Development of Bioinformatics and its application on Biotechnology By Wong Tak Hong

What is Bioinformatics? (1) -use of computer to store, analysis and manipulate biological information

What is Bioinformatics? (2) -manage and manipulate sequence data -use that sequence data in the analyses of gene, protein, and DNA function -designing novel and incisive algorithms -create new/maintain existing databases of information -allowing open access to the records held within them

Onset of Bioinformatics -Huge advances in the fields of molecular biology and genomics especially after Human Genome Project -This cause massive amount of biological information available

Onset of Bioinformatics 2

What is developed? -Biological databases are consistent data that are stored in a uniform and efficient manner -These databases contain data from a broad spectrum of molecular biology area -Primary databases contain -information and annotation of DNA protein sequences -DNA and protein structures and DNA and protein expression profiles                                      

Genbank -First database setup to store DNA sequence data, set up In 1982 -manage by National Centre Biotechnology Information -currently holds about 17 billion bases from more than 100,000 organisms -Each of the sequences are given an ID number for easy identification in the database http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html

-a comprehensive database of DNA and RNA sequences EMBL (European Molecular Biology Laboratory) Nucleotide Sequence Database -a comprehensive database of DNA and RNA sequences -manage by European Bioinformatics Institute (EBI) -information collected from the scientific literature and patent applications -supported by 17 countries in Western Europe -currently contains nearly more than 10 million bases http://www.ebi.ac.uk/embl/

SwissProt: -a database of protein sequence, function and structure -manage by European Bioinformatics Institute -provides a high level of integration with other databases -a very low level of redundancy (means less identical sequences are present in the database) http://www.ebi.ac.uk/swissprot/                                      

EC-ENZYME: The 'ENZYME' data bank contains the following data for a characterized enzyme: -EC number -Recommended name and Alternative names -Catalytic activity -Cofactors -Pointers to the SWISS-PROT entry that correspond to the enzyme -diseases associated with a deficiency of the enzyme

Website of EC-enzyme http://www.biochem.ucl.ac.uk/bsm/dbbrowser/protocol/ecenzfrm.html

Protein Data Bank -manage by Research Collaboratory for Structural Bioinformatics (RCSB) -a collection of all publicly available 3D structures of proteins, nucleic acids, carbohydrates -variety of other complexes experimentally determined by X-ray crystallography and NMR http://www.rcsb.org/pdb/

How rapidly developed?

Structural Analysis -DNA sequences that encode proteins with specific function -Researchers predict the 3D structure using protein or molecular modeling -Experimentally determined protein structures (templates) are used -to predict the structure of another protein that has a similar amino acid sequence (target)

Algorithm A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.

PROSPECT -Protein Structure Prediction and Evaluation Computer Toolkit -a protein-structure prediction system -It construct a 3-D model of proteins by protein threading - Protein threading Algorithms for protein fold recognition http://www.bioinformaticssolutions.com/products/prospect.php

Example of 3D-Protein Model

Advantages in Protein Modeling -Examining a protein in 3D allows for greater understanding of protein functions -providing a visual understanding that cannot always be conveyed through still photographs or descriptions

Homology and Similarity Tools -Homology and Similarity Tools are use to analyses similarity between two sequence or structure -the degree of similarity between two sequences can be measured -applied in evolutionary studies

BLAST (Basic Local Alignment Search Tool) -homology and similarity tools -develop by NCBI -Search programs designed for the Windows platform -used to perform fast similarity searches for protein or DNA -users can retrieve results and format their results in different format

Website for BLAST http://www.ncbi.nlm.nih.gov/BLAST/

Molecular Medicine -Most of the disease has a genetic component and environmental component -we can search for the genes directly associated with different diseases -begin to understand the molecular basis of these diseases more clearly -better treatments, cures and even preventative tests to be developed

Phenylketonuria (PKU) The PAH (phenylalanine hydroxylase) gene maps on chromosome 12 PAH

Personalized Medicine -Development of the field of pharmacogenomics -study of how an individual's genetic inheritance affects the body's response to drugs -At present, doctors have to use trial and error to find the best drug to treat a particular patient -In the future, doctors will be able to analyze a patient's genetic profile and prescribe the best available drug therapy and dosage from the beginning

Microbial genomic application -MGP (Microbial Genome Project) to sequence genomes of bacteria -useful in energy production, industrial processing and toxic waste reduction -scientists can begin to understand these microbes at a very fundamental level -isolate the genes that give them their unique abilities to survive under extreme conditions

Waste clean up -Deinococcus radiodurans is known as the world's toughest bacteria -the most radiation resistant organism known -Scientists are interested in this organism because of its potential usefulness in cleaning up waste sites that contain radiation and toxic chemicals

Deinococcus radiodurans

Evolutionary studies -sequencing of genomes from different organism -evolutionary studies can be performed to determine the tree of life -find last universal common ancestor

Evolutionary studies 2

Impact of Bioinformatics 1 -Bioinformatics leads to advances in understanding basic biological processes, treatment, and prevention of many genetic diseases -Bioinformatics has transformed the discipline of biology from a purely lab-based science to an information science as well

Impact of Bioinformatics 2 -modern biology and related sciences are increasingly becoming dependent on Bioinformatics -Thus, Bioinformatics exhibits great potential in the future development of science and technology