Bionanotechnology and Biomodeling

To outline the importance and potential applications of nanotechnology as an enabling technology to biotechnology, to present state-of-the-art research in the field. The course concludes with lectures devoted to the social and economic context of nanotechnologies and to their potential risks and possible solutions. Course is a survey of biomodeling in biology, emphasizing basic principles, practical use and future perspectives. It provides teoretical and practical knowledge on work with biological databases, biological se1uence advanced and multiple sequence alignment, gene expression and prediction, protein analysis by biomodeling tools, molecular phylogeny and evolution in bioinformatics.

To outline the importance and potential applications of nanotechnology as an enabling technology to biotechnology, to present state-of-the-art research in the field.

General Biology, Biochemistry, General Genetics, Biophysics, Fundamentals of Microbiology and Immunology, General Biotechnology and Bioinformatics.

Science and history of bionanotechnology. Objectives, objects and methods of bionanotechnologies and practical application. Nanotechnology in biology, bio-technology and medicine. Risks of bionanotechnology, public health, environmental and consumer protection. The bionanotechnology of the future. Biomodeling science, practical application and perspectives. Integrity and informativeness of biological databases. Advanced database search. Specialized BLAST search. Search for weakly bound proteins (PSI-BLAST and PHI-BLAST). Use of BLAST-like bioinformatics tools (Pattern hunter, BLASTZ, BLAT, Mega BLAST). Use of BLAST in gene detection. Multiple sequence alignment. Description, use and strategies of juxtaposition. Basic methods of multiple juxtaposition. Multiple juxtaposition databases (Pfam, conservative domain database, PopSet). Database management: manual or automatic. Molecular phylogeny and evolution in bioinformatics. Phylogenetic trees of species versus phylogenetic trees of genes / proteins. Phylogenic trees based on DNA, RNA and protein sequences. Stages of phylogenetic analysis. Gene prediction and gene expression (microarray data analysis). Gene prediction methodologies and gene structural elements. Data analysis software packages, drawings, normalization. Statistical data processing (aggregate analyzes, analysis of principal components, gene classification). Protein analysis and proteomics. Protein databases. Protein identification methods. Modular structure of proteins (domains, motifs and profiles). Prediction programs (protein localization and function). Practical classes: Introduction of DNA and drugs into plant and animal cells with the help of electroporation method, and detection. Diversity and use of biological macromolecule databases. Specialized BLAST search (PSI-BLAST, PHI-BLAST). Dinosaur DNA analysis (BLAST, multiple comparison) Processing of microarray data. Prediction of eukaryotic genes (GenScan, HMMgene, NetGene2) ExPASy web portal tools in proteomics. Evolutionary velocity of human and chimpanzee mitochondrial sequences.

Gain knowledge of: basic ideas of bionanotechnologies and biomodeling and their development; methods and principles of bionanotechnological research; the problems and dangers to be solved and the possible solutions to them; the use of bionanotechnologies and biomodeling in research and the relationship with other life sciences. Gain knowledge of the use of biomodeling at the molecular, organismal and phylogenetic levels; adaptability of biological sequence alignment; methods for gene and protein prediction and expression analysis; solving phylogenetic and evolutionary problems with the help of bioinformatics tools. Understand: the significance of bionanotechnologies and biomodeling in the context of modern biology, other modern sciences, and the development of society; the application of bionanotechnologies and biomodeling in industry and research; application of biomodeling in the construction of models at different structural biological levels. Understand the possibilities of using databases of biological sequences and structures. Understand the methods and applications of constructing advanced and multiple comparisons of biological sequences and structures. Understand the possibilities and perspectives of gene and protein prediction methods and tools, and the interfaces of these methods for full annotation of biological processes at the molecular level. Understand ways to solve phylogenetic and evolutionary problems using bioinformatics tools. Will be able to: practically transfer genes and drugs to animal and plant cells using bionanotechnological tools. Will be able to efficiently search for DNA, RNA and protein molecular sequences and structures in different databases, and find information about their function and other specific information; to perform advanced and multiple comparisons of biological macromolecule sequences with different bioinformatics tools and to perform correct interpretation of comparisons. Will be able to detect genes in unnotated sequences and find connections with encoded proteins. Will be able to predict the structure and function of the protein based on nucleotide information, molar structure and other bioiformatics tools. Will be able to perform phylogenetic analysis using bioinformatics tools.