fundamental principles of biology in the cell dna comprises genes encodes rna rna produces the...
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Fundamental Principles of Biology in the Cell DNA comprises genes encodes
RNA RNA produces the Proteins
---Regulates all biological processes within the Organism
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HUMAN CELL Contains 23 pairs of Chromosomes
Composed of 30,000 to 35,000
genes
Inturn
3 billion pairs of
DNA Bases
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Human genome 23 pairs – about 30,000 – 35,000 genes
Imagine genome as a book 23pairs of chromosome as chapters Several thousand genes as pages Genes as exons with interspaced introns Codons (in the exons) in the genes as words Codons composed of bases – as long as 800
bibles If human genome read at the rate of one
word/second, for 8 hrs. a day will take a century to complete
If we write human genome bases 1 letter/millimeter, text would be as long as River Danube (about 2850 km), second largest river after Volga
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Bioinformatics encompasses
Molecular Biology(source of the data to be analyzed)
Computer Science (hardware for analysis and net work to communicate)
Data analysis algorithms
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COMPONENTS OF BIOINFORMATICS
1. Information net work2. Biodiversity information
resources 3. Protein information resources 4. Genome Information resources 5. DNA sequence analysis 6. Pair wise alignment techniques 7. Multiple sequence alignment 8. Secondary data searching 9. Building a sequence search
protocol10.Analysis packages
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We have basic understanding on howgene sequences code specific proteinsBut lacks-role of DNA in specific diseases-the functions of proteins
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THE METHODS -BIOINFORMATICS
COLLECT,STORE,RETRIVE,ANALYSE AND CORRELATE -the complex informations grouped
Thus it means to explain*Normal biological processes*Malfunctions of these processes which
lead to diseases*Approaches to improving drug discovery
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A Short History of the Development
of Bioinformatics - Electrophoresis Tiselius 1933 for
protein separation-Structure of alfa-helix and beta-sheet by Pauling and Corey 1951
Double helix model for DNA watson & Crick 1953
Protein crystallography-Pertuz’s group 1954
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-Sequences of first protein Bovine insulin by F Sanger -First integrated circuit by Jack Kilby, Texas Instruments 1958-The Advanced Research Project Agency (ARPA) of US 1958-Packet-Switching net work protocols to ARPA 1968-ARPANET created linkinging at Stanford,UCSB,Uni. Utah and UCLA 1969
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-Needleman-Wunsch Algorithm Sequence comparison Published 1970-Invent e-mail programme by Tomlinson 1971
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FIRST Recombinant DNA Molecule created by Paul Berg-1972
PDB Data Bank. Brookhaven Announced-1973
‘Ethernet’ Ph.D. awarded by Harvard University --Robert Metealfe-1973
Network ‘internet’ developed- Vintcerf &Robert-Kahn-1974
Standardised general markup Language Charles Goldfarb-1974
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Two-diamentional Electrophoresis-Separation of Proteins on SDS PAGE 1975--Isoelectric Focusing 1975
Microsoft Corporation Founded- 1975
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1977
Full Description of Brookhaven PDB published
Method for DNA sequencing by A Maxim & W Gilbert(Harward) and F Sanger UK, MRC
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1978
First Usenet connection established between Duke & Uni. North Carolina
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1980
First complete genome sequence of an organism (FX 174) contain 5,386 bp &9 protein
NMR used for protein structure
Intelligenetics Inc. founded to develop programme for DNA& Protein sequences
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1981
The Smith-Waterman algorithm for sequence publishedIBM_ introduced it PC to the market
Genetics Coputer group created as a part of Uni. Wisconsin Biotechnology Center to develop molecular Biology tools
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1983
The Compact-disc launched
Name servers are developed at Wisconsin University
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1984
Jon Postel’s Domain Name system(DNS) is placed on-line
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1985
The FASTP algorithm published
PCR –reation is described by Kary Mullis and co-workers
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1986
The term “GENOMICS” appeared first time –mapping, sequencing and analyzing gene.
This term is coined by Thomas Roderick as a name of a new Journal
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1986
Amoco Technology Corporation acquires IntelliGenetics
SWISS-PORT data base created at Dept. of Medicine * Biochemistry, University of Geneva
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1987
Yeast artificial chromosome (YAC) described- Burke et al Sci:236;806-12
Physical map of E. Coli published-Kohara et al. CELL 51:319-37
PERL (Practical Extration Report Language) Released by Larry Wall
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1988
NCBI –National Center for Bitechnology established at National Cacer Institute
Human Genome Initiative startedat NRC
Internet Computer virus desinged by a student infects 6,00 military computers in US
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1990
The BLAST Programme implemented-Altschul et al.
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1991
WWW make upUnix-like operating system establishedCreation of expressed gene tags(ESTs) by Craig Venter
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1992
Human Genome System established at Gaithersburg, MarylandThe Institute of Genomic Research(TIGR) established by Craig Venter
Mel Simon announces the use of BACs for cloning
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1994
THE PRINTS DATA BASE OF PROTEIN MOTIFS PUBLISHED BY ATTWOOD & BECK
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1995
Microsoft releases 1.0 of Internet ExplorerSun releases JAVA
Haemophilus influenzex genome (1.8Mb) sequenced
Mycoplasma genitalium genome sequenced
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1996
Genome of Saccharomyces cerevisia (Baker’s yeast) 12.1 Mb sequenced
Prosite data base reported- Bairoch et al.
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1997The genome of E. coli Published (4.7 Mbp)
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1998
Genomes of Caenorhabditis elegans & Bakers yeast publishedSwiss Institute of Bioinformatics established
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2000
Genome of Psudomonas aerginosa published (6.3 Mbp)
Arabodopsis thaliana genome sequenced (100Mb)
Drosophilla melanogaskar genome sequenced (180 Mb) sequenced
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2001
THE HUMAN GENOME PUBLISHED (3,000 Mbp)
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INDIA’S BIODIVESITY
1,26,188 species – cover all five Kingdoms2.4% land area & 8% of global
biodiversityFlowering plants : 17,000 speciesEndemic species : 5725 (33.5%)
Total endemic %W. Himalaya 5,000 1,19524E. Himalayas 6,000 1,80830Western ghats 4,000 1,50038
S.W.ghats 1,286N.W. ghats 375
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Among the 25 Hot Spots of Biodiversity of the world
- Two are in IndiaEastern Himalayas & Western
Ghats
- 26 Endemic centres also been identified in India
In Kerala:- Agasthyamala- Anamala and High ranges- Nilgiris – Silent valley, Wynadu,
Kodagu
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Great Challenges facing the humanity is how to conserve and manage the natural resources including the Biological Diversity
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TO OVERCOME THIS –Comprehensive and reliable data and information base at different spatial level (global,country and regional)
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WE should know What we hold ?? Where is it ?? How much we hold ?? How much does it worth ??
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Documenting all bioresources accurately, within a shortest possible way should be the highest priority
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BIODIVERSITY ??? Totality and variability of a species, genes and the ecosystem they occupyThree levelsGenetic (within the species)Diversity,species (organismal)Ecological (habitat)
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Article 15 of CBD would be possible only if we have high quality documentation of our biological diversity
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Biodiversity can be categorized in to different levels: molecular sequences, gene diversity, individuals, populations, species, higher taxa, habitats,ecosystems and biomes
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Role of Bioinformatics on Biodiversity 1. Characterization of biodiversity 2.Bioprospecting of medicinal plants
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Characterization of biodiversity-RAPDs, AFLPs, DNA/ Protein sequencing, Photochemical screening
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Bioprospecting includes:Identification of novel drug targets, pesticide precursor compounds, prospecting of novel genes, mapping areas cotrolling quantitative traits for development of new cultivars
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Plant Biotechnology Division developed a sample web-site on a medicinal plant Andrographis paniculata on distribution, habit, habitat, botany,R&D literature base name of scientists working etc. http://www.geocities.com/andrographis