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Nikhil U. NairAssistant Professor, Chemical & Biological Engineering, School of EngineeringAdjunct Assistant Professor, CMDB Program, Graduate School of Biomedical SciencesTufts UniversityScience & Engineering Complex #237200 College Avenue, Medford, MA 02155Email: Nikhil.Nair@tufts.eduPhone: 617-627-282Fax: 617-627-3991Research site: https://sites.tufts.edu/NairLabTwitter: https://www.twitter.com/Nair LabPublons: -nair/iGEM team: http://2019.igem.org/Team:Tuftsa. stant Professor, Department of Chemical and Biological Engineering (ChBE), TuftsUniversity, Medford, MA.Adjunct Assistant Professor, Program in Cellular, Molecular, and Developmental Biology(CMDB) of the Tufts Graduate School of Biomedical Sciences, Tufts Medical School,Boston, MAProtein Purification Scientist, Bristol Myers-Squibb, Syracuse, NYb. Professional Preparation:Cornell University, Ithaca, NYUniversity of Illinois, Champaign, IL(advisor: Huimin Zhao)University of Illinois, Champaign, IL(advisor: Huimin Zhao)Harvard Medical School, Boston, MA(advisor: Ann Hochschild)Chemical & Biomolecular Eng.Chemical & Biomolecular Eng.BSMS20032006Chemical & Biomolecular Eng.PhD2010Microbiology & ImmunobiologyPostdoc2010-2013c. Honors and Awards:As PI:2016 NIH Director’s New Innovator Award recipient2016 Tufts Faculty with Significant Impact on Undergraduate StudentsAs graduate student:2009 Hanratty Travel Award, University of Illinois, Urbana2008-2009 Mavis Memorial Fund Scholarship Award, University of Illinois, Urbana2008-2009 Drickamer Endowment Fund, University of Illinois, Urbana2008, 2009 Annual ChBE Graduate Research Symposium Award, University of Illinois, Urbana2008 Best Oral Presentation in the CMB/MBTG Research Symposium, University of Illinois, Urbana2008 Hanratty Travel Award, University of Illinois, Urbanad. Publications:Publications at Google Scholar and NCBI’s MyBibliography undergraduate; † co-first authors; * corresponding author(s)Work done as independent PI:1. V. D. Trivedi, N. U. Nair* (in preparation)2. T. C. Chappell, N. U. Nair* (in preparation)3. S. A. Amin, T. B. Nicks, V. Porokhin, N. U. Nair*, S. Hassoun* (in preparation)1

4.5.6.7.8.9.10.11.12.13.14.15.16.17.18.B. Motta Nascimento, N. U. Nair* (in preparation)J. R. Bober, K. Mohan, N. U. Nair* (in preparation)V. D. Trivedi†, T. C. Chappell†, N. U. Nair, M. Levin, C. Herrera Rincon* (in preparation)Z. S. J. Mays, T. C. Chappell, N. U. Nair*, “Quantifying and engineering probiotic bacterial adhesion tomucus”, (under revision, ACS Synthetic Biology, bioRxiv)J. R. Bober, N. U. Nair*, “Galactose to Tagatose Isomerization at Moderate Temperatures with HighConversion and Productivity”, Nature Communications, 2019 (link, bioRxiv)S. A. Amin†, E. Chavez† , V. Porokhin , N. U. Nair*, S. Hassoun*, “Towards Creating an ExtendedMetabolic Model (EMM) for E. coli Using Enzyme Promiscuity Prediction and Metabolomics Data”,Microbial Cell Factories, 2019 (link, bioRxiv)S. A. Amin, V. Endalur Gopinarayanan, N. U. Nair*, S. Hassoun*, “Establishing Synthesis Pathway-HostCompatibility via Enzyme Solubility”, Biotechnology & Bioengineering, 2019 (link, bioRxiv)V. Endalur Gopinarayanan, N. U. Nair, “Pentose Metabolism in Saccharomyces cerevisiae: The Need toEngineer Global Regulatory Systems”, Biotechnology Journal (perspective & review), 2018 (link)V. Endalur Gopinarayanan, N. U. Nair, “A Semi-synthetic Regulon Enables Rapid Growth of Yeast onXylose”, Nature Communications, 2018 9(1) (link)Associated press-release and news articles: Tufts Now!, Biofuels International, EurekAlert!, NewsWise,and MediaNet.J. R. Bober, C. L. Beisel*, N. U. Nair*, “Synthetic Biology Approaches to Engineer Probiotics and Membersof the Human Microbiota for Biomedical Applications”, Annual Review of Biomedical Engineering, 2018 20(link)Z. J. S. Mays, N. U. Nair, “Synthetic Biology in Probiotic Lactic Acid Bacteria: At the Frontier of LivingTherapeutics”, Current Opinion in Biotechnology, 2018 53 (link)M. Waller, J. R. Bober, N. U. Nair, C. L. Beisel, “Toward a Genetic Tool Development Pipeline for Hostassociated Bacteria”, Current Opinion in Microbiology, 2017 38 (link)T. C. Chappell, N. U. Nair, “Co-utilization of Hexoses by a Microconsortium of Sugar-Specific E.coli Strains”, Biotechnology & Bioengineering, 2017 114(10) (link)J. I. Marcus , S. Hassoun, N. U. Nair, “Computational Prediction of Functional Abortive RNA in E.coli“, Genomics, 2017 109(3-4) (link)N. Hassanpour, E. Ullah, M. Yousofshahi, N. U. Nair, S. Hassoun, “Selection Finder (SelFi): AComputational Metabolic Engineering Tool to Enable Directed Evolution of Enzymes”, MetabolicEngineering Communications, 2017 4 (link)Work done as post-doctoral fellow:19. S. R. Goldman†, N. U. Nair†, C. D. Wells, B. E. Nickels, A. Hochschild, “The Primary σ Factorin Escherichia coli Can Access the Transcription Elongation Complex from Solution in vivo”, eLife, 2015 4(link)Work done as graduate student:20. J. Lian, T. Si, N. U. Nair, H. Zhao, “Design and Construction of Acetyl-CoA Overproducing Saccharomycescerevisiae Strains”, Metabolic Engineering, 2014 24 (link)21. J. Sun, Z. Shao, H. Zhao, N. U. Nair, F. Wen, J.H. Xu, H. Zhao, “Cloning and Characterization of a Panel ofConstitutive Promoters for Applications in Pathway Engineering in Saccharomycescerevisiae”, Biotechnology & Bioengineering, 2012 109(8) (link)22. Y. Zou, H. Zhang, T. W. Johannes, R. D. Woodyer, N. U. Nair, J. S. Bruznelle, W. van der Donk, H. Zhao, S.K. Nair, “Crystal Structures of Phosphite Dehydrogenase Provide Insights into Nicotinamide CofactorRegeneration”, Biochemistry, 2012 51(21) (link)23. N. U. Nair, H. Zhao, “Selective Reduction of Xylose to Xylitol from a Mixture of HemicellulosicSugars”, Metabolic Engineering, 2010 12(5) (link)2

24. N. U. Nair, W. L. Tang, D. E. Eriksen, H. Zhao, “Industrial Applications of Enzymes as Catalysts”, Manualof Industrial Microbiology and Biotechnology (3rd edition), R. H. Baltz, J. E. Davies, A. L. Demain (editors),ASM Press 2010 (link1, link2)25. C. A. Denard, N. U. Nair, H. Zhao, “Engineering of Enzymes for Selective Catalysis”, Current OrganicChemistry, 2010 14(17) (link)26. F. Wen, N. U. Nair, H. Zhao, “Protein Engineering in Designing Tailored Enzymes and Microorganisms forBiofuels Production” Current Opinion in Biotechnology, 2009 20(4) (link)27. N. U. Nair, H. Zhao, “Improving Protein Function by Directed Evolution”, The Metabolic PathwayEngineering Handbook, C. D. Smolke (editor) CRC Press 2009 (link)28. N. U. Nair, H. Zhao, “Mutagenic Inverted Repeat Assisted Genome Engineering (MIRAGE)”, Nucleic AcidsResearch, 2009 31(1) (link)29. N. U. Nair, H. Zhao, “Evolution in Reverse: Engineering a D-Xylose-specific XyloseReductase”, ChemBioChem 2008 9(8) (link)30. N. U. Nair, H. Zhao, “Biochemical Characterization of an L-Xylulose Reductase from Neurosporacrassa“, Applied & Environmental Microbiology, 2007 73(6) (link)e. Patents1. H. Zhao, N. U. Nair, M. Racine, R. Woodyer, “Production of xylitol from a mixture of hemicellulosicsugars”, US 96245172. H. Zhao, N. U. Nair, “Xylose reductase mutants and uses thereof”, US 8822661f. Presentations & Posters(underlined) presenting authorInvited Talks:1. N. U. Nair, “What is Synthetic Biology?”, Intellectual Property Law in the Age of Synthetic Biology,Medford, MA, 10/13/20152. N. U. Nair, “Synthetic Biology in the Nair Lab”, Department of Biology, Tufts University, Medford, MA,11/5/20153. N. U. Nair, “Using Synthetic Biology to Engineer Programmable Therapeutic Bacterial Vectors”, Cellular,Molecular, and Developmental Biology Program, Graduate School of Biomedical Sciences, Tufts MedicalSchool, Boston, MA, 1/17/20174. N. U. Nair, “Engineering and Programming Microbes”, Tufts Giving, Tufts University, Medford, MA,3/24/20175. N. U. Nair, “Using Synthetic Biology to Engineer the Gut Microbiome and Treat Inborn Errors ofMetabolism (IEMs)” World Orphan Drug Congress USA, Washington, D. C., 4/19/20176. N. U. Nair, “New Design Rules for Engineering a Non-native Nutrient Assimilation System” Society forIndustrial Microbiology & Biotechnology (SIMB) Annual Meeting, Denver, CO, 7/31/20177. N. U. Nair, “Elucidating Design Rules to Engineer Non-Native Nutrient Assimilation ( and also onengineering gut microbes as therapeutic vectors)”, Department of Chemical & Biomolecular Engineering,North Carolina State University, Raleigh, NC, 9/8/20178. N. U. Nair, “Engineering a Gut Microbe to Treat Inborn Errors of Metabolism” American Institute ofChemical Engineers (AIChE) Annual Meeting, Minneapolis, MN, 11/01/20179. N. U. Nair, “On How to Convince Microbes to not be Picky Eaters”, Department of Chemical &Biomolecular Engineering, Cornell University, Ithaca, NY, 1/29/201810. N. U. Nair, “How to Convince Microbes to not be Picky Eaters”, Department of Chemical & BiomolecularEngineering, University of Illinois, Urbana, IL, 9/13/201811. N. U. Nair, “How to Convince Baker’s Yeast to not be a Picky Eater”, Department of Chemical & BiologicalEngineering, Iowa State University, Ames, IA, 2/7/20193

12. N. U. Nair, “Biomolecular Systems to Study and Engineer Microbiota and Probiotics”, American Institute ofChemical Engineers (AIChE) Annual Meeting, Orlando, FL, 11/12/2019 (accepted invitation)Contributed Talks:1. N. Hassanpour, B. Gaynor, M. Yousofshahi, S. Hassoun, N. U. Nair, “Automated Selection Finder (ASF) ForDirected Evolution”, International Workshop on Bio-Design Automation, Boston (IWBDA), MA, 6/11/20142. J. I. Marcus, S. Hassoun, N. U. Nair, “Search for Functional Abortive RNAs in E. coli”, Tufts SummerScholars Seminar, Tufts University, 8/8/20143. N. Hassanpour, E. Ullah, M. Yousofshahi, S. Hassoun, N. U. Nair, “Enabling Selection in Directed Evolutionof Enzymes Via Cellular Engineering”, Synthetic Biology, Engineering, Evolution, and Design (SEED)Meeting, Boston, MA, 6/12/20154. N. Hassanpour, E. Ullah, M. Yousofshahi, S. Hassoun, N. U. Nair, “Enabling Selection in DirectedEvolution of Enzymes via Cellular Engineering (SelFi)”, American Institute of Chemical Engineers (AIChE)Annual Meeting, Salt Lake City, UT, 11/10/20155. J. I. Marcus, B. Motta Nascimento, S. Hassoun, N. U. Nair, “Discovery and Design of Novel RegulatoryNoncoding RNA in Bacteria”, American Institute of Chemical Engineers (AIChE) Annual Meeting, Salt LakeCity, UT, 11/12/20156. J. I. Marcus, B. Motta Nascimento, S. Hassoun, N U. Nair, “Discovery and Design of Novel RegulatoryNoncoding RNA in Bacteria” American Chemical Society Biotechnology Division (ACS BIOT) SpringMeeting, San Diego, CA, 3/13/20167. V. Endalur Gopinarayanan, N. U. Nair, “Re-engineering Signal Transduction Enables Efficient NutrientAssimilation”, American Chemical Society Biotechnology Division (ACS BIOT) Spring Meeting, San Diego,CA, 3/13/20168. N. Hassanpour, E. Ullah, M. Yousofshahi, S. Hassoun, N. U. Nair, “SelFi: Selection Finder for the DirectedEvolution of Enzymes”, American Chemical Society Biotechnology Division (ACS BIOT) Spring Meeting,San Diego, CA, 3/14/20169. T. C. Chappell, K. Vik, N. U. Nair, “Engineered Microconsortium of Lactic Acid Bacteria to CombatWound Infections” American Institute of Chemical Engineers (AIChE), San Francisco, CA, 11/17/201610. T. C. Chappell, N. U. Nair, “Engineered Consortium Overcomes Substrate-Induced Inefficiencies in HexoseCatabolic Pathways”, American Institute of Chemical Engineers (AIChE) Annual Meeting, San Francisco,CA, 11/18/201611. V. Endalur Gopinarayanan, N. U. Nair, “Engineered Signal Transduction Coupled with Gene CircuitsEnables Efficient Assimilation of Native and Foreign Nutrients in Saccharomyces cerevisiae”, AmericanInstitute of Chemical Engineers (AIChE) Annual Meeting, San Francisco, CA, 11/14/201612. S. Amin, V. Endalur Gopinarayanan, N. U. Nair, S. Hassoun, “Enhancing Pathway Synthesis Using GeneticInformation” American Institute of Chemical Engineers (AIChE) Annual Meeting, San Francisco, CA,11/15/201613. Z. S. J. Mays, N. U. Nair, “Developing Microbiome-bots to Treat Inborn Errors of Metabolism”, AmericanChemical Society Biotechnology Division (ACS BIOT) Spring Meeting, San Francisco, CA, 4/2/201714. B. Motta Nascimento, N. U. Nair, “Engineering Biosynthetic Routes to High-performance Non-naturalPolymers”, American Chemical Society Biotechnology Division (ACS BIOT) Spring Meeting, San Francisco,CA, 4/3/201715. V. Endalur Gopinarayanan, C. Hubert, E. Paul, N. U. Nair, “New Design Rules for Engineering a NutrientAssimilation System”, Biochemical & Molecular Engineering XX Meeting, Newport Beach, CA, 7/19/201716. V. Endalur Gopinarayanan, N. U. Nair, “On how to convince microbes to be a less picky eater”, SyntheticBiology, Engineering, Evolution, and Design (SEED) meeting, Scottsdale, AZ, 6/6/201817. S. A. Amin, N. U. Nair, S. Hassoun, “Expecting the Unexpected: Synthesis Pathway-Host IncompatibilityDue to Metabolic Network Disruption”, American Institute of Chemical Engineers (AIChE) Annual Meeting,Pittsburgh, PA, 10/31/20184

18. V. D. Trivedi, V. Endalur Gopinarayanan, N. U. Nair, “A Semi-Synthetic Regulatory Infrastructure CanRemodel Yeast Global Phenotypic State for Rapid Growth on Non-Native Nutrients of Choice”, AmericanInstitute of Chemical Engineers (AIChE) Annual Meeting, Pittsburgh, PA, 11/1/201819. J. R. Bober, N. U. Nair, “Balancing Kinetic and Thermodynamic Barriers to Isomerization Catalysis inProbiotic Lactobacillus plantarum”, American Institute of Chemical Engineers (AIChE) Annual Meeting,Pittsburgh, PA, 11/1/201820. Z. S. J. Mays, N. U. Nair, “Engineering “Sticky” Probiotics”, American Chemical Society BiotechnologyDivision (ACS BIOT) Spring Meeting, Orlando, FL, 4/1/201921. T. C. Chappell, N. U. Nair, “Using a Consortium of Lactic Acid Bacteria (LAB) to Combat Biofilms andInfections”, American Chemical Society Biotechnology Division (ACS BIOT) Spring Meeting, Orlando, FL,4/2/201922. V D. Trivedi, N. U. Nair, “Developing and Characterizing Peptide Bacteriocins as AntimicrobialTherapeutics”, American Chemical Society Biotechnology Division (ACS BIOT) Spring Meeting, Orlando,FL, 4/3/201923. J. R. Bober, N. U. Nair, “Surpassing Multiple Barriers to Isomerization Catalysis for Tagatose Biosynthesis”,Enzyme Engineering XXV, Whistler, British Columbia, Canada, 9/16/2019Contributed Posters:1. N. Hassanpour, B. Gaynor, M. Yousofshahi, S. Hassoun, N. U. Nair, “Automated Selection Finder (ASF) forDominant Positive Enzyme Phenotypes”, Boston Bacterial Meeting (BBM), Cambridge, MA, 6/12/20142. J. I. Marcus, S. Hassoun, N. U. Nair, “Search for functional abortive RNAs in E. coli”, Tufts SummerScholars Poster Session, Tufts University, Medford, MA, 10/9/20143. J. I. Marcus, S. Hassoun, N. U. Nair, “Search for Functional Abortive RNA in Bacteria”, Synthetic Biology,Engineering, Evolution, and Design (SEED) Meeting, Boston, MA, 6/12/20154. V. Endalur Gopinarayanan, N. U. Nair, “Engineering a Synthetic Regulon in Saccharomyces cerevisiae forEfficient Xylose Utilization”, Synthetic Biology, Engineering, Evolution, and Design (SEED) Meeting,Boston, MA, 6/12/20155. J. I. Marcus, S. Hassoun, N. U. Nair, “Mining for novel regulatory noncoding RNA in bacteria” BostonBacterial Meeting, Cambridge, MA, 6/18/20156. E. Paul, V. Endalur Gopinarayanan, N. U. Nair, “Engineering a sensor in S. cerevisiae for arabinoseutilization”, The Leadership Alliance National Symposium (LANS), Stamford, CT, 7/25/20157. N. Hassanpour, E. Ullah, M. Yousofshahi, N. U. Nair, S. Hassoun, “Selection Finder (SelFi) for DirectedEvolution of Enzymes” Computational Aspects of Biological Information (CABI) Symposium, Cambridge,MA, 12/1/20158. T. C. Chappell, K. Vik, N. U. Nair, “Combating P. aeruginosa Biofilms by Engineering a Lactic AcidBacteria Microconsortium”, Boston Bacterial Meeting (BBM), Cambridge, MA, 6/14/20169. J. R. Bober, Z. Mays, M. E. Allen, N. U. Nair, “Microbiome-bots for the Treatment of Inborn Errors ofMetabolism”, Boston Bacterial Meeting (BBM), Cambridge, MA, 6/14/201610. J. R. Bober, Z. S. J. Mays, M. E. Allen, N. U. Nair, “Microbiome-bots for the Treatment of Inborn Errors ofMetabolism”, American Institute of Chemical Engineers (AIChE) Annual Meeting, San Francisco, CA,11/14/201611. S. Amin, V. Endalur Gopinarayanan, N. U. Nair, S. Hassoun, “Enhancing Pathway Synthesis Using GeneticInformation”, Computational Aspects of Biological Information (CABI) Symposium, Cambridge, MA,11/30/201612. K. Zachary, J. R. Bober, H.-H. Hsu, X. Jiang, N. U. Nair, “Immobilization of Bacillus subtilis throughphotopolymerization”, Tufts University REU Poster Session, Medford, MA, 8/15/201713. E. Chicklis, S. A. Amin, V. Endalur Gopinarayanan, N. U. Nair, S. Hassoun, “Accounting for MetabolicDisruption in Biological Pathway Synthesis”, Tufts University REU Poster Session, Medford, MA, 8/15/201714. S. Amin, V. Endalur Gopinarayanan, N. U. Nair, S. Hassoun, “ProSol DB: A Protein Solubility Database”,ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB),Cambridge, MA, 8/20/175

15. B. Motta Nascimento, N. U. Nair, “Characterizing and Engineering of a Membrane Enzyme for BiosyntheticProduction of New Polymers”, Boston Bacterial Meeting, Cambridge, MA, 6/1/201816. J. R. Bober, N. U. Nair, “Balancing Kinetic and Thermodynamic Barriers to Isomerization Catalysis inProbiotic Lactobacillus plantarum”, Boston Bacterial Meeting, Cambridge, MA, 6/1/201817. B. Motta Nascimento, N. U. Nair, “Characterizing and Engineering of a Membrane Enzyme for BiosyntheticProduction of New Polymers”, Protein Society 32nd Annual Meeting, Boston, MA, 7/12/1818. J. R. Bober, N. U. Nair, “Balancing Kinetic and Thermodynamic Barriers to Isomerization Catalysis inProbiotic Lactobacillus plantarum”, Protein Society 32nd Annual Meeting, Boston, MA, 7/12/1819. V. Endalur Gopinarayanan, N. U. Nair, “Developing a Rational Design Paradigm for Non-Native SubstrateAssimilation for S. cerevisiae”, Metabolic Engineering 12, Munich, Germany, 6/26/1820. E. Chavez, S. A. Amin, N. U. Nair, S. Hassoun, “Building a Better Metabolic Model of E. coli Using EnzymePromiscuity”, Tufts University REU Poster Session, Medford, MA, 8/7/201821. T. B. Nicks, N. U. Nair, “Engineering the Natural Competence Machinery of Bacillus subtilis”, BostonBacterial Meeting, Cambridge, MA, 6/6/201922. V. D. Trivedi, N. U. Nair, “Role of Charge-based Interactions in Bacteriocin Pediocin PA-1 Function”,Boston Bacterial Meeting, Cambridge, MA, 6/6/2019g. FundingTotal funding received by Nair lab (9/2013 – current): 3,138,506All amounts include direct costs (DC) and facilities and administration (F&A) overhead.Current and Completed Extramural Grants:CurrentDP2-HD091798 (PI: Nair)9/30/2016 – 8/31/20210.75 summerNational Institutes of Health 2,340,000Metabolic Engineering in Humans: Altered Gut Microbes as a Therapeutic PlatformCBET-1935354 (PI: Nair)12/1/2019 – 11/30/2022National Science Foundation 323,320A Foundational Platform to Engineer Synthetic Heterotrophy in Yeast0.30 summerCCF-1909536 (PI: Hassoun, Co-PI: Nair, Liu)10/1/2019 – 9/30/20220.10 summerNational Science Foundation 499,970 (Nair portion: 123,363)Tools and Experimental Validation for Predicting Enzymatic Promiscuity and its ProductsGrant #503763 (PI: Nair, Co-PI: Camilli)7/8/2018 – currentn/aDepartment of Energy JGI DNA Synthesis Prog. 50 Mb synthetic DNA (in-kind support)Developing Bacillus subtilis Endospore-display as a Platform for Rapid Cell-free Pathway Prototyping andBioprocessingR01-GM132391 (PI: Hassoun, Co-I: Nair 4)11/1/2019 – 10/31/20240.50 summerNational Institutes of Health 2,076,876 (Nair portion: 21,898)Computational Techniques for Advancing Untargeted Metabolomics AnalysisCompletedCCF-1421972 (PI: Hassoun, Co-PI: Nair)8/14/2014 – 7/1/20180.05 summerNational Science Foundation 309,774 (Nair portion: 116,349)Design Tools and their Experimental Validation for Synthetic Biological SystemsR03-HD090444 (PI: Nair)8/18

2013-Present Assistant Professor, Department of Chemical and Biological Engineering (ChBE), Tufts University, Medford, MA. 2017-Present Adjunct Assistant Professor, Program in Cellular, Molecular, and Developmental Biology (CMDB) of the Tufts Graduate School of Biomedical Sc

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