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MIT Industrial Liaison Program March 2009 |

Toxicology Research This survey by MIT's Industrial Liaison Program identifies selected research in the area of chemical and environmental toxicology, toxicogenomics and epidemiology at MIT. For more information, please contact MIT’s Industrial Liaison Program at +1-617-253-2691.

TOXICOLOGY .................................................................................................................................................................. 4 CENTER FOR ENVIRONMENTAL HEALTH SCIENCES ........................................................................................................ 4

CEHS Pilot Projects..................................................................................................................................................... 4 (1) "Changes in the Spectrum of tRNA Secondary Modifications as Biomarkers of Exposure" ............................................5 (2) "Structural Studies of DNA Repair Protein Human Alkyladenine Glycosylase"...............................................................5 (3) "Inflammation-associated Prostate Cancer: Development of Mouse Models for Assay of Environmental Contaminants" ...............................................................................................................................................................................5 (4) "Direct Coupling of Nanofluidic Preconcentration System and Conventional Mass Spectrometry"................................5 (5) "Detection of Toxic Events in the Liver in vivo using Single Wall Carbon Nanotubes" ..................................................5 (6) "Exploring DNA Damage Response Networks with High-Dimensional Information Theoretic Statistics" ....................6

The CEHS Bioengineering for Toxicology Research Core ....................................................................................... 6 The CEHS Mutation and Cancer Research Core....................................................................................................... 6 The CEHS Environmental Health Systems Research Core ....................................................................................... 6

RESEARCH THRUST AREA: COMPUTATIONAL BIOENGINEERING, GENOMICS, SYSTEMS AND SYNTHETIC BIOLOGY............................................................................................................................................................................ 7

Application of Optimal Experimental Design in the Context of Systems Biology.................................................... 7 PROF. ERIC J ALM............................................................................................................................................................. 7

Alm Laboratory for Microbiology: Evolutionary, Ecological & Environmental Systems Biology ....................... 7 Induced and Targeted Mutagenesis of Plastid Encoded Genes..................................................................................................8

PROF. PETER C DEDON ..................................................................................................................................................... 8 Dedon Lab..................................................................................................................................................................... 9 Genomic Determinants of DNA Damage.................................................................................................................... 9

PROF. WILLIAM M DEEN.................................................................................................................................................. 9 The Nucleotide Pool as a Target for Nitrosative Deamination During Inflammation .......................................... 10 Toxicity of Endogenous Nitric Oxide ........................................................................................................................ 10

PROF. BEVIN P ENGELWARD .......................................................................................................................................... 11 Engelward Lab ........................................................................................................................................................... 13

Research Areas in the Engelward Laboratory:..........................................................................................................................14 PROF. JOHN M ESSIGMANN ............................................................................................................................................ 14

Essigmann Lab ........................................................................................................................................................... 15 Site specific mutagenesis by DNA adducts...............................................................................................................................15

PROF. JAMES G FOX........................................................................................................................................................ 17 Animal Model and Pathology Facilities Core .......................................................................................................... 18 Pathogenesis of Helicobacter Induced Hepatitis and Tumorigenesis .................................................................... 18 “Nitric oxide shown to cause colon cancer: Study offers proof of compound's role in disease”......................... 18

PROF. ERNEST FRAENKEL............................................................................................................................................... 19 Fraenkel Lab: Systems Biology of Disease.............................................................................................................. 19

Disease.........................................................................................................................................................................................20


Using High-throughput Data to Understand and Modify Biological Systems........................................................................20 PROF. LINDA G GRIFFITH ............................................................................................................................................... 20

Microscale Liver and Bone Marrow Tissue Engineering........................................................................................ 22 A Cell Culture Assay for Gene-Damaging Chemicals ............................................................................................. 22

PROF. LEONA D SAMSON ............................................................................................................................................... 23 Samson Lab: ............................................................................................................................................................... 23

Toxicogenomics ..........................................................................................................................................................................24 Gene Environment Interactions..................................................................................................................................................24 Genomic Phenotyping.................................................................................................................................................................24 Spontaneous Mutagenesis ..........................................................................................................................................................25

“Prenatal arsenic exposure detected in newborns: Research could lead to test for screening populations for the poison”.................................................................................................................................................................. 25 “DNA-damage test could aid drug development” ................................................................................................... 27

PROF. RAM SASISEKHARAN............................................................................................................................................ 28 Sasisekharan Laboratory ........................................................................................................................................... 29

Glycobiology ...............................................................................................................................................................................29 Human Pathophysiology & Biotherapeutics .............................................................................................................................29 Carbohydrate-Mediated Mechanisms of Tumor Progression ..................................................................................................30

DR. PAUL L SKIPPER....................................................................................................................................................... 30 PROF. STEVEN R TANNENBAUM .................................................................................................................................... 30

Biological Engineering Accelerator Mass Spectrometry (BEAMS) Laboratory ................................................... 31 Research in Toxicology .............................................................................................................................................. 32 Nitric Oxide: Chemistry and Pathophysiology......................................................................................................... 32 Tissue Engineering for Drug Development and Chemical Toxicity ....................................................................... 32 Quantitative Ultramicro Measurements for Drug and Carcinogen Metabolism................................................... 32

PROF. WILLIAM G THILLY ............................................................................................................................................. 33 PROF. FOREST M WHITE ................................................................................................................................................ 34

Forest White Lab ........................................................................................................................................................ 35 Epidermal Growth Factor Receptor Signaling Network ..........................................................................................................35 T Cell Signaling ..........................................................................................................................................................................35 Technology Development...........................................................................................................................................................36

DR. JOHN S WISHNOK (PETE) ........................................................................................................................................ 36 PROF. GERALD N WOGAN .............................................................................................................................................. 36

Fluorescence Labeling of Nucleoside Adducts for Molecular Epidemiology ........................................................ 38 REALITY MINING............................................................................................................................................................. 38

Epidemiology and Information Dissemination......................................................................................................... 39


TOXICOLOGY

CENTER FOR ENVIRONMENTAL HEALTH SCIENCES Director: Prof. Leona D. Samson, Professor of Toxicology, and Biological Engineering, http://web.mit.edu/be/people/samson.shtml Deputy Director: Prof. Peter C. Dedon, Professor of Toxicology and Biological Engineering Associate Head, Department of Biological Engineering, http://web.mit.edu/be/people/dedon.shtml The mission of the MIT Center for Environmental Health Sciences (CEHS) is to take a leadership role in facilitating and promoting research into the biological effects of exposure to environmental agents in order to understand and predict, how such exposures affect human health. Three fundamental components influence the health effects of environmental exposures: the nature of the exposure itself, the duration of that exposure, and how well the exposed organism is equipped to deal with the exposure, in other words, the organism’s genetic susceptibility. These are the broad-brush strokes of what environmental health sciences research is all about. As Director and Deputy Director of the CEHS, Professors Samson and Dedon believe that it is their role to identify and bring together appropriate MIT faculty members who are doing top-notch research that is relevant to the environmental health sciences. To this end, the goals of the MIT CEHS are to achieve the following: one, to create an intellectual hub (and sub-hubs) that will foster multidisciplinary approaches to environmental health research questions; and two, to support centralized resources and facilities for groups of investigators that would be impractical, implausible or impossible for individual investigators to support and maintain. We are currently expanding our overall mission to address Global Environmental Health issues. Toward this end the MIT CEHS, along with the Johns Hopkins Center in Urban Environmental Health, plans to launch a Global Alliance that will start with the Chulabhorn Research Institute in Thailand and the National University of Singapore and which will hopefully grow to include a number of developing countries, particularly in Asia… More at http://cehs.mit.edu/

CEHS Pilot Projects A significant portion of the Center's funding is allocated for Pilot Projects. Pilot projects are particularly important to the Center because they foster innovative research, help to broaden membership, and facilitate collaborations between research groups that might not otherwise occur. The goals of the MIT CEHS Pilot Project Program are to achieve the following: • Provide initial support for investigators to establish new lines of research in environmental health • Allow exploration of possible innovative new directions representing a significant departure from

ongoing funded research for established investigators in environmental health sciences • Stimulate investigators from other areas of endeavor to apply their expertise to environmental

health research Six pilot projects with a start date of April 1, 2008:


(1) "Changes in the Spectrum of tRNA Secondary Modifications as Biomarkers of Exposure" Prof. Peter C. Dedon, Professor of Toxicology and Biological Engineering Associate Head, Department of Biological Engineering, http://web.mit.edu/be/people/dedon.shtml This project will explore the utility of RNA secondary modifications as biomarkers of exposure. The development of bioanalytical methods for characterizing the spectrum of RNA 2˚ modifications will be useful for many studies beyond those emphasizing biomarker development, such as defining the poorly characterized spectrum and function of secondary modifications of nucleobases in rRNA, miRNA, and other RNA species.

(2) "Structural Studies of DNA Repair Protein Human Alkyladenine Glycosylase" Catherine Drennan, Professor of Chemistry and Biology, http://web.mit.edu/chemistry/www/faculty/drennan.html This project is to understand how the cell protects against DNA alkylation by environmental carcinogens.

(3) "Inflammation-associated Prostate Cancer: Development of Mouse Models for Assay of Environmental Contaminants" Dr. Susan Erdman, Principal Research Scientist, Division of Comparative Medicine; Assistant Director, Chief of Clinical Resources; http://web.mit.edu/comp-med/postdoc/dcmstaff.html This project is to develop novel mouse models of prostate cancer for study of environmental contaminant exposures in humans. This project will utilize these mice to test whether inflammation and environmental contaminants may act as co-factors that promote prostate cancer development. The goal is to provide murine models to study prostate cancer in humans.

(4) "Direct Coupling of Nanofluidic Preconcentration System and Conventional Mass Spectrometry" Jongyoon Han, Associate Professor of Electrical Engineering and Biological Engineering, http://web.mit.edu/be/people/han.shtml This project will couple a nanofluidic peptide/protein preconcentrator chip to mass spectrometry (MS) via various dispensing methods and to qualify it as efficient front-end signal enhancement tool for MS. Using the proposed solution, the concentration of low-abundance peptides and proteins can be increased by several orders of magnitudes on chip and sent to mass spectrometer directly without any manual transfer. This way, biologically significant, but highly diluted biomolecules can be detected at unprecedented high sensitivity with minimal sample loss.

(5) "Detection of Toxic Events in the Liver in vivo using Single Wall Carbon Nanotubes" Michael Strano, Charles (1951) and Hilda Roddey Career Development Associate Professor of Chemical Engineering, http://web.mit.edu/cheme/people/profile.html?id=31 Steven Tannenbaum, Underwood-Prescott Professor of Chemistry and Toxicology, http://web.mit.edu/chemistry/www/faculty/tannenbaum.html Gerald Wogan, Professor of Chemistry and Biological Engineering, Emeritus, http://web.mit.edu/be/people/wogan.shtml


This project is to develop the DNA-SWNTs sensors for in vivo detection of toxic events associated with DNA damage. The objective is to further validate the identification method in vitro and in vivo using the mouse liver as a model and to demonstrate the detection of chlorambucil as a model DNA damaging agent.

(6) "Exploring DNA Damage Response Networks with High-Dimensional Information Theoretic Statistics" Professor Bruce Tidor, Professor of Biological Engineering and Computer Science Associate Chair of the Faculty, http://web.mit.edu/be/people/tidor.shtml This project is to refine, adapt, and apply the methods for use of datasets relevant to environmental-health interactions.

The CEHS Bioengineering for Toxicology Research Core This Research Core represents an exciting new direction for the CEHS that will bring many of the strengths of the Biological Engineering Department and the emerging Computational and Systems Biology Initiative (CSBi) into the Center. The approaches that will be adopted here include the following: using engineered tissues (such as liver and bone marrow) to monitor and dissect biological responses to toxic environmental agents; linking systematic experiments to quantitative models of cellular responses to damaging agents (the CSBi paradigm as shown in the adjacent figure); developing genomic and proteomic approaches for these systematic measurements; and applying state-of-the-art mechanical engineering to devise new ways of monitoring biological events and single molecule biochemical events… More at http://cehs.mit.edu/research.html#Bioengineering_and_Toxicology

The CEHS Mutation and Cancer Research Core This Research Core builds upon the historical strength of the Center. Collectively this group addresses how exposure to DNA damaging agents affects the health of cells, tissues, animals, people and populations, and in particular how these agents cause cancer and contribute to other diseases associated with the aging process. The damaging agents include reactive oxygen and nitrogen species, alkylating agents, and radiation (all ubiquitous in our environment) and the tools used include x-ray crystallography, state-of-the-art mass spectrometry, organic chemistry and biochemistry, bacterial and yeast model organisms, cultured mammalian cells, mathematical modeling of signal transduction pathways, RNAi manipulation of gene expression, transgenic and knock-out mouse model systems, genetic polymorphism detection in human populations, transcriptional profiling, functional genomics and the accompanying bioinformatics required to analyze the data. The goals are to determine the molecular details of how exposure to environmental agents cause detrimental health effects, and perhaps more importantly to determine the molecular details of how cells, tissues, animals, and people ameliorate these detrimental effects. See http://cehs.mit.edu/research.html#Mutation_and_Cancer

The CEHS Environmental Health Systems Research Core This Research Core is to understand, holistically, the relationships that link ecological processes and human health. This includes the traditional 'fate and transport' model (in which chemical releases are transported and modulated by processes in the ecosystem, thus governing the extent of human exposure to the chemicals). However, advances over the past decade mandate a broader


view of environment-health linkages, in which genomics and ecology play an increasingly prominent and important role. Future advances require better understanding of evolution, gene flow, and ecosystem processes along with progress in chemical and physical modeling and measurement. Gene flow, for example, can affect the distribution of pathogenicity, or the acquisition of antibiotic resistance or biodegradative capability in microbial communities. Ecosystem processes govern the nature of coexisting populations at scales from that of the gut to that of continents, with direct effects on humans at all scales… More at http://cehs.mit.edu/research.html#Environmental_Health_and_Systems

RESEARCH THRUST AREA: COMPUTATIONAL BIOENGINEERING, GENOMICS, SYSTEMS AND SYNTHETIC BIOLOGY Faculty: Prof. Bruce Tidor (MIT), Eugenio Ferreira and Isabel Rocha (U. Minho) MIT Portugal Bio-E Research [Research thrust area identified for collaborative Portuguese and MIT faculty and doctoral student research project.] This thrust area is focused on: (i) Application of optimal experimental design techniques in the context of System Biology; (ii) Synthetic Biology by the design of bacteria to produce therapeutic agents and the use of life bacteria as targeted delivery systems; and (iii) Toxicogenomics to elucidate gene-environment interactions and favors the establishment of parallelisms between different organisms with impact in Environmental Safety and Human Health, Agriculture and Biotechnology. http://www.mitportugal.org/bioengineering-systems/research.html#thrust3

Application of Optimal Experimental Design in the Context of Systems Biology Systems biology is expected to bring major benefits to industrial biotechnology especially in the development of efficient cell factories, by speeding up the development process, and ensuring that new products can be brought to the market faster or that there can be a faster improvement of existing bioprocesses. Therefore, the ultimate aims of this project are associated with aiding efforts to the optimization of industrial biotechnology processes like the production of bulk chemicals (e.g. succinate or lactate), biofuels (e.g. bioethanol) and specialty chemicals (e.g. vitamins and antibiotics). A set of mathematical and computational techniques will be developed and applied to the problem of designing efficient and informative experiments for the identification of kinetic models representing metabolic reactions.

PROF. ERIC J ALM Henry L Doherty Assistant Professor of Ocean Utilization; Assistant Professor of Biological Engineering; Associate Member, Broad Institute; http://cee.mit.edu/alm http://almlab.mit.edu/ALM/ALM.html ; http://csbi.mit.edu/people/alm.html

Research in the Alm group includes both computational/theoretical and experimental approaches to understanding the evolution of microorganisms, emphasizing a 'systems-level' perspective.

Alm Laboratory for Microbiology: Evolutionary, Ecological & Environmental Systems Biology The Alm lab develops complementary computational and experimental methods for studying microbial evolution. Ongoing projects include the detection of selection in ancestral bacteria, the experimental evolution of marine Vibrio, and the refinement of the Tree of Life. More at http://almlab.mit.edu/ALM/Research/Research.html


Induced and Targeted Mutagenesis of Plastid Encoded Genes Diatoms belong to the most abundant microalgae in our oceans. Due to their vast abundance and ecological success their contribution (20%) to the global annual biomass production equals the productivity of the rain forests. Focusing on the marine Diatom Phaeodactylum tricornutum we are studying a unique mechanism that allows us to induce random mutagenesis within in a plastid encoded target gene. So far mutagenesis was induced in psbA (encoding for the D1 protein of photosystem II) and the 16S rRNA gene. Currently we examine how precisely we are able to restrict mutagenesis to an area of interest. Besides understanding the underlying molecular mechanism, we are also interested in providing a useful tool for bioengineering purposes. So far, possible target genes only include genes that - after experiencing point mutations - can induce a selectable phenotype. To overcome this restriction we use fluorescence-activated cell sorting to establish the selection of mutants with deviating photosynthetic phenotypes. http://almlab.mit.edu/ALM/Research/Entries/2008/5/6_Induced_and_targeted_mutagenesis_of_plastid_encoded_genes.html

PROF. PETER C DEDON Professor of Toxicology and Biological Engineering; Associate Department Head, Biological Engineering (BE); Deputy Director, Center for Environmental Health Sciences (CEHS) http://web.mit.edu/be/people/dedon.htm ; http://dedon.mit.edu/index.html ; http://csbi.mit.edu/people/dedon.html

Dr. Peter C. Dedon of the Division of Toxicology joined the MIT faculty in 1991. He was named the first Samuel A. Goldblith Career Development in 1993 and was promoted to full professor without tenure in 2003. After obtaining an undergraduate degree in toxicology at St. Olaf College, he earned the M.D. and Ph.D. in pharmacology at the University of Rochester. Before coming to MIT, he did postdoctoral research in biology at the University of Rochester and in biological chemistry and molecular pharmacology at Harvard Medical School. Professor Dedon's research crosses the boundaries of cancer pharmacology and genetic toxicology. It has led to important discoveries that advance the understanding of the mechanisms by which drugs and carcinogens damage DNA and cause mutations. He is a world leader in demonstrating how experimental results on DNA in vitro apply to DNA in living cells. The model compounds he has used for this work are a class of antibiotics called enediynes and the surprising results he has obtained with these compounds may lead to the development of more potent anti-cancer drugs. Dedon's work includes the interactions of most genotoxins with DNA, which have been studied with isolated, naked DNA, an essential simplification for determining gross chemical mechanisms. DNA rarely exists as such in the living organism, however, in which it is packaged along with proteins into the compact mass of chromatin. There is evidence to suggest that chromatin structure changes the way genotoxins interact with DNA in vivo, and it is the long-term objective of the research in Dr. Dedon's laboratory to delineate the rules that govern the interactions of small molecules with chromatin from toxicologic, pharmacologic and biochemical points of view. An understanding of the role that chromatin structures play in the biochemistry of DNA-interactive agents is essential to the design of selective chemotherapeutic agents and


chemical probes of DNA and chromatin structure, and to the understanding of the mechanisms of mutagenicity, carcinogenicity, and DNA-directed toxicity of small molecules.

Dedon Lab http://dedon.mit.edu/index.html

Genomic Determinants of DNA Damage One of the major challenges in understanding mutagenesis and carcinogenesis is to define the relationship between DNA damage and mutations or cell death. Central to this problem is the question of what determines the location and quantify of DNA damage arising in cells by endogenous processes or by exposure to genotoxic agents. The location of DNA lesions is generally presumed to be a critical determinant of the cellular response, yet we know little about the determinants of damage location. Nor is there information, beyond the level of individual genes, about the larger picture of differential rates of repair across the genome. Damage patterns and trends that occur consistently are more likely to be important in the cellular response than those that occur in isolation, and there is abundant evidence that genotoxic agents do not damage DNA randomly. To better identify the determinants of DNA damage in cells, we have developed a research program to map sites of DNA damage produced by well characterized drugs and toxins across an entire genome and correlate the damage locations with features of genomic organization and nuclear architecture.

PROF. WILLIAM M DEEN Carbon P Dubbs Professor of Chemical and Biological Engineering; Graduate Registration Officer (Chem-E) http://web.mit.edu/cheme/people/faculty/deen.html http://web.mit.edu/wmdeen/www/index.html http://web.mit.edu/be/people/deen.htm Deen’s Research Focus: Bioengineering, Transport Phenomena, Membrane Separations The common theme of our research group is the application of engineering principles to biological materials or systems. Most of the problems we work on are motivated by a desire to understand normal or pathophysiological processes occurring in the body, and their implications for the prevention, diagnosis, or treatment of human disease. Much of the work entails collaboration with physicians, physiologists, and other biological scientists. One area of focus involves the fundamentals of water and macromolecule transport in liquid-filled spaces of molecular dimensions. This is important for understanding mass transfer in body tissues, as well as for designing membranes or other separation devices. A key objective of our work is to develop models to predict transport hindrances in porous or fibrous materials, based on the size, shape, and electrical charge of the permeating molecule and the nanostructural properties of the material. The theoretical models are tested using membranes or gels of well-defined structure. They are used also to interpret experiments that probe the permeability properties of mammalian kidney capillaries in health and disease. We are endeavoring to relate the ultrastructure of those capillaries to their transport characteristics, through detailed analyses of convection and diffusion at the cellular and subcellular levels.


Another area of interest is transport and reaction of nitric oxide (NO) in biological systems. It has been shown in recent years that NO is synthesized throughout the body and that it is a key intercellular messenger molecule (e.g., in the regulation of blood pressure). Transient increases in NO synthesis are important also in the response of the immune system to infection, in that the toxicity of NO helps to kill invading microorganisms. However, sustained high levels of NO synthesis (as may occur with chronic infection or inflammation) carries with it the risk of collateral damage to host tissues, including mutational changes that may lead to cancer. To provide insight into the biological effects of NO and of the various reactive NOx species derived from NO, we are studying reaction kinetics and diffusion in aqueous solutions and cell cultures. Using such data, we are developing computational models to predict the consequences of NO synthesis by cells in vivo or in vitro.

The Nucleotide Pool as a Target for Nitrosative Deamination During Inflammation The goal of this research project is to explore the cellular purine nucleotide pool as a potential target for damage caused by chemical mediators of inflammation. The hypothesis driving these studies is that the broader cellular distribution and the greater solvent exposure of free nucleosides and nucleotides will lead to significantly higher level of reactivity of their base moiety with inflammation-related chemical agents. This hypothesis is being tested by developing novel analytical methods and kinetic models of the behavior of the nucleotide pool under inflammatory stress.

Toxicity of Endogenous Nitric Oxide Researchers in numerous branches of medicine and physiology have discovered in recent years that nitric oxide (NO) is routinely synthesized by cells throughout the body, and that maintaining proper concentrations of it is essential for good health. It helps regulate blood pressure, affects clotting, assists the communication among neurons, and plays a role in the immune response to infections, among other beneficial actions. But, unfortunately, NO is both toxic and mutagenic if present in excess, and there are situations in which its production is apparently over stimulated. The sustained, high rate of NO synthesis by immune cells during chronic inflammations provides an example, and may explain the statistical link between persistent inflammations and certain forms of cancer. Chemical damage to cellular proteins, lipids, and DNA results not so much from NO itself, but from a variety of trace nitrogen oxides formed when NO is oxidized in biological fluids. Professor Deen's group has been investigating the fundamental aspects of the production and fate of NO and related nitrogen oxides in biological systems in collaboration with several faculty in the Biological Engineering Division. To assess health risks and design interventions, one needs to know which compounds actually mediate the various harmful effects of excess NO. Underlying that effort is the need to know what their concentrations are near an NO source (e.g., an activated macrophage), and over what distances those concentrations remain elevated. A chemical engineering problem emerges: The concentration fields must reflect the interplay between rates of reaction and diffusion. The modeling problems are made challenging by the complex chemistry, which includes enzymatic sources and sinks for NO, a network of inorganic oxidations that yield other reactive nitrogen oxides, and the interactions of the nitrogen oxides with soluble or structural biomolecules. The geometric complexity of tissues, and even of cell culture systems used to study NO toxicity, adds its own difficulties. Experimentally, few of the compounds of


interest are present at measurable concentrations, and their levels must be inferred from analyses of oxidation end products and biomarkers (e.g., trace levels of nitrogen oxide-modified proteins). The work in Professor Deen's group has yielded several recent insights. A reaction-diffusion model developed to describe the fate of NO released by macrophages cultured on plates revealed that some species will be present only in the immediate vicinity of the cells, but others will exist throughout the culture medium. Accordingly, various chemical reactions will be spatially segregated, even in extracellular fluid. Experiments varying the depth of the liquid medium indicated that NO strongly inhibits its own synthesis by macrophages, a phenomenon that has been demonstrated previously with isolated enzymes but not with intact cells. An analysis of the kinetics of NO production and consumption in macrophages suggested that the maximum NO concentration that can be achieved at any cell number density is about 1 M. This was the first indication of a possible upper limit for NO concentrations at sites of inflammation. Knowing better what to mimic, an apparatus was designed to permit "target cells" (cells that do not produce NO) to be exposed to controlled, micromolecular levels of NO for up to several days. In collaboration with Professor Gerald N. Wogan of the Biological Engineering Division, the effects of NO concentration and total dose (area under the concentration curve) were then characterized in terms of cell survival and several types of cellular damage. It was found that there are dual thresholds for NO toxicity. Toxic effects were not seen unless a minimum concentration and a minimum dose were both exceeded. The concentration threshold for the cell lines used was about 0.5 M (about half the inferred physiological maximum). This is the first quantitative demonstration of toxicity thresholds for NO, and is stimulating a new round of experiments to examine the underlying intracellular events. An important objective in the next few years will be to develop reaction-diffusion models for tissues that will provide a rational means to extrapolate kinetic, diffusional, and cell culture data to pathophysiological conditions in the body.

PROF. BEVIN P ENGELWARD Associate Professor of Biological Engineering; Secretary of the MIT Faculty http://web.mit.edu/be/people/engelward.htm http://web.mit.edu/engelward-lab/

Bevin Engelward graduated from Yale University in 1988. Her formative scientific experience came from studies in the laboratory of Thomas Steitz where she learned crystallographic techniques and about protein and DNA structure. After working as a microscopist for a year and working as a database designer at a software company in Cambridge for a year, Bevin Engelward returned began graduate studies at the Harvard School of Public Health. Thanks to "real world experience", Bevin's appreciation for the luxury of academia drove her to pursue the best training possibilities available. She attended 5 graduate level Biology/Genetics/Biochemistry courses at MIT along with many courses at Harvard. Bevin chose to do her thesis work in the laboratory of Leona D. Samson in the Department of Molecular and Cellular Toxicology. Professor Samson's high standards and forward thinking research agenda were inspirational. Bevin Engelward's thesis work included cloning and characterizing a mammalian DNA repair enzyme. Her studies involved biochemical, cell biological, and mouse work, culminating with the creation of a mouse lacking the 3-Methyladenine DNA Glycosylase DNA repair gene. While still a graduate student, Bevin Engelward applied for a faculty position at MIT in the Division of Toxicology. After being accepted for the position, she graduated from Harvard in 1996 and continued her work in Professor Samson's laboratory as a Post-doctoral fellow for one year. Bevin


Engelward started her own research group at MIT in July 1997. Her research group is interested in the interplay between DNA repair and recombination. Ultimately, Dr. Engelward hopes that her research will contribute to improved ability to identify people who are born with increased susceptibility to cancer so that they can take appropriate precautionary measures. As a toxicologist who studies DNA repair, she is also driven to do research that will help in the identification of agents in our environment that put people at risk for cancer or other diseases. The research goal is to help figure out which agents in our environment are most threatening to human health and which genes are most important for keeping people healthy. It is becoming increasingly clear that people's susceptibility to many diseases, including cancer, is intimately linked to their genetic make up. For example, 55-75% of women who inherit mutations in the BRCA1 gene will get breast cancer before the age of 70. What other genes are important in preventing cancer? What precautions might help prevent cancer and other diseases? In our research, we take advantage of chemical and genetic tools to dissect the consequences of particular DNA adducts, we study the mechanisms that cells use to repair DNA damage, and we study the effects of certain DNA repair deficiencies on susceptibility to cancer. The mission is to use basic research to help solve problems in public health. DNA sequences provide the information necessary for life. However, our genome is constantly under attack by chemicals that destroy the structure of DNA, creating permanent mutations in the DNA sequence. Such mutations can promote diseases, aging, and cancer. Fortunately, the cells have evolved sophisticated mechanisms to repair DNA damage. Research is focused on revealing the molecular mechanisms that cells use to tolerate and repair DNA damage. DNA repair in human cells is a complex process involving nearly a dozen different pathways and over 100 different genes. Analogous repair processes in E. coli and yeast involve many fewer genes, but share fundamental principals. The research is aimed at revealing the underlying principals of DNA repair and the molecular mechanisms that cells use to tolerate DNA damage. Thus, studies of E. coli and yeast lay the foundation for our studies in mammalian cells and mice aimed at elucidating analogous, yet more complex, processes in mammals. DNA damage is inevitable, stemming both from endogenous cellular metabolites as well as agents in our environment. One of today's most pressing public health problems is our lack of knowledge of the types of exposures that are carcinogenic. As Bioengineers, the research is aimed at solving real-world problems using the most appropriate, accurate and quantitative tools available. Consequently, the research approaches are broad -- ranging from biochemistry to genetics to animal studies. Toxicology within BEH: Bevin is a part of the group of toxicology faculty within the Division of Bioengineering and Environmental Health. The toxicology group is focused on molecular mechanisms leading to toxic impacts of chemicals on cellular processes, and is not conducting research in traditional industrial toxicology subjects, which lean toward researching how chemicals affect animal health, as models for human health impacts. With the emphasis on researching the molecular basis for toxicology, this group is contributing toward an overall biological/chemical/engineering systems emphasis in the research on cell biology within BEH. This rigorous approach is a key part of the strategy of BEH that is designed to differentiate it from bioengineering programs at other universities. Bevin's General Research Focus is studying the causes of genetic change in humans -- DNA recombination and deletion -- that lead to loss of genetic information and point mutations. These


types of genetic change lead to cell death, cancer, and other diseases as well as to species evolution. Bevin, her four graduate students and two post-docs are working in two main research areas, funded by NIH and NCI: (1) Developing tools and methods for detection of genetic change in bacteria, yeast, mammalian cell and mouse models. Current slow, manual methods are being advanced toward faster, automated methods that should lead eventually to high-throughput methods in the next five years. (2) With Peter Dedon, studying how endogenous NO, which is released by macrophages as part of the inflammation process, causes DNA rearrangements and point mutations that lead to physical sequence changes.

Engelward Lab http://web.mit.edu/engelward-lab/ It is now well established that cancer is caused by the accumulation of mutations in oncogenes and tumor suppressor genes. In some cases, cancer (and other genetic diseases) can be traced back to single base changes, while in other cases, the root cause can be a large scale gain or loss in DNA sequence information. Such large scale sequence rearrangements are an important class of mutations that not only promote cancer, but also promote aging and other genetic diseases. A major goal of the Engelward laboratory is to help reveal genetic and environmental factors that promote large scale sequence rearrangements in mammals. By understanding the causes of sequence changes, we will become better able to mitigate disease. There are two major classes of large scale sequence changes: those that are caused by joining of DNA ends with minimal influence from DNA sequence, and those that are caused by large scale misalignments of homologous sequences. We are primarily interested in the latter, so called homologous recombination events, and we have applied and developed a number of approaches for detecting this class of sequence change in E. coli, yeast, mammalian cells, and in mice. Most of the approaches developed in this laboratory depend upon a fluorescent readout, which makes it relatively fast and easy to assess the frequency of cells that harbor a particular sequence change (they fluoresce green or yellow, for example). In this laboratory, we created the first mouse in which rare cells that have undergone a homologous recombination event at an integrated transgene can be detected via a fluorescent readout. Using existing and novel tools developed in this laboratory, we have studied both genetic and environmental factors that modulate the frequency of homologous recombination in several species. Some of the things that we have learned are that relatively subtle changes in the structure of DNA can induce large scale sequence changes; that either too much or too little of certain DNA repair enzymes can promote recombination events; that inflammatory chemicals are highly recombinogenic in eukaryotic cells, and that recombination events can be induced as a consequence of heritable changes in the epigenome. Ongoing studies are primarily focused primarily on the effects of radiation and inflammation on genomic stability. In addition to studies of homologous recombination, we are also focused on technology development. Currently, we are developing novel approaches for detecting DNA damage and for measuring DNA repair. Using lab-on-a-chip technologies, we have created a higher throughput assay for detecting DNA damage in isolated mammalian cells, and we are optimizing methodology for applications in cancer research and environmental health.


Research Areas in the Engelward Laboratory: http://web.mit.edu/engelward-lab/research.htm 1. Developing New Tools for Studying Homologous Recombination 2. Understanding Natural Causes of Homologous Recombination 3. Understanding the Underlying Causes of Homologous Recombination

PROF. JOHN M ESSIGMANN William R (1956) and Betsy P Leitch Professor of Chemistry, Toxicology and Biological Engineering http://jessig.mit.edu/jmegroup/ http://web.mit.edu/be/people/essigmann.htm http://web.mit.edu/chemistry/www/faculty/essigmann.html http://csbi.mit.edu/people/essigmann.html Research in the Essigmann laboratory focuses on how cells respond to DNA damaging agents. When cells are exposed to radiation, certain chemicals (including nearly all carcinogens) and some antitumor agents, the normal nucleotides of the genome become chemically altered to form covalent adducts. John Essigmann's research focuses on how repair enzymes remove structural damage from DNA and on how the adducts that evade repair either kill cells or induce mutations and cancer. Our studies on mutagenesis typically start with the synthesis of an oligonucleotide containing a DNA adduct that has not been studied before from the biological perspective. Recombinant DNA techniques are then used to insert the modified oligonucleotide into the genome of a virus at a preselected site. The modified genome is then introduced into cells, where the DNA replication and repair systems act upon the single DNA adduct. Progeny DNA molecules are isolated, and the appropriate area of the genome is sequenced in order to establish the nature and frequency of the mutation(s) induced. Work on the mechanisms of antitumor drug action focuses in part on cisdiamminedichloro-platinum(II) (cisplatin), which binds to DNA to form adducts that block the enzymes associated with tumor cell DNA replication and transcription. We discovered that the transcription factor hUBF, which controls rRNA production, binds tightly to the major DNA adduct of cisplatin. The Kd of this association is in the pM range, which is within threefold of the binding affinity of hUBF for the rRNA promoter. Current efforts are aimed at establishing whether cisplatin adducts act as decoys that disrupt transcription of the rRNA gene and other genes regulated by related transcription factors. The third area of research in the Essigmann laboratory concerns the synthesis of programmable therapeutics. Bifunctional molecules are being prepared in which a DNA damaging warhead is linked to a molecular recognition domain for proteins that are over expressed in tumors (e.g., steroid receptors). Following DNA damage, the molecular recognition domain attracts the over expressed nuclear proteins. The formation of the protein-adduct complex sterically hinders the repair of the adduct, causing the adduct to persist and enhancing the likelihood that it will kill the cell. In non-tumor cells, adduct repair is rapid and hence those cells suffer less toxicity. Molecules have also been designed to alter the ability of specific transcription factors to function normally. In cancer cells, many transcription factors are over expressed and they are therefore targets for this therapeutic strategy. Because the protein recognition domain can be tailored to attract many different tumor specific proteins, the general approach has been termed "fatal engineering." Out


of these efforts, molecules that have shown promise in vivo against breast and prostate cancer have been evolved. The one developed against prostate cancers is of particular interest because it circumvents that apoptotic blockade that typically protects prostate cancer cells from therapeutic alkylating agents.

Essigmann Lab http://jessig.mit.edu/jmegroup/research.htm Cellular Responses to DNA Damage: The research objective of the Essigmann laboratory is to understand the relationship between the structures of lesions formed in the genome by DNA damaging agents and the specific biological endpoints of mutation, cancer, and cell death. In the area of carcinogenesis, we probe the molecular etiology of human cancer. Our parallel studies on antitumor drugs focus upon uncovering the mechanism of action of existing drugs. Based upon that understanding, we design novel compounds that could be useful for the treatment of cancer. Background. The biological effects of ionizing radiation, most chemical carcinogens, and many antitumor drugs are dependent upon the ability of these agents to act as electrophiles in the vicinity of DNA (inside broken lines). Chemical carcinogens, for example, are either inherently electrophilic or they are activated to reactive species by cellular enzymes. Electrophiles are also produced intracellularly by normal metabolic processes. Similarly, reactive compounds are produced by inflammatory cells of the immune system. The reactive intermediates modify DNA, RNA and protein, forming covalent adducts in which the chemical residue is joined to nucleophilic atoms of the constituent nucleotides or amino acids. Adducts within DNA have special significance in view of their potential to force replication or repair errors and thus lead to heritable genetic alterations. The resulting mutations may constitute an important step in the pathway leading to neoplastic transformation. The work of this laboratory addresses the biochemical mechanisms by which cells respond to specific forms of DNA damage. The rationale of our work stems from the possibility that the DNA adducts caused by DNA damaging agents will be either mutagenic or cytotoxic, or both.

Site specific mutagenesis by DNA adducts http://jessig.mit.edu/jmegroup/mutagenesis.htm Exposure of cells to DNA damaging agents usually results in the formation of a vast population of structurally heterogeneous carcinogen-DNA adducts. It is hypothesized that misreplication of adducts initiates cells along the pathway to malignancy. A large body of evidence indicates, however, that only a subset of the adduct population is likely to contribute to mutagenicity and carcinogenicity. When we began our work, a central problem in the field of carcinogenesis was the lack of an experimental system to identify which DNA lesion gave rise to which types of mutations. Our laboratory established such a system. [As shown in this figure,] the genome of a virus or plasmid is processed by using recombinant DNA techniques to situate a small gap at a specific site. An oligonucleotide containing a single DNA adduct is then synthesized and ligated into the gap. The site specifically modified genome is introduced into a bacterial or mammalian cell, allowed to replicate intra- or extra-chromosomally and, finally, progeny are isolated. Reduction in the yield of progeny is an indication of the genotoxicity of the adduct. We also determine the type, amount, and genetic requirements for


mutagenesis induced by the adduct. This technology enables one to rank the mutagenic and genotoxic potentials of the various adducts that form in the genomes of cells treated with DNA damaging agents. Using this system we have defined the genetic effects of the DNA lesions induced by oxidants and ionizing radiation, simple alkylating agents, aflatoxin B1, cisplatin, 4-aminobiphenyl, 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx), and vinyl chloride. Our future studies will be in three areas: (i) understanding how aflatoxin B1 (AFB1) causes mutations that give rise to tumors, (ii) understanding how oxidized DNA bases give rise to mutations and (iii) trying to apply knowledge of mutagenesis toward the development of safer drugs. AFB1 is a major cause of concern worldwide owing to its ability to induce liver cancer. In earlier studies we showed that the exo-epoxide of AFB1 gives rise to its DNA adducts, and recently we showed that the N7 guanine adduct formed by the epoxide has a mutational signature that matches (in terms of genetic requirements) that of the toxin in cellular systems. Human tumors from Asia and Africa, where exposure to AFB1 is a major problem, show the same mutation as seen in our studies. In the epidemiological studies, p53 genes from tumors showed a G to T transversion and, interestingly, most of those studies show a striking clustering of the transversions at a specific position in the protein -- at codon 249. We plan to study the mechanism by which this hotspot arises. Specifically, we are constructing shuttle vectors that will contain the individual AFB1-DNA adducts at each site of possible adduct formation in the region of the p53 mutational hotspot. The extreme lability of N7 guanyl adducts has prevented the study of many of AFB1 adducts in this or any sequence context. Fortunately we were able to overcome that obstacle due to a recent chemical advance, and we are now able to synthesize the desired oligonucleotides for genome construction. We shall introduce the vectors into human cells and determine whether the mutational context specificity seen in intact organs is also seen in cell culture systems in which the vector integrates into the host genome. One special feature of our work plan is the use of a hepatitis virus driven system in which the promoting effect of viral infection on mutation or selection of mutant cells will be examined; hepatitis B infection is almost always associated with a high risk to aflatoxin carcinogenesis in humans. Other studies will focus on continuing our study of the mutagenic effects of alkyl and oxidized DNA bases. We identified 8-oxoguanine some years ago as a premutagenic lesion and it is now believed to be the second most frequent contributor to spontaneous mutations in aerobic organisms. Despite much effort the major contributor to spontaneous adduct driven mutations has evaded identification. We are involved in a systematic search for novel mutagenic lesions formed by oxidation. By identifying the DNA adducts of environmental carcinogens and drugs that are deleterious to humans, we can implement intervention strategies that minimize risk to humans who are exposed to these agents. In the preceding paragraph we indicate how this goal could be achieved with drugs. Using oxidized DNA bases as a second example, knowledge of the lesions giving rise to cancer allows one to identify risk factors (i.e., genetic defects in the repair of that adduct) and even strategies to suppress the formation of the genotoxic adducts.


PROF. JAMES G FOX Professor of Toxicology; Director, Division of Comparative Medicine (DCM) http://web.mit.edu/be/people/fox.htm http://web.mit.edu/afs/athena/org/c/comp-med/ James G. Fox is Professor and Director of the Division of Comparative Medicine and a Professor in the Division of Biological Engineering at MIT. He is also an Adjunct Professor at Tufts University School of Veterinary Medicine and the University of Pennsylvania, School of Veterinary Medicine. He is a Diplomate and a past president of the American College of Laboratory Animal Medicine, past president of the Massachusetts Society of Medical Research, past chairman of AAALAC Council, past chairman of the NCCR/NIH Comparative Medicine Study Section. He also is an elected fellow of the Infectious Disease Society of America. Professor Fox is the author of over 440 articles, 75 chapters, 3 patents and has edited and authored 8 texts with another 4 in press, in the field of in vivo model development and comparative medicine. He has served on the editorial board of several journals and is currently a member of the NIH/NCRR Scientific Advisory Council. He has received numerous scientific awards including the AVMA’s Charles River Prize in Comparative Medicine, the AALAS Nathan Brewer Scientific Achievement Award, and the AVMA Excellence in Research Award. He has been studying infectious diseases of the gastrointestinal tract for the past 30 years and has focused on the pathogenesis of Campylobacter spp. and Helicobacter spp. infection in humans and animals. His laboratory developed the ferret as a model for both campylobacter and helicobacter associated disease as well as the first rodent model to study helicobacter associated gastric disease including gastric cancer. Dr. Fox is considered the international authority on the epidemiology and pathogenesis of enterohepatic helicobacters in humans and animals. He is largely responsible for identifying, naming, and describing many of the diseases attributed to various Helicobacter species; most notably their association with hepatitis, liver tumors, inflammatory bowel disease and colon cancer in mice. His laboratory most recently has described the pivotal role that Helicobacter spp. play in the development of the gallstones in mice fed a lithogenic diet; thus linking this finding to his earlier description of Helicobacter spp. associated chronic cholecystitis and gallstones in Chilean women a population at high risk of developing gallbladder cancer. He also has had a long-standing interest in zoonotic diseases as well as biosafety issues associated with in vivo models. His past and current research has been funded by NIH and NCI, as well as by private industrial sources, for the past 30 years. He has been the principal investigator of an NIH postdoctoral training grant for veterinarians for the past 19 years. He consults nationally and internationally with government, academia and industry. In 2004 Professor Fox was elected to the Institute of Medicine of the National Academy of Sciences. Fox has had a longstanding research interest in infectious diseases of the gastrointestinal tract and their oncogenic potential. The ferret has been developed in his laboratory as an experimental model because this species has many similarities in anatomy and physiology to those observed in the human. For example, the Fox lab has used the ferret on NIH supported grants as (1) a model of carotenoid metabolism (2) to study enteric campylobacteriosis and (3) investigations regarding proliferative bowel disease caused by a novel Desulfovibrio sp. Also the pathogenic bacterium, Helicobacter mustelae in the ferret gastric mucosa has been extensively characterized. This bacterium causes inflammatory lesions, including ulcers and multifocal atrophic gastritis, a premalignant lesion as well as being directly linked to gastric adenocarcinoma and MALT lymphoma. This finding is of considerable interest in connection with studies of Helicobacter pylori gastric infection in humans and its relationship to gastritis, ulcers, and most recently


gastric adenocarcinoma and MALT lymphoma. A mouse model of Helicobacter-induced gastritis developed in our laboratory is also being used to study pathogenesis, therapeutic modalities and immunization strategies. His laboratory also isolated, characterized, and named H. hepaticus, which is responsible for a new murine disease, "H. hepaticus induced hepatitis." In A/JCr mice and B6C3F1 (the mouse hybrid used in NTP carcinogenesis bioassays), the organism induces hepatic adenomas and heptocellular carcinomas. Ongoing studies are designed to determine in vivo molecular events operable in the tumorigenic process.

Animal Model and Pathology Facilities Core A substantial fraction of the research carried out in the CEHS involves the use of animal models of human disease. To meet this need, the Animal Models and Pathology Facilities Core, directed by Professor James Fox, provides numerous services to Center members, including overseeing husbandry for all the animals used by CEHS members (rats and mice), development of transgenic knock-out and knock-down animal models, histopathology, advanced tissue imaging, DNA sequencing, real-time PCR and other technologies related to cell and molecular biology, as well as the services of board certified pathologists. The Core is comprised of the facilities, services and expertise of the Division of Comparative Medicine at MIT, directed by James Fox. The goal of this project is to understand how toxic environmental agents perturb biological systems and to determine how such perturbations may affect human health.

Pathogenesis of Helicobacter Induced Hepatitis and Tumorigenesis To determine the oncogenic potential of H. hepaticus and study in vivo molecular events operable in the tumorigenic process.

“Nitric oxide shown to cause colon cancer: Study offers proof of compound's role in disease” Anne Trafton, MIT News Office, January 19, 2009, http://web.mit.edu/newsoffice/2009/colon-cancer-0119.html

Researchers long ago established a link between inflammation, cancer and the compound nitric oxide, which may be produced when the immune system responds to bacterial infections, including those of the colon. However, the exact nature of the relationship was unknown -- until now. Scientists from MIT's Division of Comparative Medicine and Department of Biological Engineering have found that nitric oxide produced by inflammatory cells during bacterial infection can cause colon cells to become cancerous. The finding suggests that blocking the compound may help prevent or treat colon cancer, the third most common form of cancer in the United States. The researchers, led by James Fox, director of the Division of Comparative Medicine (DCM), report their findings in the Jan. 19 online edition of the Proceedings of the National Academy of Sciences. Many years ago it was discovered that gastrointestinal infection by H. pylori is often linked to cancer in humans; a related bacteria called H. hepaticus has similar effects in mice.


Nitric oxide is produced during the inflammatory response to such bacterial infection, but it has been unclear whether it was damaging cells or protecting them. By studying mice, the MIT team found that nitric oxide produced by different types of cells has different effects. "Nitric oxide delivered by inflammatory cells, in particular, is important in causing changes in intestinal epithelial cells, setting the stage for cancer development," said Susan Erdman, principal research scientist in the Division of Comparative Medicine and lead author of the PNAS paper. In mice infected with H. hepaticus, the researchers found that blocking an enzyme needed to produce nitric oxide reduced colon cancer rates. More work is needed to study the exact effects of nitric oxide and develop potential clinical therapies for colon cancer, Erdman said. "Therapies will need to be targeted to inhibit the damaging effects of nitric oxide while preserving as many of the protective elements of nitric oxide as possible," she said. "This study is a wonderful example of the value and final product that results from an interdisciplinary team effort," said Fox. Other authors of the paper are Varada Rao, former postdoctoral fellow in the DCM; Theofilos Poutahidis, visiting scientist in the DCM; Arlin Rogers, principal research scientist in the DCM; Christie Taylor, research technician in the DCM; Erin A. Jackson, research technician in the DCM; Zhongming Ge, molecular biologist in the DCM; David Schauer, professor of biological engineering; Gerald Wogan, professor emeritus of biological engineering; and Steven Tannenbaum, professor of biological engineering.

PROF. ERNEST FRAENKEL Eugene Bell Career Development Assistant Professor in Tissue Engineering http://web.mit.edu/be/people/fraenkel.htm http://fraenkel.mit.edu/ http://csbi.mit.edu/people/fraenkel.html Ernest Fraenkel is combining structural analysis, bioinformatics and biochemistry to predict the interaction of proteins. He expects that this work will ultimately lead to a better understanding of how signals propagate in cells, providing insight into the biology of cancer and development. Fraenkel received his Ph.D. in Biology from MIT in 1998, and came to the Whitehead Institute from Harvard University. Fraenkel is a 2001 Leonard T. Skeggs Jr. Fellow and has received fellowships from the Damon Runyon-Walter Winchell Cancer Research Fund and the Howard Hughes Medical Institute.

Fraenkel Lab: Systems Biology of Disease http://fraenkel.mit.edu/ We are developing computational and experimental approaches to search for new therapeutic strategies for diseases. New experimental methods make it possible to measure cellular changes across the genome and proteome. These technologies include genome-wide measurements of transcription, of protein-DNA interactions (ChIP-Seq), of genetic interactions, and of protein modifications. Each data source provides a very narrow view of the cellular changes. However, by


computationally integrating these data we can reconstruct signaling pathways and identify previously unrecognized regulatory mechanisms that contribute to the etiology of disease and may provide new approaches for treatment. Current projects focus on the study of cancer, neurodegenerative diseases and diabetes.

Disease We are creating systems biology methods to identify potential therapeutic targets. Our approach integrates data from a variety of sources including high-throughput genetic interaction screens and transcriptional profiling to uncover pathways that are altered in disease. Currently, we are collaborating with members of the Lindquist Lab to analyze the causes of neurodegenerative diseases. We are exploring the mechanisms of toxicity of alpha-synuclein and huntingtin, proteins which cause Parkinson’s and Huntington’s diseases, respectively. We seek to discover the pathways that are altered by these proteins at early stages of disease, when pharmaceutical intervention could potentially prevent neurodegeneration.

Using High-throughput Data to Understand and Modify Biological Systems We are developing new computational and experimental approaches to understanding how transcription, signaling and metabolism change during development, in disease and in response to environmental change. High-throughput technologies including expression microarrays, genome-wide chromatin immunoprecipitation, proteomics and metabolomics are providing increasingly detailed views of the state of molecules in vivo. Our goal is to synthesize these data to create a systems level understanding of cellular processes.

PROF. LINDA G GRIFFITH School of Engineering Professor of Teaching Innovation; Professor of Mechanical and Biological Engineering; Director, Biotechnology Process Engineering Center (BPEC) http://web.mit.edu/be/people/griffith.htm http://meche.mit.edu/people/faculty/index.html?id=32 http://web.mit.edu/lgglab/index.html http://csbi.mit.edu/people/griffith.html Linda Griffith is a Biological Engineering and Mechanical Engineering at MIT. Professor Griffith joined MIT as a postdoctoral associate. She was appointed assistant professor of health sciences and technology and chemical engineering (1991-93), assistant professor of chemical engineering (1993-96), associate professor of chemical engineering without tenure (1996), and was tenured in 1998, and full professor in 2002. She is director of the Biotechnology Process Engineering Center, director of the Bioengineering for Toxicology Research Core of the Center for Environmental Health Sciences, and chair of the Undergraduate Curriculum Committee for Biological Engineering. Griffith received a bachelor's degree from Georgia Tech. in 1982 and a Ph.D. degree from the University of California at Berkeley in 1988, both in chemical engineering. Following a postdoc with Robert Langer and Joseph Vacand at MIT and Children's Hospital, she joined the faculty at MIT in 199 1, teaching at MIT and Harvard Medical School. Griffith conducts research in the field of biomaterials and devices for tissue and organ regeneration. Her research combines molecular design and synthesis of biornaterials as well as design and synthesis of macroscopic 3-D devices for therapeutic and in


vitro use. Several of her patents are in commercial development. More than 30 masters students, doctoral students, and postdoctoral associates have completed training under her supervision or co-supervision. Griffith is a co-founder of Therics, Inc. and has served as consultant or scientific advisory board member for Advanced Tissue Sciences, AstraZeneca, Biohybrid Technologies, Corning, Cytotherapeuctics (Stem Cells, Inc.), DuPont, Schroeder Ventures, Therics, The Whitaker Foundation, Harvard School of Dental Medicine, and the Illinois Institute of Technology Pritzker Institute of Medical Engineering. Her work has been featured on several television documentary shows including Scientific American Frontiers hosted by Alan Alda. Her awards include the Popular Science Brilliant 10 award, NSF Presidential Young Investigator Award, MIT Class of '60 Teaching Innovation Award, along with named lectures at academic institutions and societies. She is a Fellow in the Cambridge-MIT Institute. She has served as co-chair of the Materials Research Society Annual Spring Meeting, the Keystone Tissue Engineering Meeting, and the joint NSF-NIH Workshop on Bioengineering and Bioinformatics Training and Education, and is a member of the Advisory Council for the National Institute for Dental and Craniofacial Research at NIH. Professor Griffith's research can be categorized within the rapidly-emerging field of bioengineering termed "tissue engineering". This field can be defined as the manipulation of cells using biochemical factors, synthetic materials, and mechanics, to form multi-dimensional structures that carry out the functions of normal tissue in vitro or in vivo. My work focuses on controlling the spatial and temporal presentation of molecular ligands and physical cues which are known to influence cell behavior. Current projects include: (1) synthesis of new materials that control cells from the solid phase at a microscopic level and synthesis of new three-dimensional architectures that guide tissue morphogenesis at a macroscopic level; (2) determination of cell/matrix organizational principles to provide a basis for future developments in synthesis. Research in Tissue Engineering. Broadly defined, tissue engineering is the process of creating living, physiological, 3D tissues and organs. The process starts with a source of cells derived from a patient or from a donor. The cells may be immature cells, in the stem cell stage, or cells that are already capable of carrying out tissue functions; often, a mixture of cell types (e.g., liver cells and blood vessel cells) and cell maturity levels are needed. Coaxing cells to form tissue is inherently an engineering process, as they need physical support (typically in the form of some sort of 3D scaffold) as well as chemical and mechanical signals provided at appropriate times and places to form the intricate hierarchical structures that characterize native tissue. The process of forming tissues from cells is a highly orchestrated set of events that occur over time scales ranging from seconds to weeks and dimensions ranging from 0.0001 cm ? 10 cm. Research projects in the lab address problems across this spectrum. At one end, we study basic biological and biophysical processes at the molecular and cellular level. This helps us understand what processes the cells need help with, and what events they can accomplish themselves. Work at this end of the spectrum has led to the development of new tools for biologists to use in fundamental studies of cell behavior. At the other end of the spectrum, we develop new materials and devices that are needed to direct the process of tissue formation, under the classical engineering constraints of cost, reliability, government regulation, and societal acceptance. We are also developing new integrated micro-bioreactor systems to grow 3D tissues for use in drug discovery and development, and as physiological models of human diseases such as hepatitis. Research and development in this area includes integration of materials and scaffold engineering with computation models of fluid flow and nutrient metabolism.


Microscale Liver and Bone Marrow Tissue Engineering http://web.mit.edu/lgglab/research/index.html#microscale Many therapeutic applications of tissue engineering involve disease processes that might be prevented or treated if better drugs were available or if the processes could be better understood. Animal models, although they provide great insight into human disease, sometimes fall short of capturing the full spectrum of human pathologies and responses to therapy and are not readily adaptable to high throughput studies. Cell culture models, although high throughput, often fail to replicate physiological processes adequately. For example, liver cells lose their susceptibility to hepatitis infection and many aspects of drug metabolism when they are taken from the body and placed in culture. We are thus developing microscale 3D tissues in order to capture higher order physiological behavior of human tissues in vitro in a reasonably high throughput format. One application area is development of physiological models of liver. The in vivo microenvironment of hepatocytes includes signaling mechanisms mediated by cell-cell and cell-matrix interactions, soluble factors, and mechanical forces. In an attempt to mimic key facets of the in vivo microenvironment, we have developed a microfabricated bioreactor system that fosters three dimensional tissue morphogenesis under continuous perfusion conditions. A key feature of the bioreactor is the distribution of cells into many tiny (~0.001 cm 3) tissue units that are relatively uniformly perfused with culture medium. The total mass of tissue in the system is readily adjusted for applications requiring only a few thousand cells to those requiring over a million cells by keeping the microenvironment the same and scaling the total number of tissue units. We are currently conducting fundamental studies characterizing cell dynamics and liver-specific gene expression as a function of several system parameters, and using and modifying the system for a range of applications including prediction of drug toxicity, evaluation of liver responses to environmental toxins, and models of cancer metastasis. A second application area is development of in vitro models for assessment of toxicity in the hematopoietic system. Here, we are employing an in vitro erythropoiesis culture system developed by the Lodish lab, and attempting to build a quantitative model of responses to agents that damage DNA, such as chemotherapeutic drugs.

A Cell Culture Assay for Gene-Damaging Chemicals Principal Investigator: Prof. Harvey F Lodish Other Investigators: Prof. Linda G Griffith, Prof. Leona D Samson Depts/Labs/Centers: Department of Biology In collaboration with the laboratories of Professors Leona Samson and Linda Griffith, extended our in vitro culture system for erythroid progenitors into an assay for genotoxicity. Assays that predict toxicity are an essential part of drug development and many drugs fail in phase I clinical trials; therefore, there is a demand for models that can better predict human responses. The mouse in vivo micronucleus assay is a robust toxicity test that assesses the genotoxic effect of drugs- especially those that induce breaks in DNA - by detecting chromosome fragments that remain in the reticulocyte after enucleation; an in vitro correlate to this assay might allow extension to human cells and thus better predictive power in drug development. As first steps in developing a toxicity assay, Joe has adapted our in vitro erythropoiesis culture system to induce optimized erythropoietic growth from the Lin- population of adult murine bone marrow. Using this system he demonstrated that exposure to genotoxicants induces micronucleus -formation in this culture system. In particular, Joe showed that addition of the alkylating agents BCNU,


MNNG, and MMS to this culture system induces both a cytotoxic response and an increase in micronucleus frequency within the reticulocyte population. This increase in micronucleus production following exposure to these alkylating genotoxicants provides a clear signal of the genotoxic mechanism that likely induced the observed erythropoietic toxicity.

PROF. LEONA D SAMSON Ellison American Cancer Society Research Professor; Professor of Toxicology and Biological Engineering; Director, Center for Environmental Health Sciences (CEHS) http://web.mit.edu/be/people/samson.htm http://samsonlab.mit.edu/ http://csbi.mit.edu/people/samson.html B.Sc. Biochemistry, Aberdeen University, Scotland 1974; Ph.D. Molecular Biology, Imperial Cancer Research Fund and University College, London University, England 1978; Director, MIT Center for Environmental Health Sciences, MIT, 2001; Affiliate, MIT Center for Cancer Research, 2001; Adjunct Professor of Toxicology, Harvard School of Public Health, 2001; Executive Committee, MIT Computational and Systems Biology Initiative (CSBi).

Samson Lab: http://samsonlab.mit.edu/ Alkylating agents represent an abundant class of chemical DNA damaging agent in our environment and they are toxic, mutagenic, teratogenic and carcinogenic. Since we are continuously exposed to alkylating agents, and since certain alkylating agents are used for cancer chemotherapy, it is important to understand exactly how cells respond when exposed to these agents. The repair of DNA alkylation damage provides tremendous protection against the toxic effects of these agents and our aim is to understand the biology, the biochemistry, and the genetics of numerous DNA repair pathways that act upon DNA alkylation damage. Organisms separated by enormous evolutionary distances employ similar proteins to protect against DNA damage, and we know that bacteria, yeast, and human cells induce the expression of specific sets of genes in response to such damage. Our studies on the response of Escherichia coli, Saccharomyces cerevisiae and human cells to alkylating agents have become intimately intertwined. Much of our previous work was based on the findings that bacterial DNA repair functions can operate in eukaryotic cells, and vice versa, i.e., eukaryotic DNA repair functions can operate in bacterial cells. We exploited this phenomenon to clone a large number of yeast, mouse and human DNA alkylation repair genes, and we are using these cloned genes to gain a thorough understanding of how eukaryotic cells respond to alkylating agents. Moreover, we have extended our alkylation toxicity studies from the cellular level to the whole animal level. Specifically, we have: (i) produced transgenic and knock-out mice with altered DNA repair capabilities and are now measuring their susceptibility to alkylation toxicity; and (ii) transferred DNA alkylation repair genes to bone marrow cells to determine whether such gene therapy could confer a useful level of extra resistance in the bone marrow of chemotherapy patients.


Toxicogenomics http://samsonlab.mit.edu/toxicogenomics.html Toxicogenomics is a new scientific field that elucidates how the entire genome is involved in biological responses of organisms exposed to environmental toxicants/stressors. Our laboratory uses transcriptional profiling to study gene expression changes induced by DNA damaging chemicals in order to better understand their mechanisms of action. We perform studies in a variety of model systems including yeast, bacteria, cultured mammalian cells, and in vivo experiments in mice. We are fully equipped to run Affymetrix GeneChip© oligonucleotide arrays or a variety of other platforms through our collaborations with MIT BioMicroCenter. We are a member of the Toxicogenomics Research Consortium whch consists of six Cooperative Research Members (CRMs), two Resource Contractors, and NIEHS Extramural Staff. The CRMs include 5 academic centers and the NIEHS Microarray Group. These include: Duke University, Fred Hutchinson Cancer Research Center, MIT, NIEHS Microarray Group, OHSU, and UNC.

Gene Environment Interactions http://samsonlab.mit.edu/geneenvironment.htm When cells are exposed to DNA damaging agents a signal is generated such that the transcription of various genes is altered. We have used Affymetrix oligonucleotide DNA chip analysis to monitor the transcriptional response of the entire S. cerevisiae genome (i.e., all 6,200 genes) in response to a number of different alkylating agents. To our surprise, we have identified hundreds of responsive genes and have uncovered a hitherto unknown response that links ubiquitin-mediated protein degradation and DNA repair. We are currently exploring the biological roles that the large number of responsive genes plays in protecting cells against alkylation toxicity. Signals can also be generated, in cells exposed to alkylating agents, which trigger cell cycle checkpoint arrest or apoptosis. We are also dissecting the molecular mechanisms by which alkylating agents signal these very important downstream events. Samson, a professor of both biology and biological engineering, and head of MIT’s Center for Environmental Health Sciences, is a toxicologist. This means her interests include the factors -- ultraviolet radiation, selected chemicals, components of cigarette smoke -- that can trigger cancer.

Genomic Phenotyping http://samsonlab.mit.edu/genomicphenotyping.html We have generated a genomic phenotyping database identifying hundreds of S. cerevisiae genes important for viable cellular recovery after mutagen exposure. Systematic phenotyping of 1,615 gene deletion strains produced distinctive signatures for each of four mutagens. Computational integration of the database with 4,025 interacting proteins, comprising the yeast interactome, identified several multi-protein networks important for damage recovery. Some networks were associated with DNA metabolism and cell cycle control functions, but most were associated with unexpected functions such as cytoskeleton remodeling, chromatin remodeling, and protein, RNA and lipid metabolism. Hence, a plethora of responses other than the DNA damage response are important for recovery.


Spontaneous Mutagenesis http://samsonlab.mit.edu/spontaneousmutagenesis.html An increase in spontaneous mutations is associated with increased cancer risk. Our laboratory has shown that a simple imbalance between the first two enzymes involved in DNA base excision repair can increase the rate of spontaneous mutations several hundred-fold. Specifically, the S. cerevisiae MAG1 3-methyl-adenine DNA glycosylase, when expressed at high levels relative to the apurinic/apyrimidinic endonuclease (APN1), increases spontaneous mutation by up to approximately 600-fold in S. cerevisiae and approximately 200-fold in E. coli. Genetic evidence suggests that, in yeast, the increased spontaneous mutation requires the generation of abasic sites and the processing of these sites by the REV1/REV3/REV7 lesion bypass pathway.

“Prenatal arsenic exposure detected in newborns: Research could lead to test for screening populations for the poison” David Chandler, MIT News Office, November 22, 2007, http://web.mit.edu/newsoffice/2007/arsenic-1122.html The children of mothers whose water supplies were contaminated with arsenic during their pregnancies harbored gene expression changes that may lead to cancer and other diseases later in life, MIT researchers reported in a new study. In addition to establishing the potential harmful effects of these prenatal exposures, the study also provides a possible method for screening populations to detect signs of arsenic contamination. This is the first time evidence of such genome-wide changes resulting from prenatal exposure has ever been documented from any environmental contaminant. It suggests that even when water supplies are cleaned up and the children never experience any direct exposure to the pollutant, they may suffer lasting damage. The research was published in the Nov. 23 issue of PLoS Genetics (published by the Public Library of Science). The evidence comes from studies of 32 mothers and their children in a province of Thailand that experienced heavy arsenic contamination from tin mining. Similar levels of arsenic are also found in many other regions, including the U.S. southwest. The research was led by Mathuros Ruchirawat, Director of the Laboratory of Environmental Toxicology of the Chulabhorn Research Institute (CRI) in Thailand, and Leona D. Samson, Director of MIT's Center for Environmental Health Sciences (CEHS) and the American Cancer Society Professor in the Departments of Biological Engineering and Biology at MIT. The first author of the study was Rebecca C. Fry, a research scientist at CEHS. Co-authors included Panida Navasumrit of the CRI and Chandni Valiathan, graduate student at MIT's Computational and Systems Biology Initiative. The team analyzed blood that had been collected from umbilical cords at birth. The exposure of mothers to arsenic during their pregnancy was independently determined by analyzing toenail clippings--the most reliable way of detecting past arsenic exposure.


The team found a collection of about 450 genes whose expression had been turned on or turned off in babies who had been exposed to arsenic while in the womb. That is, these genes had either become significantly more active (in most cases) or less active than in unexposed babies. "We were looking to see whether we could have figured out that these babies were exposed in utero" just by using the gene expression screening on the stored blood samples, Samson said. "The answer was a resounding yes." Further, the team found that a subset of just 11 of these genes could be used as a highly reliable test for determining whether babies had been born to mothers exposed to arsenic during pregnancy. Since blood samples are already taken routinely for medical tests, this may provide an easier way of screening for such exposure. The gene expression changes the group found in the exposed children are mostly associated with inflammation, which can lead to increased cancer risk. Recognizing the damaging effects of the arsenic exposure, "the government has provided alternative water sources" to the affected villages, Fry said, which means that following these children as they grow older (they are now toddlers) has the potential to show how long-lasting the effects of the prenatal exposure may be. However, she adds, this may be complicated by the fact that many people are still using the local water for cooking. It's not yet clear how long the changes may last. "We will be testing whether these gene expression changes have persisted in these children," Fry said. This is the first time such a response to prenatal arsenic exposure has been found in humans. But it is not entirely unexpected, Samson explains, because "in mice, when mothers are transiently exposed to arsenic in the drinking water, their progeny, in their adult life, are much more cancer-prone." Further research could include studies of possible ways of reversing or mitigating the damage, perhaps through dietary changes, nutritional supplements or drug treatments to counteract the gene expression changes. Also, the group plans to do follow-up studies in different locations and with larger groups of subjects to confirm the value of the 11 "marker" genes as a reliable indicator of arsenic exposure. The researchers also aim to determine whether the gene expression changes are specific to arsenic. This study is an example of the CEHS's efforts to promote collaborative interdisciplinary research into global environmental health issues, specifically in the developing world. This research was funded by the National Institutes of Environmental Health Sciences and the Chulabhorn Research Institute.


“DNA-damage test could aid drug development” Eric Bender, Whitehead Institute, May 14, 2007, http://web.mit.edu/newsoffice/2007/dna-damage.html In the daunting marathon that leads to successful drugs, promising drug candidates must pass toxicity tests before entering clinical trials. Researchers from MIT and the Whitehead Institute have developed a cell culture test for assessing a compound's genetic toxicity that may prove dramatically cheaper than existing animal tests. This assay would allow genetic toxicity to be examined far earlier in the drug development process, making it much more efficient. Like the current FDA-approved test, the new test looks for DNA damage in red blood cells formed in the bone marrow of mice. The precursors to red blood cells are handy for this because such cells normally lose their nucleus during the last stage of red cell formation, and DNA-damaged precursors generate red blood cells containing an easily detected "micronucleus" consisting of fragments of nuclear DNA. Unlike the current procedure, which injects the compound into a live mouse, the new assay is a cell-culture system that could allow hundreds or thousands of tests to be performed from the bone marrow of a single mouse, and potentially from human bone marrow. Joe Shuga, the graduate student in chemical engineering who developed the assay, is in the unusual position of being a graduate student in three labs, those of Professors Linda Griffith, Harvey Lodish (a Whitehead member) and Leona Samson. "We're all faculty in the biological engineering department, and collaborative projects like this are what the department was intended to do," says Griffith, senior author of a paper on the work to be published online in the Proceedings of the National Academy of Science the week of May 14. "This is an example of taking fundamental lab science and doing something useful with it," says Lodish, whose lab has extensively studied the process by which red blood cells are generated. Shuga first worked with postdoctoral researcher Jing Zhang in the Lodish lab to adapt techniques from an established cell-culture system based on mouse fetal liver cells to create a new system based on adult red cell precursors from mouse bone marrow. Shuga patiently optimized the system, which allows the precursor cells to proliferate and differentiate in the normal way, dividing four or five times before losing their nucleus and becoming immature red blood cells. Shuga then studied the way these developing cells reacted to three toxic DNA- damaging agents whose effects had been studied by Samson's lab and found the results correlated well with results from the existing test. Additionally, he experimented with mutant mice created by Samson's lab that are deficient in certain DNA-repair systems. The bone marrow cells derived from these mice, and the cells cultured from that bone marrow, proved more sensitive to the toxic agents than were the cultured cells from normal mice, further confirming the results. With the new assay, "instead of testing one chemical and one dose in one animal, you'll be able to take one animal, get the bone marrow out and test a thousand different conditions," says Samson, the American Cancer Society Research Professor. "You'll be able to look in more detail at different doses given at different times in the cell differentiation process." "This is a much cheaper assay that's at least as predictive as previous assays," emphasizes Griffith, "and drug developers can afford to use it a lot earlier in the drug development process."

http://web.mit.edu/newsoffice/2007/dna-damage.html

http://web.mit.edu/newsoffice/2007/dna-damage.html


It also could help to avoid issues with animal testing. "The European Union is trying to minimize animal testing," Shuga points out. "A ban on animal testing of cosmetic products goes into effect in 2009." Next steps in the research, which may be carried out by industry partners, will be to test the assay in rats and other organisms, and with a wide variety of other toxic chemicals. "This research is the first stage in a new type of clinical drug toxicity test," says Lodish. "And although we haven't done it, you may be able to extend the technique to humans. Humans are the gold standard in that one wants an assay that directly predicts toxicity in humans, not animals, and you could obtain human bone marrow that's left over from medical procedures." "If you could change the micronucleus assay to have a human cell readout, that would be pretty amazing," says Samson. Down the road, she suggests, such a test might offer a new way to examine how different individuals respond to chemotherapeutic agents. "The presumption is that, for some biological processes, in vitro human models could be closer to in vivo human than in vivo mouse," notes Shuga. "That premise will be tested in coming years as new systems become available." Shuga has additional affiliations with the Whitehead Institute and MIT's Center for Environmental Health Sciences (CEHS); Samson is director of CEHS and has an appointment in MIT's Department of Biology; Lodish also has an appointment in biology; and Griffith has appointments in biology and in the Department of Mechanical Engineering. This work was funded by the Cambridge-MIT Institute, Amgen, the National Institutes of Health and the National Science Foundation.

PROF. RAM SASISEKHARAN Edward Hood Taplin Professor of Biological Engineering and Health Sciences and Technology Underwood-Prescott Professor; Co-Director, Harvard-MIT Division Health Sciences and Technology (HST) http://web.mit.edu/be/people/sasisekharan.htm http://web.mit.edu/tox/sasisekharan/ http://hst.mit.edu/servlet/ControllerServlet?handler=PeopleHandler&action=viewOne&id=HST001007 http://web.mit.edu/ki/faculty/sasisekharan.html http://hst.mit.edu/public/people/faculty/facultyBiosketch.jsp?key=Sasisekharan Professor Sasisekharan is currently the Underwood-Prescott Professor of Health Sciences and Technology (HST) and Biological Engineering (BE) at MIT, and is a member of the Koch Institute for Integrative Cancer Research and the Center for Environmental Health Sciences. He joined the MIT faculty in 1996, following appointments as an instructor at HMS and as an HST postdoctoral fellow. He holds a Ph.D. in Medical Sciences from Harvard Medical School, an M.S. in Biophysics from Harvard University and a B.S. in physical sciences from Bangalore University in India. Sasisekharan became the new Director of the Harvard-MIT Division of Health Sciences & Technology on December 10, 2008. He will share the leadership of HST with David E. Cohen, the

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Director for HST at Harvard, Associate Professor of Medicine and HST at Harvard Medical School, and Director of Hepatology at Brigham and Women's Hospital. Professor Sasisekharan's research objective is to contribute to the discovery and distribution of therapeutics that alleviate suffering and promote human health. His research is highly multidisciplinary, integrating a broad range of technologies for the study of complex polysaccharides that are involved in many disease processes. His work has laid the foundation for the development of novel therapeutics for applications to problems as diverse as stroke and bird flu leading to the creation of several companies. Dr. Sasisekharan has won numerous awards, including the 1999 Burroughs Wellcome Fund Young Investigator Award: Awarded to the most promising young faculty members who bring new ways of thinking and new experimental approaches to life sciences; 1999 Beckman Foundation Young Investigator Award: Awarded to the most promising young faculty members in the chemical and life sciences (this is one of the most prestigious awards or recognition for a junior faculty member in the U.S); 1999 Edgerly Science Partnership Award; the 1998, 1999, 2000 and 2001 CaPCure Award, CaPCure Foundation: Award given to outstanding prostate cancer research programs and the 2003 Global Technovator Award. He earned the B.S. from Bangalore University (1985), the M.A. from Harvard University (1987) and the Ph.D. from Harvard Medical School (1992). He joined the MIT faculty in 1996 and was promoted to associate professor in 2000. He is the graduate officer for the Applied Sciences track of the Biological Engineering Graduate program. Dr. Sasisekharan is a member of the Steering Committee of the International Consortium for Functional Glycomics and has served on study section panels of the National Institutes of Health. He has founded biotechnology companies and is or has been an advisor to Research Institutes, Venture Funds, Biotechnology or Pharmaceutical Companies.

Sasisekharan Laboratory http://web.mit.edu/tox/sasisekharan/ The Sasisekharan group employs a multidisciplinary strategy to develop tools to study glycans such as the glycosaminoglycans with an ultimate goal towards the development of novel pharmacological approaches to alleviate glycan-mediated disease processes.

Glycobiology http://web.mit.edu/tox/sasisekharan/research/glycobiology.html In the recent past, biomedical scientists have been primarily concerned with intracellular events at the genetic and protein levels. Recently, a wealth of new information has revealed that extracellular environment exert tremendous influences in normal and aberrant pathophysiology. Our efforts are thus largely associated with a third class of important biomolecules that occur extracellularly—the glycans.

Human Pathophysiology & Biotherapeutics http://web.mit.edu/tox/sasisekharan/research/pathophysiology.html Complex glycans—located at the surfaces of cells, deposited in the extracellular matrix, and attached to soluble signaling molecules—play a crucial role in the phenotypic expression of

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cellular genotypes. We are investigating the indispensable role of these molecules in human physiology as well as in disease processes. Complex glycans act on a multicellular level, at the interface between cells, tissues, and organs, to coordinate biological processes. From a biological perspective, complex glycans represent a promising, but to date largely untapped, source for the development of novel therapeutics. Our lab has been exploring various biotherapeutic applications.

Carbohydrate-Mediated Mechanisms of Tumor Progression Increasingly in recent years, the extracellular matrix is being recognized as a key modulator of cell behavior in physiological and pathological processes. We seek to explore the role of the cell's external milieu, specifically the carbohydrate component, in tumor progression and associated pathological processes. Using new enzymatic and analytical tools for dissecting the structure-function relationships of carbohydrates in these processes, we seek to increase our understanding of tumor biology as well as to identify new therapeutic targets. Further, we utilize the information gained about these relationships to aid in the development of novel therapeutic strategies.

DR. PAUL L SKIPPER Principal Research Scientist, Department of Biological Engineering http://web.mit.edu/toxms/www/paul.htm http://web.mit.edu/toxms/www/who.htm Areas of Interest and Expertise: Molecular Dosimetry of Carcinogen Exposure in Human Populations Chemical Carcinogenesis Sub-Micro Analysis Chemical and Biological Aspects of Food Safety and Cancer Etiology Toxicology and Epidemiology [See Tannebaum projects below]

PROF. STEVEN R TANNENBAUM Underwood-Prescott Professor of Toxicology; Professor of Chemistry; Center for Biomedical Engineering; Center for Environmental Health Sciences; Computational and Systems Biology Initiative; Institute for Soldier Nanotechnologies http://web.mit.edu/chemistry/www/faculty/tannenbaum.html http://web.mit.edu/be/people/tannenbaum.htm http://web.mit.edu/toxop/www/ http://web.mit.edu/tox/www/Faculty/tannenbaum.html Steven Tannenbaum is the Underwood-Prescott Professor of Toxicology and Professor of Chemistry. Dr. Tannenbaum studies the etiology of cancer in high-risk populations. This is done by developing appropriate in vivo and in vitro models for comparison and extrapolation to humans, and through the measurement of carcinogen adducts covalently bound to biological macromolecules. Dr. Tannenbaum is developing analytical methods for the quantitation of toxicologically significant compounds by monitoring their reaction products in human or animal blood. The proposed method would be applicable to many carcinogens, mutagens, and other reactive chemicals. The results would allow more accurate assessments of human risk, and more

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precise epidemiological investigations of the links, for example, between exposure to carcinogens and human cancer. N-nitroso compounds may be formed endogenously from nitrite and a variety of nitrogen-containing compounds. The substances thus formed may be toxic and carcinogenic and have been implicated in the etiology of certain cancers in humans, including that of the stomach, lower GI tract, bladder, and esophagus. Dr. Tannenbaum's research program encompasses many of the factors which influence this process. Tannenbaum’s interests include biochemistry and toxicology. In particular, he studies the relationship between exposure to environmental and endogenous chemicals and risk of cancer and other diseases. This approach utilizes chemical reactions, components of cells, cells in culture, and animal models for development of chemical biomarkers for application to human populations. The Quantification of Human Exposure to Carcinogens -- Some environmental chemicals pose risks to human health. The accurate assessment of these risks requires quantitative data on human exposure. Such data are currently estimated from measurements of the chemicals in air, water or food. Direct measurements in human blood, urine, or tissues have generally not been attempted, since the compounds involved are usually short-lived and present in low levels. We have developed an analytical approach for the quantitation of toxicologically significant compounds by monitoring their reaction products to human proteins. The proposed method is applicable to many carcinogens, mutagens, and other reactive chemicals. The results allow more accurate assessments of human risk, and more precise epidemiological investigations of the links, for example, between exposure to carcinogens and human cancer. The basis of this research is as follows. Compounds such as carcinogens are toxic often because they react within the body to modify the genetic material (DNA). The same electrophiles that react with DNA also react with proteins. Since DNA is repaired and proteins are not, the protein serves as a template for carcinogen exposure. Measurement of protein adducts is therefore a useful approach for human biomonitoring and investigation of the effect of metabolic polymorphisms. Detection of protein adducts in human requires analytical tools that are both sensitive and specific. The laboratory specializes in the application of mass spectrometry and laser fluorescence methods to these problems.

Biological Engineering Accelerator Mass Spectrometry (BEAMS) Laboratory Principal Investigator: Prof. Steven R Tannenbaum Other Investigators: Rosa G Liberman, Dr. Paul L Skipper, Dr. John S Wishnok (Pete) The Biological Engineering Accelerator Mass Spectrometry [BEAMS] Lab at MIT was established to be a high-throughput facility for biomedical applications of AMS such as pharmacokinetics, metabolite profiling, toxicology, and microdosing…

The BEAMS Lab engages in collaborative research with academic and industrial partners. It is also a center for research into improving the accessibility of AMS to chemical analysts with a new, more compact spectrometer under construction and continuing development of sample interfaces… See: http://web.mit.edu/beams/

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Research in Toxicology Principal Investigator: Prof. Steven R Tannenbaum Other Investigators: Dr. Paul L Skipper, Dr. John S Wishnok (Pete) Ongoing research in toxicology is centered about two major foci: quantifying DNA damage induced by carcinogenic and cytogenic agents, and using isotope-directed fractionation to isolate and identify biomarkers of chemical exposures. DNA damage resulting from attachment of radiolabeled chemical entities has been a focus of research utilizing AMS since attention first turned to biomedical applications. In support of research conducted in the Tannenbaum laboratory, we are analyzing DNA samples from a wide range of experiments aimed at characterizing the interactions of a group of monocyclic amines with DNA under conditions of in vitro exposure mediated by reconstituted metabolic systems, in cell culture systems, and in animal models. The amines of interest are those newly implicated through epidemiological studies as human bladder carcinogens. In collaboration with Prof. Essigmann’s laboratory at MIT, we are performing AMS analyses of DNA that becomes the target of developmental cancer chemotherapeutic agents designed to exhibit high tissue specificity… More at http://web.mit.edu/beams/research/tox.html

Nitric Oxide: Chemistry and Pathophysiology Our laboratory has been interested for many years in the formation, distribution, and metabolism of nitrate, nitrite, and N-nitroso compounds. This work led to our discovery of the endogenous synthesis of nitrogen oxides and eventually the discovery of nitric oxide as a biological molecule. At present our laboratory is conducting research on the pathophysiological consequences of nitric oxide and its oxidation products. This encompasses cell-mediated nitrosation, free-radical reactions, and oxidation. We are particularly interested in the nature of chemical damage to DNA and its genotoxic consequences. From a health point of view this is important for the inflammatory state and for various infections and diseases that increase the risk of cancer. We are also interested in the inhibition of these reactions by antioxidants and other substances that offer protection from oxidative stress. http://web.mit.edu/srtlab/research/index.html

Tissue Engineering for Drug Development and Chemical Toxicity Cells placed in culture generally lose at least some key differentiated physiological functions that they normally exhibit as part of organized tissues in the body. Thus, while cultured cells may be adequate for some applications in drug metabolism and detection of toxins, they are certain to fail for others. We have developed an in vitro organized tissue-based sensor for detection of unknown toxins and rapid screening of drug metabolism. The technology combines a unique chip-based micro tissue arrangement with mass spectrometric and optical sensors to detect changes in tissue behavior and measure primary and secondary biochemical transformations of drugs and toxins. http://web.mit.edu/srtlab/research/index.html

Quantitative Ultramicro Measurements for Drug and Carcinogen Metabolism We are developing new approaches to measure the fate of drugs and chemicals in the classical paradigm for drug metabolism: Absorption, Distribution, Metabolism, Excretion (ADME). The methods include variations in biological Mass Spectrometry and Laser-Induced Fluorescence Spectroscopy. An important new, unique tool is an Accelerator Mass Spectrometer for C14 and

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tritium that will be directly coupled to gas and liquid chromatography. These tools will enable us to conduct "Nanotracing" of molecules in humans at heretofore unexplored levels. http://web.mit.edu/srtlab/research/index.html

PROF. WILLIAM G THILLY Professor of Professor of Genetics, Toxicology and Biological Engineering, http://web.mit.edu/be/people/thilly.htm , http://epidemiology.mit.edu/

The work of the Thilly lab encompasses the study of genetic change in humans, both germinal and somatic changes causing or increasing the age specific probability of disease. We begin with a mathematical analysis of the age specific mortality rates for human disease which we have collected and computed for individual birth cohorts using data from 1900 forward. With these data and quantitative models of time dependent accumulation of somatic mutations we have been able to calculate the fraction of the American population at risk of death by diseases such as cancer at any site, cardiovascular or cerebrovascular disease, diabetes and several others. These studies have shown us that for the most prevalent human cancers unconnected with smoking, those of the colon, breast and prostate have shown no change in the population at risk from birth cohorts of the mid-nineteenth century to the present day. Other cancers such as leukemia, lymphoma and brain cancer have shown marked increases apparently unconnected to cigarette use. Stomach cancer has shown a precipitate decline in risk fraction. We interpret these data to demonstrate a clear environmental risk condition for cancers for which the risk has changed for the birthyear cohorts examined, roughly 1840 -1950. Thilly's approach also shows that the risk of lung cancer has risen as a simple linear function of cigarette usage with the same relationship observed for both males and females. Further analyses of these data indicated that the parameters of somatic mutation rates and adenoma growth rates were historically constant or nearly constant even while the fraction of risk for certain cancers, including lung cancer significantly increased or decreased. This in turn suggests that environmental determinants of risk for these diseases are not effecting mutation rates or cell turnover or growth rates in normal tissues or adenomas. These hypotheses derived from analyses of the public health record appear to be consistent with direct measurements made in the laboratory in experimental animals and humans. In studies of mitochondrial DNA mutations in cultured human cells and various human organs, an essentially identical pattern of point mutations was discovered. When these studies were extended to the mitochondrial DNA of bronchial epithelial cells of identical twins discordant for cigarette smoking, the number and patterns of mutation were identical. This near identity led to the conclusion that mitochondrial point mutations are spontaneous in origin and not induced by exogenous mutagenic chemicals despite their presence in the environment. [It has since been found that a subset of these mutations are created when human mitochondrial DNA polymerase is used to copy the mitochondrial DNA sequence studied.] In nuclear DNA, the work is extended by direct comparison of smokers and nonsmokers using assays for point mutations at six separate positions in the H-RAS, TP53 and HPRT genes. First results indicate that the increase in mutant fractions in smokers is less than twofold, a value consistent with that derived from analysis of mortality data for lung cancer in birth cohorts which did or did not have access to cigarettes. Furthermore, it was discovered that a significant subset of human inherited and somatic point mutations [in the HPRT gene] are created by treating human


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cells with a concentration of a chemical which induces formation of 106 methyl guanine in DNA at levels found in normal human tissues. One interpretation is that spontaneous formation of this intermediate accounts for about a quarter of human base pair substitutions which account for about 3/4 of all human inherited disease. The technology for performing the mutation assays in human cells and organs was developed in the laboratory in the past decade. Much of it is based on tour development of constant denaturing capillary electrophoresis (CDCE) which permits the isolation of measure and sequence mutants more than 95% of the human genome with a sensitivity of 2 x 106. CDCE technology itself is based on application of statistical mechanics to calculation of equilibrium melting temperatures for DNA duplex sequences; its application permits separation of mutant from nonmutant sequences. More recently, Thilly's lab has extended the use of CDCE to the determination of the number and kind of point mutations in human populations. These inherited mutations are a mixture of a vast majority which have no effect on reproductive capacity (nondeleterious) or longevity (nonharmful) and a small faction which are deleterious, harmful or both. We have already demonstrated the discovery of inherited point mutations in mixtures of blood samples from 5000 juveniles at levels below 103 and have discovered some alleles at these low frequencies which are elevated in African American populations. Thilly has proposed a means to study human populations in such a way that deleterious alleles and harmful alleles may be readily identified within demographically distinct groups. Current Challenges: Studies of organs and tissues to identify causes of cancer remain the focus of the research in Thilly's laboratory. He is currently trying to create a successor Center to the CEHS to house this research, and welcomes contact from companies interested in sponsoring research on environmental causes of cancer and the cellular processes leading to cancer. His work on epidemiology and the assembly of the database has been his own project, not funded at MIT. He would like to seek some funding to support its expansion. Mortality Analysis: http://epidemiology.mit.edu/

PROF. FOREST M WHITE Associate Professor of Biological Engineering; Computational and Systems Biology Initiative; Koch Institute for Integrative Cancer Research (KIICR); Biotechnology Process Engineering Center; Center for Environmental Health Sciences http://web.mit.edu/be/people/white.htm http://web.mit.edu/fwhitelab/ http://web.mit.edu/ki/faculty/white.html http://csbi.mit.edu/people/white.html

Forest White is an expert in phosphoproteomics, the measurement of how proteins are phosphorylated in cells and tissues. Protein phosphorylation is a key mode of energy transport that affects cellular signaling and is key in all cellular processes. He holds a doctorate in analytical chemistry from Florida State University, and worked as a post-doctoral associate in proteomics and immunology with Don Hunt at University of Virginia. Before coming to MIT, White spent 2-1/2 years developing phosphoproteomics methods and equipment for MDS Proteomics.

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His research will focus on global mapping of protein phosphorylation events in the cell. His intent is to catalogue novel phosphorylation sites, and determine what they do, and to combine all this information into methods to compare quantitatively the phosphorylation states of cells over a time course. This research will allow researchers to watch signal transduction cascades firing off over time, enabling comparisons between, for example, normal and cancerous cells, or normal and diabetic tissues. The method could study processes like apoptosis (cell death) as well. By seeing the different signal transduction cascades in cells, new drug targets could be identified, and by studying the alteration in the cascades in treated cells, new ways to modulate cell signaling could be studied to develop improved drugs for a wide range of diseases. Thus this research has promise as a means to improve new drug discovery and preclinical evaluation of drug metabolism and toxicology. White's group will house the skills of proteomics, analytical chemistry (primarily mass spectroscopy), molecular and cell biology, medicinal chemistry, bioinformatics and statistics. He is also co-supervising a student working with Profs. Wittrup and Lauffenburger on EGF receptor signaling research, a related topic. He will be an active contributor to CSBi's research.

Forest White Lab The goal of research in the White lab is to understand how protein phosphorylation-mediated signaling networks drive biological responses to cellular stimulation. If we take a cue-signal-response view of biological systems, we can present the systems with different cues, such as agonists or antagonists, over-expression, mutation, or knock-down of components in the network and monitor biological responses including proliferation, cell motility, endocytosis, and invasiveness. Quantification of the signaling networks which result from each of these cues and drive the corresponding biological response should provide key information regarding the mechanism by which the cue relates to the response. A protein may have multiple phosphorylation sites which control different biological functions and show unique phosphorylation dynamics. A site-specific high-resolution map of the signaling network, with associated temporal dynamics, will enable improved computational modeling of the systems and provide predictive power for more effective targeted interventions in aberrant signaling networks. More at: http://web.mit.edu/fwhitelab/

Epidermal Growth Factor Receptor Signaling Network Within this framework, a significant fraction of research in the group is centered on the Epidermal Growth Factor Receptor (EGFR) signaling network, quantifying temporal dynamics of protein phosphorylation within the EGFR network while monitoring changes in the network induced by perturbations at the ligand and receptor level. The goal of this research is to answer several questions in oncogenic signaling: how does the EGFR signaling network change when different ligands (e.g. EGF, TGF-alpha, heregulin) are used to stimulate EGFR or EGFR family members, how do mutations within EGFR or over-expression of EGFR family members affect the signaling network, and what role does the EGFR signaling network play in cancer progression?

T Cell Signaling T cell signaling is another focus area within the lab, specifically aimed (1) at the signaling networks involved in T cell response to peptide ligand stimulation, with the goal of identifying defective signaling processes which may lead to autoimmune disorders such as Type 1 diabetes,

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and (2) at signaling networks downstream of IL-2, IL-15, CD3, and CD28 stimulation, with the goal of monitoring the network response to combinations of cytokine stimulations.

Technology Development To interrogate the signaling networks in these diverse biological systems, we use hybrid quadrupole time-of-flight mass spectrometers coupled with stable-isotope labeling, affinity chromatography, and LC-MS/MS to quantify temporal dynamics of tyrosine phosphorylation on hundreds of proteins simultaneously with site-specific resolution typically from several million cells. After gathering and analyzing the data, we are working with the Lauffenburger and Tidor labs in the Biological Engineering Division at MIT to develop better methods of computational analysis and modeling of signaling networks. These models will then be used to predict biological and signaling network responses to additional perturbations to the system.

DR. JOHN S WISHNOK (PETE) Senior Research Scientist, Department of Biological Engineering; Director, Mass Spectrometry Laboratory http://web.mit.edu/toxms/www/pete.htm , http://web.mit.edu/toxms/www/wtmsl.htm , http://web.mit.edu/be/people/wishnok.htm

John S. (Pete) Wishnok’s research interests include biological mass spectrometry, chemical carcinogenesis, molecular dosimetry, and nitric oxide biochemistry. Biology and biological engineering are being increasingly driven by advances in bioanalytical techniques and instrumentation. My research is focused on applications of biological mass spectrometry for the characterization and quantitation of DNA and protein damage caused by exposure both to xenobiotic substances and to endogenous compounds that are formed during various metabolic pathways. In the case of xenobiotics, e.g., smoking-related or diet-related carcinogens, quantitation of modifications to DNA or proteins can provide estimates of individual exposure to the active forms of these substances. DNA or protein modifications arising from endogenous substances, e.g., peroxynitrite, can provide valuable clues towards the biochemistry of their formation and often towards the subtle but important balances between essential vs damaging levels of nominally normal metabolites.

PROF. GERALD N WOGAN Professor of Chemistry and Biological Engineering, Emeritus; Center for Environmental Health Sciences http://web.mit.edu/be/people/wogan.htm , http://web.mit.edu/gnwlab/ http://web.mit.edu/chemistry/www/faculty/wogan.html

Professor Wogan's research concerns two major areas: DNA damage and genetic alterations in carcinogenesis; and molecular markers of exposure to environmental carcinogens. The objective of the first area is to elucidate relationships between DNA damage induced by chemical carcinogens and genetic alterations associated with tumor initiation and development. Particular emphasis is placed on studies of carcinogens thought to be of importance as risk factors for human cancers, and the program is structured to include methodologies that can be applied in

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concurrent parallel studies in appropriate experimental models and in humans known to be exposed to the carcinogens. Current evidence indicates that DNA damage caused by carcinogens is a critical initiating event in cancer, and investigation of damage induced by environmental carcinogens that are risk factors for human cancers remains a continuing interest. Current projects involve characterization of mutations induced in various experimental systems by nitric oxide and oxygen radicals. These reactive species are of interest because they are produced by cells involved in tissue inflammation, which is in turn an important risk factor for some major forms of cancer, including the stomach and liver. Nitric oxide and reactive oxygen species can induce a wide spectrum of DNA damaging lesions, but which these contribute to cancer initiation is currently unknown. Part of our program concerns characterization of mutations induced by these agents under controlled conditions in well-characterized experimental systems. Mutational spectra induced by reactive derivatives of nitric oxide are being characterized in shuttle vectors after repair and replication in bacterial and human cells. Mutagenesis is also being studied in target cells co-cultured with macrophages induced to produce nitric oxide over prolonged periods of time, as experimental surrogates for cells exposed in vivo to prolonged inflammation. These processes are also being investigated in SJL mice, which spontaneously develop pathologic states involving endogenous production of high levels of nitric oxide. The second area of research emphasis concerns molecular markers of exposure to environmental carcinogens. Accurate assessment of cancer risks represented by environmental carcinogens and formulation of effective intervention strategies require quantitative data on levels of human exposure to specific carcinogens. Historically, data of this kind have been calculated from measurements of concentrations of the chemicals in food, water or air, coupled with estimates of intake, a procedure of very limited accuracy for quantifying exposures of individuals within populations. Our research program seeks to address this objective through development of molecular markers of exposure that can be applied in determining the significance of carcinogens as risk factors for human cancers. We have characterized the DNA reaction products of aflatoxin B1 and developed analytical procedures of adequate sensitivity to measure DNA adduct levels in tissues and body fluids of humans exposed through dietary contamination. Analogous methods have also been developed for quantification of adducts of the carcinogen with serum albumin. Using these analytical methods, studies of populations known to be exposed to aflatoxin and at high risk of liver cancer in Guangxi Province, PRC and in The Gambia have been conducted in collaboration with cancer epidemiology groups of the University of Southern California, Johns Hopkins University, and the Shanghai Cancer Institute. We have demonstrated that exposure of individuals to the carcinogen can be accurately quantified by this approach, and that such persons are at high risk for development for the cancer, in particular those who are simultaneously infected by the hepatitis B virus. We have recently developed a novel analytical method for detection of DNA adducts of all classes of carcinogens. This methodology is being applied in evaluating the significance of oxidative DNA damage products associated with chronic inflammation as well as specific chemical carcinogens (heterocyclic aromatic amines) in the etiology of other major forms of cancer, including stomach, colon and bladder. Data produced from these studies will be important in the development of preventive and intervention studies to minimize the impacts of these carcinogens as cancer risk factors. The major focus of my research program is to identify risk factors for major forms of human cancers, with particular emphasis on defining contributions of both endogenous and exogenous chemicals to cancer causation. One aspect of our current work focuses on mechanisms through


which chronic inflammation increases risk for gastric, liver and other forms of cancer, with particular emphasis on nitric oxide (NO) overproduction by inflammatory cells. Specific projects involve characterization of mutagenic and carcinogenic responses to NO-induced DNA damage in experimental models including plasmids, cultured cells and transgenic mice. The second major focus of our current work concerns chemical carcinogens as risk factors for colorectal and bladder cancer. We are developing ultrasensitive and specific analytical technology for detecting and quantifying DNA adducts formed by aromatic and heterocyclic amines in cells and tissues following exposure. The analytical technology is being applied in the molecular epidemiology of colorectal and bladder cancers in collaboration with investigators at the University of Southern California. The rationale underlying our work is that effective strategies for cancer prevention and control must be based on data generated by investigation of molecular and cellular mechanisms underlying carcinogenesis.

Fluorescence Labeling of Nucleoside Adducts for Molecular Epidemiology The second research focus is molecular markers of exposure to environmental carcinogens. Accurate assessment of cancer risks from carcinogen exposure requires quantitative data on individual human exposure to specific carcinogens. Detection and analysis of specific carcinogen-damaged DNA bases (DNA adducts) resulting from endogenous or exogenous exposures to carcinogens is essential not only for quantifying biologically effective doses, but also for establishing relationships between exposure and cancer risk. To meet this need, we have developed and validated a sensitive and specific procedure based on fluorescence labeling of DNA adducts combined with HPLC-laser-induced fluorescence detection. The fluorescent dye BODIPY FL has been used to label deoxynucleoside adducts of the aromatic amine 4-aminobiphenyl, a bladder carcinogen widely disseminated in the environment, and PhIP, a heterocyclic amine formed during cooking of high-protein foods. The labeling reaction is carried out on adducts at picomolar to nanomolar concentrations, and the fluorescent product is detected and quantified by HPLC/laser-induced fluorescence. This analytical method is being used for analysis of aminobiphyenyl-deoxyguanosine levels in DNA isolated from urinary bladder in a case-control study of bladder cancer… More at http://web.mit.edu/gnwlab/research/index.htm

REALITY MINING Nathan Eagle, Prof. Alex (Sandy) Pentland MIT Media Lab Reality Mining defines the collection of machine-sensed environmental data pertaining to human social behavior. This new paradigm of data mining makes possible the modeling of conversation context, proximity sensing, and temporospatial location throughout large communities of individuals. Mobile phones (and similarly innocuous devices) are used for data collection, opening social network analysis to new methods of empirical stochastic modeling. The original Reality Mining experiment is one of the largest mobile phone projects attempted in academia. Our research agenda takes advantage of the increasingly widespread use of mobile phones to provide insight into the dynamics of both individual and group behavior. By leveraging recent advances in machine learning we are building generative models that can be used to predict what a single user will do next, as well as model behavior of large organizations… More at http://reality.media.mit.edu/

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Epidemiology and Information Dissemination Computational epidemiology is the study of modeling disease propagation. In order to understand and control the spread of pathogens, it is essential to establish some of the key parameters associated with disease transmission. Determining the basic reproductive ratio (Ro) of a disease, for example, is the primary objective for many epidemiological studies. Ro defines the number of secondary cases produced by an infected individual in an entirely susceptible population. Ideally, health policies can attempt to change the parameters involved in its formulation in order to control a pathogen's spread. Unfortunately, is notoriously difficult to measure, and must be derived indirectly. Mathematical models have played an important role in assessing and understanding the dynamics of disease transmission in human populations. For example, the proportion of individuals requiring vaccination for the eradication of a disease may be formulated using Ro. The majority of epidemiological models are based on a compartmental, SIR framework; the host population is partitioned into those that are susceptible, infected, or immune to a particular pathogen… More at http://reality.media.mit.edu/epidemiology.php

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