PI: Maffini, Maricel
Title: The Role of the Stroma in Carcinogenesis
Abstract:  Mammary gland (MG) tumor susceptibility to the carcinogen N-nitrosomethylurea (NMU) varies considerably among rat strains. Wistar-Furth (WF) rats are highly susceptible, whereas Copenhagen (COP) rats are resistant. Although the initial pre-neoplastic changes in the epithelium of both rat strains are similar, in COP rats the lesions disappear prematurely and do not complete the neoplastic transformation. This process of “redifferentiation/normalization” occurs within 2 months of NMU exposure. Meanwhile, the same pre-neoplastic lesions develop in the WF rats and progress into tumors. No differences were found in proliferation or apoptosis rates, incidence of Ha-ras gene mutations, etc. that would explain such a different response to the same injury. Recently, using WF rats, we showed that non-exposed mammary epithelial cells (MEC) developed neoplasias when placed into NMU-exposed mammary stroma. In contrast, recombinants of non-exposed stroma and NMU-exposed MEC developed phenotypically normal ducts, suggesting damage to the stroma initiates the neoplastic transformation of non-exposed MEC. We hypothesize that the tumor-resistant phenotype in COP rats is due to the stroma ‘s ability to reverse the damage generated by the exposure to NMU through the “normalization” of stromal-epithelial interactions in their MGs. This hypothesis will be tested through two different approaches: (1) by recombining either the stroma or epithelium component of the tumor-resistant COP MG with either the epithelium or stroma of the tumor-susceptible WF rats. These recombinants will be introduced into an immunotolerant host such as the SCID mouse, and (2) by identifying which genes are differentially expressed in the MG stroma of either COP or WF rats exposed to NMU.

PI: Malamy, Michael
Title: Genetic Systems to Study Virulence in Bacteroides
Abstract: This study will focus on factors that allow the obligate anaerobe Bacteroides fragilis, although a component of the normal colonic microbiota, to be a successful pathogen. These include its ability to withstand an aerobic environment (aero-tolerance) during early stages of infection; the presence of systems to import heme into the cell for the heme-dependent pathways of central metabolism and defense against reactive oxygen species; the ability of B. fragilis to remove sialic acid residues from host components, and its virtuosity in obtaining nutrients for growth in vivo from complex oligosaccharides and glycoproteins. Specific aims include:
1) To continue to study factors that allow B. fragilis to withstand prolonged oxygen challenge (aerotolerance): We propose that activities in the B. fragilis periplasm serve as the initial line of defense to combat the formation of reactive oxygen species (ROS), protect sensitive targets from ROS challenges and to reverse ROS damage. In addition we have identified specific functions (superoxide dismutase, SOD), and an extensive gene cluster (the Bat operon) that are required for aerotolerance. We will test the hypothesis that the Bat operon forms a multi-protein complex in the cell membrane that plays an important role in exporting reducing potential from the cytoplasm to the periplasm.
2) Acquisition of iron and heme is important for B. fragilis growth in vitro and in vivo. We will study the process of heme uptake in B. fragilis by the heme permease systems whose genes and functions we have described We will also continue to study the heme-dependent, and Fe-S cluster-containing enzymes in the dual pathways of central metabolism to establish their roles in aerotolerance and in providing energy during oxygen challenge.
3) To investigate the composition, functions and control of operons for the acquisition of growth substrates from the infected host. We will focus on the operon containing the neuraminidase (nanH1) gene and several other glycohydrolases capable of converting the complex Lewis antigen found on the surface of many human cells to individual monosaccharides. We will continue to analyze the operon for NANA utilization, the NanLET operon and to define the sites in the three NanR repressed promoters for NanR binding. We will determine if neuraminidase is a virulence factor because it supplies NANA for growth, or because its activity alters the surface of host cells, or both.

PI: Mann, Anthony
Title: High Energy Physics at Tufts University
Abstract:  The main effort in the coming year will be to complete the analyses of our atmospheric neutrino data, our search for baryon instability, and our study of the cosmic ray sun shadow and its variation with the solar cycle. It is possible that the Soudan 2 detector (then to be known as THESEUS) will be turned back on at the time of the NuMI beam startup in late 2004. We think THE SEUS could provide valuable information to the MINOS project on possible 1 appearance effects; we would be active workers in the recommissioning of the Soudan 2 detector for that purpose. We propose to participate in the preliminary design work on possible future projects We are excited by the physics potentials of the NuMI off axis experiment, the future linear collider, and the UNO project. We intend that our participation in this preliminary work will enable us to contribute more effectively to the projects when they reach the development stage.

Two of our ongoing experiments, DONUT and E791, are in a phase of reduced activity at Tufts. We propose to continue some work on E791; in particular we will continue our search for the charmed baryon E.  With regard to MINOS, we are now well into the production and installation stage, and our group is participating in the development of analysis tools. The Tufts multiplexing-box assembly factory is operating efficiently and will complete its assignment of 225 such boxes early in 2003 In addition, we will be contributing to MINOS construction and assembly at the Soudan mine Should Fermilab approve a MINOS shield for atmospheric neutrino studies we will participate in its construction, whether it be a newly con structed scmtillator shield or the redeployment of the Soudan 2 proportional tube shield to the MINOS cavern.  During the next several years Colhder Run 2 at Fermilab will be in full gear, hopefully with much increased luminosity Our CDF group will fully participate in running the CDF detector and in the analysis of the new data We will continue our tf analysis using the Dahtz-Goldstein-Shwa statistical method of determining production rates and the top quark mass, we will also examine possible contributions of new physics to the tf production We intend to proceed with the search for the Higgs as well as supersymmetric particles. In addition, the study of B-meson physics and charm physics will be a priority.  The group plans to participate in work towards developing new ways to tag b-quarks by combining information from different taggers, possibly using neural nets or multivariate analysis We also intend to continue our activity in the CDF Avanced Analysis Group.  A major long term committment of the group for the period beyond MI NOS and CDF is the ATLAS experiment at LHC Prof Shwa has taken a leading role in the U S effort and will continue to chair the ATLAS/MONARC working group of the National Computing Board Simulations of the ATLAS distributed computing system will continue We have shown it may be possible to significantly improve the precision of the electroweak mixing angle from the asymmetry in leptonic Z decays and this work will also continue. We will also continue our work within the BMC on instrumentation contributions to the monitored drift tube production facilities.  The theoretical investigations into the phenomenology of top production and properties will continue, in particular the work on the incorporation of spin correlations to test Standard Model expectations and sharpen the determination of top quark mass. In addition we will continue to study the role of polarization and spin transfer in various fragmentation and production processes, and we will extend the study of hadronic contributions to the tensor charge of the nucleon.  We propose some modest improvements in our computing facilities to  meet the needs of the projects described above.

PI: Mazurana, Dyan
Title: Regional Gender and Generational Analysis of Armed Conflict, Peace and Justice Processes, and Disarmament, Demobilization, and Reintegration of Northern Uganda, Eastern Uganda, and Southern Uganda
Abstract:  The current research is a multi-year, regional, comparative study on the root causes and drivers of these armed conflicts. The study also examines the on-going peace and justice processes and the official and community-based disarmament, demobilization, and reintegration (DDR) programs and the shifts in livelihoods over the conflicts. The study is being conducted in Northern Uganda, Eastern Uganda, and Southern Sudan and will link up with current research underway by Tufts University in Darfur. The topics with the study are analyzed using a variety of perspectives to develop and enable a holistic understanding of the crises. In particular, we use gender and generational perspectives throughout the work, this includes paying attention to the roles, experiences, and voices of women and girls. In seeking more enduring solutions to peace and human security in countries and regions experiencing armed conflict, the United Nations Security Council Resolution 1325 and the United Nations Secretary-General Kofi Annan in his study Women, Peace and Security and subsequent Report called upon the Security Council and Member States to:  Identify and utilize local sources of information on the impact of armed conflict, and the impact of interventions — peacekeeping, peace-building, humanitarian operations, disarmament, demobilization and reintegration programmes, and reconstruction — on women and girls, and on the roles and contributions of women and girls in conflict situations, including through the establishment of regular contacts with women’s groups and networks.  These and other recent reports by the Secretary-General highlight the importance of research and gender analyses in developing better understanding of and responses to armed conflict, peace processes, and long-term peacebuilding. Indeed, in the present study, the use of gender and generational perspectives has already revealed aspects of the conflicts that have not been adequately addressed in the past. In addition, these perspectives should make important contributions towards best policy and practice for the key processes underway in the region, most notably, peace negotiations, disarmament, demobilization, and reintegration, transitional justice, protection efforts, reconciliation, conflict prevention, and strengthening sustainable livelihoods.

PI: McKeown, Nicola
Title: Carbohydrate Nutrition and Cardiovascular Disease: The Role of the Insulin Resistance Syndrome
Abstract:  The IRS currently affects an estimated 32 million adults in the United States. This syndrome not only contributes to the type 2 diabetes epidemic, but also atherosclerosis, endothelial dysfunction, and CVD. Recently, it has been found that individuals with this syndrome are at a three-fold greater risk of coronary heart disease (CHD) and stroke and a five-fold greater risk of CVD. The role of diet in the etiology of the IRS is poorly understood and limited to only a few observational studies. Pereira and colleagues recently reported that a high dairy intake was inversely associated with the IRS. Mennen and colleagues found that middle-aged men consuming more than 200g of bread per day had a 50% lower risk of developing this intermediate syndrome, compared to men eating less that 50g of bread per day. These findings, however, were not confirmed among women, and the authors could not differentiate between whole and refined grain breads. Our proposed study will be the first to examine several aspects of carbohydrate nutrition in relation to developing the IRS, rather than limiting diet associations to individual risk factors. As an outcome of the proposed investigation, we expect to determine which aspects of diet, related to the quality and quantity of carbohydrate intake, affect this intermediate syndrome. The research proposed in this investigation is significant because by identifying dietary patterns that can modulate the risk of the IRS and its sequelae, we will potentially reduce an individual’s risk of developing CVD.

PI: McMillan, Margaret
Title: HIV/AIDS, Health Behavior, and the Income Gradient: Evidence from South Africa
Abstract:  Using individual- and household-level survey data from the Africa Centre for Health and Population Studies, our research will examine the links between health behaviors and socio-economic status (SES), particularly income. The aim is to document whether household resources contribute to the health gradient—the observed positive correlation between health and wealth or other measures of SES—through better knowledge and awareness of HIV/AIDS, less risky sexual behavior, and/or less participation in other behaviors damaging to health (such as tobacco use or heavy drinking). Primary research questions include:

(1) What is the relationship between income and (a) number of sexual partners; (b) condom use; or (c) other health-related behavior such as smoking and drinking?

(2) Which socio-economic factors other than income (such as schooling) are correlated with number of sexual partners and condom use?

(3) To what extent do these relationships differ between men and women?

PI: McMillan, Nora
Title: Sasakawa Young Leaders Fellowship Fund
Abstract:  The primary purpose of the SYLFF Fellows’ Mobility Program (FMP) is to contribute to and enrich the academic and cultural learning of SYLFF fellows by providing SYLFF/FMP awards for non-degree study and research at another participating SYLFF institution. The secondary purpose of the FMP is to strengthen the linkages among SYLFF institutions and fellows.

PI: McNinch, George
Title: Reductive Groups in Positive Characteristic
Abstract: The broader impacts of the proposed research include the advancement of mathematical knowledge and learning, and the advancement of the mathematical working infrastructure through collaborations and the rapid electronic dissemination of the results of the research. The project will assist the graduate teaching role of the author. The project will support mathematical collaborations of the author with mathematicians at other institutions. Finally, the author will continue to make results of supported research available through use of the arXiv preprint server; this permits timely dissemination of the results, and supports a significant tool in the working infrastructure of modern mathematics. 

PI: Miczek, Klaus
Title: Psychomotor Stimulants and Aggression in Animals
Abstract: Epidemiological data, statistics on perpetrators of violent crimes and of victims of violence under the influence of drug as well as neurobiological evidence link social stress and drug use. The proposed research aims to characterize the common behavioral and neural features of individuals who experience salient types of social stress and who self-administer psychomotor stimulants and opioids in a compulsive-like manner, and to define the neural circuits for these apparently opposing activities. Ostensibly aversive events such as social defeat stress and euphorogenic effects such as those produced by cocaine or opioids share physiological and corticolimbic circuits. First, experiments are designed to identify the critical behavioral and mesocorticolimbic features of brief episodes of social defeat stress, chronic subordination stress, and impulsive aggressive behavior as potential determinants for the transition to compulsive-like intravenous self-administration of cocaine, d-amphetamine or morphine. We aim to characterize the transition from regulated to dysregulated drug taking by studying the long (>24 h) drug binge as a model. Secondly, the neurobiological mechanisms for the behavioral sensitization that results from repeated episodes of social defeat stress will be characterized with a focus on glutamatergic, GABAergic and serotonergic modulation of mesocorticolimbic dopaminergic pathway. In vivo microdialysis measurements aim to reveal the emerging neural sensitization in the microcircuit consisting of amgydaloid and cortical structures modulating the VTA DA system. Thirdly, neuropharmacological experiments are designed to examine the role of NMDA and AMPA glutamatergic receptos, GABAA receptors, and subtypes of the 5-HT receptor families in modulating activity in the mesocorticolimbic DA pathway for their relevance in sensitization to social stress and in the transition to intense dysregulated cocaine and morphine self-administration in stress-sensitized animals. It is anticipated that the sensitizing effects of social stress experiences can be reversed or protected against by targeting the modulatory influences on the VTA system. Reversal of cross-sensitization from stress may be a means by which to prevent the transition to out-of-control compulsive-like drug taking.

PI: Milbury, Paul
Title: Distribution of Anthocyanins in Tissues of Blueberry-Fed Pigs
Abstract: Working with Dr. Wilhelmina Kalt at the Atlantic Food and Horticulture Research Centre, we will analyze tissues of BB-fed pigs for BB flavonoids and their metabolites. Determining levels of BB components in these pig tissues will be extremely important, since this study has already demonstrated other BB-dependent effects (e.g. blood lipids), in spite of a high basal level of flavonoids in the pig diet. Analyzing pig tissues for ACNs and possibly other BB flavonoids, will allow a complete characterization of their bioavailability, including theft dose response, metabolism, and tissue distribution, as well as the impact of different levels of non-BB flavonoids in the basal diet.

Objective 1. Determine the optimal extraction methodologies and chromatographic methods (HPLC-ECD, HPLC-MS and HPLC-UV diode array) for the quantitative recovery and aimlysis of ACNs from several pig tissues, including eye, brain (3 regions), liver, kidney, muscle, small and large intestines, as well as urine, plasma and feces.

Objective 2. Determine the levels and distribution of ACNs in tissue collected from the USHBC-fiinded pig study by Kalt et al.

PI: Minear, Larry
Title: Humanitarianism and War Project
Abstract:  Building on the past decade and with an eye to the evolution of the wider humanitarian enterprise in the coming years, the H&W Project has identified a number of objectives for Phase 5, primarily in the areas of research, education, and institutional change. The objectives include: (1) to enhance further the professionalism of the humanitarian practitioner community by encouraging greater attention to humanitarian principles and to the political context in which activities are undertaken; (2) to contribute to the increased effectiveness of humanitarian activities by identifying recurring challenges and highlighting best practices for meeting them; (3) to engage donor governments more fully and self-critically in issues of humanitarian policy and practice; (4) to engage the wider public on the issues of humanitarian principle and practice, both through writings for the general public (e.g., op-eds) and through nurturing constituencies for assistance and protection activities (e.g., through NGOs); (5) to demonstrate the utility of more creative and routine interaction between practitioners and social science researchers; (6) to build upon and nurture the Project’s existing network of professional contacts and connections with an eye to deepening the existing dialogue; and (7) to disseminate more widely and innovatively materials produced in earlier phases of the project.

PI: Moore, Claire
Title: The Coupling of mRNA Transcription and 3' End Formation
Abstract: The emerging model of eukaryotic mRNA synthesis is that transcription and mRNA processing events are carefully orchestrated in vivo by a physical association of the different machineries. For example, RNA polymerase II affects the efficiency of 3' end processing, and processing factors affect the efficiency of transcription termination downstream of poly(A) sites. We are interested in the precise molecular mechanisms involved in the coordination of these two events and have identified several new points of interaction between transcription and cleavage/polyadenylation factors. These findings suggest that the presence of processing factors at the promoter might affect the efficiency and/or specificity of transcription initiation and facilitate recycling of RNAP II back to the promoter for another round of transcription. This may serve as a mechanism to insure the proper loading of processing factors onto the transcriptional complex, and in turn, the subsequent polyadenylation of the transcript, which is essential for optimal export, translation, and turnover of mRNA. To investigate this issue, we propose the following specific aims:
1. Can the activity of Ssu72 in transcription be separated from its role in 3" end cleavage? We have found that Ssu72, previously identified as a protein affecting initiation, is directly involved in mRNA 3'end cleavage. We will analyze an existing collection of ssu72 mutants to try to separate the cleavage activity of Ssu72 from a function in transcription initiation and develop new assays to help discriminate these functions.
2. What is the functional significance of the interactions of Sub1 and Ssu72 with Pta1, and how are these interactions regulated? Ssu72 and Sub1 were initially identified based on genetic interactions with TFIIB. We have found that these proteins genetically interact with the Ptal subunit of Cleavage/Polyadenylation Factor (CPF). Moreover, they physically bind Pta1 in a mutually exclusive manner. We will test the hypothesis that sequential interactions of Pta1 with Ssu72 and Sub1 are important for efficient initiation and/or cleavage of pre-mRNA. 3. Does Swd2 function in mRNA synthesis as part of CPF? This protein is intimately associated with CPF and the Set1 histone methylase. However, Swd2 depletion has no effect on 3' end processing, but causes inefficient transcription termination and reduced mRNA levels. We will test the hypothesis that Swd2 affects termination by recruiting Set1 to the transcription complex. We will identify the contact point of Swd2 with CPF and examine how disruption of this interaction affects mRNA synthesis. A genetic screen will be used to identify other important functional interactions with Swd2.

PI: Moore, Claire
Title: Molecular Mechanism of mRNA 3' End Formation in Yeast
Abstract: The post-transcriptional acquisition of a poly(A) tail onto the 3' ends of eukaryotic mRNAs is an essential process that promotes transcription termination and transport of mRNA from the nucleus and serves as an additional point at which the cell can regulate the type and amount of mRNA derived from a particular gene. The poly(A) tail is also important for optimal translation and for determining mRNA stability. Polyadenylation requires site-specific endonucleolytic cleavage of the primary transcript followed by poly(A) addition to the upstream product. These steps are closely coupled in vivo, but can be experimentally uncoupled in vitro and assayed separately. While many of the protein components required for each step have been identified, much less is known about the biochemical nature of the process. Using the yeast S. cerevisiae as a model eukaryote, we will address the following specific aims:
1. Analysis of the molecular mechanism by which yeast cleavage factors recognize and cleave the mRNA precursor in the 3' untranslated region. These experiments will determine what constitutes the core cleavage complex, and how these factors interact with each other and with the RNA to mediate this step of the reaction.
2. Investigation of the molecular linkage between the mRNA 3'-end processing machinery and the mRNA transport apparatus. This aim seeks to identify connections between disassembly of the polyadenylation complex and assembly of the transport complex. We will ask when the cleavage/polyadenylation factors leave the polyadenylated product, and whether this recycling is facilitated by transport factors. A closely related issue is when transport factors join the mRNA, and whether their recruitment is assisted by the polyadenylation factors. With the research proposed here, we hope to derive a dynamic model of the complex that cleaves mRNA precursor. This work should provide insight into how this complex sets the stage for subsequent polyadenylation and transport of the mRNA. A better understanding of the basic mechanism will also make it easier to determine how polyadenylation is coordinated with other nuclear events and how the cellular environment modulates the activity or levels of the factors involved in this essential process.

PI: Must, Aviva
Title: Obesity and Psychopathology: A Longitudinal Study of Youth
Abstract: Obesity and mental illness are two of the largest health issues the United States is currently facing, and their burden to society in human suffering, health care costs, and lost productivity is immense. The known psychosocial consequences of obesity include reduced educational attainment and lower rates of marriage. In adults presenting for the treatment of obesity, co-morbid psychopathology is increased. Widespread stigmatization of obese children is manifested through teasing and increased social stress. Nonetheless, the epidemiology of psychological outcomes subsequent to obesity has not been well characterized, and associations between obesity and psychopathology have frequently been assessed in clinical samples, or have used cross-sectional study designs. The proposed analyses make use of comprehensive data, from a longitudinal community study of determinants of psychological health from childhood to early adulthood, to characterize the specific psychological consequences of obesity and associations with relative weight during adolescence, and to assess the role of psychopathology on the development of obesity. Psychopathology is assessed based on standard Diagnostic and Statistical Manual of Mental Disorders (DSM) diagnostic criteria as well as by symptom scales. With longitudinal statistical modeling, the bi-directional associations of adolescent relative weight with anxiety disorders, mood disorders, and overall psychopathology will be assessed. The extent to which mediating and moderating factors contribute to the development of adolescent obesity and influence subsequent psychopathology will be examined. Relative weight will be assessed based on body mass index (BMI) calculated from self-reported height and weight. The Centers for Disease Control's BMI growth reference will be used to determine age- and sex-specific BMI z-scores. Obesity will be defined as a BMI score above the 85th percentile from the CDC growth reference. Understanding the psychological consequences of obesity will allow for increasingly focused research in prevention and treatment efforts aimed at reducing psychological and physical suffering from obesity and from mental illness.

PI: Nickerson, Raymond
Title: Probabilistic Reasoning
Abstract: The research literature on cognition contains numerous findings that have generally been taken as evidence of human irrationality manifesting itself in a variety of guises and contexts. Many of the more widely cited evidences of irrationality have to do specifically with probabilistic reasoning. Illustrative topics include the gambler's fallacy, framing effects, illusory correlation, the conjunction fallacy, sample-size insensitivity, the "hot-hand" illusion, false consensus, and hindsight bias, among others. The work proposed here is motivated, in part, by the belief that many of the published experiments that have produced results that have been interpreted as evidence that people's intuitions about probability are faulty have used problems that are ambiguous or incompletely stated. A primary goal of the proposed studies is that of determining the sensitivity of certain experimental results to the specifics of the wording of problems that have been used to study probabilistic reasoning. People's intuitions about probability may indeed be faulty in specific ways, but to show them to be so it is essential that problems be stated unambiguously and completely; otherwise one cannot be sure that the problems on which participants worked are those that the investigators intended that they attempt to solve. We describe three experimental paradigms that we propose to use in this program to study the effects of problem ambiguity and incompleteness on how people deal with probabilistic problems. We expect to use as participants some people who have had some training in probability theory or closely related subjects (statistics, stochastic processes, combinatorics) and some who have not. We do not intend that our research be limited to these paradigms, but they represent our current thinking about reasonable points of departure for data collection. We expect that the design of experiments to be run after the first few will be influenced by what is learned in the initial studies described herein.

The proposed work continues a long-term interest of the principal investigator in the theoretical question of what it means to be rational, and in the practical question of how people might be taught to reason more effectively. The specific focus is an empirical extension of recent theoretical and review work by the principal investigator on probabilistic reasoning in particular. The results of the proposed experiments should enhance our understanding of how people deal with probabilistic situations, of the kinds of assumptions they make to resolve ambiguities or to fill in missing information, and of what might be done to improve people's ability to reason probabilistically. We consider such results to be important for both theoretical and practical purposes. Theories of cognition must be based on such results if they are to provide accurate representations of people's probabilistic intuitions and capabilities. From a practical perspective, the results should have implications for decision-making, policy formulation and instruction. They should inform such questions as: how to improve the intuitive grasp of probability concepts by people who have had no formal training in probability
theory, how best to communicate probabilistic information (e.g., information about the seriousness of specific risks or threats) to the general public, and how to improve the formal teaching of probability and closely related concepts.

PI: Nurminskaya, Maria
Title: Evaluation of T-Gases as Regulators of VSMC
Abstract: Cardiovascular calcification (mineralization) is a common pathologic condition associated with ageing, diabetes, and chronic renal insufficiency. It often leads to stroke, amputation and ischemic heart disease. The contribution of VSMCs, trans-differentiated to acquire the osteoblast phenotype, in depositing mineralized matrix is well established. However, the mechanisms and regulators of such trans-differentiation are not understood yet. The original proposal aimed to evaluate our hypothesis that extracellular enzymes transglutaminases (TOases) niay promote trans differentiation in vascular smooth muscle cells (VSMCs), and induce VSMCs to deposit mineralized matrix. This hypothesis derived from our published and preliminary data including: (1) co-localization of TGases with areas of calcification in the arteries; (2) induction of matrix calcification in VSMC cultures by exogenous TGase; and (3) the ability of TGases to promote maturation and matrix mineralization in preosteoblasts. The following specific aims were proposed: (1) To examine the TOases-induced acquisition of osteoblast phenotype by VSMC in vitro, and (2) To identify TGase-binding proteins in VSMCs to elucidate further cellular mediators of TGase-induced changes in VSMCs. In addition, we proposed to analyze whether exogenous TOase activates LRP/b-catenin signaling in VSMC.

PI: Orians, Colin
Title: Dissertation Research: Does Herbivory Signal Plants to Increase Nitrogen Uptake and Bolster Nitrogen and Starch Storage?
Abstract: Mobilization of stored starch is important for plant tolerance to herbivory. The amount of stored starch is assumed to be independent of herbivory. However, preliminary results indicate that plants might increase storage in response to herbivory.  In Populus, allocation of 11C to lower stem and roots increased in response to jasmonic acid (JA), an important signal molecule in defense induction. This study will determine whether JA and insect herbivory results in (1) increased allocation of carbon and nitrogen to storage compounds in the stem and roots, and (2) increased nitrogen uptake and assimilation.  Immediate processes will be studied in vivo using radio-tracers (11C, 13N), and subsequent partitioning and chemical allocation will be examined using stable isotopes (13C, 15N) and destructive sampling. Increased nitrogen uptake and C and N allocation to storage compounds following initiation of herbivory would indicate that lants can adjust their metabolism to maximize chances of surviving defoliation and improving regrowth. This pioneering research of storage regulation in response to herbivore signals will be necessary to understand how plants have evolved to cope with herbivory. Moreover, an improved understanding of plant tolerance may influence commercial cultivation practices, and could generate insights for manipulating plants to increase tolerance.  

PI: Orians, Colin
Title: Tufts REU Site: Mentoring Biological Research As A Collaborative Enterprise
Abstract: The Tufts University Biology Department has a long-standing commitment to mentoring undergraduates in research, as well as a strong track record of highly productive interdisciplinary research collaborations. As science is an increasingly collaborative enterprise, it has become essential to combine expertise of researchers from diverse fields. Today's students thus require training not only in discipline-specific research skills, but also in how to build successful collaborations. This REU Site proposal, if funded, will allow undergraduate students to experience biological research as a collaborative enterprise, with each student learning from two mentors. In addition, our REU program will allow us to extend this unique training to underrepresented minorities and other students lacking comparable research opportunities.

We will offer a 10-week summer program in which 12 students (half from outside Tufts) will work on one of eight collaborative, interdisciplinary projects combining faculty expertise in animal behavior, endocrinology, conservation biology, development, plant ecology, and molecular biology. The goals of this summer program are: (1) to increase students. Proficiency in biological research and collaborative skills, (2) to educate and inspire students toward future eresearch careers, (3) to develop students. ability to effectively communicate scientific results, and (4) to extend these opportunities to underrepresented minorities. Each student will work closely with two mentors to combine research techniques from different fields, and to design and conduct an independent project. The program will include activities that foster studentstudent interactions, including seminars, field trips, site visits and a student symposium. In addition, weekly discussions will focus on ethics, the interface between science and policy, scientific communication skills, and careers in science. Tufts University has shown major institutional commitment to this program by providing fully subsidized, on-campus housing for all REU students, as well as contributing summer salary support to the PI administering this program. Applicants should contact Dr. Colin Orians at colin.orians@tufts.edu or Department of Biology, Tufts University, Medford, MA 02155.

PI: Ortiz, Daniel
Title: ABC Transporter Binding Proteins and Trafficking
Abstract: The ABC (ATP-Binding-Cassette)-type protein BSEP (ABCB11) is essential for bile formation. BSEP resides primarily in the canalicular membrane of hepatocytes and mediates ATP-dependent transport of conjugated bile acids from cytoplasm to bile. Correct targeting and recycling to the apical membrane are fundamental to BSEP function and regulation. Mutations that cause BSEP retention in the endoplasmic reticulum produce Progressive Familial Intrahepatic Cholestasis type II. Additionally, BSEP removal from the canalicular membrane is associated with drug and sepsis induced intrahepatic cholestasis. BSEP mobilization and targeting to the apical membrane are mediated by association with factors that connect the transporter to sorting and trafficking networks. We previously identified proteins that interact with BSEP in the apical domain and regulate its plasma membrane delivery and endocytosis. However, there is no information regarding proteins that bind BSEP and regulate its progress through the early secretory pathway or exit from the Trans Golgi Network, which represents the central sorting hub of the vesicular transport network. We have identified two proteins, a clathrin adaptor and a putative endoplasmic reticulum sorting receptor, which interact with BSEP and influence its apical membrane expression. The goal of the proposed research is to investigate the role these proteins play in regulating BSEP trafficking. Experiments in Aim 1 will clarify which aspect of the BSEP trafficking itinerary in polarized cells and hepatocytes is controlled by interaction with the clathrin adaptor. Aim 2 focuses on determining the extent to which accessory proteins, which form a macromolecular complex with BSEP and the clathrin adaptor, participate in BSEP delivery to the plasma membrane. Specific Aim 3 will investigate the relevance of an endoplasmic reticulum resident protein, which directly interacts with BSEP, to transporter maturation and vesicular trafficking to the Golgi. We will also ascertain whether overexpression of the interacting protein improves trafficking of BSEP PFIC II mutants. Inherited or acquired defects that compromise BSEP expression in the canalicular membrane are likely causes of intrahepatic cholestasis. Therefore, elucidating pathways that govern transfer and recruitment of ABC-transporters to the apical membrane, and identification of proteins which control these processes, will provide critical insight into mechanisms underlying cholestasis and suggest targets for drug design.

PI: Panetta, Karen
Title: REU Supplement: Research Experience of Undergraduates in Simulation and Modeling
Abstract: The main purpose of this supplemental work will be to provide an undergraduate experience with modeling, design and test issues for MEMS components. Supplementary funding will allow the student the opportunity to work as a technical contributor on a team, get exposure to simulation and modeling issues and collaborate with professional engineers at industrial technology companies. The student will also learn about fault modeling, and testing methodologies and their importance for developing quality products. The emphasis of our research is developing models and fault models that accurately encapsulate MEMS devices that can be seamlessly integrated into our simulator environment. To accomplish this, many tasks have been underway that have included developing the simulator to accept behavioral and structural models. The simulator can integrate multiple models at varying levels of detail. This allows us to construct large system simulations and focus on the propagation of faults through models, as well as observing the cause-effect relationships of faults in a system within an efficient simulation environment.

PI: Panjwani, Noorjahan
Title: Corneal Epithelial Cell Surface Glycoconjugates
Abstract: The failure of the epithelium to migrate over the wound or of the migrated epithelium to remain adherent to the substratum may lead to the development of a number of debilitating clinical conditions of the cornea including recurrent erosions and persistent epithelial defects. We established during the previous funding period that two carbohydrate binding proteins, galectins-3 and -7, are among the key molecules which mediate corneal epithelial cell migration. For an understanding of the mechanism by which galectins-3 and -7 mediate corneal epithelial cell migration, in Aim 1, we shall identify and characterize the corneal epithelial cell surface and extracellular matrix (ECM) glycoproteins which serve as counterreceptors of galectins-3 and -7, and will establish whether the lectins modulate corneal epithelial cell migration by binding to well-known integrins, growth factor receptors, and/or ECM molecules. In Aim 2, using small interfering RNA (siRNA) and/or antisense adenoviral constructs, cDNA microarrays and glycogene arrays, we shall determine whether galectin-3 mediates corneal epithelial cell migration indirectly by modulating the expression of key adhesion and/or signal transduction molecules. In Aim 3, by determining whether galectins-3 and/or -7 modulate the activation of specific kinases (focal adhesion kinase, protein kinase B, MAP kinases) that are well known for their role in cell migration, we shall establish whether the lectins mediate corneal epithelial cell migration by modulating specific signal transduction pathways. The proposed studies will contribute to a better understanding of the molecular basis of corneal epithelial cell migration and should ultimately help find novel therapeutic strategies for treating nonhealing corneal wounds. In addition, this study will contribute to the basic understanding of the general disorders of impaired or delayed re-epithelialization including chronic wounds in the elderly, decubitus ulcers, and venous stasis ulcer of the skin, conditions that together affect millions of individuals worldwide.

PI: Pokras, Mark
Title: Seabird Ecological Assessment Network (SEANET)
Abstract: With generous support from the Geraldine R. Dodge Foundation, Tufts Center for Conservation Medicine I Wildlife Clinic (Tufts CCM) established SEANET, the Seabird Ecological Assessment Network in fall 2002. This large-scale, comprehensive ecosystem health program focuses on seabirds as indicators of marine, coastal, and human health. A network of over 60 seabird and ecological health organizations from Canada to New Jersey has been established, ‘citizen-scientist’ beached bird surveys launched with over 300 volunteers, and data on seabird mortality, population distribution, ocean contamination, and coastal land use, are being collected for a SEANET GIS-based repository.  This project sustains a long-term marine and coastal ecosystem health monitoring project using seabirds as sentinels, fostering participation by citizen scientists ranging from adult volunteers to school children. We are collaborating with numerous partners (inch ding Wildlife Trust and the New York Bioscape Project). With the USGS National Wildlife Health Center we continue to develop and maintain a comprehensive distributed Internet mapping resource to facilitate research and applications of diverse data sets, including beached bird mortality data, bird population data from birders, data from pelagic seabird surveys, and Census of Marine Life data. We will continue to utilize information technology to map, distribute and analyze marine and coastal bird population and mortality data, ocean contamination, biotic and abiotic coastal and marine factors, and emerging diseases.

PI: Pokras, Mark
Title: Training Tomorrow's Leaders: Energizing a New England Conservation Medicine Network Through Innovative Student Training
Abstract: To investigate and solve such complex problems requires the combined expertise of professionals trained in a variety of disciplines. As noted historian Theodore Zeldin commented, “Most advances in science have been the result of intermediaries venturing beyond the boundary or the paradigms of their disciplines, uniting insights which come from different kingdoms of knowledge.”

PI: Poltorak, Alexander
Title: Genetic Dissection of Lipopolysaccharide Response
Abstract: The lipopolysaccharide (LPS) signaling pathway has been analyzed using combination of biochemical and genetic methods. However, not all of the proteins that participate in LPS recognition have been identified. In order to find more of them, several inbred strains of mice were evaluated on their LPS response and genetic basis of the differences in this response was examined. Among them, BALB/C and C3H/HeN strains differ significantly in their response to LPS. To further determine the relationship between TLR4 LPS response, (BALB/C x C3H/HeN) F2 intercross mice were analyzed on their LPS response and genotyped for TLR4 locus. These data show that although there is functional polymorphism in TLR4 observed between BALB/C and C3H/HeN mice, additional genes are clearly involved in LPS response. In order to map these genes, the panel of F2 mice was expanded and subjected to genome wide screening with all progeny genotyped for TLR4 locus. Genetic analysis of 80 meioses revealed that hyporesponse of BALB/C mice to LPS is linked to loci on chromosomes 6 and 17. To further characterize candidates and to improve resolution of genetic mapping, two congenic strains were constructed: one with BALB/C allele of TLR4 on C3H/HeN background and another - with HeN allele of TLR4 on BALB/C background. These strains were further analyzed to determine the level of their response to LPS. Two new loci, termed Lpml and Lpm2, may be assumed to contribute to the LPS response. The elucidation of Lpml and Lpm2 will represent an important advance, in that many genes that are known to contribute to complex traits can be identified by such approach. Similar strategy was employed for analysis of intercross response to peptidoglycan in F2 intercross animals. Elucidation of a precise mechanism of anti-bacterial response in a mouse model will undoubtedly contribute to the studies of host resistance to infectious diseases in humans.

PI: Prevelakis, George
Title: Balkans Conference in Hellenic and Southeastern European Studies
Abstract:  The Balkan question has been more or less “forgotten” in Western Europe and even more in the United States. However most of the problems of the 1990s remain unresolved. A new crisis is more than probable, although it is difficult to predict its timing. Even without an open crisis, the Balkan situation is extremely grave. Security is guaranteed only through the existence of a series of quasi-protectorates, the economic conditions remain disappointing and the steps towards Democratization are uncertain. The economic, political and moral burden of the Balkans remains very heavy. In addition, the Balkans function as a dangerous hearth of organized crime and corruption, threatening neighboring countries, one of which is Greece. Attracting attention and promoting understanding of the Balkans is therefore as important today as it was in the early 1990s.  To create interest again, it is necessary to associate the Balkan questions with themes which, for one reason or another, appear more relevant. For the American public, the question of Iraq comes first (and will probably continue to attract attention in the foreseeable future) while the Atlantic relationship (especially in its most acute form, i.e. the French-American relationship) is also a focus of interest. The proposed conference will combine those three elements (Balkans, Middle East and French-American relations). The linkage of those apparently different themes will be furnished through the following theoretical framework: 

1. During the Cold War, the Eastern Question, perceived as the struggle to dismantle the Ottoman Empire and to share its possessions, was considered as belonging to history. However, the Balkan crises, the difficulties to solve the Palestinian question (in spite of the end of the Cold War), the Gulf Wars and the Al-Quaeda threat have shown that the territories which belonged to the Ottoman Empire continue to constitute sources of international instability. The Eastern Question has reappeared under a new form. The focus today is on the more or less successful efforts to introduce the Western Geopolitical model in a region which had lived for centuries under a very different system, rather than the dismemberment of the Ottoman Empire. This new definition of the Eastern Question links the past with the present. 

2. The Eastern Question is usually studied from the regional perspective. This approach leads to fragmentation of perceptions and finally to confusion. Instead of going through a series of case studies, this conference will try to reunify the theoretical questioning in order to understand not only the western influence on eastern peripheries, but also how the various impulses from the “East” have been (and are) interpreted in the “West”; and how those interpretations influence in their turn the relationships between the various components of the “West” as well as that between “East” and “West”. 

3. Among the various “external” actors of the traditional Eastern Question, two proved to be the most influential. They were both “western”: France and Great Britain. Since the Greek Civil War and the Suez Canal crisis, the USA have replaced the British, preserving thus the Anglo-Saxon Mediterranean presence. France lost a large part of her influence in the Mediterranean, but has retained the most powerful Mediterranean presence among the European countries. Her policy has been to integrate her traditional Mediterranean interest in the context of a wider European involvement. Thus, the new terms of the old French-British competition/cooperation in the Eastern Mediterranean are not completely different from the old. If the transatlantic couple (USA/EU) is the actual focus of the renewed Eastern Question,  the French role and tradition is the only credible European alternative in the face of the Anglo-American perspective. The French opposition to the US policy towards Iraq in 2003 clearly illustrated the danger of a new divide on the renewed Eastern Question; a divide which can lead to growing transatlantic misunderstandings, crippling thus the efforts to solve the problems of the Balkans and of the Middle East.  It is not surprising that the dialogue on the Balkans (and to a lesser degree on the Middle East) between intellectuals and academics of French and of English expression is almost inexistent. One of the ambitions of the proposed conference is to initiate exchange of ideas. A chair with Balkan affinities will thus be able to contribute to French-American dialogue, breaking with the opposite tradition (western efforts to facilitate dialogue in the East).  The invited personalities cover a wide sphere of French (or French speaking) approaches: from members of the “pure” research community (like Xavier Bougarel) to influential intellectuals (like Regis Debray) and to Ambassadors and other policy makers (like Michel Foucher, one of the Rambouillet protagonists). They also represent a variety of disciplines and specializations: Marc Ferro (a very well-know historian), Violette Rey (a leading geographer), Guy Hermet (a highly respected political scientist), specialists of religion (Gilles Kepel, Jean-Francois Colosimo) etc. Finally, a few relatively younger researchers (like Yves Tomic, Emmanuelle Boulineau) will offer a view of the newer generation of French research on questions of religion, politics and territoriality in the Balkans.  The final list of participants and the program of the three-day conference will be determined by a Fletcher scientific committee comprising Georges Prevelakis, Alan Henrikson, Leila Fawax and Andrew Hess.  The papers of the conference will be published as the first volume of the Karamanlis Geopolitical Series. The Balkan question has been more or less “forgotten” in Western Europe and even more in the United States. However most of the problems of the 1990s remain unresolved. A new crisis is more than probable, although it is difficult to predict its timing. Even without an open crisis, the Balkan situation is extremely grave. Security is guaranteed only through the existence of a series of quasi-protectorates, the economic conditions remain disappointing and the steps towards Democratization are uncertain. The economic, political and moral burden of the Balkans remains very heavy. In addition, the Balkans function as a dangerous hearth of organized crime and corruption, threatening neighboring countries, one of which is Greece. Attracting attention and promoting understanding of the Balkans is therefore as important today as it was in the early 1990s.  To create interest again, it is necessary to associate the Balkan questions with themes which, for one reason or another, appear more relevant. For the American public, the question of Iraq comes first (and will probably continue to attract attention in the foreseeable future) while the Atlantic relationship (especially in its most acute form, i.e. the French-American relationship) is also a focus of interest. The proposed conference will combine those three elements (Balkans, Middle East and French-American relations). The linkage of those apparently different themes will be furnished through the following theoretical framework:  1. During the Cold War, the Eastern Question, perceived as the struggle to dismantle the Ottoman Empire and to share its possessions, was considered as belonging to history. However, the Balkan crises, the difficulties to solve the Palestinian question (in spite of the end of the Cold War), the Gulf Wars and the Al-Quaeda threat have shown that the territories which belonged to the Ottoman Empire continue to constitute sources of international instability. The Eastern Question has reappeared under a new form. The focus today is on the more or less successful efforts to introduce the Western Geopolitical model in a region which had lived for centuries under a very different system, rather than the dismemberment of the Ottoman Empire. This new definition of the Eastern Question links the past with the present.  2. The Eastern Question is usually studied from the regional perspective. This approach leads to fragmentation of perceptions and finally to confusion. Instead of going through a series of case studies, this conference will try to reunify the theoretical questioning in order to understand not only the western influence on eastern peripheries, but also how the various impulses from the “East” have been (and are) interpreted in the “West”; and how those interpretations influence in their turn the relationships between the various components of the “West” as well as that between “East” and “West”.  3. Among the various “external” actors of the traditional Eastern Question, two proved to be the most influential. They were both “western”: France and Great Britain. Since the Greek Civil War and the Suez Canal crisis, the USA have replaced the British, preserving thus the Anglo-Saxon Mediterranean presence. France lost a large part of her influence in the Mediterranean, but has retained the most powerful Mediterranean presence among the European countries. Her policy has been to integrate her traditional Mediterranean interest in the context of a wider European involvement. Thus, the new terms of the old French-British competition/cooperation in the Eastern Mediterranean are not completely different from the old. If the transatlantic couple (USA/EU) is the actual focus of the renewed Eastern Question,  the French role and tradition is the only credible European alternative in the face of the Anglo-American perspective.  The French opposition to the US policy towards Iraq in 2003 clearly illustrated the danger of a new divide on the renewed Eastern Question; a divide which can lead to growing transatlantic misunderstandings, crippling thus the efforts to solve the problems of the Balkans and of the Middle East.  It is not surprising that the dialogue on the Balkans (and to a lesser degree on the Middle East) between intellectuals and academics of French and of English expression is almost inexistent. One of the ambitions of the proposed conference is to initiate exchange of ideas. A chair with Balkan affinities will thus be able to contribute to French-American dialogue, breaking with the opposite tradition (western efforts to facilitate dialogue in the East).  The invited personalities cover a wide sphere of French (or French speaking) approaches: from members of the “pure” research community (like Xavier Bougarel) to influential intellectuals (like Regis Debray) and to Ambassadors and other policy makers (like Michel Foucher, one of the Rambouillet protagonists). They also represent a variety of disciplines and specializations: Marc Ferro (a very well-know historian), Violette Rey (a leading geographer), Guy Hermet (a highly respected political scientist), specialists of religion (Gilles Kepel, Jean-Francois Colosimo) etc. Finally, a few relatively younger researchers (like Yves Tomic, Emmanuelle Boulineau) will offer a view of the newer generation of French research on questions of religion, politics and territoriality in the Balkans.  The final list of participants and the program of the three-day conference will be determined by a Fletcher scientific committee comprising Georges Prevelakis, Alan Henrikson, Leila Fawax and Andrew Hess.  The papers of the conference will be published as the first volume of the Karamanlis Geopolitical Series.