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Funded Research Abstracts

PI: Adler, James
Title: Collaborative Research: Advanced Numerical Techniques for the Simulation of Magnetohydrodynamics
Abstract:
The overall objective of this research is to develop numerical models and efficient energy-consistent methods for simulation of complex fluid systems and to obtain physically-accurate solutions for magnetohydrodynamic (MHD) systems, in particular. This work focuses on minimizing the computational cost of approximating solutions to these systems in order to develop practical simulations for this type of problem. The bottom line is to further develop discretization and solution algorithms that yield the most accuracy per computational cost. This is achieved by deriving discrete energy laws for MHD systems and proving that they are consistent with the continuous mathematical model. The investigators accomplish this by using the Energetic-Variational Approach (EVA) to further investigate the MHD model itself and determining which "flavor" of the MHD equations is the simplest model that captures the relevant physics. One of the main issues with using finite-element methods for solving complex fluid and electromagnetic problems has been the precise preservation of divergence-free solutions. Here, the investigators analyze discretization methods that satisfy these quantities accurately, while remaining amenable to efficient solution. Finally, the main bottleneck in the discretization methods used so far is the slow convergence of the linear solvers. By further developing multigrid methods for systems of partial differential equations, the investigators create a robust and efficient algorithm for these complex systems.

The development of an efficient simulation framework for MHD systems has a major impact on the study of fusion energy, as this model is used to describe various phenomena that occur in fusion reactors, including tearing mode and sawtooth instabilities. With projects such as the International Thermonuclear Experimental Reactor (ITER) in France and the National Ignition Facility (NIF) at Lawrence Livermore National Lab attempting to obtain sustainable fusion energy, scientific computing in fields related to these projects is critical. In addition, the numerical tools being developed, such as energy-preserving finite-element discretizations and optimal multigrid solvers for systems of PDEs, are applicable to a wide variety of other problems in multi-physics and multi-scale systems.

PI: Admassu, Berhanu
Title: Supporting Government Guidelines for Water Development in the Somali Regions of Ethiopia
Abstract:
The output of this project is a Somali Regional government good practice guideline for water development, published by the regional government in Somali and English.

The guidelines will act as a point of reference for assessing new water development programs at the design stage, and will assist government, donors and NGOs to move towards a long-term regional water development plan. Experience indicates that if official guidelines are used in Ethiopia, over time the guidelines become de facto policy before formal policy change occurs. The development of the guidelines is an initial milestone in this longer-term process.

The process of guidelines development includes specific deliverables by three Working Groups viz. a “Human Water” group, a “Pastoral and Agropastoral” group and an “Agriculture” group, as already agreed with the stakeholder forum. These deliverables include literature reviews, expert consultations, and specific applied research, impact assessment or economic analysis depending on identified evidence gaps. The exact number and scope of studies, impact assessments, or economic analyses will not be known until each Working Group has finalized its literature review and identified evidence gaps. Provisionally, and based on previous experience with this overall approach, we expect the process to result in:

  • at least three literature reviews;
  • at least five specific studies, impact assessments or economic analyses.

PI: Anwer, Sawkat
Title: Role of Protein Kinase C in Isoforms in Bile Formation and Cholestasis
Abstract:
The long-term goal of this proposal is to understand the mechanism of canalicular bile formation and cholestasis. Our present understanding of the pathogenesis of cholestasis is based on studies to define the physiological regulation of transporters involved in bile formation and their deregulation in cholestasis. During the last granting period we have defined the role of aPKCζ, Rab4 and phosphorylation in Ntcp translocation and started defining the role of nPKCδ, nPKCε and p38 MAPK in Mrp2 translocation. The present proposal extends these studies to further define the role of nPKCδ and nPKCε in Ntcp/NTCP and Mrp2/MRP2 translocation/retrieval. One of the key goals is to define the mechanism involved in opposing effects of these kinases in hepatocytes. The following hypotheses are proposed:

  1. nPKCδ-pThr505 mediates translocation of Ntcp/NTCP by cAMP and translocation of Mrp2/MRP2 by cAMP and TUDC to the plasma membrane.

  2. nPKCε mediates TLC-induced retrieval of Mrp2/MRP2 from the plasma membrane by phosphorylating MARCKS and/or Mrp2/MRP2, and cAMP and TUDC reverse this effect by inhibiting TLC-induced nPKCε activation.

Proposed studies will be conducted in perfused livers and hepatocytes from rat livers, primary human hepatocytes and hepatic cell lines. In addition, studies will be conducted in perfused livers and hepatocytes isolated from nPKCδ-/- and nPKCε-/- mice to further confirm the role of these kinases. Role of these kinases will be evaluated by manipulating their activity and expression using chemical inhibitors, wild type-, constitutively active- and dominant negative-plasmids and Si- and/or ShRNA. Immunofluorescence and co-immunoprecipitation studies will be used to determine colocalization of desired proteins in subcellular organelles and with other proteins. Collectively, proposed studies should further define the role of nPKCδ in Ntcp/NTCP and Mrp2/MRP2 translocation, the role of nPKCε in Mrp2/MRP2 retrieval, and mechanism of reversal of TLC-induced cholestasis by cAMP and TUDC. Since a kinase may produce beneficial or toxic effect in an isoform specific manner, a better understanding of isoform specific effects should allow for better therapeutic agents that could avoid potential liver toxicity.

PI: Anwer, Sawkat
Title: Summer Programs for Veterinary Students
Abstract:
The overall objective of this training program is to help students crystallize their interest in research, to make them aware of their research potential and to familiarize them with the opportunities inherent in a research career by exposing them to an active biomedical research environment. The following specific areas were emphasized during the training period:

  1. How to evaluate a scientific article
  2. How to design an experiment
  3. How to organize and critically analyze data
  4. How to translate data into hypothesis
  5. How to transmit research information in writing and speech

PI: Asztalos, Bela
Title: The Effect of Niacin on HDL Remodeling
Abstract:
Niacin, or vitamin 83, is synonymous of nicotinic acid and nicotinamide and serves as a precursor of cellular Nicotinamide Adenine Dinucleotide (NAD) and Nicotinamide Adenine Dinucleotide Phosphate (NADP). In some instances, scientists have been able to link the lipid-modifying effect of niacin to the reduction in coronary disease progression or even to regression. Because of these clinical observations, there is an increased interest in the understanding of the mechanism of action of niacin on lipoprotein metabolism.

Hypothesis:

Niacin treatment will alter HDL remodeling in a favorable way in HIV positive subjects. Niacin treatment-mediated changes in the HDL subpopulation profile will be significantly associated with changes in viral dose.

Objectives:

To better understand the underlying mechanism of niacin-mediated High Density Lipoprotein (HDL) increase and remodeling in vivo in a population where the major lipid disorder is low HDL level. Define the effect of niacin on the Apolipoprotein A-1 (apoA-1)-conwining HDL subpopulation profile in an HIV positive population. Determine the associations between HDL-subpopulation profile and viral dose by correlating viral dose to the various HDL subpopulations.

Approach:

The apoA-1-containing High Density Lipoprotein (HDL) subpopulations will be measured by non-denaturing two-dimensional gel electrophoresis and image analyses in 700 subjects. The lipids and Apolipoprotein A-1 (apoA-1) concentrations will be measured by an Olimpus AU 400 automated analyzer using kits F from Roche. The study is blind for the investigators and code will be broken after the result is sent to the statistician. Data will be analyzed with appropriate statistical analyses.

PI: Bachovchin, William
Title: Using FAP to Selectively Target Epithelial Cancers
Abstract:
Fibroblast activation protein (FAP) is a serine protease expressed on the surface of tumor-associated fibroblasts (TAFs) in epithelial cancers and expressed to a lesser extent in healthy tissues. FAP appears to promote tumor growth, and FAP+ TAFs appear to suppress tumor killing by effector T cells (Teff). However, the role of FAP proteolytic activity in these effects is not fully understood. For instance, is FAP proteolytic activity involved in immunosuppression by FAP+ TAFs? Is FAP proteolytic activity involved in tumor promotion by non-immune effects? Indeed, it is possible that FAP promotes tumor growth by several mechanisms.

Mechanistic knowledge of FAP is needed for evaluation of its potential as a target for drug discovery. Understanding of the possible immunoregulatory functions of FAP is particularly important. Cancer vaccines can prime T cells against tumor antigens; but the immune responses seldom produce durable tumor regression clinically. Immunosuppression of T cells by FAP+ TAFs at the tumor site seems likely to contribute to the failure of cancer vaccines. Consequently, pharmacological agents that inhibit or ablate FAP+ TAFs could relieve immunosuppression and act as adjuvants that enable cancer vaccines to achieve clinical efficacy.

To date, the unavailability of pharmacological inhibitors that target FA with selectivity over related serine proteases has hindered investigation of FAP proteolytic activity in cancer. Non-specific inhibitors have yielded results that implicate serine proteases in tumor growth and immune regulation; but the relevant target in vivo remains elusive. Bachovchin et al. recently discovered how to make FAP-selective inhibitors and cytotoxic pro-drugs that are targeted by FAP to the tumor site. The agents will be used to probe FAP and FAP+ TAF function in models of epithelial cancer in which FAP is known to promote tumor growth. Investigation of two different pharmacological approaches — FAP inhibition and cytotoxic ablation of FAP+ TAFs — will reduce risk of failure in the early stages of the project.

The Specific Aims include: comparison of antitumor effects achieved by inhibition of FAP activity versus pharmacological ablation of FAP+ TAFs, characterization of the possible immune or non-immune mechanisms of action, and evaluation of the feasibility of FAP-targeted anticancer agents by determining therapeutic index and characterizing mechanism-based toxicities that might arise due to expression of FAP in some normal tissues. It will be important to evaluate any hematopoietic toxicity of FAP-targeted agents that might arise from interactions with FAP-expressing stromal fibroblasts in bone marrow.

The proposed research will address basic questions about the functions of FAP in tumor progression and support the long-term goal of developing a FAP-targeted pharmacological approach to cancer treatment.

PI: Beaulieu, Marie-Claire
Title: Digital Humanities in the Classroom: Bridging the Gap between Teaching and Research
Abstract:
The Department of Classics at Tufts University is designing and testing an integrated platform on which students will collaboratively transcribe, edit, and translate Latin and Greek texts creating vetted open source digital editions. This project, while giving students the opportunity to work with original untranslated documents, also contributes to the efforts of the scholarly community worldwide to meet the challenge of publishing large numbers of primary source documents online while preserving high editorial standards. The students' work will be vetted by experts, encoded in XML TEI following best practices in the Digital Humanities and published online in the Tufts Digital Library and the Perseus Digital Library, which receives more than 700,000 visits a month. The integrated platform will be made available as open-source software and can be used as a model for editing and translating any source documents in any language and any Humanities field.

PI: Bers, Marina
Title: Collaborative Research: ScratchJr: Computer Programming in Early Childhood Education as a Pathway to Academic Readiness and Success
Abstract:
This collaborative project between Tufts University and the Massachusetts Institute of Technology is researching and developing a new version of the Scratch programming language to be called ScratchJr, designed specifically for early childhood education (K-2). The current version of Scratch, which is widely implemented, is intended for ages 8-16 and is not developmentally appropriate for young children. This work will provide research-based evidence regarding young children's abilities to use an object-oriented programming language and to study the impact this has on the children's learning of scientific concepts and procedures. The team will develop ScratchJr in an iterative cycle, testing it in both the Devtech lab at Tufts and the Eliot Pearson lab school and with a wider network of early childhood partners. At the end of the three-year project, ScratchJr will have been tested with approximately 350 students in K-2, 40 parents, and 58 early childhood educators.

ScratchJr will have three components: 1) a developmentally appropriate interface, with both touch screen and keyboard/mouse options; 2) an embedded library of curricular modules with STEM content to meet federal and state mandates in early childhood education; and 3) an on-line resource and community for early childhood educators and parents. The research questions focus on whether ScratchJr can help these young children learn foundational knowledge structures such as sequencing, causality, classification, composition, symbols, patterns, estimation, and prediction; specific content knowledge; and problem solving skills.

PI: Bers, Marina
Title: Ready for Robotics: The Missing T and E of STEM in Early Childhood Education
Abstract:
The project investigates the use of robotics into early childhood education. It address two objectives: to develop and evaluate a low-cost, developmentally appropriate robotic construction kit specifically designed for early childhood education (PreK-2) and to pilot a robotics-based professional development model for early childhood educators to teach engineering and technology. A number of research questions are included. To what extent did participating teachers gained knowledge about robotics, engineering and programming, and pedagogies? To what extent have they increased their familiarity of, comfort with, and understanding of the use of robotics in early childhood? To what extent participating in the institute can support the passage from knowledge to action? What processes/standards are used by early childhood teachers to integrate engineering and technology into their traditional curriculum? Do teachers adopt the robotics kit and curriculum for their classrooms? How do they adapt it to their own practices? What are the factors that predict successful outcomes in terms of adoption and adaptation? To what extent has the teaching practice of the teachers changed in a way that demonstrates understanding of the role of T and E in early childhood education?

For robotics to be successfully integrated into the early childhood classroom, there are three factors that need to be considered: the robotics technology needs to be developmentally appropriate and low-cost; and teachers should be exposed to professional development. This project addresses these issues. It contributes to the emerging field of robotics in education by addressing the needs of an educational segment, early childhood, where there is a lack of new technologies and approaches to teach technology and engineering in a developmentally appropriate way.

PI: Black, Lauren
Title: Restoring LV Function Post-MI Using Fibrin-Gel Based Engineering Myocardium
Abstract:
Cardiovascular disease can lead to myocardial infarction (MI) and subsequent heart failure. There are currently a number of therapies aimed at preventing or treating heart failure post-MI. Only heart transplantation replaces infarcted myocardium to restore heart function, but there is a paucity of donor hearts and the incidence of cardiovascular disease continues to rise. A new and innovative option is the use of "heart patches" created in vitro for implantation in vivo. The research proposed in the independent phase of this award aims to address 2 critical issues pertaining to the function and eventual use of such heart patches: 1) the effect of a biomimetic culture environment on tissue morphology and function, and 2) the efficacy of myocardial equivalents biomimetically-engineered in vitro in restoring left ventricular function post-MI.

The overall hypothesis of this work is that myocardium engineered in vitro in biomimetic culture conditions restores post-MI left ventricular function better than cell therapy-based methods of repair. The environment at the Tufts University uniquely positions me to address this hypothesis, as the world-renowned Tissue Engineering Research Center and Molecular Cardiology Research Institute are both located nearby. This environment will give me the opportunity to augment my already considerable background in tissue mechanics and tissue engineering methods with cardiac anatomy and physiology in health and disease and cardiac surgical techniques. The continuation of my career plan during the independent phase includes gaining more expertise in cell and tissue culture techniques and bioreactor development, while learning new skills in areas including cardiac surgical techniques and physiological evaluation in a rat model of MI.

The ultimate goal of the project is to leverage these skills to directly compare the efficacy of myocardial tissue engineered in vitro with current cell-therapy based methods of cardiac repair in restoring function to the left ventricle post-MI. This research is especially critical considering the continuing rise in incidence of heart disease. The results of this research may help elucidate design parameters that are critical to the creation of functional myocardium engineered in vitro and thus advance the concept of the "heart patch" closer to reality.

PI: Black, Lauren
Title: The Role of the Extracellular Biophysical and Biomechanical Milieu in CHDs
Abstract:
Congenital heart defects (CHDs) are the leading cause of death in infants and young children and those suffering from congenital diaphragmatic hernia and associated CHDs (particularly with left heart hypoplasia (LHH)), have high mortality. The dominant hypothesis is that the CHDs result from mechanical factors leading to altered blood flow in the left heart, such as compression of the left heart by visceral structures protruding into the thoracic cavity. In mild LHH, left ventricular dimensions tend to normalize after birth and hernia repair, further implicating the role of altered mechanical loads in certain forms of CHD. Decreased cardiac tropoelastin and procollagen gene expression and decreased left ventricular function in LHH compared to normal hearts suggest that significant deviations from normal ECM composition and mechanical properties of the myocardium occur. Given that ECM properties can affect various cell functions including proliferation, differentiation, and phenotype, any deviations from the normal composition and stiffness of the ECM in the progression of CHD would have a significant impact on the myocytes, resulting in profound alterations to the development and function of the myocardium. Additionally, altered flow through the developing heart will affect mechanical strain in the ventricular wall, and studies have demonstrated that changes in mechanical strain can significantly impact cell function.

We hypothesize that by mimicking changes in ECM composition, stiffness, and/or mechanical strain associated with LHH, we will be able to guide embryonic myocytes towards the LHH phenotype while mimicking the healthy embryonic heart environment will lead to normal myocyte development. In Aim 1, we will use nitrofen-induced congenital diaphragmatic hernia in developing rat embryos to generate models of CHD. Healthy and diseased hearts from embryonic and fetal stages will undergo decellularization to obtain cardiac ECM which will be assayed to determine any compositional differences and alterations in mechanical stiffness. At these same life stages, we will characterize native myocyte proliferation and maturation in healthy and CHD hearts. We will then culture embryonic/fetal myocytes isolated from healthy and CHD ventricles in rationally altered 2D environments that mimic different combinations of healthy and diseased biophysical properties using an ECM-coated polyacrylamide (PA) gel system and assess whether stiffness and composition act synergistically or antagonistically, and whether "healthy" biophysical cues can drive "diseased" myocytes towards a healthy phenotype. In Aim 2, we will subject embryonic and fetal myocytes to mechanical strain of varying amplitude and frequency and assess the proliferation, maturation, and function of myocytes from healthy and CHD hearts. These studies are novel and will represent one of the first experiments to assess the role of altered biophysical and biomechanical signaling in the development of cardiac pathologies during growth in utero.

Mentor: Black, Lauren
Fellow: Williams, Corin
Title: Towards Repairing Congenital Heart Defects: The Effects of Fetal Cardiac Extracellular Matrix on Myocyte Proliferation
Abstract:
Congenital heart defects (CHD) are the leading cause of mortality in live-born infants. Hypoplastic Left Heart Syndrome (HLHS) is a rare CHD that requires several major reconstructive surgeries. However, the reconstructed heart does not replicate normal anatomy and function, and many patients suffer from serious secondary complications throughout life. Cardiac tissue engineering is especially promising for treating HLHS by creating living functional heart tissue that can grow with the child. However, creating functional heart tissue in vitro remains a major challenge, as mature cardiomyocytes (CMs) are mostly non-proliferative. While embryonic and fetal CMs are highly proliferative and can restore function in damaged or diseased hearts, the causes of decreased CM proliferation and loss of cardiac regenerative capacity after birth are still largely unknown. Elucidating factor that promotes CM proliferation will greatly impact tissue engineering and regenerative approaches to treating CHD in children. The extracellular matrix (ECM) modulates a variety of cell functions, including proliferation, and there is evidence that ECM composition and stiffness of the heart change during development and maturation.

The hypothesis of this project is that recapitulation of the fetal ECM environment will promote the proliferation of CMs; specifically, it is expected that the features of fetal cardiac ECM that promote CM proliferation are the cues that are lost or diminished in the adult heart. The hypothesis will be systematically tested in vitro, to determine the individual and combined effects of ECM composition and stiffness in 2D and 3D culture, and in vivo, as an initial step towards future clinical translation For ECM composition studies, native fetal and adult rat hearts will be decellularized to obtain ECM and then solubilized and adsorbed onto tissue culture dishes. Primary neonatal rat CMs will be seeded onto cardiac ECM-coated substrates and assayed for proliferation. In parallel, the effects of substrate stiffness will be determined. Decellularized and native hearts will undergo mechanical testing to determine the stiffness of the ECM. Polyacrylamide (PAAm) gels will be made with stiffnesses that mimic fetal and adult hearts.

In these studies, Collagen I will be used at the same ligand density in fetal vs. adult stiffness gels to decouple composition from stiffness. To investigate the combined effects of ECM composition and stiffness on CM proliferation, solubilized cardiac ECM will be incorporated into PAAm gels. The ECM/stiffness combination that results in highest CM proliferation will be used to guide the design of an injectable ECM-based biomaterial. The 3D gel will be characterized and optimized in vitro and will reveal whether 2D vs. 3D culture has different effects on CM proliferation. The ECM gel which results in greatest cell viability, infiltration, and proliferation in vitro will be tested in vivo for its effects on stimulating CM proliferation in neonatal rats.

The results of this work will significantly impact future cardiac tissue engineering approaches through the development and characterization of ECM-based biomaterials that promote CM proliferation and regeneration of cardiac tissue.

PI: Bohm, Alex
Title: Selection of the 3' end mRNA Processing Site by Cleavage Factor I
Abstract:
Gene expression is the process of synthesizing functional proteins using information stored in the nucleus as DNA and transmitted to cellular sites of protein synthesis in the form of mRNA molecules, produced by copying (transcribing) DNA. An essential step in gene expression is the precise trimming of the 3'-ends of messenger RNA (mRNA) molecules by 3'-end processing enzymes that recognize specific RNA sequences. This process determines the length of each mRNA molecule and affects the efficiency with which it is utilized as a template for protein synthesis. Roughly half of human genes contain more than one potential site of 3'-end processing and are subject to alternative processing. Selection of the appropriate processing site is particularly important in the synthesis of proteins involved in immune responses and in cell differentiation. This project uses yeast as a model system to study the mechanism of 3'-end processing and focuses on an evolutionarily conserved complex of five proteins called Cleavage Factor I (CF I) that recognizes mRNA signal sequences which define the sites of 3'-end processing. The research will utilize single-particle electron microscopy, coupled with RNA foot-printing and molecular modeling techniques to construct models of the overall structure of CF I and elucidate how it recognizes mRNA signal sequences and directs processing of the 3'-ends of mRNAs. Yeast genetics, coupled with biochemical binding experiments, will be used to verify and refine the resulting molecular models. This work is of fundamental importance because mRNA 3'-end processing affects the expression of all proteins in all eukaryotic cells.

PI: Booth, Sarah
Title: Vitamin K Analysis of Food and Dietary Supplements
Abstract:
To identify and quantify vitamin K and related compounds in representative samples of foods and dietary supplements to improve and expand analyses to the USDA Nutrient Databases.

PI: Bridges, Robert
Title: NCRR Research Training for Tufts Veterinary Students
Abstract:
There is a crucial need for veterinarians with research training to participate in academic as well as corporate based research in the fields of animal and human health. Veterinarians trained in this century need to acquire the scientific skills and technical training together with the conceptual framework to participate both as independent researchers and collaborators to meet the projected national research needs in the biomedical sciences.

The objective of the proposed training described here is to provide bright, and highly-motivated veterinary students with a one year, in-depth research experience in a productive and active research setting. Training will involve the use of animal models to develop skills at hypothesis-based, biomedical research. Over a five year period, our aim is to train ten students (2/year). Applicants will be actively recruited from incoming and existing veterinary classes at Tufts Cummings School of Veterinary Medicine with an effort to insure minority student participation. Participants receive 12 months of consecutive research training following completion of their second year of veterinary school. The training is integrated into a Master of Science degree program (D.V.M./M.S.) specifically designed for trainees in this program. This degree program includes limited course work and complementary seminars. Program faculty consists of 12 NIH supported faculty members from both our basic and clinical departments. Using animal models that include pigs, horses, sheep, goats, cats, dogs, rats, and mice, program faculty will provide intensive laboratory training in the research areas of infectious diseases, reproductive biology, digestive diseases, neuroscience and behavior, nutrition, and respiratory physiology.

Our long-term objective is to make this research training experience an effective launching pad for career involvement in biomedical research for Tufts' graduates. The success of the program will be evaluated by determining the number and quality of trainees that integrate health science research into their professional careers.

PI: Brugge, Douglas
Title: Community Assessment of Freeway Pollution and Health
Abstract:
We propose a CBPR study of the relationship between air pollution gradients and health effects in individuals living next to major highways. There is evidence that:

  1. People living close to highways experience significantly elevated exposures to constituents of motor vehicle exhaust including ultrafine particles (UFP; 0.01-1 microns) and black carbon

  2. That motor vehicle pollution is associated with cardiac mortality and morbidity in adults, and asthma and reduced lung function in children

C-reactive protein (CRP), an inflammatory marker of risk for cardiac illness, has been shown to increase in response to changes in particulate exposure, making it a viable indicator of the potential impact on cardiac health. Our core study involves measuring 5 traffic-related pollutants (i.e., UFP, PM2.5, NOx, CO, black carbon, particulate PAH) in 6 neighborhoods within 400 meters of highways through in the Boston area. A background site >1000m from highways will also be monitored. We will complete a scientific survey of residents living in the neighborhoods to determine pediatric asthma prevalence. We will determine the time residents spent within the near highway zone currently and rigorously measure highway pollution gradients in the neighborhoods. We will document exposures at work, school and while commuting. For a subset of non-smoking households we will obtain pulmonary function tests from children and analyze multiple blood samples per person from adults for CRP and fibrinogen. Our study will be:

  1. The first to test associations between highway pollution gradients and biological markers of health

  2. The first CBPR study of highway pollution

  3. The most comprehensive collection of data on time spent in the exposure zone and many confounders and effect modifiers

We will conduct bivariate and regression analyses and have developed preliminary mathematical models that frame our approach to analyzing the large set of data. Our team consists of faculty at Tufts University and 6 co-investigators from community organizations that are concerned about the impact of highways on the health of residents in their communities. We will train and hire field staff from the communities and have an advisory board. We will link community participation to the science through participation in our steering committee and through our advisory board. Our study is designed to report useful information locally as well as influence pressing national policy needs.

Mentor: Bunnell, Stephen
Fellow: Lewis, Juliana
Title: Investigating the Homing and Engraftment of CML Stem Cells in the Bone Marrow
Abstract:
Chronic Myeloid Leukemia (CML) is a hematopoietic stem cell (HSC) malignancy that is induced upon the balanced translocation of chromosomes 9 and 22 and the resulting formation of a Philadelphia (Ph) chromosome. The product of the Ph chromosome is the BCR-ABL tyrosine kinase. The constitutively active tyrosine kinase activity of BCR-ABL is the crux of the malignancy and causes defective integrin signaling and adhesion in HSCs. Recent studies in our laboratory indicate an abnormal and increased dependency on selectins and their ligands for homing and engraftment of these leukemic stem cells within the bone marrow (BM) niche. The main objectives of this proposal are to 1) investigate and further define the nature of the adhesive molecules that contribute to engraftment of malignant stem cells in CML patients and 2) develop methods that will block engraftment of CML stem cells without affecting the engraftment of normal stem cells.

To induce CML in donor stem cells we will employ our BCR-ABL transduction/transplantation model system. To delineate the critical adhesion molecules that mediate malignant stem cell engraftment compound donor and/or recipient mutant mice will express genetic mutations for adhesion molecules expressed in HSCs or BM endothelium, respectively. These BM transplantation studies will collectively determine the critical adhesion factors for engraftment of leukemic stem cells. Neuraminidase, anti-selectin reagents, monoclonal antibodies and small molecule selectin antagonists will be tested for their efficacy to block CML stem cell engraftment first in a murine model for CML and then using xenografts of human CML stem cells transplanted into NOD/SCID/γc-deficient mice. The observations from these studies will engender novel clinically applicable methods for blocking CML stem cell engraftment in autographed patients.

PI: Bunnell, Stephen
Title: Mechanisms of Integrin-Mediated Costimulation in T Cells
Abstract:
The integrin α4β1 (VLA-4) contributes to the etiology of common autoimmune disorders, including multiple sclerosis, inflammatory bowel disease, and systemic lupus erythematosus. Although VLA-4 is widely viewed as contributing to T cell function by directing cell trafficking and by enhancing cell adhesion, VLA-4 potently costimulates T cell activation. The mechanisms underlying this costimulation are not well understood and may play a significant role in the etiology of human immune disorders.

Our long-range goal is to understand how to manipulate the costimulatory functions of VLA-4 in order to regulate T cell activation in vivo. Our immediate objective is to determine how VLA-4 modulates T cell responses to antigen. Here, we present preliminary data characterizing a previously unknown effect of VLA-4 ligation on the movement of signaling complexes induced by the TCR.

Our specific hypothesis is that structures containing SLP-76 and ADAP are required for the transmission of tension-dependent costimulatory signals initiated upon VLA-4 ligation. The rationale for the proposed work is that it will provide an enhanced understanding of the fundamental mechanisms that enable the integration of the signaling pathways downstream of the TCR and VLA-4.

Three aims will examine how ADAP contributes to T cell costimulation and how cytoskeletal tension contributes to VLA-4 dependent costimulatory signals:

  1. How does ADAP contribute to the assembly and translocation of SLP-76 microclusters?

  2. How does costimulation depend on the VLA-4-dependent immobilization of microclusters?

  3. How does cytoskeletal tension contribute to T cell costimulation by VLA-4?

These studies explore a novel effect of VLA-4 ligation, the lateral immobilization of TCR-induced complexes, and use it as a tool to dissect the pathways involved in costimulation by VLA-4. We expect these studies to define the mechanisms by which VLA-4 ligation costimulates T cell activation. This will have a positive impact on our understanding of autoimmune disease, and will assist in the identification of unique intracellular targets for drug development. This work will also generate insights into the systems linking cell shape to cell growth and proliferation, providing useful insights into cancer.

PI: Burgess, Kristine
Title: Evaluation of Metformin on Growth Inhibition and Cytotoxicity in Canine Cancer Cell Lines
Abstract:
Spontaneous cancer in the dog is the leading cause of disease related deaths with estimates at 4 million cases per year. For most tumors the use of conventional cancer treatments can provide disease remissions, but unfortunately most cancers will recur over time. It is believed these relapses occur as a result of cancer stem cells that can evade cell death induced by chemotherapy treatments. A therapy that is directed at these stem cells would provide a key component in cancer cell killing by targeting those cells that escape traditional chemotherapy drugs. In both human and veterinary oncology, there is a real need for cancer stem cell targeted therapy, which has the potential to impact both early and late stages of cancer development.

Metformin (dimethylbiguanide) is an established oral anti-diabetic drug that has been used in humans for >25 years. Epidemiological studies have revealed that diabetics treated with metformin have reduced risk of developing various types of cancer. Indeed, studies completed on human breast and other cancer cell lines have demonstrated inhibition of cell growth including breast cancer stem cells when exposed to metformin.

We hypothesize that the anti-proliferative/anticancer effects of metformin seen in human cancers occur in established canine mammary and other canine cancer cell lines. Also, we hypothesize that canine cancer stem cells are growth inhibited by metformin in vitro. Successful completion of this study will provide information necessary to proceed to a phase III clinical trial in dogs with spontaneous forms of cancer.

PI: Camilli, Andrew
Title: Medically Oriented Research in Graduate Education
Abstract:
Tufts University Sackler School of Graduate Biomedical Sciences proposes a new training program that will serve as a blueprint for integrating medical knowledge and clinical perspective into PhD education. Building from strength in graduate education and research, the MERGE-Infectious Disease (MERGE-ID) program will combine PhD training in the basic microbiology and immunology of pathogenic organisms and host interactions with in-depth exposure to the pathogenesis, diagnosis, prevention, treatment and epidemiology of infectious disease. The program will retain discipline-specific depth and add new courses that integrate clinical exposure from day one of the program throughout the training.

A basic researcher and a clinician-scientist expert in ID will equally co-mentor each trainee in laboratory rotations and in hypothesis driven thesis research that addresses a question of clinical importance. Trainees will complete discipline-specific courses as well as an ID-Problem-Based Learning course, a specialized team-taught pathogenesis module that integrates human physiology and pathology with in-depth study of human pathogens, and an intensive three-month Clinical Practicum based on their dissertation research. Seminars and enrichment activities that focus on interaction with clinical ID fellows and physicians will supplement the training.

Four students, specifically selected for MERGE-ID will be admitted to the program each year, bringing the cohort to 16 by the fourth year of the program. When our trainees complete their education, we expect them to conduct highly effective, clinically relevant research that integrates basic approaches to medical problems. Based on the results from ongoing evaluation of the program, we propose to expand the MERGE-ID model to create similar programs focused on other disease-related areas before the end of the funding period.

PI: Camilli, Andrew
Title: Role of c-di-GMP Signaling in Vibrio cholerae Virulence
Abstract:
Knowledge is very limited with respect to how facultative pathogens, i.e., pathogens that spend portions of their life cycles both inside and outside of the human body, adapt to drastically changing conditions when passing from a human host into an environmental reservoir. Advances in understanding of the basic mechanisms of adaptation during this transition are needed to provide new molecular targets and strategies for limiting transmission, dissemination and environmental persistence, and thus reduce the large medical burden imposed by this diverse group of pathogens. In the facultative, water-borne pathogen Vibrio cholerae (the causative agent of cholera), signaling by the intracellular secondary messenger molecule cyclic diguanylate (c-di-GMP) leads to the repression of virulence genes, and at the same time, the induction of environmental survival genes. At a late stage of infection, just prior to excretion of V. cholerae in watery stool, expression of three genes that encode c-di-GMP synthetases is induced, leading to the hypothesize that c-di-GMP mediates the transition from a state of virulence to one of environmental suitability.

In this project the role of c-di-GMP in the biology of V. cholerae late in infection and in the process of dissemination will be determined using genetic and biochemical methods, including some novel methods created for these studies. In addition, the roles of a family of five c-di-GMP-binding proteins in transducing the c-di-GMP signal into biological changes will be determined. It is anticipated that this work will provide a working model of the central regulatory pathway in V. cholerae that represses virulence gene expression and induces expression of genes important for dissemination. It is also anticipated that these studies will have application to a broad range of bacterial pathogens since most contain multiple c-di-GMP synthetic, degradative and sensory proteins.

PI: Camilli, Andrew
Title: Study of Transmissible Forms of Vibrio cholerae
Abstract:
Vibrio cholerae is a facultative pathogen and the causative agent of cholera. Hallmarks of the disease include profuse watery diarrhea resulting from the action of secreted cholera toxin, and deadly, explosive outbreaks. The strong link between epidemics and human overcrowding in areas with untreated drinking water suggests an efficient mode of fecal-oral transmission via an aquatic intermediate. In support of this notion, we discovered that V. cholerae exit cholera victims in a heightened state of transmissibility (referred to as “hyperinfectivity”), which persists for several hours after shedding into pond water. Knowledge of the molecular basis for this phenotype, and a general characterization of this transmissible form of V. cholerae, would contribute to the design of vaccines to prevent cholera at the initial stage of infection.

In prior work, we discovered that motility in the absence of chemotaxis is one determinant of hyperinfectivity. To identify additional determinants aiding in transmission, we measured global transcriptional changes in human-shed V. cholerae during the transition to an aquatic microcosm. This analysis revealed a number of regulators and effectors that potentially contribute to cholera transmission. In related work, we used a genetic selection to identify genes that are ‘pre-induced’ at late stages of infection and which subsequently play roles in the transition of V. cholerae to aquatic environments.

In Aims 1 and 2 of this project, we propose to determine if genes regulated late in infection or in cholera stool play important roles in the transition pond water and in hyperinfectivity. Transcriptional regulators with important roles in these phenotypes will be further analyzed by transcriptional profiling to define their corresponding regulons. In Aim 2, we also propose to measure and correlate changes in the transcriptome and proteome of cholera stool V. cholerae during the transition to pond water. In Aim 3, we propose to apply knowledge of the effectors of transmission to develop and test a mucosal vaccine in a mouse maternal model of immunization and challenge of pups.

We hypothesize that an acellular vaccine expressing a repertoire of antigens that are stably expressed on the surface of transmissible forms of V. cholerae will provide enhanced protection to challenge by the transmissible form of this pathogen. These studies will establish a basis for understanding both the hyperinfective phenotype of V. cholerae and its transition to aquatic environments. This knowledge will enhance our understanding of transmission of this and perhaps other water-borne pathogens, helping pave the way to development of novel vaccines that target transmissible forms of facultative pathogens.

PI: Canyes, Barbara
Title: MACC AmeriCorps Student Leaders in Service
Abstract:
Massachusetts Campus Compact, Connecticut Campus Compact and the University of Sacred Heart, a consortium of 90 colleges and universities, propose to continue into a new grant cycle with a strategic national service initiative that will simultaneously 1) advance the public service mission of higher education; 2) leverage resources for the benefit of communities throughout our region; 3) develop students as civic leaders. With nine years of experience with Education Award Programs, Massachusetts Campus Compact will act as the lead for the program.

Annually, over 675,000 students are enrolled in higher education institutions in MA, CT, and PR. However, according to the Corporation for National and Community Service Report, Volunteering in America, on average less than a quarter of these college students are volunteering in their communities. AmeriCorps Student Leaders in Service seeks to take advantage of the unharnessed resource of young people creating change in their communities. College students who actively volunteer are more likely to actively participate in civic life as adults. AmeriCorps Student Leaders in Service will be a vehicle for college students to be more active in their local communities by developing their civic skills and beliefs as they recruit their peers to volunteer alongside them. In the current economic climate, community-based organizations rely even more on skilled volunteers to increase their capacity. This program will help fulfill that need.

AmeriCorps Student Leaders in Service will capitalize on the skills, energy and passion of one of the greatest resources in Massachusetts, Connecticut and Puerto Rico, our college students. This program will continue to empower college students to connect campuses and communities from across all three regions through active citizenship and service. As AmeriCorps members, 325 college students will each provide direct service to community and faith-based organizations, through tutoring, mentoring, addressing immediate needs of food, clothing, and shelter, and a variety of other efforts. Through their service, students will additionally build the capacity of campus-community partnerships for long-term sustainability through volunteer recruitment and coordination and service program management and development. This aligns with the Corporation for National and Community Service's goals of mobilizing more volunteers, engaging students in communities and ensuring a brighter future for America's youth.

Furthermore, AmeriCorps Student Leaders in Service will strengthen the civic mission of higher education by creating a pathway to lifelong civic engagement for college students. This assertion has been confirmed by the Massachusetts Campus Compact's previous AmeriCorps Education Award grant. College students enrolled as AmeriCorps members reported an increased belief in their ability to create change along with stronger civic competencies and leadership skills. A significant majority reported that their experience in AmeriCorps service contributed to a deeper understanding of their role as citizens and enhanced their understanding of the needs facing their communities. Students also reported that they will continue to serve within the community throughout college and after graduation.

PI: Capiro, Natalie
Title: Evaluation of Partitioning Electron Donors for Enhanced Bioremediation of Chlorinated Solvent Source Zones
Abstract:
Recent studies have demonstrated that microorganisms are capable of biodegradation within close proximity to chlorinated solvent source zones. This biological activity can enhance (accelerate) aqueous dissolution (removal) of chlorinated solvents, and has the potential to provide more effective source zone treatment, thereby reducing potential exposure and remediation costs. However, the performance of bioremediation, and more specifically, biologically-enhanced dissolution, faces two challenges: sustained release of electron donor (food source) and delivery of electron donor to the intended target.

To overcome these limitations, a potential alternative are partitioning electron donors (PEDs), organic compounds (e.g., n-butyl acetate) that are relatively water soluble, but also partition into (directly mix with) chlorinated solvents. When a PED is delivered to the subsurface contaminant source zone, it preferentially partitions into the organic separate phase chlorinated solvent, and then slowly dissolves back into the passing groundwater along with the contaminant. This strategy of electron donor delivery is intended to promote the growth of chlorinated solvent degrading bacteria in close proximity to the contaminant source zone, while minimizing consumption of electron donor in microbial processes not associated with chlorinated solvent bioremediation (e.g., methane production).

The specific objectives of this research are designed to assess the physical, chemical and biological processes that govern PED delivery, mass transfer, and consumption to support sustained microbial biodegradation in chlorinated solvent source zones. A combination of laboratory-scale experiments and mathematical modeling will be conducted using trichloroethene (TCE) as a representative contaminant. The research program is structured around four tasks that will:

  1. evaluate and select PEDs for detailed study based on abiotic and biotic batch reactor studies,

  2. quantify PED delivery and release, and rates of bioenhanced dissolution and degradation in columns containing residual TCE in comparison to current electron donor delivery approaches,

  3. measure the spatial distribution and temporal evolution of PED delivery/release, TCE dissolution and degradation, and microbial communities in heterogeneous aquifer cells to assess the potential for improved bioremediation under more realistic conditions, and

  4. implement mathematical models to obtain mass transfer and utilization rate parameters from experimental data, and predict responses to alternative PED delivery strategies and subsurface aquifer conditions to support potential scale up to field-application.

PI: Castellot, John
Title: Regulation of Uterine Fibroids by CCN5
Abstract:
Leiomyomata (fibroids) are a non-malignant neoplasia of uterine smooth muscle cells (UtSMC) that afflict approximately 20% of all women and 80% of black women in the U.S. The most common tumor in women, fibroids cause severe pain and bleeding as well as infertility. Though temporary respite from the symptoms can be achieved by medical and surgical interventions, the only treatment that prevents recurrence is hysterectomy. More than 200,000 hysterectomies are performed annually in the U.S., with direct health care costs exceeding $2B; the emotional distress caused by loss of the uterus is incalculable. Despite its prevalence and severity, this condition has received sparse attention in the basic research community until quite recently. If we are to advance our understanding of the pathogenesis and improve treatment options for fibroids, it is critical to elucidate the mechanisms that underlie UtSMC proliferation.

Work in our laboratory showed that the growth-arrest protein CCN5 was nearly absent in human fibroids, yet abundant in the normal myometrium of the same patients. We have also demonstrated that the CCN5 protein blocks human UtSMC proliferation in culture and in animal models by >80%. Gene profiling indicates that CCN5 regulates clusters of genes that control mitogenic signal transduction and cell cycle progression. These observations underpin our central hypothesis that CCN5 has a key role in maintaining normal smooth muscle function in the uterus, and that dysregulation of CCN5 expression is a major factor in the pathogenesis of fibroids. A corollary hypothesis is that administration of CCN5 will reduce or prevent fibroid formation. To test these hypotheses, in this revised proposal we will carry out structure-function analyses to determine the mechanisms by which CCN5 regulates UtSMC function using a combination of in vitro and in vivo model systems. Using immunocompromised mice implanted with human fibroid UtSMC engineered to express CCN5, we will determine if CCN5 or related peptides can suppress fibroid formation.

These experiments are designed to provide a comprehensive assessment of the effects of CCN5 in human UtSMC from the molecular to the physiologic and pharmacologic levels. We hope the results of the proposed work will provide new insights into the pathophysiologic role of CCN5 in fibroids, and lead to novel therapeutic targets for treating this important women’s health issue.

PI: Catley, Andrew
Title: Livestock Emergency Guidelines and Standards: Support to Phase III
Abstract:
Throughout the developing world, livestock are a crucial livelihoods asset for vulnerable communities. In the face of continued political instability, conflict, population growth and climate change, natural and man-made disasters affect increasing numbers of people globally. The Livestock Emergency Guidelines and Standards (LEGS) are a set of international standards and guidelines for the assessment, design, implementation and evaluation of livestock interventions to assist people affected by humanitarian crises. The ultimate aim of LEGS is to improve the quality and livelihoods impact of livestock-related projects in humanitarian situations.

In early 2009 and with OFDA support, LEGS was published and made available as a free soft copy from the LEGS website, and as a hard copy version. After publication, a global LEGS training program was developed and tested, and LEGS was translated into French and Arabic. From mid 2009 to mid 2011 LEGS training courses were run in eight regions, and national courses in 14 countries. Combined with various regional and national awareness-raising events, these activities have helped to start to establish LEGS as the key point of reference for the design of livelihoods-based livestock programs in humanitarian crises. LEGS has attracted broad stakeholder acceptance and support, and continues to be overseen by a Steering Group comprising FAO, ICRC, Tufts University, African Union and Vetwork UK. Post publication activities were largely funded by ECHO and DFID, as part of a funding strategy to ensure broad donor support. In May 2011, LEGS was recognized as a Companion Module to Sphere, further reflecting its growing acceptance by the international humanitarian community.

Despite the good progress made by LEGS, there is still a considerable amount of work to be done to institutionalize LEGS in the humanitarian sector. For example, LEGS trainees now need to actually apply LEGS in new projects and evaluate the impact, and far more people need to know about LEGS, be trained, and use the guidelines. The momentum created by LEGS so far provides a strong platform for further work, but critically, the core coordination and management capacity of LEGS needs to be continued.

PI: Cebe, Peggy
Title: Confinement in Electrospun Polymer-Based Nanocomposites, with Research Opportunities for Deaf and Hard of Hearing Interns
Abstract:
Non-woven membranes will be created using very small diameter fibers, on the nano-scale, by applying a high electric field to a solution containing polymer and additives (such as carbon nanotubes or clay). Nanofibers formed this way are stronger and more heat resistant compared to conventional large diameter fibers. The processing conditions and nature of the additive will be varied to see which combinations yield nanofibers with the best properties. These non-woven fabrics are candidate materials for use as filtration membranes, in catalysis, for drug delivery, and as a component of smart clothing materials. Both national and international collaborations have been established for conducting this research using specialty equipment and novel processing conditions. To provide research opportunities for students with disabilities, four deaf and hard of hearing undergraduate students will participate in an internship, and perform research on the project during the summer months. These interns will learn to make the non-woven nanofibers, heat treat them, and study their physical properties.

PI: Cebe, Peggy
Title: Individual PAESMEM Nomination of Peggy Cebe: Internship Program for Deaf and Hard of Hearing Students
Abstract:
Dr. Peggy Cebe, professor of physics at Tufts University, has served as mentor and role model for undergraduate students over her twenty-two year academic career. Ninety one students have performed scientific research in her polymer materials laboratory, including 42 females, 14 minorities, and 26 students with disabilities. The special program developed by Prof. Cebe for the latter group of students with disabilities forms the basis for the PAESMEM nomination. In 2003, Prof. Cebe began a unique program to provide research internships and intense mentoring to deaf and hard of hearing (DHH) undergraduate summer interns. To date, twenty six DHH students have participated, performing research leading to co-authorship of scientific publications and presentations at national scientific meetings.

To bring deaf and hard of hearing students into the larger scientific community as professionals, they must have positive scientific experiences at a formative time in their educational lives. Prof. Cebe provides this type of opportunity in a specific and well-integrated learning experience centered on the topic of "polymer materials." In each year of the program, a small group, of four-five deaf or hard of hearing students, participates in a summer internship at Tufts University, performing hands-on laboratory work, making and testing polymer-based materials. Associated classroom lessons prepare the interns for the laboratory work by providing the scientific underpinnings, including introduction to the chemistry and physics of polymers. Tufts faculty, postdoctoral associates, graduate and undergraduate students are all involved in providing educational opportunities for the DHH interns, and in this way "hearing" persons also become educated and find reward and inspiration in working closely with students with disabilities.

The specific program objectives are to:

  1. Increase the interns' knowledge about polymers and polymer blends, and their use in fuel cell technologies;

  2. Increase the interns' confidence in performing laboratory work;

  3. Demonstrate the importance of teamwork as an approach to real-time problem solving;

  4. Improve group presentation communication skills;

  5. Impart knowledge of the standards of ethics associated with the scientific endeavor; and, as part of sustainability for the future,

  6. Conduct outreach to DHH middle and high school students to encourage their participation in STEM disciplines.

DHH interns make and characterize polymer materials for ultimate use as novel proton exchange membranes for hydrogen fuel cell technologies. They fabricate films, electro-spun fibers, and/or oriented tapes, and characterize the structure and properties of the resulting materials. This research will contribute to a fundamental understanding of the effects of composition and thermal treatment on polymer films, and ultimately on the potential of these polymer blends to serve as proton exchange membranes.

PI: Chakravorti, Bhaskar
Title: Investing in Africa: Context for Assessing Risk and Return in the World's Most Fragmented—and Promising—Emerging Market Conference
Abstract:
On April 23-24, 2012, The Fletcher School hosted a conference entitled “Investing in Africa: Context for Assessing Risk and Return in the World's Most Fragmented — and Promising — Emerging Market.” The event brought together resources from across Tufts University, including the IBGC and CEME, the Feinstein International Center, the World Peace Foundation, the Institute for Human Security, and faculty members from multiple disciplines. Fletcher faculty chaired, and drove the intellectual content of, each conference panel.

Policy makers, academics, and businesspeople need to know how to harness Africa's promise while minimizing and meeting its challenges. Business interest in Africa has picked up dramatically of late, with its natural resources, human potential, growth statistics, and many of the region's underlying fundamentals providing positive outlook for investment and development. However, Africa remains challenged on many fronts. It is not a monolith: its diverse countries, industries, people, infrastructures, governments, and economies mean that investment decisions can be complicated. Moreover, Africa hosts significant barriers to development, including political upheavals, famines, civil wars, diseases, intractable sociocultural issues, and unstable political institutions. Through this conference The Fletcher School aimed to examine these competing variables in order to provide contextual insight for assessing risk and return in the continent's key emerging economies.

PI: Chang, Remco
Title: CGV: Small: Toward Objective, In-Situ, and Generalizable Evaluation of Visual Analytics by Integrating Brain Imaging with Cognitive Factors Analysis
Abstract:
Evaluating complex, interactive visual analytics systems is challenging for many reasons. The exploratory nature of using visualization makes quantitative measurements of individual components of the visualization task infeasible. The range of potential users and their differing goals render standardized metrics too restrictive. And environmental conditions can influence experimental outcomes, making it difficult to compare and generalize the results of separate evaluations. Although numerous methods have been proposed for evaluating visualizations and HCI, few can be readily applied to objectively evaluate visual analytics systems in real-world settings.

In this project the PI will address this open challenge by developing a method to evaluate complex, interactive visual analytics systems using objective measures that can be performed in-situ to yield reproducible, generalizable results. His approach is to integrate noninvasive brain imaging using functional near-infrared spectroscopy (fNIRS) and cognitive factors measurements. The PI argues this will allow him to address issues in visual analytics evaluation by explaining the user's cognitive processes at a deeper level. Lightweight, noninvasive brain imaging techniques such as fNIRS have become more mature and reliable in recent years. fNIRS is easy to set up, robust to movement, and has been demonstrated in studies to be effective in determining a user's cognitive load, preferences, and perception when using a visualization. Cognitive factors such as locus of control, spatial visualization ability, and perceptual speed have recently been shown to correlate with a user's ability to interact with a visualization, and can be generalized to predict the behavioral patterns of users with different cognitive profiles. Both approaches aim to better understand the user's cognitive state and abilities. In this research cognitive factors measurements will provide low-level, baseline information about the user which is stable and unchanging ("traits"), while fNIRS provides immediate, real-time feedback on the user's current cognitive state when interacting with a visualization ("states"). In practice, without accounting for the individual user's traits, it is difficult to generalize the signals provided by fNIRS (for example, right- and left-handed subjects produce very different brain signals). By combining information on both "traits" and "states," evaluation results can generalize to a larger population based on cognitive profiles.

The PI and his team have conducted two preliminary experiments that demonstrate the feasibility of the approach. They have replicated the classic experiment by Cleveland and McGill using fNIRS, and successfully distinguished participants' brain signals when using bar charts versus pie charts. In another experiment, they successfully correlated participants' locus of control with their ability to use hierarchical visualizations with different visual metaphors.

PI: Chen, Jake Jinkun
Title: Adiponectin Promotes Osseointegration of Dental Implants in Type II Diabetes Mellitus Patients
Abstract:
The increased prevalence of diabetes mellitus has become a public health problem. There is evidence that diabetes mellitus has a negative influence on bone formation and remodeling and reduces osseointegration of implants. Adiponectin, an adipose-derived hormone, has a variety of biological functions including increasing insulin sensitivity and anti-inflammation. Besides, adiponectin inhibits osteoclastogenesis and increases osteoclast apoptosis, while enhancing expression levels of osteogenic transcription factors and bone matrix proteins.

The overall aim of this research project is to investigate the effects of adiponectin on osseointegration of dental implants in the type II diabetes mellitus (T2DM). To mimic the clinical gene therapy and cell based therapy, purified globular adiponectin, human adiponectin in a carrier, and adiponectin overexpressing BMSCs will be injected systemically or applied locally to accelerate bone regeneration and dental implant osseointegration in T2DM.

Based on previous results, either systemic infusion or local application of adiponectin will promote osseointegration of dental implants in T2DM. Ultimately, the aim is to create an option to improve success rate of dental implants in T2DM and facilitate immediate loading by the replenishment of adiponectin in T2DM patients.

PI: Chen, Jake Jinkun
Title: Therapeutic Strategies for Treating Type 2 Diabetes Mellitus-Associated Periodontitis
Abstract:
Periodontitis is twice as prevalent in diabetics as in non-diabetics. Diabetic periodontal diseases are more severe and refractory because T2DM and obesity trigger the release of excess inflammatory factors, such as TNF-α and IL-6, which in turn stimulate osteoclasts to resorb the alveolar bone that supports the teeth.

Adiponectin, a fat cell derived hormone, is emerging as a potent molecule with multiple biological functions including regulating insulin sensitivity, suppressing inflammation, and improving diabetic symptoms. It also promotes osteoblastic differentiation and bone formation. Our recent studies have shown that adiponectin inhibits osteoclast differentiation and increases osteoclast apoptosis.

Our long-term objective is to identify and characterize an ideal endogenous mediator as a potent therapeutic remedy for the treatment of the widely prevalent T2DM-associated periodontitis. The objective of this application is to investigate the mechanisms of adiponectin in the pathogenesis of T2DM-associated periodontitis and to specifically reconstruct the inflammatorily damaged periodontal tissues by the replenishment of adiponectin in vivo. The central hypothesis to be tested is that the decreased level of adiponectin, together with the consequent removal of its suppressive effects on osteoclasts and proinflammatory factors, contributes to the pathogenesis of T2DM and T2DM-associated periodontitis. Also, a systemic adiponectin infusion promotes the reconstruction of the damaged periodontal tissues.

Aim 1: Using an animal model for the first time to determine the effects of anti-inflammatory factor in periodontal pathogenesis including inhibition of differentiation of osteoclasts that directly resorb alveolar bone.

Aim 2: To determine the therapeutic effect of systemic adiponectin infusion in dampening inflammation and in reconstruction of damaged periodontal tissues in vivo.

PI: Chen, Oliver (Chung-Yen)
Title: Evaluation and Screening of Pistachio Extracts for UV Photoprotection and Skin Health in a 3-Dimensional Human Skin Equivalent Tissue Model
Abstract:
Skin health requires a variety of genetic, environmental, and hormonal mechanisms. Pistachios contain an array of antioxidants. Although a variety of natural antioxidants, including flavonoids like catechins from green tea and carotenoids like xanthophylls from marigold flowers, appear to provide antioxidant benefits to the skin, the interactive effect of pistachio antioxidants have yet to be explored. Thus, we propose employing a novel, validated 3-dimensional (3D) human skin cell model to investigate whether antioxidants found in pistachios could protect modeled human skin against UV-induced damage through a medium application.

Our hypothesis is that pistachio extract (PE) and selected constituents will protect human skin equivalents (HSE) against UVA induced damage.

We plan to test our hypothesis by pursuing the following specific aims:

  • Specific Aim 1: Determine the optimal doses of PE and selected constituents (lutein, γ-tocopherol, chlorophyll, and cyanidin-3-galactoside) that maintain or improve skin health.

  • Specific Aim 2: Determine the UV protective capacity of PE.

A human skin equivalent (HSE) tissue will be first constructed. Primary human keratinocytes and fibroblasts obtained from newborn foreskins will be cultured for subsequent incorporation into skin equivalents. Subsequently, pistachio extract and lutein, γ-tocopherol, chlorophyll, and cyanidin-3-galactoside in DMSO will be applied into culture medium. Two hours after nutrient administration, HSE will be exposed to UVA at 35J/cm2. At 48 h post UVA exposure, HSE and medium will be harvested for following assays, including hematoxylin and eosin (H&E) morphology, histological analyses of apoptotic cells using Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay, proliferation, differentiation, and presence of superficial fibroblasts, and secretion of growth factors.

PI: Chen, Oliver (Chung-Yen)
Title: Long-Term Effect of a Cranberry Beverage on Urinary Anthocyanin Status and LDL Oxidation in Moderately Hypercholesterolemic Overweight/Obese Adults: A Randomized, Double-Blind, Placebo-Controlled Clinical Trial
Abstract:
The putative health benefits of cranberries and related products include protection against urinary and gastrointestinal infections and cardiovascular disease. The compounds responsible for the mechanisms of bioactivity have not been fully elucidated, although the focus of most cranberry research has centered on subclasses of polyphenols, especially anthocyanins and proanthocyanins. Previously, we have reported in an acute study in patients with coronary artery disease that cranberry anthocyanins were quickly bioavailable and rapidly eliminated from. Further, our preliminary data obtained from an Ocean Spray-sponsored pharmacokinetic study showed that 6 anthocyanins and 8 anthocyanin glucuronides were detected in the urine of 10 healthy older men and postmenopausal women consuming an 8 oz. serving of low-calorie, sugar-free cranberry juice cocktail (54% juice). However, the extent of anthocyanin accumulation after long term consumption of a cranberry beverage remains to be examined. The information on urinary anthocyanin status gathered from this study will help interpret the outcomes of clinical trials of cranberry products.

Lipid peroxidation products are formed during normal cell metabolism via production of an excess of free radicals that can react with unsaturated fatty acids, particularly LDL. Once LDL is oxidized, it is taken up by macrophages through scavenger receptors whose expression is not controlled by cholesterol loading. The accumulation of oxidized LDL (ox-LDL) in macrophages is the first step in the formation of lipid laden foam cells with the ultimate development of atherosclerotic lesions. Thus, information on circulating oxidized LDL can help provide evidence about the health benefits of constituents in cranberry beverages on the risk of cardiovascular disease.

Objectives:

  • To determine anthocyanins and anthocyanin glucuronide metabolites in 24-h urine samples of subjects consuming a cranberry beverage for 12 wk.
  • To determine oxidized LDL in plasma samples of subjects consuming a cranberry beverage for 12 wk.

PI: Chen, Oliver
Title: The Effect of Whole Almonds on Glucoregulation, Endothelial Function, Inflammation, Lipid Profile, and Oxidative Stress in Chinese Patients with Type 2 Diabetes
Abstract:
The benefit of nuts in lowering serum cholesterol has been largely substantiated, with a consequent FDA-approved qualified health claim for the reduction of risk for coronary heart disease. In addition, nut consumption has been associated with improvement in biomarkers of inflammation, endocrine dysfunction, and oxidative stress that are related to the risk of cardiovascular disease (CVD). Our previous study demonstrated almonds (~60 g/d) improved lipid profile, glucoregulation, inflammation, and oxidative stress in 20 Chinese patients with type 2 diabetes mellitus (T2DM). To follow-up and expand this work with a more robust trial, we propose a larger (n = 40), longer-term (90-d) investigation of the effect of almonds (~60 g/d) on adipokine regulation, endothelial function, glucoregulation, inflammation, lipid profile, and oxidative stress in Chinese patients with T2DM as compared to a placebo control.

The main goal of the randomized, crossover, placebo-controlled, controlled feeding trial is to determine if 3-month supplementation of ~60 g/d almonds that are incorporated into the NCBP step II diet to replace 20% calories will improve measures of glucoregulation, endothelial function, adipokine regulation, inflammation, oxidative stress, and lipid profile.

The clinical trial will be conducted at Taipei Medical University in Taiwan. We will conduct a 7-mo randomized, cross-over, placebo controlled clinical trial in which all meals will be provided to all subjects. During the first 2 wks (run-in period), all subjects will receive a control diet resembling a typical Taiwan diet, prepared based on the NCEP Step 2 guidelines. During the following 3 mo (Phase I), subjects will be randomized to receive either the control diet or the control diet with whole almonds (~60 g/d) incorporated to replace 20% calories. After a 2-wk washout period during which all subjects will once again receive the control diet, subjects will receive the opposite diet to the one assigned during the Phase I for the other 3 months (Phase II). The caloric content of each diet will be adjusted to each subjects’ energy needs to prevent any change in body weight. The following biomarkers will be determined at the baseline and end of each dietary intervention: Glucoregulation: fasted serum HbA1c, glucose and insulin, postprandial serum glucose and insulin, and urinary C-peptide; Endothelial Function; brachial artery FMD and serum nitric oxide, e-selectin, endothelial-1 (ET-1), and intracellular adhesion molecule-1 (ICAM-1); Adipokine Regulation: serum adiponectin, leptin, and resistin; Inflammation: serum high-sensitivity C-reactive protein (CRP), interleukin (IL)-6, IL-10, retinol binding protein-4 (RBP-4), and tumor necrosis factor (TNF)-α; Oxidative Stress: urinary isoprostanes (adjusted for creatinine) and serum protein carbonyls and oxidized LDL; and Lipid Profile: serum cholesterol, triglycerides, and apolipoproteins A1 and B.

PI: Chen, Oliver
Title: Urinary Proanthocyanidin (PAC) A2 as a Biomarker of Compliance to Intake of Cranberry Products – A Pilot Study
Abstract:
Apparent lack of compliance in long-term clinical trials to the daily consumption of cranberry juice has confounded the interpretation of several studies investigating the effect of this beverage on health outcomes, particularly urinary tract infections. A-type proanthocyanidins (PACs) are phytochemicals not commonly found in plant foods; however, cranberries are a rich, natural source of A-type PACs. Thus, PAC-A2 may be served as a useful biomarker of cranberry intake.

We hypothesize that PAC-A2 could serve as a valid biomarker of cranberry intake.

The objective is to determine whether urinary PAC-A2 concentration (adjusted for creatinine) in young, healthy females consuming a cranberry beverage will increase with frequency of consumption of a cranberry beverage.

We will conduct an 8-wk clinical trial with 5 generally healthy premenopausal women, age 20-40 y, with a BMI of 18.5-25 kg/m2. The study design with a 6 progressive dosing scheme will be arranged to test the utility of PAC-A2 as a biomarker of compliance by testing actual intakes of a cranberry beverage:

  1. consume only 1 time on the first day (wk 1);
  2. 2 times – on the first and last days (wk 2);
  3. 3 times – at the beginning, middle, and end of the test period (wk 3);
  4. 4 times with one day of non-compliance falling on the last day (wk 4);
  5. 4 times with one day of compliance falling on the day before the last day (wk 5); and
  6. full compliance for 7 d (wk 6).

Urine samples (24-h collected on the last day and morning spot urine samples collected on the following day) collected from each dosing scheme will be analyzed for PAC-A2 using LC-MS/MS.

PI: Chiesa, Luisa
Title: Superconducting Technology for Magnet Systems in Fusion Machines
Abstract:
Superconducting magnets play a key role for the confinement of plasma in a large fusion energy machine providing magnetic fields high enough to confine the plasma and produce substantial fusion power density. The magnet components alone account for a considerable fraction (~30% for ITER) of the investment in the fusion machine (~50% of the magnet system cost is for superconducting materials). High field fusion magnets of Nb3Sn low temperature superconductors have showed unexpected sizable degradations compared to the expected currents estimated from single strand values. Those degradations are due to the inherent mechanical loads caused by thermal contractions and operational electro-magnetic forces. ITER model coil tests have shown the degradations could be as high as 50% in fusion magnets.

My long term career goal is to pursue research and education in superconducting materials and magnet systems for fusion machines. The objective of this project is to understand the electromechanical behaviors of superconducting materials both low (LTS) and high temperature superconductors (HTS).

PI: Chisholm, Karen
Title: MACC AmeriCorps*Vista Program (2012-2013)
Abstract:
Massachusetts Campus Compact (MACC) is a statewide consortium of 73 colleges and universities committed to developing the civic skills of students, building partnerships with the community, and integrating civic engagement with teaching and research. Through technical assistance, grant distribution, training, and resource development, MACC aids students, faculty, staff and presidents in developing and improving community service and service-learning programs to respond to specific local and regional needs throughout Massachusetts. MACC supports the leveraging of college and university resources to address community problem-solving and directly target issues faced by low-income communities.

Non-profit community based organizations (CBOs) face a number of challenges in their respective communities. These can include an increasing demand for their services that does not match their capacity; fewer resources; unmet funding needs; and increasing need for assessment and evaluation. Developing a partnership with a neighboring college and/or university can be an effective way to respond to these challenges.

The MACC VISTA program has been successful in deepening higher education's impact on low-income communities through a focus on the development of sustainable internal systems for civic engagement and the development of partnerships between colleges and community-based organizations. As a result of MACC VISTA efforts, there are more partnerships between community-based organizations and colleges and universities. There are more students civically engaged in their communities through volunteer opportunities, community service federal work-study, and service learning programs, among other things. Overall, there is an increased capacity for institutions of higher education to continue to serve communities in meaningful ways.

PI: Chishti, Athar
Title: Calpain-1 Signaling Pathways in Platelets
Abstract:
The overall aim is to test the hypothesis that calpain-1 regulates platelet signaling events by modulating the activity of PTP1B by a conserved mechanism.

PI: Chishti, Athar
Title: Cytoskeletal Regulation of Erythorocyte Glucose Transporter-1
Abstract:
The overall aim is to test the hypothesis that the spectrin-actin junctions play a critical role in the maintenance of red blood cell shape and membrane properties. This hypothesis will be tested by identifying new membrane receptors for dematin and adducing in both erythroid and non-erythroid cells.

PI: Chiu, Chung-Jung
Title: Development of a Prediction Model for Advanced Age-Related Macular Degeneration
Abstract:
Age-related macular degeneration (AMD) is a progressive disease, the advanced forms of which account for over 50% of legal blindness in the US. Vision impairment due to advanced AMD also significantly reduces quality of life and consumes a large portion of Medicare budget. Diminishing the modifiable risk factors for the progression of AMD could lead to significant clinical benefit and save health care cost. However, early identification and close follow-up of patients at high risk of developing advanced AMD are essential to allow for implementing strategies to delay progression of the disease to stages when vision is compromised. Recently, using the Age-Related Eye Disease Study (AREDS) dataset PI (Chiu) developed a prediction model for advanced AMD (c-index=0.877). However, validation analysis of this AREDS model in the Blue Mountains Eye Study (BMES) cohort indicated that it is necessary to use data from multiple cohorts to develop a prediction model with maximal generalizability.

Our objective is to use risk factor information provided in the patient history and clinical eye examinations to develop a widely applicable tool for the early prediction of advanced AMD.

PI: Cochran, Brent
Title: RNAi Screen of the Glioblastoma Stem Cell Kinome under Hypoxia and Normoxia
Abstract:
Glioblastomas are highly aggressive brain tumors with a mean survival time of only 14 months. There is increasing evidence that brain tumors and glioblastomas in particular are driven by a subpopulation of cancer stem cells. It has recently been possible to isolate and maintain continuously in culture these putative tumor stem cells. These cells grow as neurospheres and retain the ability to differentiate into neurons and astrocytes despite being highly tumorigenic mouse xenografts. We have developed methods for high throughput screening of these GBM stem cells using RNAi. Here we propose to comprehensively identify kinases that are required for the growth and survival of glioblastoma stem cells under normoxic and hypoxic conditions. We will focus on kinases since they are druggable targets for which a great many inhibitors are already available and for which several have already been clinical successes.

Our first aim will be to perform shRNA screens of the human kinome to identify kinases commonly required for the growth and survival of glioblastoma stem cell lines. Our preliminary results indicate that the kinases required for tumor stem cell growth are distinct from the kinases required for growth of traditional serum grown cell lines. Thus, these screens are likely to uncover new kinase targets for glioblastoma therapy. Moreover, glioblastomas are known to be tumors that have hypoxic microenvironments that can limit the efficacy of traditional therapies. Our evidence indicates that glioblastoma stem cells actually thrive under hypoxia. Our preliminary data also indicates that there are kinases that are required for tumor stem cell growth under normoxic conditions, but not hypoxic conditions and vice versa. Identifying the kinases that are required for growth and survival under hypoxic conditions is thus critical for elimination of cancer stem cells in the tumor. Thus, we will screen these GBM stem cells under both hypoxic and normoxic conditions.

In the second aim, we will investigate the cellular functions of kinases identified in the RNAi screens. In addition, we will determine whether key kinases identified in the screen are in fact activated in primary human glioblastomas, and determine whether inhibition of these kinases in mouse xenografts will inhibit tumor growth. Results of these studies should identify and prioritize new kinase targets for treatment of glioblastoma.

PI: Coffin, John
Title: Molecular Biology of Retroviruses
Abstract:
Retroviruses are important causes of cancer and other diseases, such as AIDS, in humans and other animals. Because they are relatively simple and have a very close association with the cells of their host, they provide scientists with powerful tools to understand the workings of the normal cell as well as how small changes in genes cause a normal cell to become a cancer cell. Work in my laboratory is directed toward obtaining a better understanding of fundamental aspects of the interaction between the cells and the viruses they grow in. Our current research is directed toward several aspect of this interaction. We are studying how the virus "sees" the target cell and enters it to start the replication cycle. The ability of retroviruses to integrate or merge their genetic information in the form of DNA called a provirus also allows them to become part of the inherited genetic information of humans and other vertebrates. The contribution of such endogenous viruses to evolution is another interest of my laboratory. These agents are important causes of breast cancer and leukemia in mice; we are initiating a program test their role in human disease. Finally, we are interested in the evolution of the viruses themselves – how they change from relatively benign to highly dangerous agents of serious disease, such as AIDS and cancer. We are developing both theories of virus evolution and model systems to test those theories.

PI: Coffin, John
Title: Retrovirus Evolution
Abstract:
Retroviruses exhibit a wealth of evolutionary phenomena, including the ability to undergo rapid genetic change in response to varying selective pressure; the ability to vary in the use of host cell receptors; and the ability to become integrated in the genome of their host species and passed down through the generations as endogenous proviruses. In the prior project period, we have studied all these aspects of retrovirus evolution:

  • We have looked at the mechanism of evolution of env genes by analyzing an unusual mutant that extends the host range of ALV beyond chicken, to quail, dog, and even human cells.

  • We have isolated and studied an unusual mouse endogenous provirus that appears to occupy a special phylogenetic location between mouse and non-mouse species.

  • We have extensively analyzed the coevolution of humans and their endogenous proviruses, particularly the relatively recently inserted HERV-K family.

  • We have developed sophisticated mathematical models for the evolution of replicating virus populations, describing the effects of mutation, selection, drift, linkage, and recombination on the accumulation (or loss) of deleterious mutations.

Future work will address the following aims:

  1. How do retroviral envelope genes evolve to use new receptors and to alter other important properties? We will use our extended host range mutants to test specific hypotheses for this process.

  2. What are the functional and pathogenic properties of human endogenous retroviruses, particularly HERV-K? Can we isolate infectious virus? Is their expression or reintegration associated with malignancy?

  3. How do important the forces of mutation, selection, recombination, and drift combine to direct retrovirus evolution? We will combine mathematical and in vitro modeling of virus replication to test specific evolutionary models.

PI: Cook, Robert
Title: Mechanisms of Avian Visual Perception, Cognition, and Action
Abstract:
Vision is one of the enduring puzzles of modern cognitive science and elucidating the mechanisms of visual object perception presents a particular challenge. Nothing in the reflected light that arrives at the retina contains direct information about the location, shape, size, or number of objects in view. Understanding how the brain processes visual stimuli to derive this information would be a major advance in visual science. Because birds are active and mobile, avian visual systems must resolve the same problems that have driven theoretical advances in human and machine vision research. Examining these issues in such small, non-mammalian systems adds substantially to the development of a unified general theory of vision. Using our well-developed psychophysical techniques based on discrimination learning, we propose to evaluate this problem by examining in how starlings and pigeons process visual stimuli in controlled analytical contexts. This will be the first parallel comparison of visual processing in two avian species.

The overall objective of this application is to investigate and compare how these species solve central problems of visual cognition and object perception as related to the processing of illumination and shading, edge processing and figural grouping, and the recognition and classification of behavior and action. Our specific aims include:

  1. Equating our procedures for the comparative examination of visual processing in these species;
  2. Examining the processing of surface shading and its contributions to object and depth perception;
  3. Examining edge and figural grouping processes in shape perception; and
  4. Examining the mechanisms of visually-mediated action and movement recognition.

The current project is a part of our long-term objective to understand the proximate psychological, computational and neural mechanisms by which different pattern recognition systems perceive, recognize, categorize, integrate, understand, and respond to complex visual information. The unique combination of visual power, small size, and different neural organization exemplified by birds offers a special scientific opportunity for better understanding this extremely important sensory modality and how it functions and is implemented across different classes of animals. This comparison will address whether there are only a few biologically plausible mechanisms for rapid visual processing of objects or whether there are multiple routes to functional vision in highly mobile organisms. Because there is strong evolutionary pressure for highly efficient and rapid computation of visual information placed on the small, highly visual brain of birds, our results will contribute directly to the practical development of treatments, corrective solutions or prostheses for humans with a variety of visual disorders and to the design of visual sensors for self-guided bio-mimetic robotic devices.

PI: Crane, Gregory
Title: CNR and the Perseus Collaboration
Abstract:
Our overall goal is to develop generalized infrastructure that enhances the role that textual sources can play in formal teaching and research, as well as in the broader life of society. We wish to support a global republic of letters, one that bridges stubborn boundaries not only of space but also of language and culture as well. A speaker of Chinese should, in this environment, be able to work closely with sources on the Greco-Roman world that survive in Greek and Latin. American citizens, intrigued by visions of Ancient Chinese culture that they have encountered, whether in formal study or in popular culture, should likewise be able to work directly with sources in Chinese.

Our work during 2012/2013 will focus on the following tasks:

  1. Developing a digital humanities curriculum in Italian, Arabic and English
  2. Localization of Perseus Infrastructure. with an initial focus on Italian and Arabic
  3. Addition of early modern Italian authors to the Perseus Digital Library
  4. Aligning efforts at Perseus and CNR to work with Classical Arabic
  5. Additional improvements to processing of source texts

PI: Crane, Gregory
Title: DC: Large: Collaborative Research: Mining a Million Scanned Books: Linguistic and Structure Analysis, Fast Expanded Search, and Improved OCR
Abstract:
The Center for Intelligent Information Retrieval at UMass Amherst, the Perseus Digital Library Project at Tufts, and the Internet Archive are investigating large-scale information extraction and retrieval technologies for digitized book collections. To provide effective analysis and search for scholars and the general public, and to handle the diversity and scale of these collections, this project focuses on improvements in seven interlocking technologies:

  1. Improved OCR accuracy through word spotting, creating probabilistic models using joint distributions of features, and building topic-specific
    language models across documents;

  2. Structural metadata extraction, to mine headers, chapters, tables of contents, and indices;

  3. Linguistic analysis and information extraction, to perform syntactic analysis and entity extraction on noisy OCR output;

  4. Inferred document relational structure, to mine citations, quotations, translations, and paraphrases;

  5. Latent topic modeling through time, to improve language modeling for OCR and retrieval, and to track the spread of ideas across periods and genres;

  6. Query expansion for relevance models, to improve relevance in information retrieval by offline pre-processing of document comparisons; and

  7. Interfaces for exploratory data analysis, to provide users of the document collection with efficient tools to update complex models of important entities, events, topics, and linguistic features.

When applied across large corpora, these technologies reinforce each other: improved topic modeling enables more targeted language models for OCR; extracting structural metadata improves citation analysis; and entity extraction improves topic modeling and query expansion. The testbed for this project is the growing corpus of over one million open-access books from the Internet Archive.

PI: Crane, Gregory
Title: The Hellespont Project: Integrating Arachne and Perseus
Abstract:
We propose to combine and expand the collections of two of the oldest and most established digital projects in Classical Studies – Arachne at the University of Cologne and Perseus at Tufts University – and thus to create a single comprehensive digital library about the ancient world. The resulting collection will contain CIDOC-CRM metadata for more than 250,000 archaeological sites and objects, MODS/FRBR bibliographic records for editions of every major Greek and Latin author whose work survives either in the manuscript tradition or in substantial fragments, and TEI P5 compliant XML transcriptions for 20 million words of Greek and Latin primary sources, as well as for more than 50 million words of archaeological documentation, major lexica, commentaries, and encyclopedias. The lead partners at Cologne and Tufts University are, in addition, already collaborating closely with computer science projects at Leipzig and the University of Massachusetts at Amherst and dedicated to the analysis of text from the humanities and classics. This collection will therefore include a range of metadata extracted from existing databases and mined from the full text of much larger collections, including content relevant to classical studies in JSTOR and in the 1.5 million books from the Internet Archive (IA) alone. Users of Arachne and Perseus will have access to the full collections available in each. More importantly, everything that we produce will be available for download under a Creative Commons License in formats that conform to optimal standards and best practices. The German Archaeological Institute (DAI) will, for example, be able to integrate a new generation of cataloguing data into its Zenon Union Catalogue, and general repositories such as the Hathi Trust, internet giants such as Google, and small groups of collaborators and individual researchers will be able to present and extend the work that we conduct to serve the study of the Greco-Roman world in ways that we cannot now predict.

Both Arachne and Perseus have devoted substantial resources to collecting digital images of archaeological sites and objects. The CIDOC-CRM metadata will facilitate the distribution of approximately 150,000 images of Greco-Roman antiquity, but in this project we will also focus upon the challenge of documentation. With the rise of inexpensive digital cameras and the increasing acceptance of flashless photography in museums, the challenge has shifted from collecting digital images to contextualizing and analyzing the many images becoming available online. In an August 2009 visit to Berlin, American PI Crane, for example, took more than 300 digital pictures in an intensive visit of the Antikensammlung and Pergamonmuseum, including many details not visible in published images. What is still lacking for users of these images is information necessary to enhance their understanding of them, descriptions of traditional museum catalogues but the full record, textual and material, of the Greco-Roman world.

PI: Crott, Jimmy
Title: Effect of Maternal B Vitamin Intake on Intestinal Tumorigenesis in Offspring
Abstract:
Parental diet and exposures are being increasingly recognized as determinants of disease risk in offspring. Indeed there are already epidemiological studies indicating that maternal diets high in folate are protective against several pediatric cancers. Our contribution has been to demonstrate that maternal supplementation with vitamins B2, B6, B12 and folate can suppress, while mild deficiency can promote, intestinal tumorigenesis in mouse offspring. We also observed a decrease in Sfrp1 expression, elevation in Sfrp1 promoter methylation and elevation total B catenin in the small intestine of offspring with decreasing maternal B vitamin intake, together pointing towards as a de-repression of the Wnt pathway. Although our observations constitute a highly biologically plausible mechanism they do not definitively prove causality. Now, using a Sfrp1 knockout mouse, we hope to address this.

We hypothesize that B maternal B vitamins are protective against offspring intestinal tumors by preventing a methylation and suppression of Sfrp1 expression. We aim to test this by repeating our previous study using Apc1638N mice that also lack Sfrp1. In this fashion, we anticipate that Sfrp1 knockout will ablate the protective effect of B vitamins, thereby proving a true causal role for the Wnt pathway, starting at Sfrp1. Briefly, Sfrp1-/- female mice will be fed diets either mildly deficient, adequate, or supplemented with vitamins B2, B6, B12 and folate for 4 weeks before being mated with Apc1638NSfrp1-/- mice. All Apc1638NSfrp1-/- offspring will be maintained on a replete diet, irrespective of their mother's diet, for 8 months. After this time animals will be studied for the presence of tumors as well as activation of the Wnt pathway and the downstream processes of apoptosis and proliferation.

The relevance of this work is underscored by the fact only around one-third of US women report taking vitamins containing folate before conception and that mild inadequacies of B2, B6, B12 occur in 10-50% of the US and European populations. This contribution is significant because understanding how B vitamins modulate the development of cancer in individuals and their offspring is essential for developing intelligently-constructed and effective measures that will utilize these vitamins in the prevention of cancer.

PI: Crott, Jimmy
Title: Effect of Paternal B Vitamin Intake on Intestinal Tumorigenesis in Offspring
Abstract:
Parental diet and exposures are increasingly recognized as determinants of disease risk in offspring. Our contribution here has been to demonstrate that maternal supplementation with vitamins B2, B6, B12 and folate can suppress, while mild deficiency can promote, intestinal tumorigenesis in mouse offspring. We propose that modulating paternal diet will have similar effect on tumorigenesis in offspring. This issue is of importance because there may exist an opportunity to exploit a previously ignored means to lower the incidence of cancer in our society. Unlike the situation for expectant mothers, there are no dietary recommendations for men prior to conception and the incidence of mild deficiencies of vitamins B2, B6, B12 remains high in the US (10-50%). Furthermore, despite the rarity of folate deficiency in the US, our data in mothers indicates that intakes above and beyond those considered adequate are required to maximally suppress intestinal tumorigenesis in offspring and that intakes considered 'adequate' are associated with elevated tumor incidence in offspring.

Our long term goal is to minimize the risk of cancer in offspring by optimizing diet throughout the life cycle, including that of both parents. The objectives of this application are to determine whether paternal supplementation and depletion with vitamins B2, B6, B12 and folate can alter tumor incidence in offspring and to gain an understanding of the mechanisms involved. We hypothesize that supplemental quantities of vitamins B2, B6, B12 and folate in the paternal diet will suppress, while combined mild deficiency will promote tumorigenesis in offspring. Furthermore, that such effects will be associated with the prevention or promotion of deleterious promoter methylation and gene expression changes of members of the "Wnt" signaling pathway, a pathway that regulates cell division and death and is commonly disrupted in colorectal cancer.

The primary specific aim of this proposal is to determine whether paternal supplementation of mild depletion of vitamins B2, B6, B12 and folate alters the incidence of intestinal tumors in offspring. A secondary aim is to determine whether observed changes in tumor incidence are associated with changes in the expression and methylation of Wnt pathway genes in the normal intestinal mucosa. This contribution is significant because understanding how B vitamins modulate the development of cancer in individuals and their offspring is essential for developing intelligently-constructed and effective measures that will utilize these vitamins in the prevention of cancer.

PI: Cunningham, Suzanne
Title: The Effect of Heart Failure on Circulating Endothelial Progenitor Cell Concentrations in the Dog
Abstract:
Cardiovascular disease is a significant cause of morbidity and mortality in the dog, estimated to affect at least 11% of the total canine population and more than 30% of dogs over the age of 10 years. The precise etiologic factors underlying the development and progression of both vascular disease and cardiomyopathy remain elusive, but both of these afflictions are progressive conditions that ultimately result in congestive heart failure (CHF). Once CHF develops, treatment is limited to symptomatic management and death typically occurs from refractory dyspnea or euthanasia within months to a year of diagnosis.

The normal vascular endothelium maintains a vasodilatory, anti-inflammatory, and anti-proliferative homeostatic state. Impaired function of the vascular endothelium accompanies CHF in humans and is associated with inappropriate vasoconstriction, diminished tissue perfusion, reduced exercise tolerance, and disease progression. A recent study from our group has also identified endothelial dysfunction in dogs with CHF, demonstrating an association between worsening endothelial function and increase in CHF severity. Circulating bone-marrow-derived endothelial progenitor cells (EPCs) play a crucial role in the maintenance and repair of the vascular endothelium. In addition to their crucial role in angiogenesis, EPCs may promote regeneration of injured myocardium by releasing paracrine factors to mobilize tissue resident cardiac progenitor cells, thus improving myocardial function. As such, alterations that reduce the availability of EPCs shown in human patients with CHF may contribute to and worsen endothelial and cardiac dysfunction. Reduced circulating EPC concentrations in people also serve as independent predictors of the development of a major cardiovascular event in humans.

A decrease in the number of circulating EPCs accompanying CHF has been hypothesized to result from exhaustion of the bone marrow reservoir, reduced cell mobilization from the bone marrow, and an increase in the frequency of apoptosis. Moreover, inflammatory mediators such as C-reactive protein and tumor necrosis factor (TNF-α) are increased in CHF and have been shown to exert direct inhibitory effects on EPC differentiation, survival, and function. Consequently, human patients with CHF and endothelial dysfunction who have the greatest need for the reparative functions of EPCs paradoxically have the lowest circulating numbers of these cells. Research has shown that transplantation of EPCs via intracoronary infusion in human patients suffering from myocardial infarction results in a significant increase in left ventricular contractile function, and the possibility of EPC-based therapy for canine heart disease merits further exploration.

Though EPCs typically circulate in relatively low numbers, a variety of flow cytometric protocols and cell culture techniques have been utilized to identify EPCs from whole blood. However, to date, no single standard method has been established to best isolate and characterize circulating EPCs in people or dogs because of the lack of unifying phenotypic markers. The lack of consensus results from the change in phenotypic markers as the progenitor cells mature. In the bone marrow, EPCs are thought to be CD45-, CD34+, CD133+, and VEGFR-2+. As these cells mature to early circulating EPCs, they remain CD34+ and VEGFR-2+ but become CD133+. Even more differentiated cells are thought to lose the CD34 marker and start expressing markers similar to mature endothelial cells such as von Willebrand Factor (vWF), CD31, VE-cadherin, endothelial nitric oxide synthase (eNOS), CD146, and uptake acetylated LDL. However, the exact points at which these changes in marker expression occur are still unknown. To date, our laboratory has cultured potential endothelial cells from canine peripheral blood that are CD34-/CD45+/CD146+ where the CD146 marker intensity increases after 1 passage of the cell culture.

Hypothesis:

Circulating bone-marrow-derived EPCs can serve as a biomarker for cardiovascular disease. To our knowledge, EPC concentrations have not been characterized in dogs with naturally occurring CHF. The purpose of this study is to validate the protocol currently under development in our laboratory for the identification and isolation of circulating EPCs in dogs, and to subsequently characterize changes in circulating EPC concentrations in dogs with CHF. We hypothesize that a decrease in circulating EPC concentration will accompany CHF in dogs, and that EPC numbers will increase with successful short-term CHF therapy. We expect that the results from this study will help further the understanding of the role that EPCs play in cardiac repair in dogs with heart disease and will help guide future research into stem-cell-based therapeutics to treat or delay the progression of cardiovascular disease.

Aims:

  1. To validate our method for isolating EPCs from canine peripheral blood
  2. To quantify the difference in EPC concentration between dogs with and without CHF

PI: Danahy, Ethan
Title: InterLACE: Interactive Learning and Collaborative Environment
Abstract:
This project, under the Tufts University Center for Engineering Education and Outreach (CEEO) designs, constructs, and field-tests a web-based, online collaborative environment for supporting the teaching and learning of inquiry-based high school physics. Based on prior NSF-funded work on RoboBooks, an interactive digital workbook environment, the team is customizing the platform to include scaffolds and other supports for learning physics, fostering interaction and collaboration within the classroom, and facilitating a design-based approach to scientific experiments. The InterLACE team hypothesizes that technology seamlessly integrating physics content and process skills within a classroom learning activity will provide a wide variety of student benefits, ranging from improved learning outcomes and increased content knowledge to gains in attitudinal and social displays as well.

The hypothesis for this work is based on research that indicates teachers believe proper implementation of design-based, inquiry projects are time consuming and can be difficult to manage and facilitate in classrooms without great scaffolding or other supports. Using design-based research with a small number of teachers and students, the PIs iteratively develop the system and supporting materials and generate a web-based implementation that supports students through the various stages of design inquiry. A quasi-experimental trial in the final years of the project is used to determine the usability of the technology and efficacy of the system in enhancing teaching and learning. Through the tools and activities developed, the researchers anticipate showing increases in effective inquiry learning and enhanced accessibility to meet the needs of diverse learners and teachers, leading to changes in classroom practice.

Through this project the PIs (1) gain insights that will enable them to refine the InterLACE platform so it can be implemented and brought to scale in the near terms as a support for design-based inquiry science projects, and (2) advance theory, design and practice to support the design of technology-based learning environments, and (3) understand how connecting students hypotheses, ideas, and data impacts their learning of physics content and scientific inquiry skills.

PI: Davies, Paul
Title: Novel Actions of Neurosteroids on GABAA Receptor Trafficking
Abstract:
Tonic inhibition determines the excitability of neurons and the activity of neuronal circuits through the persistent activity of specialized populations of high affinity extrasynaptic γ-aminobutyric acid A receptors (GABAARs), that are the principle targets of neurosteroids. Neurosteroids are widely accepted as endogenous regulators of GABAergic inhibition. Fluctuations in the levels of neurosteroids are accepted to play a critical role in epilepsy, and are also relevant to autism, anxiety, depression, premenstrual syndrome and schizophrenia. However, to date, there is a fundamental gap in understanding how fluctuations in the levels of neurosteroids change extrasynaptic GABAAR subunit expression levels, which are a significant factor in the changes in GABAergic inhibition that occur in a plethora of neuropsychiatric disorders.

Our long-term goal is to fully understand the mechanism by which neurosteroids influence the expression levels of extrasynaptic GABAARs. In this proposal we will address the role that neurosteroids play in protein kinase C (PKC)-dependent phosphorylation of α4 subunit-containing GABAARs. We will determine how this influences the cell surface accumulation of the GABAAR subtypes that mediate tonic inhibition. Our central hypothesis is that neurosteroids modulate the phosphorylation of GABAARs assembled from α4β3 and δ subunits, which mediate the majority of tonic inhibition in the dentate gyrus and thalamus. Neurosteroids specifically potentiate PKC-dependent phosphorylation of serine 443 (S443) in the α4 subunit. This increased phosphorylation leads to enhanced insertion of receptors composed of α4β3 and δ subunits into the plasma membrane that originate within the secretory pathway. These enhancements of receptor cell surface stability are responsible for sustained increases in the efficacy of tonic inhibition. Guided by strong preliminary data, this hypothesis will be tested by pursuing three specific aims:

  1. Determining the role of PKC-dependent phosphorylation in modulating the specific cell surface accumulation of GABAARs that mediate tonic inhibition
  2. Visualizing neurosteroid-mediated changes in cell surface stability and membrane trafficking of GABAARs and
  3. Ascertaining the effects of neurosteroid-dependent phosphorylation on the activity of GABAARs and the efficacy of tonic inhibition.

In summary this proposal will demonstrate a new and unexpected mechanism by which neurosteroids exert persistent and sustained changes in the efficacy of tonic inhibition. Understanding neurosteroid-mediated changes in phosphorylation and cell surface expression of GABAARs has the potential to translate into better understanding of neuropsychiatric disorders. Moreover such information is likely to lead to the development of more efficacious treatments for anxiety, depression, premenstrual syndrome, schizophrenia and substance abuse.

PI: Davis, Barbara
Title: Evaluating Grading Systems for Accurate Prognosis of Canine Cutaneous Mast Cell Tumors
Abstract:
This proposal addresses the need to develop biomarkers specific to canine cutaneous mast cell tumors (MCT) that can be used to quantitatively, efficiently and accurately predict tumor behavior. In dogs, mast cell tumors are one of the most common cancers, comprising up to 21% of all canine skin cancers. Clinical outcomes of cutaneous MCT can vary from easily cured isolated tumors to fatal metastases. Failure to accurately predict the outcome can result in patients being subjected to painful and expensive treatments unnecessarily or, conversely, not getting the intensive treatment they need. The current markers for MCT only accurately predict outcome in a small number of patients. Moreover, these techniques are subjective and labor-intensive. A major effort is underway to develop molecular and biological tests for diagnosis and prognosis in human oncology. We intend to apply this approach to canine cutaneous MCT, through active collaborations between pathologists at Tufts Cummings School of Veterinary Medicine and veterinary oncologist and molecular biologists at the Broad Institute who have identified a number of unique potential biomarkers for canine MCT.

PI: Dawson-Hughes, Bess
Title: A Pilot Study of the Effect of Dietary Fat Type and Amount on Vitamin D3 Absorption
Abstract:
This is a single blind, randomized, controlled 1-day study in which healthy Caucasian men and postmenopausal women age 50 years and older will be studied between October 1 and May 15, when skin synthesis of vitamin D is relatively low. Up to 65 subjects will be enrolled in order to have 60 completers. Subjects will be randomly assigned to one of three meal conditions – high MUFA/PUFA (30 completers), low MUFA/PUFA (15 completers), or fat-free (15 completers). Within the high MUFA/PUFA group, subjects will be randomized to the standard 50,000 IU dose of D3 (15 completers) or to the lower, more commonly consumed dose of 800 IU of vitamin D3 (15 completers). The two vitamin D doses will be accompanied by 800 IU of deuterated D3, so that absorption can be measured precisely. Subjects will come to the center at 7:00 am for a blood draw, breakfast meal, vitamin D dosing. They will return that evening for blood draws at 10, 12, and 14 hours after receiving the vitamin D. All meals on the study day will have the same nutritional composition as their breakfast meal and will be provided by the HNRCA. The plasma D3 and deuterated D3 will be quantified by LC MS and lipids and fatty acid levels will also be assayed. Changes in the three meal groups will be compared as will the fractional absorption from the two vitamin D doses.

PI: Dawson-Hughes, Bess
Title: Musculoskeletal Benefits of Bicarbonate in Older Adults – A Dose-Finding Trial
Abstract:
With aging, men and women develop a mild and progressive metabolic acidosis. This occurs as a result of declining renal function and ingestion of acid-producing diets. There is extensive evidence that severe metabolic acidosis causes bone and muscle loss, but the impact of the chronic, mild acidosis on bone and muscle in older individuals has not been established. In our recently completed NIH-funded trial in 171 older men and women, alkalinizing the diet with a bicarbonate supplement daily for 3 months significantly reduced urinary excretion of N-telopeptide (NTX), a marker of bone resorption, and urinary nitrogen, a marker of muscle wasting. Moreover, bicarbonate supplements significantly improved muscle performance in the women. These and other data support a potential role for bicarbonate as a means of reducing the musculoskeletal declines that lead to extensive morbidity and mortality in the elderly. Before proceeding to a long-term bicarbonate intervention study, however, it is important to identify the dose of bicarbonate most likely to be optimal and to characterize the subjects who benefit most from it.

The proposed dose-finding study will extend our previous work in this area by evaluating the effects of placebo and two doses of bicarbonate on urinary NTX and nitrogen excretion and on lower extremity performance. The lowest dose we plan to test is similar to the dose shown in our recent trial to be effective. The proposed study is a double blind, randomized, placebo-controlled, parallel-group trial in which 138 men and 138 women, age 60 and older, will take potassium bicarbonate in doses of 1.0 or 1.5 mmol/kg of body weight or placebo daily for three months. Changes in urinary excretion of NTX and nitrogen and in selected measures of lower extremity performance will be compared across the three groups. The safety and tolerability of the interventions will also be evaluated. This investigation should provide needed information on the appropriate dosing regimen and on the study population that should be enrolled in a future long-term bicarbonate intervention trial to assess the long-term effects of this simple, low cost intervention on important clinical outcomes including rates of loss in bone and muscle mass, falls, and fractures.

PI: Dawson-Hughes, Bess
Title: Role of Sclerostin in Glucose Metabolism
Abstract:
Our overarching goal is to understand the mechanisms by which bone affects glucose metabolism. The specific goal of this proposal is to define the potential role of circulating sclerostin, likely acting through the Wnt β-catenin signaling pathway, as a determinant of fasting plasma glucose in normal and high risk pre-diabetic older adults. We will accomplish this goal by measuring serum sclerostin and β-catenin levels in stored samples taken at the beginning and end of a randomized, placebo-controlled trial conducted in healthy men and women age 65 years and older. Subjects were treated with 700 IU of vitamin D3 plus calcium (500 mg) or placebo daily for 3 yrs. Of the 314 subjects, 92 had pre-diabetes (fasting glucose levels of 100-120 mg/dl) at baseline. The subjects with pre-diabetes, particularly those in the placebo group, had significant increases in fasting plasma glucose over the 3-yr period.

Total body bone mineral content is available in all subjects at baseline and 3 years. Serum sclerostin may be influenced by the amount of bone tissue and this association will be examined in baseline measurements. We will also determine whether changes in serum sclerostin are influenced by 3-yr changes in bone mineral content. Understanding this relationship will be useful to the field, and it may enhance our ability to identify associations between sclerostin and glucose metabolism.

Specific Aim 1: To determine whether starting sclerostin and β-catenin levels or their 3-yr changes predict the 3-yr changes in fasting glucose or insulin levels in subjects with normal and impaired fasting glucose levels.

Hypothesis: Subjects with pre-diabetes, when compared with normal subjects, will have higher starting sclerostin levels and greater increases over 3 years; these differences will be due to impaired Wnt β-catenin signaling, manifested by lower starting levels and greater 3-yr declines in serum β-catenin levels.

Specific Aim 2: To define the association between total body bone mineral content (BMC) and serum sclerostin levels at baseline and to determine whether 3-yr changes in serum sclerostin are associated with 3-yr changes in total body BMC.

PI: Degterev, Alexei
Title: Mechanistic Analysis of Necrostatins: Specific Inhibitors of Programmed Necrosis
Abstract:
Necrosis, a catastrophic cell death caused by overwhelming stress, is a major contributor to human disease. However, very little effort has been made to develop therapies targeting pathologic necrosis due to its perceived uncontrollable nature. This notion has been recently challenged through the discovery that necrosis can result from the activation of intrinsic cellular regulatory pathways, suggesting that necrosis can be specifically targeted for inhibition. As a direct demonstration of the feasibility of this approach, we have developed potent and selective small molecule inhibitors of such regulated necrosis or “necroptosis”. Furthermore, we have used one of these molecules, Necrostatin-1, to demonstrate that necroptosis is an important component of acute pathologic injury in vivo in the case of ischemic brain and heart damage and endotoxic liver destruction. Discovery of necrostatins provides an unprecedented opportunity to develop novel necrosis-specific therapies for human disease.

In preliminary studies, we identified five structurally distinct necrostatins in a cell based high-throughput screen of 100,000+ compounds. Surprisingly, all necrostatins inhibit necroptosis at the level of RIP kinase complex, an established mediator of necroptosis induction, suggesting that it is a key step of this pathway susceptible to inhibition. Interestingly, while all necrostatins act through a similar target, they display distinct activities in different cells, suggesting the possibility of developing cell type-specific inhibitors. In this proposal, we will further investigate the mechanism of necrostatins’ activity in vitro and in vivo.

In Aim 1, we will investigate in vitro interactions of necrostatins with RIP and associated factors using combination of biochemical, mass spectrometry, medicinal chemistry and structural biology methods. In Aim 2, we will apply the insights from Aim 1 to identify key parameters defining differential cellular sensitivity to necrostatins in order to develop specific markers for predicting optimal strategy for necroptosis suppression in various paradigms of pathologic necrosis. In Aim 3, we propose to study how in vitro activities of necrostatins translate into therapeutic benefit in the animal model of acute liver injury.

Overall, our project should further define necroptosis as the key component of pathologic injury and provide mechanistic basis for development of novel necroptosis-specific therapies.

PI: Degterev, Alexei
Title: Molecular and Functional Analysis of Necrotosis Activation Complex
Abstract:
Extensive evidence suggests that two “classic” cell death pathways, apoptosis and necrosis, do not encompass the full variety of physiological and pathological cell death mechanisms. Our and other laboratories have established the existence of a common third pathway, termed “programmed necrosis” or “necroptosis.” Necroptosis is a regulated cell death pathway with phenotypic features of necrosis. It is activated in cells that are induced to undergo apoptosis, yet prevented from its completion. We have recently developed a potent and selective small molecule inhibitor of necroptosis, Necrostatin-1, and using this molecule has demonstrated the important role of necroptosis in various paradigms of pathologic cell death in vitro and in vivo. Discovery of necroptosis offers unique opportunity to develop novel therapies specifically targeting necrotic component of pathologic cell death, which was previously not pursued due to the notion that necrosis is an unregulated form of death.

However, little is currently known regarding the specific mechanisms of activation and execution of necroptosis. Ser/Thr kinase RIP has emerged as the key upstream activator of necroptosis. Furthermore, we have recently established that RIP kinase activity is a specific cellular target of Necrostatin-1 and several other structurally unrelated potent necrostatins that were also developed in our laboratory, highlighting the critical role of RIP kinase in necroptosis. In our preliminary studies, we developed new assays to specifically measure RIP kinase activation and necroptosis induction. We performed preliminary mass spectrometry-based characterization of RIP kinase that led to the identification of a number of novel and specific posttranslational modification (phosphorylation) events that are potentially involved in the regulation of necroptotic activity of RIP. We also demonstrated the feasibility of assessing dynamic changes in the composition of the endogenous RIP interactome using mass spectrometry analysis.

Our current proposal focuses on further studies of the mechanism of necroptosis induction by RIP kinase. The specific aims of the project include confirming the role of RIP phosphorylation changes, previously identified by us, in the activation of necroptosis; characterization of RIP kinase activation process in vitro and in vivo using phosphospecific RIP antibodies and RIP kinase assay; dissection of RIP interactome using high resolution mass spectrometry followed by functional characterization of the role of RIP interacting factors in necroptosis initiation; and establishing the feasibility of the necroptosis inhibition by necrostatins as a new direction for cytoprotective therapies against acute pathologic necrosis.
Overall, our studies will provide important new insights into the regulation of necroptosis through elucidating the molecular basis of the induction of the key upstream step in necroptosis, RIP kinase activation, and will validate a potential new direction for therapeutic inhibition of pathologic necrosis through selective targeting of necroptosis-specific initiation factors.

PI: DeWaal, Alex
Title: Documentation, Research and Writing on the African Union High Level Implementation Panel for Sudan
Abstract:
The African Union High Level Implementation Panel (AUHIP), chaired by Pres. Thabo Mbeki, was mandated by the African Union (AU) Peace and Security Council in 2009 to further the implementation of the AU High Level Panel on Darfur recommendations on Darfur and to facilitate the completion of the Comprehensive Peace Agreement. The Panel played a central role in the events of the critical period covering the elections of 2010, the referendum and the independence of South Sudan, the crises in Southern Kordofan and Blue Nile, and the current crisis of political, economic and military conflict between Sudan and South Sudan.

The project asks: what did the AUHIP achieve? The project posits that the assessment of achievements- in the near term by those who participated in the process and the long-term by researchers- is made possible only by establishing the record of the AUHIP's work. Therefore, the project will provide a forum for reflection by key Panel staff, archive the materials related to the AUHIP, and catalyze discussions between Panel staff and specialists on Sudan and conflict resolution.

The project will document and archive all materials related to the work of the AUHIP, as much as is possible will be made publicly available. It will convene a workshop involving the AUHIP staff, in which the relevant staff members are commissioned to produce narrative accounts of their particular roles that can accompany the archived material. It will host a symposium in which senior staff of the AUHIP present papers to a group that also involves specialists on Sudan and on conflict resolution. Finally, it will produce a book capturing these reflections and analysis.

PI: Dodman, Nicholas
Title: Feline Wool Sucking Study
Abstract:
"Wool sucking" is a behavioral condition that involves the repetitive searching, suckling, chewing and ingestion of non-food items. While items made of wool can be the preferred substrate, cats may also seek out and chew items made of cotton, rubber, nylon, paper, cardboard and plastic (e.g. plastic grocery bags, plastic wrap). A negative consequence of this behavior is breakdown of the human-animal bond due to owners' frustration with property damage and restricting their cats' access to favored items. In its most severe form, the cat cannot be maintained safely as an indoor cat. While wool sucking behavior can occur in any cat breed, the incidence is higher in oriental breeds, suggesting a genetic susceptibility.

To identify potential genetic components of the compulsive "wool sucking" behavior in cats, DNA samples will be collected via saliva from normal and affected Siamese and Birman cats. Since "wool sucking" is an excellent model in a domesticated animal of human obsessive-compulsive behaviors, the identification of a genetic susceptibility locus could lead to novel cellular pathways that facilitate development of carrier testing, as well as better treatment options for both cats and humans with these disorders.

PI: Dorfmann, Luis
Title: Anisotropic Magneto-Sensitive Composites
Abstract:
Magneto-sensitive composites change their shape and properties in response to magnetic stimulation. Among the various classes of smart materials, in which non-mechanical excitation fields are used to induce mechanical deformations, the class of magneto-sensitive composites is an outstanding one. These composites undergo large deformations, extract large forces, their response time is short, they can be remotely activated, and their manufacturing is relatively simple. Consequently, they can be used in variety of applications such as switches, sensors, actuators and manipulators, vibration isolation, and energy harvesting devices. Moreover, the fact that permanently magnetized inclusions are available may result in a unique response, which is yet to be explored. However, the constitutive description of these materials, where geometrically nonlinear deformations of heterogeneous and anisotropic materials on top of inherently nonlinear magneto-mechanical coupling must be accounted for, is quite complicated.

We wish to exploit possible procedures and advance a framework for tackling the nontrivial aspects associated with magneto-sensitive composites. At the scientific level we will be using and developing modern homogenization techniques in the context of a most demanding application. The unique class of magneto-sensitive composites with permanently magnetized inclusions will be explored together with the role of the inclusions spatial arrangement. Analytical results will be compared with corresponding numerical simulations that incorporate simultaneous solutions of magnetic and elastic problems. The goal is to bring relevant data from the microscopic level up to the macroscopic one in terms of anisotropic energy-density functions that will be made available and implemented numerically for both the scientific and the engineering communities.

PI: Duchin, Moon
Title: Canada/USA Mathcamp: Research in Pairs and Scholarships for Students
Abstract:
Canada/USA Mathcamp is an intensive five-week summer program for mathematically talented high school students. Every year, Mathcamp brings together 110-120 exceptional teenagers from the United States, Canada, and around the world, and creates an environment where they can "live and breathe mathematics". Both intellectually and socially, it is a life-changing experience for many of these students, most of whom have never had a true peer group before coming to Mathcamp. The program takes place on a different college campus each summer; working mathematicians are recruited from across all specialties (and ranging from postdocs to superstar researchers) to visit for a week and participate in the mathematics instruction. Access to working mathematicians at Mathcamp helps meet an intellectual need for the students, many of whom do not have the mathematical resources at home to pursue their interests.

PI: Duchin, Moon
Title: CAREER: Finer Coarse Geometry
Abstract:
The research themes in this proposal are centered in geometric group theory and geometric topology, but have connections to several other fields, including number theory, combinatorics, convex geometry, dynamics, and probability. Geometric group theory is most often focused on quasi-isometry invariants: measurements that are insensitive to bounded (additive and multiplicative) distortion of distances. This allows us to pass between the study of groups and the spaces they act on geometrically, and between different Cayley graphs for finitely generated groups. A unifying theme for the research projects described here is the pursuit of "finer" approaches to asymptotic geometry through the use of more sensitive measurements. In particular, the PI proposes to study large-scale geometric statistics that are not invariant under quasi-isometry. This point of view facilitates the study of randomness and asymptotic density in groups, and of properties of "typical" geodesics in spaces.

The ideas in play here have already led the PI and her collaborators to new density results in free abelian groups and the Heisenberg group; new invariants used to further the classification program for right-angled Artin groups; and progress in the study of Teichmueller geometry. Statistical geometry is broadly applicable in a range of settings outside pure mathematics, from computer science to medicine - wherever geometric models are made and long-term probabilistic prediction is required. In addition to the research program, this proposal describes a collection of educational projects: principally, the development of an organizational infrastructure for Research Labs engaging faculty and students from a wide variety of institutions. Each lab will work on a cluster of problems around a coherent mathematical nucleus, with opportunities for mutli-level teaching, learning, exploration, and collaboration. There will be conferences and journal issues coordinated with these Labs, guided by the principles of combining expository soundness with research value and emphasizing collaboration.

PI: Dulla, Chris
Title: Disrupted Gluamatergic Maturation in a Model of Polymicrogyria
Abstract:
Brain development is an exquisitely complex process. When development is disrupted there can be serious consequences on brain function and quality of life. A type of disruption of brain development known as polymicrogyria (PMG) will be investigated because people who suffer from PMG have a high (80%) incidence of epilepsy and are generally not well treated by anti-epileptic drugs nor by brain surgery. In PMG, brain cells release too much of the neurotransmitter glutamate in the wrong brain regions and that they may not remove glutamate quickly enough to maintain brain function. Novel drugs will be tested which increase the brain's ability to remove glutamate and which could decrease seizure activity.

PI: Dulla, Chris
Title: Impact of Astrocytic Glutamate Transport on Epilepsy Associated with Developmental Cortical Malformations
Abstract:
Diseases of cortical malformation cause approximately 25% of all cases of epilepsy. They are also the most common cause for surgical resection of epileptic brain tissue. Almost 80% of people with a cortical malformation suffer from epilepsy and greater than 70% of those people have seizures which are not managed by anti-epileptic drugs. Novel treatment strategies are urgently needed to treat this problematic group of epilepsies.

In this proposal we will address the hypothesis that loss of astrocytic glutamate reuptake during the development of a cortical malformation acutely disrupts glutamate homeostasis and has long term effects on synaptic connectivity and cortical network function. Normally, astrocytes remove the neurotransmitter glutamate via glutamate transporters. In diseases of cortical malformation, however, astrocytes become reactive which we believe decreases their ability to remove extracellular glutamate. In the developing cortex glutamate directly drives synapse formation. Therefore, we hypothesize that loss of astrocytic glutamate reuptake during the development of a cortical malformation increases extracellular glutamate levels which promotes excitatory synapse formation and leads to long term cortical hyperexcitability. We will test our hypothesis utilizing cutting-edge imaging techniques, electrophysiological recording from astrocytes, in vivo assays of cortical excitability and molecular disruption and augmentation of astrocyte glutamate transport.

Our experiments are extremely innovative. We have developed a novel rodent model of cortical malformation which closely replicates focal cortical dysplasia type 1, a disease with no current animal model. We will utilize exciting, novel glutamate biosensor imaging techniques to assay network function and astrocytic glutamate reuptake. We will record cortical glutamate transporter currents, which have not previously been investigated, and we will do so in the malformed cortex. We will utilize laser-scanning photostimulation to spatially map how astrocytic glutamate reuptake is altered in the malformed cortex. Utilizing molecular modulation of astrocytic glutamate transport, we will test whether developmental loss of astrocytic glutamate transport is sufficient to induce cortical hyperexcitability and whether increasing glutamate reuptake in the malformed cortex interrupts epileptogenic processes which we believe lead to later network dysfunction. Importantly, we will utilize drugs which are already clinically available to increase glutamate reuptake. Should this approach successfully attenuate cortical hyperexcitability it could be rapidly translated into a potential anti-epileptogenic clinical tool.

Mentor: Durant, John
Fellow: St. Vincent, Allison
Title: Developing Time-Resolved Models for Predicting Atmospheric Concentrations of Highway-Generated Nanoparticles in Urban Neighborhoods
Abstract:
Environmental and Water Resources Engineers study natural and man made environmental systems for the dual purpose of improving human health and protecting the natural environment. This scientific knowledge informs environmental regulations and natural resource management. Through the Tufts University Program in Environmental and Water Resources Engineering (EWRE), I expect to expand on my undergraduate degree in environmental engineering from MIT to better augment the knowledge of environmental systems related to public health that is available to policymakers and private citizens. The EWRE Ph.D. program at Tufts requires fifteen courses, three of which are core classes (Chemical Principles in Environmental and Water Resources, Transport Principles in Environmental and Water Resources Engineering, and Environmental and Water Resources Systems). As a first semester student, I am currently taking the first two core classes. The remaining courses will be directed towards acquiring knowledge required for development of the thesis, with courses on such topics as air pollution science and modeling, numerical methods, and environmental statistics. In addition, all Ph.D. candidates must pass a qualifying exam consisting of both written and oral components to be formally admitted to doctoral candidacy. In addition, students must pass a proposal defense, a final dissertation defense, and submit a written thesis to be awarded a degree.

PI: Economos, Christina
Title: ChildObesity180 – Communications
Abstract:
Childhood obesity is the pre-eminent public health issue of our time. Today, one-third of children in America are overweight or obese — and on track to experience catastrophic health conditions, swamp healthcare budgets, and create unprecedented challenges across society. Our vision is to reverse the trend and eliminate this epidemic in a generation's time.

We believe in taking action. Not later, but now. This epidemic is too important to wait another moment. We believe in addressing this national challenge by bringing together leaders from across the spectrum. We have attracted outstanding individuals from the private, public, academic, and non-profits worlds, drawn by a unique opportunity to initiate real change. Each of us is a leader in our own field. We have checked our individual agendas at the door, committed to the cause of serving the common good.

PI: Economos, Christina
Title: ChildObesity180 Core Strategic Partnership with the JPB Foundation
Abstract:
Obesity is the single largest health problem in the United States and in the rest of the developed world, across all age groups. We believe, and evidence supports, that the greatest opportunity for impact lies with children. Today, a full one-third of children are overweight or obese; these children may be the first generation in history to have a shorter life expectancy than their parents. The prevalence of obesity in school-aged children has tripled and, for certain elementary and middle school ages, even quadrupled over the past three decades. According to the CDC, children who are obese are more likely to have cardiovascular risk factors, bone and joint problems, sleep apnea, and social and psychological problems. Further, children who are obese are likely to be obese in adulthood, with increased risks of type II diabetes, heart disease, stroke, osteoarthritis, many types of cancer, and decreased long-term cognitive and mental health.

At an annual estimated cost of $270 billion in the US alone, this is an epidemic with catastrophic implications. Preventable diseases related to obesity are major contributors to rising healthcare costs, diminished worldwide economic competitiveness, and decreased military readiness. Unless we address it with careful consideration and a sense of urgency, the obesity epidemic will have a devastating ripple effect across all segments of society. ChildObesity180, through its innovative approach of working across sectors, is uniquely positioned to work toward this shared objective.

ChildObesity180 seeks to have a collective, concentrated impact that effectively eliminates the U.S. childhood obesity epidemic in a generation's time.

The obesity landscape is complex, with overlapping causes, factors, and potential solutions. There is an urgent need to address this crisis and seemingly no shortage of ideas or interventions aimed at achieving this objective; however, many of these initiatives work in isolation with little synergy, information sharing, or collaborative problem solving. A long-term, coordinated strategic approach, developed through collaboration across multiple sectors, is required to turn the tide on obesity and ultimately reduce the prevalence of overweight and obesity among children.

ChildObesity180 seeks to provide an integrated national strategy and become a major catalyst to prioritize and drive the necessary systemic changes to reverse childhood obesity within one generation's time. The organization promotes interdisciplinary dialogue in the development of a strategic plan to influence the complex systems that have fueled the obesity epidemic. Twenty leaders have been drawn from government, academia, public health advocacy, community organizations, healthcare, the food industry (manufacturers, retailers, and restaurants), and children's media to serve as ChildObesity180 Members and Liaisons.

At the first meeting of ChildObesity180, the Members and Liaisons agreed on the one goal and mission that brought them together and continues to guide all of our work-to have a measurable impact on reversing the trend in childhood obesity. We will achieve this goal by leveraging the power of a partnership of national leaders from multiple sectors working together in coordination with partner organizations on innovative initiatives to accelerate and increase impact. ChildObesity180 ensures that in all work, interactions, and initiatives we are acting in the best interest of children with the highest integrity to protect and enhance the reputations and standing of all contributing organizations, partnerships, and individuals.

PI: Economos, Christina
Title: ChildObesity 180: Reverse the Trend
Abstract:
There is growing recognition that obesity is the single largest health problem in the United States and the rest of the developed world. At an annual estimated cost of $270 billion in the U.S. alone, this is an epidemic with catastrophic implications. Preventable diseases related to obesity are major contributors to rising healthcare costs, diminished worldwide economic competitiveness, and decreased military readiness. Unless we address it with careful consideration and a sense of urgency, the obesity epidemic will have a devastating ripple effect across all segments of society. The Robert Wood Johnson Foundation, having recognized the urgent need to address this crisis, has stepped forward with a major commitment to fund those organizations and programs which are most likely to play a role in reversing the epidemic and improving the health of children. ChildObesity180, through its innovative approach of working across sectors, is uniquely positioned to work with the Robert Wood Johnson Foundation to achieve this shared objective.

ChildObesity180 seeks to provide an integrated national strategy and become a major catalyst to prioritize and drive the necessary systemic changes to reverse childhood obesity within one generation’s time. The group promotes interdisciplinary dialogue in the development of a strategic plan to influence the complex systems that have fueled the obesity epidemic. Seventeen leaders have been drawn from government, academia, public health advocacy, community organizations, healthcare, the food industry (manufacturers, retailers, and restaurants), and children’s media to serve as ChildObesity180 Charter Members and Liaisons.

Over the past twelve months, the ChildObesity180 group has drawn up a strategic action plan and has selected its initial priorities; seed grants from the Robert Wood Johnson Foundation have supported this work. Over the proposed grant period, we will continue to cultivate engagement from committed national leaders across multiple sectors while expanding our innovative organizational model to support the implementation of a diverse portfolio of large-scale initiatives. Working with traditional and non-traditional partners, we will utilize best practices from across sectors to initiate long-term, sustainable change. As we conduct this work, we will maintain a focus on generating and broadly disseminating knowledge resulting from ChildObesity180’s impact and application of innovative and collaborative strategies. Success means that our nation will be set on a dynamic new course—a “180” that reverses the trend and lowers the overall prevalence of childhood obesity for current and future generations of children. Our children deserve our best effort.

PI: Economos, Christina
Title: Healthy Kids Out of School
Abstract:
The obesity epidemic impacts all aspects of health, capability, and well-being at individual, community, and societal levels. Over the past three decades, rates of childhood obesity have doubled for children ages 2-5, quadrupled for children ages 6-11, and tripled in children ages 12-19. Both sides of the energy balance equation factors related to energy intake and energy expenditure-contribute to this epidemic.

Throughout the day there are many opportunities to expose children to healthy foods and physical activity; yet, for the majority of children these opportunities are not being realized. While significant efforts are currently aimed at improving the school wellness environment, childhood obesity prevention programs for the out-of-school (OST) time environment are not as well established. The majority of school-aged children in the U.S. are currently enrolled in OST activities, including after school, weekend, and summer activities. However, there has been great variability in the foods and beverages served and opportunities for physical activity offered to children participating in these programs. Given our long history working with OST programs and their potential for high impact, we have identified these programs as promising partners for promoting healthy habits and preventing childhood obesity.

To realize this potential, the "Healthy Kids Out of School" initiative of ChildObesity180 has assembled an unprecedented group of nine leaders from some of the country's largest OST organizations to leverage their enormous reach and implement three guiding principles for health, wellness, and obesity prevention. By doing so, tens of millions of children who participate in these programs will now hear consistent messages, consume healthier snacks and beverages, and be offered increased opportunities for physical activity.

The principles are:

  • Drink right: Choose water instead of sugar-sweetened beverages.
  • Move more: Boost movement and physical activity in all programs.
  • Snack smart: Fuel up on fruits and vegetables.

PI: Economos, Christina
Title: Tufts-USDA Doctoral Fellowship in Childhood Obesity Prevention
Abstract:
There is growing recognition that obesity is the single largest health problem in the United States. At an annual estimated cost of $270 billion in the U.S. alone, this is an epidemic with catastrophic implications. The goal of this proposal is to help reverse the trend in childhood obesity by obtaining funds for the education and training of three doctoral fellows committed to research careers in childhood obesity prevention. The John Hancock Research Center for Physical Activity, Nutrition and Obesity Prevention at the Friedman School of Nutrition at Tufts University is uniquely positioned to fulfill the needs of the Targeted Expertise Shortage Area (TESA) for Food Science and Human Nutrition-specifically, reduction of childhood obesity (relevant discipline N). Our goals are aligned with one of USDA/NIFA's five priority areas: Childhood Obesity Prevention.

The eight core faculty engaged in this program have national and international research reputations in relevant fields: childhood obesity, nutrition, exercise, sociology, epidemiology, communications, behavior change, and public policy. The broad range of resources provided through the doctoral training will prepare the three fellows to critically examine childhood obesity prevention at many levels. Faculty will mentor and guide fellows throughout their doctoral training, which includes appropriate coursework, a qualifying examination, and original, high-quality research. The training that the fellows receive will prepare each of them to become future leaders in the field. Their collective research will generate knowledge and improve our understanding of childhood obesity prevention, with the ultimate goal of reducing obesity rates among children and adolescents.

PI: Ellis, Julie
Title: SEANET: Coastal Surveillance by Citizens: A Powerful Early Warning System
Abstract:
Seabirds are sensitive indicators of ocean health because they rely heavily on the marine environment, they collectively number in the millions, and some species are very sensitive to human activities. Although live seabirds are easy to see on a beach, they are difficult to accurately identify and quantify. In contrast, with proper training and a field guide anyone can identify a seabird carcass. The Seabird Ecological Assessment Network (SEANET) is the only program in the U.S. conducting standardized beached bird monitoring along the Atlantic coast (http://seanetters.wordpress.com). Based at the Cummings School of Veterinary Medicine at Tufts University, the program monitors disease outbreaks, contaminant levels and oil spill events and provides baseline data on seabird mortality throughout the Atlantic coast. SEANET staff trains and coordinates a network of “citizen scientist” volunteers who perform monthly or twice-monthly walks on assigned beaches. The volunteers collect data on beach characteristics, weather, live and dead seabirds and shorebirds, oiling rates, and human generated debris.

Mentor: Fahey, Jeanne
Fellow: Frank, Emily
Title: Obstacles to Assessing Nutrition Assistance amongst Low Income Youth and Their Families
Abstract:
Since 1980, childhood obesity has nearly tripled. As of 2011, nearly 17% of children ages 2-19 were obese. Poverty is a risk factor both for childhood obesity and food insecurity (having limited or uncertain access to adequate food). In the past, food insecurity was generally associated with becoming underweight. However, recent data suggests that it is possible to be both obese and insecure, and it is hypothesized that food insecurity might actually be a risk factor for obesity.

The Healthy Hearts Program at Oakland Children's Hospital works with morbidly obese youth and their families to maintain or decrease the child's Body Mass Index (BMI). In this program, children and their families meet with pediatricians, dieticians, psychologists, and exercise specialists for a series of visits that are 2-4 weeks apart. At this clinic, 58% of patients are Latino, 18% are African American, 12% are White, and 6% are Asian. 54% of the patients come from a household with an annual income under $30,000 and 29% live in a household with an annual income of less than $15,000.

Recently, the clinic has begun screening patients for food insecurity, and has found that approximately 43% of its patients report being food insecure. Yet only about half of these food insecure families are using Supplemental Nutrition Assistance Programs (SNAP, i.e. food stamps). Currently, the clinic does not have a system in place to follow up on this concern. This study seeks to determine barriers for food insecure families in accessing and utilizing food stamps and alternative free food sources and to help connect these families to these resources.

Hypothesis:

The barriers for food insecure families to access and utilize food stamps and alternative sources of free food can be overcome through interventions to ease their connection to these resources.

Aim 1: To explore the reasons food insecure families are not accessing food stamps and alternative sources of free food.

Aim 2: To connect families who are interested to the food stamp program and other available food sources provided through the Alameda County Food Bank.

Aim 3: To follow up with families who were connected to these resources to determine whether they contacted them, whether they have begun using them, and what obstacles to access and use remain.

PI: Fantini, Sergio
Title: Near-Infrared Spectral Imaging of the Breast for Cancer Detection and Monitoring
Abstract:
This project involves (1) the development of a novel instrument for optical imaging of the human breast, and (2) pilot clinical tests to demonstrate the effectiveness of the proposed instrument in detecting breast cancer and monitoring response to neoadjuvant therapy of breast cancer. The proposed instrument features levels of spatial sampling (25 points/cm2 on the x-y scanning plane), spectral sampling (0.5 points/nm over the wavelength band 650-1000 nm), and temporal resolution (20 full spectra/s) that are not simultaneously achieved by any existing optical mammography instrument. These instrumentation capabilities will be used to enhance the information content of optical mammograms in terms of spatial information (depth discrimination, tomographic reconstruction of hemoglobin/water/lipid/scattering-parameters distributions), quantitative oximetry, and temporal hemodynamics characterization. The clinical tests will specifically test the hypothesis that intrinsic optical contrast provided by hemoglobin, water, lipids, and scattering parameters in breast tissue allows for the detection of breast cancer, its discrimination from benign breast lesions, and for monitoring effectiveness of neoadjuvant breast cancer therapy.

The broad objective of this project is the development of optical mammography as a stand-alone clinical tool for breast cancer detection, and for monitoring effectiveness of therapy.

PI: Feig, Larry
Title: The Function of the Ras-Related Ral Proteins
Abstract:
The overall goal of this proposal is to exploit our understanding of the Ral signaling cascade to reveal how it contributes to cancer in both tumor cells and adjacent stromal fibroblasts. RalA and RalB are members of the Ras superfamily that become activated by a distinct set of guanine nucleotide exchange factors, like RalGDS, in response to a variety of extracellular signals. Once activated, Ral proteins influence a unique set of downstream signaling molecules that regulate multiple cellular processes including vesicle trafficking, apoptosis, cell migration and cell proliferation. A key property of the Ral signaling cascade is that it is stimulated by Ras proteins. In many studies, including those involving RalGDS knockout mice, the Ral signaling cascade supports Ras-induced oncogenic transformation, however the mechanisms involved are poorly understood. Thus, there is intense interest in revealing how the Ral signaling cascade contributes to cancer.

In order to understand how Ral GTPases function in squamous carcinoma of the skin, where activated Ras is often an important component, we used a bioengineered tissue model of human skin that allows us to manipulate the Ral signaling cascade in both epithelial and stromal compartments. We found that RalA plays a cell-type dependent role in Ras-mediated squamous cell carcinoma. In keratinocytes of the epithelium, RalA inhibits, rather than supports tumorigenesis, since suppression of RalA expression enhances tumor progression at least in part by promoting cell invasiveness, through its effector protein the exocyst subunit Exo84 and decreased E-cadherin stability. Moreover, tumor progression in this model system is associated with, and requires, down-regulation of RalA levels. RalB knock-down complements the effects of RalA inhibition by enhancing keratinocyte proliferation. Specific Aim I will elucidate how RalA and RalB play these surprising tumor-suppressing activities, and reveal how tumor progression down-regulates RaIA levels in cells to allow tumor progression.

In fibroblasts of the dermis, RalA has the opposite function. It supports tumorigenesis, since RalA knock-down in these cells blocks the invasive properties of adjacent epithelial cells. Specific Aim 2 will reveal the mechanism behind this striking phenomenon and test the hypothesis that at least part of the tumorresistant phenotype of RalGDS knockout mice is due to the loss of this protein in dermal fibroblasts. Finally, we will test the exciting possibility that the components of a RalA signaling cascade in genetically stable fibroblasts represent new drug targets to block the formation of not only skin squamous carcinoma but also breast adenocarcinoma.

PI: Feig, Larry
Title: Genetic Analysis of Ras and G Protein Function
Abstract:
The execution of complex functions and their breakdown in disease involves the interplay between an animal’s genetics and environment. The overall goals of this proposal are to reveal how Ras-family GTPases influence signaling networks that control synaptic plasticity, and how an “enriched environment” (EE) alters these networks to change the way synaptic plasticity is induced in adolescent mice and remarkably, across generations.

One focus of this proposal is on GRF1 and GRF2, which form a family of multi-catalytic, calcium-stimulated, guanine nucleotide exchange factors that have the potential to activate both Ras and Rac GTPases. Despite these similarities, we found that GRF1 and GRF2 promote opposing forms of synaptic plasticity induced by NMDA-type glutamate receptors (NMDA-Rs) beginning at early adolescence. GRF1 promotes long-term depression (LTD), while GRF2 promotes long-term potentiation (LTP), at least in part, because they regulate different MAP kinases. The experiments combine genetic, biochemical and electrophysiological studies to reveal how GRF1 and GRF2 respond to different upstream signals, and how signaling downstream from their Ras- and Rac-activating domains is differentially regulated in the hippocampus. These experiments will add new insight into how specificity is achieved in neuronal signal transduction. They will also add significantly to our understanding of the molecular basis of LTP and LTD induction. Defects in these well-established cellular paradigms of learning and memory are thought to contribute to a variety of neurological and mental health disorders.

A second focus of this proposal concerns how environmental stimulation, involving exposure to novel objects, enhanced socialization and voluntary exercise particularly during pre-adolescence, changes the way LTP is induced. We discovered that adolescent enrichment unlocks a previously unidentified latent signaling pathway that promotes LTP in mice and rescues defective LTP and contextual fear memory in GRF knockout mice. Even more dramatic is our finding that these effects of pre-adolescent enrichment are passed on to the next generation through their adolescence. The experiments described will use multiple approaches to reveal how this novel EE-gated signaling pathway promotes LTP, and how EE unlocks this cascade to affect synaptic plasticity and memory across generations. A better understanding of the transgenerational effects of the environment on brain function may reveal new approaches to overcome neurological and mental health disorders.

PI: Flytzani-Stephanopoulos, Maria
Title: Atomic-Scale Alloys as Energy- and Cost-Efficient Catalysts for Fuels and Chemicals Production
Abstract:
Understanding the molecular-scale adsorption and dissociation behavior of a number of small molecules on catalytically relevant surfaces is crucial for the design of better working catalysts. More efficient, low-cost processes for the production of fuels and chemicals may be developed as a result. Professors Maria Flytzani-Stephanopoulos, Georgios Kyriakou and Charles Sykes form a team at Tufts University, Medford, MA which is receiving an award to utilize their expertise in heterogeneous catalysis and surface science to identify the factors that lead to enhanced catalytic activity and high selectivity of single-atom alloys, particularly aimed at small molecule activations. Their aim is to develop materials and methodologies that will enable wide ranging academic, technical and industrial applications of these catalysts for heterogeneous hydrogenations. The approach is to use a minority metal component such as Pd present as isolated atoms in another metal like Cu, such that the former induces different catalytic properties on the latter. In this example, the Pd atoms can serve to dissociate H2 molecules, and spill over atomic hydrogen to the host metal. Hence the Pd atoms serve as conduits of H atoms to the Cu surface which can now facilitate hydrogenation reactions with gaseous H2, reactions which have been impossible in the previous literature. This novel catalyst system not only reduces the higher temperatures typically required to activate H2 on Cu catalysts and hence reduces waste heat in products but also allows for more selective hydrogenations to proceed at lower temperatures without decomposition observed on the pure metals. In addition to these benefits, alloy particles in which the expensive, active element is atomically dispersed should dramatically reduce the cost of the catalyst materials.

PI: Flytzani-Stephanopoulos, Maria
Title: Metal Ion Sites on Oxide Supports as Catalysts for the Water-Gas Shift and Methanol Steam Reforming Reactions
Abstract:
The overall goal of this project is to elucidate how catalysis is manifested by stabilized atomic dispersions of metal ions on oxide supports. This is particularly important for the catalytic reactions of interest to fuel reforming for hydrogen generation where atomically-dispersed metals on various oxide surfaces have been identified as the active sites. Working with trace amounts of precious metals is both intriguing fundamentally as well as of great practical interest in our continual search for low-cost, efficient and stable catalysts for the conversion of fuels to hydrogen under highly demanding operating conditions, such as in practical low-temperature fuel cell systems. The current DOE project investigates trace amounts of sub-nm clusters and ions of gold or platinum in nanostructured oxides (ceria, iron oxide, zinc oxide) as potential new catalysts meeting these requirements. Our findings to date point to the importance of the particle size, shape, and oxygen defect density of the host oxide for proper distribution of the active metal sites to effectively catalyze the low-temperature water-gas shift and methanol steam reforming reactions. In an exciting new development, we have shown how to turn the Pt/SiO2 system, from a totally inactive state for the low-temperature water-gas shift reaction to a catalyst superior to Pt/CeO2 by simply adding alkali to the surface. The alkali-promoted Pt(OH)x site is active and stable up to ~350°C. All indications point to a support-independent active site, therefore allowing tremendous flexibility in catalyst design. Low-cost, abundant supports rather than the rare earths can now be employed. In the proposed work, we are extending our investigation to understand the electronic and ligand effects of metal-metal oxide and alkali atom interactions at the atomic scale, making particular use of atomic-layer deposition for controlled metal site decoration of support surfaces, and of state-of-the-art scanning tunneling microscopy/spectroscopy to follow atom-atom-oxygen interactions. The complementary catalysis and surface science studies, aided also by computational investigations, will provide a comprehensive approach to understand atomic-scale catalysis, using as examples the water-gas shift and methanol reactions which remain of interest to this project.

Novel preparation methods to control the size and shape of oxide nanoparticles, applied successfully in the project to date, will continue in the new phase. Particles with special surface planes preferentially exposed, and decorated with Au, Pd, Pt, or bimetallics provide a viable new way to study crystal surface reactivity and structure sensitivity of reactions at normal pressures. For example, we have shown that the {110} surface of ceria and the {0010} polar surface of ZnO nanocrystals are the best in providing the largest number of stably bound Au-O sites, and thus maximum activity for the WGS and SRM reactions. These studies will continue and extend to other systems to probe metal-support interactions and specific structure — function correlations. Finally, we will continue and extend to other systems the use of in situ techniques for gaining mechanistic insights of the reactions under investigation; in situ XANES/EXAFS has been used in the current project to follow the structural evolution of gold clusters on CeO2 and Fe3O4; and the stability of Pt-Ox-K-(OH) clusters on silica as a function of gas composition and temperature.

The project involves a close collaboration of a team of academic investigators at Tufts, Columbia, and Wisconsin. The advancement in our understanding and considerable progress made in our project over the past three years, has enabled us to sharpen our objectives as outlined above. New scope to the proposed collaborative effort has been added as necessary to obtain key answers and meet our objectives in an effective manner. Our on-going collaborations with scientists at Brookhaven National Lab (EXAFS, HREM, TR-XRD) will continue and be strengthened as they are essential to the success of our program.

PI: Ford, Lawrence
Title: Research on Fluctuations of Gravity and Quantum Fields
Abstract:
This project will entail theoretical studies of several aspects of quantum fluctuations of spacetime and related issues. A key problem in any quantum theory of gravity is understanding these fluctuations and their physical effects. One will be the effects of quantum energy density fluctuation in the early universe, especially in the context of inflationary cosmology. Previous studies by the PI and his collaborators indicate that these effects may be larger than one would have naively guessed, and possibly large enough to cause observable effects today. A related topic is the study of the probability distribution for quantum energy density fluctuations. A better understanding of this distribution, especially the part which describes rare but large fluctuations, can have applications to several questions in quantum theory and cosmology. Other aspects of the project will include a search for secular effects from quantum gravity fluctuations, that is, effects which can accumulate over the history of the universe. If such effects exist and can be detected, it would lead to significant insights. The project will also involve a search for laboratory experiments to detect such effects as negative energy and lightcone fluctuations in analog systems.

PI: Forgac, Michael
Title: Structure, Mechanism and Regulation of the V-ATPases
Abstract:
The long term goals of this research are to determine the mechanism and regulation of the vacuolar (H+)-ATPases (V-ATPases). The V-ATPases are ATP-dependent proton pumps that function in both normal and disease processes, including membrane traffic, viral infection, urinary acidification, bone resorption and tumor invasion. V-ATPases are multisubunit complexes composed of a peripheral V1 domain that hydrolyzes ATP and an integral V0 domain that translocates protons. V-ATPases are regulated in vivo by reversible dissociation of the V1 and V0 domains.

The first objective of this proposal is to test the role of helical swiveling within the V0 domain in proton transport. We have obtained evidence for helical swiveling (rotation of a helix about its long axis) in both subunit a and the proteolipid subunits. We hypothesize that swiveling of helices containing transport critical residues functions in proton translocation through V0.

The second objective of this proposal is to elucidate the mechanism by which glucose regulates V-ATPase assembly in yeast. We have developed a novel genetic screen for regulators of V-ATPase assembly and used this screen to identify the Ras/cAMP/PKA pathway as a key regulator. We hypothesize that there are novel regulators in addition to PKA that control V-ATPase assembly, and have recently identified protein phosphatase PP1 as one such regulator.

We will test these hypotheses and achieve our objectives by pursuing the following Specific Aims:

  • Specific Aim 1 – To test the hypothesis that helical swiveling within the V0 domain functions in proton transport, we will determine the effect of intramolecular, disulfide-mediated cross-linking between adjacent helices within both subunit a and subunit c' on proton transport activity. We expect that if helical swiveling is required for proton transport, preventing helical swiveling by cross-linking adjacent helices within subunit a or subunit c' will inhibit activity.

  • Specific Aim 2 – To determine the mechanism by which glucose regulates V-ATPase assembly in yeast, we will identify and characterize additional novel regulators of V-ATPase assembly using our modified genetic screen. These regulators include both essential and non-essential genes whose mutation blocks V-ATPase dissociation or reverse PKA-mediated assembly.

The proposed research is significant because it will greatly advance our understanding of the mechanism by which V-ATPases carry out proton transport and facilitate the identification of novel regulators of V-ATPase assembly. Because V-ATPases are highly conserved between yeast and mammalian cells, as is the use of regulated assembly to control V-ATPase activity, and because regulators such as glucose, PKA and aldolase control assembly in both yeast and higher eukaryotes, these studies will likely provide important insight into control of V-ATPase assembly in mammalian systems. These insights will in turn facilitate the development of therapies to modulate V-ATPase activity that could prove effective in the treatment of diseases, such as viral infection, osteoporosis and cancer, in which V- ATPases participate.

PI: Frank, Eric
Title: Electrophysiological Studies of Synapse Formation by Regenerating CST Axons
Abstract:
Most functional deficits after spinal cord injury are caused by the disruption of nerve fibers that project longitudinally and interconnect the brain and spinal cord. In principle, there are two possible strategies for re-building functional circuits to repair this loss of communication: nerve fibers that were not damaged can be stimulated to sprout collateral axons and build compensatory connections, and injured axons can be stimulated to grow across the lesion to reconnect with their original targets. Major progress has been made recently in promoting sprouting and regeneration of the corticospinal tract (CST), a major pathway for controlling movement. It is not known; however, if these sprouted and regenerated CST axons can re-establish functional synaptic connections. This proposal addresses that second step, determining if sprouting or regenerating CST axons can make functional synaptic contacts with their normal target neurons in the spinal cord. Recent studies have shown that genetic deletion of PTEN in CST neurons results in robust contralateral sprouting of their axons in the spinal cord following ablation of the contralateral CST and also promotes unprecedented regeneration of CST axons across spinal cord lesions. It remains unknown, however, if sprouted or regenerated axons can make functional synaptic connections. A major target of CST axons in mice is Clarke's column neurons, located in the C11 – L2 segments of the spinal cord, in close proximity to the CST. We propose to utilize in vivo electrophysiological approaches to assess the ability of re-growing CST axons form functional synapses with Clarke's column neurons.

In the first aim, we will induce the axons in one CST to sprout into the contralateral spinal cord by interrupting the other CST via a unilateral pyramidotomy in PTEN-deleted mice. We will test if sprouted CST axons establish functional synaptic connections by selectively stimulating the CST while recording intracellularly from Clarke's column neurons. We can thus test if axonal sprouts can form functional synapses with appropriate synaptic targets in the spinal cord. In the second aim, the CST will be lesioned bilaterally by a complete spinal cord crush at T10. This surgical procedure interrupts all axons that project through the crush region. After allowing CST axons to regenerate through the lesion in PTEN-deleted mice, we will record intracellularly from Clarke's column neurons just caudal to the crush while stimulating the CST at cervical levels above the crush. These experiments will test if CST axons regenerating through the lesion are able to form functional synaptic connections below the lesion.

Taken together, these experiments will allow us to assess an important functional aspect of sprouting and regenerating CST axons, namely their ability to form functional synaptic connections. These results should provide direct insights into designing therapeutic strategies for re-establishing corticospinal connections and promoting functional recovery after spinal cord injuries.

PI: Frank, Eric
Title: Repair of Root Avulsions in Brachial Plexus Injuries
Abstract:
Injuries to the brachial plexus, an important class of spinal cord injuries, disrupt nerve conduction between the arm and the spinal cord, resulting in loss of both sensation and movement in the limb. In many of these injuries, the spinal roots are stretched such that their attachments to the cord are broken, or avulsed. The anatomical discontinuity between the roots and the cord prevents regrowth of sensory axons into the cord, thereby blocking recovery of function. The objective of this project is to develop a reliable method for reattaching avulsed dorsal roots firmly to the spinal cord to permit sensory axon growth through the dorsal root into the cord, and to determine an effective therapy to promote the re-establishment of functional synaptic connections with spinal neurons. The first aim of this proposal is to develop a technique, already used in preclinical models of peripheral nerve repair, for bonding the avulsed root to the cord. In the second aim, we will test various doses and durations of pharmaceutical treatments to promote robust regeneration of sensory axons into the cord and re-establishment of functional synapses with appropriate spinal targets.

PI: Frank, Nicholas
Title: Use of Compounded Thyrotropin-Releasing Hormone in the Response Test for Pituitary Pars Intermedia Dysfunction
Abstract:
One of the major limitations of diagnostic testing for pituitary pars intermedia dysfunction (PPID) is the sensitivity of available diagnostic tests. The two most commonly used diagnostic tests, resting adrenocorticotropin hormone (ACTH) concentrations and the dexamethasone suppression test, can yield negative results in horses with early PPID. Of the tests available, the thyrotropin-releasing hormone (TRH) response test is the most likely to detect early PPID. Unfortunately, TRH is not commercially available and has to be prepared in the laboratory using a chemical purchased from a laboratory reagent supplier. This problem has limited the use of the TRH response test and left many horses with early PPID undiagnosed.

One solution to this problem is to identify a source of TRH that will be available to all practitioners. Wedgewood Pharmacy has worked with our research group to address this issue and prepared 1-ml syringes containing TRH for use in the field. The proposed study will examine the efficacy of this product. While the company has offered to provide the product for testing, they are not interested in funding a study to determine its efficacy because TRH is unlikely to generate significant revenue.

We hypothesize that TRH produced by a commercial compounding pharmacy is effective in stimulating ACTH release in horses with PPID.

Specific Aims:

  1. To compare the efficacy of compounded TRH with regular TRH in PPID testing.
  2. To measure the repeatability of the TRH response test when two tests are performed sequentially, separated by a 60-minute interval

PI: Gaither, Sarah
Title: Mixed-Race Perceptions: Fluidity in Categorization, Racial Identity and Behavior
Abstract:
The multiracial population faces unique challenges in navigating social situations, reporting constantly having to "choose" one of their racial identities, but this research has not used a behavioral focus. This series of experiments aim to: 1) examine the role racial identification plays concerning face processing for biracial individuals; 2) highlight behavioral differences for biracial individuals within various social contexts; and 3) create one of the first stimuli sets comprised of biracial individuals. These results will add to a growing literature regarding the behavioral tendencies of multiracial individuals, one of the fastest growing populations, yet one we still know little about.

PI: Garlick, Jonathan
Title: iPSC-derived Repair-Responsive Fibroblasts to Heal Diabetic Foot Ulcers
Abstract:
Diabetic foot ulceration (DFU) is a major problem that significantly impairs quality of life of the patient, leads to prolonged hospitalizations and may require major amputation, demonstrating the urgent need to develop next generation treatments for these and other chronic wounds. To fill this critical gap in patient care, novel sources of autologous cells that are more repair-competent are immediately needed.

Our long term goal is to develop a therapeutic approach, based on induced pluripotent stem cell (iPSC) technologies that will reverse DFU fibroblasts from a non-healing to a healing phenotype by treating these cells in situ, directly in the patient's wound without needing to remove and culture them. To lay the groundwork for this, the immediate goal of our project is to greatly improve the wound repair potency of DFU fibroblasts following their reprogramming to iPSC, that will reveal how "epigenetic memory" (patterns of DNA methylation retained from the cell type reprogrammed) can best be exploited to acquire a spectrum of pleiotrophic effects that will trigger wound repair. In light of the emergence of epigenetics as a critical regulator of the "metabolic memory" linked to diabetic cell dysfunction, DFU fibroblasts are likely to be controlled by epigenetic mechanisms (miRNA, histone modification and DNA methylation). As a result, we expect iPSC reprogramming to reset the epigenome and reverse "metabolic memory" to improve repair after iPSC differentiation.

The overall objective is to develop new sources of autologous, repair-competent fibroblasts using iPSC technologies that will dramatically improve DFU therapy. Our central hypothesis is that DFU fibroblasts will become repair-competent when reprogrammed to iPSC and subsequently differentiated to a fibroblast lineage by acquiring repair-promoting functions that will be mediated by epigenetic controls. The rationale for our research is based on exciting new preliminary data that has established the augmented healing potential of iPSC-derived fibroblasts (iPDK) and in vivo models of diabetic wound repair developed in our labs that will determine this repair potential. To test this hypothesis, we have developed skills and data that support the feasibility of this approach by establishing that iPSC-derived fibroblasts are more versatile than their parental fibroblasts.

We plan to test our central hypothesis by pursuing the following specific AIMS:

  • AIM 1: Identify cellular functions that trigger repair-competency when repair-deficient, DFU fibroblasts are reprogrammed to iPSC and differentiated to fibroblasts

  • AIM 2: Reveal if the switch to repair-competency is linked to distinct DNA methylation profiles, histone modifications or miRNA signatures that regulate repair functions in iPDK fibroblasts

  • AIM 3: Establish repair efficacy of iPSC-derived fibroblasts in two, well-established animal models of diabetes and optimize their delivery to heal diabetic wounds.

Ultimately, this knowledge has the potential to transform the care of patients suffering from DFUs and will be widely applicable to many other types of non- healing wounds, as well as to periodontal disease and aging-related diseases.

PI: Garven, Grant
Title: Physiochemical Evidence of Faulting Processes and Modeling of Fluid Flow in Evolving Fault Systems in Southern California
Abstract:
We are advancing our studies of the geohydrology and geochemistry of active faults and young petroleum reservoirs in southern California, including the South Ellwood field in the Santa Barbara basin (SBB), the Newport-Inglewood Fault zone (NIFZ) in the Los Angeles basin, and the Lost Hills field in the San Joaquin basin (SJB). Subsurface core samples, outcrop samples, well logs, reservoir properties, pore pressures, thermal gradients, fluid compositions and structural-seismic sections are being studied to characterize the geohydrologic/diagenetic history and degree of compartmentalization for these known fault networks in a transpressional tectonic setting. We are also investigating the isotopic and trace elements signatures in calcium carbonate minerals, including vaterite that characterizes rapid CO2 degassing, as observed in scales from production well tubing in several petroleum and geothermal reservoirs. These data provide the constraints for our geohydrologic models that are being developed to predict fluid pressures, multiphase fluid saturations, rates and patterns of deformation and fluid flow, subsurface temperature, geothermal heat flow, and fluid geochemistry associated with large fault systems.

Mentor: Georgakoudi, Irene
Fellow: Quinn, Kyle
Title: Non-Invasive Optical Biomarkers to Quantify Engineered Bone Tissue Development
Abstract:
Bone tissue regeneration is necessary to restore skeletal function following a variety of clinical procedures, including bone fracture repair, reconstructive surgery, and spinal fusions. Tissue-engineered bone offers a number of advantages over traditional bone grafts used for the repair and regeneration of bone. However, the current methods employed to evaluate and optimize the growth of engineered bone tissue lack the spatial and temporal resolution to characterize the dynamic cell-matrix interactions that occur during tissue development. The objective of this project is to develop quantitative optical biomarkers to identify and monitor changes in the biochemical, microstructural, and overall mechanical properties of engineered bone tissue during its in vitro development. This work focuses on the dynamic changes that occur as three-dimensional silk scaffolds seeded with human mesenchymal stem cells develop into functional bone tissue. The central hypothesis of this proposal is that endogenous optical signals can be measured non-invasively using multi-photon imaging and depth-resolved light scattering spectroscopy to determine the biochemical and microstructural properties of the developing tissue. To test this hypothesis, the intrinsic fluorescence and light scattering signals from different cellular and extracellular matrix components will be identified in Aim 1 and correlated with traditional histological and molecular biology techniques. The optical biomarkers for microstructural organization identified in Aim 1 will be used to predict the overall mechanical function of the bone tissue in tension and compression in Aim 2. Collectively, these aims will provide a unique understanding of how the biochemical status and mechanical function of engineered tissue changes during osteogenesis. By using only non-invasive techniques that identify intrinsic sources of optical contrast, the outcomes of this proposed research can be used to optimize the future approaches to engineering functional bone tissue and will enable a means to monitor engineered constructs as they are incorporated into native tissue following surgical repair.

PI: Georgakoudi, Irene
Title: Optical Biomarkers for the Non-invasive Detection of Early Cancer
Abstract:
Most cancers develop in the uppermost layer of tissue that covers our body cavities and organs. If cancer changes are detected when they are confined to this superficial layer, they can be treated effectively. Unfortunately, these early lesions are very small and are difficult to detect using standard equipment that is used in a doctor’s office. Their accurate detection usually requires invasive, costly, labor intensive and time-consuming procedures. Our long term goal is to develop optical, noninvasive imaging methods that enable improved cancer detection in its early stages with instrumentation that is portable, provides results immediately and can be operated without highly specialized training. Towards this aim, we have begun to identify optical signals that rely on the natural ways with which cells and tissues interact with and modify light depending on their biochemical composition and organization. We have also found that a set of such signals does change when precancerous cells are present, either in experimental models of tissue or in live human tissues.

In this proposal, we plan to identify how changes in optical signals are related to specific microscopic changes that are commonplace in early cancers. The optical techniques that we will use include a combination of methods, some of which we have invented, that can be implemented together to provide complementary information about the function and structure of the specimen from microscopic to macroscopic scales. The studies we will perform are particularly relevant to cancers caused by a virus (human papillomavirus), such as those in the uterine cervix, head and neck. However, because development of these cancers involves aberrations in cellular pathways that are disturbed in many cancers, we expect that the methods we develop will be even more broadly applicable. Since these methods are noninvasive (i.e. do not require a biopsy) and rely on entirely natural sources of contrast (i.e. no stains are needed), they can be easily transferred to the clinical setting. Therefore, we expect that these methods will improve the rates at which we detect cancers at a stage when effective treatments are available and will, thus, have a positive impact on patients' lives.

PI: Georgakoudi, Irene
Title: Optical Monitoring of Engineered Tissues
Abstract:
Our long-term goal is to develop non-invasive, optical technologies to monitor the functional development of engineered tissues in vitro and in vivo. The objective of this application is to develop optical biomarkers based on endogenous sources of optical contrast that obviate the use of exogenous stains and can be used to report quantitatively on the biochemical and structural composition of engineered tissues. The proposed studies focus on the characterization of adipose and bone engineered tissues developed from silk scaffolds seeded with human mesenchymal stem cells.

The central hypothesis of the application is that linear and non-linear depth-resolved imaging methods based on the natural light scattering and fluorescence signatures of cell and matrix components of engineered tissues can be developed to report on the dynamic changes that occur prior to and following implantation of engineered tissues. Our hypothesis is based on preliminary evidence acquired from in vitro samples, which indicate that endogenous optical signals can be used to monitor changes in the biochemistry and morphology of differentiating stem cells, silk scaffolds and deposited collagen.

The rationale for the proposed research is that the establishment of non-invasive methods that allow monitoring of the dynamic changes that occur within engineered tissues will play an essential role in the development and optimization of innovative, functional engineered tissue constructs. To achieve our goal we will characterize the endogenous fluorescence and light scattering signals from different cell and matrix components of engineered tissues developed in vitro (Aim 1). We will develop a system that will optimize acquisition of these optical signals from animals (Aim 2) and we will use these biomarkers to characterize non-invasively the integration of these engineered tissues in vivo following implantation either within a mammary fat pad or a cavarial bone defect mouse model (Aim 3). This will be the first time that dynamic monitoring of the biochemical and structural function of implanted engineered tissues is achieved in vivo using non-invasive means based on endogenous optical signals.

PI: Goldberg, Jeanne
Title: The GREEN (Growing Right: Eating Eco-Friendly and Nutritious) Project
Abstract:
Poor diet quality in children contributes to obesity, chronic disease, and diminished quality of life. Many efforts have focused on foods provided in schools. But elementary school children regularly bring snacks and lunches. Little attention has been directed toward improving the nutrient profiles of foods brought from home. The proposed intervention, The GREEN (Growing Right: Eating Eco-friendly and Nutritious) Project takes advantage of a natural synergy between healthy eating and eco-friendly behaviors to address the quality of foods brought to school from home. Our novel, school-based communications campaign will combine messages about the nutritional and eco-friendly qualities of foods. Our target population is third and fourth graders and their caregivers in Eastern Massachusetts.

Our central hypothesis is that at the end of one school year, children who receive a campaign with combined healthy eating and eco-friendly messages will show greater improvement in diet quality and eco-friendliness of snacks and lunches brought from home than those who receive healthy eating communications alone or those in a control group. The theory-based multi-channel communications campaign will be developed on the basis of qualitative research with the target population. For the campaign, schools will be randomized to three conditions to receive:

  1. Healthy eating and eco-friendly messages;
  2. Healthy eating only messages; or
  3. Delayed healthy eating eco-friendly messages after serving as controls.

The primary outcome is change in the number of servings of fruits and vegetables brought to school. Secondary outcomes will include changes in the quantity of sugar-sweetened beverages and processed, energy-dense foods, as well as the weight of trash associated with foods brought from home. Baseline and outcome assessments of these outcomes will be made using digital photography. After the GREEN Project has been implemented, the RE-AIM framework will be used to make revisions to the intervention which will then be disseminated to the delayed intervention group. This design will provide an opportunity to test the feasibility of replication. If successful, this novel approach, taking advantage of the synergy between healthy eating and eco-friendly messages, could be extended to elementary schools across the US and adapted to other populations. In addition, the strategy might be extended to other behaviors affecting personal health that can be tied to eco-friendly behaviors.

PI: Gorbach, Sherwood
Title: Center for Metabolic Research on HIV and Drug Use
Abstract:
Five years ago, the Tufts Nutrition Collaborative – Center for Drug Abuse and AIDS Research (TNC-CDAAR) was funded by NIDA as just one of two CDAAR's in the nation. The CDAARs were charged with the following mission: to foster a collaborative approach to drug abuse and addiction research; to enable studies that would not occur without the climate, facilities, and resources that a research center can uniquely provide; to serve as a resource to attract established and promising investigators into drug abuse research; and to provide opportunities for research training, career development, and mentoring. The TNC-CDAAR was formed as a partnership between three East Coast Institutions (Tufts, Brown and Johns Hopkins) with a specific focus on studying nutritional and metabolic disorders among HIV-positive and HIV-negative drug users. Over the past five years, we have expanded the TNC-CDAAR to include collaborators from 3 international sites: Argentina, India, and Vietnam.

Our major accomplishments, thus far, have been to:

  1. design and implement several new studies to assess and compare the prevalence and incidence of specific nutritional and metabolic disorders in drug users of different ethnicities, both in the U.S. and abroad;
  2. develop training materials, protocols, and manuals for investigators who want to undertake similar studies in their localities;
  3. help in the development of new grant proposals in Center-related areas of research; and
  4. become a resource center on nutrition and metabolic disorders in drug users.

The TNC-CDAAR will continue to operate five of its original six cores: Administrative (Core A), Developmental (Core B); Drug User Resources (Core C); Nutrition and Metabolism (Core D); and Epidemiology and Biostatistics (Core F). Core E (Endocrine) will be merged with Core D and a new core on Hepatitis and Liver Function (Core G) will be added. This new core was developed in response to the needs of TNC-CDAAR investigators and members who have found that nutritional and metabolic abnormalities are likely linked not only to HIV, but also to chronic liver disease among persons who use drugs.

The center will continue to work to raise awareness of the importance of nutritional and metabolic disorders on outcomes in the drug using population and to encourage investigators to include studies of nutritional and metabolic status in their research in drug using populations. The five center cores will continue to work synergistically to provide a multitude of services for center members.

PI: Greenberg, Andrew
Title: Age Dependent Role of Bisphenol A in Obesity and Insulin Resistance
Abstract:
The objective of this application is to determine the doses and mechanism(s) by which early-life exposure to the ubiquitous industrial chemical, bisphenol A (BPA), promotes insulin resistance (IR) and type 2 diabetes (T2DM) in adults. Prior studies and preliminary data from this investigative team suggest that early-life (perinatal) exposure to BPA promotes IR and T2DM by increasing adiposity, altering pancreatic insulin secretion, and in females, promoting a phenotype similar to human polycystic ovarian syndrome (PCOS), which typically includes obesity and IR. The rationale for the proposed studies is that public health policy regarding the prevention of insulin resistance and T2DM will be significantly enhanced by definitive, mechanistic studies of BPA's role in promoting obesity and/or dysregulating glucose and insulin homeostasis. Accordingly, this project will investigate the effects of early BPA exposure (gestation through postnatal day 21) on the development of IR, T2DM and obesity in male and female rats and potential ovarian dysfunction in female rats. Glucose homeostasis, adiposity and adiposity-related biohumoral and tissue read-outs will be monitored at 4, 8, 12 and 18 months in male and female rats exposed to vehicle and 4 different doses of BPA. Blood and tissues (white and brown adipose depots, pancreas, liver, skeletal muscle and ovaries) will be collected for various biohumoral, histological, biochemical, gene expression and epigenetic analyses.

Specific Aim 1 will determine the dose(s) of perinatal BPA exposure that dysregulate glucose/insulin homeostasis in adult rats and will determine the chronology and progression of this dysregulation. Specific Aim 2 will test the hypothesis that BPA-induced IR reflects the metabolic and inflammatory impacts of obesity and/or hormonal dysregulation in females. Specific Aim 3 will identify BPA-induced transcriptional and epigenetic changes (DNA and histone methylation) in both white and brown adipose tissue that are associated with the development of IR and/or obesity. Completion of Aims 1-3 and integration of their results will provide an in-depth assessment of the effects of early-life BPA exposure on the development of impaired glucose homeostasis, IR and T2DM in the adult and the associated BPA-induced adipose, pancreatic and ovarian changes that may promote this metabolic dysregulation.

The significance of the proposed studies lies in their ability to identify the multiple effects of BPA exposure on gene expression, metabolism, body composition and hormones that may be contributing to societal increases in obesity, IR and T2DM.

PI: Greenberg, Andrew
Title: Estrogen Replacement in Postmenopausal Women
Abstract:
When women undergo menopausal transition, their risk of developing central adiposity, diabetes and cardiovascular disease increases greatly. Estrogen treatment of postmenopausal women results in protection against diabetes and is thought to improve body composition. However, the mechanisms and pathways that underlie the ability of estrogen to protect against body fat accumulation and diabetes in humans are unknown. Previously, we have demonstrated that estrogen administration to ovariectomized mice reduces adipocyte size, reduces adipocyte death and adipose tissue inflammation, increases activation of oxidative metabolic pathways in muscle and appears to improve insulin sensitivity. An important objective of our OSQR is to understand the mechanisms that underlie adipocyte death and adipose tissue inflammation. Estrogen may protect against adipocyte death and additionally estrogen may promote adipocyte hyperplasia which we hypothesize would protect against adipocyte death. We also hypothesize that increasing oxidative metabolism in muscle may protect against the development of adipocyte hypertrophy and adipocyte death.

In this proposal we will determine the whole body and tissue specific effects of estrogen in postmenopausal women and determine whether estrogen attenuates the detrimental metabolic effects of energy surplus in postmenopausal women. We propose to determine the effects of delineating the mechanisms by which estrogen is beneficial by providing estrogen via a skin patch, which is more physiologic than oral administration of estrogen, to early postmenopausal women. With the knowledge gained in this study, we will be able to develop nutrition therapies that will result in healthy aging in women. Women entering the study will participate in a double blind randomized placebo controlled trial and receive estrogen for 3 months. We will characterize glucose-insulin homeostasis using an intravenous glucose tolerance test. We plan to perform adipose and skeletal muscle biopsies to allow us to understand the cellular and molecular mechanisms by which estrogen acts on these tissues. Body composition studies will be performed using DEXA. Additionally, at the end of three months, subjects will participate in a three-day overfeeding study to determine effects of estrogen on the metabolic effects of energy surplus.

Upon completion of this study we will be able to develop a more rational nutritional approach to aiding women as they undergo the menopause transition which places them at increased risk of developing central adiposity, diabetes, and heart disease.

PI: Greenberg, Andrew
Title: Research Training Program in Nutrition, Obesity and Metabolic Disease
Abstract:
The objective of this proposal is to obtain funds for the training of PhD scientists committed to academic careers that have a research focus integrating the interaction between nutrition and metabolism. More specifically to understand, prevent, and treat metabolic diseases which include diabetes, obesity and associated complications, such as nonalcoholic fatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH), and kidney disease. The importance of training future researchers in these areas is evident due to the growing epidemic of these disorders in the United States.

The rationale for this proposal is based on the firm belief that nutrition is one of the most significant, if not the significant environmental factor that may be modified to prevent, delay or ameliorate obesity and metabolic disorders. This proposal therefore seeks funds to train the next generation of nutrition research investigators to address an understanding of metabolism and metabolic dysfunction at the molecular, cellular, whole body and/or population levels. Support is requested for five pre-doctoral training slots for each of the proposed five years.

All trainees are first admitted to a graduate degree program at the Gerald J. and Dorothy R. Friedman School of Nutrition Science and Policy, located on the Health Science Campus of Tufts University, and, after one year of coursework and laboratory rotations are eligible to be admitted to the proposed training program. Acceptance into the training program is predicated upon outstanding academic and research achievement during the first year. Each of the faculty mentors have appointments within the Health Science Campus and will provide exemplary research training to pre-doctoral students interested in the broad research areas of obesity, diabetes, metabolism, digestive diseases, endocrinology, genomics and gene therapy, epidemiology, and related diseases of the kidney and pancreas.

Mentor: Greenberg, Andrew
Fellow: Bowman, Thomas
Title: Role of Perilipin in Hepatic Steatosis and Metabolism
Abstract:
The purpose of this application is to train the applicant to become a productive, independent investigator in obesity-related diabetes research. The applicant's long-term goal is to elucidate the molecular mechanisms by which fatty acids are partitioned in cells and the effects of fatty acid on regulating obesity associated insulin resistance. The proposed studies will provide the applicant with the opportunity to build on existing knowledge in lipid metabolism, insulin action, rodent and human physiology and biochemistry. Specifically the applicant will obtain expertise in cell culture and microscopy techniques, protein kinase signaling, lipid metabolism, molecular biological techniques, and glucose clamp analyses. The training plan will also provide training and experience in writing manuscripts, grant proposal development, group presentations, and increased scientific independence.

In concordance with a goal of NIDDK funded obesity research, the long term objective of the proposal is to understand at the cellular level mechanisms linking obesity and overnutrition to insulin resistance. Perilipin is a protein that localizes at the surface of intracellular lipid droplets (LD) where triacylglycerol (TAG) is stored and regulates fatty acid release from stored TAG. Although perilipin is abundantly expressed in human hepatocytes within steatotic livers it is not expressed within steatotic livers of obese mice. Preliminary data from our laboratory confirm this finding, and also that ectopic expression of perilipin in isolated mouse hepatocytes induces and enhances formation of hepatic lipid droplets.

The proposed project will test the hypothesis that perilipin expression in human hepatocytes acts to sequester fatty acids as TAG into LD, thereby reducing TAG secretion and preventing the effects of fatty acids to promote insulin resistance. The applicant will test this hypothesis, in Aim 1, using primary human hepatocytes and HepaRG human hepatoma cells, which express perilipin, and examining the effects of perilipin knockdown; as well as using adenoviruses used to express perilipin with isolated mouse hepatocytes. These hepatocytes will be incubated with oleic and/or palmitic acid to mimic in vivo trafficking of fatty acids to the liver and facilitate TAG accumulation. In Aim 2 we will extend our studies to examine the effects of perilipin expression within hepatocytes in vivo, by creating a transgenic mouse with hepatocyte-specific expression of perilipin and inducing obesity with a high fat diet. This hypothesis driven proposal will produce novel insights and understanding about the role of perilipin in regulating hepatic lipid metabolism and the pathogenesis of insulin resistance.

Mentor: Greenblatt, David
Fellow: Hanley, Michael
Title: Effects of Anthocyanins on Cytochrome P450 Enzymes and P-Glycoprotein
Abstract:
Anthocyanins are a class of flavonoids found in many berry fruits, including blueberries. Public interest in blueberries and other anthocyanin-containing products has increased in recent years due to their reported health-promoting properties. In turn, the concomitant consumption of anthocyanin-containing products with prescription drugs is likely to occur. Unfortunately, little information is currently available regarding the potential drug interaction risks associated with anthocyanins.

The objective of this proposal is to establish the effects of anthocyanins on the cytochrome P450 (CYP) enzymes and the drug transporter, P-glycoprotein. In Aim 1, we will determine the potential of anthocyanins and anthocyanidins to inhibit GYP activity in vitro. In preliminary work, blueberry juice inhibited the in vitro activity of CYP3A and CYP2C9 at concentrations that could easily be achieved in the gastrointestinal tract after BBJ consumption.

Consequently, in Aim 2, we will ascertain the clinical relevance of these in vitro interactions by conducting pharmacokinetic studies in which blueberry juice will be co-administered with the probe substrates buspirone (CYP3A) and flurbiprofen (CYP2C9). Since alterations in the activity of P-glycoprotein can also influence drug disposition.

In Aim 3, we will examine the effects of anthocyanins and anthocyanidins on P-glycoprotein-mediated fexofenadine transport across Caco-2 cell monolayers. Taken together, the knowledge gained from these studies will help ensure the safe use of anthocyanin-containing products by the public.

PI: Griffin, Timothy
Title: Training Leaders to Understand and Integrate Agricultural, Food, and Environmental Sciences
Abstract:
A new generation of agricultural professionals is needed, empowered with an integrated understanding of policy, agricultural sciences, production agriculture, food systems analysis, and environmental resource management. With rising concern about food borne diseases such as E. coli 0157H7, the impact of global climate change on food security, water scarcity, and the standoff over agricultural subsidies in the Doha Round, the national and global need for such professionals is urgent. There is a lack of new ideas to address these and other pressing issues and no clear path to a future food system that is sustainable for both humans and the natural environment. The Agriculture, Food and Environment (AFE) Program within the Friedman School of Nutrition Science and Policy at Tufts University is uniquely designed to train this new generation of leaders. Our mission is to educate students to evaluate the environmental, political, economic and social aspects of food production and distribution. As such AFE is well suited to fulfill the needs of the CRSEES TESA for Training in Sustainable Sciences.

PI: Griffiths, Jeffrey
Title: Hospital and Household Studies of Respiratory Cryptosporidiosis and Transmission
Abstract:
Human Cryptosporidium (Cr.) transmission has been thought to occur only via fecal-oral, water-, or food-borne routes. We recently found that 35% of Ugandan children with Cr. diarrhea and cough were PCR sputum-positive, suggesting that respiratory tract (RT) infection occurs frequently in children with Cr. Infection. This suggests that Cr. transmission may occur via aerosols or respiratory droplets ejected during coughing. Using linked hospital and household studies, we will assess the clinical and public health significance of RT infection. We hypothesize that RT infection has clinical sequelae; and that prior exposure to Cr. may limit RT infection, in contrast to malnutrition or HIV which may facilitate or worsen clinical RT infection. Further, we surmise that parasite species affects the propensity for RT infection. Finally, we hypothesize that children with RT infection have increased propensity for transmission of Cr. to others.

Aim 1 is a hospital-based study that will assess severity of RT illness and possible modifying factors. We will enroll Ugandan children aged 9-36 months who (Group A) have primary diarrhea and unexplained cough or tachypnea; or (Group B) primary clinical pneumonia with or without diarrhea. The respiratory status of all children will be rigorously assessed, including pulse oximetry. Both groups will be screened for Cr. in the stool, and eligibility for sputum induction after clinical and laboratory testing affirms the procedure can be safely performed. Prior Cr. exposure will be judged via two novel immunological methods, salivary antibody to gp15 and an indirect immunofluorescence assay against replicating Cr. grown in vitro. Nutritional status will be gauged via anthropometrics, hemoglobin, and serum albumin. HIV testing, if consented to, will be performed. Sputum isolates of Cr. will be speciated via RFLP analysis. Concurrent RT infections will be exhaustively assessed by standard microbiology, multiplex PCR, and staining for HIV-related organisms. Children identified in Aim 1 will then serve as index children for household transmission studies under Aim 2A. We will visit households of index children to characterize the clinical history, enteric and RT Cr. status, and exposure history (with salivary antibody to gp 15) of household members, at the time of presentation of the index child and 2 weeks later. We will then compare transmission rates in households of children with and without RT Cr. infection in both a retrospective and prospective fashion. To address the hypothesis that adults with RT Cr. could act as agents of transmission, under Aim 2B we will establish whether there is any evidence of RT Cr. in adults using an inexpensive, efficient approach testing thousands of specimens – by re-screening sputa collected for tuberculosis testing for Cr. This group is enriched with persons with HIV.

PI: Guyer, Samuel
Title: CAREER: Cooperative Virtual Machines: Mechanisms, and Policies for Application-Aware Runtime Services
Abstract:
Modern managed programming languages, from Java and C# to JavaScript and Ruby, provide a compelling set of software engineering advantages over traditional languages like C and C++. Unfortunately, they continue to suffer from a range of well-documented performance problems. Their inefficient use of memory, in particular, imposes a significant penalty, with debilitating consequences for the quality and capacity of critical server software built in these languages. In spite of intensive research and development, these problems have remained stubbornly unsolved. As a result programmers face a difficult dilemma: choose a safe and secure managed language, but take a major performance hit, or continue taking their chances with C and C++.

This project explores a new approach, called cooperative virtual machines, which attacks the problem by improving communication and cooperation between the programmer and the managed language runtime system (the virtual machine). The key idea is that with extra information, virtual machines can provide much more efficient services because they are customized to each application's needs. The project involves building new tools for exploring and quantifying memory performance, designing a configurable garbage collector for large server applications, and developing techniques to give programmers more control over the low-level representation and management of data structures. Significant improvements in memory utilization and performance will allow existing computing infrastructure (hardware and software) to deliver higher quality services to more users. A crucial component of this project is improved pedagogical tools and techniques to help new programmers reason about the performance of these complex systems.

PI: Guyer, Samuel
Title: SHF: Small: Dynamic Detection of Heap-Based Bugs
Abstract:
Identifying bugs in software continues to be a challenging, but essential problem to solve. One particularly difficult task is ensuring the integrity of large-scale data structures stored in memory. Existing bug-finding techniques, such as static analysis of the code, have not been effective on this problem, especially for complex and highly dynamic software, such as web applications.

This project explores a new technique for checking data structures dynamically as the program executes. Dynamic checking is effective and precise, but must be efficient in order to avoid significantly slowing program execution. The key idea in this work is to piggyback checking on the garbage collector, which already periodically visits all data structures in the program. An efficient and precise tool for detecting data structure errors could be widely deployed to improve the reliability of critical software infrastructure.

The project consists of three specific avenues of research. The first involves developing a declarative language for expressing dynamic data structure properties, building on existing techniques from static analysis and verification. The second investigates the class of properties that can be checked during a single pass of the garbage collector. The third builds on the machinery of concurrent garbage collection, allowing heap checks to proceed concurrently with the application on available extra CPU cores.

PI: Harris, Jonathan
Title: Core Support for the Global Development and Environment Institute
Abstract:
The goal of the Research and Policy Program is to deepen public understanding and influence public debate over environmental and development problems and policies. Complementing GDAE's educational and theoretical efforts, the program's main goals are to identify the appropriate role for market-based instruments and develop alternative proposals that make use of a wider range of policy measures. The principal research area is Globalization and Sustainable Development, which for eleven years has offered policy oriented research on international trade and development. The program also includes collaborative work with the Stockholm Environment Institute on the economics of climate change, and ongoing work on economics for health and the environment.

In the coming two-year period, the Research and Policy Program will focus on key areas of debate in global governance, with climate as a cross-cutting theme. These include:

  • Trade and Investment Agreements – The Obama Administration seems intent on continuing the trade policies of prior administrations, based on the failed NAFTA model. GDAE will bring its deep critique of this approach to debates over: pending trade agreements with Korea, Colombia and Panama; the proposed TransPacific Partnership; the Doha Round of the World Trade Organization; and bi-lateral investment treaties with key trading partners. This draws on eleven years of research on the "Lessons from NAFTA."

  • Foreign Investment – The global economic crisis precipitated new debate over international financial flows. GDAE will continue its work on China's foreign investment in Latin America, the role of capital controls in trade and development, and the management of sovereign debt. Through a number of established media GDAE's Kevin Gallagher has become a platform for playing a leadership role in the debate over the role of foreign capital in international development.

  • Global Governance of Food and Agriculture – The global food price crisis has stimulated a re-examination of the governance of global agricultural trade and development. CWAE's Timothy A. Wise will analyze both U.S. and international policy responses with particular attention to the role of smallholders employing sustainable fanning practices. His work covers a wide range, from U.S. farm policy to the role of commodity speculation in food price increases. GDAE also researches the impacts of South American agricultural expansion on the environment.

  • Intellectual Property for Development – GDAE will continue to examine the ways in which Latin American countries have shaped their national intellectual property regimes and the impacts on development and innovation

PI: Harris, Jonathan
Title: Theory and Education
Abstract:
The U.S. economy is failing across a broad front — environmentally, socially, financially, and politically. Deep, systemic change is needed to promote a transition to a new economy, one where the acknowledged priority is to sustain human well-being and the natural world we inhabit. There is growing awareness of the need for change, reflected in the Occupy Wall Street protests and widespread social discontent with inequality, unemployment, and environmental degradation. What is needed is a vision for alternative priorities and institutions both for the United States and for the rest of the world.

The Global Development and Environment Institute (GDAE) is an interdisciplinary research institute at Tufts University, working to reform economic theory, transform the way economics is taught, and reshape economic policies to promote sustainable and equitable development. As the world reels from on-going global economic and ecological crises, the need to re-examine economic theory and practice is ever more urgent. Since 1993, GDAE has distinguished itself as one of the leading sources of new thinking in economics, bringing fresh insights into the classroom with innovative curriculum materials and into policy debates with rigorous, policy-relevant research.

GDAE's Theory and Education Program understands the essential role played by curricular materials in the continuum where theory is needed to strengthen vision, and without vision constructive change is almost impossible. Our focus on a wide variety of educational materials is based on the recognition that if students continue to be offered only the standard fare in economics we are leaving out a critical piece of the package needed for constructive change in our socio-economic system.

PI: Harris, Jonathan
Title: Theory and Education Program Support
Abstract:
The educational materials created at GDAE have the overall goal of changing the content, the assumptions, and the status-quo-preserving ideology of college economics curricula. We are aware that our efforts alone cannot bring about such change, but in nearly 20 years of focusing on this goal we have produced a substantial base of exceptionally useful materials. The new materials we are developing are taking into account new information on growing environmental threats and depletion and degradation of resources, as well as changing attitudes among a public that, since 2008, has become increasingly aware of unjust divisions of power, influence and money in the economy- divisions that also hinder attempts to address environmental problems. The largest single portion of our efforts is focused on incorporating the latest knowledge about environmental and social issues into new editions of our three basic textbooks. Specifically, our goals for the next two years are:

  • To put onto our website 3 new curricular modules. 15 modules are now freely available, at http://www.ase.tufts.edu/gdae/education_materials/modules.html. We have tracked about 52,000 separate downloads of modules from the GDAE website.

  • To complete a new-edition of GDAE's environmental economics text, Environmental and Natural Resource Economics

  • To complete new editions of two other textbooks, Microeconomics in Context and Macroeconomics in Context

  • To complete distribution of our Social Science Library (SSL) to all university libraries in 137 of the world's poorest countries.

PI: Hashley, Jennifer
Title: Massachusetts Beginning Farmer Agricultural Alliance
Abstract:
The objectives are:

  1. Establish the Massachusetts Beginning Farmer Agricultural Alliance (BFAA) – a statewide collaboration of beginning farmers, farm service providers, and farm support agencies – to expand use of new and existing agricultural education and technical assistance resources.

  2. Farmland access: Develop a statewide farmland outreach, training and technical assistance program to connect new producers to farmland resources.

  3. Develop a statewide livestock training and technical assistance program.

PI: Hatini, Victor
Title: Cellular Interactions in Patterning and Morphogenesis
Abstract:
Apical constriction is an ancient developmental process that triggers key morphogenetic events such as neurulation in vertebrates and gastrulation in insects. However, the pathways involved are not fully understood. During pupariation, presumptive leg joints undergo apical constriction and epithelial invagination to initiate joint morphogenesis. We hypothesize that the process is mediated by an increase in actomyosin contractility and a decrease in cell-cell adhesion. The goal of this grant is to study the roles of the Rho GTPases Rho1, Rac1 and Cdc42 and their regulators, the RhoGEFs and RhoGAPs, in controlling the stability and turnover of adherence junctions (AJs), and the contribution of these genes to apical constriction and epithelial invagination during joint morphogenesis. We find that the inhibition of Rho1 or the activation of Rac1 or Cdc42 blocks joint morphogenesis. We also find that RhoGAP68F (GAP68F), a putative GAP for Cdc42, and RhoGAP5A (GAP5A), a putative GAP for Rac1, are expressed at presumptive joints and are required to initiate joint morphogenesis. We provide strong preliminary evidence to suggest that these regulators act through distinct pathways to control apical constriction.

To test the role of the Rho GTPases and their regulators in apical constriction we propose the following specific AlMs:

  • AIM 1: We will test the hypothesis that Rho1, Cdc42 and Rac1 respectively regulate the influx, efflux and the stable pool of AJs at the ZA to promote apical constriction.

  • AIM 2: Large-scale interaction screens identified Rab4 and Sec3 as partners of GAP68F suggesting that GAP68F inhibits endocytic recycling from two distinct recycling routes to decrease the surface expression of AJs and thereby adhesive cell-cell contacts. In agreement, we find accumulation of GAP68F in the endocytic compartment. Therefore, we will test the hypothesis that GAP68F inhibits endocytic recycling and thereby adhesive cell-cell contacts to promote apical constriction.

  • AIM 3: We find that GAP5A is enriched at or near the zonula adherence (ZA). We will test the hypothesis that GAP5A acts at the ZA to decrease the stability of AJs and thereby adhesive cell-cell contacts to promote apical constriction.

The successful completion of these studies will highlight the contribution of junctional stability and endocytic trafficking to apical constriction and epithelial invagination with implications to vertebrate systems.

PI: Haydon, Philip
Title: Astrocyte-Neuron Signaling
Abstract:
Researchers are increasingly aware that astrocytes respond to neuronal activity with Ca2+ signals that can induce the release of chemical transmitters. The roles of these gliotransmitters in the control of neural function and behavior are poorly defined. Our studies have revealed that astrocytes are responsible for the control of extracellular adenosine that activates neuronal adenosine 1 receptors (A1R). The expression of a dominant negative dnSNARE domain in astrocytes, to inhibit the release of gliotransmitters, causes a reduction in the magnitude of CA3-CA1 long term potentiation (LTP), as well as a reduction in synaptic N-methyl-D-aspartate receptor (NMDAR) current (prelim studies) and impairments in sleep homeostasis. Since Ca2+ supplied by NMDARs is essential for the induction of LTP, we propose a novel hypothesis linking astrocyte-derived adenosine with NMDARs and LTP: Astrocyte-derived adenosine acting through A1 receptors enhances synaptic NMDAR currents and consequently the magnitude of NMDAR-dependent LTP.

To test this hypothesis we will use conditional astrocyte-specific transgenic mice that allow both activation and inhibition of glial signaling pathways. We have four specific aims: First, we will test the hypothesis that astrocyte-derived adenosine acting on A1 receptors regulates synaptic NMDAR currents. Second, we will test the hypothesis that astrocytic Ca2+ signaling promotes NMDAR-dependent LTP. Third, we will test the hypothesis that astrocytic enhancement of LTP is mediated via A1 receptor-dependent augmentation of NMDA receptors. There are likely to be wide ranging effects of adenosine, NMDAR and LTP on behavior. To maintain focus we will build on our recent studies in the fourth specific aim to identify roles for astrocyte-Ca2+ signals and adenosine in the control of sleep homeostasis.

This project will provide entirely new information on the role of astrocytes in brain function. Using molecular genetic studies in situ and in vivo we will determine under which conditions astrocytes contribute to information processing and behavior. Since we propose that astrocyte-derived signals regulate NMDA receptors, receptors known to be central to numerous disorders, this project has the potential to identify novel glial targets to enhance learning and memory and to treat sleep disorders.

PI: Haydon, Philip
Title: Glial Dependent Modulation of Depressive Like Behaviors
Abstract:
Sleep abnormalities are co-morbid with many psychiatric conditions though whether sleep disorders are a cause or consequence of depression is unclear. A total night of sleep deprivation has immediate antidepressive actions in the clinical population, although the signaling pathway is unknown. We propose that adenosine underlies the antidepressive effects of sleep deprivation because i) adenosine regulates sleep, ii) sleep deprivation elevates adenosine, and iii) single nucleotide polymorphisms in adenosine transporters and a metabolic enzyme have been identified in patients with depression with disturbed sleep.

We demonstrated that astrocytes contribute to the behavioral responses to acute sleep deprivation. We conditionally expressed the SNARE domain of a vesicle protein in astrocytes to impair exocytosis resulting in reduced extracellular adenosine, as assessed by reduced basal activation of neuronal A1 receptors (A1R), reduced slow wave activity (SWA) during non-rapid eye movement (NREM) sleep and impaired recovery sleep following sleep deprivation. We hypothesize that the antidepressive effects of acute sleep deprivation are mediated by astrocyte-derived adenosine acting on neuronal A1 receptors.

Aim 1: We will test the hypothesis that astrocytic modulation of sleep homeostasis contributes to antidepressive effects of sleep deprivation. We will determine whether a total night (12h) of sleep deprivation leads to antidepressive like effects, then using dnSNARE mice will ask whether the astrocytic sleep homeostat is required to mediate depressive-like responses.

Aim 2: We will test the hypothesis that A1 receptors are required to mediate the antidepressive-like effects of sleep deprivation. We will determine whether 12h of sleep deprivation leads to enhanced activation of A1R and using central delivery of A1R antagonists and A1R knockout (A1R-/-) mice we will determine whether antidepressive-like effects of sleep deprivation require A1R.

Aim 3: We will test the hypothesis that sustained (12h) pharmacological activation of central A1R will produce antidepressive like effects. We will deliver A1R agonists intracerebroventricularly (i.c.v.) and will ask whether the activation of this receptor pathway yields antidepressive like effects.

Aim 4: We will determine the role of frontal cortex in contributing to antidepressive effects of sleep deprivation. We will expand preliminary c-fos immunoreactivity studies and the use of novel Tet Tag transgenic mouse that enables GFP-labeling of c-fos active neurons to identify sleep deprivation activated neurons of the frontal cortex. Finally, we will virally transduce frontal corex astrocytes with dnSNARE and ask whether region specific transduction inhibits antidepressive effects of sleep deprivation.

The identification of a signaling pathway underlying antidepressive like effects of sleep deprivation has the potential to for the future development of glial-based therapeutics for the immediate relief of depression.

PI: Haydon, Philip
Title: Roles for Astrocytes in Mediating Responses to Alcohol
Abstract:
Alcohol has numerous actions in the nervous system mediated through multiple transmitter signaling pathways. Both acute and chronic actions of alcohol modify sleep related behaviors through undefined mechanisms. We have shown that astrocytes, a type of glial cell, modulate sleep homeostasis by an adenosine receptor 1 (A1R)-dependent mechanism. We have novel evidence that molecular genetic manipulations directed at this glial pathway also impact alcohol-induced behaviors. We propose that alcohol activates the adenosine-dependent astrocytic cell and molecular signaling pathway that normally contributes to the homeostatic drive to sleep. Our overriding hypothesis is that an astrocytic source of adenosine mediates behavioral sensitivity to alcohol, and that the comorbidity of alcoholism and sleep disruptions involves long-term perturbations of this adenosine pathway.

This project will be divided into three sections. Initially, we will identify the astrocyte-based signaling pathways that contribute to acute effects of alcohol on behavior (Aim 1). Subsequently, we will study how pre-existing impairments in sleep homeostasis impact alcohol behaviors (Aim 2), and how chronic alcohol exposure modifies sleep homeostasis (Aim 3). Despite numerous clinical reports that emphasize the correlation between sleep homeostasis and alcohol behaviors, few experimental models have been developed to explore this relationship. The significance of this project is reflected in the development of novel experimental models and multiple techniques that will be used to identify the interaction between alcohol behaviors and sleep impairments. The approaches described below offer distinct opportunities for therapeutic intervention.

The proposed study uses an innovative integration of multidisciplinary approaches to study the involvement of the astrocyte-dependent sleep homeostat as a key mediator of acute and chronic effects of alcohol. Since astrocytes are now known to express G protein coupled receptors that are not expressed in neurons, results may also enhance the future potential to identify novel targets for ameliorating sleep impairments that haunt recovering alcoholics.

PI: Haydon, Philip
Title: Roles for Gliotransmission in Substance Abuse
Abstract:
Synaptic plasticity is at least one of the cellular underpinnings of addiction to drugs of abuse. NMDA receptors, which are necessary for some forms of synaptic plasticity, play pivotal roles in mediating behavioral responses to cocaine. Infusion of cocaine can lead to NMDA receptor-dependent long term potentiation of synaptic transmission in the ventral tegmental area (VTA). Infusion of NMDA receptor antagonists into the VTA prevent cocaine-induced conditioned place preference. We will test the novel hypothesis that astrocytes are critical for the control of NMDA receptor function, synaptic plasticity, and as a consequence addictive behaviors.

There is a new appreciation for roles of astrocytes in the control of synaptic transmission. In 1994, we discovered that astrocytic Ca2+ signals stimulate the release chemical transmitters from these glia. Since then we and others have shown that this process of gliotransmission can regulate neuronal excitability and synaptic transmission leading to the idea of the Tripartite Synapse, which accounts for roles of astrocytes in synaptic transmission. Using lines of inducible, astrocyte-specific transgenic mice impaired in gliotransmission we have made two observations essential for this project: First, inhibiting gliotransmission significantly reduces synaptic NMDA receptor density. Second, this inhibition of gliotransmission blunts cocaine-induced conditioned place preference. Given the known importance of NMDA receptors in mediating rewarding properties of drugs of abuse we hypothesize that astrocytes regulate neuronal NMDA receptor density and synaptic plasticity and thereby behavioral responses to drugs of abuse.

Specific Aim I: Test the hypothesis that gliotransmission regulates functional NMDA receptor density on dopaminergic neurons in the VTA.

Specific Aim II: Test the hypothesis that gliotransmission promotes synaptic plasticity in the VTA.

Specific Aim III: Test the hypothesis that gliotransmission is essential for cocaine-induced behavioral response.

Systematically evaluating the role of gliotransmission in synaptic plasticity and behavioral responses to drugs of abuse promises to offer new insights into the cellular mechanisms underlying addiction. Since astrocytes express unique receptors that could be targeted therapeutically, success in this project may offer a new approach to prevent and treat addictions.

Mentor: Haydon, Philip
Fellow: McIver, Sally
Title: The Role of Gliotransmission in Mediating the Central Effects of Alcohol
Abstract:
Much attention has been given to the neurochemical and synaptic changes that influence the behavioral effects of alcohol, with emphasis placed on neuronal mechanisms of action. The potential role of astrocytes as targets or mediators of the central effects of alcohol is largely unknown, and is the major focus of this proposal. The rationale behind the proposed studies is in part based on two key findings from the literature: that acute alcohol exposure causes increased extracellular adenosine via blockade of the equilibrative nucleoside transporter 1, and that sensitivity to and consumption of alcohol can be mediated by activation of the src family kinases (SFK) and a known substrate, the NR2B subunit of the NMDAR. Using an astrocyte-specific transgenic mouse, called dnSNARE, we have shown that an astrocytic source of adenosine acting on A1 receptors (A1R) influences NMDAR-mediated synaptic activity and membrane expression of NR2B. In preliminary studies, dnSNARE mice exhibited increased sensitivity to the acute effects of alcohol and decreased alcohol consumption, supporting the involvement of astrocytes in alcohol behaviors. Collectively, this evidence led to the hypothesis that an astrocytic source of adenosine acting on A1Rs contributes to the synaptic and behavioral changes occurring in response to alcohol exposure.

The proposed experiments are designed to establish the potential link between astrocytes and the effects of alcohol on A1R activation and NMDAR-mediated synaptic activity. In the first aim, dnSNARE mice will be tested to determine sensitivity to the hypnotic and motor impairing effects of alcohol, and for consumption of and preference for alcohol. The second aim will employ pharmacology in dnSNARE and control mice to examine whether these characteristic alcohol behaviors involve A1R activation, independently and/or in concert with downstream changes in activation of SFK and the NR2B subunit of the NMDAR. In the third aim, electrophysiology will be used to compare the effects of alcohol on synaptic transmission in brain slices from dnSNARE and control mice, and to test whether astrocyte-regulated activation of A1Rs, SFK, and NR2B mediates alcohol-induced changes in synaptic transmission. By identifying a novel astrocytic target of alcohol, results from these studies have a unique potential to impact the development of therapies for treatment of alcohol abuse and dependence.

Mentor: Haydon, Philip
Fellow: Blutstein, Tamara
Title: The Role of Gliotransmission in Sleep Homeostasis
Abstract:
Over ten years ago the idea of a tripartite synapse, which suggested that synaptic transmission involved three components, a presynaptic terminal, a postsynaptic terminal and a glial cell, was put forth to the scientific community. Since then tremendous advances have been made in the field of glial biology, and it is now well-accepted that glial cells are active participants in synaptic transmission and can release chemical transmitters, in a process called gliotransmission, which can influence synaptic activity and behavior. Our lab has developed a transgenic mouse model which specifically impairs gliotransmitter release in astrocytes via the inducible expression of a dominant negative SNARE (dnSNARE) protein driven by a GFAP promoter. Using this model we have shown that gliotransmission is involved in the modulation of sleep homeostasis. More specifically, astrocytic SNARE dependent gliotransmitter release is necessary for the accumulation of sleep pressure and contributes to the impairment of working memory following sleep deprivation in an A1R dependent manner.

The goal of this proposal is to further explore the role of gliotransmission in sleep homeostasis and cognition. First, we propose to determine the identity of the gliotransmitter. The effects we observe are A1R dependent which has led us to propose that astrocytic release of ATP, which is converted extracellularly to adenosine, is the putative gliotransmitter. Thus, we will directly measure extracellular adenosine levels in wild-type and dnSNARE animals during sleep deprivation. Next, we will seek to identify the activating signal for gliotransmitter release. Nitric oxide (NO) is also involved in sleep homeostasis and has been shown to increase extracellular adenosine levels, making it an intriguing potential candidate molecule for the initiation of gliotransmitter release. Thus, we will test whether NO can induce an astrocytic SNARE sensitive increase in extracellular adenosine and sleep pressure. Finally, we will assess whether the increased adenosine tone contributes to the cognitive deficits seen after sleep deprivation. The proposed experiments will take advantage of my existing skills in in vivo microdialysis and molecular biology while allowing me to gain skills in EEG/EMG recordings, electrophysiology and behavior. Sleep is important to overall health and affects all aspects of human behavior. This makes it imperative to understand the homeostatic mechanisms that underlie sleep and wakefulness and identify new regulatory targets, such as glial cells.

PI: Heldwein, Ekaterina
Title: Structural Mechanism of Herpesvirus Egress
Abstract:
Herpesviruses are a family of human pathogens that establish lifelong latent infections from which viruses periodically reactivate, causing a number of ailments. Reactivations are responsible not only for a significant disease burden but also for a high rate of new infections. During reactivation, multiple infectious progeny virions are assembled and released from the cell in a process called egress. The first step in this process is nuclear egress whereby assembled nucleocapsids exit the nucleus into the cytoplasm. Although key viral nuclear egress participants have been identified, critical mechanistic details are lacking.

The long-term goal of this research is to elucidate the process of nuclear egress at the atomic level for two alphaherpesviruses, herpes simplex (HSV) and pseudorabies (PRV). The objective of this proposal is to initiate a biophysical, biochemical, and structural characterization of the HSV-1 nuclear egress complex UL31/UL34 (NEC). This research is driven by a hypothesis that the NEC enables primary envelopment by a mechanism similar to that of matrix proteins of negative-stranded RNA viruses and cellular ESCRT-III proteins, which promote budding by deforming the membrane in an oligomerization-dependent manner.

Aim 1 will focus on the determination of the affinity and stoichiometry of UL31/UL34 interactions, mapping of the minimal fragment of each protein that can form the NEC, and initiation of crystallization trials with the goal of determining the structures of UL31, UL34 and the UL31/UL34 complex.

Aim 2 will test the hypothesis that purified HSV-1 NEC can deform membranes in vitro in the absence of other viral or host proteins, in oligomerization-dependent manner.

The proposed studies will provide important insights into the structure of the NEC and the mechanism by which it enables membrane deformation during nuclear egress. Obtaining the crystal structures of UL31, UL34, and the NEC would be a significant achievement that would have a major impact in the field of herpes virology. Known functional data can be mapped onto the structures to obtain insight into the structural basis of functional phenotypes. In the future, this knowledge will allow for the structure-guided design of drugs targeting these interfaces. Showing that the purified NEC alone can deform membranes in vitro not only will demonstrate that it is necessary and sufficient for this process but will also allow the development of an in vitro assay in which the membrane deformation activity of UL31 and UL34 mutants can be correlated with their in vivo budding phenotypes.

In the future, the results obtained in the course of the proposed work will form the foundation for a subsequent R01 application to elucidate fully the mechanism of herpes virus egress.

Mentor: Hinds, Philip
Fellow: Bryan, Crystal
Title: The Role of pRb-dependent Ihh in Osteogenesis and Osteosarcoma
Abstract:
The retinoblastoma protein (pRb) is a tumor suppressor that is found mutated or dysregulated in most human cancers. It is most commonly directly affected in retinoblastoma and osteosarcoma. To appreciate why direct mutation of pRb is important in cancer development in certain tissues, understanding its role in normal development is essential. Through various studies, the sponsor's lab found that pRb is necessary for lineage commitment of osteoblasts and that there are more bipotent progenitors in the calvarium of animals lacking pRb, which could contribute to malignant phenotypes. The lab also found more recently that Indian hedgehog (Ihh) is downregulated in Rb1-/- calvarial cells during differentiation, implicating this factor as a potential mediator of pRb's function in bone development and cancer.

The purpose of this project is to determine the role of Ihh in lineage commitment of osteoblasts as well as the possible roles for Ihh as a mediator of pRb function in osteosarcoma. Using both in vitro and in vivo tools, the bipotency/stemness of calvarial cells lacking Ihh will be assessed to determine if Ihh is necessary for osteoblast commitment. This will be accomplished by first differentiating the cells into adipocytes and osteoblasts to determine if Ihh-/- calvarial cells are bipotent. Stemness will be assessed by serially differentiating these cells, that is, differentiating with osteogenic media until full differentiation has been achieved, then replating and differentiating again. In addition to these studies, the effect of adding Ihh to pRb-deficient calvarial cells during differentiation will be assessed utilizing recombinant Ihh (rIhh) and the adipoctye/osteoblast differentiation protocols. It is expected that loss of Ihh will increase the pool of bipotent progenitor cells in the calvariu (similar to pRb loss) and that adding rIhh to Rb1-/- cultures will impair their bipotent capabilitis.

The effect of Ihh loss in an osteosarcoma model will also be assessed to determine a role for Ihh in bone tumorigenesis. To this end, animals will be mated to carry conditional alleles of Trp53 and Ihh, after which both will be deleted in osteoblasts by introducing an Osterix-Cre allele into this population. Animals will be monitored for osteosarcoma formation and tumor cells will be isolated and characterized to assess their adipocyte and osteoblast differentiation abilities. In addition, the loss of both p53 and Ihh in osteoblast commitment and differentiation will be assessed using calvarial cells from E18.5 embryos and differentiating these cells with osteogenic media. It is expected that Ihh loss will contribute to transformation of osteoblasts and promote tumorigenesis.

PI: Holcomb, Phillip
Title: The Neuro-cognition of Word Comprehension
Abstract:
The mental and underlying neural (neuro-cognitive) operations involved in the comprehension of words are fundamental to language based communication. Understanding how the brain identifies individual words from around fifty thousand or so possibilities in less than half a second, has been a continuing challenge for theorists in psychology, neuroscience and education. Finding the answer to this and related questions would represent a major step forward in basic language science, but also would provide a framework for helping isolate the neuro-cognitive locus of deficits in certain developmental language disorders.

The overall goal of the proposed research is to continue our study of word comprehension processes from a neuro-cognitive perspective. The experiments outlined in this proposal are focused on providing answers to questions about the temporal dynamics (ERPs) and now the spatial organization (MEG and fMRI) of the neural networks that underlie the comprehension of words.

The proposed research has four specific aims. In Aim 1 we propose to test a series of predictions about the temporal dynamics of visual word comprehension derived from our recently elaborated Bi-modal Interactive Activation Model (BIAM) of word processing. Experiments are proposed that use our well understood ERP masked priming paradigm, as well as two new novel experimental techniques. We will also extend the scope of our research in three new directions. In Aim 2 we propose a novel series of ERP studies designed to expand our study of comprehension to the auditory modality using our newly developed dichotic priming task. These studies will allow us to better elaborate the auditory side of the BIAM. In Aim 3 we propose experiments that test predictions from the BIAM at the interface between visual and spoken word processing, a level we hypothesize is critical to the process of learning to read. Finally, in Aim 4 we propose to augment our work on the temporal dynamics of word comprehension by using multi-modal imaging techniques. This will provide much needed information about the spatial organization of the neural networks involved in word comprehension and will allow us to add an anatomical component to our BIAM of word comprehension.

Our long term goal is to extend these studies to normal children as well as those with word processing deficits including dyslexia and SLI.

PI: Hollander, Justin
Title: A Cross-National Comparison of Urban Shrinkage in Quebec, Canada and New England, USA
Abstract:
While both the U.S. and Canada continue to struggle with economic challenges, the outcomes of decline have been manifested at the neighborhood level with increasing numbers of foreclosures, vacant, and abandoned housing in New England but with more stable outcomes in Quebec. I propose to conduct a comparative study of governmental and economic policies in Quebec and New England by looking closely at how demographic and economic conditions have shifted during the last four years of contraction in the two regions. The hypothesis is that patterns of economic change during this period of contraction are distinct across the two regions and that difference can be attributed to national, provincial/state, and local policies. The results are expected to illuminate key environmental and sustainability issues in both countries, helping to guide future governmental and economic policymaking.

PI: Hollister, Robert
Title: Youth Economic Participation Initiative
Abstract:
The Talloires Network is a coalition of universities – 230 institutions in 62 countries enrolling over 6 million students – that are moving beyond the ivory tower to tackle pressing societal problems. The Network is the primary global alliance committed to strengthening the civic roles and social responsibilities of higher education. It mobilizes its members to improve community conditions and, in the process, to educate students to be leaders for change. Our vision is that a decisive majority of universities worldwide collaborate actively with the communities where they are located; that institutions of higher education become dramatically more effective engines of social and economic development; that they systematically partner with NGOs, government agencies and private businesses; and that the gold standard in higher education is the "engaged university," one that achieves both positive community impacts and academic excellence.

Developed in collaboration with The MasterCard Foundation, the Talloires Network Youth Economic Participation Initiative (YEPI) responds to the pervasive gap between the realities of the job market in many developing countries and the ability of university-educated youth to successfully participate in the economy. Understanding that universities hold an important responsibility to address this issue, the YEPI aims to apply the extensive expertise and person power of university civic engagement programs to tackle the youth economic participation crisis. Strategically changing how institutions of higher education educate their students can significantly improve the ability of educated youth to engage in economic participation, either through employment, or through entrepreneurship.

YEPI aims to achieve this goal by demonstrating, documenting and disseminating best practices for university-community partnerships that promote the economic participation of educated youth. In addition, it will encourage its own member institutions and others to adopt these policies and practices, and provide guidance on how to do so. The Initiative will perform these functions through two principal sets of activities: A Demonstration Grants Program and a Global Community of Practice. The Demonstration Grants Program will award 8-12 grants to Talloires Network member institutions in developing countries 1. Grants will be awarded to institutions that demonstrate a record of success in implementing innovative community-based programs, and that propose creative approaches to facilitating students’ transition from university to employment and job-creation. Demonstration projects will document lessons learned that we will disseminate among Talloires Network institutions and encourage them to use.

The Community of Practice is a concerted strategy to facilitate the sharing of knowledge among universities around the world about the role of higher education institutions in promoting the economic participation of educated youth. The Community of Practice will reinforce multiple core functions of the Talloires Network – the exchange of best practices, capacity-building, brokering joint projects, and collective action to strengthen civic engagement programs. It will both enable the Talloires Network to integrate YEPI findings and recommendations into all Network activities, and also include a series of activities – such as a web platform, moderated online discussions, and trainings – specifically dedicated to the exchange of knowledge about youth economic participation. The Talloires Network will partner with the youth consultancy group DECODE to run a stakeholder-led design process for the Community of Practice using DECODE's Innovation Engine methodology.

PI: Hopwood, Jeffrey
Title: DARPA-2011-Microplasma Array
Abstract:
The proposed work will develop and demonstrate a two-dimensional array of microwave resonators used to generate a surface-conformal array of microplasmas. Control of the microplasma distribution will be achieved by the selection of drive frequency and programming a control logic layer of transistor switches. The electrode design will be tailored to ensure maximum achievable plasma density and minimize switching times. Microplasma arrays will facilitate two novel signal processing paradigms: as actively-configurable metamaterials for multiband tunable absorbers/reflectors and as the platform for the next generation of millimeter-wave spatiotemporal signal processing using a microplasma-based switch matrix embedded within millimeter-wave modules.

Mentor: Hu, Linden
Fellow: Klein, Brian
Title: Determination of Porphyromonas Antimicrobial Resistance Mechanisms by Tn-Seq
Abstract:
Porphyromonas gingivalis, an anaerobic, Gram-negative bacterium, is an important organism in the pathogenesis of periodontitis. Antibiotics are used in the treatment of severe periodontitis and recently growing resistance to antibiotics in clinical P. gingivalis isolates has been reported. Metronidazole is a nitroimidazole with activity against many anaerobic bacteria, including P. gingivalis. Resistance to metronidazole has now been reported as high as 22%, but little is known about the mechanisms of resistance.

In this proposal, I will use transposon mutagenesis to identify genes and gene networks involved in the development of metronidazole resistance. In my preliminary work, I have created two transposon mutant libraries in different strains of P. gingivalis using a Mariner-based transposon system. This transposon system has advantages compared to prior transposon libraries in P. gingivalis due to ability of Mariner to insert randomly as to create highly saturated libraries with insertions throughout the genome. Using this library, I have already identified previously unrecognized pigmentation mutants of P. gingivalis. Interestingly, some of these pigmentation-defective Pg mutants are resistant to metronidazole.

In this proposal, I will first establish the role of pigmentation in resistance to metronidazole by performing complementation and characterization of the pigmentation mutants I have isolated. The transposon I used is adapted for use with massively-parallel sequencing to identify the relative fitness of mutants in the library with a technique called Tn-seq. To uncover additional non-pigment related genes involved in metronidazole resistance, I will perform a screen of the entire library using Tn-seq to identify mutants that are either enriched or eliminated on exposure to different concentrations of metronidazole. Finally, I will perform clinical sampling for P. gingivalis from patients with periodontal disease and employ targeted gene sequencing of metronidazole resistance genes identified in Aims 1 and 2, to determine whether mutations associated with in vitro resistance to metronidazole are found in patients with clinically resistant isolates of P. gingivalis.

This project is expected to shed new light on mechanisms of P. gingivalis resistance to an important antimicrobial agent. In the process I will be developing new tools and learning techniques that have the potential to be applied to multiple aspects of P. gingivalis virulence and that will prepare me for a future in oral microbiological research.

PI: Hynes, Morgan
Title: Preparing Engineers to Educate Now
Abstract:
The Tufts University Noyce capacity building project aims to bolster Tufts' newly instituted Master of Arts in Teaching Engineering program that prepares engineers as grades 5-12 engineering teachers. The project team composed of faculty from Mechanical Engineering, Computer Science, and Education recognizes the need for a multi-faceted approach:

  1. Attract and recruit engineering undergraduates and practicing professionals to become engineering teachers,
  2. Build partnerships with local schools and engineering teachers to serve as M.A.T. in Engineering candidates cooperating teachers, and
  3. Effectively prepare M.A.T. in Engineering candidates through innovative coursework, engineering faculty advisors, and other programmatic supports.

The approach includes new course development where engineering faculty work with education faculty to incorporate education themes and ideas in graduate level engineering content courses and year-round programming with all stakeholders (undergraduate engineering students, M.A.T. candidates and graduates, cooperating in-service teachers, and engineering and education faculty).

PI: Imanishi-Kari, Thereza
Title: The Effect of Innate Immunity on B Cell Tolerance
Abstract:
Recent evidence increasingly points to the importance of antibodies specific for RNA antigens in the pathogenesis of SLE. Using a novel mouse model in which RNA-specific B cells are generated and easily tracked, and in which clinical SLE pathologies are recapitulated, new and critical information on the pathogenesis of SLE will be obtained. The mouse line to be used, 564lgi, was generated in our laboratory and has already made an important contribution to the emerging understanding of the role played by TLRs, in particular TLR7, in the development of SLE. In this system, on the non-autoimmune C57BL/6 background, most RNA-reactive B cells undergo receptor editing, while those that retain their RNA-specificity become anergic by multiple criteria. Yet class-switched pathogenic autoantibodies are produced by a T-independent, but TLR7-dependent mechanism. Thus, either anergic RNA-specific lgM+ B cells are capable of activation and differentiation into lgG producing cells in response to self-antigen, or a subpopulation of these cells is able to evade anergy, namely those that have undergone CSR in the bone marrow during B cell development in response to self-antigen encounter. In the current proposal, these two models will be tested in detail. In either case, the signals required for differentiation into antibody producing cells and the extent to which there are contributions from non-B cells will be determined. Finally, the effect of autoimmune-prone backgrounds on the regulation of RNA-specific B cells in the 564lgi system will be studied. These experiments will help unravel the mechanisms by which RNA-specific B cells become activated and produce pathogenic autoantibodies in SLE.

PI: Isberg, Ralph
Title: Analysis of the Interplay between Cell Adhesion and Bacterial Protein Translocation
Abstract:
Misregulation of host cells is a common tactic of bacterial pathogens. In particular, proteins translocated by type III secretion systems (TTSS) encoded by Gram-negative organisms can disrupt a wide range of cellular processes. Many pathogens also encode specialized adhesion systems whose activities, at least superficially, appear unrelated to misregulation. In fact, it is not unusual to find that the activities of the translocated substrates can interfere with the activity of the adhesion protein. Selective pressure clearly has forced maintenance of these supposedly antagonistic proteins, so it is likely that in many cases these proteins collaborate in a fashion that promotes colonization and the establishment of the disease state. It is important to determine how these factors collaborate, because several proteins with very different biochemical activities may act together to alter the regulation of a single downstream target. Such information should allow simplification of drug discovery, as very different proteins that appear to be at war with each other may feed into a single pathway that can be targeted therapeutically.

This proposal will focus on the TTSS of Yersinia pseudotuberculosis and its relationship to the outer membrane protein invasin, which promotes bacterial uptake into host cells with concurrent activation of mammalian cell small GTPases. Many of the translocated substrates of the TTSS, called Yops, appear to interfere with invasin function by inactivating these GTPases. Using invasin and YopT, this application will test the hypothesis that, rather than compete with each other, the Yops and invasin collaborate to allow misregulation of host cells. To pursue this goal, the fate of a photoactivated fluorescent derivative of the small GTPase will be followed in response to invasin engagement of host cell receptors. The ability of functional engagement of receptors to form a pool of the GTPase that is readily accessible to YopT will be determined. In addition, a combined photoactivation/photobleaching strategy will be introduced to the microbial pathogenesis field, in order to identify the site in the cell where YopT encounters the small GTPase. In so doing, the model will be tested that bacterial interactions with host cell surface receptors control the site in the cell where YopT ultimately contacts the small GTPase.

The long-term goal of these studies is to determine how the entire pool of TTSS substrates cross-regulates the function of other virulence-associated proteins at the site of bacterial adhesion, in a disease-promoting network. The ability to disrupt collaborative bacterial virulence factor interactions that promote the disease process is critical for identifying strategies that maintain immune function in the presence of pathogen attack.

PI: Isberg, Ralph
Title: Molecular Analysis of Microbial Pathogens
Abstract:
This is for continuation of a rigorous predoctoral Training Program that focuses on the molecular analysis of microbial pathogens. Experimental research training is the primary focus of this program. A key and complementary component of the Training Plan is the requirement for PhD students to have exposure to problems in clinical medicine through participation in a seminar course and in clinical rounds. The training program is designed to provide students with the tools to become independent research scientists in academia or industry while in parallel providing a deep understanding of current problems in clinical infectious diseases. The Training Program is a track within the interdepartmental Graduate Program in Molecular Microbiology and draws faculty members from the Departments of Molecular Biology and Microbiology, Biochemistry, Medicine, Molecular Physiology and Pharmacology, and Pathology. All investigators have a common interest either in pathogenic microorganisms or in restriction of pathogens in cell or animal models.

The varied research interests of the group include:

  1. bacterial pathogenesis, including the study of colonization, intracellular growth, toxin expression and development of tools to study microbial genes expressed during animal infections;
  2. viral pathogenesis and replication;
  3. viral persistence and oncogenesis;
  4. viral and bacterial evolution during disease;
  5. development of novel anti-parasitic and anti- fungal strategies;
  6. protein secretion and the analysis of yeast, parasite and bacterial surfaces;
  7. regulation of gene expression and cell growth in microbial model systems;
  8. analysis of developmental stages in fungal pathogens;
  9. mouse models of innate immunity; and
  10. microbial interaction with effectors of acquired immunity.

The members of this Program use genetic and biochemical strategies to analyze microbial pathogens as well as animal infection models. This Program has a long history of having a strong collaborative spirit of learning and research among faculty and students. Recruitment and admission strategies have been highly successful, with an excellent minority recruitment program, as over 20% of the students are members of underrepresented minority groups. The overwhelming majority of the 175 Ph.D. graduates of the Department since 1964 are currently employed in research positions in academics and industry, with approximately 40% of the graduates who have finished postdoctoral training obtaining faculty positions. The Program is overseen by the Training Committee, a group of internationally recognized bacteriologists and virologists who participate in the graduate education of all trainees. The application is for five years of support for 5 predoctoral trainee positions per year. Trainees are chosen by a rigorous selection process and are supported for 2 years.

Mentor: Isberg, Ralph
Fellow: De Jesus-Diaz, Dennise
Title: Molecular Analysis of the Interaction between Legionella pneumophila and Its Host
Abstract:
Legionnaire's disease is a pneumonia that results from aerosolized water sources containing the bacterial pathogen Legionella pneumophila, which initiates disease by replicating within lung macrophages. Although the bacterium is capable of growing extracellularly, it is thought that in the environment it primarily replicates within amoebae. Once inside host cells, Legionella has the capacity to modulate host cell processes in order to form a compartment surrounded by endoplasmic reticulum, where the bacteria resides and replicates. Formation of this compartment, known as the Legionella Containing Vacuole (LCV), requires the presence of the bacterial Dot/lcm system, a Type IV Secretion System (T4SS). Numerous studies have highlighted the importance of the T4SS in modulating the host endocytic and secretory pathways to form the LCV, but little is known about host factors outside of the early secretory apparatus that could modulate intracellular growth. A large-scale RNAi screen demonstrated that depletion of host proteins involved in cell cycle control or initiation of protein synthesis resulted in enhanced intracellular growth of the bacterium, consistent with the model that disruption of the host cell cycle stimulates intracellula replication.

The goal of this fellowship proposal is to understand how host factors involved in cell cycle control and translational initiation contribute to bacterial proliferation. Experiments will be performed to:

  1. Determine if L. pneumophila is able to control the host cell cycle to stimulate intracellular replication; and

  2. Determine if L. pneumophila translocated proteins play are role in stimulating bacteria growth by modulating host translation and cell cycle networks.

The results acquired from the proposed experiments will allow the determination of why cell cycle disruption stimulates L. pneumophila intracellular growth, with the intention of determining if the microorganism replicates preferentially in terminally differentiated cells.

Mentor: Isberg, Ralph
Fellow: Geisinger, Edward
Title: Type VI Protein Secretion in an Emerging Multidrug-Resistant Pathogen
Abstract:
Hospital-acquired infections due to multidrug-resistant bacteria are a major cause of increased morbidity and mortality in patients with weakened immunity. A leading agent of such infections is the bacterium Acinetobacter baumannii. This microbe causes invasive infections, including pneumonia and sepsis, that in recent years have become increasingly severe and antibiotic-resistant, raising the specter that they may one day be untreatable. New ways to prevent and treat infections with A. baumannii are urgently needed, but alarmingly little is known about how these bacteria cause disease.

Recent evidence indicates that these bacteria induce adherence-dependent cytotoxicity toward cultured epithelial cells; however, the mechanisms used by A. baumannii to intoxicate cells upon adhesion are unclear. The goal of the proposed studies is to understand how these microbes interact with human cells and how such interactions undermine normal cellular processes, promoting infection. Towards this goal, this proposal aims to characterize in detail a contact-dependent protein delivery system, known as a Type VI Secretion System (T6SS) that is present in clinical strains of A. baumannii responsible for recent epidemics. These systems play a role in host infections by a range of microbes, but the system is undefined in A. baumannii. The proposed work will determine which cells are targeted by the A. baumannii T6SS, identify the effector proteins it sends into these cells, and examine the functional roles of the system and its effectors in host interactions and pathogenesis. These aims will be accomplished by analyzing the transfer of reporter fusions into target cells, conducting directed genome-wide screens for effectors, and examining the effects of T6SS- and effector-null mutants on bacterial toxicity and the host innate immune response during interactions with host cells in culture and in a murine model of pneumonia.

These studies will break new ground on the mechanisms used by A. baumannii to promote infection and will address key gaps in our understanding of T6SS pathobiology. Ultimately, this information will uncover targets for novel anti-infective treatments and vaccines against highly drug-resistant bacteria. The training experience will broaden my expertise in molecular biology, teach me new techniques in mammalian cell culture and animal models, and advance my understanding of the pathogenesis of infectious diseases.

PI: Islam, Shafiqul
Title: IGERT: Water Across Boundaries – Integration of Science, Engineering and Diplomacy
Abstract:
This Integrative Graduate Education and Research Training (IGERT) award supports the development of an interdisciplinary graduate training program at Tufts University, focused on water diplomacy. The goal is to prepare students who can think across natural and societal boundaries and generate actionable knowledge to help resolve water problems with competing needs.

The origin of many water problems is a dynamic consequence of competition, interconnections, and feedback among variables in the natural and societal domains. While scientific formulation and engineering solutions are necessary to address these needs, societal and political contexts must be an integral part of long-term solutions. Formulation and framing of water problems are intricately linked; consequently, variables in natural and societal domains cannot be treated independently. A main feature of this IGERT is the synthesis of these viewpoints — through integration of knowledge from science, engineering, policy and diplomacy—critical to effective water management solutions. This IGERT will prepare a new cadre of water professionals with strong disciplinary grounding and experience as problem solvers with interdisciplinary expertise and negotiation skills. Strong institutional support and proposed innovations—e.g., integrating scientific assessment and policy relevance to create actionable knowledge, exploratory research experience in real world settings, opportunities for national and international field work, and engaging students in synergistic interdisciplinary activities—will transform this IGERT project into a process that will continue to produce a new generation of water professionals with the skills and aptitude to cross boundaries and create an impact far beyond this grant.

PI: Islam, Shafiqul
Title: RCN-SEES A Global Water Diplomacy Network: Synthesis of Science, Policy, and Politics for a Sustainable Water Future
Abstract:
Conflicts over water continue to increase around the globe at local, national, regional and international scales arising from complex interactions of natural, societal, and political forces. While efforts to theorize about water systems have been many, the tools and techniques available to pursue and implement these theories in practice have often led to science that is 'smart but not wise'. It is important to integrate scientific learning with the complex contextual reality of real world water problems to find solutions where societal and political aspects are incorporated. Such solutions to water problems bridge the divide between theory and practice. This Research Coordination Network will create a “Water Diplomacy” approach to address complex water problems where natural, societal, and political elements cross multiple boundaries and interact in unbounded, uncertain and nonlinear ways. This approach, rooted in emerging ideas of complexity theory and negotiation, seeks to synthesize scientific objectivity with contextual reality and create actionable water knowledge. The Water Diplomacy approach posits that water resources could be more effectively managed by understanding the interaction among individual components within the natural, societal and political systems using recent developments in network theory.

This RCN will examine the adequacy of the Water Diplomacy Framework with three propositions that challenge the conventional wisdom about water management: (a) water is not a fixed resource; (b) water networks are open and continuously changing; and (c) uncertainty, variability, nonlinearity, and feedback are not exogenous. Building on these three propositions, this RCN will explore and demonstrate the utility and effectiveness of cooperative rather than competitive approaches to decision-making to address and resolve water conflicts. The community building activities will focus on two interrelated goals: (i) engage scholars and professionals from different domains of expertise to examine three propositions in a range of field-based settings; and (ii) develop technology-enhanced opportunities in data management and social networking to produce, refine, and share results and best practices with the global community.

 

 

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