DOCSLIB.ORG

Table of Contents Introduction 2 the CIG at a Glance 2 the CIG Scientific Advisory Committee 3 Message from the Director 4 Highlights 5

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Table of Contents Introduction 2 the CIG at a Glance 2 the CIG Scientific Advisory Committee 3 Message from the Director 4 Highlights 5 Table of Contents INTRODUCTION 2 The CIG at a glance 2 The CIG Scientific Advisory Committee 3 Message from the Director 4 Highlights 5 RESEARCH 6 Richard Benton Chemosensory perception and evolution in insects 8 Béatrice Desvergne Networking activity of nuclear receptors during development and in adult metabolic homeostasis 10 Christian Fankhauser Light regulation of plant growth and development 12 Paul Franken Genetics and energetics of sleep homeostasis and circadian rhythms 14 David Gatfield Molecular mechanisms of circadian gene expression 16 Nouria Hernandez Synthesis of non-coding RNAs by RNA polymerases II and III: mechanisms of transcription regulation 18 Winship Herr Molecular epigenetics 20 Henrik Kaessmann Functional evolutionary genomics in mammals 22 Liliane Michalik Molecular control of skin homeostasis 24 Alexandre Reymond Genome structure and expression 26 Andrzej Stasiak Functional transitions of DNA structure 28 Mehdi Tafti Genetics of sleep and sleep disorders 30 Bernard Thorens Physiological genomics of energy homeostasis 32 Walter Wahli The multifaceted roles of PPARs and micronutrients in health and disease 34 Other groups at the Génopode 36 CORE FACILITIES 40 Genomic Technologies Facility (GTF) 42 Protein Analysis Facility (PAF) 44 Core facilities associated with the CIG 46 EDUCATION 48 Courses and lectures given by CIG members 50 Doing a PhD or a Postdoc at the CIG 51 Symposia and seminars 52 The CIG and the public 56 PEOPLE 58 1 Introduction THE CENTER for INTEgratiVE GEnomics (CIG) at A glanCE The Center for Integrative Genomics (CIG) is a department of the Faculty of Biology and Medicine (FBM) of the University of Laus- anne (UNIL). Its main missions are to pursue cutting edge research, to deliver the highest quality teaching to students, and to inform the public at large. It encompasses 14 research groups working on genome structure and function using a large number of techniques and experimental systems, as well as two core facilities dedicated to providing the latest equipment and knowledge in genomics and proteomics to researchers at the UNIL and beyond (see chapter “core facilities”). The CIG research groups are involved in numer- ous collaborative research projects and programs both within Swit- zerland and at the international level (see chapter “research”). To train tomorrow’s scientists, CIG members are involved in the teaching program of the UNIL and contribute to developing new education programs. The Center proposes seminars, lectures, and scientific meetings for the scientists of the Lemanic region and beyond. Moreover, its members organize and actively participate in activities geared to the public at large (see chapter “education”). The CIG is currently composed of more than 200 members origi- nating from some 30 different countries, who together contribute to the development of its research, its core facilities and its educa- tional activities (see chapter "people"). 2 Message from the SAC Scientific Advisory Committee members From the perspective of the Scientific Advisory Committee (SAC) the CIG continues to be an increasingly dynamic presence within the Swiss and the international scientific communities. During the last Prof. Robert EISENMAN Prof. Ivan STAMENKOVIC several years the ties between the CIG, the UNIL and other scientific (President of the SAC) Director of Departement institutions in Switzerland have been strengthened as CIG faculty Fred Hutchinson Cancer of Experimental Pathology play teaching and administrative roles within the UNIL community Research Center University of Lausanne and as the CIG collaborates in numerous multi-institute initiatives. A University of Washington Lausanne, Switzerland noteworthy example is the new UNIL/CIG/Swiss Institute for Bioin- School of Medicine, formatics/Vital IT doctoral program in Integrative Experimental and Seattle, USA Prof. Markus STOFFEL Computational Biology (IECB) with its aim to train a new generation Institute of Molecular of biologists proficient in both laboratory benchwork and computa- Prof. Steve BROWN Health Sciences tional analysis. Director of MRC Harwell Swiss Federal Institute Mammalian Genetics Unit of Technology Zurich (ETHZ) The CIG continues to appoint and promote faculty of the highest Harwell, UK Zurich, Switzerland caliber and to recruit first-rate trainees to its laboratories. The SAC considers the diversity of the scientific programs within the CIG to Overall, the Advisory Committee Prof. Nicolas GALTIER Prof. Gisou VAN DER GOOT be one of its major strengths. Research in contemporary biology has Institut des Sciences Global Health Institute become increasingly multi-disciplinary and the diverse programs of views the CIG as a vibrant and de l’Evolution Ecole Polytechnique Fédérale de the CIG foster interactions between fields and unexpected synergies collegial institution that has Montpellier, France Lausanne (EPFL) between laboratories as well as providing a unique training environ- succeeded in attracting excellent Lausanne, Switzerland ment for graduate students and postdoctoral fellows. The shared- Prof. Ueli GROSSNIKLAUS use core facilities required to support these diverse research tech- scientists at every career level. Institute of Plant Biology Prof. Veronica nologies (e.g. Protein Analysis, Genome Technologies) appear to be University of Zurich VAN HEYNINGEN up-to-date, well-managed, and widely-used by the CIG and UNIL Robert N. Eisenman Zurich, Switzerland Medical Research Council (MRC) departments. President the Scientific Advisory Committee Human Genetics Unit During our last visit in June 2012 the SAC met with the CIG lead- Prof. Ueli SCHIBLER Western General Hospital ership, the Dean of the Faculty of Biology and Medicine, technical funding sources and the UNIL. In addition, it will be important for Department of Molecular Biology Edinburgh, United Kingdom staff, administrators and assistants (graduate students and postdoc- the institute to become more proactive in identifying future employ- University of Geneva toral fellows). We noted that a number of issues raised during previ- ment opportunities for talented CIG postdoctoral fellows and gradu- Geneva, Switzerland ous visits, primarily concerning the desire for increased involvement ating students especially given the limited number of available aca- of assistants, administrators and technical staff in decision making demic positions. Increasing interactions with the biotechnology and processes at the CIG, are being satisfactorily addressed. In addition pharmaceutical industry may be useful in this regard and addition- avenues for more open communication have been established and ally provide avenues for translation of basic science discoveries. an ombudsman has been appointed to help resolve issues arising among assistants and faculty. Moreover, the director and faculty Overall, the Advisory Committee views the CIG as a vibrant and col- have approved implementation of a rigorous faculty review plan that legial institution that has succeeded in attracting excellent scientists will continue to ensure allocation of space and resources based pri- at every career level. Many of their recent discoveries are highlighted marily on scientific excellence. in this 2011-2012 Scientific Report. Under the leadership of the insti- tute’s director, Prof. Nouria Hernandez, and with the support of the While the CIG is clearly capable of building on its considerable UNIL, we expect that the CIG will continue to evolve and to make strengths, it nonetheless faces a number of challenges in the near important contributions to the scientific community. future. For example, hiring and promotion of CIG faculty and the launching and maintenance of new scientific initiatives will require Robert N. Eisenman increased, and relatively stable, financial support from both external President the Scientific Advisory Committee 3 Introduction Message from the Director How to ensure that a department remains highly productive and It is incredibly important that young people joining a department competitive? In my last director’s report, I wrote about the CIG con- be assured that, if they deserve it, they can progress in their career, sidering implementing some form of faculty evaluation process. i.e. they can be tenured and then promoted. Promotions should be This is now set and done! The CIG faculty has voted favorably on based on performance, not on the number of years one has spent in a proposal for a review, every five years, of its tenured professors, a particular position, not on age (neither too old or… too young!), based on letters from external experts and a formal review by the and certainly not on departmental budgets. This is important not CIG Scientific Advisory Committee, with consequences on space and only to maintain the motivation of faculty already in the department, resources. This is an impressive illustration of the dedication of the but also to attract new young faculty, who want to know that they CIG faculty, who accepted to be regularly reviewed with the goal of are joining a meritocracy– that, if they do well, their accomplish- allowing the CIG to use its resources in the best possible way in the ments will be recognized. long term. The counterpart of endorsing faculty promotions when deserved is Evaluation of tenured faculty is an important tool in keeping a that retiring associate and full professors should not be replaced by department dynamic, but there is a second, at least as important associate or full professors, as is often the case
Load more

Recommended publications
  • The Ins and Outs of Circadian Timekeeping Steven a Brown* and Ueli Schibler†
    gd9507.qxd 11/10/1999 12:14 PM Page 588 588 The ins and outs of circadian timekeeping Steven A Brown* and Ueli Schibler† Recent research in Drosophila and in mammals has generated The mechanism by which light signals entrain the clock is fascinating new models for how circadian clocks in these another topic of intense interest, and will be our other focus. organisms are reset by light and how these clocks, in turn, direct circadian outputs. Though light perception by the central clock is Central clock mechanisms: a brief summary ocular in mammals, it probably proceeds via a mechanism In all cases examined to date, circadian clocks have been separate from traditional visual transduction. In Drosophila, one cell-autonomous: a single cell can generate and maintain mechanism is non-ocular and is in fact present in many different self-sustained circadian oscillations. The molecular basis tissues. In both organisms, the cryptochrome family of for these rhythms may rely on a negative feedback loop in photoreceptor-like molecules plays a role in the circadian clock, which clock proteins negatively regulate their own abun- though their function is incompletely understood. Moreover, dance or activity. This regulation may occur both at the although a master clock resides in the brain, a functional clock transcriptional and at the post-transcriptional level. For appears to reside in most cells of the body. In these tissues, at example, in the bread mold Neurospora crassa, the Fre- least some output genes are controlled at the transcriptional quency protein negatively regulates its own transcription level directly by clock proteins; others appear to be regulated by by interfering with the ability of the White-collar-1 and cascades of circadian transcription factors.
    [Show full text]
  • WO 2013/102674 A2 11 July 2013 (11.07.2013) W P O P C T
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2013/102674 A2 11 July 2013 (11.07.2013) W P O P C T (51) International Patent Classification: (74) Agent: CABINET PLASSERAUD; 235 cours Lafayette, C12N 1/15 (2006.01) F-69006 Lyon (FR). (21) International Application Number: (81) Designated States (unless otherwise indicated, for every PCT/EP20 13/050 126 kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (22) Date: International Filing BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, 4 January 2013 (04.01 .2013) DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (25) Filing Language: English HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, (26) Publication Language: English ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, (30) Priority Data: NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, 61/583,559 5 January 2012 (05.01 .2012) US RW, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, (71) Applicants: NOVARTIS INTERNATIONAL PHAR¬ ZM, ZW. MACEUTICAL LTD.; 13 1 Front Street, Hamilton (BM). GLYKOS FINLAND OY [FI/FI]; Viikinkaari 6, FI- (84) Designated States (unless otherwise indicated, for every 00790 Helsinki (FI).
    [Show full text]
  • Gastronauts Symposium Booklet
    DUKE / DUKE-NUSDUKE / DUKE-NUS GASTRONAUTSGASTRONAUTS SINGAPORESINGAPORE A GLOBAL SYMPOSIUMA GLOBAL ON GUT-BRAIN SYMPOSIUM MATTERS ON GUT-BRAIN MATTERS 3 - 4 MAY 20183 - 4 MAY 2018 CONTENTS 03 Message from Co-Chairs 04 Symposium Highlights 08 SESSION ONE Session Chair: Diego Bohórquez Speaker 1.1 Raphael H. Valdivia Speaker 1.2 Jonathan Kotula Speaker 1.3 Xiuqin Zhang Speaker 1.4 Matthew Chang 14 SESSION TWO Session Chair: Irene Miguel-Aliaga Speaker 2.1 Feifan Guo Speaker 2.2 Walter Wahli Speaker 2.3 Paul M Yen Speaker 2.4 Greg S. B. Suh 20 DISCUSSION Chair: Pae Wu Iain Dickson Jermont Chen Justin Gallivan Robert Kokoska 21 SESSION THREE Session Chair: Xiling Shen Speaker 3.1 John Furness Speaker 3.2 Arthur Beyder Speaker 3.3 Nicholas Spencer Speaker 3.4 Sven Pettersson CONTENTS 27 SESSION FOUR Session Chair: Raphael H. Valdivia Speaker 4.1 Nick Barker Speaker 4.2 Xiling Shen Speaker 4.3 Hyunsoo Shawn Je Speaker 4.4 Maxime M. Mahe 33 SESSION FIVE Session Chair: Nicholas Spencer Speaker 5.1 Lawrence Carin Speaker 5.2 John Doyle Speaker 5.3 Warren Grill 38 SESSION SIX Session Chair: Arthur Beyder Speaker 6.1 Karl Herrup Speaker 6.2 David L. Silver Speaker 6.3 Rodger A. Liddle 43 SESSION SEVEN Session Chair: John Furness Speaker 7.1 Diego Bohórquez Speaker 7.2 Luis R. Saraiva Speaker 7.3 Irene Miguel-Aliaga Speaker 7.4 Ivan de Araujo MESSAGE FROM CO-CHAIRS Dear Gastronauts, On behalf of the organising committee, we are thrilled to welcome you to Singapore: A place known for its cultural tapestry Diego Bohórquez Assistant Professor of Medicine and where people from around the globe and Neurobiology Duke University come to imagine new possibilities.
    [Show full text]
  • 2009 Riboclub Program
    RiboClub 2017 in association with the Swiss National Center of Competence in RNA & Disease. September 24-28 RNPs: the Good, the Bad and the Ugly Insights into RNA-protein complex assembly and function in health and disease Hotel et Villégiature Chéribourg 2603 Chemin du Parc Orford (Magog) Quebec, Canada Sunday, September 24th 15:00 – 18:00 Registration for early arrivals 18:00 – 19:30 Welcome reception 19:30 – 21:30 Opening dinner Monday, September 25th 08:00 – 08:45 Registration 08:45 – 08:55 Opening Notes and Announcements (Sherif Abou Elela) 08:55 – 09:10 Welcome Notes by Beat Nobs, Ph.D., Swiss Ambassador to Canada 09:10 – 09:15 Presentation of Keynote speaker (Oliver Mühlemann) 09:15 – 10:15 Keynote presentation From bench to clinical trial: microRNA 122 as an antiviral target for hepatitis C virus Peter Sarnow, Stanford University, Stanford 10:15 – 10:45 Coffee break Session 1: Non-coding RNA function Chair: Martin Jinek (Host: Benoit Chabot) 10:45 – 10:50 Introduction by Martin Jinek 10:50 – 11:05 Mbnl1-dependent mis-regulation and mis-splicing of a conserved myogenic lncRNA in myotonic dystrophy type 1 Pascal Chartrand, Universite de Montreal, Montreal 11:05 – 11:30 Non-canonical function of DGCR8 controls mESCs exit from pluripotency Constance Ciaudo, ETH Zurich, Zurich 11:30 – 11:45 microRNAs use different ways to regulate gene expression in animals Martin Simard, Universite Laval, Quebec 11:45 – 12:10 Structure, evolution and targeting of non coding RNAs Gabriele Varani, University of Washington, Seattle 12:10 – 12:35 Structural
    [Show full text]
  • The for Report 07-08
    THE CENTER FOR INTEGRATIVE GENOMICS REPORT 07-08 www.unil.ch/cig Table of Contents INTRODUCTION 2 The CIG at a glance 2 The CIG Scientific Advisory Committee 3 Message from the Director 4 RESEARCH 6 Richard Benton Chemosensory perception in Drosophila: from genes to behaviour 8 Béatrice Desvergne Networking activity of PPARs during development and in adult metabolic homeostasis 10 Christian Fankhauser The effects of light on plant growth and development 12 Paul Franken Genetics and energetics of sleep homeostasis and circadian rhythms 14 Nouria Hernandez Mechanisms of basal and regulated RNA polymerase II and III transcription of ncRNA in mammalian cells 16 Winship Herr Regulation of cell proliferation 18 Henrik Kaessmann Mammalian evolutionary genomics 20 Sophie Martin Molecular mechanisms of cell polarization 22 Liliane Michalik Transcriptional control of tissue repair and angiogenesis 24 Alexandre Reymond Genome structure and expression 26 Andrzej Stasiak Functional transitions of DNA structure 28 Mehdi Tafti Genetics of sleep and the sleep EEG 30 Bernard Thorens Molecular and physiological analysis of energy homeostasis in health and disease 32 Walter Wahli The multifaceted roles of PPARs 34 Other groups at the Génopode 37 CORE FACILITIES 40 Lausanne DNA Array Facility (DAFL) 42 Protein Analysis Facility (PAF) 44 Core facilities associated with the CIG 46 EDUCATION 48 Courses and lectures given by CIG members 50 Doing a PhD at the CIG 52 Seminars and symposia 54 The CIG annual retreat 62 The CIG and the public 63 Artist in residence at the CIG 63 PEOPLE 64 1 Introduction The Center for IntegratiVE Genomics (CIG) at A glance The Center for Integrative Genomics (CIG) is the newest depart- ment of the Faculty of Biology and Medicine of the University of Lausanne (UNIL).
    [Show full text]
  • Circadian Rhythms: Mop up the Clock !
    Article Circadian rhythms: Mop up the clock ! BROWN, Steven, SCHIBLER, Ulrich Abstract All circadian clock genes discovered in Drosophila have mammalian counterparts with extensive sequence homology. Similarities and differences have been identified between insect and mammalian oscillators. Recent studies have shed new light on two mammalian clock components: Mop3 and Per2. Reference BROWN, Steven, SCHIBLER, Ulrich. Circadian rhythms: Mop up the clock ! Current Biology, 2001, vol. 11, no. 7, p. R268-R270 DOI : 10.1016/S0960-9822(01)00135-X Available at: http://archive-ouverte.unige.ch/unige:123132 Disclaimer: layout of this document may differ from the published version. 1 / 1 R268 Dispatch Circadian rhythms: Mop up the clock! Steven A. Brown and Ueli Schibler All circadian clock genes discovered in Drosophila have cryptochrome (cry). The products of these clock genes can mammalian counterparts with extensive sequence be assembled into a negative feedback loop that provides homology. Similarities and differences have been a plausible molecular mechanism for rhythm generation identified between insect and mammalian oscillators. (for review, see [5]). Recent studies have shed new light on two mammalian clock components: Mop3 and Per2. In the proposed circuitry, Clk and Cyc — transcription factors with PAS-helix-loop-helix domains — activate the Address: Département de Biologie Moléculaire, Sciences II, Université de Genève 30, Quai Ernest Ansermet, CH-1211 Genève-4, transcription of the per and tim genes. Per and Tim proteins Switzerland. then block transcription of their own genes. As a conse- E-mail: [email protected]; [email protected] quence, Per and Tim levels decrease, and a new 24 hour wave of per and tim transcription can initiate.
    [Show full text]
  • EMBO Facts & Figures
    excellence in life sciences Reykjavik Helsinki Oslo Stockholm Tallinn EMBO facts & figures & EMBO facts Copenhagen Dublin Amsterdam Berlin Warsaw London Brussels Prague Luxembourg Paris Vienna Bratislava Budapest Bern Ljubljana Zagreb Rome Madrid Ankara Lisbon Athens Jerusalem EMBO facts & figures HIGHLIGHTS CONTACT EMBO & EMBC EMBO Long-Term Fellowships Five Advanced Fellows are selected (page ). Long-Term and Short-Term Fellowships are awarded. The Fellows’ EMBO Young Investigators Meeting is held in Heidelberg in June . EMBO Installation Grants New EMBO Members & EMBO elects new members (page ), selects Young EMBO Women in Science Young Investigators Investigators (page ) and eight Installation Grantees Gerlind Wallon EMBO Scientific Publications (page ). Programme Manager Bernd Pulverer S Maria Leptin Deputy Director Head A EMBO Science Policy Issues report on quotas in academia to assure gender balance. R EMBO Director + + A Conducts workshops on emerging biotechnologies and on H T cognitive genomics. Gives invited talks at US National Academy E IC of Sciences, International Summit on Human Genome Editing, I H 5 D MAN 201 O N Washington, DC.; World Congress on Research Integrity, Rio de A M Janeiro; International Scienti c Advisory Board for the Centre for Eilish Craddock IT 2 015 Mammalian Synthetic Biology, Edinburgh. Personal Assistant to EMBO Fellowships EMBO Scientific Publications EMBO Gold Medal Sarah Teichmann and Ido Amit receive the EMBO Gold the EMBO Director David del Álamo Thomas Lemberger Medal (page ). + Programme Manager Deputy Head EMBO Global Activities India and Singapore sign agreements to become EMBC Associate + + Member States. EMBO Courses & Workshops More than , participants from countries attend 6th scienti c events (page ); participants attend EMBO Laboratory Management Courses (page ); rst online course EMBO Courses & Workshops recorded in collaboration with iBiology.
    [Show full text]
  • Role of the Nuclear Receptor Rev-Erb Alpha in Circadian Food Anticipation and Metabolism Julien Delezie
    Role of the nuclear receptor Rev-erb alpha in circadian food anticipation and metabolism Julien Delezie To cite this version: Julien Delezie. Role of the nuclear receptor Rev-erb alpha in circadian food anticipation and metabolism. Neurobiology. Université de Strasbourg, 2012. English. NNT : 2012STRAJ018. tel- 00801656 HAL Id: tel-00801656 https://tel.archives-ouvertes.fr/tel-00801656 Submitted on 10 Apr 2013 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. UNIVERSITÉ DE STRASBOURG ÉCOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTE CNRS UPR 3212 · Institut des Neurosciences Cellulaires et Intégratives THÈSE présentée par : Julien DELEZIE soutenue le : 29 juin 2012 pour obtenir le grade de : Docteur de l’université de Strasbourg Discipline/ Spécialité : Neurosciences Rôle du récepteur nucléaire Rev-erbα dans les mécanismes d’anticipation des repas et le métabolisme THÈSE dirigée par : M CHALLET Etienne Directeur de recherche, université de Strasbourg RAPPORTEURS : M PFRIEGER Frank Directeur de recherche, université de Strasbourg M KALSBEEK Andries
    [Show full text]
  • Molecular Modelling for Enzyme-Inhibition: a Search for a New Treatment for Cataract and New Antimicrobials and Herbicides
    Molecular Modelling for Enzyme-Inhibition: A Search for a New Treatment for Cataract and New Antimicrobials and Herbicides A thesis submitted in partial fulfilment of the requirements for the Degree of Doctor of Philosophy in Biochemistry at the University of Canterbury Christchurch New Zealand Blair Gibb Stuart March 2010 Contents CONTENTS ACKNOWLEDGEMENTS 1 ABSTRACT AND PUBLISHED WORK 2 1 INTRODUCTION 6 1.1 Calpain and the cataract hypothesis 6 1.2 Proteases 7 1.3 Calpains 10 1.4 Structure of the eye, cataract and the importance of an anti-cataract drug 14 1.5 The β-strand: important for protease recognition 15 1.6 Computer modelling programs 17 1.7 References 20 2 DEVELOPMENT OF A CALPAIN MODEL FOR DOCKING STUDIES 27 2.1 Introduction 27 2.1.1 Overview of calpain model development 27 2.2 Calpain X-ray crystal structures 28 2.2.1 The first published structures 28 2.2.2 Calpain constructs 1KXR and 1MDW 30 2.3 Exploring the calpain construct 1KXR to develop a viable model for Glide docking experiments 33 2.4 The InducedFit docking model 37 Contents 2.5 Conclusion 37 2.6 References 39 3 MOLECULAR MODELING OF ACYCLIC INHIBITORS 43 3.1 Introduction 43 3.1.1 Natural inhibitors 43 3.1.2 Modified natural inhibitors 45 3.1.3 Lead compound: SJA-6017 46 3.2 Docking studies of known inhibitors 46 3.2.1 Compounds of Inoue et al 46 3.2.2 Docking results for the Inoue et al compounds 50 3.3 Docking Studies of SJA-6017 analogues 58 3.3.1 N-Heterocyclic dipeptides 58 3.3.2 Docking results of N-heterocyclic dipeptides 60 3.4 Docking studies of diazo and
    [Show full text]
  • Downloading the Nucleotide Sequences and Scanning Them Against the Database
    An in silico analysis, purification and partial kinetic characterisation of a serine protease from Gelidium pristoides A dissertation submitted in fulfilment of the requirement for the degree of Master of Science (MSc) Biochemistry by Zolani Ntsata Supervisor: Prof. Graeme Bradley 2020 Department of Biochemistry and Microbiology Declaration I, Zolani Ntsata (201106067), declare that this dissertation, entitled ‘An in silico analysis and kinetic characterisation of proteases from red algae’ submitted to the University of Fort Hare for the Master’s degree (Biochemistry) award, is my original work and has NOT been submitted to any other university. Signature: __________________ I, Zolani Ntsata (201106067), declare that I am highly cognisant of the University of Fort Hare policy on plagiarism and I have been careful to comply with these regulations. Furthermore, all the sources of information have been cited as indicated in the bibliography. Signature: __________________ I, Zolani Ntsata (201106067), declare that I am fully aware of the University of Fort Hare’s policy on research ethics, and I have taken every precaution to comply with these regulations. There was no need for ethical clearance. Signature: _________________ i Dedication I dedicate this work to my grandmother, Nyameka Mabi. ii Acknowledgements Above all things, I would like to give thanks to God for the opportunity to do this project and for the extraordinary strength to persevere in spite of the challenges that came along. I am thankful to my family, especially my grandmother, for her endless support. I would also like to acknowledge Prof Graeme Bradley for his supervision and guidance. Thanks to my friends and colleagues, especially Yanga Gogela and Ntombekhaya Nqumla, and the plant stress group for their help and support.
    [Show full text]
  • Cell Size Regulation, a Mechanism That Controls Cellular RNA Accumulation
    Cell Size Regulation, a Mechanism That Controls Cellular RNA Accumulation: Consequences on Regulation of the Ubiquitous Transcription Factors Oct1 and NF-Y, and the Liver-enriched Transcription Factor DBP Edward E. Schmidt and Ueli Schibler Department of Molecular Biology, University of Geneva, Sciences II, CH-1211 Geneva-4 Switzerland Abstract. Cell sizes can differ vastly between cell per protein DBP correlate closely to cellular Downloaded from http://rupress.org/jcb/article-pdf/128/4/467/1401380/467.pdf by guest on 24 September 2021 types in individual metazoan organisms. In rat liver, RNA:DNA ratios. Our results suggest that DBP spleen, and thymus, differences in average cell size mRNA levels, like rRNA levels, are transcriptionally roughly reflect differences in RNA:DNA ratios. For determined. Thus the dbp gene, like the ribosomal example, hepatocytes were found to have a cytoplas- genes, may be subject to cell size regulation. As a mic:nuclear volume ratio and an RNA:DNA ratio consequence, nuclei from liver, a tissue with a very which were 34- and 21-fold higher, respectively, than large average cell size, accumulated higher levels of those in thymocytes. RNA synthesis per DNA- DBP protein than nuclei from small-celled tissues, equivalent in the hepatocytes was 25-fold greater than such as spleen or lung. In contrast to DBP, the ubiq- that in thymocytes, suggesting that differences in over- uitous transcription factors Octl and NF-Y escaped all transcriptional activity, not differences in overall cell size control. Nuclei from most tissues contained RNA stability, were primarily responsible for deter- similar amounts of these factors irrespective of cell mining cellular RNA:DNA ratios.
    [Show full text]
  • Identification and Characterization of a Bacterial Glutamic Peptidase
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Copenhagen University Research Information System Identification and characterization of a bacterial glutamic peptidase Jensen, Kenneth; Østergaard, Peter R.; Wilting, Reinhard ; Lassen, Søren F. Published in: BMC Biochemistry DOI: 10.1186/1471-2091-11-47 Publication date: 2010 Document version Publisher's PDF, also known as Version of record Citation for published version (APA): Jensen, K., Østergaard, P. R., Wilting, R., & Lassen, S. F. (2010). Identification and characterization of a bacterial glutamic peptidase. BMC Biochemistry, 11(47). https://doi.org/10.1186/1471-2091-11-47 Download date: 07. Apr. 2020 Jensen et al. BMC Biochemistry 2010, 11:47 http://www.biomedcentral.com/1471-2091/11/47 RESEARCH ARTICLE Open Access Identification and characterization of a bacterial glutamic peptidase Kenneth Jensen1,2*, Peter R Østergaard1, Reinhard Wilting1, Søren F Lassen1 Abstract Background: Glutamic peptidases, from the MEROPS family G1, are a distinct group of peptidases characterized by a catalytic dyad consisting of a glutamate and a glutamine residue, optimal activity at acidic pH and insensitivity towards the microbial derived protease inhibitor, pepstatin. Previously, only glutamic peptidases derived from filamentous fungi have been characterized. Results: We report the first characterization of a bacterial glutamic peptidase (pepG1), derived from the thermoacidophilic bacteria Alicyclobacillus sp. DSM 15716. The amino acid sequence identity between pepG1 and known fungal glutamic peptidases is only 24-30% but homology modeling, the presence of the glutamate/ glutamine catalytic dyad and a number of highly conserved motifs strongly support the inclusion of pepG1 as a glutamic peptidase.
    [Show full text]