PI: Abramson, Daniel
Title: Architecture in the Age of Obsolescence
Abstract: I propose during a twelve-month fellowship period to draft the manuscript of a book provisionally titled “Architecture in the Age of Obsolescence.” This project explores how the idea of obsolescence first came to be applied to the built environment in the early twentieth century, and then how the paradigm of obsolescence became a dominant theme through the early 1970s, productive alike of modernist experimentation and populist counter reaction. Like the theme of obsolescence, the book is international in scope, but one of its particular focuses is mid-century Britain. “Architecture in the Age of Obsolescence” looks closely and extensively at the obsolescence preoccupations of Reyner Banham, Cedric Price, Archigram, Richard Liewelyn-Davies, John Weeks, and Peter Cowan, as well as the linked roles played by the welfare state and academe.

PI: Abriola, Linda
Title: Identification and Protocol Development for Characterization of DNAPL Source Zone Architecture and Associated Plume Response
Abstract: Widespread use of chlorinated ethenes, such as trichloroethene (TCE) and tetfachioroethene (PCE), in dry cleaning and degreasing operations has led to groundwater contamination at thousands of industrial facilities and governmental installations. The majority of contaminant plumes at such sites emanate from aquifer regions containing dense nonaqueous phase liquid (DNAPL). Although significant effort has been directed toward improving methods for recovering DNAPL from the subsurface, it is now generally accepted that no single technology will result in complete mass removal. Recently, focus has shifted from complete mass removal to quantifying the benefits and limitations of partial mass removal. Research has revealed that there is a strong link between source zone architecture (local-scale DNAPL distribution) and down gradient plume response to partial mass removal. Our work on SERDP Project ER-1293, suggests that features of a DNAPL distribution, such as ganglia-to-pool (GTP) ratio, may be (i) of far greater importance for source zone remedy selection and analysis of technical feasibility and (ii) far easier to estimate in practice than the precise spatial distribution of the DNAPL saturations. While the GTP ratio has been demonstrated useful in the assessment and prediction of system behavior in simulated and laboratory experiments, no general guidance exists for its quantification in practice, nor is it clear that the GTP ratio is the most appropriate parameter to characterize long term plume response to mass removal in the field. Thus, there is a clear need for systematic development and assessment of alternative metrics to quantify DNAPL architecture based upon field-observable parameters.

The primary objective of this research is to develop and demonstrate a comprehensive approach for field characterization of DNAPL source zones which quantifies the key features that control plume response. This goal will be accomplished by:

• identification of the most information rich metrics for linking NAPL architecture to plume response,
• development and refinement of in situ test methods and modeling tools that can be used to quantify identified metrics in targeted regions of the source zone,
• integration of these metrics and tools with current characterization methods for an overall source zone assessment protocol, and
• development of simplified models for prediction of plume response.

The research approach will integrate batch, column and aquifer cell experiments with mathematical modeling and processing tools to identify and quantify features of the DNAPL architecture controlling the down gradient plume response. The utility of the developed protocol and modeling tools will be demonstrated at a field site(s) to be selected in conjunction with personnel at the Air Force Center for Environmental Excellence (AFCEE) (Ms. Erica Becvar), using existing databases (e.g., the Environmental Resources Program Information Management System (ERPIMS)).

The proposed research is intended to provide site managers and regulatory agency officials with an improved understanding of how plume response is coupled to DNAPL architecture. The suite of protocols and models developed in this research will provide site managers with specific tools that can be employed for source zone characterization and remedy screening. Anticipated deliverables include:

• identification of key metrics for characterization of DNAPL source zone architecture,
• targeted methods for quantifying source architectural metrics,
• an integrated protocol for source zone characterization, and
• simplified modeling tools to assist site managers in source characterization and prediction of remedy performance.

The primary audience for the project deliverables and related research findings are site managers and regulatory officials responsible for overseeing and/or approving the remedial options for DNAPL source zones. The proposed project will culminate with a field demonstration of the integrated protocol where the technologies will be transitioned to personnel at the Air Force Center for Environmental Excellence (AFCEE). Technical information will also be disseminated through peer reviewed publications, conference presentations, and recognized internet remediation organizations.

PI: Afsar, Mohammed
Title: The Scattering and Absorption Characteristics of Two Samples of Dyed Corn Meal at W-Band Frequencies
Abstract: The Tufts University proposes to perform the electromagnetic measurement of two dyed corn meal samples. The transmission and reflection measurement will be carried out utilizing unique Backward wave based quasi-optical spectrometer system at W-band frequencies as well as the dispersive Fourier transform spectroscopy. Both instrumentations and associated measurement techniques were developed by the PT. This is the only facility in the world that can provide such measurements with unprecedented accuracy. The data will be collected as scattering parameter, refractive index, and absorption coefficient from 75 GHz to 110 GHz at room temperature. A report will be prepared and submitted as a final product.

PI: Ambady, Nalini
Title: Nonlinguistic Dialects: Behavioral and Neural Correlates
Abstract: The overarching goal of this application is to test a theory regarding nonlinguistic dialects. Six sets of studies are proposed to test the hypotheses that nonlinguistic emotional dialects are (a) acquired through cultural exposure and (b) provide cues as to cultural identity. Further, (c) emotional dialects of majority group members are understood more accurately by minority group members than vice-versa; (d) emotional dialects are associated with distinct neural patterns of activation; (e) emotional dialect acquisition shows a similar early developmental trajectory to linguistic dialect acquisition, and, (f) bicultural individuals fluent in different emotional dialects will code-switch between dialects in response to subtle primes.

The 12 proposed studies are designed to examine emotional communication by members of diverse cultural and ethnic groups from Japan, India, and the United States. Within these groups, both majority as well as minority group members will be examined. Both the results and the stimuli collected for these studies involving emotions expressed in 3 different channels (the face, body, and voice) from diverse cultural and ethnic groups will be shared and disseminated to other scientists to enhance research and knowledge in this area.

The proposed research should have important implications for mental health and inter-group relations. Being less able to understand the emotions being communicated by members of other ethnic or cultural groups probably contributes heavily to a lack of empathy and understanding of less familiar others as well as to inter-group prejudice and discrimination. This work has implications for diverse interactions such as in the client-provider relationships, in which members of diverse ethnic and cultural groups have to interact and sustain relationships.

PI: Anwer, Sawkat
Title: Mechanism of Canalicular 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. Cyclic AMP stimulates bile formation by translocating solute transporters to the plasma membrane and reverses acute cholestasis associated transporter dislocation. The focus of the present proposal will be to further characterize the signaling pathways involved in cAMP-mediated transporter translocation and reversal of transporter dislocation in acute cholestasis. The following hypotheses are proposed:

• cAMP stimulates Ntcp translocation by dephosphorylating Ntcp at S226 via activation of PP2B and/or inhibition of ERK1/2.

• PKC-zeta mediates cAMP-induced Ntcp translocation by facilitating PKB activation in hepatocytes.

• cAMP stimulates translocation of Ntcp, Bsep and Mrp2 by activating PKC-delta and/or p38 MAPK.

• cAMP reverses TLC-induced retrieval of Bsep and Mrp2 by reversing the effect of TLC on PKC-alpha and/or PKCE.

• cAMP stimulates net translocation of Ntcp by stimulating Rab4-mediated exocytotic insertion and/or by inhibiting Rab5-mediated endocytic internalization.

Proposed studies will be conducted in perfused rat livers, rat hepatocytes and HUH-7 cell lines. Hepatocytes and HUH-7 cells transfected with wild-type and mutant Ntcp will be used to determine the role of phosphorylation in Ntcp translocation. Role of various kinases will be evaluated by manipulating their activity using chemical inhibitors, wild-type and dominant negative plasmids and siRNA. Immunofluorescence and co-immunoprecipiation studies will be used to determine colocalization of Rab proteins with Ntcp. Collectively, proposed studies should provide further insights into signaling pathways by which cAMP stimulates bile formation and reverses acute cholestasis. In addition, these studies should help define the role of Rab proteins in cAMP-induced vesicle trafficking.

PI: Anwer, Sawkat
Title: Short-Term Training in Health Professional School
Abstract: The overall long term objective of this proposal is to stimulate research interests in talented veterinary students and to expose them to opportunities inherent in a research career. The program will provide research training opportunities for veterinary students in the following biomedical research areas: digestive diseases, infectious diseases, biotechnology/reproductive biology, neuroscience/behavior, and international/wild life medicine. This program is specifically designed to introduce students to active biomedical research environments and to train them in following specific areas: critical evaluation of published data, development of hypothesis, preparation of research proposals, experimental designs, research ethics, analysis and organization of data, and oral and written presentations of results. The proposed program will accept 15 students per year, and the students will be selected on a competitive basis. All first and second year veterinary students will be eligible to submit a research proposal using a standard format with input from a program faculty of his/her choice. The submitted proposals will be evaluated and ranked in order of merit by a faculty committee using predefined criteria. Apart from the scientific merit of the proposal, preference will be given to minority students, to be actively recruited, and students who exhibit willingness to continue to conduct research beyond this training period. Training during the months of June, July and August will take place in established laboratories with ongoing projects and funding. Each trainee will attend a seminar series conducted by the program faculty, submit a written report and make a oral presentation at the annual veterinary student research day. The success and impact of the program will be evaluated by using a survey method to determine the number of trainees actively involved in biomedical research following their initial training period.

PI: Azuma, Chieko
Title: Identifying Mutations in Genes Associated with Canine Hemangiosarcoma: Denser Fine Mapping of the Associated Locus in Chromosome 5
Abstract: Hemangiosarcoma (HSA), a malignant tumor of blood vessels, is a significant health concern in dogs, with a reported incidence of up to 2% of all tumors. NSA can affect all dogs, but a particularly high disease incidence has been reported in certain breeds, such as golden retriever (15%), German shepherd (10%), and Labrador retriever. The higher incidence in these particular breeds suggests that genetic risk factors exist. We have identified seven regions in the canine genome associated with HSA in golden retrievers using a newly developed powerful analytical method in order to search for small differences in the patterns of DNA. Subsequently, DNA patterns have been compared with five other breeds and all risk factors appear to be shared with at least one other breed. We now aim to perform denser fine mapping to validate and further narrow down the associated locus on chromosome 5 which is the most likely to contain a gene associated with hemangiosarcoma. Once the mutations have been identified and their presence in different breeds assessed, it will be possible to rapidly develop genetic tests for carriers of HSA. Ultimately, understanding of the disease biology will lead to prevention and better treatment of NSA.

PI: Balbach, Edith
Title: Organized Labor and Tobacco Industry
Abstract: While the shared interests that unions and public health have in worker health has led to cooperation on many health issues, it has often not led to such cooperation on tobacco control. While some unions have been supportive of tobacco control efforts, many have not, and a number have adopted pro-tobacco industry positions, especially protesting tax increases and assisting in the defeat of smoke free air legislation.  We will build on our previous study of the relationship between organized labor and public health and continue to explore ways to improve that relationship, which has the potential to improve the health of blue collar and service sector workers, a group with higher than average smoking rates. Our overall research goal is to continue to build an understanding of the relationships among the tobacco industry, organized labor, and public health, focusing on state level activity in nine states. To achieve this goal, we will pursue three specific research aims:

Specific Aim #1: Continue our comprehensive search of the tobacco industry databases for materials related to the political interactions among public health, organized labor and the tobacco industry, focusing in this renewal on the state level issues related to smoke free worksites and excise tax increases.

Specific Aim #2: Develop nine case studies based on research conducted under Specific Aim #1, using additional information found through the labor press, local newspapers, and other written sources, and through interviews with key labor leaders and public health activists.

Specific Aim #3: Using comparative case analysis, synthesize the nine case studies conducted under Specific Aim #2 with three state level case studies completed under parent grant (2002-2005) to build a comprehensive study of public health's efforts to work with organized labor on excise taxes and smoke free worksites.

To lower the high number of deaths caused by smoking, public health must lower smoking rates. Two of the leading interventions to achieve this reduction are worksite restrictions and excise tax increases. To implement these interventions in states with strong unions, public health must work with organized labor. This project will study the factors that facilitate and impede that relationship with a goal of improving it.

PI: Barber, Lisa
Title: COTC008: Evaluation of the mTOR Inhibitor Rapamycin in Dogs with Osteosarcoma
Abstract:

1. To compare the tolerance and safety of three rapamycin treatment schedules in dogs with osteosarcoma pulmonary metastasis.
2. To compare the effects on immune function and on AKT-mTOR axis modulation in peripheral blood mononuclear cells (PBMC) of three rapamycin treatment schedules in dogs with osteosarcoma pulmonary metastasis.
3. To determine if rapamycin administration results in objective responses in dogs with radiographically evident osteosarcoma pulmonary metastases.

PI: Bers, Marina
Title: Tangible Programming in Early Childhood: Revisiting Developmental Assumptions through New Technologies
Abstract: The focus of this project is on computer programming and robotics in early elementary school, with an emphasis on kindergarten. The goal is to understand what is developmentally appropriate for young children in light of novel human-computer interaction techniques that provide more age-appropriate access to technology. At the heart of this proposal is the claim that, for a variety of reasons, modern graphical user interfaces (GUI) are ill-suited for use in early elementary school, especially for computer programming activities. This project proposes to build on emerging tangible user interface (TUI) technology to create a tangible programming language for young children. That is, rather than using a mouse or a keyboard to write programs to control robots, children will instead construct programs by connecting smart wooden blocks shaped like jigsaw puzzle pieces. In a similar spirit, the project proposes to re-envision robotics as an activity having less to do with constructing robots out of expensive and intricate parts (such as LEGOs) and more to do with constructing artistic creations out of arts and crafts goods and recycled materials. Over the course of three years, the project will build on existing research to develop novel technology and a complementary kindergarten robotics-based curriculum. In addition, it will develop a research protocol and experimental tasks in order to study children’s learning in this domain. The project will then evaluate the effectiveness of both the technology and the curriculum in four kindergarten classrooms.

PI: Bers, Marina
Title: Zora: A Virtual Community for Pediatric Transplant Patients
Abstract: The proposed research project explores the potential of virtual environments to improve adherence to the onerous medical regimens followed by pediatric (ages 11-15) transplant patients, and to support the formation of a peer network with positive effects towards psychosocial development and transitioning back to school.

Advances in medicine are allowing pediatric patients with chronic illnesses to survive. However, medical treatments demand a life-time commitment to invasive interventions and a medical regime which is accompanied by side effects. Research has shown that pre-teens and teens have difficulties making lifestyle adjustments that might disrupt their academic and social life and complying with medicine intake and dietary restrictions. Long-term studies that follow patients who have received a transplant in their childhood into adulthood are still few, but all emphasize the importance of psycho-social supports.

The proposed project explores the potential of new technologies to address this challenge. It utilizes the Zora virtual world to help children with a severe condition that are geographically isolated to adhere to their medical regimen, transition into school routines, and create a virtual peer support group. Zora is an Internet-based environment that provides easy-to-use tools for young people to create a three dimensional virtual city where they can communicate and create interactive objects, as well as share their stories.The project will follow directly from my NSF-funded study with pediatric post-transplant patients at Boston Children’s Hospital. Preliminary analysis has shown positive results. One of the significant issues that emerged as crucial both for social adjustment and for medical adherence was transitioning back to school. The proposed project will focus on this and will also extend the current Zora community to bone marrow transplant patients from Tufts’ Floating Hospital for Children, thus enabling a larger virtual community that will provide a meaningful experience for the patients and a larger data set for analysis. Four sets of data will be collected:

1. data pertaining to Zora use and participant feedback;
2. data pertaining to the positive development of youth through the use of Zora;
3. data about patients’ medical adherence; and
4. data related to school transitioning.

The project will investigate the way psychosocial support programs are currently conceptualized, not only for transplant pediatric patients, but for other children and families with critical medical conditions that share a need for better ways to adjust back to their social and academic life, for finding a peer-social network for support and for engaging in behaviors that will improve their medical adherence.

PI: Blanco-Pillado, Jose Juan
Title: String Theory Cosmology
Abstract: This proposal will explore how one can find a natural way to embed a period of cosmological inflation within recently proposed string theory compactification mechanisms. The first part of the research will consider a version of modular inflation called racetrack inflation developed by the PI and his collaborators. Modular inflation uses the potentials generated for the moduli fields that occur in string theory compactifications as the source of the negative pressure required for the inflationary period. In this picture the mechanism for reheating will be studied and the generation of fluctuations in the Cosmic Microwave background due to iso-curvature perturbations.

The PI will also investigate other typed of inflation that can occur in string theory compactifications. The second aspect of the proposal will be a detailed study of D-Brane inflation. In this picture the scalar field responsible for inflation parameterizes the position of a brane along the internal manifold. One possible consequence of this picture is that during inflation there is brane-antibrane annihilation which could lead to the production of cosmic strings which have observable cosmological effects.

The broader implications of this proposal are that if string theory can be directly verified (or falsified) by measurement of cosmological parameters this would be very important. The PI intends to create a web page for the general public explaining the main results of his work. He also intends to get involved with Physics Theory-Net and give lectures at local high schools.

PI: Booth, Sarah
Title: Dietary and Non-Dietary Components of Vitamin K Metabolism
Abstract: Vitamin K has a role in bone health, but little is known about vitamin K metabolism in aging and in maintenance of bone mass. The limited understanding of vitamin K metabolism impedes the establishment of dietary recommendations for vitamin K, and the interpretation of results from clinical trials on vitamin K supplementation and bone health of women in a narrow age group. The proposed study is the first to assess the role of dietary and other factors that influence the response to vitamin K status and bone turnover to vitamin K depletion and repletion in adults. This study also compares the absorption efficiency and body retention of vitamin K relative to current vitamin K status. Men and women [21 younger (21-40y) and 21 older (60-80y)] will participate in a 65-d metabolic study, with a 5-d run-in period, followed by a 30 d dietary vitamin K restriction period (10 µg/d), and ending with a 30 d dietary vitamin K supplementation period (500 µg/d). Coagulation times will be monitored during the dietary restriction period. Serial measurements of vitamin K status, markers (plasma phylloquinone, urinary Gla, serum %ucOC and plasma PIVKA-II and urinary vitamin K metabolites) and of bone turnover (serum osteocalcin and NTx) will show the response of vitamin K to dietary manipulation for both age groups under identical controlled dietary conditions. Deuterium-labeled vitamin K in collards will be used to compare the absorption of vitamin K during a vitamin K-deplete state (21 d of dietary vitamin K depletion) to that of a vitamin K-replete state (21 d of dietary vitamin K repletion). Vitamin K is transported in triglyceride-rich lipoproteins, which may vary among individuals due to differences in adiposity and lipid homeostasis. Therefore, measurement of body composition by DXA and plasma lipids (total and individual lipoproteins) will provide insight into the role of lipids in absorption and transport of vitamin K. The findings of the proposed study are critical for the interpretation of the epidemiologic and clinical data used to determine the protective role vitamin K may have in chronic disease prevention.

PI: Bowdler, Michelle
Title: Tufts Community Cares: A Suicide Prevention Program
Abstract: A Suicide Prevention Program will work with Tufts University faculty, staff, targeted student groups including peer leaders, students from Tufts’ six Culture Centers (Africana, Asian American, International, Latino, LGBT, and Women’s) and the general student population, and families to support a comprehensive suicide prevention program. Its goals are to increase awareness of signs and symptoms of depression, student distress, suicide risk and available resources; decrease barriers to help-seeking, including stigma, lack of awareness, misinformation or other factors that inhibit students’ utilization of mental health or other supports; and enhance linkages within the community between mental health/substance abuse services, and gatekeepers, students, families, and other sources of support.

The activities of the program include conducting bi-annual enhanced faculty, staff and student gatekeeper trainings, conducting seven focus groups with target student populations noted above to gather information for program development and implementation, creation of bi-annual family wellness newsletters and year long universal programming to reduce stigma. Both formative and summative evaluations will be used to enable the capture of data regarding: 1) satisfaction with gatekeeper training, culturally appropriate educational sessions, the family newsletter and universal programming on-campus; 2) learning about suicide prevention methods and available resources for assistance; and 3) performance of suicide prevention counseling and referral methods. As data will be collected from a multitude of sources, the linking of data across participants and elements will be possible.

PI: Bridges, Robert
Title: Endocrine Regulation of Maternal Behavior
Abstract: The long-term goal of this project is to identify the neural and neurochemical mechanisms underlying the regulation of maternal behavior and to elucidate potentially novel mechanisms of neural plasticity associated with the expression of maternal behavior in the adult mammal. The specific hypothesis that will be tested is that the induction, maintenance, and retention of maternal care are under endocrine regulation by a neural lactogenic system, a system that displays significant plasticity as a function of reproductive experience. The first series of studies will examine the role of the neural prolactin (PRL) receptor in the initiation of maternal behavior. Using a rat model, we will determine whether placental lactogens, like PRL, act via the PRL receptor to stimulate the onset of behavior. A second study will use the novel PRL receptor antagonist, S179D-PRL, which will be administered centrally to test the hypothesis that activation of the PRL receptor by lactogenic hormones around the time of birth is essential for the normal onset of maternal care. The third study using ISHH will measure how pregnancy concentrations of progesterone (P) and estradiol affect expression of mRNA for neural PRL receptors. Then, central sites of P action will be examined to see how P affects the onset of maternal care and to delineate a mechanism of P’s action in the initiation of maternal behavior. A second series of experiments will determine the involvement of the endocrine system in ongoing maternal care. First, the effects of exposure to PRL-secreting ectopic pituitary grafts on pup-directed maternal care and maternal aggression will be measured. Then, the effects of central administration of the PRL receptor antagonist, S179D-PRL, will be examined in lactating rats. The third set of experiments will delineate the role of the endocrine system in the retention of maternal behavior. The involvement of PRL in the opioid-mediated establishment of the retention of maternal behavior will be assessed. Finally, the effects of prior maternal experience on activation of the neural lactogenic system will be measured to see whether prior maternal experience up-regulates the brain PRL system and makes the female more sensitive to her own neural hormones. The results of these investigations will delineate common endocrine and neurochemical regulators of maternal care in mammals, present a new model for examining neuroplasticity in the adult female, and provide a basis for evaluating the effects of endocrine and neurochemical imbalances on mother-young interactions.

PI: Brizuela, Barbara
Title: Young Children's Numerical Representations Across Different Systems
Abstract: The proposed project will explore, in children, the connections among three representations of the number system: nonverbal, written, and oral. I will follow two groups of children (one in the Boston area of the United States [US], and one in Argentina) during their first grade of schooling (approximate age 6). The basic question underlying this research is:

• What are the connections in the ways in which children represent (through production and interpretation) a number in writing, orally, and noverbally?
• Are there differences in how children represent numbers in these three dimensions in different languages (English and Spanish)?

Past research shows that different kinds of representation involves distinct intellectual challenges (e.g., Dehaene, 1997; Gelman & Butterworth, 2005; Gelman & Cordes, 2001; Gelman & Gallistel, 1978, 2004; Power & Dal Martello, 1990; Saxe, 1979; Scheuer et al, 2000; Seron & Fayol, 1994). Past research has usually focused on children’s performance on each of these modes of representation in isolation. For instance, previous studies (e.g., Fuson & Kwon, 1992; Miura & Okamoto, 1989; Power & Dal Martello, 1990; Ross, 1986; Scheuer, 1996; Seron & Fayol, 1994; Sinclair & Scheuer, 1993) have focused on place value, notation, number decomposition, and oral numeration, without exploring the relationships of these aspects with one another.

More recent research has shown the need for exploration of the potential connections among these different representations (e.g., Alvarado, 2002; Brizuela, 2004; Scheuer et al, 2000; Seron & Fayol, 1994). For example, Scheuer et al (2000) discuss distinct types of incorrect numerical notation strategies used by children and speculate that perhaps these different strategies stem from different ideas in children about the concept of number, yet their study only focuses on written numbers. The study here proposed is novel in that I seek to explore the connections among these different—yet related—modes of representation.

Other studies also set the ground for the need to look at children’s representation of number across different systems. Namely, studies carried out by Power and Dal Martello (1990) and by Seron and Fayol (1994), who studied Italian children and French and Walloon children, respectively. The first study left unanswered what role the spoken numbers had played in children’s performance. The second study was designed as a follow-up experiment aimed at answering this specific question. Not surprisingly, certain incorrect syntactical responses were seen only among French children, which are very similar to errors produced by French adult aphasics (DeLoache & Seron, 1982). The Walloon children had difficulties in transcoding from oral to written numbers due to the production of the written numbers themselves. Thus, connections across representational systems are important and fully reflecting and understanding the nature of these connections is a worthwhile endeavor.

PI: Brodley, Carla
Title: III-CXT-Medium: Interdisciplinary Machine Learning Research and Education
Abstract: This project is encouraging interdisciplinary machine learning research and education that integrates the use of machine learning into the application areas, solves real science problems, and serves as a catalyst for new research in both machine learning and the application domains. We are investigating four basic machine learning issues that arise when working with real-world applications:

1. Optimizing over choices available when generating training data
2. Assessing and improving the quality of training data
3. Designing specific algorithms and methods for time series and feature-based data
4. Developing methods for abstaining during classification

Our research is motivated by on-going collaborations with researchers to create solutions for: training an artificial nose (Chemistry, Tufts); land-cover mapping from remotely sensed data (Geography, Boston University); classification of sky surveys (Astronomy, Harvard); non-invasive glucose monitoring (Biomedical Engineering, Tufts); and liquification prediction (Civil Engineering, Tufts). The successful application of machine learning to each of the five tasks will have significant impact on the lives of humans. Our education initiatives have two complementary goals:

1. To educate computer science students on how to conduct interdisciplinary machine learning research.
2. To educate professors, graduate students and undergraduates from science, engineering and medicine on how to recognize and pose problems as machine learning and data mining problems.

PI: Brugge, Douglas
Title: Community Assessment of Freeway Pollution and Health (CAFEH)
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; and (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, CC, 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, and
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.

PI: Bullock, Peter
Title: A Chemical Genetic Approach to Inhibiting T-ag Assembly on the Viral Origin
Abstract: One of the critical events during the replication of many DNA viruses is the binding of “initiator proteins” to origins of replication. Once bound to the origins of replication, the virally encoded initiator proteins frequently assemble into higher oligomeric complexes. Our long-term goal is to develop a systematic approach for the isolation of inhibitors that will selectively block the assembly of viral initiators on origins of replication. These inhibitors will serve as useful reagents for exploring biological activity and as lead compounds for drug design.

The systematic approach that we will utilize is an extension of recently described chemical genetics methods. A critical component of this technique is the use of split intein based vectors to generate diverse cyclic-peptide libraries in E. coli cells. This is a very cost effective method for generating complex, but very stable, libraries. Using straightforward genetic screens, the libraries will be searched for members that are able to disrupt the assembly of a prototype viral initiator termed Simian Virus 40 T-antigen. The advantages of selecting cyclic peptide inhibitors that block T-antigen oligomerization include the fact that much of T-ag’s structure has been determined and T-ag’s interaction with the Simian Virus 40 origin is understood in great detail. Furthermore, inhibitors of T-ag oligomerization are clinically relevant. For example, 5V40 T-ag may be a human health issue; although interpretations remain uncertain, data have linked it to a variety of human cancers including mesothelioma and non-Hodgkins lymphomas (reviewed in Vilchez and Butel (2004) Clinical Microbiology Reviews 17: 495-508). Furthermore, 5V40 virus is closely related to two human viruses, BK and JC virus. These viruses induce a number of diseases in humans, including cancer. In addition, JC virus induces progressive multifocal leukoencephalopathy (PML); a disease that occurs in patients whose cellular immunity has been impaired. Indeed, approximately 5% of patients with AIDS have PML. Therefore, the approach that we propose to use to isolate inhibitors of T-ag assembly may identify lead compounds against BK and JC viruses. More importantly, these experiments will serve to demonstrate that the chemical genetic approach that we describe is a general method for the isolation of inhibitors against viral initiators. Once the feasibility of the approach is demonstrated, similar experiments will be conducted with the viral initiators encoded by other DNA viruses, such as those encoded by Herpes simplex virus and different strains of human papillomavirus. Thus, the approach described herein might facilitate the isolation of compounds with broad clinical relevance.

PI: Bunnell, Stephen
Title: Unraveling Integrin-Mediated Inflammatory Signaling Pathways Using Dynamic Imaging Techniques
Abstract: Mounting evidence suggests that inflammatory T cell responses play a major role in atherosclerosis, and therefore increase the risks of cardiovascular diseases such as heart attack and stroke. Integrin ligands are upregulated in atherosclerotic lesions and influence the progression of atherosclerosis. Although integrins govern the recruitment of immune cells to sites of inflammation, integrins also transmit costimulatory signals that sensitize T cells to antigen and promote the production of inflammatory T helper 1 (Th1) cytokines. In this manner, integrins may contribute to the development of atherosclerosis by sensitizing T cells to antigens that pose little intrinsic threat. Our SPECIFIC HYPOTHESIS is that integrins enhance the production of inflammatory T helper 1 (Th1) cytokines by directly stabilizing antigen-induced signaling complexes.

To test how integrins influence the development of inflammatory responses, we developed novel methods of visualizing T cell receptor (TCR)-induced signaling complexes in real time. Here, we will determine how the Th1-promoting integrin VLA-4 impacts the formation of these TCR-induced microclusters, and test whether VLA-4 drives Th1-biased signals by altering microcluster formation, persistence, or movement.

AIM 1: How are the TCR and VLA-4 induced signaling pathways coupled?
We propose that the signaling proteins associated with the TCR and VLA-4 form molecular bridges that integrate the signals from these receptors. We will determine which proteins co-localize with the TCR and VLA4 in model systems and in physiological immune synapses. Nanometer-scale interactions among these proteins will be assessed using FRET.

AIM 2: Which signaling molecules are essential for VLA-4 mediated costimulation?
We propose that VLA-4-associated signaling molecules promote inflammatory signaling by stabilizing TCR signaling complexes. We will identify these proteins by pairing cytokine production assays with dominant-negative and RNAi-mediated knock-down strategies.

AIM 3: How do essential signaling molecules potentiate inflammatory signaling?
Specific molecular interactions involved in VLA-4 mediated complex stabilization and inflammatory signaling will be identified. Functional and imaging assays will be performed to evaluate mutant variants of the proteins implicated in these processes.

PI: Bunnell, Stephen
Title: Visualizing the Mechanisms of Integrin-Mediated Lymphocyte Costimulation
Abstract: Autoimmune diseases and immunodeficiencies result when the immune system incorrectly perceives the threat posed by self-antigens or by pathogens. Costimulatory molecules play an essential, but poorly understood, role in this process. Integrins are costimulatory molecules that respond to ligands upregulated by the inflammatory processes associated with infection and autoimmune disease. The loss of proper integrin function leads to profound immunodeficiencies, and aberrant integrin activation is associated with common autoimmune diseases. To understand how immune responses are controlled, we developed a novel method to visualize the signaling complexes induced by the T cell receptor (TCR) in real time. How integrins modulate the signals transmitted by the TCR remains unresolved. Here, we have adapted these assays to reveal how integrins impinge on the signaling complexes induced by the TCR. Our specific hypothesis is that integrins influence the course of immune responses and autoimmune disorders by directly interacting with and enhancing the signaling complexes induced by the TCR. In this proposal we will employ the integrin VLA-4 as a model costimulatory protein. VLA-4 is a critical lymphocyte integrin with well-characterized functions in cell adhesion and signaling. VLA-4 has also been implicated in the etiology of autoimmune disorders, such as multiple sclerosis. The mechanisms by which VLA-4 costimulates T cell activation are not well understood. These studies will provide insights into general mechanisms of integrin signaling and costimulation that are relevant to normal immune function and autoimmune diseases.

Our imaging system, capable of revealing molecular interactions at the TCR in real time, in living cells, provides an ideal basis for these studies. Using this system, we have, for the first time, presented direct evidence of a qualitative effect of integrin engagement on the signaling molecules associated with the TCR; namely, we have shown that VLA-4 immobilizes and increases the persistence of these signaling complexes, an effect that is perfectly correlated with effective costimulation. This breakthrough was possible because of our unique ability to track the persistence and movement of individual signaling complexes overtime, using our dynamic imaging techniques. Here, we will extend our imaging techniques to explore protein localization and proximity in the immune synapses of living T cells. To do so, we will dynamically visualize multiple proteins in three dimensions, perform FRET experiments in live cells, and automate the reconstruction of immune synapses overtime. Our immediate goal, which is to characterize the signals that link VLA-4 to the TCR, will be pursued in the three aims below:

Aim 1: What molecules link VLA-4 to the TCR, as assessed by FRET microscopy? We propose that TCR and VLA-4-associated signaling proteins form a molecular bridge that integrates the signals from these receptors. We will determine which proteins co-localize with the TCR and VLA-4 in the immune synapse. Direct, nanometer-scale interactions will be confirmed by assessing fluorescence resonance energy transfer (FRET) between these proteins.

Aim 2: Which signaling molecules are essential for VLA-4 mediated costimulation? We propose that TCR and VLA-4-associated signaling molecules play critical roles in the integrin-induced stabilization of the TCR signaling complex. We will identify these proteins by using dominant-negative and RNAi-mediated knock-down strategies.

Aim 3: How do essential signaling molecules exert their costimulatory function? We propose to identify the specific molecular interactions involved in costimulation and complex stabilization by performing mutational analyses of proteins implicated in these processes.

By revealing the mechanisms of costimulation by integrins, these studies will identify targets for the development of small molecule therapeutics for autoimmune diseases.

PI: Burgess, Katrina
Title: Can Mexican Migrants Improve Local Governance in Their Communities of Origin? Designing Public-Private Partnership to Leverage Collective Remittances
Abstract: The proposed project aims to understand and promote the conditions under which civic associations formed by Mexican migrants living in the United States (HTAs) can contribute to more transparent and accountable governance in their communities of origin. The laboratory for exploring this question is the “Three-for-One Program for Migrants” (3x1 Program) created by the Mexican government in 2002 to leverage migrant philanthropy for local development. Besides providing matching funds to support community projects co-financed by HTAs, the 3x1 Program offers various opportunities for HTAs to influence and monitor resource management and project implementation by the local government.

The proposed project has a research component and an outreach component:
The research component aims to develop a systematic analysis of the conditions under which HTAs are willing and able to serve as effective social monitors in their communities of origin. Building on an ongoing study of 100 3x1 projects in 60 communities in 17 municipalities in the Mexican states of Michoacán and Zacatecas, it proposes to conduct household surveys in Mexico and surveys of HTA leaders in the United States to test hypotheses regarding the determinants of the relative effectiveness of social monitoring by HTAs. The findings of these surveys would be used to generate both theoretical and practical conclusions. Theoretically, they would help bridge the largely disconnected literatures on migrant transnationalism and local governance and accountability. Practically, they would generate policy recommendations for enhancing transparency and accountability in the management of co-financed projects and suggest possibilities for creating multiplier effects that would improve civil society and engagement overall in the affected communities. These conclusions would be disseminated through a book manuscript, academic journal articles, policy papers, a project website, and presentations at academic, policy outreach, and governmental institutions.

The outreach component aims to use the project’s research to spark an exchange of ideas among practitioners regarding best practices in transnational public-private partnerships such as the 3x1 Program. This component would involve organizing a 2 1/2 day workshop in Mexico City in which the findings, implications, and lessons of the research would be shared with and discussed by HTA leaders, local community organizers, government officials, NGOs, and scholars from Mexico, the United States, and other high-migration countries in Latin America. The main themes would be: (1) strengthening transnational linkages between HTAs and their hometowns; (2) encouraging and improving government outreach to HTAs; and (3) promoting transparency and accountability in the management of co-financed projects. Besides generating new ideas and networking opportunities for participants in transnational public-private partnerships, the workshop would aim to promote a richer dialogue between HTAs and NGOs working more broadly on governance issues.

PI: Canyes, Barbara
Title: MACC AmeriCorps Student Leaders in Service
Abstract: Campus Compact is a membership organization of over 1000 colleges and universities nationwide dedicated to the civic mission of higher education. Member campuses in Massachusetts have a longstanding commitment to the value of service in education. Our membership is representative of every sector of higher education (community colleges, technical colleges, schools of art and design, Ivy League universities, land grant institutions, faith-based colleges, etc.), and is dedicated to meeting community needs through teaching, service and research. Each institution has a wide variety of programs and departments from offices of financial aid to campus volunteer centers that involve students, faculty and staff to meet the needs of local communities.

On behalf of our 66 member colleges and universities, Massachusetts Campus Compact proposes to continue into a new grant cycle with a strategic national service initiative that will simultaneously advance the public service mission of higher education, leverage resources for the benefit of communities throughout our region, and develop students as civic leaders.

MACC AmeriCorps Student Leaders in Service will capitalize on the skills, energy and passion of one of the greatest resources in Massachusetts, our college students. This program will empower college students to connect campuses and communities from across the Commonwealth through active citizenship and service. As AmeriCorps members, 325 college students will each provide direct service to faith-based and community organizations. Through their service, students will build the capacity of campus-community partnerships for long-term sustainability through volunteer recruitment and coordination, service program management and development, and by improving community knowledge of the Community Federal Work-Study program and other partnership-building resources. To support these efforts, the AmeriCorps members will recruit additional college student volunteers who will provide hours of service to local community based organizations, strategically aligning 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.

Through service activities, student AmeriCorps members will learn to navigate community and campus systems, work with diverse stakeholders and use their unique skills to meet pressing community needs. The program will challenge students to assume leadership roles in the development of campus partnerships with community-based organizations and to develop competencies enabling them to be effective participants in public problem solving.

PI: Castellot, John
Title: Development of a Biochemically Functionalized, Silk-Based Vascular Graft
Abstract: We hypothesize that a stable, long-term reduction in restenosis and restoration of a functional artery wall will require cell-specific vascular grafts that suppress SMC hyperplasia while permitting EC regeneration. To work towards this translational goal, we propose to use tissue engineered vascular grafts (TEVG) which are biomechanically robust, non-thrombogenic and biologically compatible. Silk fibroin derived from Bombyx morii (silkworm) cocoons is an excellent candidate for tissue engineering applications, as it is mechanically robust, chemically modifiable, biocompatible, and immunologically inert. The silk-based grafts have clear advantages over existing technology, in that silk fibroin materials have demonstrated mechanical strength sufficient to withstand arterial pulse pressure and can be biochemically modified 2. In Aim 1, we will develop a silk-based small-diameter vessel capable of sustained release of heparin, which we will measure over time in conjunction with biological activity as indicated by inhibition of smooth muscle cell proliferation. In Aim 2, we will biochemically functionalize a silk vessel to incorporate and release VEGF and CCN5, specific modulators of ECs and SMCs respectively, and determine success using tissue-culture based assays. Finally, Aim 3 utilizes a pulsatile flow bioreactor to test the hypothesis that biochemically functionalized vessels in conjunction with arterial flow conditions are sufficient to differentiate endothelial progenitor cells (EPCs) to ECs. Achievement of this goal will be determined by assessing a “molecular fingerprint” characteristic of developing endothelium. Thus, in this study, we will design a vascular graft using silk fibroin modified with cell-specific molecules to selectively control cell behavior leading to re-endothelialization and prevention of restenosis.

PI: Catley, Andy
Title: Policy and Institutional Support to Livestock Development Relief in Pastoral Areas of Ethiopia
Abstract: It is widely recognised that livestock are the crucial livelihoods asset for pastoralists in Ethiopia, and vulnerability is directly related to access to livestock resources and livestock-derived benefits. In common with other countries in the Horn of Africa region, livestock interventions in Ethiopia can be categorized as ‘relief’ or ‘development’ projects. However, the frequent provision of relief has often disrupted development work and to date, there have been few attempts to view livestock projects from a livelihoods perspective or within a “developmental-relief” framework. In summary, these approaches view relief as a means not only to save human lives but also to protect and enhance livelihoods in the long-term.

The Ministry of Agriculture and Rural Development (MoARD) in Ethiopia increasingly supports pastoralism through policies which aim to link pastoralists to a growing livestock export trade, and provide them with improved veterinary services by supporting privatised and veterinary-supervised community-based systems. The linkages between pastoralism, vulnerability, animal health and trade are becoming more obvious to the MoARD as new markets enable pastoralists to convert livestock into cash.

This proposal uses the USAID Pastoralist Livelihoods Initiative (PLI) Program to begin to address issues of policy coherence in the general area of pastoralism as a viable livelihood, and more specifically in developing policies and best-practice for livestock developmental-relief approaches. The PU Program includes four separate NGO consortia for PLI component 1 (stocking rates and production of livestock optimized) and 1 US university for sheep and goat management; 1 NGO for component 2 (early warning and response systems); 1 NGO for component 3 (market development) and 1 US university for livestock sanitary standards and marketing. This proposal aims to ensure technically proficient and harmonised implementation of these interventions, and systematic impact assessment and research to draw lessons to inform policy and best-practice within an overall drought contingency plan. To create government leadership of the policy process, the project will support a national multi-stakeholder Pastoralist Livestock Policy Forum (PLPF) to be convened by the MoARD. Within the PLPF, four Working Groups will be established to examine each type of livestock intervention in the PLI, identify key policy issues, support impact assessment and research, and make recommendations accordingly. A fifth Working Group will be used to examine an additional policy issue with a view to achieving progress within the two-year project period. This fifth issue has been provisionally identified as rangeland degradation due to bush encroachment. In addition to these activities, the project will use awareness-raising and training events to expose the other government ministries to the benefits of pastoralism and its potential contribution to economic, market-led growth in Ethiopia.

The final outputs of the project will be a national livestock development-relief policy framework and guidelines, a national policy forum which will continue to function after the PU to address a broader range of issues around pastoralism and livestock, and a more propastoralist approach within federal government as a whole. The project builds on the USAID funded work of Tufts University in the Horn of Africa since the early 1990s, and the Feinstein International Famine Center since 1996. The latter includes successful coordination of large-scale livestock programs projects and policy reform. The project also complements existing USAID support to pastoralism and livestock interventions in Ethiopia through the FOCUS, PARIMA, STI and other initiatives.

PI: Cebe, Peggy
Title: Constraints in Semicrystalline Polymers during the Transition from Liquid to the Solid State
Abtract: The confining effect of crystals, during the transformation from liquid to semicrystalline solid of semicrystalline polymers, will be investigated in this research program. The research will answer the following specific questions about structure and relaxation dynamics vis-a-vis confinement.

1. Does the length, xCRR, of cooperatively rearranging regions, CRRs, at the glass transition correlate with the development of the solid fraction, the crystal fraction, or both?
2. Do the alpha relaxation (glass transition) dynamics vary in a manner correlated with the development of these same fractions?
3. What is the structure of the resultant nanophases during solidification? 

The answers to these questions will provide a fundamental level of understanding about the relationship between the crystals and the non-crystalline portions of the semicrystalline polymer, as confinement occurs during the transition from the liquid to the solid state. A major and novel aspect of this research will be the use of quasi-isothermal measurements of the reversing heat capacity to study the time development of formation of the crystal constraints. The time development of the solid fraction and the crystalline fraction, respectively, will be assessed from the earliest stages of crystallization through spherulite impingement, and finally to completion of the crystallization process. The alpha relaxation (glass transition process) will be studied using dielectric relaxation spectroscopy and lamellar structure will be determined using small angle X-ray scattering and atomic force microscopy.

Plastics are ubiquitous materials in everyday life. The majority of commercially useful plastics are processed using heat and pressure to form them into desired shapes. An important class of plastics comprises those that also have the ability to crystallize during processing. The crystals have very complicated shapes and tend to form in clusters. But in a very simplified picture, the crystals act like miniature staples, holding the plastic together on the nanometer length scale, and preventing the constituent molecules from shifting around. To improve the ultimate properties of the plastics, it is important to: understand when and how the staples form; characterize the actual crystal shape, size, and organization; and determine how crystals restrict the motion of the other molecules. This research will lead to new products and processing strategies for plastics, improving our global competitiveness. The program also serves to educate the next generation of scientists, with a special focus and outreach to students who are deaf or hard of hearing.

PI: Chisholm, Karen
Title: MACC AmeriCorps*VISTA Program (2008-2009)
Abstract: Through the MACC VISTA program, VISTA Volunteers will have long-range measurable impacts on faculty, staff, students and community members in at least 35 communities in Massachusetts. By expanding the ability of campuses to establish partnerships throughout the local community, assuring the quality of service delivery, and promoting the “training of trainers” model, each VISTA Volunteer will allow this impact to reach the greatest number of people within campus environments and low-income communities. Each VISTA Volunteer will have one-on-one, ongoing contact with campus community members and will provide extensive training on broad issues and specific topics relevant to each community. The VISTA Volunteers will also plan a year-long student leadership training program that will impact a minimum of 60 students as direct participants and an even larger number of their peers and community members as recipients of training and service.

With the expansion in federal funding for America Reads initiatives, many campuses are faced with the challenge of providing new literacy tutoring placements for Federal Work Study (FWS) students, and ensuring the quality of program delivery. MACC VISTA Volunteers will assist colleges in developing and implementing America Reads programs on at least 15 college campuses. They will recruit and train tutors, organize and implement trainings and support both the student volunteers and the school site contacts in order to assure the development of a quality program to benefit the children of Massachusetts. MACC VISTA Volunteers will also assist campuses in planning and developing quality placements for mathematics tutors under the new America Counts initiative.

Massachusetts Campus Compact (MACC) is a membership organization of college and university presidents leading 45 Massachusetts institutions of higher education in building a state-wide collaboration to promote service as a critical component of higher education. 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. We currently have 19 VISTA Volunteers serving 23 campus communities. Some results at mid-year include the placement and training of at least 444 tutors in 53 elementary schools, outreach to 694 community organizations and the initiation of 97 new community partnerships. The MACC VISTAs also complement our other grant programs and MACC’s statewide coalition by working on three significant network initiatives: an Alternative Break Weekend in Holyoke, MA where 37 people worked on 4 projects over 2 days. The Student Network Conference, our statewide students in service conference with 20 workshops and over 200 attendees; and the MACC Leaders program with 64 student leaders. VISTA Volunteers complement our grant funded programs. Eighteen of MACC’s Learn and Serve subgrantees and After School grant programs benefit from the support of a VISTA.

PI: Choi, Sang Woon
Title: Genomic DNA Methylation and Biohazard Associated Carcinogenesis
Abstract: To determine the relationship among DNA methylation, B-vitamin status, and the risk of biohazard associate cancer, we would like to propose to measure genomic methylation status of DNA samples from studies conducted by the Division of Cancer Epidemiology and Genetics at the NIH. Genomic DNA methylation is an important epigenetic mechanism for cancer development as well as a cancer biomarker that can be easily affected by B-vitamins status.

PI: Choi, Sang Woon
Title: A Nested Case-Control Study of DNA Markers of One-Carbon Metabolism and the Risk of NHL and Multiple Myeloma in PLCO Study
Abstract: To determine whether genomic DNA methylation, a biomarker of one-carbon metabolism, is associated with non-Hodgkin lymphoma (NHL) and multiple myeloma.

PI: Coffin, John
Title: The Significance of Polymorphic Endogenous Retroviruses to Human Mental Health
Abstract: Human endogenous retroviruses (HERVs) result from the integration of retroviral DMA into germ cells. The HERV-K (HML-2) proviruses represent the most recently integrated HERV group. Although most are defective, HML-2 proviruses with intact open reading frames in some or all genes exist. HML-2 have been under purifying selection, suggesting reinfection, and their insertion rate appears constant during hominid evolution. HML-2 expression has been associated with brain disorders, particularly schizophrenia, by the presence of viral particles, genomic RNA, or transcripts. The consequences of HERV expression in human brain tissue are poorly understood. We hypothesize the existence of an replication competent HML-2 provirus whose expression has negative genetic effects on nearby cells. Although infectious viruses could potentially be generated from multiple loci in trans, an intact provirus could alone produce infectious virus, the most likely candidates for which are very recent insertions. We propose to identify novel HML-2 polymorphic insertions in humans using a combination of blotting, PCR, cloning, and sequencing. The incidence of each newly identified HML-2 provirus and disease will be analyzed in a high-throughput PCR screening of human DNA samples. Finally, we will look for HML-2 insertions in DNA extracted from schizophrenia-associated brain tissue against age-matched controls using blotting and PCR techniques. New, clonal HML-2 insertions detected in such an analysis would provide strong evidence of an expressed, replication competent HML-2 provirus. Close proximity of a new integration to a host coding region will be considered as preliminary evidence for a model of transcriptional alteration, and would provide the basis for further studies. An inherited HML-2 provirus with a significant incidence in patients with schizophrenia would be an important discovery. This knowledge would affect not only the diagnosis of the disease, but strategies for prevention and treatment could be adjusted appropriately as an alternative to current methods. Schizophrenia currently affects about one percent of the United States population and costs the public nearly $100 billion each year (National Institutes of Mental Health). Recently integrated proviruses may be genetically linked to this mental disorder through the expression of inherited endogenous loci, the most likely of which belong to the HERV-K (HML-2) group of retroviruses. The goal of this proposal is to clarify the relationship between HML-2 expression and schizophrenia by either establishing a genetic linkage of an inherited provirus with the disorder, or demonstrating the presence of novel proviruses in brain tissue from the patients diagnosed with schizophrenia versus age-matched controls.

PI: Cook, Robert
Title: Mechanisms of Avian Object Perception and Recognition
Abstract: The goal of this research is to understand how animals, and more specifically birds, perceive and learn about the world. In particular, the Principal Investigator is investigating how birds perceive objects and whether the cognitive and brain mechanisms involved are the same as or different from those of humans and other animals. Pigeons are ideal for such comparative cognitive studies because they have evolved small, powerful, central nervous systems capable of exceptional visual perception and complex discrimination learning.  The objectives of the research are to advance three related lines of investigations looking at how pigeons detect and recognize the edges of objects, detect and recognize changes in an object when it moves or rotates, and how complex objects are broken by into smaller parts for the purposes of recognition. These are universally agreed on by vision scientists to be fundamental issues in understanding the mechanisms of visual perception. Visual perception continues to be one the most demanding and difficult biological riddles to solve. For example, it is still beyond our capacities to build a visually-directed robot that can match a chickadee's ability to move through a visually noisy forest canopy. Examining these perceptual mechanisms in small visually sophisticated animals, like birds, is a key step towards solving such questions. This research will immediately impact our understanding of the visual, neural, psychological mechanisms by which complex animals, including humans, perceive the world. This type of comparative research is also part of a larger scientific enterprise by many scientists to understand the evolution and mechanisms of cognition and behavior and their functions in the natural world by investigating the distribution of behavioral similarities and differences among a wide variety of animal species in both laboratory and field settings. Beyond its scientific importance to theories of animal behavior, the proposed research has broader impacts and applications to human health, welfare, and education. This research is part of the general effort to understand how the brain generates and controls behavior. An understanding of the mechanisms of how small biological systems work may lead to the practical engineering of similar smart systems for a variety of purposes (e.g., compact visual prostheses for the blind, autonomous robots for search and rescue, efficient information transmission algorithms). Activities related to the research will be used to educate and train students at the graduate, undergraduate, secondary and primary levels of education. Outreach programs using the internet will also be pursued.

PI: Court, Michael
Title: Acetaminophen Pharmacogenetics
Abstract: Acetaminophen (APAP) is the most commonly used medication in the United States but is also the most frequent cause of drug-induced hepatotoxicity. The long-term objective of this research is to elucidate the pharmacogenetic mechanisms that contribute to variability in individual risk for APAP-induced hepatotoxicity. Our working hypothesis is that genetic polymorphisms that modify the expression and function of enzymes and regulatory proteins involved in APAP toxification and detoxification can be used to identify individuals that have increased risk for APAP hepatotoxicity. The major focus of this work are genes encoding the enzymes that have been identified as critical to these pathways, including the UDP-glucuronosyltransferases (UGTs), sulfotransferases (SULTs), and cytochromes P450 (CYPs). In preliminary work, we established UGT1A1, 1A6, and 1A9 as major APAP glucuronidation enzymes, and identified 3 linked amino acid polymorphisms in the UGT1A6 gene that alter APAP glucuronidation by recombinant enzyme, and also 3 linked SNPs in the 3'-UTR region shared by all UGT1A isoforms that were associated with higher APAP glucuronidation in a human liver bank. Consequently, in Aim 1, we propose to elucidate the molecular mechanisms underlying the effects of the UGT1A6 cSNPs and the UGT1A 3'-UTR SNPs on APAP glucuronidation through studies of protein stability/localization, mRNA stability, and translation efficiency. In Aim 2, we will determine the effect of these UGT polymorphisms and other known functional polymorphisms in the SULT and CYP genes on rates of APAP glucuronidation, sulfation, and oxidation measured in volunteers that receive a therapeutic dose of APAP. We will also determine whether metabolism of APAP is different in African-Americans compared with European-Americans (a novel and untested hypothesis). In Aim 3, we will utilize DNA samples from 2 ongoing studies of APAP-induced hepatotoxicity to determine whether this validated subset of UGT, CYP, and SULT polymorphisms can be used to identify patients predisposed to developing hepatotoxicity resulting from APAP use (overdose or unintentional toxicity).

PI: Court, Michael
Title: Curcumin-Piperine Interaction with Human CYP3A and Phase 2 Enzymes
Abstract: The use of complementary and alternative medicines has increased dramatically over the past decade as the benefits of these natural medications are realized. Although herbal medicines are commonly believed to be a safer alternative to traditional medications, physicians are increasingly concerned about interactions between these medications. One reason for this concern is that unlike traditional medications, safety and drug interaction data is not required by the FDA prior to the sale of herbal supplements to consumers. Often, such interactions are only discovered after a serious and sometimes life-threatening event has occurred. Curcumin, an herbal supplement of recent clinical interest, is in clinical trials for the treatment of several advanced cancers and Alzheimer's disease. However, limited data has been generated examining curcumin's potential for drug-herb interactions due to inhibition of the major drug metabolizing enzymes. Prior to the broader therapeutic application of curcumin, curcumin's potential for these drug-herb interactions should be investigated. Here, we propose to test the effect of curcumin on the in vitro metabolism of midazolam and acetaminophen, index substrates for phase I (cytochrome P450 isoform CYP3A) and phase II (UDP-glucuronosyltransferase and sulfotransferase) drug metabolism, respectively. Curcumin, due to its limited bioavailability, is often administered with a bioavailability enhancing agent, piperine, which may increase the likelihood of curcumin to cause drug-herb interactions. Therefore, we also propose to test the effect of piperine and a combination of curcumin-piperine on midazolam and acetaminophen metabolism in vitro. Furthermore, we will verify our in vitro results with an in vivo clinical study examining the effects of a curcumin-piperine combination on the pharmacokinetics of a single dose of acetaminophen or midazolam in a randomized 4-way crossover study in healthy volunteers. The results from this study will provide important information on the potential of curcumin-piperine to inhibit the metabolism of co-administered drugs and cause drug-herb interactions. Ultimately, this information can be used by physicians to help guard patients from potentially unsafe combinations of herbal and traditional medicines.

PI: Cowen, Lenore
Title: Computational Methods for Wrapping and Threading Remote Protein Homologs
Abstract: The "twilight zone" is a term coined by Burkhard Rost to refer to remote protein homologs whose sequence similarity to proteins of known structure is sufficiently low that computational detection of the homology becomes quite challenging. We propose to construct new threading methods that extend protein structure prediction and sequence/structure alignments further into the "twilight zone." We attack the problem on two fronts: first, we intend to extend the "wrapping" methods we designed to successfully attack two hard special cases of this problem to other SCOP superfamilies. This involves casting the pairwise dependencies in the wrapping portion of the energy function into the general framework of Markov Random Fields, while still allowing them to wrap multiple aligned sequences to narrow the search space; then using a more sophisticated energy function based on a backbone-dependent rotamer library for sidechain packing. Second, our programs for the beta-helix and trefoil folds used human intervention to construct the core structural templates on which we are wrapping the sequences to predict whether they could fold into these structures or not. In order to construct a general threading program with reasonable fold library coverage for the PDB, we need to solve the challenge of automating the construction of a structural template from a set of proteins that, for example, all belong to the same SCOP superfamily. Most current threading programs train too closely to a backbone of one particular structure to be able to capture remote homologs. We propose a novel multiple structure alignment that adds geometric flexibility to capture similarities between more distant homologs, from which more general core templates can be abstracted. The applications of better computational protein structure prediction to speed up medical discovery are well-known. BetaWrap, our first beta-helix prediction program, already uncovered a previously-unknown relationship between the beta-helix fold and the virulence of microbial pathogens. A striking prediction of the BetaWrap program is that the beta-helix fold is predicted for many surface adhesins, toxins, and other recognition/penetration proteins of human pathogens. Our prediction that a major pollen allergen forms the beta-helix shape has just recently been confirmed experimentally.

Advances in computational protein structure prediction can help guide prediction of protein function, and thus speed medical discovery. This proposal is especially targeted at improving prediction of beta-structural motifs, which include many protein families that are important for bacterial pathogenesis, with representatives from whooping cough toxin (beta-helices) to the botulism toxin (beta-trefoils).

PI: Crane, Gregory
Title: A Reading Environment for Arabic and for Islamic Culture
Abstract: Students learning Arabic or reading English texts about Islamic Culture are confronted with a dizzying set of references as well as quotations from religious texts and classical poems that are part of the vocabulary of even ordinary, and apparently, unrelated discourse, understood by native speakers but unintelligible to outsiders. This project develops and evaluates a reading environment, based on automatic linking within a digital library framework, that automatically provides lexical and/or encyclopedic background information adapted to individual users. The work proposed here transfers digital library research to a pedagogical setting. Heavy and growing usage of a reading environment for Greco-Roman culture suggests that a similar set of tools may attract substantial use for Arabic and Islamic studies. This project goes beyond implementation, studying the impact of these technologies on two core groups of learners: Arabic language students moving beyond annotated texts and to real world Arabic, and students reading texts about Islamic culture, especially non-specialists from other disciplines. We focus upon two broad areas. First, to what extent does this reading environment enhance existing practice? Can readers move more quickly through new text? Can readers begin working with culturally complex documents at an earlier stage? Second, to what extent does this reading environment change the goals of learners? Can they address more challenging topics? Do they make broader use of more complex source materials? We will examine three core user groups: 1) students enrolled in Arabic courses at Tufts University; 2) students working with Islamic cultural materials as part of courses taught as International Relations; 3) individuals making use of the reading environment online from outside Tufts. Instruments include reading comprehension tests for both Arabic and English texts on Islamic culture, field observations of practice, structured interviews with students, instructors and focus groups, and analysis of lookup patterns. By encoding our data in standard formats, we can represent that information in a range of forms, not only as text on text but printed as braille and as sound generated by speech synthesizers.

The materials produced under this grant will be made available under the open access terms defined for the Tufts University Open Courseware Initiative (http://ocw.tufts.edu), providing a public commitment, backed by the university leadership, to make these results freely available.

PI: Crane, Gregory
Title: Building a Greek Treebank
Abstract: While the Cantus Foundation support is aimed at Greek, overlap with Cybereditions, NEH/IMLS, NEH R&D can support work by David and students on the Latin Treebank. We can thus continue to augment the Latin Treebank and to make sure that we have a system that is able to support both languages.

The following table lists definite texts that we definitely want to cover. These include Homer, Hesiod, Pindar and selections of Greek epic, the surviving plays of Greek Tragedy and Comedy and several of the most important Platonic dialogues. For now, we assume that we are doing whole dialogues (e.g., all of the Republic). Second list of possible texts suggests authors from whom we can draw selections to round out our target of 1,000,000 words.

PI: Crivello, Natalia
Title: Folate Deficiency, Brain Lipids, and Amyloid Toxicity in APP/PS1 Mice
Abstract: The objectives of this application are to identify the metabolic underpinnings of the association between dietary folate deficiency, choline-containing lipid metabolism, and cognitive impairment in APP/PS1, double transgenic mouse model of AD. The proposed study was designed to test the hypothesis that introduction of folate deficiency at early age challenges the status of choline-containing lipids in the hippocampus and cortex, shifting accumulation of Aβ at earlier age, and contributing to cognitive dysfunctions.

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 have 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: Dobrow, Julia
Title: Media and Public Service Program Editing Lab
Abstract: With the addition of a new editing lab, the MPS Program will be able to expand in many ways. First, we will be able to start up the Tufts Film Unit, a program associated with an advanced filmmaking class, in which students will take on projects for non-profit “clients” and produce films for community groups on social issues. Second, we will be able to offer additional film classes we cannot currently offer due to space constraints. Third, this space can be used by students and faculty in several other programs on campus, including the growing digital photography program (a joint venture between Tufts and the Museum School), the Exposure Project (http://www.tuftsgloballeadership.org/programs/exposure.html), the animation and multimedia courses given in the Tufts Engineering School and the digital music courses offered through the music department. We believe this investment will be both large and long lasting, not just for the MPS program but also for the entire Tufts campus.

In addition, we are working to develop partnerships with a number of organizations outside of Tufts that will provide students with new ways to use the capabilities of the editing lab. For example, we are working with Press Pass TV (http://www.presspasstv.org/), an organization that teaches inner-city minority high school students basic broadcast journalism skills. Our students will be working with the high school students to help them develop, shoot and edit stories. Another partnership is with the New England News Forum (http://www.newenglandnews.org/), an organization devoted to finding news stories not covered by mainstream news organizations and disseminating them. A new editing lab will help our students to develop and produce stories that can be posted through this organization, potentially reaching thousands of people. Having a dedicated editing facility will also be the catalyst for new partnerships and opportunities, as well. Lastly, we are reaching out to communities through a program we’re developing to teach teachers about media literacy. The Tufts Summer Media Literacy Institute will be launched in summer 2008 and is designed to help teachers who work in both urban and suburban K-12 schools to develop ways to integrate media literacy into already existing curriculum. The new editing lab will enable us to develop a component of the Institute that focuses on learning how to edit. Since a central tenet of media literacy is understanding production, the new media lab will be an important resource that will play a key role in enabling us to reach out into many communities around social change filmmaking.

PI: Dolan, Kathy
Title: Oral Health Across the Commonwealth - Sealant Program Extension
Abstract: TUSDM seeks a multi-year grant to expand and enhance its sustainable, comprehensive community-based oral health care program for at-risk, underserved communities, Oral Health Across the Commonwealth (OHAC). This expansion will add critical preventive services to the care we already provide this population, further increasing access to care and improving the oral health care status of children in these communities.

Specifically, TUSDM will build upon the success of OHAC in three targeted communities — Boston, Springfield, and Lowell — by adding sealants to the primary prevention services offered. These services currently include parent and student education, a dental cleaning, a topical fluoride treatment and oral hygiene instruction; the addition of sealants will make a much-needed impact in helping reduce the incidence of dental disease for a vulnerable group of children when the intervention can be most effective: preschool through eighth grade.

A critical first-step in this process is to develop relationships with community dentists, recruiting them to conduct the required screenings prior to sealant application, and to accept referrals for more definitive dental care as needed. With proper funding we are confident of attracting dentists to participate in this well-known and well-regarded program.

Support from the Oral Health Foundation will provide funding to:

• enhance the OHAC school-based program in our targeted communities by adding a broad-based sealant program;
• develop and expand our provider network to assist with sealant screenings and to accept more MassHealth patient referrals for general care;
• design and develop patient educational and enrollment materials and resources for recruiting dentists;
• enhance reimbursement by adding an insurance coordinator to the team;
• evaluate the clinical success in terms of patient health outcomes and;
• establish a financially viable business model to ensure long-term sustainability and replicability.

PI: Donini, Antonio
Title: Phase III of Humanitarian Agenda 2015
Abstract: In May 2008 at a retreat of HA2015 researchers, FTC faculty and a few outside experts, progress in the overall research program was reviewed and avenues for future research explored. It was felt that while the four original “petals” of the HA2015 research were still valid for framing current humanitarian challenges, there were a number of emerging issues that needed to be explored. The meeting discussed the need to continue to engage with donors and humanitarian agencies on the issues emerging from HA2015, in particular the politicization and instrumentalization of humanitarian action, particularly, but not only, in the context of the global war on terror. A number of small consultations will be held on both sides of the Atlantic to pursue these issues. Various donors, NGO consortia and research institutions have already agreed to support these activities. A number of academic outputs are also planned, including articles in peer-reviewed journals and a book capitalizing on the findings of the HA2015 research.

At the same time, FTC will pursue country specific follow-up research activities. The country studies in Afghanistan, Iraq and Sri Lanka will be updated to take into account emerging humanitarian issues. Policy briefs on these countries (and others if funding is available) will be issued in the Summer/Fall of 2008.

Moreover, our work in Nepal has uncovered a number of interesting issues around the humanitarian-development relationship and the challenges of social transformation in a (hopefully) post-conflict environment that we feel that it is important to research both because they are largely un-explored and because of their potential policy implications. While funding is already available for some of these activities, a contribution from Norway would allow us to expand the depth and geographical spread of the research.

PI: Economos, Christina
Title: Children in Balance: A National Childhood Obesity Prevention Model
Abstract: Childhood obesity has reached epidemic proportions in the United States. Obesity early in life is of concern in the short term because of its immediate effects on the health and well being of young children. It is also of concern because it increases the likelihood of overweight and obesity and the risk factors associated with it later in life. Early-elementary school children in culturally diverse urban areas are at considerable risk. For that reason, over the past several years, faculty and staff at the Friedman School of Nutrition Science and Policy at Tufts University have been engaged in a community intervention to identify ways to stop this trend.

PI: Economos, Christina
Title: Understanding Childhood Obesity in a Diverse Population of Low-Income Children Living in Rural America
Abstract: U.S. Children living in impoverished rural communities have limited opportunities for physical activity and accessibility to healthy foods. Research in this area is limited as much of the work has been done in urban and suburban areas. Given the increasing obesity rates it is necessary to identify the factors that are driving this epidemic in rural areas.

Specific Aims and Hypotheses:

1. To describe the feeding and parenting styles of low income, rural parents living in four distinct areas of the U.S. (Appalachia, Central Valley, Mississippi River Delta, and the Southeast) and to examine the agreement among feeding style instruments (CFSQ/CFQ) and between feeding style and parenting style instruments (CFSQ/PDI-S).

   Hypothesis 1a: There are associations between the feeding style dimensions of demandingness and responsiveness (CFSQ) and the feeding style dimensions (CFQ) of pressure to eat, restriction, and level of monitoring.

   Hypothesis 1b: There are associations between the feeding style dimensions of demandingness and responsiveness (CFSQ) and the parenting style subscales (PDI-S) of nurturance, inconsistency, follow thru, organization, letting go, punishment, reasoning, reminding, and control.

2. To determine the relationship between parent feeding styles and child's dietary quality, energy intake, and weight status in a low income, rural population.

Hypothesis 2a: There are associations between child diet quality and parent level of demandingness (+) and responsiveness (+) toward feeding, as measured by the CFSQ, and pressure to eat (+), restriction (-), and level of monitoring (+), as measured by the CFQ.

Hypothesis 2b: There are associations between child energy intake and parent level of demandingness (-) and responsiveness (-) toward feeding as measured by the CFSQ and pressure to eat (-), restriction (+), and level of monitoring (-) as measured by the CFQ.

Hypothesis 2c: The pressure to eat score reported by parents, as measured by the CFQ, will be different between children who have a high vs. average BMI z-score.

3. To determine the relationship between physical activity-related parenting practices and parenting styles of low income rural parents and their child's physical activity level.

Hypothesis 3a: There is a positive association between a child's PA level and their parents activity-related practices score.

Hypothesis 3b: Levels of physical activity will be different in children with an authoritative parent, as measured by the PDI-S, compared to children with a nonauthoritative parent.

PI: Economos, Christina
Title: Assessing and Preventing Obesity in New Immigrants
Abstract: Immigrant populations, by virtue of being medically-underserved, low-income, and of race-/ethnic and linguistic minority status are at particularly high risk to become obese as they adapt to the obesogenic environment in which they reside once in the US. Preventive interventions developed with the active participation of these communities have the potential to prevent or moderate the weight gain.

We will demonstrate, using measures of effectiveness, the feasibility of partnering with the immigrant community in Somerville, MA to refine, implement, evaluate, and disseminate a 2-year preventive intervention to moderate or reduce weight gain in 435 mother/child dyads of new immigrants. The 435 mother/child dyads will be randomized to either receive the intervention or to serve as controls that will receive a delayed intervention, once the main trial is completed. We will enroll immigrants from Brazil, Haiti, and Latin-American countries, groups who are coming in large numbers to eastern MA, and are served by local community agencies. Intervention targets focus on 10 family-based goals in the areas of healthy eating, increased physical activity, and the reduction of sedentary behavior. Specifically, the intervention is designed to bring adults into the healthy weight range by reducing or maintaining BMI by providing education, skill development and support. In children, it will be designed to result in an increased energy expenditure of up to 125 kcals per day beyond the increases in energy expenditure and energy intake that accompany growth. Based on our formative research within these groups, intervention elements will be delivered in small groups at the agencies of our community partners. “Lifestyle coaching” sessions and support groups tailored to the specific immigrant groups' needs will capitalize on traditional healthy behaviors practiced by new immigrants and teach specific strategies that effect family environments. The proposed project reflects the ongoing work of a multidisciplinary research group and builds on two successful research initiatives in Somerville, one completed and one ongoing.

The goals of this community-based participatory research study have been developed from community interest and involvement. The community partners engaged with us to conduct the formative research used to develop this application, and will be involved in the design, recruitment, delivery, and research evaluation throughout the project. Dissemination of results to the affected community was deemed critical and will be done with the intention of strengthening community resources, preventive health care and education for immigrants. Furthermore, if successful, national dissemination of this trial can assist other communities with large immigrant populations to reduce the risk of obesity in this vulnerable population.

PI: Edwards, Aurelie
Title: Mathematical Model of Vascular and Tubular Transport in the Rat Outer Medulla
Abstract: The overall objective of the proposed work is to use mathematical modeling to gain fundamental insights into the mechanisms by which nitric oxide (NO), superoxide (O₂^-), and heme oxygenase (HO) regulate renal medullary blood flow, oxygenation, and sodium reabsorption. We will develop numerical models, with inputs from experimental data, to investigate:

1. How NO and O₂^- regulate medullary thick ascending limb (mTAL) active sodium reabsorption and oxygen consumption. We will develop a new, steady-state model of vascular and tubular transport in the rat outer medulla (OM), that accounts for the three-dimensional architecture of the medulla, the presence of red blood cells, as well as the production and consumption of oxygen, NO and O₂^-. We will determine how interactions between NO and O₂^- affect mTAL sodium reabsorption under physiological and pathological conditions. We will examine the hypothesis that NO, as an endogenous inhibitor of active transport, plays an important role in modulating the susceptibility of the medulla to anoxic injury.

2. How NO and O₂^- regulate medullary blood flow, blood distribution, and oxygen supply. We will convert the new steady-state model into a dynamic model, and incorporate the effects of vasodilation on medullary blood flow (MBF). We will examine the hypothesis that the diffusion of paracrine substances such as NO from adjacent tubules to vasa recta pericytes provides an efficient mechanism whereby local perfusion is precisely matched to tubular oxygen demand. We will determine whether the enhancement of NO generation that is mediated by constrictors of the medullary circulation (such as Angiotensin II) may serve to protect the outer medulla from ischemic injury.

3. How renal medullary heme oxygenase (HO) and its products carbon monoxide (CC) and biliverdin modulate tubular sodium reabsorption and medullary blood flow. Recent evidence suggests that the renal medullary HO/CO system constitutes a significant antihypertensive mechanism. We will incorporate into our model the activity of HO, the formation of its products, and their effects on reactive oxygen species and NO. We will examine the hypothesis that significant expression of HO in the renal medulla serves to protect this region from ischemic injury, through CO-induced vasodilation and bilirubin-mediated antioxidant effects. We will simulate the effects of renal perfusion pressure-induced elevations in medullary CO concentrations on mTAL sodium reabsorption, so as to gain some insight into the mechanisms underlying pressure natriuresis.

PI: Ekbladh, David
Title: The Great American Mission: Development and the Construction of an American World Order, 1914 to Present
Abstract: Recent U.S. involvement in Afghanistan and Iraq pushed into the limelight questions about what methods the United States and the international community will use to foster the reconstruction and development of these and other countries. A broad commitment to development as a means to “drain the swamp” to defuse the appeal of dangerous ideologies demonstrates how policymakers after September 11, 2001, again embraced development as a means to further the strategic ends of the United States. However, concepts and institutions instrumental to that policy have changed over time. While it is understood development has an extensive history as a policy mechanism, many remain unaware of how its past has shaped and constrains its application in the present. Many use terms such as “sustainable” and consciously abjure terms like “planning” when discussing development projects seen as pivotal to a particular mission, yet they may not comprehend exactly how these terms found or fell from favor. This is not the result of fuzzy theoretical debates, but the product of hard learned lessons in applying these ideas as policy internationally. Contemporary officials may not be aware of the long history of collaboration between nongovernmental groups, key international institutions, and the U.S. government to promote development for strategic ends. Lacking an understanding of how development got to where it is today, policymakers in the international community can find themselves groping as they create policies to meet a new international situation.

A historical exploration of the evolution of development as an integral element in the foreign relations of the American state, as well as international and nongovernmental organizations to build a world in their own image provides a necessary means to understand how development has come to play such an indispensable role in the wider U.S. engagement with the world. It also demonstrates how assumptions driving the concept were altered by application in the world, bequeathing many of the assumptions, institutions, and ideas actively employed in U.S. foreign policy today. As policymakers inside and outside the U.S. government grapple with changing world situations they will grasp with more certainty what was left to them, allowing fresh perspectives and, perhaps, the ability to create new options.

Present emphasis on development should be no surprise as its use to consciously shape a world amenable to the United States has a long legacy. From the late nineteenth century onward, Americans believed that the route to stability and prosperity for less developed areas lay along a path that put faith in technological cures for social, political, and economic ills. It was primarily non-governmental groups that harnessed international reform ideas emerging in the early decades of the twentieth century and fashioned them into an American style of development that was exportable to the world in direct contrast to the models offered by fascism and communism. These techniques, defined in the Depression, were the foundations of Cold War development activity of the United States government and the construction of an American dominated liberal order in opposition to other ideologies that claimed to have the correct path to modernity. In turn, the institutions and approaches established during the Cold War era remain in the skeletal structure of the international community today. Development, as contemporary concept, became deeply rooted within international life as a means to achieve political ends even as what constitutes development shifts. For the United States, development, through much of the twentieth century and into the present, has served as a powerful means to secure and legitimate an international order based on liberal principles.

PI: Ellis, Julie
Title: Surveillance for HPAI by the Seabird Ecological Assessment Network (SEANET)
Abstract: Globally, almost all detections of Asian H5N1 in a new locality have been through investigation of mortality events in wild birds or domestic poultry (Pacific Islands Fish and Wildlife Office, USFWS, and NWHC unpubl. report, 2006). Only regular and repeated surveillance of appropriate habitats have the sensitivity to detect mortality and provide opportunities to sample moribund or fresh carcasses (Guberti and Newman 2007). AI viruses have been successfully detected, as documented by the virologist (Dr. lion Ip) who conducts AI testing at the WDIN, from a variety of marine birds and mammals, both from live as well as stranded or beached animals. The benefits gained from conducting disease investigations of wildlife mortality events are not unique to AI. Many other important diseases have been discovered and described after initial detection through the wildlife disease investigation process. Increasing the frequency of surveillance to detect morbidity and mortalities in wild birds requires extensive human resources. Using ongoing surveillance programs, such as SEANET’s beached-bird monitoring, to aid in HPAI surveillance provides inexpensive samples and capitalizes on previously established programs.

According to the US Interagency Strategic Plan for an early detection system for highly pathogenic H5N1 avian influenza in Wild Migratory Birds (March 2006), “The key to successful surveillance strategy involves: 1) early detection of morbidity and mortality, 2) rapid reporting and submission of appropriate specimens to qualified diagnostic facilities, 3) immediate assessment of the field event, 4) rapid diagnosis and confirmation, 5) immediate reporting of diagnostic results once confirmed, and 6) pre-planned contingency and response training for occurrence of HPAI.”

Currently, an immediate reporting of diagnostic results does not exist for mass mortality events in seabirds on the Atlantic coast. A large die-off of shearwaters in the Southeast in July 2007 brought to light the need for such a reporting system. During this event, shearwaters were observed dead or dying on the water and on beaches in the Bahamas, Florida, Georgia, and the Carolinas. Staff at SEANET, wildlife refuges, and federal agencies (such as the WDIN) received numerous reports from members of the public and biologists. However, there was no system in place for receiving and summarizing reports, no clear mechanism through which the public could relay their observations and counts of dying or dead birds, and no real-time mechanism to track the spatial extent of the die-off. Moreover, there was confusion about what type of samples to take and where to send them, samples were sent to different testing laboratories, and there was no coordination in reporting the results of laboratory analyses. State agency staff in North Carolina and Florida attempted to compile and summarize the mortality event at a regional scale (e.g. # of dead birds and species, specimens deposited in freezers, # specimens necropsied or sent out for testing, results of tests, live birds in rehab). However, they were unable to successfully summarize this information due to the lack of coordination in reporting and the limited amount of time that agency staff could devote to this activity. SEANET can serve this role as a coordinated reporting system.

Developing an emergency response plan and contingency actions in the event of a mass seabird die-off is important to both bird conservation and HPAI surveillance.

To increase surveillance and improve coordinated reporting of morbidity and mortality events in seabirds and coastal waterbirds, we propose the following actions:

1. Recruit and train “Local SEANET Coordinators” in Northeast, Southeast and Mid-Atlantic regions of the Atlantic Flyway to help maintain regular surveillance of beaches by volunteers in each region. Coordinators would also serve as “first responders” for volunteers reporting mass seabird mortality events and would help in collecting, sampling, and shipping bird carcasses to the National Wildlife Health Center for HPAI testing. Recruiting and training of Coordinators would take place at regional workshops led by SEANET staff. Because much of the northeast region of SEANET has Local Coordinators, we will focus our efforts on recruiting and training Coordinators in the Mid-Atlantic and Southeast regions.

2. Create and distribute a Seabird Mortality Incident Emergency Response Plan in each of the three regions of the Flyway. These plans would help to solve some of the issues that arose during the shearwater die-off event in the Southeast in July 2007. The plans will include datasheets and protocols for systematic monitoring of beached birds, a uniform protocol for reporting mass seabird mortality events, a list of key contacts by state and by region, avenues for getting information out to the public about the mortality event (listservs and press releases), instructions for the safe handling and shipping of specimens to identified diagnostic facilities, and a variety of additional key information.

3. Continue work with the Wildlife Disease Information Node to develop a near-real time web-based reporting site for mass seabird morbidity and mortality events. This system can be used by SEANET collaborators, state agencies, and the public throughout the coastal regions of the Atlantic Flyway.

4. Revise the datasheets used for SEANET beached bird surveys and alter the web-based data entry system to reflect these changes. Standardized bird monitoring protocols are vital to investigations of HPAI and other sources of bird mortality on the east coast. These new datasheets will be used throughout the SEANET network of beaches in all three regions (Northeast, Mid-Atlantic, and Southeast) of the Atlantic Flyway.

PI: Ellis, Julie
Title: Common Eider Mortality Events at Cape Cod, Massachusetts: Diagnosing an Unknown Virus and the Role of Contaminants
Abstract: Common eider mortality at important overwintering sites such as Cape Cod may pose a threat to regional populations. Estimates of 3500 birds affected in 2007 exceed the annual Massachusetts harvest in 2007 (USFWS 2008), suggesting that these die-offs have management and conservation level significance. Gross necropsy of nearly 50 birds collected during the die-offs of 2007 and histopathology of a subset of those revealed that affected birds tend to be thinner than unaffected birds, and have a higher prevalence of some subtle lesions such as liver discoloration. But the overall diagnostic picture remains murky due to a lack of advanced testing. Previous Massachusetts die-offs were attributed to acanthocephalan parasites based solely on gross necropsy findings (Christiansen, unpublished data) and eider die-offs in Europe have been similarly diagnosed (e.g., Clark et al. 1958, Borgsteede 2001). However, our recent work comparing acanthocephalan numbers in die-off birds versus unaffected birds shot by hunters have demonstrated that these parasites were not the proximate cause of death as prevalence and numbers of parasites were similar between groups (Courchesne, unpublished data). Similar comparisons undertaken by European investigators have yielded the same results. (Camphuysen et al. 2002, Thieltges et al. 2006). Preliminary testing of a few elders affected during the 2007 die-offs revealed the presence of an unidentified enveloped RNA virus in some tissues (Ip, unpublished data). Its pathogenicity and significance in the die-offs is currently unknown, as is its prevalence in the wider population of eiders not affected by the die-offs. These studies highlight the need to compare eiders unaffected by the events to those from die-offs in order to accurately evaluate the role of subtle and often novel lesions. It is also clear that limiting diagnostics to gross necropsy may be misleading, and that necropsy results must be viewed in the context of additional testing.

By pursuing virus isolation and experimental infections with the virus, as well as contaminants analysis on tissues archived from the 2007 die-offs, we will seek to firmly establish a diagnosis for these events. We will be assisted in this endeavor by submission of archived tissues from unaffected birds shot by hunters. These data will also aid in understanding the associations among parasite loads, body condition, and contaminant concentrations. For instance, starvation can lead to loss of fat reserves and muscle mass, protein catabolism, and redistribution of heavy metals within organs. The more severely emaciated the animals are, the higher the metal levels in the tissues (Frank et al. 1983, Daoust et al. 1998, Debacker et al. 2000, Wayland et al. 2005). Toxic levels of metals in organs can lead to immunosuppression that may compound the stress of heavy parasite loads, opportunistic infection and starvation. Likewise, heavy parasite loads may exacerbate the effects of starvation. This research will directly address the stated Information Needs and Conservation Strategies for North American Seaducks and for common eiders specifically as detailed in the Sea Duck Joint Venture Strategic Plan 2008-2012; by assaying for contaminants and attempting to diagnose the unknown virus, and then by linking both those data sets to necropsy findings, we will meet the two aims listed: (1) sample birds for contaminants, diseases and parasites and (2) evaluate the effect of diseases.

There are three main objectives in this study:

1. Perform virus isolation on tissue samples from both birds found dead during 2007 die-offs and unaffected birds shot by hunters.
2. Perform experimental infections in mallards using the virus recovered from eiders.
3. Assay liver samples from affected and unaffected birds for both metals and organic contaminants to evaluate in light of necropsy findings and virus presence or absence.

PI: Fielding, Roger
Title: Lower Extremity Muscle Power and Function in the Elderly
Abstract: The focus of this research has been to examine the physiologic and functional effects of a muscle power training intervention in comparison to traditional progressive resistance training in a community-based group of elderly men and women with moderate mobility limitations. During the current project period, we have successfully demonstrated that peak lower extremity power is closely associated with functional limitations and self-reported disability in older community dwelling men and women. We propose to extend our previous findings by examining the physiological mechanisms that contribute to the age and gender-related declines in peak muscle power. To compliment our existing data on skeletal muscle fiber contractile properties, we will assess the neural contributions to the generation of muscle power with advancing age. We will test the hypothesis that skeletal muscle single fiber contractile properties (i.e., single fiber power, shortening velocity, specific force), neural factors (i.e., intermuscular coordination patterns, central activation ratios/and motor unit control properties) and lower extremity power will be reduced with advancing age and degree of risk for mobility disability, and these differences will be attenuated in women compared to men. Middle-aged healthy (40-55 yrs.), older healthy (70-85 yrs.), and older (70-85 yrs.) men and women at risk for mobility disability will be studied under controlled conditions (Study 1). In addition, in light of our recent observations that differences in lower extremity maximal velocity occur at relatively low external forces (e.g., 40% 1 RM) and are most closely associated with gait velocity in older individuals, we propose conducting a randomized controlled trial of high velocity low resistance exercise training in individuals at risk for mobility disability to test the hypothesis that a short-term resistance training intervention performed against a low external force and at maximum voluntary velocity will induce significant reductions in mobility disability as evidenced by improvements in gait velocity during performance of a 400 M walk in older individuals at risk for mobility disability (SPPB score ≤9, 70-85 yrs.) (Study 2). The results of these studies will have important implications in understanding the proximal determinants of physical disability in the frail elderly and in designing intervention strategies targeted at improving mobility.

PI: Flytzani-Stephanopoulos, Maria
Title: Nanostructured Metal Ion-Modified Ceria and Zirconia Oxidation Catalysts
Abstract: The overall goal of this proposal is to elucidate the role of noble metal ions as catalytic sites on oxide nanoparticle supports; and the role of oxide defects in stabilizing the added metal ions in their active state for reactions of interest to fuel reforming for hydrogen generation. The quantities and the types of the responsible defects on oxide support are strong functions of the size and surface of the nanoparticles. A novel preparation to control size and surface of oxide nanoparticles will be exploited to elucidate the correlations.

Recently at Tufts University, it was demonstrated that the activity of ceria-supported metal nanoparticles of gold or platinum catalysts for the water-gas shift reaction is NOT due to the metal nanoparticles. Rather, Au-O-Ce or Pt-O-Ce phases appear responsible for the reaction activity. Contrary to the literature, the metal particle size distribution is irrelevant for this reaction. On the other hand, the particle size and oxygen defect density of ceria are crucial for an active catalyst. These results have a major impact on catalyst design and development. For example, a very active catalyst can be prepared with a tiny amount of gold or platinum (<1.0 wt%) as long as the oxide nanoparticle support properly stabilizes an atomic dispersion of the metal. This would greatly improve the prospects of fuel processing to generate low-cost hydrogen for fuel cells and other applications.

A well-controlled preparation of non-stoichiometric, monodispersed ceria nanoparticles, also yielding a significant fraction of Ce³⁺, was developed recently at Columbia University. The preparation offers unprecedented control of the ceria nanoparticles which can be exploited to sort out catalytic mechanisms that are based on the nanoscale oxide surface and size. As the particle size decreases below 20 nm, the amount of Ce³⁺ ions in the lattice increases (to ~9% for 6 nm particles) and a concomitant lattice parameter increase is measured. In fact, the Ce³⁺/Ce⁴⁺ ratio is a strong function of the particle size. These particles are prepared at room temperature as single crystals in octahedron shape with eight (111) surfaces, or as truncated octahedrons with extra (100) surfaces. The (100) surfaces are known to have more intrinsic oxygen vacancies due to charge balance. These vacancies can stabilize the added metal ions and readily participate as sinks and sources of oxygen in the catalytic redox reactions. Particles with special surface planes will be exploited in this project to answer some of the fundamental questions.

This proposal aims at exploring and understanding the observed atomic-scale interaction of Au, Pt, Cu and other transition metals and metal oxides with cerium and zirconium oxides. Monodispersed ceria and zirconia nanoparticles with size selection and controlled surfaces will be prepared at Columbia University as model catalyst supports. Metal addition will be by deposition/precipitation or vapor phase deposition, followed by annealing and leaching to remove weakly bound metal species. Materials will be prepared for comparison by a modified gelation technique to maximize the number of M-O-S sites. At Tufts, catalytic activity will be probed for the CO oxidation reaction by several oxidants. The proposed computational effort will check hypotheses based on the experimental evidence and be used to guide further experiments. A number of key characterization techniques, such as in situ Raman and UV-VIS (DRS), HREM, and STM/STS, will be used to characterize surface ion-defect complexes, to follow the catalyst structural changes and correlate them to reactivity. Time-resolved X-ray absorption spectroscopy, in situ XANES and EXAFS experiments will be performed at Brookhaven National Laboratory under the direction of senior researchers there who will serve as no-cost collaborators in this project.

PI: Ford, Lawrence
Title: Research on General Relativity and Quantum Fluctuations
Abstract: This project will involve theoretical research on several topics related to quantum theory and gravitation. There will be special emphasis on phenomena related to quantum fluctuations including the operational meaning of spacetime geometry fluctuations, the probability distribution of quantum stress tensor fluctuations, the role of stress tensor fluctuations in inflation, and selected aspects of the Casimir force. This project seeks to integrate studies of the quantum nature of the gravitational field with studies of fluctuating electromagnetic forces. It is hoped that this type of investigation will lead to a deeper understanding of both types of phenomena.

This project is expected to have a broader impact through possible benefits to other fields of science, to education, and to technology. It will entail international collaborations, and hence help to forge links with researchers in other countries. The insights and techniques of this work may be useful outside of the specific subfields of physics being investigated. The project will further education through the training of graduate students and by the involvement of faculty at primarily teaching institutions. It should also produce examples which can be used to explain some of the concepts of quantum theory and relativity to students on a variety of educational levels. The work on Casimir forces may eventually be useful in nanotechnology where a better knowledge of Casimir forces is likely to become important for the construction of small scale devices.

PI: Forgac, Michael
Title: Structure, Mechanism and Regulation of the V-ATPases
Abstract: The long term objectives of this proposal are to determine the structure, mechanism and regulation of the vacuolar (H⁺)-ATPases (or V-ATPases). The V-ATPases are responsible for acidification of intracellular compartments in eukaryotic cells and serve an important function in a variety of cellular processes, including receptor-mediated endocytosis, intracellular membrane traffic, protein processing and degradation and coupled transport of small molecules. V-ATPases in the plasma membrane of specialized cells also function in renal acidification, pH homeostasis, bone resorption and tumor metastasis. Understanding how V-ATPases are regulated is thus crucial to understanding many disease processes, including viral entry, osteoporosis and metastasis.

The V-ATPases are organized into two functional domains: a peripheral V₁ domain responsible for ATP hydrolysis and an integral V₀ domain responsible for proton translocation. Electron microscopic images of the V-ATPase complex reveal multiple connections between the V₁ and V₀ domains. To determine the arrangement of subunits within the V-ATPase complex, unique cysteine residues will be introduced into the B subunit and used as sites of attachment of a photoactivated crosslinker. In addition, electron microscopy of complexes decorated with subunit-specific antibodies will be performed. The function of a unique domain of the catalytic A subunit will be addressed by deletion and random mutagenesis. The structure of the 100 kDa a subunit and its interactions with the proteolipid subunits of the V₀ domain will be determined using cysteine mutagenesis, chemical labeling and disulfide bond formation. Finally, the in vivo dissociation of the V-ATPase complex, which has been proposed to be an important regulatory mechanism, will be investigated. Dissociation in response to glucose depletion will be compared in V-ATPases located in different intracellular compartments and mutants defective in dissociation will be selected and analyzed. These studies should provide further insight into the structure and regulation of this important family of (H⁺)-ATPases.

PI: Garven, Grant
Title: Physiochemical Evidence of Faulting Processes and Modeling of Fluid Flow in Evolving Fault Systems in Southern California
Abstract: Faults are potentially important pathways for fluid migration as well as barriers to fluid flow (e.g. Knipe, 1993; Antonellini and Aydin, 1995; Haneberg, 1995; McCaffrey et al., 1999; Cox et al., 2001; Borja and Aydin, 2004). In mature sedimentary basins where formation permeability is low due to diagenesis, the faults may be the only feasible pathway for significant fluid movement. Wherever subsurface storage or production of fluids is contemplated, such as CO2 sequestering (Bruant et al., 2002), the integrity of local fault system relative to the reservoir seal has to be considered. Faults can also be important for the transfer of heat, which in turn can influence thermally sensitive diagenetic processes such as hydrocarbon maturation and oil trapping (Philippi, 1965; Waples, 1980; Wieck et al., 1995; Person et al., 1996; Zhang et al., 2005), carbonate/quartz cementation, hydrothermal ore mineralization (Sibson et al., 1975; Garven et al., 2001; Simms and Garven, 2004), and contact metamorphism (Ague and Rye, 1999; Dipple et al., 2005). Changes in fluid pressures within fault zones also play an important role in earthquake rupture nucleation and recurrence (Blanpied et al., 1992; Nur and Walder, 1992; Sibson, 1992; Hickman et al., 2000; Stanislavsky and Garven, 2002).

In basins with complex structural histories, faults may change character, both with respect to style of movement as well as sealing properties (e.g. Byerlee, 1990; Scholz, 1990; Gordon and Flemings, 1998; Fisher and Knipe, 2001; Cox et al., 2001; Rowland and Sibson, 2004). In this proposal, we plan to capitalize on our previous studies of faults and their hydraulic properties in southern California.

We propose to build on our previous DOE funded results (Boles-Garven), by pursuing significant leads that have resulted from these studies. We propose to utilize newly acquired data sets from the current expanded exploration/development activities of oil companies in Southern California. These data offer a unique opportunity to leverage oil company data, which are extremely expensive to acquire, towards a fundamental understanding of fault permeability and faulting processes. Our proposed study is a true collaborative effort, combining field and analytical observations from the Boles team at UC Santa Barbara with hydrogeologic and poroelastic deformation modeling generated by the Garven team at Tufts University.

The basic questions being investigated are:

1. What is the spatial distribution of permeability within a fault system, how does it evolve over time in basins that have changed from extensional to convergent stress regimes, and how is it affected by multiphase fluid flow?
2. What is the geochemical evidence for magnitude and rate of fluid and heat transfer along faults?

We propose to investigate by geochemical flow modeling, field and lab experimental studies, the effects of rapid degassing on carbonate geochemical signatures and answer these questions.

PI: Geck, Peter
Title: Do Stem Cells from the Fetus Contribute to Breast Cancer?
Abstract:

INNOVATION: We present an unexplored, novel concept based on recent compelling sets of data:

1. We propose that post-pregnancy mammary glands are chimeras and integrate Stem cells from the fetus;
2.  the process increases the ratio of immature progenitors that have a critical role in breast cancer, and
3. Y chromosome analysis (male fetus) can validate the hypothesis and offers future screening markers.

The concept presents a new mechanism in breast cancer (BrC), and new avenues in screening and prevention.

RATIONALE: The exchange of fetal and maternal cells during pregnancy results in the integration of fetal, multipotent progenitors in the mother. The established fetomaternal microchimerism (MC) appears to be stable for life in most mothers. The biological significance of the discovery is that these cells, called Pregnancy Associated Progenitor Cells (PAPC) represent a surprising, third type of progenitor pool (in addition to embryonic and adult stem cells), with major biological implications. By homing in normal regenerative processes, they can rejuvenate stem cell pools and may contribute to the lifespan advantage for women. On the other hand, their negative roles in autoimmunity and cancer have also been reported. Y chromosome markers (male fetus) detect the fetal lineage and were shown in several maternal tissues. Curiously, no data are available on fetal progenitors in the human mammary gland, although the hormonal regeneration-degeneration cycles render the mammary gland a prime target for fetal progenitor integration.

HYPOTHESIS: Based on the above, we postulate that the fetal progenitor lineage is highly represented in the mammary gland with a critical role in breast cancer. Two biological outcomes are considered:

1. PAPC integration may correctly rejuvenate the stem cell pool and protects from breast cancer. This effect on breast cancer is unstudied, only a correlation was shown with low circulating MC cells. The study did not rule out, however, that fetal cells can be cleared from circulation by the immune booster of a growing cancer.

2. PAPC integration is initially beneficial, but immunological tolerance gradually breaks down, particularly against Y-chromosome-specific antigens. In fact, this breakdown-scenario is well-documented to play a critical role in a set of autoimmune diseases. Coincidentally, breast cancers also show high correlations with other autoimmune symptoms and develop extensive (auto?)-immune-inflammatory histology. The persistent inflammation alters the stroma and damages the progenitor niche. We propose that as a result, the differentiation programs in the fetal (and/or maternal) progenitor lineages fail and progress to breast cancer. Involvement of fetal cells in cervical cancer has been shown and suggests a similar mechanism.

OBJECTIVES: It is now generally accepted that breast cancers initiate from cancer stem/progenitor cells or equivalents. Our innovative idea, therefore, that post-partum mammary glands may harbor a novel, third kind of “xenograft” progenitor pool is of great significance. Our major objective is to investigate, for the first time, if breast cancer is microchimerism related. We propose to detect Y-chromosome markers in breast cancer samples to establish correlations with breast cancer. The experiments, as designed, will be highly informative at any outcomes. Our baseline is expected to be ca. 20% positive for a Y chromosome marker in normal controls (ca. 80% of women with BrC were pregnant, ca. half carried male fetuses and ca. half of those developed long-term microchimerism = 20%). Results of <20% Y-positive will show that microchimerism protects from cancer, while results >20% will suggest that microchimerism initiates cancer.

SPECIFIC AIM 1: will establish the methodology for Y-marker detection in breast cancer samples from commercially available tissue-arrays. Methods for microdissection, DNA extraction and PCR design for Y-specific sequences will be optimized.

SPECIFIC AIM 2: will analyze a number of breast cancer samples and normal controls for the presence of fetal progenitor microchimerism to establish correlation patterns.

PI: Gorbach, Sherwood
Title: HIV Infection in Drug Users in Two International Sites
Abstract: We propose to conduct longitudinal observational studies in two countries - India and Vietnam - each with significant problems of drug abuse and increasing incidence of HIV. In both countries, the HIV epidemic is rapidly emerging as a direct result of injection drug use. Furthermore, the governments of both countries have recently initiated programs to provide combination antiretroviral therapy to HIV-infected patients. An important goal of this proposal is to initiate research in these countries to establish baseline nutrition and metabolic status of HIV-infected patients prior to widespread access to HAART and to follow participants who start on a first-line HAART regimen to document the natural history of treated HIV infection in these countries. This is an important window of opportunity to conduct the proposed studies as, over time, access to patients who are HAART-naive may be diminished and regimens will become more complicated. Our specific aims are as follows:

1. To characterize and compare HIV-negative and HIV-positive (HAART and non-HAART) injecting drug users (IDUs) in terms of:

   1. types, frequency and patterns of illicit drug use,
   2. co-morbidities,
   3. nutritional and metabolic abnormalities, and
   4. clinical outcomes;
      
      
2. To examine the independent contributions of adherence to HIV medications, psychosocial factors (e.g. depression), and socioeconomic factors (e.g. food insecurity) to the development or persistence of nutritional and metabolic abnormalities; and
   
   
3. To establish an infrastructure and ongoing presence in these countries so that with the increasing availability of interventions for HIV, we will have populations on which to build future studies.

Results from these international studies will not only provide important data for HIV-infected patients within these countries, but will also serve as comparisons for U.S. based studies. Comparison of findings between U.S. and international studies will help expand our understanding of the causes and consequences of metabolic complications in chronic HIV infection in the U.S. Furthermore, the results of this project will help to identify generalized malnutrition or specific micronutrient deficiencies in the local populations that may be amenable to nutritional interventions for delaying HIV disease progression. These might include vitamin supplementation and/or dietary counseling to improve the quality of food intake.

PI: Gorbach, Sherwood
Title: Center for Metabolic Research on HIV and Drug Use
Abstract: The aim of this Center is to provide scientific resources for studying the nutritional, endocrine, and metabolic aspects of HIV infection in chronic drug users of different ethnicities (Caucasian, Hispanic, and African-Americans) who are using various types of illicit drugs. HIV-positive drug users face a unique set of issues and challenges that may exacerbate their illness, including poor nutrition, inadequate medical care, difficulties adhering to complicated therapeutic regimens, and the use of specific drugs known to impair metabolic function. Investigation of the overall nutrition, endocrine, and metabolic effects of HIV infection in the general HIV-positive population, however, seldom extends to the drug using population, a group in which 50% of new HIV infections occurs. This Center will consist of 6 Cores: Administrative, Developmental, Drug User Resources, Nutrition and Metabolism, Endocrine, and Epidemiology/Biostatistics. The Center will build upon an existing infrastructure of studies in drug users at four East Coast institutions (Tufts University School of Medicine in Boston, Massachusetts; Brown University School of Medicine in Providence, Rhode Island; Johns Hopkins Medical Institutions in Baltimore, Maryland; and the New York Academy of Medicine, in New York City, New York). Tufts has developed programs in specific nutrition and metabolic aspects of HIV infection and has a research program in Hispanic drug users with and without HIV. Brown University has developed expertise in conducting research among specialized populations, including injection drug users, substance abusing women, and incarcerated drug users. Johns Hopkins has research in endocrine disorders among drug users with HIV, and has active longitudinal studies of African-American injection drug users. The New York Academy of Medicine’s Center for Urban Epidemiologic Studies has several ongoing research studies related to HIV infection in drug using populations. The proposed Center will combine the complementary resources and expertise that exist at each of the collaborating sites to develop a new research program that will focus on the nutritional, metabolic, and endocrine abnormalities in HIV-positive and HIV-negative drug users.

PI: Greenberg, Andrew
Title: Research Training Program in Nutrition and Chronic Disease
Abstract: The objective of this proposal is to obtain funds for the training of PhD scientists committed to academic careers in nutrition research and chronic disease prevention. The importance of training future researchers in these two areas follows from our increasing awareness that nutrition is an underlying pathogenic component of many chronic diseases. These include obesity, diabetes and its complications, non-alcoholic steatohepatitis (NASH), digestive diseases, chronic kidney disease (CKD), hepatic and colon cancer and cardiovascular disease. Although these disorders have traditionally been viewed as pathologies of the middle-aged and/or elderly, it is now clear that appropriate interventions for these conditions need to be initiated decades earlier in the life cycle. Interventions that can delay or prevent chronic disease(s) afford potentially profound public health benefit, both from reduced morbidity and mortality as well as from cost savings. A recent (2000) CDC study reported that obesity alone accounts for 9% ($180 billion) of national health care costs. The rationale for this proposal is based on the firm belief that nutrition is the most significant and tractable environmental factor that can be modified to prevent or delay chronic disease. This proposal therefore seeks funds to train the next generation of nutrition research investigators to address chronic disease prevention at the molecular, cellular, organismal and/or population levels. Support is requested for six predoctoral training slots for each of five years.

All trainees are first admitted to a graduate degree program at the Friedman School and, after one year of coursework, are eligible to be admitted to the Training Program. Acceptance into the Training Program is predicated upon outstanding academic and research achievement during the first year. Faculty preceptors on the Boston Health Sciences Campus, all members of Tufts University's Friedman School of Nutrition Science and Policy, will provide exemplary research training to predoctoral students interested in the broad research areas of obesity, diabetes, metabolism, digestive diseases, endocrinology, genomics and gene therapy, epidemiology, and diseases of the kidney and pancreas. Program administration and trainee supervision will be the responsibility of the Program Director and a Steering Committee, which will meet every 6 months to review and discuss trainee progress and program enrichment. We sincerely believe that the proposed Training Program is a true investment in both the scientific future of the trainees and the public health of this nation.

PI: Griffiths, Jeffrey
Title: Air Pollution and Respiratory Disease Traineeship
Abstract: Acute respiratory infection (ARI) is responsible for 19% of all deaths worldwide among children less than five years old. Environmental factors such as air pollution have been hypothesized to increase the risk of incidence for ARI in young children. Malnutrition is also known to suppress the immune system that renders a child more susceptible to ARI. This five-year traineeship aims to link environmental pollutants, while controlling for host nutritional factors, to an overall increase in the incidence of respiratory diseases in Ecuadorian children. Air pollution in Quito, Ecuador will be closely monitored by the City of Quito and using mobile handheld monitors to allow a time-series and geographical analysis of respiratory disease in a cohort of children already enrolled in an NIH-funded study. These data will be used to statistically analyze adverse respiratory health outcomes in variably malnourished Ecuadorian children as it relates to air pollution. In addition, molecular and microbiologic analysis will establish a spectrum of pathogens that cause disease.

PI: Griffiths, Jeffrey
Title: Innovative Water and International Research Curricular
Abstract: This application proposes to support two interdisciplinary research curriculum objectives.

The first is to devise and implement a 'Water and Health' interdisciplinary course at Tufts University, which has recently started an interdisciplinary, all-University program focusing on drinking water. This program is a partnership of the Tufts University Schools of Arts and Sciences, Engineering, the Fletcher School of Law and Diplomacy, the School of Veterinary Medicine, and the School of Medicine. In order to meet the challenge of developing an integrated approach across disciplines to understand and solve global water issues, Tufts has launched the "Water: Systems, Science, and Society" PhD and MS Program. The purpose of the program is to provide the interdisciplinary tools and perspectives need to manage water-related problems. This program enjoys the highest level support at Tufts, including the participation of the President as a WSSS faculty member.

The second objective is to make concrete an internet based, interdisciplinary curricular linkage between Tufts' Graduate Program in Public Health, and specific East African centers of excellence in public health training and research. The PI has cultivated educational and research linkages at both the University and individual faculty level in East Africa since the fall of 2000 in pursuit of this objective. The purpose of this objective is to develop interdisciplinary shared courses or modules that will lend themselves to the teaching of research methods, and to the building of research networks.

PI: Harris, Susan
Title: Vitamin D, Glucose Control and Insulin Sensitivity in African-Americans
Abstract: Poor vitamin D status and type 2 diabetes mellitus (T2DM) are both more common among older blacks than whites, but it is uncertain whether the two are causally linked in that group. Although there is compelling evidence from a variety of study types that adequate vitamin D may reduce the risk for T2DM in whites, recent evidence from NHANES III demonstrated an association of vitamin D with diabetes in whites but notin blacks (Scragg 2004). This may reflect an adaptive response to low vitamin D levels among blacks (Harris 2006), but the central hypothesis of this proposal is that providing enough supplemental vitamin D to blacks (raising their blood levels higher than that of most in NHANES III) will improve blood measures related to diabetes risk. The proposed study is a 12-week randomized, double-blind, placebo-controlled experiment designed to examine the effect of vitamin D supplementation on glucose control and insulin sensitivity in non-diabetic black men and women. This study would be the first to examine the effect of vitamin D supplementation on intermediary variables related to T2DM in African-Americans given enough vitamin D to achieve what are hypothesized to be optimal blood levels of the vitamin.

Specific Aims:

Aim 1: To determine whether supplementation with 50 µg/d of vitamin D will improve glucose control and insulin secretion.

Hypothesis: Vitamin D supplementation for 12 weeks, compared with placebo, will, 1) reduce fasting plasma glucose, 2) during an oral glucose tolerance test, blunt the increase in 2-hour plasma glucose and increase the 30-minute ratio of serum insulin to plasma glucose and 3) reduce glycosolated hemoglobin.

Aim 2: To determine whether vitamin D supplementation for 12 weeks will improve insulin sensitivity.

Hypothesis: Vitamin D supplementation for 12 weeks, compared with placebo, will 1) reduce fasting serum insulin, 2) reduce C-peptide hormone, and 3) decrease the homeostasis model analysis insulin resistance index (HOMA-IR).

PI: Hashley, Jennifer
Title: Innovative Programs for Outreach and Training Opportunities to Develop New Farmer Enterprises for Socially and Disadvantaged Farmers
Abstract: The New Entry Sustainable Farming Project (NESFP) with its multiple partners has been assisting immigrants and refugees to develop commercial farming opportunities across Eastern Massachusetts. We run a four-year land-based program for beginning farmers combining outreach, training and technical assistance (T&TA), and assist other producers with farm planning, farm and financial management, production, marketing, employment links, farm jobs referrals and other outreach services. We will now expand to serve farm workers, interns, and other US-born socially disadvantaged constituencies, and adding several innovative program components. Our outreach will promote farming to wider audiences; and Explorer classes will provide farm planning and assessment opportunities. Employment and mentoring referrals will provide farmers hand-on experience that also pays wages. Connections to other T&TA opportunities will be encouraged. Training will expand to include both crops and animal husbandry courses and applied field experiences. To reach more farmers, we will develop easy-to-use online course and webcasts. Additional articles, guides, video clips, and weblinks to USDA and other service providers will be posted and widely promoted. Comprehensive hands-on technical assistance will be provided to program enrollees and more widely through a new email and telephone “Distance Assistance” service. A state-wide guide will add additional information about accessing and using multiple farm resources. Farmers will get help finding and securing farmland. Farm clusters will bring diverse farmers together to share experiences and problem solving. Guides to USDA and other farm services will be developed in readable Plain Language and some materials translated to Spanish. Results will be widely disseminated.

PI: Hassoun, Soha
Title: Multi-Resolution Partitioning and Kinetic Function Estimation for Dynamic Biochemical Network Model Development
Abstract: This interdisciplinary research investigates creating dynamic models of biological systems with predictive power that is beyond the capabilities of current generation of descriptive, static models. A biological system such as a cell can be conceptualized as a complex integrated network of biochemical reactions. Metabolic reactions are an important class of reactions performing essential cellular functions such as energy generation, biosynthesis, and harmful waste and byproduct elimination. Predictive models of cellular metabolism offer broad benefits as tools for both basic and applied research. In the context of public health, metabolic models can be used to integrate new laboratory and clinical data on drug efficacy, to compare healthy and diseased tissues, and to predict potentially harmful side effects of new drugs under development. Metabolic models also play an essential role in biotechnology as they enable the design and optimization of genetically engineered microbial cells that produce industrially useful bulk and value-added chemicals (e.g. biofuels).

This research focuses on two innovative modeling techniques for metabolic networks. The driving principle for both techniques is integration of structural and functional analyses. The first technique is multi-resolution structural modeling, which combines top-down modularization and bottom-up functional abstraction of individual reactions. The second technique compensates for incomplete information during mathematical modeling. This work investigates a co-estimation of reaction rate law functions and relevant parameters for each dominant reaction set while using noisy data for model calibration. The two modeling techniques and their associated algorithms are tested on experimental data collected from cultures of liver cells (hepatocytes), a representative and well-studied model system with biochemical complexity and relevance to public health. The modeling techniques obtained through this study feature generic aspects, e.g., mathematical abstraction of directed and time-varying interactions, which apply not only to metabolic networks but also other types of important biochemical (e.g., signaling, gene regulatory, etc.) networks.

PI: Hata, Akiko
Title: Role of BMPRII Mutants in the Pathogenesis of Pulmonary Hypertension
Abstract: Pulmonary hypertension (PH) is characterized by an increase in pulmonary vascular resistance that impedes ejection of blood by the right ventricle, leading to right ventricular failure. Primary PH (PPH) is a rare but progressive disease with a mortality of 30 percent over 4 years. Recently, germline mutations in bone morphogenetic protein receptor type II (BMPRII), a member of the transforming growth factor β (TGFβ) receptor family, have been found in over 50 percent of familial PPH patients and in 30 percent of sporadic cases of PPH. Mutations have been found in the extracellular, ligand binding, and cytoplasmic serine/threonine kinase domains, as well as the long carboxyl-terminal region (tail domain). The long-term objective of this application is to understand the molecular mechanism(s) by which BMPRII mutations contribute to the pathogenesis of pulmonary arterial hypertension. We found that BMPs promote, apoptotic cell death in normal human pulmonary artery smooth muscle cells (PASMCs). BMP-mediated apoptosis in PASMCs is associated with activation of caspases-3, -8, and -9, cytochrome c release, and downregulation of Bcl-2. PASMCs expressing mutant forms of BMPRII identified in PPH patients are resistant to BMP-mediated apoptosis. The specific hypothesis to be tested is that mutation(s) in the BMPRII disrupts BMP-mediated apoptosis in PASMCs, which is required for maintenance of normal cell number in the pulmonary vasculature. In Specific Aim 1, we will characterize the apoptotic-signaling pathway mediated by BMP7 in PASMCs. In Specific Aim 2, we will characterize the biological activities of BMPRII mutants found in PPH and generate transgenic mice expressing a BMPRII tail domain truncation mutant gene in smooth muscle to examine the role of this mutant BMPRII in vivo. We recently discovered that neuronal cell death-inducible putative kinase (NIPK) interacts with the tail domain of BMPRII in mammalian cells. NIPK contains a ser/thr kinase-like domain. Therefore in Specific Aim 3, we will focus on the functional role of the interaction between NIPK and the tail domain of BMPRII in the regulation of BMP-mediated signaling pathways. These studies will elucidate the mechanism of BMP-dependent apoptosis in PASMCs and the role of the tail domain of the BMPRII in the regulation of the BMP signaling pathway, which is of fundamental importance to understanding the molecular mechanisms underlying the pathogenesis of pulmonary hypertension.

PI: Hatini, Victor
Title: Cellular Interactions in Patterning and Morphogenesis
Abstract: During development, cell fates are established by signals that emanate from specialized "organizer" regions. How these signals direct cells to differentiate migrate, and alter their shape during development is a fundamental yet poorly understood question. The analysis of Hedgehog (Hh) and Wingless (Wg) signaling in Drosophila embryonic epidermis is contributing novel insights into these fundamental developmental problems. Preliminary work identified three conserved genes drumstick (drm), lines, and bowl. Their gene products interact physically to mediate patterning by the epidermal organizer. In imaginal discs, these gene products control epithelial morphogenesis by signals distinct from Hh and Wg.

Genetic and biochemical experiments suggest the following model to be tested in Aims 1 and 2: Lines targets Bowl for degradation via the ubiquitin-proteasome pathway; Drm inhibits Lines to shield Bowl from degradation; Drm accomplishes this function by localizing Lines to the cytoplasm. Specific Aim 1 is designed to test how Lines decreases the abundance of Bowl. A combination of genetic, molecular, and pharmacological approaches in cell culture and in vivo will link the activity of Lines to proteasomal, or non-proteasomal pathways. Specific Aim 2 is designed to test whether Drm localizes Lines to the cytoplasm to stabilize Bowl and whether Drm accomplishes this function by decreasing Lines-Bowl interaction.

Molecular genetic experiments suggest that Lines blocks epithelial folding in imaginal discs, whereas Drm inhibits Lines, and thereby activates Bowl, to initiate epithelial folding. Specific Aim 3 utilizes a combination of loss- and gain-of-function experiments in mosaic clones to test the model.

The proposed experiments will help explain how primary organizing signals direct cells to differentiate and alter their shape during development. Insight from this work may apply to vertebrate development where parallel pathways operate. In addition, the proposed experiments will provide essential insights into the regulation of the ubiquitin-proteasome system (or another proteolytic system) in a developmental setting. Insight from this work may suggest new strategies for reversing diseases that arise from constitutive degradation of key regulatory proteins.

PI: Haydon, Philip
Title: Reciprocal Signaling between Synapses and Astrocytes
Abstract:

Aim I: We will test the hypothesis that the diacylglycerol (DAG) arm of the phospholipase C (PLC) pathway is required to stimulate ATP release from astrocytes.

Aim II: Synaptically-stimulated release of purines from astrocytes causes a contrast enhancement between neighboring active and inactive synapses.

Aim III: Astrocyte-derived purines block the induction of LTP.

Aim IV: By integrating the level of neuronal activity astrocytes have anti-convulsant actions through their control of extracellular adenosine.

PI: Haydon, Philip
Title: Roles for Gliotransmission in Seizure-Related Disorder
Abstract:

Aim I: We will determine whether status epilepticus induces a change in the Ca²⁺ signaling, properties so that glial Ca²⁺ signals have a higher oscillation frequency and become a cell-wide process, rather than being restricted to local microdomains.

Aim II: We will determine whether the neuronal NR2B-containing NMDA receptor, which is known to couple to a cell death pathway, is selectively activated by this gliotransmission pathway during the period of enhanced Ca²⁺ excitability that follows status epilepticus.

Aim III: We will determine whether the enhanced Ca²⁺ signaling within astrocytes that follows seizures leads to enhanced glial glutamate release that excites neighboring pyramidal neurons through NR2B subunit-containing NMDA receptors.

PI: Haydon, Philip
Title: Purinergic Transmission Mediated by Astrocytes
Abstract: Astrocytes release a number of gliotransmitters which modulate the function and excitability of associated neurons. These include ATP and its derivative adenosine which act to depress neuronal activity. Increases in astrocytic intracellular calcium can be used as an indication of phospholipase C activity and ATP release. Preliminary evidence indicates that status epilepticus (SE) results in a prolonged increase in calcium excitability in cortical astrocytes that is temporally correlated with SE-induced neuronal death. I will use two-photon microscopy to ask if astrocytic calcium oscillations and wave propagation in the hippocampus are affected by SE. I will also use animals with impaired astrocytic ATP release to examine whether ATP released from astrocytes is necessary for in vivo hippocampal calcium wave propagation. These animals will also be used to determine if astrocytic ATP and adenosine can reduce the amount of SE-induced neuronal death in the hippocampus.

PI: Haydon, Philip
Title: Astrocyte Neuron Signaling
Abstract: During the past decade a growing body of evidence has accumulated to indicate that glial cells, and in particular astrocytes, play active roles in information processing (Haydon, 2001). Since astrocytes are juxtaposed with the capillaries and with end-feet on endothelia, and since astrocytic processes enwrap synaptic terminals, it is likely that astrocytes serve regulatory functions in controlling blood flow and synaptic transmission (Haydon, 2001; Raichle, 2001). We hypothesize that astrocytic calcium levels are the key integrative signal for the regulation of these two diverse functions. Specifically, we hypothesize that neuronal activity-induced astrocytic calcium signaling regulates: 1) the synthesis within the astrocyte of the vasodilator nitric oxide (NO), and 2) a feedback regulation of the synapse mediated by the calcium-dependent release of glutamate from astrocytes. Using calcium and nitric oxide imaging, confocal microscopy, electrophysiology, photolysis and adenovirus to overexpress SNARE protein fragments and G-protein-coupled receptors we will test four hypotheses:

1. Physiological calcium signaling in astrocytes stimulates nitric oxide production, which in turn regulates calcium homeostasis.
2. Neuronal activity causes the synthesis of nitric oxide in astrocytes.
3. SNARE proteins are essential for the release of glutamate from astrocytes.
4. The release of glutamate from astrocytes modulates synaptic transmission in hippocampal slices.

By performing these studies we will obtain new insights into the roles of astrocytes in the CNS. Since astrocytes can integrate neuronal inputs and release glutamate in response to elevated internal calcium, the demonstration of a role for astrocytes in the control of the synapse will change the way we view information processing in the nervous system.

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.

PI: Herbert, Jean
Title:  Osher Reentry Scholars Program (REAL Program)
Abstract: Since 1970, Tufts University has offered adults the opportunity to continue their undergraduate education. The Resumed Education for Adult Learners or R.E.A.L Program enables highly-motivated adults to earn an undergraduate degree at a selective, private institution. Instead of a separate or extension program for adults, R.E.A.L. students attend the same courses and earn the same degree as other Tufts undergraduates, and participate in every aspect of campus life — clubs, studying abroad, tutoring opportunities, internships and joining sports teams — while also receiving individual attention from admission to graduation to help meet their unique academic needs.

R.E.A.L. students are at least 24 years of age and have had various circumstances occur that caused their collegiate studies to be interrupted. Drug or alcohol problems; not mentally prepared for college right after high school; started working or got married (and started a family) right after high school; realization that promotions are out of reach without an undergraduate degree, or just didn’t have the financial means — whatever the reason — R.E.A.L. offers these students a second chance, especially when most selective colleges would not consider such candidates because of their earlier poor academic record. Many R.E.A.L. students have demonstrated success in community college. Others have an extensive career history, and great motivation to expand their knowledge. Realizing they can do well in academics, these students are now eager for a greater challenge that other four-year institutions do not offer. The admissions process ensures that all applicants to R.E.A.L. are evaluated on criteria relevant to their experience.

For R.E.A.L. students, the transition to college life can be exciting and frightening at the same time. Although all students are adjusting to college life the first semester, unlike traditional-age students, R.E.A.L. students do not have access to dorm mates, upper classmen and RAs to help them “find their way”. To assist students, a one-half credit seminar is taken the first semester which has two purposes: to serve as a support group, and to help students “learn the ropes” by bringing in guest speakers from various university areas to provide information on available resources in a quick and efficient way. Additionally, this seminar is held in dedicated space for R.E.A.L., which includes a conference room that also serves as a study area, a lounge, and a kitchen which encourages students to meet and support each other.

To ensure academic success, R.E.A.L. addresses the unique challenges our adult students face. One challenge for returning students is adjusting to the rapid pace of courses. Typically, students are used to handling 4 or 5 classes at a community college, in addition to working 20-40 hours a week. Because students must transition from a working/student life to a full-time student life, R.E.A.L. works with students to improve their study skills and time management. Also, because it was found that many students had to drop a class their first semester, R.E.A.L. instituted a policy that new students only take 3 classes. Of course, those students that can handle a full course load are encouraged to do so, and by the second semester all students maintain a full course schedule. However, having a reduced schedule the first semester makes it easier for students to adjust to the different classroom pace.

Another challenge for returning students is the classroom environment itself. Most students come from the community college setting which is very age diverse. Aside from feeling odd being the oldest student in the class, more often R.E.A.L. students are initially intimidated by the high intellect of their younger counterparts. Through the seminar, students are excited and challenged, not frustrated in class discussions. This reminds them why they selected Tufts — to find the intellectual curiosity in others that they themselves have. They enjoy and want to be challenged by faculty and other students. Integrating with the undergraduates creates a positive influence for every R.E.A.L. student to reach their full potential.

R.E.A.L. alumni play a crucial role in measuring the effectiveness of the program. After graduation, alumni are asked to evaluate the program and offer suggestions for improvements. This method has been very successful, resulting in several improvements to R.E.A.L. One such improvement involved the math requirement for a Tufts undergraduate degree. Although several R.E.A.L. students excel in math, most took low-level algebra for their Associate’s degree, and now find the demanding math classes difficult. R.E.A.L. responded by offering extra tutoring sessions in math. Now, all our students are successfully completing the math requirement when they first enroll. Another improvement was implementing wireless capabilities in the R.E.A.L. lounge area. Originally, this area was set up for only one computer, which was provided for students who couldn’t afford their own. Now, more and more students are coming with their own laptops requiring greater wireless capabilities.

Alumni narratives also provide an opportunity to identify areas for improvement. Additionally, they clearly demonstrate how grateful students are for the opportunity and how their lives have been affected by having an undergraduate degree.

PI: Herman, Ira
Title: Initiation of Tumor Angiogenesis: A Role for Cancer Stem Cells?
Abstract: Currently, controversy exists regarding the derivation of the tumor microvasculature. One theory holds that the endothelial cells present within tumors originate from local capillaries, which are beckoned to the incipient tumor via diffusible factors or microniche created by the tumor-derived cells. Another theory states that the tumor vasculature is derived, in part, from bone marrow-derived endothelial progenitor cells (EPC), which are mobilized to the peripheral circulation and take up residence within the remodeling tumor microvasculature. However, the presence of these bone marrow-derived EPC within tumor microvessels has not been conclusively established, leaving the regulatory role that such a progenitor cell population could play in orchestrating the initiation or progression tumor angiogenesis equivocal. Interestingly, it has been recently revealed and preliminary data presented indicate that some populations of cancer stem cells express CD133, which is also vascular endothelial surface marker. CD133, which is expressed and present on EPC is also expressed on bone marrow-derived EPC, together with the cell surface marker, CD34. Based on these recently published findings and preliminary data presented, here, we postulate that the local tissue microenvironment, including the cancer stem cell niche, itself, induces the in situ formation of endothelial progenitor cells directly from CD133+ cancer stem cells. Further, we hypothesize that these EPC derived from CD133+ cancer stem cells elaborate an endothelial progenitor population that initiates tumor angiogenesis and enables integration with the host’s microvasculature, therein sustaining cancer cell and tumor progression. Consistent with this hypothesis are findings that normal neural stem cells can differentiation into vascular endothelial cells.

To directly test whether CD133+ cancer stem cells are vasculogenic, i.e. able to induce and/or initiate tumor angiogenesis, we will carry out pilot studies to establish whether CD133+ cancer stem cells from glioblastomas are able to directly give rise to endothelial progenitors and capillary endothelial cells in vitro. Using well characterized populations and established methods, we will interrogate whether glioblastoma-derived cancer stem cells, which have been previously shown to express the EPC surface marker CD133, can acquire an endothelial phenotype and give rise to the de novo formation of an integrated tumor microcirculation. Further, we will take advantage of our long standing experience and expertise in angiogenesis-related research to establish whether known angiogenic inducers and novel angiogenesis-inducing peptides produced in the Herman lab foster the in situ differentiation of cancer stem cells directly into endothelial progenitors. Results of this exploratory pilot project will not only help to elucidate the molecular and cellular mechanisms governing the initiation of tumor angiogenesis, but successful outcomes will provide important new insights that will likely give rise to the paradigm-shifting realization that cancer stem cells, themselves, elicit and elaborate a tumor microvasculature required for tumor progression in vivo.

PI: Hess, Andrew
Title: The Fletcher School - United Arab Emirates International Relations Training Program
Abstract: The Fletcher School International Relations Training Program will develop an innovative multi-disciplinary curriculum that will prepare participants for the political, economic, and security demands of today’s international relations environment.

To compete in the globalized world of the 21st century, it is crucial to understand the complex and dynamic processes of change, navigate multicultural environments, and manage enterprises across cultures and among diverse organizations. Increasingly, individuals working in foreign affairs and the military need to possess a nuanced understanding of international organizations, both governmental and nongovernmental, and implement policies across disciplines. The senior officials participating in the Fletcher School Training Program will be trained in developing a global perspective required to interact and operate in an environment characterized by international organizations and issues.

The Fletcher School’s multidisciplinary approach will impart a nuanced understanding of the security, political, economic, cultural and technological pressures that continue to shape the world. As part of this multi-disciplinary approach to international relations, the Fletcher School Training Program will incorporate workshops, training seminars and, where appropriate, field trips to move beyond the academic understanding of the classroom into the practical day-to-day skills and cultural competence that a diplomatic training demands. These workshops may include trainings in: Public Speaking, Media Relations, and Multilateral Mediation. These training exercises will allow participants to interact in seminars with policy makers, experience first hand the functioning of international organizations and institutions and, most importantly, to apply and test their recently acquired classroom knowledge to a real world setting.

PI: Hibberd, Patricia
Title: Improving the Quality of Care for the Treatment of Childhood Pneumonia
Abstract: Tufts University School of Medicine and the Indira Gandhi Government Medical College Nagpur, India, affiliated with Lata Medical Research Foundation, are proposing to expand their longstanding multidisciplinary collaboration and partnership in the study of childhood pneumonia and are applying to participate in the Global Network for Women's and Children's Health Research. The goal of this participation is to improve scientific knowledge and outcomes in neonates and young children and to expand capacity and infrastructure in the research unit at Nagpur, India. Their proposal for the Global Network application focuses on childhood pneumonia. Every year, at least 2 million children under age 5 die of pneumonia - more than the number of children who die of AIDS, malaria and measles combined. Mortality is highest in children who are hypoxemic or infected with HIV, where mortality rates are as high as 80%. Hypoxemia has long been recognized as an important predictor of mortality and poor outcome in childhood pneumonia. The World Health Organization's case-management strategy uses woefully inadequate clinical signs to detect hypoxemia, missing about 30% of children who are hypoxemic. These children do not receive much needed oxygen therapy and bear the brunt of adverse outcomes. Investment in pulse oximetry to detect hypoxemia in rural and district hospitals worldwide has not occurred, partly because no clinical trial has been conducted to determine whether access to pulse oximetry is either life-saving or cost-effective. We propose that Global Network sites conduct a cluster randomized trial to evaluate whether access to pulse oximetry and training providers in its use to guide oxygen therapy decreases treatment failure and mortality in children with pneumonia. The study will be conducted in rural hospitals that currently have no access to pulse oximetry. We will assess whether this approach is cost effective. We will also determine the microbiologic predictors of treatment failure and mortality in the eras of HIV infection and increasing antimicrobial resistance, as the etiology of pneumonia in the community setting in developing countries has not been studied since the 1980s. Introduction of pulse oximetry is a simple, easy to use, inexpensive and highly relevant technology that has the potential to improve outcomes, in a sustainable way, for one of the most pressing global health problems - childhood pneumonia.

PI: Hollander, Justin
Title: EMPTIED OUT: Strategic Planning Research to Assist Congregation Beth Israel in Understanding and Responding to Declining Community Membership
Abstract: Malden has been home to Congregation Beth Israel for over one-hundred years. The community’s membership has grown and declined in that time. Unlike other older, established communities in inner-suburban/urban areas, Beth Israel has worked remarkably hard in the past few years to grow. It appears that a series of incentives, programming, and outreach has generated some growth in the community. But, that growth has not met the expectations of the congregation.

In this project, we propose to study the wider trends in Orthodox Jewish community building and growth throughout the Northeast, look closely at other Boston-area communities, and perform an assessment of Beth Israel’s efforts to date. As a result of this research, we will be able to make a series of recommendations to help Beth Israel chart a path forward.

PI: Hollander, Justin
Title: Acton Community Visualization Study
Abstract: This is a collaborative project between the Department of Urban and Environmental Policy and Planning (UEP) at Tufts and the Town of Acton to assess, design, and execute effective strategies for educating citizens about their planning options. Faced with regional development pressures, Acton citizenry stands to benefit from visualizing the various paths the town could take in the near future. Tufts faculty and students have the background and training to help craft community visualizations that help citizens understand what can otherwise be the rather abstract arcane language of planning. This project will support one second-year graduate student at UEP to work closely with the Town, while conducting the work necessary for a Master’s thesis.

UEP has a strong track record of working with communities, with results to show for it. Just last year, Professor Hollander and a team of four students conducted a community outreach, visualization, planning, and design study for a vacant lot in Salem, Massachusetts which received a national student project award from the American Institute of Certified Planners. The report they produced helped the City of Salem obtain a $474,000 grant from the state, and $200,000 from the EPA. This proposed effort could also bolster future Town of Acton efforts to obtain external funding for community outreach and planning efforts.

Approach
Under the supervision of Professor Hollander, a graduate student in the Department of Urban and Environmental Policy and Planning will support the Town of Acton’s computer visualization efforts. The student will work closely with Town officials in devising an applied research project that will benefit ongoing efforts to enhance citizen education about planning options. Professor Hollander and the graduate student will leverage existing resources at Tufts University to explore the potential for improving land use planning in Acton through the use of three-dimensional, online, virtual worlds. Just this year Tufts established a National Science Foundation funded Center for Scientific Visualization whose main feature is a 4 foot by 8 foot high-resolution display wall. The display wall has capabilities for three-dimensional viewing and could be used to help Acton residents virtually walk-through a variety of land use planning growth scenarios.

PI: Huber, Brigitte
Title: HERV-K18 as a Risk Factor for CFIDS
Abstract: The etiology of Chronic Fatigue Syndrome (CFS) is far from understood and is likely due to multiple genetic components. Infection with EBV and treatment with IFN-α have been implicated in the pathogenesis. Our laboratory has shown that EBV-infection, and exogenous IFN-α, activate transcription of the env gene of a Human Endogenous Retrovirus, HERV-K18. This provirus is normally silent, but when induced it encodes a superantigen (SAg), which is a class of proteins that is capable of deregulating the immune system. Three alleles of HERV-K18 env have been documented, K18.1, K18.2, K18.3, whose gene products have SAg activity, but are predicted to differ biochemically and functionally. Our working hypothesis is that HERV-K18 is a risk factor for CFS. In a pilot study, the allele and genotype distributions of the HERV-K18 env gene were compared between various groups of CFS patients and healthy controls. Although only a limited number of samples were available in the various cohorts, the odds ratios that were obtained were statistically significant. The most intriguing interpretation of these data are that they provide genetic evidence for the unique etiology of at least one group of CFS patients. Thus, it may be possible to delineate different subtypes of CFS, depending on the clinical history of the patients. It is now proposed to substantiate these pilot results, using a much larger cohort of 400 CFS patients associated with EBV that has been assembled by the co-investigator, Dr. Renee Taylor. Dr. Ben Katz, board certified in both Pediatrics and Pediatric Infectious Diseases, will clinically evaluate the patient cohort, and Dr. Inga Peter, a genetic epidemiologist and biostatistician, will oversee the statistical analyses. In addition, the expression pattern of the HERV-K18 SAg during active disease versus intermission will be measured. Furthermore, T cell stimulatory activity of this SAg, expressed on peripheral blood lymphocytes of patients during the course of the disease, will be tested ex vivo, using a T cell hybridoma reporter assay that has been developed in our lab. Since SAg-activated T cells produce massive quantities of chemokines, lymphokines and neurokines, the expression of the HERV-K18 SAg could influence not only the immune system, but other organs as well. A positive association between CFS and either HERV-K18 alleles or expression patterns would open new avenues for the development of clinical treatments of this chronic disease.

PI: Imanishi-Kari, Thereza
Title: The Effect of Innate Immunity on B Cell Tolerance 
Abstract: Autoreactive B cells first encounter antigen in the bone marrow. The result of this encounter can be receptor editing, clonal deletion or anergy. Purified immature B cells undergo apoptosis in response to BCR crosslinking. However, when such B cells are in the presence of BM cells, they respond to BCR crosslinking by expressing Rag genes, a precursor to receptor editing, rather than by dying. This emphasizes the importance of the bone marrow microenvironment to normal tolerance induction. We propose that in autoimmune-prone mice, features of the BM environment actually subvert normal tolerance mechanisms by inducing the activation, expansion, and differentiation to antibody forming cells, of nucleic acid-specific autoreactive B cells.

In order to test our hypothesis we will use a novel site-directed BCR transgenic mouse line developed in our lab. This line, which we call 564 Igi, contains the rearranged heavy and light chain genes (VDJ and VJ) of an autoreactive hybridoma, 564, targeted respectively to the endogenous J_H and Jk loci. The 564 hybridoma in Elisa assays is reactive with ssRNA, ssDNA, and DNA/histone complexes. In our recent published results, we have found in the 564 Igi systems that 564+ B cells, although anergic by multiple criteria can be synergistically activated to proliferate in vitro by simultaneous coengagement of BCR and TLR7. Class switched 564 antibodies are found in the sera of 564 Igi mice and by 13 months of age 564-containing immune deposits and pathology are seen in the kidney.

The following specific aims are proposed in this research proposal:

1. Determine the molecular mechanisms by which autoreactive B cells are activated, induced to proliferate and secrete autoantibodies.
2. To determine what are the differences between autoimmune and normal autoreactive B cells and
3. To determine what are the roles of TLRs 7, 8 and 9 and the effects of type 1 IFN on the in vivo proliferation, survival and autoantibody secretion by 564Igi autoreactive B cells wild type and autoimmune background.

Understanding how, where and when B cells are activated and break down tolerance to self antigens are important for the development of new approaches to treat many chronic autoimmune diseases.                                 

PI: Isberg, Ralph
Title: Molecular Basis of Yersinia-Host Cell Interaction
Abstract: The long-term objective of these studies is to determine how an enteropathogenic bacterium is able to enter within host cells and to evaluate the role of mammalian cell receptors in promoting uptake. As a model system, Yersinia pseudotuberculosis is being studied in order to gain detailed information on the function of bacterial- and host-encoded internalization factors. Specifically, Y. pseudotuberculosis invasin-integrin interaction will be studied, and host-encoded factors that modulate receptor-mediated bacterial internalization will be identified. Uptake promoted by invasin depends upon high affinity binding to its receptors, regulated by the concentration of receptor available to participate in uptake. To further investigate the molecular mechanism of uptake, the following experiments will be performed:

1. A model for the binding of a single invasin molecule to multiple host receptors will be tested, by analyzing the subunit structure of invasin and determining the stoichiometry of invasin-receptor interaction;
2. the region of the integrin heterodimer involved in invasin binding will be determined by performing two novel mutant selection for altered receptor interaction;
3. the role in bacterial uptake of the beta-1 integrin will be investigated by analyzing the binding of mammalian cell cytoplasmic components to hybrid protein harboring this domain;
4. functional studies on the role of mammalian cytoplasmic components will be performed using a newly-developed perforated cell assay, allowing evaluation of the biological roles of factors identified in other Aims; and
5. the role of invasin in intestinal infections will be analyzed, using invasin mutations resulting in partially functional proteins.

Bacterial uptake by host cells is a common step in establishing disease by a number of bacterial pathogens. Investigation of this process will result in important information on how enteric diseases are initiated, and provide a potential source for the development of new chemotherapies that block this step in the infection process. In addition, identification of the components that allow a simple organism to enter an animal cell could result in new techniques to introduce therapeutic agents that would otherwise not be able to enter the host cell.

PI: Isberg, Ralph
Title: Molecular Analysis of Microbial Pathogens
Abstract: This application requests support for continuation of a rigorous predoctoral training Program that focuses on the molecular analysis of microbial pathogens. The Program is interdepartmental and is centered around the Department of Molecular Biology and Microbiology, with members being drawn from the Departments of Biochemistry, Medicine, Infectious Diseases, and Pathology. All investigators have either a common interest in pathogenic microorganisms, restriction of pathogens in cell or animal models, in basic processes performed by such microorganisms, or have complementary expertise in molecular biology. 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. sporulation as model regulatory and pathogenic system;
4. protein secretion and the analysis of microbial surfaces, including those of pathogenic bacteria and yeast; and
5. regulation of gene expression and cell growth in microbial model systems;
6. analysis of developmental stages in fungal pathogens;
7. mouse models of innate 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, with 20% of the students being members of underrepresented minority groups, as defined by NIH guidelines. The overwhelming majority of the 140 Ph.D. graduates of the Department since 1964 are currently employed in research positions in academics and industry, with approximately 50% of the graduates who have finished postdoctoral training currently holding 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. All faculty members of the Program have individual NIH grants or other forms of support. The application is for 5 years, with 5 predoctoral trainees requested for each of years 01-05.

PI: Islam, Shafiqul
Title: Variations and Trends in Fall Precipitation Over the Central United States: Issues of Physical Mechanisms, Circulations Anomalies and Boundary Forcing
Abstract: There is a broad consensus among climate models that a warming world will lead to a drier climate over most of the subtropical United States. Yet, observational evidence suggests that total precipitation and stream flow have increased across the United States over the last several decades with the largest increases generally observed in fall across the central United States. Identification of origins for the observed precipitation trends may be complicated by an apparent fall dry bias in current climate models. Most coupled climate models significantly underestimate precipitation over the Mississippi basin during fall, limiting our ability to skillfully predict future changes in precipitation or attribute the recently observed trends to anthropogenic origins. This apparent inconsistency between observed trends in fall precipitation and the dry bias in climate models motivates the Principal Investigators (PIs) to better understand and identify the dominant mechanisms that produce trends and variations in fall precipitation.

The relationship between atmospheric circulations and surface climate over the United States in winter and summer has been the subject of many observational and modeling studies. Relatively little attention has been paid to fall precipitation, limiting our knowledge of the space-time variations and predictability of fall climate. A key goal of this research is to understand the long-term trend and the decadal variability of fall precipitation over the central United States. To achieve this goal, the PIs will focus on three broad questions:

1. What mechanisms are important to produce trends and decadal variations in fall precipitation across the central United States and how well are they represented in current generation climate models?
2. In what ways and why these mechanisms are particularly dominant in fall and not in other seasons?
3. Can the physical linkages between decadal variations in fall precipitation and Pacific or Atlantic Sea Surface Temperature (SST) be identified?

The PIs will begin by expanding their ongoing observational data analyses and existing results from the literature to further establish the associational link among fall precipitation variations, circulation anomalies, and boundary forcing. Then, they will attempt to identify possible physical mechanisms that can explain the observed correlation and associational links. A main outcome of this research will be a better understanding and identification of the dominant atmospheric processes responsible for the spatially coherent trends and decadal variations in fall precipitation and how they differ from other seasons.

This research would address questions related to origin and nature of fall precipitation variability and trends at the seasonal, inter-annual, and decadal time scales. Most of the existing studies consider precipitation variations in winter and summer seasons only. The fall transition season was not considered separately in any of the future climate change assessments, such as those by the Fourth Assessment Report of the Intergovernmental Panels on Climate Change (IPCC). Results from this research will provide new insight on why a large increase in precipitation is primarily observed in the central United States in fall and why current climate models are unable to capture this trend.

This collaborative partnership between the Tufts University and Columbia University builds on mutually synergistic expertise in water cycle research, atmospheric dynamics, and hydrology. This partnership will be further strengthened through co-advising of PhD students and involvement of undergraduate students through summer internships. The PIs will integrate findings from this research to develop an interactive multimedia education module on Precipitation Variations over the United States to be used as a three-week teaching instrument for our dual-level (senior undergraduates and first year graduate students) course on Environmental Signal Processing. They will present their results in national conferences and archival journals and publish their findings in diverse media formats so they will be readily available to journalists, teachers and the general public.

PI: Islam, Shafiqul
Title: Collaborative Research: A Precipitation Dipole in Eastern North America: Issues of Space-Time Variability and Physical Mechanisms
Abstract: Recent studies suggest that precipitation over Eastern North America (ENA) exhibits a dipole pattern of wet and dry conditions between the central United States and eastern Canada, with particular prominence at decadal timescales and considerable contribution to local trends, but which is largely erased in the usual calculations of area-averaged trends. The associated trend toward increased Central US precipitation is not well reproduced in current models and is contrary to the usual expectations of drying in the continental interior with a warmer climate. Decreasing precipitation over eastern Canada is also contrary to model projections of generally wetter conditions nearer the coasts. Several fundamental questions have yet to be addressed: What are the underlying dynamics and key physical mechanisms? How closely is it related to large-scale climate variability? What processes are setting the decadal timescale?

The goals of this project are to determine the underlying dynamics of the dipole pattern and its connections to large-scale climate variability and trends. The three primary objectives of the proposed work are to: 1) determine the timescales, seasonality, and structure of the dipole pattern, 2) examine the dynamics of the precipitation changes in terms of the hydrologic budget, moisture transport, and storm track variability, and 3) use a hierarchy of models to investigate the influence of large-scale variability on the dipole mode. To investigate the underlying mechanisms, we will test a set of hypotheses on the local forcing of the precipitation via moisture flux and thermodynamically-forced vertical velocity, and on the large-scale controls on the regional circulation via both baroclinic and barotropic response to tropical convection.

We will expand our observational data analyses to establish and clarify the link among precipitation variations, circulation anomalies, and boundary forcing that may create a precipitation dipole over ENA. We will then investigate the links to large-scale climate variability and tropical forcing. This is perhaps one of the first attempts to understand and characterize the existence of a precipitation dipole over ENA. Our methodology — which builds on our ongoing and previous work — was briefly tested and some preliminary results are presented in the proposal. We will conduct observational analysis of a range of hydrologic and atmospheric variables to determine the structure of the seasonal and spatial pattern. We will analyze the observed hydrologic budget, moisture transport, shifts in the storm tracks, and transient-mean flow interaction to investigate the internal dynamics of the dipole, using both simple compositing and pattern-based analysis techniques such as Principal Component Analysis. We will use multiple estimates of precipitation and atmospheric circulation to alleviate known data quality issues. For dynamical investigations, we will use a range of models of increasing complexity: a global barotropic (one-layer) model linearized about a zonally-varying mean flow, a tropical Gill-Matsuno model with generalized heating, and the NCAR Community Atmospheric Model, which we have modified to allow imposition of convective anomalies.

This collaborative project between the Tufts University and University of Massachusetts builds on mutually synergistic expertise in water cycle research, atmospheric dynamics, and hydrology. This partnership will be further expanded through co-mentoring of a post doctoral fellow, PhD students and involvement of undergraduate and high school students through summer internships. The proposed research addresses several important scientific questions, including the dynamics of large-scale atmospheric influences on hydrology, mechanisms of hydrologic variability at decadal and longer timescales, and trend attribution over different regions of ENA. There is also considerable societal relevance: understanding these regional changes in precipitation and their long-term variations has important implications on how, and to what extent, long-term variations in precipitation over ENA can be predicted and managed. The results are also relevant to agriculture (e.g., winter wheat) and, potentially, to water trade with Canada and increased terrestrial carbon fluxes to stream.

PI: Jackson, Rob
Title: TUSM/T–NEMC Center Core for Neuroscience Research
Abstract: This application requests funds to establish a NINDS Center Core to augment the research capabilities of NINDS and other neuroscience investigators at Tufts School of Medicine (TUSM) and the affiliated medical center Tufts–New England Medical Center (T–NEMC). Within the research labs of TUSM and T–NEMC, there are 17 NINDS-funded research projects, spanning most areas of contemporary neuroscience research. Most of our Tufts NINDS investigators are members of the Sadder School Graduate Neuroscience Training Program, a highly collaborative group of 28 neuroscientists from TUSM and T–NEMC. This is a rapidly evolving program that includes 6 new neuroscience departmental faculty and a total of 12 new TUSM or T–NEMC neuroscientists hired within the last 6 years. Due to the rapid growth of our program, we have become concerned with providing adequate research core facilities to neuroscience investigators, and have held planning meetings to determine the need for additional or expanded core facilities. The award of NINDS Center Core funds will permit us to integrate faculty and research facilities from TUSM and T–NEMC, with the primary intent of providing needed services to NINDS investigators. A related goal is to foster collaborative research among the large collection of NINDS investigators at TUSM and T–NEMC. Importantly, the TUSM/T–NEMC NINDS cores will be available to other investigators at TUSM, T–NEMC, and Tufts University. The establishment of these cores is greatly aided by the expressed support of Tufts University, TUSM, and T-NEMC, who are providing assistance, funds and space for the establishment of a NINDS Center Core. The administration of the new center core will be based in the TUSM Department of Neuroscience. Supervision for the center core will be provided by the P.I., Dr. F. Rob Jackson, and an advisory committee including core directors and outside scientists with relevant expertise.

PI: Jacob, Robert
Title: HCC: Human-Computer Interaction and Brain Measurement Using fNIR Spectroscopy
Abstract: There has been much previous research in the general area of brain-computer interfaces (BCI), which has primarily aimed to help people with severe motor disabilities interact with their environment by translating their brain activity into specific device control signals. Users who are completely paralyzed ("locked-in") or those who lack muscle control (e.g., people with cerebral palsy or stroke victims) can use BCIs to answer simple questions, to control their environment, and for word processing. But the variety of brain imaging techniques that have been tried to date for BCIs have all suffered from serious drawbacks, so that communicating through such systems is currently time consuming and mentally demanding. Open research challenges concern the accuracy of BCIs (systems often misinterpret a user's intentions), and the information transfer rate of such systems (which is often too slow for use in real world settings). In this project, the PIs will build on their experience in designing, implementing, and evaluating non-command, adaptive user interfaces (e.g., based on eye movement), to advance BCI by bringing to bear emerging technology for measuring brain activity using functional near infrared (fNIR) spectroscopy coupled with machine learning to analyze user data in human-computer interaction. While fNIR technology is still in its infancy, the PIs expect its use as a real-time input to an adaptive interface to break new ground. The PIs believes that this combination will also lead to new, more objective methods for evaluating next generation interaction styles for BCI in general. The PIs' approach is a natural extension of and will exploit their prior work relating to the concept of reality-based interaction, which focuses on the ways that new interaction styles exploit the user's pre-existing skills and expectations from the real world more than trained computer skills, while at the same time helping to differentiate mental effort devoted to interface-related or syntactic aspects from that devoted to the underlying task or semantic aspects.
This project will develop technologies of immediate benefit to users with motor disabilities. Additionally, the work will open up a new area of BCI research (namely, relating to interfaces that can dynamically adapt in real time to the user's cognitive load), and will advance the theory and evaluation of interaction styles in general.

PI: Jacques, Paul
Title: Cardioprotective Effects of Dietary Flavonoids in the Framingham Offspring Cohort
Abstract: There is a great deal of controversy about the potential effects of food flavonoids on cardiovascular disease risk. This is, in part, a consequence of the absence, until recently, of a complete food flavonoid database and the potential for differential effects of the various classes of flavonoids. Some epidemiological evidence of cardiovascular disease risk reduction is available for the flavanol class (including catechins and flavanones). Epidemiological evidence is available, though variable, for the flavone, flavonol and isoflavone classes whereas associations between the anthocyanins and cardiovascular risk have not been investigated. The goal of the present study is to further our understanding of the role of dietary flavonoids in cardiovascular disease by examining the relation between intake of the different flavonoid classes and various intermediate markers of cardiovascular disease. Specifically, we will examine the associations between five classes of dietary flavonoids (flavanols, anthocyanins, flavones, flavonols, and isoflavones) and the following CVD risk factors: inflammatory markers including C-reactive protein, interleukin 6, monocyte chemoattractant protein-1, and tumor necrosis factor—alpha; fibrinolytic factors including fibrinogen and P-selectin; lipids including high density lipoprotein cholesterol, low density lipoprotein cholesterol, total cholesterol, and triglycerides; endothelial function by assessed by flow mediated dilation (brachial artery reactivity); and blood pressure. Our hypothesis is that a higher intake of the flavanol class of flavonoids (which includes the catechins, proanthocyanidins, and flavanones) is associated with a healthier profile of intermediate markers of cardiovascular disease risk. In contrast to the flavanols, intakes of other classes of flavonoids (anthocyanins, flavones, flavonols, and isoflavonoids) are not expected to be as strongly associated with lower CVD risk as indicated by intermediate biomarkers. We plan to examine this hypothesis using previously collected and measured data from the seventh examination of Framingham Heart Study Offspring Cohort. Working with the Framingham investigators, we will link an enhanced and updated flavonoid database to dietary information collected with a food frequency questionnaire. Amounts of each food flavonoid will be entered in a database for each item on the questionnaire. The extended database will allow more complete assessment of flavonoid intakes than has previously been possible. It should be noted that the study investigators have extensive experience with addition of flavonoids to other food frequency questionnaires, and therefore we anticipate no problems in accomplishing this. The proposed project presents an efficient and effective means to examine the potential relationship between flavonoids and cardiovascular disease risk.

PI: Jacques, Paul
Title: Disparate Effects of Vitamin E on CVD Events in Persons with and without CVD
Abstract: Several large observational cohort studies have shown protective associations between vitamin B supplements and cardiovascular disease. Randomized trials have so far failed to show significant protective effects on CVD risk, but most of these trials have been conducted in participants with pre-existing vascular disease. The controversy has further been rekindled by two studies that have been published last year that reported increased risk of all-cause mortality (from CVD and cancer) and congestive heart failure (CHF) in individuals taking high-dosage vitamin E supplements. Again, the majority of subjects included in these trials had pre-existing chronic diseases. No conclusions can be drawn from these studies with regard to the effect of vitamin B supplementation in individuals without preexisting CVD. In addition, none of the above mentioned intervention studies analyzed gamma-tocopherol, a common form of vitamin E in the American diet, with regard to vascular or CHF risk. Supplementation with alpha-tocopherol, which is the major form of vitamin E used in supplements, reduces plasma gamma-tocopherol levels. It is important to study the effects of both forms of tocopherol because some recent in vitro and animal studies suggest that gamma-tocopherol has high antioxidant and anti-inflammatory properties.

The objectives of the proposed project therefore are to investigate [1] whether vitamin E supplementation is associated with increased risk for CVD, in subjects with and without preexisting CVD; and specifically to evaluate effect modification by prevalent CVD status; and [2] examining the interrelations of gamma- and alpha-tocopherol status with respect to CVD and CHF risk.

For this, we propose to analyze data from participants from the Framingham Heart Study examination cycle 20 and from the Offspring examination cycle 5. The aims based on plasma alpha- and gamma-tocopherol will be limited to a subset of over 1000 participants from examination 20 of the original cohort. We propose to examine the following hypotheses:

1. Vitamin E supplement use is associated with an increased risk of death and CVD in participants with prevalent CVD, but not in individuals without prevalent CVD;
2. Plasma alpha- and gamma-tocopherol levels will interact with each other in respect to CVD risk such that with high alpha tocopherol levels in the presence of low gamma-tocopherol levels will be associated with increased risk of death and CVD in participants with prevalent CVD, but not in individuals free of prevalent CVD;
3. Vitamin B supplement use is associated with increased LV mass internal dimensions and wall thickness in participants free of MI and CHF;
4. Plasma alpha and gamma tocopherol levels will interact with each other in respect to LV function and structure such that with high alpha tocopherol levels in the presence of low gamma-tocopherol levels will be associated with increased LV mass, increased LV internal dimensions and increased LV wall thickness in participants free of myocardial infarction and CHF.
5. Subjects’ health status modifies the cross-sectional relation between vitamin E supplement use and plasma α- and γ-tocopherol levels.

This project will help to clarify the role of vitamin E in development and progression of cardiovascular disease, and to identify the basis for differing results derived from the observational studies and intervention trials examining the relation of vitamin E and CVD. Our findings will allow for a better understanding of the function of dietary antioxidants in development of CVD, the major age-related chronic disease among Americans.

PI: Jay, Daniel
Title: Inhibiting Surface HSP90 to Limit Metastasis
Abstract: The vast majority of breast cancer-related deaths are due to secondary tumors after metastasis. There is currently no effective therapy to limit metastasis. Our long term objective is to develop new therapies that reduce cancer invasion, a critical first step in metastasis. This proposal is based on our observations that a novel extracellular form of the molecular chaperone hsp90a is required for cancer invasion by the activation of the matrix metalloproteinase MMP2. Hsp90 has been implicated in cancer and hsp90 inhibitors with anti-tumor activity are currently in clinical trials. These drugs may be problematic in that they interfere with the many intracellular functions of hsp90. Our findings suggest our main hypothesis that inhibiting extracellular hsp90a will decrease invasion and thus limit metastasis. This presents an opportunity for novel anti-cancer therapy by inhibiting invasion without interfering with the myriad intracellular functions of hsp90. To support this idea, we will address three specific aims. We will determine the mechanism of how hsp90a functions on the outside of cancer cells (Aim 1). We will then use this information to develop and test extracellular hsp90 inhibitors (Aim 2). We already have one impermeant hsp90 inhibitor in hand and several candidates for neutralizing single chain antibodies from our collaborators at NCI and Xerion Pharmaceuticals. Finally, we will test the best of these inhibitors of extracellular hsp90a for their ability to limit metastasis in a new model developed by our collaborators at Tufts using human breast cancer cells metastasizing to human bone explants in immunocompromised mice (Aim 3). Thus, these experiments take us from an initial discovery of hsp90a function with cell-based assays to in vivo animal models taking an interdisciplinary approach to address a key issue of human health: limiting metastasis to improve breast cancer prognosis. These studies aim to expedite the translation of our basic research into a potential therapy. If successful, the proposed work would provide data for developing future clinical studies and thus impact human health.

PI: Jay, Daniel
Title: Proteome Signatures and Target Validation in Lymphomas
Abstract: To address tumor diversity and their varied responses to chemotherapy, we require the ability to custom design treatment for each tumor. The goal of pharmacogenomics is to generate gene expression signatures for tissue using microarrays that are then correlated with prognosis or response to therapeutics. However, much of the complexity and diversity of response may be due to proteomic differences. Thus far, probing for proteomic diversity and linking this to therapeutic efficacy has been difficult. Our overall goals are to develop surface proteome signatures (SPS) and perform functional proteomic target validation analysis directly on primary tumor tissue. There is a great need to assess the efficacy of different chemotherapy combinations directly on patient tissue samples. A major difficulty is this respect is our inability to assess the small amounts of primary tumor tissue available from patient-derived samples. As part of our previous IMAT-funded research, we developed a library of single chain (scFv) phage display antibodies that recognize approximately 500 components of the surface proteome. In this work we also developed high-throughput methods for immunocytochemistry (ICC) using scFvs and apoptosis assays that use small number of cells (<500) per assay. Together, these developments allow us to generate SPS and measure apoptosis after chemotherapy treatment using small amounts of primary tumor tissue. Cells will be tested with a battery of drugs alone and in combination and analyzed for apoptosis. Thus, a differential response to therapeutics will be correlated with a SPS. We will develop and test these assays in the R21 phase using thymic lymphoma mouse cell lines derived from three mouse models: transgenic MyrAkt and two genetic deletions, PTEN-/+ or p53-/-. This is an ideal model system, as the primary tumors are genetically defined by single oncogenic mutations. We will establish SPS for cell lines derived from thymic lymphoma lines from these mice. We will test for the efficacy of different drug regimens to obtain the optimum combination for inducing apoptosis of the cells. We will then test these drug combinations in primary tumor tissue from MyrAkt mice. We will also address the causal link between SPS and drug response and will test the functional role of scFvs that are biomarker candidates. In the R33 phase we will test the predicted optimal drug regimen on thymic lymphomas in the three mouse models, examining tumor load and survival. We will also characterize ten of the scFvs as potential biomarkers or targets for drug discovery. Our studies complement pharmacogenomics and provide a novel route to pharmacoproteomics.

PI: Joseph, Paul
Title: Documenting Local Justice
Abstract: For the past twenty-two years, Northern Uganda has endured a civil war between the Government and the Lord’s Resistance Army (LRA). In 2003, UN Undersecretary General for Humanitarian Affairs Jan Egeland described the conflict as “the biggest forgotten, neglected humanitarian emergency in the world.” 1.9 million people were displaced by the conflict, which was characterized by child soldiers, abduction, and the frequent use of rape. A ceasefire was finally reached in 2006 and peace talks have steadily moved forward in Juba, Sudan ever since.

Though the International Criminal Court indicted five of the top LRA commanders, the overwhelming majority of ex-combatants and abductees will return to their communities under the government’s amnesty program. Reintegrating former fighters into their communities is crucial if the region is to heal, move forward, and achieve a sustainable peace. There has been much discussion about which justice and peace-building mechanisms can best achieve this reconciliation. Currently, local practices are being ignored and local involvement in the process is minimal.

Mato Oput and Kayo Cuk are restorative justice processes used by two of the ethnic groups deeply affected by the conflict, the Acholi and the Langi respectively. Both processes are based on a protracted period of conflict mediation, culminating in a ritual ceremony that involves the perpetrator’s confession and compensation to the victim. Acholi and Langi religious, political and cultural leaders advocate for the use of Mato Oput and Kayo Cuk as justice approaches that resonate within communities and promote grassroots reconciliation. However, there is no written record of the use of such processes for war-related crimes. Thus, there continues to be confusion and skepticism both within the international community and Ugandan society about the effectiveness and legitimacy of the two processes.

Prominent political leader Norbert Mao suggested that the students could provide a needed service in Uganda by creating a casebook of how Mato Oput and Kayo Cuk rituals have been used for war-related crimes. Prime Minister Olwitingol emphasized the value of multimedia documentation. Our personal goal is to document fifty rituals over the course of the summer, compiling them into a formal casebook. We will then present hard copies of the casebook to the “Civil Society Organizations for Peace in Northern Uganda” (CSOPNU), the district governments and other key stakeholders in the transitional justice process. We will also film, photograph and audio-record the ceremonies and interviews with key stakeholders, when appropriate and after receiving consent. CSOPNU, for example, as a coalition of civil society organizations in Northern Uganda, can use our casebook as an advocacy tool. The multimedia presentation will go to cultural leaders, NGOs, community-based organizations, and the heads of clans. As the transitional justice process in Northern Uganda moves forward, the casebook along with the multimedia documentation will be helpful to these actors as they try to build sustainable peace in their communities.

Through the casebook, we believe that we can portray these reconciliation processes in an accessible format that makes sense to national and international stakeholders, and that demonstrates the nuances of the ceremony. We believe that peace begins with community involvement and agency. An inclusive reconciliation process that includes local conceptions of justice is crucial to the development of a sustainable peace. The casebook and multimedia presentation are locally relevant and will ideally increase understanding of and incorporation of the practices at the national and international level, while ideally helping to give war survivors a greater stake in the reconciliation process.

The in-field portion of the project will involve traveling to Gulu, Uganda for a period of ten weeks during the summer of 2008. Based on previous research, we currently have over one hundred confirmed contacts in Uganda as well as access to Gulu and Makerere University’s reference libraries, research assistants, translators, and technical legal assistance for the casebook portion of the project. Interviews and recorded oral recollections from survivors, perpetrators, and community leaders will be transcribed. In turn we will create a PDF version of the casebook available online through the Gulu District website as well as a hard copy of the book for the above-mentioned stakeholders. Another key element in making this project successful is the empowerment of local community members. One of the participants has previously established contacts in Gulu and Makerere Universities, which will allow for collaboration with Ugandan students, making this a team-based process. A primary goal is to ensure the project’s longevity through this collaboration. Media-training organizations, such as Barefoot Productions, who have a base in Lango, will ideally be a part of this as well.

The second phase of the project will be a multimedia presentation to be used for education, advocacy and awareness. The presentation will be based on the filming, photographing, and audio-recording of the reconciliation ceremonies and of Acholi and Langi voices describing their experiences with these ceremonies, gathered in a visually appealing format. We will share the presentation alongside a panel on transitional justice in Uganda scheduled to take place at Tufts University during the fall of 2008. We will seek guidance from Tufts faculty involved in transitional justice in identifying international stakeholders with whom we can also share this presentation. It will also be used in a student taught “Explorations Course” on transitional justice that one of the applicants intends to co-teach during the Fall Semester of 2008. Student activism groups, such as Pangea, can use it for awareness projects. Finally, we will also show our multimedia presentation in the Boston area through a connection with Project: Think Differently, an organization dedicated to social change and awareness through supporting relevant music, film, and other forms of media.

PI: Joyner, Valencia
Title: BRIGE: Multi-Spectral, High-Frequency Imaging Sensors for Frequency-Domain Biomedical Imaging
Abstract: The proposed research and educational efforts focus on the development and application of a new class of image sensor architectures with transformative effects on biomedical optical diagnostics. The aim is to further advance the field of near-infrared spectroscopy by developing miniaturized, multi-spectral, imaging sensors with pixel-level RF detection and signal processing. The proposed work will improve image resolution, reduce acquisition time, and enable portability of frequency-domain diffuse optical tomography (FD-DOT) systems. A mixed-mode design methodology for high-sensitivity optical imaging sensors optimized for phase-sensitive detection of RF-modulated optical signals will be explored. The optical and electrical performance of photodetector structures in nanometer-scale VLSI technologies will be evaluated with an emphasis on the affect of new high-k dielectric materials and metal layer stacking on photoresponse.

The resulting research will have broader impacts in many areas, including medical optical diagnostics, high-performance image sensor technology, and the semiconductor industry workforce. A central focus of the proposed activities is to broaden opportunities to students from underrepresented groups and engage students at all levels in interdisciplinary research and integrated circuit design training. A summer enrichment program will be launched, incorporating IC CAD tool training, coursework, a team-based research project, and visits to labs/companies in the greater Boston area. There is a strong mentoring and training component for students at all levels.

PI: Joyner, Valencia
Title: Collaborative Research: 3D Integrated Imaging Receivers for 10-Gb/s Free Space Optical MIMO
Abstract: The objective of this research is to create a new class of power-efficient imaging photoreceivers to reach an aggregated data rate of 50 gigabits per second and beyond for broadband wireless optical communication. The approach is to develop a large array of planar tessellated photodetectors with a rate of 10 gigabits per second per pixel. The array includes diversity selection circuits, which are implemented using an optical multi-input/multi-output configuration.

With respect to intellectual merit, this project addresses two well-known challenges in optical wireless communication, channel scintillation and optical beam alignment. The research explores power-efficient InGaAs metal-semiconductor-metal photodetectors that are integrated with silicon integrated circuits for multifunctional operation (decision, amplification, and computing), and the implementation of multi-input/multi-output architectures for signal processing of massive amounts of data. This research is expected to augment the body of knowledge on carrier drift characteristics in the photodetectors at low voltage bias and the physics of complex three-dimensional optoelectronic device structures. This research also explores heterogeneous integration of compound semiconductor device on silicon circuits using three-dimensional wafer bonding for photoreceiver applications.

With respect to broader impacts, the research has the potential to benefit a variety of applications, including wireless networks with reduced security vulnerabilities, networks able to transfer high-resolution digital images in the midst of equipment sensitive to electromagnetic interference in healthcare settings; and optical interconnects in large-scale data centers. A cross-university curriculum is addressed, covering multi-disciplinary topics in information theory, system-level design, analog circuits, device physics, fabrication and integration. Various programs are used to recruit students from underrepresented groups. K-12 outreach efforts are coordinated through the Tufts Center for Engineering Educational Outreach.

PI: Kaplan, David
Title: Bone Regeneration via Silk Biomaterials
Abstract: Critical sized bone defects caused by injury, disease or congenital malformations, remain a challenging problem in orthopedic medicine. Current options to restore full function to such bone defects are limited due to slow rates of regeneration of native bone tissue, second site morbidity, poor mechanical stability and lack of integration with surrounding tissues depending on the mode of clinical repair utilized. New options to accelerate the rate and extent of new bone formation, as well as integration to surrounding tissues are needed to overcome current limitations. In this competitive renewal application, a novel silk protein matrix will be bioengineered to optimize these goals to achieve large defect bone regeneration. The proposed studies build off of the results from the current grant that demonstrated the unique and useful attributes of a silk fibroin protein 3D porous matrix for in vitro and in vivo bone regeneration. In the proposed research, our goal is to accelerate the rate and extent of bone formation and integration across the defect through the combined delivery of BMP-2 and VEGF in the 3D protein matrices, and to incorporate bioengineered peptide adhesives to promote interactions with adjacent parent bone. These enhanced, degradable and biocompatible 3D porous silk matrices functionalized with growth factors and adhesion capabilities will be studied in a rat critical sized femur defect model to optimize their design. Subsequent to optimization, in the final aim of the study, the implants will be assessed in a critical-size goat femur defect model. Our goal is to conclude the study with an optimized design for these new 3D porous protein matrices in order to pursue human clinical trials. Outcome assessments for the three aims will be based on mineral density, homogeneity of mineral distribution and mechanical integrity of the repairs in the small and then large animal critical sized defects. To achieve the goals, an interdisciplinary team of investigators has been assembled to address the challenges with expertise in biomaterial matrix design, stem cell biology, biomechanics, imaging and veterinary medicine.

PI: Kaplan, David
Title: Tissue Engineering Resource Center
Abstract: The field of tissue engineering has been propelled in recent years by advances in cell and molecular biology, biomaterials science and engineering and bioreactor design and function. With the resulting avalanche of information, the complexity of the interactions needed to achieve desired tissue outcomes in vitro to adequately address clinical needs in vivo represents a growing challenge. It is difficult for any one laboratory to deal with all of the scientific and technological issues involved. The proposed Tissue Engineering Resource Center (TERC) will integrate cell biology, biomaterials and bioreactor systems, built upon strong core knowledge in each of these areas, to provide a systems approach to the field of tissue engineering and the associated service to address laboratory and clinical challenges. The core research projects in the Center will focus on (1) stem/progenitor cells - stem cell biology characterization expansion differentiation, (2) bioinductive scaffolds - structurally and functionally tailored, and (3) advanced bioreactors - with enhanced environmental controls and a capability for nondestructive real time assessments. A unique Center will be established and hosted by an academic consortium led by Tufts University, MIT and the University of Toronto. The Center will couple the capabilities of these laboratories through a Core Service Lab operated at Tufts to provide outside researchers full access to the latest techniques integrated in one location to solve complex challenges in the field. The Service Core will focus on the integration of scaffolds, stem cells and complex reactors to achieve new fundamental insights for use in the field, targeted tissues for clinical needs, and general service to support investigators. The Center will also interface with and complement other Centers with relevant components in tissue engineering - such as the Imaging Center at Harvard-MGH and Biomaterials Center at the NIST. The Center will host a number of collaborations with other laboratories related to specific enhancements of the core projects, such as tissue engineering of human ligaments using transfected stem cells. Information on scientific and technological advancements will be actively communicated through workshops, courses, symposia and educational outreach by the core at Tufts with additional outreach through MIT and Toronto. The Service Core will also provide essential support to help new industries in the field move ahead in the current challenging economic climate.

PI: Kaplan, David
Title: Bioemulsifying Vaccine Delivery System for Immunomodulation
Abstract: In our recent studies we have demonstrated that the biopolymeric emulsifier, emulsan, possesses exciting potential with regard to dual function (direct emulsification and immunomodulation). In particular, a compelling set of features including structural tailorability, innate ability to carry proteins, easy and large scale synthesis, lack of toxicity (to the extent tested thus far), and strong indication of vaccine efficacy and immunomodulation prompt the plans in the present proposal. The structural features of these novel biopolymeric systems can be 'tailored' through a combination of physiological control and/or genetic engineering and we have demonstrated that alteration in structure of these bioemulsifiers directly relates to changes in solution properties (e.g., emulsification, surface tension) and biological function (e.g., macrophage activation such as TNF). In vivo, vaccine efficacy has been demonstrated in a number of animal studies including with a DNP-hapten carrier, Lyme and Yersinia. Based on these prior data, the hypothesis in this proposal is that structural variants of these microbial exopolysaccharides can provide new insight into our understanding of mechanistic features of the polymer interactions with the innate immune system and lead to the identification of promising candidate vaccine adjuvants. These data would lead to new and more effective vaccine adjuvants, an area of strong clinical need. The unique and powerful dual function of emulsification properties of these polymers combined with strong structural tailorability, suggests that new and useful functional adjuvants can be obtained. The studies planned will focus on biological preparation and assessment of these bioemulsifiers. An interdisciplinary team of scientists with expertise in biopolymer engineering, immunology and disease models, will conduct the proposed studies and has also been involved in the collection of the Preliminary Data. The specific aims include:

1. Synthesis and characterization of emulsan structural variants.
2. Assessments of innate immune recognition of the structural variants.
3. Assessment of the variants in an in vivo vaccine disease model based on the utilization of emulsan with a recombinant Yersinia pseudotuberculosis vaccine to induce protective immunity in a murine disease model.
4. The efficacy of emulsans in intranasal delivery of the vaccine formulation.

The proposed studies will provide a solid foundation upon which to correlate emulsan structure and cellular responses leading to specific levels and types of immunological activities. Furthermore, lead adjuvant candidates will result from the study in preparation for formulation studies and clinical trials in future work.

PI: Kaplan, David
Title: Developing Biomaterial Scaffolds that Delay Senescence in Mesenchymal Stem Cells
Abstract: Adult mesenchymal stem cells (MSCs) offer enormous potential for regenerative therapies, but occur in low frequency in bone marrow, lack the ability to continuously divide under traditional ex vivo tissue expansion methods and eventually lose their differentiation potential. These factors limit the clinical efficacy of MSC therapies. The most promising approach to extend the expansion potential of MSCs in vitro is the cultivation of cells on extracellular matrix (ECM) proteins, where integrin-ligand binding between cells and the ECM are known to activate cellular processes such as proliferation, differentiation, and survival. Our objectives are to translate what is known about the role of ECM/MSC interactions in the aging process into a new generation of scaffold designs containing the appropriate chemical signals and physical features capable of regulating stem cell behavior. For this work, silk fibroin proteins will be used as a biomaterial scaffold onto which a variety of signaling molecules will be incorporated. Specific targets include cell adhesion peptides derived from collagen, and factors that activate telomerase to extend telomeres during cell division thus prolonging the life span of the cell. The chemical signaling identity and density of the peptide displays on the 3D silk scaffolds will be optimized independently in order to decouple and isolate the effects on aging of MSCs. In depth chemical and physical characterization of these modified scaffolds, and the morphology, growth rate, differentiation potential, and production of ECM proteins by the MSCs expanded on these modified 3D scaffolds will be studied and quantified along with appropriate controls. Osteogenic markers of MSCs expanded on these scaffolds will be monitored and compared to ascribe changes in cell behavior to the matrix composition. The goal of developing cell culture scaffolds that can delay senescence of MSCs to prolong their proliferative lifetimes would allow for long-term expansion of the cells ex vivo, enabling clinical use of MSCs in a broad range of cell therapies and tissue-engineered devices.

PI: Kaplan, David
Title: Biosensor Devices to Monitor Water and Food Quality
Abstract: The focus is to develop low cost biosensors for food and water assessment by exploiting raw materials easily accessible in India, upon which the biosensors will be generated. The technology is derived from nanopatterning and novel processing of silk proteins into optically clear films to generate the base materials upon which antibodies or other receptors can be immobilized via facile methods, to functionalize the silk platform for selective purposes to environmental contamination in water or food. The optical features of the silk films will provide for direct readout of contaminants.

PI: Kaplan, David
Title: New Biomaterials for Cornea Replacement
Abstract: Corneal damage causes significant vision loss in the general world population, second only to cataracts. Corneal replacement is a developing technology that is rapidly becoming a necessity for many patients. Many of the reasons for corneal replacement therapies include scarring from disease (e.g., herpes infection) or complications from LASIK; hereditary problems (e.g., Fuch's disease) and complications from other surgeries (e.g., cataracts). Current strategies employed for corneal grafting make use of allogenic or synthetic materials. These strategies are only partially effective, however, and may stimulate host immune responses that result in tissue rejection. In addition, there is the potential for transfer of diseases from unhealthy donor organs. These issues are compounded by the growing use of corrective eye surgery which renders corneas unsuitable for grafting which will further impact the availability of acceptable allogenic supplies. A cornea replacement that alleviates these issues would be a clinically important advance, and this is the goal of the present exploratory proposal (R21). The hypothesis is that a unique protein-biomaterial system based on silk fibroin can be bioengineered to match cornea functional requirements in combination with cornea-specific cells, to thus serve as a cornea replacement. The proposed system will exploit the novel material features of silk fibroin that include: slow degradation, biocompatibility, full optical transparency and mechanical durability for handling, suturing and ocular pressure requirements. The research team has the required background with silk material designs to meet the material performance requirements and the experience with the cornea cell biology to characterize the material-cell interactions outlined in this project. We will: (Aim #1) prepare and characterize the required protein films and assess cornea cell interactions (both rabbit and human) with these materials, and (Aim #2) assess a system concept that will mimic the native cornea in terms of a lamellar structure incorporating rabbit fibroblast, epithelial and endothelial cells with their appropriate extracellular matrix deposition. The outcome of this effort will be initial cornea designs to move forward into an R01 for animal studies related to cornea replacements. An interdisciplinary team has been assembled to meet the challenges and all of the required analytical tools are in place to address the experimental scope. A cornea tissue system that slowly degrades to allow for host native tissue replacement would offer a significant advancement in corneal transplantation technology. An R21 mechanism is proposed as this is a new exploratory initiative, building upon a solid foundation of prior research in both laboratories, but towards an entirely new tissue construct with new challenges and complexities. Corneal damage causes significant vision loss in the general world population; it is second only to cataracts. There is a need to develop a readily available corneal tissue supply for transplantation in both the US and the rest of the world to meet the challenge of combating this prevalent form of vision loss. A unique protein-biomaterial system constructed from silk fibroin and cornea-specific cells can be bioengineered to serve as a total cornea replacement. The proposed system will exploit the novel biomaterial features of silk fibroin to produce a readily available supply of corneal tissue that will meet, or exceed, the biocompatibility and material properties of current allogenic transplant tissue.

PI: Kaufman, Gretchen
Title: Dog Sterilization/Vaccination Program at IAAS, Nepal
Abstract: The Nepal Dog Sterilization and Rabies Control Project is now in its 4th year of funding from the Elinor Paterson Baker Foundation. In these 4 years we have successfully established a surgical facility at the Institute of Agriculture and Animal Science (IAAS) School of Veterinary Medicine; provided training and support for 2 veterinary surgeons and animal care staff; enabled the development of an active and comprehensive canine surgical curriculum for Nepalese veterinary students; and helped to institute a community based dog sterilization and rabies control program in Chitwan (in full operation for 2 years). 73 veterinary students have passed through the program to date. 363 dogs have been sterilized, 777 dogs have been vaccinated, and 8 communities have been impacted. This program has gained recognition by government and international agencies working in Nepal as a key partner in the country-wide effort to control rabies and improve the health of people and dogs in Nepal. This has been achieved despite the incredible challenges created by political turmoil and instability and through a sometimes violent and uncertain evolution towards democracy for one of the poorest countries in the world.

The IAAS program is graduating Nepalese veterinarians with a comprehensive understanding of and the necessary skills for humane dog population control and rabies prevention. The surgical facilities built through this program have broadened students opportunities for small animal and ruminant surgical experience to include not only spay and castration but also gastrotomy, enterotomy, and caesarian section. Graduates are using their newly developed skills and knowledge all over the country. In addition the program has significantly strengthened the mission of the Veterinary School and has led to stronger relationships with surrounding communities. Renewed support from the Elinor Patterson Baker Foundation will continue the efforts of Tufts University, the IAAS Veterinary School, and the Humane Society of the United States, to support humane dog population control and rabies prevention in Nepal.

PI: Kehayias, Joseph
Title: Assessment of Energy Intake in Free-Living Subjects Using Stable Isotopes
Abstract: Obesity is a problem of energy balance. When energy expenditure does not keep up with intake, then adipose tissue accumulates to excess levels. Modern tools are available for monitoring two of the three components of the energy equation: body composition and energy expenditure. Energy intake, however, is still evaluated by standard self-report questionnaires on food intake. The questionnaire-based tools are useful in providing data on dietary patterns, but can be inaccurate and biased especially for overweight individuals who may underreport their energy intake.

The purpose of the proposed exploratory research is to develop a practical tool that can measure average energy intake in free-living adults. In this proposal we present evidence that simple monitoring of isotope clearance in breath CO₂ can provide quantitative information on fat, protein and carbohydrate intake. Our approach includes both mathematical modeling and clinical validation. The mathematical model will simulate the kinetics of C-13 labeled fatty acid as a function of fat, protein and carbohydrate intake, body composition, and energy expenditure. A dose of C-13 labeled fatty acid is followed by C-13 detection in breath for several days. Work with a preliminary computer simulation model indicates that fat and protein intake have different and predictable effects on the shape of the C-13 elimination curve. The detailed kinetic parameters of the isotope clearance will be measured experimentally. A second experiment will test the hypothesis that the C-13/C-12 ratio in breath after dosing with C-13 labeled fatty acid is an index of total fuel intake, by using a total body carbon pool model and dosing with every meal. The outcome of this research will be a fully developed stable-isotope-based tool to serve energy balance studies by evaluating energy intake. If successful, it will become for energy intake what doubly labeled water is today for energy expenditure.

PI: Kirshen, Paul
Title: Dairy Farm Management Practices for the Control of Cryptosporidium in Surface Waters
Abstract: This project examines the link between dairy farm practices and environmental management strategies to varying surface water loads of Cryptosporidium parvum (CP) and associated health risks in downstream communities. The hypothesis is that agricultural practices and environmental management strategies significantly affect surface water levels of CP and partially determine risk of exposure in downstream communities. The Merrimack River provides an excellent opportunity to research CP by virtue of its proximity to upstream dairy farms, its contribution to municipal drinking water in downstream communities, and prior research detecting CP both in the river and in the downstream community of Lowell, Massachusetts.

PI: Kumamoto, Carol
Title: Intestinal Colonization by C. albicans and Enteric Bacteria
Abstract: Oropharyngeal candidiasis (OPC), a common opportunistic infection in AIDS patients, is believed to arise from Candida albicans organisms that were apparently benignly colonizing the patient. Commensal C. albicans organisms typically colonize the GI tract and female vagina, and to some extent the oral cavity or the skin. In an immunocompromised host, commensal colonizers undergo a conversion to invasive pathogens that are capable of causing a wide spectrum of diseases. Although commensal C. albicans is thus important as the source of pathogenic organisms, little is known about the nature of commensal colonization and the factors that control it. The research proposed in this application seeks to understand C. albicans activities that are important during colonization and the effect of C. albicans colonization on host physiology.

The first specific aim of the proposed research is to study the effects of C. albicans mutations on the ability of mutants to colonize. In the second specific aim, the hypothesis that colonization with C. albicans results in increased host susceptibility to bacterial infection will be tested. Because of the high incidence of OPC in AIDS patients, it is likely that AIDS patients are frequently colonized by C. albicans. In addition, studies in mice indicate the T cells are important in limiting the population size of C. albicans in the intestinal tract. Therefore, it is likely that AIDS patients are colonized to high level by C. albicans. The hypothesized increase in susceptibility to bacterial infection caused by C. albicans colonization may thus contribute to the susceptibility of AIDS patients to diarrheal disease. When a patient develops candidiasis, the organisms responsible for the infection are organisms that were previously carried in the patient's body without causing disease. Although there are many studies that have examined the events that occur during disease, few studies have focused on learning about the growth of the organism before disease arises. The goal of this research project is to understand what the organism does to colonize the host and to understand how colonization affects the health of the host with particular emphasis on its influence on the course of infection by enteric pathogens.

PI: Kumamoto, Carol
Title: Oligofructose Utilization in Streptococcus Pneumoniae
Abstract:  

Specific Aim 1: Identify and locate inulinase activity in S. pneumoniae.

Hypothesis: Growth on inulin induces inulinase activity that is localized to the cell wall.

Experimental Approach: To test for inulinase activity in S. pneumoniae, cells will be grown in semi-defined minimal medium supplemented with either 0.5% inulin or 0.2% glucose as a non-inducing control. Inulinase activity will be detected by running whole cell lysates on a zymogram in which inulin is partially dissolved in the polyacrylamide mix prior to casting a native gel. After separation of proteins by electrophoresis, the gel will be incubated at 37°C to allow inulinase to hydrolyze the substrate. Enzymatic activity within lanes will be detected as a violet band after staining the gel with both 2,3,5-triphenyltetrazolium chloride and coomassie brilliant blue as described previously (Gabriel and Wang, 1968). To determine the subcellular location of inulinase activity, S. pneumoniae will be separated into cell wall, membrane and cytoplasm fractions and analyzed by zymogram as described above.

Predicted Results and Interpretations: Cells are expected to grow in both inulin and glucose, as indicated by increased turbidity over time. In the zymogram experiments, any violet band in the gel will indicate inulin breakdown and therefore inulinase activity. We predict that inulinase activity in S. pneumoniae is only induced in the presence of inulin and therefore a violet band(s) is expected in whole cell lysates from cells grown in inulin but not in cells grown in glucose. We further predict that inulinase activity in the gel will be seen in the cell wall fraction and perhaps the membrane fraction, but not the cytoplasmic fraction. Such a surface localization would be favorable to hydrolysis of host inulin prior to uptake of the hydrolysis products. If inulinase activity is detected in cells grown on inalin and glucose, then inulinase may be constitutively expressed. If no inulinasc activity is detected in the whole cell lysates or subcellular fractions, then the zymogram assay conditions (e.g., buffer composition and pH) may need to be optimized.

Specific Aim 2: Identify inulinase and transport proteins required for growth in inulin.

Hypothesis: Several cell wall and membrane protein mutations will limit cell growth in inulin Proteins identified will have detectable inulinase activity and transport activity, respectively.

Experimental Approach: Random mutations in S. pneumoniae will be made using a mariner-based transposon system as described previously (Akerley et al., 1998) and screened for mutants unable to grow on inulin. We will pick 9,600 colonies into duplicate 96-well plates, one plate with inulin and the other with glucose as carbon source. Wild type and susH colonies will be included as positive and negative controls, respectively. The plates will be incubated and screened for lack of growth on inulin but not glucose. Identified mutants will be complemented in irons to confirm the role of the mutated gene.

Predicted Results and Interpretations: Any mutants that do not grow normally in inulin represent genes that are essential or that play roles in inulin growth; growth curves will indicate the extent of the growth defect. We expect to identify both the surface inulinase and transport system for the inulin hydrolysis products. If we identify only susH as a candidate inulinase, then it is possible SusH is present both within the cytoplasm and on the cell surface, as has been observed for some glycolytic enzynics (Kolberg et al., 2006). In this case, we would epitope tag SusH and test for surface localization by Western blotting the cell wall fraction.

Identifying and characterizing inulinase activity and associated transport proteins that are required for growth in inulin will further our understanding of how S. pneumoniae utilize oligofructose sources. Our findings may lead to an understanding of how these bacteria acquire a major carbon source during colonization of the nasopharynx and lung.

PI: Kumar, Krishna
Title: Protein Design Using Unnatural Amino Acids
Abstract: Membrane proteins make up roughly a third of the human proteome and are over represented in drug targets. The broad long-term goal of this project is to be able to specify and control structure of membrane soluble protein components so that they can be used in therapeutic intervention. Soluble proteins display a bipartite architecture with hydrophilic exteriors and hydrophobic interiors. We have introduced a novel binary patterning scheme for use in membrane environments by use of highly fluorinated amino acids. The work proposed here will focus on understanding fundamental energetics of the interaction of fluorinated amino acids in model systems followed by detailed characterization in aqueous solution. Fluorinated amino acids will also be used to modulate the bioactivity and stability of antimicrobial and therapeutic peptides. Furthermore, designed transmembrane peptides that associate in micelles and phospholipid vesicles will be thermodynamically characterized using disulfide exchange assays and tested for their specificity in choosing binding partners. The information gleaned from the above studies will be used to create ion channel and pore forming bundles within membranes. These assemblies will be further studied using biophysical techniques. The design and characterization studies proposed here should facilitate the construction of membrane transport agents and also allow for activation (or) inhibition of therapeutically relevant membrane embedded proteins.

PI: Kumar, Krishna
Title: Acquisition of a 500 MHz NMR Spectrometer
Abstract: The NMR spectrometer will enable research by a diverse group of researchers in the chemical and biological sciences ranging from characterization of organometallic/protein complexes and cellulose polymers, to the analysis of non-natural fluorinated peptides and post-translational modifications of proteins that direct supramolecular self-assembly.

Nuclear Magnetic Resonance (NMR) spectroscopy is one of the most powerful tools available to chemists for the elucidation of the structure of molecules. It is used to identify unknown substances, to characterize specific arrangements of atoms within molecules, and to study the dynamics of interactions between molecules in solution. Access to state-of-the-art NMR spectrometers is essential to chemists who are carrying out frontier research. The results from these NMR studies will have an impact in synthetic organic/inorganic chemistry and biochemistry.

PI: Kuperwasser, Charlotte
Title: Elucidating the Origins of Breast Cancer Heterogeneity
Abstract: Breast cancer remains a deadly disease for American women, with over 200,000 new diagnoses of invasive cancer and over 40,000 deaths each year. Over the past two decades, enormous strides have been made in understanding the genetic and molecular defects in breast cells that result in cancerous behavior. While these findings are most illustrative, they fail to explain how the different types of breast cancer seen in the clinic arise. Breast cancers can be categorized into five classes based on their molecular profiles, with these profiles correlating with different patient outcomes. The poor understanding of factors that contribute to the formation of different breast tumor types and thus, different patient outcomes, has hindered the development of useful targeted therapies, especially for highly aggressive cancers such as basal-type ER-/PR-/Her2- tumors, where current therapies have limited effectiveness.

Studies of blood cancers provide strong evidence that the heterogeneity observed in leukemias is due in part to the differences in the cell types that acquire mutations along the development of the blood lineage. This understanding of the cellular origins of leukemia is in part responsible for the rapid development of treatments for this disease has been more rapid than with solid tumors. In contrast, for breast cancer, it is not known how the cell type of origin, and/or the genetic mutations contributes to the development of the various types of cancer that are encountered in the clinic. Therefore, understanding the cellular origins of the various types of breast cancers is critical for the accelerated development of treatments for this disease.

When cells from established or engineered breast cancer cell lines are introduced into immunocompromised mice, they usually form tumors that bear little resemblance to the breast cancers encountered in the oncology clinic. Thus, many of these tumors are constituted largely if not exclusively by the malignant breast cancer cells. In contrast, microscopic examinations of actual human breast cancers reveals that these tumors are actually highly complex tissues composed of a number of distinct types of cells, with the carcinoma cells constituting only one of these many cell types. We have developed a novel mouse model that allows us to re-create normal and malignant human breast tissues. With this model system, we have created different stages of human breast cancer development, including hyperplasia, carcinoma in situ, and invasive human breast carcinomas, which resemble actual primary breast cancers seen in patients both genetically and biologically. Using this model system, we propose to determine if breast cancer heterogeneity is due to the nature of the breast cell types which acquire mutations. To this end, we propose to determine if different breast cell types, which-contain the same mutated genes cause different types of breast cancers comma and whether this also accounts for the differences in metastatic potential. This research will give us new insights into how breast tumor sub-types arise and will potentially provide a new model system to study the formation of aggressive cancers. In the long term this work may provide the foundation for developing diagnostic markers for earlier detection of breast cancer and identifying new drug targets for tumors that are resistant to current treatments.