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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. -
CURRICULUM VITAE George M. Weinstock, Ph.D
CURRICULUM VITAE George M. Weinstock, Ph.D. DATE September 26, 2014 BIRTHDATE February 6, 1949 CITIZENSHIP USA ADDRESS The Jackson Laboratory for Genomic Medicine 10 Discovery Drive Farmington, CT 06032 [email protected] phone: 860-837-2420 PRESENT POSITION Associate Director for Microbial Genomics Professor Jackson Laboratory for Genomic Medicine UNDERGRADUATE 1966-1967 Washington University EDUCATION 1967-1970 University of Michigan 1970 B.S. (with distinction) Biophysics, Univ. Mich. GRADUATE 1970-1977 PHS Predoctoral Trainee, Dept. Biology, EDUCATION Mass. Institute of Technology, Cambridge, MA 1977 Ph.D., Advisor: David Botstein Thesis title: Genetic and physical studies of bacteriophage P22 genomes containing translocatable drug resistance elements. POSTDOCTORAL 1977-1980 Postdoctoral Fellow, Department of Biochemistry TRAINING Stanford University Medical School, Stanford, CA. Advisor: Dr. I. Robert Lehman. ACADEMIC POSITIONS/EMPLOYMENT/EXPERIENCE 1980-1981 Staff Scientist, Molec. Gen. Section, NCI-Frederick Cancer Research Facility, Frederick, MD 1981-1983 Staff Scientist, Laboratory of Genetics and Recombinant DNA, NCI-Frederick Cancer Research Facility, Frederick, MD 1981-1984 Adjunct Associate Professor, Department of Biological Sciences, University of Maryland, Baltimore County, Catonsville, MD 1983-1984 Senior Scientist and Head, DNA Metabolism Section, Lab. Genetics and Recombinant DNA, NCI-Frederick Cancer Research Facility, Frederick, MD 1984-1990 Associate Professor with tenure (1985) Department of Biochemistry -
Introduction to the Cell Cell History Cell Structures and Functions
Introduction to the cell cell history cell structures and functions CK-12 Foundation December 16, 2009 CK-12 Foundation is a non-profit organization with a mission to reduce the cost of textbook materials for the K-12 market both in the U.S. and worldwide. Using an open-content, web-based collaborative model termed the “FlexBook,” CK-12 intends to pioneer the generation and distribution of high quality educational content that will serve both as core text as well as provide an adaptive environment for learning. Copyright ©2009 CK-12 Foundation This work is licensed under the Creative Commons Attribution-Share Alike 3.0 United States License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/3.0/us/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California, 94105, USA. Contents 1 Cell structure and function dec 16 5 1.1 Lesson 3.1: Introduction to Cells .................................. 5 3 www.ck12.org www.ck12.org 4 Chapter 1 Cell structure and function dec 16 1.1 Lesson 3.1: Introduction to Cells Lesson Objectives • Identify the scientists that first observed cells. • Outline the importance of microscopes in the discovery of cells. • Summarize what the cell theory proposes. • Identify the limitations on cell size. • Identify the four parts common to all cells. • Compare prokaryotic and eukaryotic cells. Introduction Knowing the make up of cells and how cells work is necessary to all of the biological sciences. Learning about the similarities and differences between cell types is particularly important to the fields of cell biology and molecular biology. -
Cell Growth-Regulated Expression of Mammalian MCM5 and MCM6 Genes Mediated by the Transcription Factor E2F
Oncogene (1999) 18, 2299 ± 2309 ã 1999 Stockton Press All rights reserved 0950 ± 9232/99 $12.00 http://www.stockton-press.co.uk/onc Cell growth-regulated expression of mammalian MCM5 and MCM6 genes mediated by the transcription factor E2F Kiyoshi Ohtani1, Ritsuko Iwanaga1, Masataka Nakamura*,1, Masa-aki Ikeda2, Norikazu Yabuta3, Hiromichi Tsuruga3 and Hiroshi Nojima3 1Human Gene Sciences Center, Tokyo Medical and Dental University, Tokyo 113-8510, Japan 2Department of Developmental Biology, Graduate School of Dentistry, Tokyo Medical and Dental University, Tokyo 113-8549, Japan; 3Department of Molecular Genetics, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan Initiation of DNA replication requires the function of family (MCM2-7) that have been identi®ed in yeast, MCM gene products, which participate in ensuring that Xenopus, and human. Mcm proteins seem to regulate DNA replication occurs only once in the cell cycle. the initiation at the replication origin where the loading Expression of all mammalian genes of the MCM family of the proteins onto the origin recognition complex is induced by growth stimulation, unlike yeast, and the (ORC) is regulated by Cdc6 and cyclin-dependent mRNA levels peak at G1/S boundary. In this study, we kinases (Donovan et al., 1997; Tanaka et al., 1997). examined the transcriptional activities of isolated human However, the mechanism(s) by which Mcm proteins MCM gene promoters. Human MCM5 and MCM6 control the initiation of DNA replication remains promoters with mutation in the E2F sites failed in unclear. promoter regulation following serum stimulation and Xenopus Mcm proteins seem to be able to access exogenous E2F expression. -
Mutation Rates of Escherichia Coli with Different Balanced Growth Rates: a New Fluctuation Test Protocol and Phenotypic Lag Adju
Mutation rates of Escherichia coli with different balanced growth rates: a new fluctuation test protocol and phenotypic lag adjustments by Christian Terry Henderson Barna A thesis presented to the University of Waterloo in fulfilment of the thesis requirement for the degree of Master of Mathematics in Applied Mathematics Waterloo, Ontario, Canada, 2020 c Christian Terry Henderson Barna 2020 Author's Declaration I hereby declare that I am the sole author of this thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. ii Abstract Bacteria are the oldest, most abundant life form on the planet, and every other organ- ism's livelihood is dependent on them. The bacteria Escherichia coli (E. coli) is commonly used in microbiology as a model organism to give insight into the functions of bacteria and cells in general. Of particular interest in these studies is the methods with which bacteria grow and evolve. Growth is what propagates a bacteria's species; whereas evolution is what allows them to adapt to the ever-changing world. Evolution is made possible by mutations which change a bacterium's DNA. In 1943, Luria and Delbr¨uck developed a method, called a “fluctuation test", to estimate mutation rates from the number of mutants in a collection of parallel cultures exposed to a selecting agent after growth. The original fluctuation test methodology suffers from two major limitations. First, the bacteria are not in a re- producible, balanced state of growth throughout the test. -
Population Dynamics
FOCUS ON BACTERIAL GROWTH EDITORIAL Population dynamics This Focus issue on bacterial growth, highlights the versatility and adaptability with which bacterial cells respond to their environmental and community context. Bacteria have an immense capacity to grow. As men- antagonizing each other; for example, by the secretion of tioned by Megan Bergkessel, David Basta and Dianne toxins or through the type VI secretion system. By con- Newman on page 549, if Escherichia coli were to con- trast, mutualistic clonemates growing next to each other tinue exponential growth, a single bacterial “cell would often cooperate; for example, through the secretion of grow to a population with the mass of the Earth within 2 public goods. days”. However, bacteria rarely encounter perfect growth To regulate cooperative behaviour, bacteria use quo- conditions outside of the laboratory: nutrients are lim- rum sensing, whereby the concentrations of secreted sig- ited, the bacteria have to compete with other cells for nalling molecules inform bacteria about the surrounding resources or they are under attack by other bacterial population density. On page 576, Bonnie Bassler and Kai species, host defences or antimicrobial therapy. Thus, Papenfort review quorum sensing systems in Gram- bacteria have developed a wide variety of mechanisms negative bacteria, highlighting the different signalling that enable them to optimize their growth patterns molecules, receptors and response networks. They also according to the surrounding conditions. This Focus describe the broad effects that quorum sensing can have issue explores factors that influence bacterial growth by not only enabling communication between members dynamics and how bacterial populations respond to of one bacterial species but also between species, gen- them; for example, by forming biofilms and produc- era and even kingdoms; for example, between the gut ing a structured extracellular matrix, by executing microbiota and the mammalian host. -
Real-Time Egg Laying Dynamics in Caenorhabditis Elegans
UNIVERSITY OF CALIFORNIA, IRVINE Real-time egg laying dynamics in Caenorhabditis elegans DISSERTATION submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in Biomedical Engineering by Philip Vijay Thomas Dissertation Committee: Professor Elliot Hui, Chair Professor Olivier Cinquin Professor Abraham Lee 2015 c 2015 Philip Vijay Thomas TABLE OF CONTENTS Page LIST OF FIGURES iv ACKNOWLEDGMENTS v CURRICULUM VITAE vi ABSTRACT OF THE DISSERTATION viii 1 Introduction and motivation 1 1.1 The impact of C. elegans in aging and lifespan studies along with current limitations . 1 1.2 Starvation and its effect on worms . 4 1.3 Microfabricated systems for C. elegans biology . 5 2 Real-time C. elegans embryo cytometry to study reproductive aging 7 2.1 High capacity low-weight passive bubble trap . 8 2.2 Microfluidic device layout . 10 2.3 Tuning habitat exit sizes to flush out embryos while retaining worms . 11 2.4 Equal flow resistance to make identical habitats . 12 2.5 Video enumeration of eggs . 13 2.6 Switching between discrete and continuously varying media concentrations . 15 3 Optimizing worm health in C. elegans microfluidics 17 3.1 E. coli densities of 1010 cells/mL maintain egg-laying in liquid worm culture 18 3.2 E. coli biofilms in devices . 19 3.3 Amino acid addition to S-media, γ irradiation of bacteria, and elevated syringe temperatures are ineffective in reducing biofilms in devices . 20 3.4 Use of a curli major subunit deletion strain significantly reduces biofilm in S-media . 23 4 Conclusions and future directions 26 Bibliography 30 ii A Appendix Title 41 A.1 Methods . -
Microbiology Immunology Cent
years This booklet was created by Ashley T. Haase, MD, Regents Professor and Head of the Department of Microbiology and Immunology, with invaluable input from current and former faculty, students, and staff. Acknowledgements to Colleen O’Neill, Department Administrator, for editorial and research assistance; the ASM Center for the History of Microbiology and Erik Moore, University Archivist, for historical documents and photos; and Ryan Kueser and the Medical School Office of Communications & Marketing, for design and production assistance. UMN Microbiology & Immunology 2019 Centennial Introduction CELEBRATING A CENTURY OF MICROBIOLOGY & IMMUNOLOGY This brief history captures the last half century from the last history and features foundational ideas and individuals who played prominent roles through their scientific contributions and leadership in microbiology and immunology at the University of Minnesota since the founding of the University in 1851. 1. UMN Microbiology & Immunology 2019 Centennial Microbiology at Minnesota MICROBIOLOGY AT MINNESOTA Microbiology at Minnesota has been From the beginning, faculty have studied distinguished from the beginning by the bacteria, viruses, and fungi relevant to breadth of the microorganisms studied important infectious diseases, from and by the disciplines and sub-disciplines early studies of diphtheria and rabies, represented in the research and teaching of through poliomyelitis, streptococcal and the faculty. The Microbiology Department staphylococcal infection to the present itself, as an integral part of the Medical day, HIV/AIDS and co-morbidities, TB and School since the department’s inception cryptococcal infections, and influenza. in 1918-1919, has been distinguished Beyond medical microbiology, veterinary too by its breadth, serving historically microbiology, microbial physiology, as the organizational center for all industrial microbiology, environmental microbiological teaching and research microbiology and ecology, microbial for the whole University. -
The Era of Microbiology: a Golden Phoenix
RESEARCH REVIEW INTERNATIONAL MICROBIOLOGY (2006) 9:1–7 www.im.microbios.org Stanley Maloy* The era of microbiology: Moselio Schaechter a Golden Phoenix Center for Microbial Sciences, San Diego State University, San Diego, California, USA Summary. The discoveries over the last decade have demonstrated that micro- biology is a central scientific discipline with practical applications in agriculture, medicine, bioremediation, biotechnology, engineering, and other fields. It is clear that the roles of microbes in nature are so diverse that the process of mining this genetic variation for new applications will continue long into the future. Moreover, the rapid rate of microbial evolution ensures that there will be no permanent solu- tion to agricultural, medical, or environmental problems caused by microbes. These problems will demand a continual stream of creative new approaches that evolve along with the microbes. Thus, the excitement of this field will continue Received 10 January 2006 long into the future. However, these opportunities and imperatives demand a deep Accepted 6 February 2006 understanding of basic microbial physiology, genetics, and ecology. Major chal- *Corresponding author: lenges that lay ahead are to impart the broad training needed to entice and enable S. Maloy the next generation of microbiologists, and to educate the public and government Center for Microbial Sciences representatives about the continued and critical importance of this field for health San Diego State University and the economy. [Int Microbiol 2006; 9(1):1-7] 5500 Campanile Drive San Diego, CA 92182-4614, USA Tel. 1- 619-5947123. Fax 1- 619-5945676 Key words: development of microbiology · microbial ecology · microbial cell Email: [email protected] biology · integrative microbiology the natural environment, and to monitor the physiology of sin- Introduction gle cells under defined conditions. -
Erwin Chargaff 1905–2002
NATIONAL ACADEMY OF SCIENCES ERWIN CHARGAFF 1 9 0 5 – 2 0 0 2 A Biographical Memoir by SEYMOUR S. COHEN with selected bibliography by ROBERT LEHMAN Any opinions expressed in this memoir are those of the authors and do not necessarily reflect the views of the National Academy of Sciences. Biographical Memoir 2010 NATIONAL ACADEMY OF SCIENCES WASHINGTON, D.C. ERWIN CHARGAFF August 11, 1905–June 20, 2002 BY SEYMOUR S . COHEN 1 AND ROBERT LEHMAN N 1944, AS VARIOUS ARMIES WERE planning to invade central IEurope, the recently naturalized U.S. citizen and Columbia University biochemist had learned of the report of O. T. Avery and his colleagues that the deoxyribonucleic acid (DNA) of a specific strain of pneumococcus constituted the genetically specific hereditary determinant of that bacterium. Almost alone among the scientists of the time, Chargaff accepted the unusual Avery report and concluded that genetic differ- ences among DNAs must be reflected in chemical differences among these substances. He was actually the first biochemist to reorganize his laboratory to test this hypothesis, which he went on to prove by 1949. His results and the subsequent work on the nature of DNA and heredity transformed biomedical research and training for the next fifty years at least, and established potentialities for the development of biology, which have created economic entities and opportunities, as well as major ethical and political controversies. Trained as an analytical chemist, Chargaff had never imagined that he would help to solve a major cytological problem. Reprinted with the permission from Proceedings of the American Philosophical Society (vol. -
Chemical Heritage Foundation Boris Magasanik
CHEMICAL HERITAGE FOUNDATION BORIS MAGASANIK Transcript of an interview Conducted by Sondra Schlesinger In three sessions between 1993 and 1995 This interview has been designated as Free Access. One may view, quote from, cite, or reproduce the oral history with the permission of CHF. Please note: Users citing this interview for purposes of publication are obliged under the terms of the Chemical Heritage Foundation Oral History Program to credit CHF using the format below: Boris Magasanik, interview by Sondra Schlesinger, 1993-1995 (Philadelphia: Chemical Heritage Foundation, Oral History Transcript # 0186). Chemical Heritage Foundation Oral History Program 315 Chestnut Street Philadelphia, Pennsylvania 19106 The Chemical Heritage Foundation (CHF) serves the community of the chemical and molecular sciences, and the wider public, by treasuring the past, educating the present, and inspiring the future. CHF maintains a world-class collection of materials that document the history and heritage of the chemical and molecular sciences, technologies, and industries; encourages research in CHF collections; and carries out a program of outreach and interpretation in order to advance an understanding of the role of the chemical and molecular sciences, technologies, and industries in shaping society. BORIS MAGASANIK 1919 Born in Kharkoff, Russia, on December 19 Education 1941 B.S., biochemistry, City College of New York 1948 Ph.D., biochemistry, Columbia University Professional Experience Columbia University 1948-1949 Research Assistant, Department -
Bacteria Podcast.Pages
podcasts Encyclopedia of Life eol.org Bacteria Podcast and Scientist Interview Bacillus subtilis Roberto Kolter of Harvard explains the relationship between one bacterium, Bacillus subtilis, and the majestic trees outside his office windows at Harvard Medical School. There’s a lot going on, down among the roots. Transcript Ari: From the Encyclopedia of Life, this is One Species at a Time. I’m Ari Daniel Shapiro. Over the last few years, we’ve created more than 60 episodes for this series. But there’s one group we’ve neglected – the bacteria. Kolter: The most spectacular aspect of life on the planet Earth is the stuff we don’t see! Ari: Roberto Kolter is a bacteria fanatic. He’s a microbiologist, after all. Ari: Kolter lifts the blinds of one of his office windows at the Harvard Medical School. He looks outside, and he says everything he sees – depends on bacteria. The people bundled up on the street below rely on the bacteria in their guts to digest their food. There’s the dirt… Kolter: A lot of that soil is actually produced by bacterial activity. Ari: Even the trees dotting the landscape. Kolter: Without the microbes, none of those trees would make it. Ari: And it’s this last point – that most plants really benefit from a remarkable relationship with bacteria – that Kolter’s especially interested in. To explain, let’s focus on a particular bacteria – a tiny rod-shaped cell called Bacillus subtilis. This little guy is everywhere on the planet. Kolter: Glaciers in Alaska, deserts in Africa, swamps in South America – just to mention a few.