Fundamental Principles of Biology in the Cell DNA comprises genes encodes

RNA RNA produces the Proteins

---Regulates all biological processes within the Organism

HUMAN CELL Contains 23 pairs of Chromosomes

Composed of 30,000 to 35,000

genes

Inturn

3 billion pairs of

DNA Bases

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

Bioinformatics encompasses

Molecular Biology(source of the data to be analyzed)

Computer Science (hardware for analysis and net work to communicate)

Data analysis algorithms

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

We have basic understanding on howgene sequences code specific proteinsBut lacks-role of DNA in specific diseases-the functions of proteins

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

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

-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

-Needleman-Wunsch Algorithm Sequence comparison Published 1970-Invent e-mail programme by Tomlinson 1971

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

Two-diamentional Electrophoresis-Separation of Proteins on SDS PAGE 1975--Isoelectric Focusing 1975

Microsoft Corporation Founded- 1975

1977

Full Description of Brookhaven PDB published

Method for DNA sequencing by A Maxim & W Gilbert(Harward) and F Sanger UK, MRC

1978

First Usenet connection established between Duke & Uni. North Carolina

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

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

1983

The Compact-disc launched

Name servers are developed at Wisconsin University

1984

Jon Postel’s Domain Name system(DNS) is placed on-line

1985

The FASTP algorithm published

PCR –reation is described by Kary Mullis and co-workers

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

1986

Amoco Technology Corporation acquires IntelliGenetics

SWISS-PORT data base created at Dept. of Medicine * Biochemistry, University of Geneva

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

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

1990

The BLAST Programme implemented-Altschul et al.

1991

WWW make upUnix-like operating system establishedCreation of expressed gene tags(ESTs) by Craig Venter

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

1994

THE PRINTS DATA BASE OF PROTEIN MOTIFS PUBLISHED BY ATTWOOD & BECK

1995

Microsoft releases 1.0 of Internet ExplorerSun releases JAVA

Haemophilus influenzex genome (1.8Mb) sequenced

Mycoplasma genitalium genome sequenced

1996

Genome of Saccharomyces cerevisia (Baker’s yeast) 12.1 Mb sequenced

Prosite data base reported- Bairoch et al.

1997The genome of E. coli Published (4.7 Mbp)

1998

Genomes of Caenorhabditis elegans & Bakers yeast publishedSwiss Institute of Bioinformatics established

2000

Genome of Psudomonas aerginosa published (6.3 Mbp)

Arabodopsis thaliana genome sequenced (100Mb)

Drosophilla melanogaskar genome sequenced (180 Mb) sequenced

2001

THE HUMAN GENOME PUBLISHED (3,000 Mbp)

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

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

Great Challenges facing the humanity is how to conserve and manage the natural resources including the Biological Diversity

TO OVERCOME THIS –Comprehensive and reliable data and information base at different spatial level (global,country and regional)

WE should know What we hold ?? Where is it ?? How much we hold ?? How much does it worth ??

Documenting all bioresources accurately, within a shortest possible way should be the highest priority

BIODIVERSITY ??? Totality and variability of a species, genes and the ecosystem they occupyThree levelsGenetic (within the species)Diversity,species (organismal)Ecological (habitat)

Article 15 of CBD would be possible only if we have high quality documentation of our biological diversity

Biodiversity can be categorized in to different levels: molecular sequences, gene diversity, individuals, populations, species, higher taxa, habitats,ecosystems and biomes

Role of Bioinformatics on Biodiversity 1. Characterization of biodiversity 2.Bioprospecting of medicinal plants

Characterization of biodiversity-RAPDs, AFLPs, DNA/ Protein sequencing, Photochemical screening

Bioprospecting includes:Identification of novel drug targets, pesticide precursor compounds, prospecting of novel genes, mapping areas cotrolling quantitative traits for development of new cultivars

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