DOCSLIB.ORG

IN BRIEF Accounted For

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
IN BRIEF Accounted For RESEARCH HIGHLIGHTS content or isochore location are IN BRIEF accounted for. The dovetailing of the authors’ experimental and bioinformatic data EVOLUTION provides extremely strong circumstan- tial evidence that L1 insertions Noise minimization in eukaryotic gene expression. decrease gene expression in vivo. Fraser, H. B. et al. PloS Biol. 27 Apr 2004 (doi:10.1371/journal.pbio.0020137) Moreover, this new work tallies with previous findings that gene expression Until now, the functional and evolutionary significance of stochastic is suppressed when full-length L1 (‘noisy’) fluctuations in the rates of protein production was a mys- sequences are inserted into introns. tery.Michael Eisen and colleagues have developed a model of sto- The authors also raise the intrigu- chastic gene expression in yeast to test their hypothesis that genes ing possibility that the mammalian that encode subunits of multiprotein complexes or that cause lethal- genome might have co-opted tran- ity when deleted would be sensitive to such variation. Their estimates scriptional suppression of L1 (which of the noise in protein production for most yeast genes confirm this probably first evolved to prevent hypothesis and indicate that natural selection minimizes noise in excessive mutagenic retrotransposi- gene expression. tion) as a mechanism for fine-tuning the relative levels of expression of dif- CANCER GENETICS ferent genes. If this model is correct, perhaps L1 is better viewed as more Impact of the KU80 pathway on NHEJ-induced of a genomic classroom assistant than genome rearrangements on mammalian cells. Han and colleagues followed up a problematic pupil? Guirouilh-Barbat, J. et al. Mol. Cell 14, 611–623 (2004) their experiments with a neat bit of Nick Campbell bioinformatics. They compared the The genomes of cancer cells are often unstable and undergo rearrange- amount of L1 sequence in the genes References and links ments. Non-homologous end joining (NHEJ), a process that joins ORIGINAL RESEARCH PAPER Han, J. S. et al. with the highest and lowest levels of Transcriptional disruption by the L1 broken ends of double-strand breaks (DSBs) in DNA, is generally expression in humans. The results retrotransposon and implications for mammalian associated with maintaining mammalian genome stability. Josée were striking: highly expressed genes transcriptomes. Nature 429, 268–274 (2004) Guirouilh-Barbat and colleagues now show that NHEJ might occur FURTHER READING Han, J. S. & Boeke, J. D. contained small amounts of L1 sequ- A highly active synthetic mammalian in two-thirds of DSB repairs. Surprisingly, their data indicate that this ence, whereas genes with low levels of retrotransposon. Nature 429, 314–318 (2004) pathway often incorporates broken DNA into new locations and so expression contained large amounts WEB SITE accounts for many genome rearrangements that are seen in cancer cells. Jef Boeke’s laboratory: of L1 sequence. These patterns hold http://www.bs.jhmi.edu/MBG/boekelab/boeke_ even when differences in total intron lab_homepage AGEING Sirt1 promotes fat mobilization in white adipocytes by repressing PPAR-γ. idea that PLZF promotes stem-cell maintenance, possibly through Picard, F. et al. Nature 2 June 2004 (doi:10.1038/nature02583) chromatin remodelling. Zfp145–/– germ cells would be channelled Premature ageing in mice expressing defective down the differentiation pathway mitochondrial DNA polymerase. at the expense of proliferating. Trifunovic, A. et al. Nature 429, 417–423 (2004) Indeed, Pandolfi and co-authors show that Zfp145–/– cells do badly Two studies provide separate molecular explanations for the ageing at repopulating testes that lack process in mammals. In yeast, the SIR2 gene is the link between stem cells, probably because so few calorie restriction and an extended lifespan. Leonard Guarente and undifferentiated cells are present. colleagues have now investigated how Sirt1 (sirtuin 1), the mam- Given the roles of PLZF in limb malian version of SIR2,mediates the same effect in the mouse. Fat development, acute-promyelocytic reduction extends the mouse lifespan, and the authors have shown leukaemia and germ stem-cell that this is caused by the ability of SIRT1 to promote fat mobiliza- differentiation, this protein tion in adipocytes by repressing the fat regulator PPAR-γ during provides an interesting link food deprivation. Nils-Göran Larsson and colleagues focussed between development, cancer instead on the mitochondrial DNA (mtDNA), which is known to biology and stem-cell maintenance. accumulate mutations with age. Mice that were defective for the Tanita Casci mtDNA polymerase PolgA — because they expressed a nuclear References and links ORIGINAL RESEARCH PAPERS Buaas, F. W. knock-in mutation that abolished the proofreading ability of the et al. Plzf is required in adult germ cells for stem polymerase — accumulated 3–5 times the number of point muta- cell self-renewal. Nature Genet. 36, 647–652 tions, aged prematurely and developed age-related features, such (2004) | Costoya, J. A., Hobbs, R. M. et al. Essential role of Plzf in maintenance of as baldness and reduced fertility. This clever experiment supports spermatogonial stem cells. Nature Genet. 36, the view that mtDNA mutations are the cause rather than the 653–659 (2004) consequence of ageing. NATURE REVIEWS | GENETICS VOLUME 5 | JULY 2004 | 487.
Load more

Recommended publications
  • It Is NOT Junk a Blog About Genomes, DNA, Evolution, Open Science, Baseball and Other Important Things
    it is NOT junk a blog about genomes, DNA, evolution, open science, baseball and other important things The Past, Present and Future of Scholarly Publishing By MIC H A EL EISEN | Published: MA RC H 2 8 , 2 0 1 3 Search To search, type and hit enter I gave a talk last night at the Commonwealth Club in San Francisco about science publishing and PLoS. There will be an audio link soon, but, for the first time in my life, Michael Eisen I actually gave the talk (largely) from prepared remarks, so I thought I’d post it here. I'm a biologist at UC An audio recording of the talk with Q&A is available here. Berkeley and an Investigator of the —— Howard Hughes Medical Institute. I work primarily On January 6, 2011, 24 year old hacker and activist Aaron Swartz was arrested by on flies, and my research encompases police at the Massachusetts Institute of Technology for downloading several million evolution, development, genetics, articles from an online archive of research journals called JSTOR. genomics, chemical ecology and behavior. I am a strong proponent of After Swartz committed suicide earlier this year in the face of legal troubles arising open science, and a co-founder of the from this incident, questions were raised about why MIT, whose access to JSTOR he Public Library of Science. And most exploited, chose to pursue charges, and what motivated the US Department of Justice importantly, I am a Red Sox fan. (More to demand jail time for his transgression. about me here).
    [Show full text]
  • Gene Co-Expression Network Mining Using Graph Sparsification
    Gene Co-expression Network Mining Using Graph Sparsification THESIS Presented in Partial Fulfillment of the Requirements for the Degree Master of Science in the Graduate School of The Ohio State University By Jinchao Di Graduate Program in Electrical and Computer Engineering The Ohio State University 2013 Master’s Examination Committee: Dr. Kun Huang, Advisor Dr. Raghu Machiraju Dr. Yuejie Chi ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! Copyright by Jinchao Di 2013 ! ! Abstract Identifying and analyzing gene modules is important since it can help understand gene function globally and reveal the underlying molecular mechanism. In this thesis, we propose a method combining local graph sparsification and a gene similarity measurement method TOM. This method can detect gene modules from a weighted gene co-expression network more e↵ectively since we set a local threshold which can detect clusters with di↵erent densities. In our algorithm, we only retain one edge for each gene, which can generate more balanced gene clusters. To estimate the e↵ectiveness of our algorithm we use DAVID to functionally evaluate the gene list for each module we detect and compare our results with some well known algorithms. The result of our algorithm shows better biological relevance than the compared methods and the number of the meaningful biological clusters is much larger than other methods, implying we discover some previously missed gene clusters. Moreover, we carry out a robustness test by adding Gaussian noise with di↵erent variance to the expression data. We find that our algorithm is robust to noise. We also find that some hub genes considered as important genes could be artifacts.
    [Show full text]
  • Trevor John Hastie 1040 Campus Drive Stanford, CA 94305 Home Phone&FAX: (650) 326-0854
    Trevor John Hastie 1040 Campus Drive Stanford, CA 94305 Home Phone&FAX: (650) 326-0854 Department of Statistics Born: June 27, 1953, South Africa Sequoia Hall Married, two children Stanford University U. S. citizen, S.A. citizen Stanford, CA 94305 E-Mail: [email protected] (650) 725-2231 Fax: 650/725-8977 Updated: June 22, 2021 Present Position 2013{ John A. Overdeck Professor of Mathematical Sciences, Stanford University. 2006{2009 Chair, Department of Statistics, Stanford University. 2005{2006 Associate Chair, Department of Statistics, Stanford University. 1999{ Professor, Statistics and Biostatistics Departments, Stanford University. Founder and co-director of Statistics department industrial affiliates program. 1994{1998 Associate Professor (tenured), Statistics and Biostatistics Departments, Stan- ford University. Research interests include nonparametric regression models, computer in- tensive data analysis techniques, statistical computing and graphics, and statistical consulting. Currently working on adaptive modeling and predic- tion procedures, signal and image modeling, and problems in bioinformatics with many more variables than observations. Education 1984 Stanford University, Stanford, California { Ph.D, Department of Statis- tics (Werner Stuetzle, advisor) 1979 University of Cape Town, Cape Town, South Africa { First Class Masters Degree in Statistics (June Juritz, advisor). 1976 Rhodes University, Grahamstown, South Africa { Bachelor of Science Honors Degree in Statistics. 1975 Rhodes University, Grahamstown, South Africa { Bachelor of Science Degree (cum laude) in Statistics, Computer Science and Mathematics. Awards and Honors 2020 \Statistician of the year" award, Chicago chapter ASA. 2020 Breiman award (senior) 2019 Recipient of the Sigillum Magnum, University of Bologna, Italy. 2019 Elected to The Royal Netherlands Academy of Arts and Science. 2019 Wald lecturer, JSM Denver.
    [Show full text]
  • Ddawson2012.Pdf (700.6Kb)
    Open Science and Crowd Science: Selected Sites and Resources Diane (DeDe) Dawson Natural Sciences Liaison Librarian University of Saskatchewan Saskatoon, Saskatchewan, Canada [email protected] Table of Contents Introduction Open Science Crowd Science Methods and Scope Open Science – Definitions and Principles Open Science – Open Lab Notebooks of Individuals and Lab Groups Open Science – Blogs Crowd Science – Projects for Individuals or Small Teams Crowd Science – Volunteer Distributed Computing Projects The Main Software Organizations Selected Projects Further Sources for Projects Selected Examples of Collaborative Science Sites for Specialists Main Software & Online Tools for Open Science Open Science Conferences and Community Conferences Further Reading/Viewing Videos Reports and White Papers Open e-Books Selected Essays, Articles, and Interviews References Introduction “To take full advantage of modern tools for the production of knowledge, we need to create an open scientific culture where as much information as possible is moved out of people’s heads and laboratories, and onto the network” (Nielsen 2011, p.183). New Internet technologies are radically enhancing the speed and ease of scholarly communications, and are providing opportunities for conducting and sharing research in new ways. This webliography explores the emerging “open science” and “crowd science” movements which are making use of these new opportunities to increase collaboration and openness in scientific research. The collaboration of many researchers on a project can enhance the rate of data-collection and analysis, and ignite new ideas. In addition, since there are more eyes to spot any inaccuracies or errors, collaborative research is likely to produce better quality results. Openness early in the research process alerts others to the work resulting in less duplication of efforts.
    [Show full text]
  • Converting Scholarly Journals to Open Access: a Review of Approaches and Experiences David J
    University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Copyright, Fair Use, Scholarly Communication, etc. Libraries at University of Nebraska-Lincoln 2016 Converting Scholarly Journals to Open Access: A Review of Approaches and Experiences David J. Solomon Michigan State University Mikael Laakso Hanken School of Economics Bo-Christer Björk Hanken School of Economics Peter Suber editor Harvard University Follow this and additional works at: http://digitalcommons.unl.edu/scholcom Part of the Intellectual Property Law Commons, Scholarly Communication Commons, and the Scholarly Publishing Commons Solomon, David J.; Laakso, Mikael; Björk, Bo-Christer; and Suber, Peter editor, "Converting Scholarly Journals to Open Access: A Review of Approaches and Experiences" (2016). Copyright, Fair Use, Scholarly Communication, etc.. 27. http://digitalcommons.unl.edu/scholcom/27 This Article is brought to you for free and open access by the Libraries at University of Nebraska-Lincoln at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Copyright, Fair Use, Scholarly Communication, etc. by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Converting Scholarly Journals to Open Access: A Review of Approaches and Experiences By David J. Solomon, Mikael Laakso, and Bo-Christer Björk With interpolated comments from the public and a panel of experts Edited by Peter Suber Published by the Harvard Library August 2016 This entire report, including the main text by David Solomon, Bo-Christer Björk, and Mikael Laakso, the preface by Peter Suber, and the comments by multiple authors is licensed under a Creative Commons Attribution 4.0 International License. https://creativecommons.org/licenses/by/4.0/ 1 Preface Subscription journals have been converting or “flipping” to open access (OA) for about as long as OA has been an option.
    [Show full text]
  • In Memoriam: PNAS Editor-In-Chief Nicholas R. Cozzarelli (1938 –2006)
    In Memoriam: PNAS Editor-in-Chief Nicholas R. Cozzarelli (1938–2006) hen Nicholas R. Cozzarelli possessed a sharp, analytical memory, became Editor-in-Chief of which perhaps explains why he initially the Proceedings of the Na- chose to study pre-law at Princeton. tional Academy of Sciences However, after some undergraduate Wof the United States of America (PNAS) research, he began falling in love with in 1995, he inherited a journal that in science, and he graduated magna cum many ways had remained unchanged laude in 1960 with a bachelor’s degree since its inception in 1914. Yet in just in biology. Afterward, he attended Yale over a decade, he had—through a com- University School of Medicine (New bination of visionary leadership and Haven, CT) but soon realized that, de- sheer force of will—transformed PNAS spite his talents, he did not want to be a and raised it to a higher level. That physician. After a year, he transferred to transformation can be seen throughout Harvard Medical School (Boston, MA) the journal, from cover to last page. to embark on a journey of research, Since 1995, PNAS has experienced a which began with his graduate studies in marked rise in the number of submis- the laboratory of E. C. C. Lin, examin- sions and published papers, an improve- ing the genes and pathways regulating ment in the quality and variety of Escherichia coli glycerol metabolism. published material, and the introduction After receiving his Ph.D. from Har- of an innovative hybrid open access vard in 1966, Cozzarelli moved to Stan- model.
    [Show full text]
  • NEHA SPENTA WADIA [email protected] • (+1) 413 695 5367
    NEHA SPENTA WADIA [email protected] • (+1) 413 695 5367 EDUCATION University of California, Berkeley, Berkeley, CA, USA August 2015 - present Biophysics Graduate Group Redwood Center for Theoretical Neuroscience • PhD in Biophysics, advised by Professor Michael DeWeese. Expected May 2021 I work on problems in statistical physics and machine learning with the aim of developing new theoretical frameworks within which to understand network-level computations in brains. University of Waterloo and Perimeter Institute for Theoretical Physics, Waterloo, ON, Canada Perimeter Scholars International • Master of Science in Physics. June 2014 • Masters Research Essay: “Adventures in Two Dimensional Heisenberg Spin Systems in the Context of Solid State NMR”, advised by Professor David G. Cory (available at http://perimeterinstitute.ca/psi_essays/2014/Neha_Wadia.pdf). • Awards: Honorary Emmy Noether Scholarship. • Class valedictorian. Amherst College, Amherst, MA, USA • Bachelor of Arts in Physics, Magna Cum Laude. May 2013 • Cumulative GPA: 3.80/4.0, Physics GPA: 3.68/4.0. • Senior Honors Thesis: “Measurements of Branching Ratios for the B(0)-X(v) Transition in Thallium Fluoride to Determine its Potential for Laser Cooling”, advised by Professor Larry Hunter (available at https://www.amherst.edu/system/files/Wadia.pdf). • Awards: Forris Jewett Moore Graduate Fellowship. August 2013 – May 2014 • Student member of the Amherst College chapter of Sigma Xi, Scientific Honors Society. RESEARCH EXPERIENCE University of California, Berkeley, Berkeley, CA, USA • Rotation Student September 2015 – November 2015 I spent ten weeks as a rotation student in the laboratory of Professor Michael Eisen, who studies the function of enhancers in the genome and the interactions between pathogenic microbes and their animal hosts within the relevant ecological contexts.
    [Show full text]
  • A Future Vision for PLOS Computational Biology
    Editorial A Future Vision for PLOS Computational Biology Ruth Nussinov1,2* 1 Basic Science Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America, 2 Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel With much trepidation I accepted the relevance. As Editor-in-Chief I will do my PLOS Computational Biology is broad; it great honor and responsibility of becom- best to have PLOS Computational Biology addresses diverse biological problems. We ing Editor-in-Chief of PLOS Computational continue these traditions. look forward to further expanding its Biology. I am fully aware of how hard it will Computational biology is often per- scope through the inclusion of outstanding be to step into the shoes of Philip Bourne, ceived as a single field; this however is methods and resource papers, opening up the Editor-in-Chief of the journal for the not the case. Like experimental biology, significant new research directions while last seven years, since it was founded by computational biology is enormously retaining and enhancing the strong scien- him, Steven Brenner, and Michael Eisen. broad; the only distinction from experi- tific merit of PLOS Computational Biology We are all deeply appreciative and mental biology is the means. This has publications. We further plan on improv- thankful to Phil for his unique role; and disadvantages and advantages: the main ing the pace of submissions processing. we are grateful that he will be continuing disadvantage is that conclusions based on PLOS Computational Biology is recognized by his association with the journal in the computations are often treated by biolo- the community as the premier journal in future in the role of Founding Editor-in- gists as less conclusive than those based on computational biology.
    [Show full text]
  • Gene Expression in Early Drosophila Embryos Is Highly Conserved Despite Extensive Divergence of Transcription Factor Binding
    Gene expression in early Drosophila embryos is highly conserved despite extensive divergence of transcription factor binding. Mathilde Paris1, Tommy Kaplan1,2, Xiao Yong Li1,3, Jacqueline E. Villalta2, Susan E. Lott1,4, Michael B. Eisen1,2 1 Department of Molecular and Cell Biology, University of California BerKeley, BerKeley, California, United States of America, 2 School of Computer Science and Engineering, The Hebrew University, Jerusalem, Israel, 3 Howard Hughes Medical Institute, University of California BerKeley, BerKeley, California, United States of America, 4 Department of Evolution and Ecology, University of California, Davis, California, United States of America. Corresponding authors: MP and MBE ABSTRACT To better characterize how variation in regulatory sequences drives divergence in gene expression, we undertooK a systematic study of transcription factor binding and gene expression in the blastoderm embryos of four species that sample much of the diversity in the 60 million-year old genus Drosophila: D. melanogaster, D. yakuba, D. pseudoobscura and D. virilis. We compared gene expression, as measured by mRNA-seq to the genome-wide binding of four transcription factors involved in early development, as measured by ChIP-seq (Bicoid, Giant, Hunchback and Krüppel). Surprisingly, we found that mRNA levels are much better conserved than individual binding events. We looKed at binding characteristics that may explain such evolutionary disparity. As expected, we found that binding divergence increases with phylogenetic distance. Interestingly, binding events in non-coding regions that were bound strongly by single factors, or bound by multiple factors, were more liKely to be conserved. As this class of sites are most liKely to be involved in gene regulation, the divergence of other bound regions may simply reflect their lack of function.
    [Show full text]
  • The Rise and Fall of a Community-Driven Model of Scientific Communication Joachim Schöpfel
    Open access - the rise and fall of a community-driven model of scientific communication Joachim Schöpfel To cite this version: Joachim Schöpfel. Open access - the rise and fall of a community-driven model of scientific communi- cation. Learned Publishing, Association of Learned and Professional Society Publishers, 2015, 28 (4), pp.321-325. 10.1087/20150413. hal-01282744 HAL Id: hal-01282744 https://hal.archives-ouvertes.fr/hal-01282744 Submitted on 13 Jun 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution - NonCommercial - NoDerivatives| 4.0 International License Open Access – The Rise and Fall of a Community-Driven Model of Scientific Communication Opinion Paper Joachim Schöpfel GERiiCO laboratory, University of Lille 3 [email protected] Key points • In 25 years, open access, i.e. free and unrestricted access to scientific information, has become a significant part of scientific communication. However, its success story should not conceal a fundamental change of its nature. • Open access started, together with the Web, at the grassroots, as a bottom-up, community-driven model of open journals and repositories. Today the key driving forces are no longer community-driven needs and objectives but commercial, institutional and political interests.
    [Show full text]
  • Michael Eisen's Angry, Hypocrisy Drenched Assault on Informed
    Michael Eisen's Angry, Hypocrisy Drenched Assault on Informed Consent using Massive Fallacious Reasoning while Ironically Brandishing the Banner of "Science" (c) Copyright 2012 David Dilworth (Eisen may have set a New World Record by committing Six Logical Fallacies with a Single Sentence.) The Genetically modified (GMO) food conflict surfaced in California where Food Safety proponents have put GMO food labeling on the November 2012 ballot so consumers can make an informed choice. GMO manufacturing corporations including Monsanto oppose labeling. Though I'd written a letter to a British researcher about iti the GMO campaign hadn't really caught my attention until I ran across an article, or more accurately found an article that ran over me and rational discourse. Entitled "The anti-GMO campaign's dangerous war on science"ii it is written by a genetic researcher in California named Michael Eisen claiming to support Open Science. The article caught my attention because I've been helping work for good science for a few decades, I'm aware of real attacks on science philosophy and credibility and I am a bit familiar with environmental impacts iii - so sounds good right ? Wow, was I ever in for a disturbing surprise. With deeply profound irony an "infuriated" Eisen claims he's fighting to defend science ("My vested interest here is science, and what I write here, I write to defend it"). Instead his article assaults and batters science reasoning and logic so relentlessly I had to set it aside for a few days to recover from my shocked dismay. "Well I'm angry, making sense gets in the way." "Coupling" British TV seriesiv If I'd found so much as one valid electronic breath defending science methodology, reasoning or logic in the article I wouldn't have written this.
    [Show full text]
  • Objectives of the Workshop May 20, 2010
    Objectives of the Workshop May 20, 2010 To crowd‐open source the electronic printing press of the 21st century with the goal of improving how science is disseminated and comprehended. The current objectives of the workshop are: 1. To define the requirements of various classes of user (reader, author, publisher, reviewer, editor, librarian etc.) that need to be met when developing research objects (RO) that extend the features of a scientific research article beyond that typically embodied in a PDF today to take full advantage of the power of the Internet. This includes, but is not limited to: a. Providing knowledge and data integration – currently the data associated with a research article are typically not available, or in a disparate database, or computationally unusable as a supplement to a PDF, b. Bringing additional senses to the problem ‐ enhance the meaning and/or comprehension of science through the use of rich media (video and podcasts) which are not included with a PDF, or if available divorced (i.e., not integrated) with the work. c. Provide reproducibility ‐ the PDF does not capture the workflow nor any of the discourse associated with the work. d. Provides Interoperability with other ROs and with other forms of discourse e.g., blogs. e. Provide interactivity ‐ the ability to interact with the content in context sensitive ways. f. Provide a living document – additional commentary, reviews, further discourse etc. can be added to the RO at any time and an audit trail maintained. g. Provide new bibliometrics – allow a more meaningful evaluation and reward system for the original work and those that critique it.
    [Show full text]