BGRS’ 2002 International Program Committee Nikolay Kolchanov, Institute of Cytology and Genetics, Novosibirsk, Russia (Chairman of the Conference) Ralf Hofestadt, University of Bielefeld, Germany (Co-Chairman of the Conference) Philip Bourne, SDSC, San-Diego, USA (Co-Chairman of the Conference) Nickolai Alexandrov, Ceres Inc., Malibu, USA Philipp Bucher, Swiss Institute for Experimental Cancer Research, Switzerland Julio Collado-Vides, National University of Mexico, Mexico Jim Fickett, AstraZeneca, Boston, USA Paolo Frasconi, University of Florence, Firenze, Italy Sergey Goncharov, Sobolev Institute of Mathematics, Novosibirsk, Russia Igor Goryanin, GlaxoSmithKline, UK Charlie Hodgman, GlaxoSmithKline, UK Elza Khusnutdinova, Institute of Biochemistry and Genetics, Ufa Sci. Centre RAS (Ufa), Russia Lev Kisselev, Engelhardt Institute of Molecular Biology, Moscow, Russia Boris Kovalerchuk, Central Washington University (Ellensburg), USA Luciano Milanesi, ITBA, Milan, Italy John Reinitz, The University at Stony Brook, N.Y., USA Akinori Sarai, RIKEN Tsukuba Life Science Center, Tsukuba, Japan Ilya Shindyalov, San Diego Supercomputer Center, USA Rustem Tchuraev, Institute of Biology, Ufa Sci. Centre RAS, Ufa, Russia Masaru Tomita, Institute for Advanced Biosciences, Keio University, Japan Edgar Wingender, GBF, Braunschweig, Germany Nikolay Yankovsky, Institute of General Genetics, Moscow, Russia Lev Zhivotovsky, Institute of General Genetics, Moscow, Russia Local Organizing Committee Dagmara Furman, Institute of Cytology and Genetics, Novosibirsk, Nadya Omelianchuk, Institute of Cytology and Genetics, Novosibirsk, Sergey Lavryushev, Institute of Cytology and Genetics, Novosibirsk, Galina Kiseleva, Institute of Cytology and Genetics, Novosibirsk, Elena Borovskikh , Institute of Cytology and Genetics, Novosibirsk, Nikolay Shkel, Institute of Cytology and Genetics, Novosibirsk, Andrey Kharkevich, Institute of Cytology and Genetics, Novosibirsk, The information about the Conference BGRS’ 2002 is presented at http://www.bionet.nsc.ru/meeting/bgrs2002/ 2 BGRS’ 2002 Our sponsors Organizers Institute of Cytology and Genetics, SB RAS Siberian Branch of the Russian Academy of Sciences Grants INTAS Conference Grant Glaxo Wellcome Inc. Russian Foundation for Basic Research Ministry of Industry, Science and Technologies of the Russian Federation Information sponsors San Diego Supercomputer Center, United States RIKEN Tsukuba Institute Bielefeld University, Faculty of Technology http://www.karger.com/ In Silico Biology Others KWESTA-group: computers, computer accessories, service 3 BGRS’ 2002 CONTENTS COMPARATIVE AND EVOLUTIONARY GENOMICS COMPARATIVE STUDY OF THE ORTHOPOXVIRUS GENES A27L, A56R, B8R, AND C11R Babkin I.V., Mikheev M.V., Shchelkunov S.N......................................................................................... 10 COMPARATIVE STUDY OF THE ORTHOPOXVIRUS GENES B19R AND B29R Mikheev M.V., Feshchenko M.V., Shchelkunov S.N.............................................................................. 13 ANALYSIS OF BACTERIAL RM-SYSTEMS THROUGH GENOME-SCALE ANALYSIS AND RELATED TAXONOMY ISSUES Vandenbogaert M., Makeev V................................................................................................................ 16 FNR/DNR/ANR-REGULON IN GAMMA-PROTEOBACTERIA Gerasimova A.V., Rodionov D.A., Mironov A.A., Gelfand M.S. ............................................................. 19 SEARCH FOR REGULATORY SIGNALS IN GROUPS OF ORTHOLOGOUS GENES OF GAMMA – PROTEOBACTERIA Danilova L.V., Gelfand M.S. ................................................................................................................... 21 TRANSCRIPTIONAL REGULATION OF A NEW BACTERIOCIN-PRODUCING SYSTEM IN STREPTOCOCCUS EQUI. Kotelnikova E.A., Gelfand M.S. .............................................................................................................. 23 SYSTEMATIC PREDICTION OF REGULATORY INTERACTIONS IN THE LACI FAMILY OF TRANSCRIPTIONAL REGULATORS Laikova O.N............................................................................................................................................ 26 PREDICTION OF NEW ENZYME INVOLVED IN PEPTIDOGLYCAN RECYCLING Panina E.M., Vassieva O., Gelfand M.S., Overbeek R. ......................................................................... 29 BIOINFORMATICS APPROACH TO ANALYSIS OF REGULATION OF AROMATIC AMINO ACIDS BIOSYNTHESIS IN BACILLUS/CLOSTRIDIUM GROUP Panina E., Vitrehschak A., Mironov A., Gelfand M................................................................................. 32 REGULATION OF THE HEAT SHOCK RESPONSE OF β-, γ- AND ε-PROTEOBACTERIA Permina E.A., Gelfand M.S. ................................................................................................................... 35 PURINE REGULON OF GAMMA-PROTEOBACTERIA Ravcheyev D.A., Gelfand M.S., Mironov A.A., Rakhmaninova A.B....................................................... 38 COMPUTATIONAL ANALYSIS OF THE BIOTIN REGULON IN BACTERIAL GENOMES Rodionov D.A., Mironov A.A., Gelfand M.S............................................................................................ 40 REGULATION OF BACTERIAL RIBOFLAVIN GENES BY A CONSERVED RNA STRUCTURAL ELEMENT Vitreschak A.G., Rodionov D.A., Mironov A.A., Gelfand M.S. ............................................................... 44 MCMC METHOD FOR IDENTIFICATION OF ALLELIC PATTERNS IN DATA WITH QUANTITATIVELY DESCRIBABLE PHENOTYPIC FEATURES Favorov A.V., Ochs M.F.......................................................................................................................... 47 S-RNASES IN THREE PLANT FAMILIES WITH GAMETOPHYTIC SELF-INCOMPATIBILITY: PHYLOGENY RELATED TO A PUTATIVE NUMBER OF S-LOCI IN ROSACEAE Alexeyenko A.V. ..................................................................................................................................... 50 SURVEY OF HUMAN NON-SYNONYMOUS SNPs Ramensky V.E., Bork P., Sunyaev S.R.................................................................................................. 53 COMPUTATIONAL BIOLOGY AND ANALYSIS OF HUMAN POPULATIONS WITH USE OF DNA MARKERS Zhivotovsky L.A. ..................................................................................................................................... 56 4 BGRS’ 2002 THE CHANNEL CAPACITY OF SELECTIVE BREEDING: ULTIMATE LIMITS ON THE AMOUNT OF INFORMATION MAINTAINABLE IN THE GENOME Watkins C.J.C.H. .................................................................................................................................... 58 METHOD OF HORIZONTAL GENE TRANSFER DETERMINATION USING PHYLOGENETIC DATA Lyubetsky V.A., V’yugin V.V................................................................................................................... 61 MINIMAL TREES IN PHYLOGENETIC SPACES Ivanov A.O., Tuzhilin A.A........................................................................................................................ 64 COMPARATIVE ANALYSIS OF CODING SEQUENCES OF APETALA1 HOMOLOGUES Omelyanchuk N.A., Gusev V.D., Nemytikova L.A., Aksenovich A.V. .................................................... 67 SYSTEM COMPUTATIONAL BIOLOGY: ANALYSIS AND MODELLING OF GENE NETWORKS AND METABOLIC PATHWAYS GENENET SYSTEM: ITS STATUS IN 2002 Ananko E.A., Podkolodny N.L., Ignatieva E.V., Podkolodnaya O.A., Stepanenko I.L., Kolchanov N.A.72 MOLECULAR-GENETICAL MECHANISMS OF ADIPOCYTE REGULATION: REPRESENTATION IN GENENET DATABASE Proscura A.L., Ignatieva E.V. ................................................................................................................. 76 GENE NETWORK OF GLUTATHIONE HOMEOSTASIS: A RESPONSE TO OXIDATIVE STRESS Kudryavtseva A.N., Stepanenko I.L. ...................................................................................................... 80 MOLECULAR GENETIC MECHANISMS REGULATING THE THYROID SYSTEM: DESCRIPTION IN THE TRRD AND GENENET DATABASES Suslov V.V., Ignat’eva E.V...................................................................................................................... 83 INTERPRETATION OF GENE NETWORKS IN THE CONTEXT OF ANOKHIN’S THEORY OF FUNCTIONAL SYSTEMS Suslov V.V., Vityaev E.E., Ignatieva E.V. ............................................................................................... 87 ORGANIZATION OF THE GENE NETWORK OF APOPTOSIS Stepanenko I.L., Grigor’ev S.A............................................................................................................... 91 GENE NETWORK OF MACROPHAGE ACTIVATION UNDER THE ACTION OF INTERFERON-GAMMA AND LIPOPOLYSACCARIDES Nedosekina E.A., Ananko E.A................................................................................................................ 94 GENE NETWORK ON CELL CYCLE CONTROL Turnaev I.I., Podkolodnaya О.А. ............................................................................................................ 97 VARIABILITY OF FLOWER DEVELOPMENT GENE NETWORKS IN SEVERAL PLANT SPECIES Aksenovich A.V. ................................................................................................................................... 101 NEGATIVE REGULATION OF PLANT PHOTOMORPHOGENESIS Smirnova O.G., Ibragimova S.S., Shavrukov Yu.N., Stepanenko I.L. ................................................. 104 A HYBRID NETWORK OF NITROGEN-FIXING NODULES: INTERGENOMIC INTERACTIONS OF BACTERIA AND HOST PLANT Ibragimova S.S., Smirnova O.G., Shavrukov Yu.N., Stepanenko I.L. ................................................