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Bioinformatics Science Projects in Novosibirsk (Siberian Branch of Russian Academy of Science)

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Bioinformatics Sciences Projects . Novosibirsk. Siberian Branch of Russian Academy of Science
List of Projects

Project description

The Project is devoted to establishment of a high performance network linking scientists from the U.S. and Russian Federation. The Institute of Cytology and Genetics of SB RAS has broad cooperation with American partners. One of the Projects is entitled "Developing modeling and bioinformatics" and sponsored by the NSF Frontiers in Integrative Biological Research (FIBR) Program.

By integrating advances in biological knowledge, biological instrumentation, applied biomathematics, and computing, the authors of this proposal will create a computational modeling tool for developmental biology research. This effort requires a multidisciplinary, multi-institutional team, which will integrate advances in mathematical models of cell regulation and development, plant developmental biology, and software architectures to produce a scalable software platform for research and educational outreach related to the developmental biology of the shoot apical meristem in Arabidopsis and more generally to the study of complex developmental biological systems.

The research under the Project will be done at the edge of two different areas of modern science: systemic biology integrating mathematics, bioinformatics, genomics, computer and systems science and developmental biology. As a result, we propose to create a first, scalable version of a general tool and to demonstrate its success in appropriate developmental biological systems beginning with plants. In greater detail, we propose a multi-disciplinary and multi-institutional team which will integrate advances in mathematical models of cell regulation and development, plant developmental biology, microscopy, image processing, bioinformatics, and intelligent software architectures, to produce a software platform capable of contributing first to the developmental biology of the shoot apical meristem (SAM) in Arabidopsis and then more generally to the study of complex developmental biological systems.

The scientific objectives of this effort also include achieving a quantitative scientific understanding of developmental systems in Arabidopsis, starting with the shoot apical meristem stem cell population and phyllotaxis. Realistic computational models of stem cell behaviour in shoot apical meristems, and of organ positioning around the shoot apical meristem, will provide software of use in modelling of development in other organisms, and in modelling any complex set of processes in multicellular tissues. It will also provide a highly specific mechanistic description and model of key aspects of plant development, Refinement and extension of the model will eventually lead to a “silicon plant,” a complete systems model of gene activity and its consequences in plant growth and development.

Another objective of the project is to study complex hierarchy of system development. In particular, shoot apical meristem development will be represented as a hierarchical system of minimal models. T his system should be self-consistent, that is, conclusions that were obtained for a model at one hierarchical level could be interpreted as the limitations for the model of the higher hierarchical level. To this aim, we plan to apply Petri nets that are useful for modeling of complex systems with parallel architecture and synchronization of events. These features are of especial importance for administration of biological systems at different levels, from gene expression, to protein synthesis, toward organism level and higher. Experimental data representation in a form of Petri nets will give some advantages, since numerous software programs are known for Petri nets analysis. Under construction of hierarchical Petri net system, the main attention will be paid to genetic systems controlling cell proliferation and differentiation, as well as to spatio-temporal interaction between these two basic processes during shoot apical meristem development.

During the Project implementation, Russian and American sides will get mutual benefits. American Partner has a great experience in studying genetic control of shoot apical meristem function in development. They have analyzed a number of mutations that affect shoot meristem size and growth, shoot apical meristem formation, and activities of floral meristems that relate to shoot apical meristem cell division patterns, have been isolated, studied in detail at the phenotypic level, cloned, and studied in detail at the molecular level. Russian team has independent but very compatible capabilities in pathway and expression informatics, so exchange of software will not be required in order to pool mutual efforts on the representation, in SBML, of broad plant development pathway knowledge and on the development of scalable regulatory network inference algorithms for plant development.

The expected outcome of the proposed work is a computational model of the developing and growing shoot apical meristem of Arabidopsis (and thus, presumably, of any dicotyledonous plant). This model will be based on microscopic observations of the cellular domains and cell division patterns in the SAM in mutants and wild-type, and will be detailed enough to allow prediction of mutant phenotypes, and therefore experimental tests of the model. The computational model will itself be adaptable to other situations of cell-cell signaling in solid tissues, and will therefore serve as the basis for a new generation of studies, in vivo and in silico, of growth and development in plants and in animals. Refinement and extension of the model will eventually lead to a “silicon plant,” a complete model of gene activity and its consequences in plant growth and development. The outreach component of the proposal is designed to raise public awareness of the critical importance of cells in plants and animals, and therefore to introduce students and adults to one of the fundamental pillars of modern biology – the understanding of which is essential for citizens to understand their own bodies and cellular processes, including illnesses such as cancer.

Broader Impact: the goal of the outreach plan is to develop, evaluate, and introduce a new set of techniques for high school and pre-service science teachers. Ultimately this will put fundamental, powerful new capabilities in the hands of the biotechnology industry.

Leaders from Russian side

Science Programs that will get novel advantages with application of modern network connection

  1. Grant Programs of the Russian Foundation for Basic Research (No. 01-07-90376, 01-07-90084, 02-07-90355, 02-07-90359, 03-07-90181-_, 03-04-48506-_, 03-04-48469-_, 03-04-48555-_, 03-07-96837, 03-07-96833-_2003)

  2. Grant Programs of Russian Ministry of Industry, Sciences and Technologies (No. 43.073.1.1.1501),

  3. Grant Programs of Siberian Branch of the Russian Academy of Sciences (Integration Projects Nos.119, 145, 142),

  4. Subcontract of the National Institutes of Health USA (No.2 R01-HG-01539-04A2).

List of benefiting US

  1. Scientific Inference Systems Laboratory Institute for Genomics and Bioinformatics
  2. University of California Irvine California Institute of Technology 1200 East California Boulevard Pasadena, California 91125
The main research Vector activities in bioinformatics are focused in:
Development of mathematical models in biotechnology, virology, immunology, ecology, molecular biology and aerobiology so as development of software supporting the models, development of databases in many fields, development of knowledge based systems in biotechnology, virology, and molecular biology. Much of the above research is being conducted under international projects (funded by ISTC, INTAS, CRDF).

Today SRC VB VECTOR has 39 active international projects. These projects involve close collaboration with CRDF, US Department of Energy, DARPA (Defense Advanced Research Projects Agency), CTR (the Cooperative Threat Reduction Program of the U.S. Department of Defense), USDA (U.S. Department of Agriculture/Agricultural Research Service),

(U.S. Department of Health and Human Services Biotechnology Engagement Program), as well as with the US leading scientific research centers.

Major areas of research pursued under international projects:

To be able to carry out these studies, we need efficient access to the following information resources:

Protein and associated topics databases

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