NATO Advanced Research Workshop

 

 

NATO Advanced Research Workshop

 

Structural Biology and Functional Genomics

 

4-8 May, 1998, ICGEB, Trieste, Italy

 

ORGANIZERS:

Sándor Pongor (ICGEB, Trieste, Italy)

E. Morton Bradbury Los Alamos National Labs, USA

 

 

PROGRAM:

 

 

MONDAY, 4 May

08.30    COURSE REGISTRATION     Foyer, ICGEB, W Building

 

09.30    WELCOME ADDRESS Seminar Room, ICGEB

            S. Pongor, ICGEB, Trieste, Italy

 

09.45    INTRODUCTION

            E. M. Bradbury, Los Alamos National Laboratory, NM, USA

 

10.00    Genome and Chromosome Organization

            U. K. Laemmli, University of Geneva, Switzerland

            "Chromosomal loops and chromatin domains"

 

11.00    BREAK

 

11:30    Genome and Chromosome Organization (cont.)

            T. Cavalier-Smith and M.J. Beaton, University of

            BritishÊColumbia, Vancouver, Canada

            "Genome size evolution in ancient eukaryote/eukaryote chimaeras:

            implications for the function of nuclear non-coding DNA"

 

12.30    Genome and Chromosome Organization (cont.)

            M. Radman, Institut J. Monod, Paris, France

            "Genome organisation and polymorphism as hallmarks of mechanisms for

            chromosomal maintenance and evolution"

 

13.30    LUNCH   Cafeteria, Ground Floor, Building C

 

14.30    Nucleic Acids Structures and DNA Supercoiling

            A. Rich, MIT, Boston, MD, USA  041 522 7034  5 8 Riva 2nd

            "Alternative DNA conformations and some Functional Properties"

 

15.30    Nucleic Acids Structures and DNA Supercoiling (cont.)

            N. Cozzarelli, University of California Berkeley, CA, USA

            "Mechanisms of Chromosome Segregation"

           

16:30    Nucleic Acids Structures and DNA Supercoiling (cont.)

            V. Ivanov, Institute of Molecular Biology, Moscow, Russia

            "A-DNA"

 

17.30    END OF SESSION/GET-TOGETHER PARTY

            Staff Common Room, ICGEB,   W Building

 

18.30    BUS TO HOTEL

 

 

TUESDAY, 5 May

09.00    Nucleic Acids Structures and DNA Supercoiling (cont.)

            D. Lilley, University of Dundee, UK

            "RNA folding and catalytic activity"

 

10.15    Nucleic Acids Structures   and DNA Supercoiling (cont.)

            G. Gupta, Los Alamos National Laboratory, NM, USA

            "Repetitive DNA Sequences in the Human Genome"

 

11.30    BREAK

 

12.00    Nucleic Acids Structures and DNA Supercoiling

            Cynthia McMurray, Mayo Medical Foundation, Rochester, USA

            "Cause and effects of DNA expansion in human disease"

 

13.30    LUNCH

 

14.15    Protein Structure and Functional Genomics

            T. Terwilliger, Los Alamos National Laboratory, NM, USA

            "Exploring Protein Structure Space: A Protein Structure Initiative"

 

15.30    Protein Structure and Functional Genomics (cont.)

            M. Galperin and E. Koonin, National Institute of Health,

            Bethesda, MD, USA

            "Comparison of complete genomes and evolution of protein families"

 

16.45    BREAK

 

17:00    Protein Structure and Functional Genomics --> Tue 17:00

            J. Sussman, Protein Data Bank (PDB), Brookhaven National

            Laboratory, CN, USA and Weizmann Institute, Rehovot, Israel,

            "Bridging the Gap Between 3D Structure and the Genome World"

 

18.00    BUS TO HOTEL

 

WEDNESDAY, 6 May

09.00    Genome and Chromosome Organization (continuation from Mon., 4 May)

            S. Oliver, UMIST, Manchester, UK

            "The Yeast Genome Project:  Systematic analysis of gene function"

 

10.15    DNA Bending and Modelling

            A. Travers, MRC Laboratory of Molecular Biology, Cambridge, UK

            "Chemical determinants of DNA flexibility and their relevance to

            nucleosome positioning"

 

11.30    BREAK

 

12.00    DNA Bending and Modelling (cont.)

            S. Pongor, ICGEB

            "Models of DNA bending"

 

13.30    LUNCH

 

14.15    DNA Bending and Modelling (cont.)

            R. Lavery, Institut de Biologie Physico-Chimique, Paris, France

            "Modelling DNA deformation and protein binding"

 

15.30    DNA Bending and Modelling (cont.)

            J. Langowski, DKFZ, Heidelberg, Germany

            "Large DNAs and chromatin studied by solution scattering and

            computer models"

 

16:45 BREAK

 

17.00    DNA Bending and Modelling (cont.)

            V. Zhurkin, National Institutes of Health, Bethesda, MD, USA

            "DNA Bending in Tetrameric Complex with Tumor Suppressor Protein p53:

            Computer Modeling and Comparison with Experiment"

 

18.00    BUS TO HOTEL

 

THURSDAY, 7 May

 

09.00    Nucleosome and Chromatin Structures

            E. M. Bradbury, Los Alamos National Laboratory, NM, USA

            "Packaging of the Genome: Nucleosome and Chromatin Structures"

 

10:15    Nucleosome and Chromatin Structures

            M. Giacca, ICGEB, Trieste

            "Origins of DNA replication in mammalian chromosomes"

 

11.30    BREAK

 

12:00    Nucleosome and Chromatin Structures (cont.)

            V. Giancotti, U. Trieste

            "Structure and function of HMGI chromosomal proteins"

 

13.30    LUNCH

 

14.30    New Approaches to Functional Genomics

            D. Bensimmon, Ecole Normale Superieure, Paris, France

            "Twisting and stretching single DNA molecules: structure and function"

 

15.45    New Approaches to Functional Genomics (cont.)

            Chris  Aston and David Schwartz, New York University, NY, USA

            "Whole genome analysis by optical mapping"

 

16.45    BREAK

 

17.00    New Approaches to Functional Genomics (cont.)

            A. Bradbury, International School for Advanced Studies, Trieste, Italy

            "Phage display and potential applications in the human genome project"

 

18.00    BUS TO HOTEL

 

FRIDAY, 8 May

 

9:00     VISIT TO THE ELETTRA SYCHROTRONE

 

            A. Savoia and F. Zanini, Elettra Synchrotron, Trieste

            The beamlines of Elettra and their applications to structural biology

 

11:00    VISIT TO THE ICGEB LABORATORIES Foyer, ICGEB, W Building

 

CLOSING OF THE WORKSHOP

 

13.30    LUNCH

 

14.30    BUS TO HOTEL

 

 

 

 

 

 

 

INVITED SPEAKERS

 

 

 

ASTON, Christopher W.

W. M. Keck Laboratory for Biomolecular Imaging, Department of Chemistry, New York University, 31 Washington Place, New York, NY 10003, USA. Telephone: +1-212-9981371; Fax: +1-212- 9954681; E-mail: astonc01@mcrcr.med.nyu.edu

 

BENSIMON, David

Department of Complex Systems, Weizmann Institute, 76100 Rehovot, ISRAEL. Telephone: +972-8-9342061/2671/3263; Fax: +972-8-9344109; E-mail: david.bensimon@lps.ens.fr, david@physique.ens.fr

 

BRADBURY, Andrew

SISSA Laboratory, ICGEB, AREA Science Park, Padriciano 99, 34012 Trieste, ITALY. Telephone: +39-40-398995; Fax: +39-40-398991; E-mail: bradbury@icgeb.trieste.it

 

BRADBURY, E. Morton

Life Sciences Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. Telephone: +1-505-6672690; Fax: +1-505-6672891; E-mail: emb@lanl.gov, bradbury@telomere.lanl.gov

 

CAVALIER-SMITH, Tom

Department of Botany, University of British Columbia, Vancouver, CANADA.  Fax: +1-604-8226089; E-mail: tom@tcs.botany.ubc.ca

 

COZZARELLI, Nicholas R.

Department of Molecular and Cell Biology, University of California, Berkeley, 401 Barker Hall #3204, Berkeley, CA 94720-3204, USA. Telephone: +1-510-6425266; Fax: +1-510-6431079; E-mail: cdea@socrates.berkeley.edu

 

GALPERIN, Michael

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bldg 38A, Bethesda, MD 20894, USA. Telephone: +1-301-4962477 ext294; Fax: +1-301-4809241; E-mail: koonin@ncbi.nlm.nih.gov, koonin@golem.nlm.nih.gov

 

GIACCA, Mauro

ICGEB, AREA Science Park, Padriciano 99, 34012 Trieste, ITALY. Telephone: +39-40-3757324; Fax: +39-40-226555; E-mail: giacca@icgeb.trieste.it

 

GIANCOTTI, Vincenzo

Dipartimento di Biochimica, Biofisica e Chimica delle Macromolecole, Università di Trieste, Via L. Giorgeri 1, 34100 Trieste, ITALY. Telephone: +39-40-6763676; Fax: +39-40-6763694; E-mail: giancot@bbcm.univ.trieste.it

 

GUPTA, Goutam

Theoretical Biology and Biophysics, T-10, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. Telephone: +1-505-6652587; Fax: +1-505-6653493, 6673493; E-mail: gxg@lanl.gov

 

IVANOV, Valerii I.

V. A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Str., 117984 Moscow, RUSSIA. Telephone: +7-095-1351255; Fax: +7-095-1351405; E-mail: chrom@imb.imb.ac.ru

 

LAEMMLI, Ulrich K.

Department of Molecular Biology, University of Geneva, 30, quai Ernest Ansermet, 1211 Geneva 4, SWITZERLAND. Telephone: +41-22-7026122; Fax: +41-22-3290696; E-mail: ulrich.laemmli@molbio.unige.ch

 

LANGOWSKI, Jörg

Division Biophysics of Macromolecules, German Cancer Research Center, Im Neuenheimer Feld 280, D-69120 Heidelberg, GERMANY. Telephone: +49-6221-423390; Fax: +49-6221-423391; E-mail: joerg.langowski@dkfz-heidelberg.de

 

LAVERY, Richard

Laboratoire de Biochimie Theorique/CNRS UPR 9080, Institut de Biologie Physico-Chimique, 13, rue Pierre et Marie Curie, 75005 Paris, FRANCE. Telephone: +33-1-43252609; Fax: +33-1-43295645; E-mail: richard@ibpc.fr

 

LILLEY, David M. J.

Department of Biochemistry, University of Dundee, Dundee DD1 4HN, UK. Telephone: +44-1382-344243, 070-500-84350 (mobile phone); Fax: +44-1382-201063; E-mail: dmjlilley@bad.dundee.ac.uk

 

MCMURRARY, Cynthia T.

Department of Pharmacology, Department of Biochemistry and Molecular Biology, Mayo Medical Foundation, Rochester, MN 55905, USA. Telephone: +1-507-2841597; Fax: +1-507-2849111; E-mail: mcmurray@mayo.edu

 

OLIVER, Steve

Department of Biomolecular Sciences, UMIST, P.O. Box 88, Sackville St., Manchester M60 1QD, UK. Telephone: +44-161-2004222, 2004203; Fax: +44-161-2360406; E-mail: steve.oliver@umist.ac.uk

 

PONGOR, Sàndor

ICGEB, AREA Science Park, Padriciano 99, 34012 Trieste, ITALY. Telephone: +39-40-3757300; Fax: +39-40-226555; E-mail: pongor@icgeb.trieste.it

 

RADMAN, Miroslav

Laboratory of Mutagenesis, Institut Jacques Monod, Université de Paris, Tour 43, 2 Place Jussieu, 75251 Paris Cedex 05, FRANCE. Telephone: +33-1-44274731; Fax: +33-1-44275716, 44277870; E-mail: radman@ccr.jussieu.fr

 

RICH, Alexander

Department of Biology, MIT, Room 68-233, 77 Massachusetts Avenue, Cambridge, MA 02139-4307, USA. Telephone: +1-617-2534715; Fax: +1-617-2538699; E-mail: cbeckman@mit.edu

 

SUSSMAN, Joel L.

Protein Data Bank, Biology Department, Bldg. 463, Brookhaven National Laboratory, Upton, NY 11973-5000, USA. Telephone: +1-516-3446355; Fax: +1-516-3442176; E-mail: jls@bnl.gov

Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, ISRAEL. Telephone: +972-8-9342638; Fax: +972-8-9344159; E-mail: joel@sgjs3.weizmann.ac.il

 

TERWILLIGER, Tom

Life Sciences Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA. Telephone: +1-505-6670072; Fax: +1-505-6653024; E-mail: terwilliger@lanl.gov

 

TRAVERS, Andrew A.

MRC Laboratory of Molecular Biology, Hills Road, Cambrige CB2 2QH, UK. Telephone: +44-223-248011; Fax: +44-223-213556; E-mail: aat@mrc-lmb.cam.ac.uk

 

ZHURKIN, Victor

Laboratory of Experimental and Computational Biology, National Cancer Institute, NIH, Bg. 12B, Rm. B116, MSC 5677, 12 South Drive, Bethesda, MD 20892-5677, USA. Telephone: +1-301-4968913; Fax: +1-301-4024724; E-mail: zhurkin@structure.nci.nih.gov

 

 

 

OTHER PARTICIPANTS:

 

:

ARANDA-ANZALDO, Armando

Laboratorio de Biología Molecular, Facultad de Medicina, UAEM, Apdo. Postal 428, C.P. 50000, Toluca, Edo. Méx, MEXICO. Telephone: +52-72-173552; Fax: +52-72-174564, 174142; E-mail: aaa@coatepec.uaemex.mx

ATALAN, Ekrem

Biology Department, Science and Art Faculty, Yuzuncu Yil University, Van, TURKEY. Telephone: +90-432-2251083 ext 1129; Fax: +90-432-2251114

 

ATHANASSIADIS, Alekos

ICGEB, AREA Science Park, Padriciano 99, 34012 Trieste, ITALY. Telephone: +39-40-3757354; Fax: +39-40-226555; E-mail: alekos@icgeb.trieste.it

 

BENETTI, Roberta

CIB, AREA Science Park, Padriciano 99, 34012 Trieste, ITALY. Telephone: +39-40-398992; Fax: +39-40-398990; E-mail: benetti@icgeb.trieste.it

 

BENVENUTI, Federica

ICGEB, AREA Science Park, Padriciano 99, 34012 Trieste, ITALY. Telephone: +39-40-3757310; Fax: +39-40-226555; E-mail: benvenut@icgeb.trieste.it

 

BOSUTTI, Alessandra

Laboratorio di Nutrizione Clinica, Istituto di Clinica Medica, Ospedale di Cattinara, Strada di Fiume, 34100 Trieste, ITALY. Telephone: +39-40-3994597; Fax: +39-40-3994593

 

BUCHTELOVA, Eva

Institute of Organic Chemistry and Biochemistry, Flemingovo nam. 2, 16610 Praha 6, CZECH REPUBLIC. Telephone: +420-2-20183292; E-mail: eva@uochb.cas.cz

 

DAPAS, Barbara

Department of Biomedical Sciences and Technologies, University of Udine, Via Gervasutta 45, 33100 Udine, ITALY. Telephone: +39-432-523121; Fax: +39-432-600828

 

DE SANCTIS, Veronica

Centro Acidi Nucleici, Ex-Istituto di Fisiologia, Università degli Studi di Roma, Piazzale A. Moro 5, 00185 Roma, ITALY. Telephone: +39-6-49912897; Fax: +39-6-49912500; E-mail: desanctis@axrma.uniroma1.it

 

DEGANUTO, Marta

ICGEB, AREA Science Park, Padriciano 99, 34012 Trieste, ITALY. Telephone: +39-40-3757325; Fax: +39-40-226555; E-mail: deganuto@icgeb.trieste.it

 

DEL TERRA, Elisa

Department of Biological Sciences and Technologies, University of Udine, Via Gervasutta 48, 33100 Udine, ITALY. Telephone: +39-432-729348, 523121; Fax: +39-432-600828

 

FABBRETTI, Elsa

ICGEB, AREA Science Park, Padriciano 99, 34012 Trieste, ITALY. Telephone: +39-40-3757310; Fax: +39-40-226555; E-mail: fabbre@icgeb.trieste.it

 

GAMEL, Katia

SISSA Laboratory, c/o ICGEB, AREA Science Park, Padriciano 99, 34012 Trieste, ITALY. Telephone: +39-40-3757355; Fax: +39-40-398991; E-mail: gamel@icgeb.trieste.it

 

GOSTISSA, Monica

CIB, AREA Science Park, Padriciano 99, 34012 Trieste, ITALY. Telephone: +39-40-398991; Fax: +39-40-398990; E-mail: gostissa@icgeb.trieste.it

 

GUBENSEK, Franc

Department of Biochemistry, J. Stefan Institute, Jamova 39, 1000 Ljubljana, SLOVENIA. Telephone: +386-61-1773250; Fax: +386-61-273594; E-mail: franc.gubensek@ijs.si

 

GUFFANTI, Alessandro

Telethon Institute of Genetics and Medicine, c/o DIBIT, Via Olgettina 58, 20132 Milano, ITALY. Telephone: +39-2-21560212; Fax: +39-2-21560220; E-mail: guffanti@tigem.it

 

HASEK, JINDRICH

Institute of Macromolecular Chemistry, 16206 Praha 6, CZECH REPUBLIC. Telephone: +42-2-360341 EXT 205; E-mail: hasek@imc.cas.cz

 

KORDIS, Dusan

Department of Biochemistry and Molecular Biology, J. Stefan Institute, Jamova 39, 1000 Ljubljana, SLOVENIA. Telephone: +386-61-1773611; Fax: +386-61-273594; E-mail: dusan.kordis@ijs.si

 

LIBERATI, Chiara

Dipartimento di Genetica e di Biologia dei Microrganismi, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, ITALY. Telephone: +39-2-26605224; Fax: +39-2-2664551; E-mail: kirasan@imiucca.csi.unimi.it

 

MANTOVANI, Fiamma

ICGEB, AREA Science Park, Padriciano 99, 34012 Trieste, ITALY. Telephone: +39-40-3757331; Fax: +39-40-226555; E-mail: mantova@icgeb.trieste.it

 

MARRO, Martin

ICGEB, AREA Science Park, Padriciano 99, 34012 Trieste, ITALY. Telephone: +39-40-3757312; Fax: +39-40-226555; E-mail: marro@icgeb.trieste.it

 

MENDOZA MALDONADO, Ramiro

ICGEB, AREA Science Park, Padriciano 99, 34012 Trieste, ITALY. Telephone: +39-40-3757325; Fax: +39-40-226555; E-mail: mendoza@icgeb.trieste.it

 

MORASSUTTI, Carla

Department of Biomedical Sciences and Technologies, University of Udine, Via Gervasutta 48, 33100 Udine, ITALY. Telephone: +39-432-523121; Fax: +39-432-600828; E-mail: carla.morassutti@dstb.uniud.it

 

NIKSIC, Martina

ICGEB, AREA Science Park, Padriciano 99, 34012 Trieste, ITALY. Telephone: +39-40-3757312; Fax: +39-40-226555; E-mail: niksic@icgeb.trieste.it

 

ODREMAN MACCHIOLI, Federico E.

ICGEB, AREA Science Park, Padriciano 99, 34012 Trieste, ITALY. Telephone: +39-40-3757316; Fax: +39-40-226555; E-mail: odreman@icgeb.trieste.it

PARONI, Gabriela

Department of Biomedical Sciences and Technologies, University of Udine, Via Gervasutta 45, 33100 Udine, ITALY. Telephone: +39-432-917165, 523121; Fax: +39-432-600828