Suggestions & Proposals
The Institute of Cytology and Genetics, Novosibirsk:
Title: Plant Gene network of transition to flowering: conservative and species specific regulatory pathways
Brief comment on the proposal content: The (preliminary) research plan might include (1) development of the ontology for fine scale expression experiments and description of phenotype abnormalities for barley and wheat using Gramine and AGNS ontology as the basis; (2) development of PGNS (Plant GeneNet supplementary database) using AGNS (arabidopsis GeneNet supplementary database) as a prototype; (3) basic annotation in AGNS the process of transition to flowering in arabidopsis; (4) further annotation in PGNS the process of transition to flowering in different plant species; (5) reconstruction of gene network of transition to flowering in arabidopsis and other species using GeneNet
(ICG) computer system; (6) comparison of the processes of transition to flowering in different species and identification of the common regulatory pathways and species specific regulatory pathways related to different growth habits; (7) arrangement of a common mathematical model of transition to flowering with specific solution for different groups of species; (8) revealing specific characters of transcription factor binding sites in promoters of genes involved in the transition to flowering, and other related topics.
Title: Modeling bacterial metabolic networks using chemical kinetic approach
Title: Automatic identification of contextual, conformational and physical chemical properties of B-DNA helix to make a quantitative prediction of biological activity of native and mutant protein-binding sites in genomic DNA of pro- and eukaryotes.
Title: Prediction of mRNA translation elongation efficiency in the single-cellular organisms
Title: Data integration in systems biology: software for database integration in common query space
Project Title: THE ORIGIN AND EVOLUTION OF X-CHROMOSOME INACTIVATION CENTRE IN MAMMALS.
Title: Bioinformatic support for molecular biology and gene engineering experiments on plants (and possibly other pro- and eukaryotic organisms)
Brief comment on the proposal content: Project may include the development of a computational system targeted on planning the gene engineering experiments. The system may include: (i) the databases on plant-specific promoters and post-transcriptional signals whose expression patterns were verified experimentally; (ii) the programs for prediction of expression efficiency of a native transgene variant in plant cells (to evaluate the necessity of modifications; the set of prediction programs may include tools for analysis of translation initiation and termination signals (contextual and structural features)), analysis of a synonymous codon content, comparison of transgene features with characteristics of high- and low expression genes of a recipient organism); (iii) the software for a transgene structure optimization (improvement of sites of initiation and termination of translation, codon content, possibly - elimination of potential sequence motifs recognized by a host cells as splicing or polyadenylation signals); (iv) automatic extraction of knowledge on metabolic (or regulatory) processes of interest as an element of gene engineering experiment planning and design.
Title: Prediction of transcription factor binding sites in plant (and other eukaryotic) genomes
Brief comment on the proposal content: The proposal may include: (1) development of combinatory SiteGA-PWM-VOBN method to increase the signal recognition sensitivity and specificity; (2) application of new technique to analysis of eukaryotic genomes to predict potential transcription factor binding sites.
Title: Analysis of alternative translation start sites to reveal new proteins and protein forms in plants and other eukaryotic organisms
Brief comment on the proposal content: The project is targeted on the computational analysis of eukaryotic mRNAs on the presence of potential alternative translation start sites and detailed bioinformatic characterization of alternative protein forms. These data may be used to guide the proteomic experiments to reveal new functional proteins.
Additional information is available from: Kochetov AV, Sarai A, Rogozin IB, Shumny VK, Kolchanov NA. The role of alternative translation start sites in the generation of human protein diversity. Mol Genet Genomics. 2005 273:491-496; Kochetov AV, Sarai A. Translational polymorphism as a potential source of plant proteins variety in Arabidopsis thaliana. Bioinformatics. 2004 20:445-447.
Title: Participation of the regulatory systems in the processes of wild cereals domestication
Brief comment on the proposal content: It has been shown for diploid T. monococcum accessions that the deletions in the promoter region of the VRN1 gene lead to a transition from winter to spring growth habit (Yan et al., 2003). The main goal of our project is an investigation of the influence of encoded by VRN1 transcription factor on the expression of the wheat genes using the DNA microarray technique. We expect to find out, which genes in the wheat genome are the target genes for the encoded by VRN1 transcription factor.
Title: Wheats genetic & phylogenetic investigations
Brief comment on the proposal content: Wheat Genetics Laboratory carries out comparative-genetic and philogenetic investigations of genera Triticum and Aegilops species. Having the world's biggest collection of diploid wheat species (about 700 accessions) we study the genetics of its morphological, biochemical and physiological traits for their further introgression into cultivated wheat species and widening their biodiversity.
Title: Investigation of plant virus resistance mechanisms
Brief comment on the proposal content: The proposal concerns investigation of plant extracellular ribonucleases and their role establishing virus resistance. It may include the cloning of nuclease-producing plants and analysis of their resistance to various viruses/viroids. The project is also targeted on the development of new technique to increase plant resistance to infections by modulating the ribonuclease expression.
Title: Investigation of proline metabolism and its role in plant resistance to various abiotic stresses
Brief comment on the proposal content: The project concerns the modification of proline metabolism by suppressing the proline dehydrogenase and/or enhancing expression of OAT and P5CS on the model of transgenic tobacco, potato and other plants. The project is also targeted on the development of new technique to increase plant resistance to various abiotic stresses (salt, cold, drought, heavy metals, etc.) by modulating the proline metabolism at various stages.