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Department of Biology, Report to the President 2016-2017
Department of Biology Academic year 2016–2017 was exciting and productive for the Department of Biology. The department is considered one of the best biological science departments in the world. Our superb faculty members are leaders in biological research and education. Some of the news regarding our faculty, research, and educational programs is highlighted below. Faculty Count and Departures During AY2017, the Department of Biology had 56 faculty members: 44 full professors, eight associate professors, and four assistant professors. Research homes are distributed among Building 68, the Broad Institute, the Koch Institute for Integrative Cancer Research, the Picower Institute for Learning and Memory, and the Whitehead Institute for Biomedical Research. In addition to 56 primary faculty members, there were six faculty members with secondary appointments in Biology. These joint faculty members provide important connections to other departments, including Brain and Cognitive Sciences, Chemistry, Biological Engineering, and Civil and Environmental Engineering. We are saddened by the loss of Professor Susan Lindquist, who passed away in October 2016. Hidde Ploegh (Whitehead Institute) moved to Children’s Hospital in January 2017. Professor William (Chip) Quinn (Biology/Brain and Cognitive Sciences) retired in July 2016. Faculty Awards Department of Biology faculty members are widely recognized for their contributions to the field. Among our core faculty are three Nobel Laureates, 30 members of the National Academy of Sciences, 28 members of the American Academy of Arts and Sciences, 14 fellows of the American Association for the Advancement of Science, four recipients of the National Science Foundation National Medal of Science, and 15 Howard Hughes Medical Institute (HHMI) investigators. -
Volume 3 Summer 2012
Volume 3 Summer 2012 . Academic Partners . Cover image Magnetic resonance image of the human brain showing colour-coded regions activated by smell stimulus. Editors Ulisses Barres de Almeida Max-Planck-Institut fuer Physik [email protected] Juan Rojo TH Unit, PH Division, CERN [email protected] [email protected] Academic Partners Fondazione CEUR Consortium Nova Universitas Copyright ©2012 by Associazione EURESIS The user may not modify, copy, reproduce, retransmit or otherwise distribute this publication and its contents (whether text, graphics or original research content), without express permission in writing from the Editors. Where the above content is directly or indirectly reproduced in an academic context, this must be acknowledge with the appropriate bibliographical citation. The opinions stated in the papers of the Euresis Journal are those of their respective authors and do not necessarily reflect the opinions of the Editors or the members of the Euresis Association or its sponsors. Euresis Journal (ISSN 2239-2742), a publication of Associazione Euresis, an Association for the Promotion of Scientific Endevour, Via Caduti di Marcinelle 2, 20134 Milano, Italia. www.euresisjournal.org Contact information: Email. [email protected] Tel.+39-022-1085-2225 Fax. +39-022-1085-2222 Graphic design and layout Lorenzo Morabito Technical Editor Davide PJ Caironi This document was created using LATEX 2" and X LE ATEX 2 . Letter from the Editors Dear reader, with this new issue we reach the third volume of Euresis Journal, an editorial ad- venture started one year ago with the scope of opening up a novel space of debate and encounter within the scientific and academic communities. -
ANNUAL REPORT 2019 1 Contents Director’S Letter 1
Whitehead Institute ANNUAL REPORT 2019 1 Contents Director’s Letter 1 Chair’s Letter 3 Members & Fellows 4–5 Science 6 Community 44 Philanthropy 56 2 The Changing Face of Discovery For 37 years, Whitehead Institute has demonstrated an ability to drive scientific discovery and to chart paths into new frontiers of knowledge. Its continuing achievements are due, in substan- tial part, to the unique capacities and dedication of Members who joined the Institute in the 1980s and ‘90s — from Founding Members Gerald Fink, Harvey Lodish, Rudolf Jaenisch, and Robert Weinberg to those who followed, including David Bartel, David Sabatini, Hazel Sive, Terry Orr-Weaver, Richard Young, and me. Those long-serving Members continue to do pioneering science and to be committed teachers and mentors. Yet we have begun an inevitable genera- tional transition: In the last two years, Gerry and Terry have closed their labs, and Harvey will do so this coming year. The exigencies of time mean that, increasingly, Whitehead Institute’s ability to maintain its vigorous scientific leadership depends on our next generation of researchers. As I move toward the conclusion of my term as director, I am particularly proud of the seven current Members and the 14 Whitehead Institute Fellows we recruited during the last 16 years. The newest of those stellar researchers joined us in 2019: Whitehead Institute Member Pulin Li and Whitehead Fellow Kipp Weiskopf. Pulin studies how circuits of interacting genes in individu- al cells enable multicellular functions, such as self-organizing into complex tissues, and her research brilliantly combines approaches from synthetic biology, developmental and stem cell biology, biophysics, and bioengineering to study these multicellular behaviors. -
Dr. David P. Bartel Journal Interviews
Home About Scientific Press Room Contact Us ● ScienceWatch Home ● Interviews Featured Interviews Author Commentaries Institutional Interviews 2008 : June 2008 - Author Commentaries : Dr. David P. Bartel Journal Interviews Podcasts AUTHOR COMMENTARIES - 2008 ● Analyses June 2008 Featured Analyses Dr. David P. Bartel A Featured Scientist from Essential Science IndicatorsSM What's Hot In... Special Topics Earlier this year, ScienceWatch.com published an analysis of high-impact research in Molecular Biology & Genetics over the past five years. The ● Data & Rankings analysis ranked David Bartel #2 among authors publishing high-impact papers in this field, based on 19 papers cited a total of 4,542 times. Sci-Bytes In Essential Science Indicators from Thomson Reuters, Dr. Bartel's record Fast Breaking Papers includes 76 original articles and review papers published between January 1, New Hot Papers 1998 and February 29, 2008, with a total of 10,386 cites. These papers can be found in the fields of Molecular Biology & Genetics, Biology & Emerging Research Fronts Biochemistry, and Plant & Animal Science. Fast Moving Fronts Research Front Maps Current Classics Dr. Bartel is a Howard Hughes Medical Institute investigator whose lab is based at the Whitehead Institute Top Topics for Biomedical Research in Cambridge, Massachusetts. He is also a Professor in the Department of Biology at MIT. Rising Stars New Entrants In the interview below, he talks with correspondent Gary Taubes about his highly cited research. Country Profiles What motivated your research originally on these small, non-coding RNAs, and particularly the 2000 Cell paper (Zamore PD, et al., RNAi: double-stranded RNA directs the ATP-dependent ● About Science Watch cleavage of mRNA at 21 to 23 nucleotide intervals," 101[1]: 25-33, 31 March 200), which is your most-highly cited paper that’s not a review? Methodology Tom Tuschl and Phil Zamore [see also] were postdocs in my lab working in collaboration with Phil Sharp Archives [see also] on the biochemistry of RNAi. -
Whitehead Institute Hosts Campbio for Middle School Students
Whitehead Institute Hosts CampBio for LINKS About Whitehead Pulse Middle School Students Contact COMMUNITY NOV E MB E R 8 , 2 0 1 3 B Y DUS TIN GRINNE L L Subscribe Upcoming events Whitehead home In August, Whitehead Institute joined with Science from Scientists to host the first CampBio, a weeklong science program bringing local middle school students to CATEG O RIES Whitehead Institute to learn firsthand how researchers answer biology’s most challenging questions. Community Events Honors and Awards Twentysix 7th and 8th graders attended the program, In the news participating in handson activities, laboratory Multimedia demonstrations and discussions with scientists. “We Research were one of the first research institutions in the area to invite high school students into our labs,” says Amy Tremblay, the Public Programs Officer in charge of SEARCH education and community outreach at Whitehead Institute. “We wanted to offer outreach programs to middle school students as well.” It’s a niche that needs to be met, Tremblay says, given the nation’s increasing commitment to STEM (for Science, Technology, Engineering, and Mathematics) education. Such is the credo of Science from Scientists, the leading inclass science/STEM enrichment program in Massachusetts, and codesigner of CampBio. This spring, Tremblay and her team worked with the Bostonbased nonprofit group to bring the summer program to life. “We’re on the cutting edge of biomedical science,” says Tremblay, “so what better place to introduce kids to research?” She says the students were surprisingly unfiltered during the week’s activities, unpressured by their peers and unafraid to ask questions about complex subjects. -
Fire Departments of Pathology and Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Room L235, Stanford, CA 94305-5324, USA
GENE SILENCING BY DOUBLE STRANDED RNA Nobel Lecture, December 8, 2006 by Andrew Z. Fire Departments of Pathology and Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Room L235, Stanford, CA 94305-5324, USA. I would like to thank the Nobel Assembly of the Karolinska Institutet for the opportunity to describe some recent work on RNA-triggered gene silencing. First a few disclaimers, however. Telling the full story of gene silencing would be a mammoth enterprise that would take me many years to write and would take you well into the night to read. So we’ll need to abbreviate the story more than a little. Second (and as you will see) we are only in the dawn of our knowledge; so consider the following to be primer... the best we could do as of December 8th, 2006. And third, please understand that the story that I am telling represents the work of several generations of biologists, chemists, and many shades in between. I’m pleased and proud that work from my labo- ratory has contributed to the field, and that this has led to my being chosen as one of the messengers to relay the story in this forum. At the same time, I hope that there will be no confusion of equating our modest contributions with those of the much grander RNAi enterprise. DOUBLE STRANDED RNA AS A BIOLOGICAL ALARM SIGNAL These disclaimers in hand, the story can now start with a biography of the first main character. Double stranded RNA is probably as old (or almost as old) as life on earth. -
Mapeig D'innovació Massachusetts
MAPEIG D’INNOVACIÓ MASSACHUSETTS SECTOR BIO-IT / DIGITAL HEALTH 9 de febrer de 2016 CATALUNYA I MASSACHUSETTS CATALUNYA MASSACHUSETTS Sup. (km²) 32,107 27,360 Habitants 7,504,008 6,349,097 PIB (milions €) 199,786 427,365 PIB per càpita (€) 26,624 67,311 Atur 17.7% 4.7% R&D sobre PIB 1.5% 5.67% Universitats 12 122 MASSACHUSETTS INNOVADOR MASSACHUSETTS INNOVADOR KEY INDUSTRIES Financial Services Technology Medicine and Life Sciences Manufacturing Fishing Tourism Big Data Digital Health LIFE SCIENCES UNIVERSITATS El sistema d’ensenyament superior de Massachusetts és dual; és a dir, format per una xarxa de centres públics i una de centres privats. La majoria de les 122 institucions d’educació superior que acull l’estat, i també les més destacades en termes d’excel·lència acadèmica i investigadora, pertanyen a l’àmbit privat, encara que la potència del sistema públic també és remarcable. llistar principals amb algun indicador RECERCA? UNIVERSITATS HARVARD Any fundació: 1636 Faculty members : 2,400 Students: 21,000 Alumni: 323,000 living alumni, Budget: $4,500 milliom MIT Any fundació: 1861 Professors (all ranks): 1,021 Other teaching staff: 809 Students: 11,319 Applicants: 18,356 Admits: 1,447 Percentage admitted: 7.9% Patents granted: 275 Budget: $2,920 million MIT Biology/bioengineering • Bioinstrumentation Engineering Analysis and • Emergent Behaviors of Integrated Cellular Systems Microscopy (BEAM) • Harvard-MIT Division of Health Sciences and • BioInstrumentation Laboratory Technology (HST) • Biological Engineering • Human Genomics Laboratory -
About Whitehead Institute for Biomedical Research Selected
About Whitehead Institute for Biomedical Research Selected Achievements in FOUNDING VISION Biomedical Science Whitehead Institute is a nonprofit, independent biomedical research institute with pioneering programs in cancer research, developmental biology, genetics, and Isolated the first tumor suppressor genomics. It was founded in 1982 through the generosity of Edwin C. "Jack" Whitehead, gene, the retinoblastoma gene, and a businessman and philanthropist who sought to create a new type of research created the first genetically defined institution, one that would exist outside the boundaries of a traditional academic human cancer cells. (Weinberg) institution, and yet, through a teaching affiliation with the Massachusetts Institute of Technology (MIT), offer all the intellectual, collegial, and scientific benefits of a leading Isolated key genes involved in diabetes, research university. hypertension, leukemia, and obesity. (Lodish) WHITEHEAD INSTITUTE TODAY True to its founding vision, the Institute gives outstanding investigators broad freedom Mapped and cloned the male- to pursue new ideas, encourages novel collaborations among investigators, and determining Y chromosome, revealing a accelerates the path of scientific discovery. Research at Whitehead Institute is unique self-repair mechanism. (Page) conducted by 22 principal investigators (Members and Fellows) and approximately 300 visiting scientists, postdoctoral fellows, graduate students, and undergraduate Developed a method for genetically students from around the world. Whitehead Institute is affiliated with MIT in its engineering salt- and drought-tolerant teaching activities but wholly responsible for its own research programs, governance, plants. (Fink) and finance. Developed the first comprehensive cellular LEADERSHIP network describing how the yeast Whitehead Institute is guided by a distinguished Board of Directors, chaired by Sarah genome produces life. -
Whitehead Faculty and Fellows Members
Whitehead Faculty and Fellows Members Ask a visiting scientist to describe Whitehead Institute and three themes David Bartel studies microRNAs and other small RNAs emerge immediately: the exceptional quality of the scientific staff, the that specify the destruction and/or translational collaborative spirit, and the ethos that encourages researchers at every level repression of mRNAs. He also studies mRNAs, focusing to share new ideas and benefit from the insights and experience of their on their untranslated regions and poly(A) tails, and colleagues. how these regions recruit and mediate regulatory processes. His lab found that microRNAs affect most human protein-coding genes, either by regulating The key to this combination of excellence and accessibility is, of course, the them or by shaping their evolution. Faculty. “From the beginning, we sought researchers who had terrific scientific instincts, but we were also looking for people who would feel comfortable in Iain Cheeseman investigates the process of our open environment,” says Founding Member Gerald Fink. “The exchange chromosome segregation and cell division. In of energy and new ideas never stops, from the formal research retreat, to the particular, he uses proteomics, biochemistry, cell faculty lunches, to the countless informal conversations in hallways and biology, and functional approaches to examine the lounges.” composition, structure, organization and function of the kinetochore — the group of proteins that assemble Whitehead Institute faculty, known as Members, are selected through a joint at the centromere and are required for chromosome appointment process with the Massachusetts Institute of Technology (MIT) segregation and cell division. Department of Biology. Whitehead Institute is solely responsible for their salary and research. -
Micrornas Generate Gene Expression Thresholds with Ultrasensitive Transitions
MicroRNAs generate gene expression thresholds with ultrasensitive transitions Shankar Mukherji1,*, Margaret S. Ebert2,3,*, Grace X. Zheng2,4, John S. Tsang5, Phillip A. Sharp2,3, and Alexander van Oudenaarden2,6,# dramatically. In particular, we show that regulation by Short Abstract — MicroRNAs are an abundant class of post- miRNAs establishes a threshold level of target mRNA below transcriptional regulator whose repressive effects are thought which protein production is highly repressed. Beyond this to have broad reach in terms of number of targets but modest threshold, there is a regime in which expression responds effect for any given target. In this study we performed a single- cell analysis of the effects of microRNA-mediated repression. ultrasensitively to target mRNA input until reaching high We observe that microRNAs generate gene expression enough mRNA levels to almost escape repression by thresholds by which target protein production is robustly miRNA. We constructed a mathematical model, similar to silenced below a given transcriptional activity and is activated models used to describe small RNA (sRNA) reguation in in an ultrasensitive fashion as the transcriptional activity is bacteria [7] and protein-protein titration effects [8,9], increased. The threshold can be tuned by modulating the describing repression of target gene expression by both non- microRNA concentration and the number of microRNA binding sites in the target 3’-UTR. catalytic and catalytic activity of miRNA. The model predicted, and experiments confirmed, that the ultrasensitive Keywords — microRNA, gene expression, post- regime could be shifted to higher target mRNA levels by transcriptional regulation transfecting additional miRNA or by increasing the number of miRNA binding sites in the 3’ UTR of the target mRNA. -
Signature of Author
Computational and experimental analysis of plant microRNAs by Matthew W. Jones-Rhoades B.A., Chemistry (1999) Grinnell College Submitted to the Department of Biology in Partial Fulfillment of the Requirement for the Degree of Doctor of Philosophy in Biology MASSACHUSETTSINSTATE at the OF TECHNOLOGY Massachusetts Institute of Technology MAY 2 7 2005 June 2005 LIBRARIES © 2005 Massachusetts Institute of Technology All rights reserved Signatureof Author.................................... ................. ................. Department of Biology x.. '"---.~ May 20, 2005 Certified by ......... · .................................................... David P. Bartel Professor of Biology Thesis Supervisor Acceptedby ... ......... Stephen P. Bell Professor of Biology Chairman, Graduate Student Committee ,' tti v ;S Computational and experimental analysis of plant microRNAs Matthew W. Jones-Rhoades Submitted to the Department of Biology on May 20, 2005 in Partial Fulfillment of the Requirement for the Degree of Doctor of Philosophy in Biology ABSTRACT MicroRNAs (miRNAs) are small, endogenous, non-coding RNAs that mediate gene regulation in plants and animals. We demonstrated that Arabidopsis thaliana miRNAs are highly complementary (0-3 mispairs in an ungapped alignment) to more mRNAs than would be expected by chance. These mRNAs are therefore putative regulatory targets of their complementary miRNAs. Many miRNA complementary sites are conserved to the monocot Oryza sativa (rice), implying evolutionary conservation based on function at the nucleotide level. The majority of predicted miRNA targets encode for transcription factors and other proteins with known or inferred roles in developmental patterning, implying that the miRNAs themselves are high-level regulators of development. Our findings indicated that miRNAs are key components of numerous regulatory circuits in plants and set the stage for numerous additional experiments to investigate in depth the significance of miRNA-mediated regulation for particular target families and genes. -
Springer A++ Viewer
PublisherInfo PublisherName : BioMed Central PublisherLocation : London PublisherImprintName : BioMed Central Primate-specific microRNAs found ArticleInfo ArticleID : 5096 ArticleDOI : 10.1186/gb-spotlight-20050620-01 ArticleCitationID : spotlight-20050620-01 ArticleSequenceNumber : 72 ArticleCategory : Research news ArticleFirstPage : 1 ArticleLastPage : 4 RegistrationDate : 2005–6–20 ArticleHistory : OnlineDate : 2005–6–20 ArticleCopyright : BioMed Central Ltd2005 ArticleGrants : ArticleContext : 130596611 Charles Q Choi Email: [email protected] Israeli scientists have identified what may be the first microRNAs specific to primates, in research published online June 19 in Nature Genetics. They suggest these new microRNAs might mean that hundreds remain to be found in the human genome. "Finding a group of genes that is specific to primates is very important for understanding our evolution, and bears significant diagnostic and therapeutic potential," lead researcher Isaac Bentwich, at Rosetta Genomics in Rehovot, told The Scientist. MicroRNAs are single-stranded RNAs roughly 22 nucleotides long that regulate gene expression by binding to target gene mRNAs. The DNA sequence that codes for a microRNA gene includes the microRNA sequence and a nearby complementary sequence that, when transcribed, form a double- stranded RNA hairpin loop. Past studies have identified 222 human microRNAs, of which scientists had confirmed the sequences of only 86 in humans. To uncover more, Bentwich and colleagues computationally folded the entire human genome into hairpins 55 nucleotides or longer. Of 11 million potential hairpins, 434,239 appeared to be viable microRNA candidates. "Conventional approaches start with genome comparisons, to identify sequences important enough to be conserved across species. This new approach doesn't start with genome alignments. This allows them to find microRNAs not conserved beyond primates," Victor Ambros of Dartmouth Medical School in Hanover, N.H., who did not participate in this study, told The Scientist.