DOCSLIB.ORG

Mechanisms of Branched Actin Network Formation Through

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mechanisms of Branched Actin Network Formation Through MECHANISMS OF BRANCHED ACTIN NETWORK FORMATION THROUGH COORDINATE ACTIVATION OF ARP2/3 COMPLEX by LUKE ANDREW HELGESON A DISSERTATION Presented to the Department of Biology and the Graduate School of the University of Oregon in partial fulfillment of the requirements for the degree of Doctor of Philosophy December 2014 DISSERTATION APPROVAL PAGE Student: Luke Andrew Helgeson Title: Mechanisms of Branched Actin Network Formation through Coordinate Activation of Arp2/3 Complex This dissertation has been accepted and approved in partial fulfillment of the requirements for the Doctor of Philosophy degree in the Department of Biology by: Bruce Bowerman Chairperson Bradley Nolen Advisor Alice Barkan Core Member J. Andrew Berglund Core Member Kenneth Prehoda Institutional Representative and J. Andrew Berglund Dean of the Graduate School Original approval signatures are on file with the University of Oregon Graduate School. Degree awarded December 2014 ii © 2014 Luke Andrew Helgeson iii DISSERTATION ABSTRACT Luke Andrew Helgeson Doctor of Philosophy Department of Biology December 2014 Title: Mechanisms of Branched Actin Network Formation through Coordinate Activation of Arp2/3 Complex Fundamental cellular processes such as motility and endocytosis rely on the actin cytoskeleton to translate biochemical protein interactions into mechanical forces. Cells utilize an extensive collection of actin binding proteins to comprehensively regulate actin networks during these dynamic cell operations. Branched actin networks, which are geometrically and functionally disparate from linear networks, are required for numerous cellular actions. Actin-related protein 2/3 complex (Arp2/3 complex) nucleates branched actin filaments upon activation by regulatory proteins known as nucleation promoting factors (NPFs). Often, several biochemically distinct NPFs are required for the same cellular structure, leading us to hypothesize that multiple NPFs can coordinately activate Arp2/3 complex to regulate the nucleation, architecture and assembly of branched networks. We identified and dissected the mechanisms of two sets of NPFs which coordinately activate Arp2/3 complex. Overall, these findings provide a better understanding of how Arp2/3 complex is activated and how cells control branched actin networks. In chapters II and III, we investigated the mechanism of synergistic activation of Arp2/3 complex by the NPFs cortactin and WASP family proteins. We found that iv cortactin accelerates the release of WASP family proteins from a branching intermediate, a previously unknown rate limiting step. Further dissection of the mechanism revealed that cortactin is specifically suited to displace WASP family proteins through a unique Arp2/3 complex binding region and target stalled branching intermediates with high affinity. Three different WASP family members were tested for their capacity to synergize with cortactin in Arp2/3 complex activation, establishing a list of cellular structures where cortactin-mediated synergistic activation is likely occurring. In chapter IV, we investigated the ability of Dip1 and Wsp1 to coordinately activate Arp2/3 complex during branched network formation. We established that Dip1 activation of Arp2/3 complex results in the formation of linear filaments which can template Wsp1 mediated branching. Subsequent kinetic data and modeling revealed that Dip1 and Wsp1 likely increase the rate of network formation by simultaneously binding to and co- activating Arp2/3 complex. These findings suggest that, together, Dip1 and Wsp1 regulate the initiation and rate of branched network assembly. This dissertation includes previously published and unpublished co-authored material and videos files. v CURRICULUM VITAE NAME OF AUTHOR: Luke Andrew Helgeson GRADUATE AND UNDERGRADUATE SCHOOLS ATTENDED: University of Oregon, Eugene, OR Iowa State University, Ames, IA DEGREES AWARDED: Doctor of Philosophy, Biology, 2014 University of Oregon Bachelor of Science, Biochemistry, 2009, Iowa State University AREAS OF SPECIAL INTEREST: Biochemistry Biophysics Microscopy PROFESSIONAL EXPERIENCE: Graduate Teaching Assistant, Department of Biology, University of Oregon, Eugene, OR, 2009-2010 GRANTS, AWARDS, AND HONORS: Pete von Hippel Scholar Award, Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, OR. 2014. NIH Training Grant: Molecular Biology and Biophysics. Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, OR. 2010-2013 Robert Stupka Memorial Scholarship. Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA. 2009 Dexter Memorial Fund. Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA. 2005/2006. Award for Competitive Excellence Scholarship. Iowa State University, Ames, IA. 2005-2009. vi PUBLICATIONS: Helgeson, Luke A, Julianna G Prendergast, Andrew R Wagner, Max Rodnick-Smith, and Brad J Nolen. 2014. “Interactions with Actin Monomers, Actin Filaments and Arp2/3 Complex Define the Roles of WASP Family Proteins and Cortactin in Coordinately Regulating Branched Actin Networks.” The Journal of Biological Chemistry 289 (42) (August 26): 28856–28869. doi:10.1074/jbc.M114.587527. Helgeson, Luke A, and Brad J Nolen. 2013. “Mechanism of Synergistic Activation of Arp2/3 Complex by Cortactin and N-WASP.” eLife 2 (September 3): e00884. doi:10.7554/eLife.00884. Hetrick, Byron, Min Suk Han, Luke A Helgeson, and Brad J Nolen. 2013. “Small Molecules CK-666 and CK-869 Inhibit Actin-Related Protein 2/3 Complex by Blocking an Activating Conformational Change.” Chemistry & Biology 20 (5) (April): 701–12. doi:10.1016/j.chembiol.2013.03.019. Liu, Su-Ling, Jordan R May, Luke A Helgeson, and Brad J Nolen. 2013. “Insertions within the Actin Core of Actin-Related Protein 3 (Arp3) Modulate Branching Nucleation by Arp2/3 Complex.” The Journal of Biological Chemistry 288 (1) (January 4): 487–97. doi:10.1074/jbc.M112.406744. Leung Daisy W, Dominika Borek, Mina Farahbakhsh, Parameshwaran Ramanan, Jay C Nix, Tianjiao Wang, Kathleen C Prins, Zbyszek Otwinowski, Richard B Honzatko, Luke A Helgeson, Christopher F Basler, Gaya K Amarasinghe. 2010. “Crystallization and preliminary X-ray analysis of Ebola VP35 interferon inhibitory domain mutant proteins.” Acta.Crystallogr. Sect. F Struct. Biol.Cryst.Commun. 66(6): 689-92. Leung Daisy W, Kathleen C Prins, Dominika M Borek, Mina Farahbakhsh, JoAnn M Tufariello, Parameshwaran Ramanan, Jay C Nix, Luke A Helgeson, Zbyszek Otwinowski, Richard B Honzatko, Christopher F Basler, Gaya K Amarasinghe. 2010. “Structural basis for dsRNA recognition and interferon antagonism by Ebola VP35”. Nature Structural & Molecular Biology. 17(2): 165-72. vii ACKNOWLEDGMENTS First and foremost, I would like to express my sincere gratitude to my mentor and thesis advisor, Dr. Brad Nolen. Under Brad‟s guidance, I developed a strong set of scientific skills which will be fundamental to my success for years to come. I am thankful to all past and present members of the Nolen lab; without them I would not have been able to accomplish my goals. I would especially like to thank Dr. Byron Hetrick for his mentoring and Dr. Su-Ling Liu who was always helpful and full of knowledge. I would like to thank my dissertation advisor committee for their assistance and words of encouragement throughout the years. Additionally, I would like to thank the University of Oregon, Institute of Molecular Biology community for their various means of support. I am thankful to my undergraduate mentor, Dr. Gaya Amarasinghe, for helping me build a solid foundation for performing rigorous scientific research. Successful science requires a clear and refreshed mind. I am especially grateful for my friends who have allowed me to maintain a refreshed mind and have made my graduate school experience memorable. Specifically, I am forever grateful to those friends who ventured into the wilderness with me to experience and explore all the beauty nature has to offer. I would especially like to thank Dr. Alesia McKeown for her invaluable companionship throughout this challenging endeavor. Alesia‟s love, support and humor constantly sustains me and brings joy to my life. Last but not least, I am forever thankful to my family for their love throughout the years. My parents, Benny and Janice, and sister, Beth, have been constant sources of inspiration, knowledge and encouragement. Without their love and support, I would not be where I am today. viii I dedicate this work to my family, past and present. Thank you for everything. ix TABLE OF CONTENTS Chapter Page I. INTRODUCTION .................................................................................................... 1 II. MECHANISM OF SYNERGISTIC ACTIVATION OF ARP2/3 COMPLEX BY CORTACTIN AND N-WASP .......................................................................... 15 Introduction ............................................................................................................ 15 Results .................................................................................................................... 19 Discussion .............................................................................................................. 43 Material and Methods ............................................................................................ 49 Bridge to Chapter III .............................................................................................. 58 III. INTERACTIONS WITH ACTIN
Load more

Recommended publications
  • PSOC@PENN SPRING-Webinars 2021 Revised
    Physical Sciences in Spring 2021 Webinar Series Oncology Center PSOC@Penn Mondays @ Noon (EST) For webinar link, please contact <[email protected]> 01.25.2021 “Predicting interactions between cell collectives and their environment” M. Lisa Manning, PhD Professor, Department of Physics, Syracuse University, NY https://thecollege.syr.edu/people/faculty/manning-m-lisa/ 02.01.2021 TBA 02.08.2021 “Abnormal Mechanics in Brain Tumors” Meenal Datta, PhD Research Fellow in Radiation Oncology, Massachusetts General Hospital https://connects.catalyst.harvard.edu/Profiles/display/Person/17 0359 02.15.2021 “Sensing matrix rigidity: transducing mechanical signals from integrins to the nucleus” Pere Roca-Cusachs Soulere, PhD Group Leader (IBEC) & Associate professor, Cellular and Molecular Mechanobiology, University of Barcelona https://www.ibecbarcelona.eu/member/156/Pere+Roca - Cusachs+Soulere/ 02.22.2021 “Host-microbiota interaction in lung cancer development and response to immune checkpoint therapy.” Chengcheng Jin, Ph.D Assistant Professor, Department of Cancer Biology, UPenn https://www.med.upenn.edu/apps/faculty/index.php/g2000 03.01.20 “Polarity signaling ensures epidermal homeostasis by coupling cellular mechanics and genomic integrity” Sandra Iden, PhD Professor, Head of Dept. Cell & Developmental Biology, Saarland University, Homburg/Saar, Germany https://www.uni-saarland.de/en/chair/iden.html 03.08.2021 “Entropy as a driver to tissue structural heterogeneity in health and disease” Zev Gartner, PhD Professor, Department of Pharmaceutical Chemistry, UCSF, California https://www.gartnerlab.ucsf.edu/people.php 03.15.2021 “T cell circuits that can sense antigen density with an ultrasensitive threshold” Rogello Hernandez-Lopez, PhD Postdoctoral Fellow, Wendell Lim Lab, UCSF https://limlab.ucsf.edu/people/rogelio.html 03.22.2021 “TBA” Robert T.
    [Show full text]
  • 2016 Symposium Program
    Center for Innovative Drug Discovery 2016 San Antonio Drug Discovery Symposium Target Discovery and Drug Development in Texas June 9th and 10th 2016 8:00 AM –5:00 PM UTSA Main Campus, University Center, Denman Ballroom UTCIDD.org Day 1 8:00 AM-8:30 AM: Continental Breakfast and Registration 8:30 AM-8:45 AM: Welcome from Symposium Co-Chairs Stanton F. McHardy, Ph.D., Co-Director, Center for Innovative Drug Discovery, Director, Max and Minnie Tomerlin Voelcker Medicinal Chemistry Core Facility, UTSA Matthew Hart, Ph.D., Director, Center for Innovative Drug Discovery High Throughput Screening Core Facility, UTHSCSA 8:45-9:00 AM: Introductory remarks Dean George Perry, Ph.D., Semmes Foundation Distinguished University Chair in Neurobiology, Dean of the College of Sciences and Professor of Biology, UTSA 9:00 AM-9:50 AM: Plenary Keynote Presentation, Chair: Stanton McHardy, Ph.D. 9:00 AM-9:50 AM: Craig Lindsley, Ph.D., William K. Warren, Jr. Chair in Medicine, Professor of Pharmacology and Chemistry, Director, Medicinal Chemistry, Vanderbilt University “ Neuroscience Drug Discovery in an Academic Environment ” 9:50 AM-10:10 AM: Coffee Break 10:10 AM-12:10 PM: Session One, Chair: Bruce Nicholson, Ph.D. Identifying and Characterizing Molecular Drug Targets 10:10 AM-10:40 AM: Michael White, Professor, Cell Biology, Associate Director, Simmons Comprehensive Cancer Center, Sherry Wigley Crow Endowed Chair in Cancer Research, Grant A. Dove Distinguished Chair for Research in Oncology UT Southwestern Medical Center “Targeting mechanistic subtypes of neoplastic disease” 10:40 AM-11:10 AM: Gaston Habets, Ph.D., Sr.
    [Show full text]
  • Scientists Identify New Paradigm in Genetics, Paving Way for Development of Better Drug Targets to Save Lives 4 December 2015
    Scientists identify new paradigm in genetics, paving way for development of better drug targets to save lives 4 December 2015 Agency for Science, Technology and Research estimated to be as low as 25 per cent, partially due (A*STAR)'s Institute of Medical Biology (IMB) and to the high number of drug candidates found to be Singapore Immunology Network (SIgN) have resistible only during trial stage. This represents the identified a new paradigm for the identification and loss of time and resources which could otherwise evaluation of genes for cell survival. By challenging have been used to develop more effective drugs long-held notions on gene essentiality and drug and therapies. development, the study holds great potential to predict future drug resistance, thereby saving lives Now, A*STAR scientists have redefined the and optimising the use of resources. The study underlying concept of gene essentiality by putting was published on 25 November 2015 in the online forth a new genetic paradigm. Previously, genes issue of Cell. were divided into non-essential ones that are dispensable for cell viability, and essential genes Traditionally, basic and applied genetics have that are required for cell survival. The new study relied on the core concept of gene essentiality, found that essential genes can be further split into which states that certain genes are essential for a two kinds - one being the kind that cells need for cell's survival. When the cells in question are survival, known as 'non-evolvable' essential genes, cancer cells or pathogenic microbes, drugs can be and the other being those that cells can find ways developed to block these essential genes, so as to to survive without, by an evolutionary process of eradicate these harmful cells.
    [Show full text]
  • Scientists Offer Insight Into Adaptive Ability of Cells 26 November 2008
    Scientists offer insight into adaptive ability of cells 26 November 2008 The Stowers Institute's Rong Li Lab has published regulation or chemotherapeutic drug treatment work findings that shed light on the ability of cells to to limit their growth." adapt to disruptions to their basic division machineries – findings that may help explain how The work establishes an exciting new path for the cancer cells elude the body's natural defense Rong Li Lab. mechanisms or chemotherapy treatment. The work was published in the November 26 issue of Cell. "These findings validated our view that evolvability is a trackable and important subject for study," said Working with yeast cells, the team disabled a Rong Li, Ph.D., Investigator and senior author on motor protein, type II myosin — which normally the paper. "We are now working to determine powers cell division — and observed the cellular whether there are many distinct mechanisms of response. As predicted, blocking division initially evolvability correlating with varying types and resulted in severe growth and cytokinesis defects. degrees of cellular disruptions. Additionally, we But after several selection passages, some cells would like to explore the possibility of predicting the were able to solve the problems. Unexpectedly, likely evolutionary paths and outcomes based on these cells ended up with more than the normal the architecture of molecular networks present in number of chromosomes. The abnormal the cell; and in extending our research into chromosome numbers led to changes in the mammalian cell systems to directly study the role of patterns of gene expression, which correlated with aneuploidy in the evolution of cancer." the cells' ability to evolve new ways to complete division and resume growth.
    [Show full text]
  • Presented by the Maryland Biophysics Program
    Movement of cells is key to life, from the collective motion of cells during development, to the migration of immune cells as they fend off invaders and deformations of neurons as they wire up the brain. Talks will feature both experiments and modeling of cell dynamics from multiple angles. 8:30 am Refreshments and on-site registration (no fee) 9:00 am Introductory Remarks 9:15 am Modeling cellular volume and pressure Sean Sun (Johns Hopkins University) regulation: Implications for cell shape and motility 10:00 am Mechanisms of actin-based force generation in Rong Li (Stowers Institute) cell polarity and cell division 10:45 am Break 11:00 am Actin-driven dynamics of the neuronal Thomas Blanpied (UMD Medical School) postsynaptic density 11:45 am Cytoskeletal dynamics during lymphocyte Arpita Upadhyaya (University of Maryland) activation 12:05 pm How cells crawl: a role for actin arcs in the Dylan Burnette (NIH) leading edge advance of migrating cells 12:25 pm Lunch and poster session* 2:00 pm Spontaneous waves and symmetry breaking of Anders Carlsson (Washington University) f-actin in cells 2:45 pm Excitable actin dynamics at the leading edge of Dmitrios Vavylonis (Lehigh University) crawling cells 3:30 pm Break 3:45 pm Cell shape dynamics: From waves to migration Wolfgang Losert (University of Maryland) Molecular force productions, cell-shape 4:05 pm changes, and tissue patterning during Glenn Edwards (Duke University) Drosophila development Reception 5:00 pm Presented by the Maryland Biophysics Program Supported by IPST, & the Biology, Chemistry, and Physics Departments Organizers: Wolfgang Losert, Arpita Upadhyaya For more information: Caricia Fisher ([email protected]) *Poster submission is encouraged.
    [Show full text]
  • Overstuffed Cancer Cells May Have an Achilles' Heel 22 July 2019
    Overstuffed cancer cells may have an Achilles' heel 22 July 2019 the June 6 issue of Nature. The new experiments focused on a chromosome number abnormality known as aneuploidy. Normal human cells, for example, have a balanced number of chromosomes: 46 in all, or 23 pairs of different chromosomes. A cell with chromosomes that have extra or fewer copies is called aneuploid. Li says, "aneuploidy is the #1 hallmark of cancer," and is found in more than 90% of solid tumor cancer types. Aneuploid yeast cells on the left have difficulty drawing When cells gain chromosomes, Li says, they also in fluorescent molecules. Whereas, the normal yeast get an extra set of genes that produce more than cells on the right are able to rapidly draw them in. Credit: the normal amount of protein that a cell makes. Rong Li and Hung-Ji Tsai This excess can give cells growth abilities they normally wouldn't have, sometimes allowing them to overgrow and develop into a tumor. In a study using yeast cells and data from cancer Because aneuploid cells have unbalanced protein cell lines, Johns Hopkins University scientists production, they have too many free-floating report they have found a potential weak spot proteins that are not organized into a complex. This among cancer cells that have extra sets of increases the concentration inside of the cell chromosomes, the structures that carry genetic compared to outside. To compensate for the material. The vulnerability, they say, is rooted in a increased concentration, the cells draw in water, a common feature among cancer cells—their high phenomenon that leads to hypo-osmotic stress.
    [Show full text]
  • Scientists Probe Mechanism of Asymmetry in Meiotic Cell Division 7 October 2008
    Scientists probe mechanism of asymmetry in meiotic cell division 7 October 2008 The Stowers Institute's Rong Li Lab has better understanding of the process of meiotic characterized a mechanism that allows for divisions and how actin generates the force to asymmetrical cell division during meiosis in power intra-cellular movements." oocytes. By tracking chromosome movement in live mouse oocytes, the team discovered that Source: Stowers Institute for Medical Research chromosomes can recruit to their vicinity a protein called formin-2. This protein allows the oocyte to retain the majority of the cytoplasm – a requirement for embryonic development after fertilization – while the other daughter cell (called a polar body) resulting from the asymmetric division gets only a minimal amount and subsequently dies. The work was published this week in the advance online publication of Nature Cell Biology. Formin-2 is an actin-nucleating protein that can promote the formation of actin filaments around the chromosomes. Actin filaments undergo dynamic elongation and shortening and, in the process, push the chromosomes towards the outer edge of the oocyte. After the chromosomes reach the periphery, the actin filaments orient the cell division plane so that most of the cytoplasm required to sustain the earliest stages of development stays with the daughter cell that retains the identy of the oocyte. "This work revealed the general mechanism by which the actin cytoskeleton drives chromosome movement in mammalian meiotic oocytes," said Hongbin Li, Ph.D., Senior Research Associate and lead author on the publication. "Our findings will enable us to carry out even more detailed dissection of the molecular components and mechanisms." "Infertility and birth defects are often related to problems during oocyte meiotic cell divisions," said Rong Li, Ph.D., Investigator and senior author on the paper.
    [Show full text]
  • ASCB Member Profile
    ASCB Profile Rong Li The old joke is that biologists were science ma- Krumlauf thought Li would be a perfect fit. jors who couldn’t do the math. The new para- “Rong’s very much a lateral thinker,” Krumlauf digm in biology? Quantify, quantify and then do says. “She’s interested not only in her own the mathematical modeling. “That puts Rong Li projects but in the research of others. We need at the leading edge,” says Andrew Murray, about that synergy in an institution like ours …because the career of his very first graduate student. Li is all science is becoming interdisciplinary. To truly now an Investigator at the Stowers Institute for integrate biology, genetics, and biochemistry with Medical Research in Kansas City. “I think Rong computational science requires some uniquely is one of those ahead of the curve,” Murray says, qualified individuals,” says Krumlauf. “Even if “in her ability to interact with quantitative sci- you have teams with individual expertise, it’s not entists and biologists.” easy for them to say to another group, ‘Please “Rong Li’s been a very successful scientist solve this problem for me.’ You need someone who’s made real contributions to understanding like Rong Li who can bridge the gap just to know how the cytoskeleton is organized,” Murray what question is being asked.” Rong Li continues. He is now at Harvard University. “Rong is able to talk with mathematicians, In 1989 Murray was a newly help them understand the minted assistant professor at nature of the problem, and the University of California, then take their solutions San Francisco (UCSF).
    [Show full text]
  • Curriculum Vitae and Bibliography
    Curriculum Vitae and Bibliography Name: Rong Li Education 1984‐1988 B.S. and M.S (Combined) Yale University New Haven, Connecticut (Mol. Biochem. & Biophy.) 1988‐1992 Ph.D. University of California, San Francisco, California (Biochem. & Biophy.) San Francisco Postdoctoral Training 1993‐1994 Postdoctoral fellow University of California, Berkeley, California (Mol. Cell Biology) Berkeley Academic Appointments Dec 1994 – Assistant Professor Department of Cell Biology Dec 1999 Harvard Medical School Jan 2000 – Associate Professor Department of Cell Biology June 2005 Harvard Medical School July 2005 – Investigator Rong Li Laboratory Present Stowers Institute for Medical Research Jan 2006 – Professor (affiliated) Department of Molecular and Integrative Physiology Present University of Kansas School of Medicine Awards and Honors 1988 Phi Beta Kappa, Summa Cum Laude, Distinction in Major, Yale University 1993 – 1994 Damon Runyon‐Walter Winchell Cancer Research Fellowship 1995 – 1997 Medical Foundation New Investigator Award 1997 – 1998 The Funds for Discovery Exploratory Award 1998 – 2000 Giovanni Armenise/Harvard Foundation Award 1999 – 2001 Hoechst Marion Roussel Research Award 2000 Biological and Biomedical Sciences Mentoring Award, Harvard Medical School 2004 – 2005 The Alexander and Margaret Stewart Trust Pilot Project Program Award 2010 – 2012 William B. Neaves Award 2012 Watkins Visiting Professorship – Wichita State University Publications I. Research Papers 1. Zhou C, Slaughter BD, Unruh JR, Guo F, Yu Z, Mickey K, Narkar A, Ross TR, McClain M and Li R. Organelle‐based aggregation and retention of damaged proteins in asymmetrically dividing cells. (2014) Cell 159:530‐542 2. Li G, Li M, Zhang Y, Wang D, Li R, Guimerà R, Gao J, Zhang MQ. ModuleRole: a tool for modulization, role determination and visualization in protein‐protein interaction networks.
    [Show full text]
  • On the Role of P53 in the Cellular Response To
    ON THE ROLE OF P53 IN THE CELLULAR RESPONSE TO ANEUPLOIDY by Akshay Narkar A dissertation submitted to Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland July 2020 © 2020 Akshay Narkar All rights reserved ABSTRACT A majority of solid tumors are aneuploid and the tumor suppressor protein 53, has been implicated as the guardian of euploid genomes in animal organisms. Experiments using transformed or non-transform human cell lines showed that aneuploidy induction leads to p53 accumulation and a consequent, p21-mediated, G1 cell cycle arrest. However, it has been controversial as to whether there is a universal signal elicited by the aneuploid state that activates p53. My PhD thesis attempts to advance our understanding of the universality of the p53 response in different cell and tissue context post aneuploidy induction. In this study, we found that, whereas adherent 2-dimensional (2D) cultures of human immortalized or cancer cell lines indeed activate p53 upon aneuploidy induction as previously reported, suspension cultures of a human lymphoid cell line undergoes a p53- independent cell cycle arrest upon aneuploidy formation. To dive deeper into the molecular mechanisms regulating p53-independent arrest post aneuploidy in Nalm6 cells we performed a genome wide CRISPR/Cas9 knockout screen. This revealed previously uncharacterized functions of PDCD5 and LCMT1 in regulating chromosomal aberrations. Recent studies highlight that tissue environment plays a critical role in regulating chromosome segregation, however the role of p53 in 3D environment is not well characterized. To our surprise, 3-dimensional (3D) organotypic cultures of cells from human or mouse neural, intestinal or mammary epithelial tissues do not activate p53 or undergo G1 arrest upon aneuploidy induction.
    [Show full text]
  • Proceedings of the Fourth International Conference on the Foundations of Information Science, Beijing, August 21–24, 2010
    tripleC 9(2): 272-277, 2011 ISSN 1726-670X http://www.triple-c.at Editorial to the Special Issue: Towards a New Science of Information – Proceedings of the Fourth International Conference on the Foundations of Information Science, Beijing, August 21–24, 2010 Wolfgang Hofkirchner*, Zong-Rong Li**, Pedro C. Marijuán***, Kang Ouyang**** * [email protected], Unified Theory of Information (UTI) Research Group, Vienna, Austria ** [email protected], Social Information Science Institute (SISI), Huazhong University of Science and Tech- nology (HUST), Wuhan, P.R. of China *** [email protected], Bioinformation Group, Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain **** [email protected], Social Information Science Institute (SISI), Huazhong University of Science and Technology (HUST), Wuhan, P.R. of China In our times, an increasing number of disciplines are dealing with information in very different ways: from the information society and information technology to communication studies (and rela- ted subjects like codes, meaning, knowledge, and intelligence), as well as quantum information, bioinformation, the knowledge economy, network science, computer science and the Internet, to name but a few. At the same time, an increasing number of scientists in the East and the West have been engaged with the foundational problems underlying this development, to such an extent that it seems the time has come to integrate disciplines revolving around information. A new scien- ce of information can be envisaged that explores the possibilities of establishing a common ground around the information concept, of constructing a new scientific perspective that connects the diffe- rent information-related disciplines and provides a new framework for transdisciplinary research.
    [Show full text]
  • Reports Report
    Cell Reports Report Negative Elongation Factor Controls Energy Homeostasis in Cardiomyocytes Haihui Pan,1 Kunhua Qin,1 Zhanyong Guo,2,3 Yonggang Ma,4 Craig April,7 Xiaoli Gao,5 Thomas G. Andrews,2 Alex Bokov,3 Jianhua Zhang,4 Yidong Chen,2,3 Susan T. Weintraub,5 Jian-Bing Fan,7 Degeng Wang,2,3 Yanfen Hu,1 Gregory J. Aune,2,6 Merry L. Lindsey,4,* and Rong Li1,* 1Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA 2Greehey Children’s Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA 3Department of Epidemiology and Biostatistics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA 4Department of Medicine, San Antonio Cardiovascular Proteomics Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA 5Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA 6Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA 7Illumina, Inc., San Diego, CA 92121, USA *Correspondence: [email protected] (M.L.L.), [email protected] (R.L.) http://dx.doi.org/10.1016/j.celrep.2014.02.028 This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/). SUMMARY an important regulator of Pol II pausing (Kwak and Lis, 2013; Yamaguchi et al., 1999). Depletion of any of the four NELF sub- Negative elongation factor (NELF) is known to enforce units results in disintegration of the entire complex and global promoter-proximal pausing of RNA polymerase II reduction of Pol II pausing.
    [Show full text]