BIOINFORMATICS PRESENTATION

Contents

Introduction to Bioinformatics DNA Microarrays Internet Sites on Web

Bioinformatics

"Bioinformatics is the field of science in which biology, computer science, and information technology merge into a single discipline”

OR The use of computational &

statistical techniques for the analysis of biological data.

In1960s: the birth of bioinformatics.

Bioinformatics (Oxford English Dictionary)

The branch of science concerned with information and information flow in biological systems, esp. the use of computational methods in genetics and genomics.

Conti….. The field of science in which biology,

computer science and information technology merge into a single discipline

History (1960s)

Over a century ago, bioinformatics work started with an Austrian monk named Gregor Mendel .

He is known as” Father of genetics “. Mendel illustrated that the

inheritance of traits could be more easily explained if it was controlled by factors passed down from generation to generation

Biologists collect molecular data: DNA & Protein sequences,gene expression, etc.

Computer scientists (+Mathematicians, Statisticians, etc.)Develop tools, softwares, algorithms to store and analyze the data.

BioinformaticiansStudy biological questions by analyzing molecular data

The field of science in which biology, computer science and information technology merge into a single discipline

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Applications Of Bioinformatics

Application of Bioinformatics The science of bioinformatics has

many beneficial uses in the modern day world. These Include the following :

Molecular medicine Microbial genome application Agriculture Animals Comparative studies Gene therapy

Molecular medicine

Human genome will have profound effects on the field of biomedical research and clinical medicine.

Every disease has a genetic component and inherited to body’s response to an environmental stress which called alterations In the genome ( e.g cancers, heart disease and diabetes)

Agriculture The sequencing of the genomes of plants

and animals should have enormous benefits for the agricultural community and can be used to search for the genes within these genomes and their functions, making them healthier, more disease resistance and more productive.

Crops Insect resistance Improve nutritional quality Grow in poorer soils and drought resistant

Animals

Sequencing projects of many farm animals including cows, pigs and sheep are now well under way in the hope that a better understanding of the biology of these organisms will have huge impacts for improving the production and health of livestock and ultimately have benefits for human nutrition.

Comparative studies Analyzing and comparing the genetic

material of different species is an important method for studying functions of genes, mechanism of inherited diseases and species evolution.

Bioinformatics tools can be used to make comparisons between the numbers, locations and biochemical functions of genes in different organisms.

Organisms that are suitable for use in experiments are termed as MODEL ORGANISMS

Gene Therapy

Gene therapy is the approach used to treat, cure or even prevent disease by changing the expression of a person’s gene.

In the not too distant future, the potential for using genes themselves to treat disease may become a reality.

Microbial genome applications Microorganisms are ubiquitous, that is they

are found everywhere. They have been found surviving and thriving in extremes of heat, cold, radiation, salt, acidity, and pressure.

By studying the genetics material of these organisms, scientists can begin to understand these microbes at a very fundamental level and isolate the genes that give them their unique abilities to survive under the extreme conditions.

Waste cleanup Climate change studies Alternative energy sources Biotechnology Antibiotic resistance Forensic analysis of microbes Bio-weapon creation Evolutionary studies

Molecular Bioinformatics

Molecular Bioinformatics involves the use of computational tools to discover new information in complex data sets (from the one-dimensional information of DNA through the two-dimensional information of RNA and the three-dimensional information of proteins, to the four-dimensional information of evolving living systems).

DNA Microarray

A Recombinant DNA Method

Also known as DNA Chip

History Microarray technology evolved

from southern blotting in 1975.

The concept of DNA microarray began in mid 1980s.

Pin based robotic system was developed by Lehrach’s group 1990.

Steve fodor develop scanner for reading the output .

Conti…

Quantitative moniter of gene expression patterns with complementary DNA microarray reported by patrick brown ,mark schena & colleagues in 1995

Mar k schena was the father of microarray technology

DNA microarray The DNA microarray is a tool used to determine

whether the DNA from a particular individual contains a mutation in genes

The chip consists of a small glass plate encased in plastic. Some companies manufacture microarrays using methods similar to those used to make computer microchips. On the surface, each chip contains thousands of short, synthetic, single-stranded DNA sequences, which together add up to the normal gene in question, and to variants (mutations) of that gene that have been found in the human population

Microarray or DNA Chip:

Every spot on the chip represents a different coding sequence from different genes.

Each spot on the chip is made of a DNA probe that can pair with the cDNA that was created.

Principle Microarrays descend from Southern and

Northern blotting. Unknown DNA is transferred to a membrane and then probed with a known DNA sequence with a label.

Hybridization In Microarrays, the known DNA sequence (or

probe) is on the membrane while the unknown labeled DNA (or target) is hybridized

Complementary nucleic acid sequence get pair via hydrogen bonds .

Wash off of non-specific bonding sequences.

Micro array

Microarray is a general term there are many type now

DNA microarray Protein microarray Tissue microarray Transfection microarray Chemical compound microarray Antibody microarray

What Can be Measured using Microarrays?1. Amount of mRNA expressed by a gene.2. Amount of mRNA expressed by an exon.3. Amount of RNA expressed by a region of DNA.4. Which strand of DNA is expressed.5. Which of several similar DNA sequences6. How many copies of a gene is present in the

genome.7. Where a known protein has bound to the DNA.

Biological Samples in 2D Arrays on Membranes or Glass Slides

Over 10,000 Hybridization Could Be Down at One Time

Several Types of Arrays Spotted DNA arrays Affymetrix gene chips Ink-jet microarrays from Agilent

Glass cDNA microarray

First type of DNA microarray technology develop

It was pioneered by Patrick brown and his colleagues at Stanford University .

Produced by using a robotic device which deposits (spots) a nanoliter of DNA onto a coated microscopic glass slides (50-150 um in diameter)

Affymetrix microarray

High-density oligonucleotide microarray often referred to as a chips which involves in situ oligonucleotide synthesis

Ink-jet microarrays from Agilent

25-60-mers “printed directly on glass slides

Flexible, rapid, but expensive

Experiment process

Collect tissue Isolate RNA Isolate m RNA Make labeled DNA copy Apply DNA Scan microarray Analyze data

Sample preparation and labeling Isolate a total RNA containing mRNA

that ideally represents a quantitative copy of genes expressed at the time of sample collection .

Preparation of cDNA from mRNA using a reverse-transcriptase enzyme .

Short primer is required to initiate cDNA synthesis.

Each cDNA (sample & control ) is labelled with fluorescent cyanine dyes (i.e cy3 &cy5)

Cell A Cell B

Hybridizaton to chip

Labeled cDNA from gene X

Spot of gene X with complementary sequence of colored cDNA This spot shows red color after scanning.

Idea of Microarray

Spotted 2-Channel Array

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Spotted arrays are printed on coated microscope slides.

2 RNA samples are converted to cDNA. Each is labelled with a different dye.

Basic Steps to Microarray: Incubation with the mixed cDNA and

the chip DNA will yield some pairing. Wash off unbound cDNA to see what

has bound to the microarray.

Visualizing Bound cDNA:

The slide with the microarray chip is placed inside a dark box where it is scanned with a high resolution laser that detects the bound fluorescent labels. The information and images are then

sent to the computer for analysis.

Analyzing the Data: Creates a ratio

image. Green images

signal expression in one condition.

Red images signal expression in one condition.

Yellow images signal expression in both conditions.

Capacities:

Not limited to human genetic material. Can be used for all species.

Can display thousands of different genes.

Allows the study of multiple genes at once.

This machine can make 48 microarrays simultaneously.

DNA (nucleotide sequences) databases They are big databases and searching either one

should produce Similar results because they exchange information

routinely.

Gene Bank (NCBI): http://www.ncbi.nlm.nih.gov

Ensembl: http://useast.ensembl.org/index.html

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DDBJ (DNA DataBase of Japan): http://www.ddbj.nig.ac.jp

TIGR: http://tigr.org/tdb/tgi

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Translated databases:TREMBL (translated EMBL):

includes entries that have not been annotated yet into Swiss-

Prot. http://www.ebi.ac.uk/trembl/access.h

tml

Most widely used sites for sequence analysis

Sites for DNA to Protein Translation: These algorithms can translate DNA

sequences in any of the 3 forward or three reverse sense frames.Translate (http://au.expasy.org/tools/dna.html)Translate a DNA sequence: (http://www.vivo.colostate.edu/molkit/translate/index.html)Translation sequence (http://www.ebi.ac.uk/emboss/transeq)

Most widely used sites for sequence analysis

Sites for alignment of 2 sequences: T-COFFEE (http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi): more accurate than ClustalW for sequences with less than 30% identity.ClustalW (http://www.ch.embnet.org/software/ClustalW.html; http://align.genome.jp)bl2sequ (http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi)LALIGN (http://www.ch.embnet.org/software/LALIGN_form.html)MultiALIGN (http://prodes.toulouse.inra.fr/multalin/multalin.html)

BioEdit :A sequence editing software package

http://www.mbio.ncsu.edu/bioedit/bioedit.html

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IDT: http://www.idtdna.com/scitools/scitools.aspxPrimhttp://frodo.wi.mit.edu/primer3/ or directly on NCBI

References: Strachan, Tom; Read, Andrew. Human Molecular

Genetics 3. pp 175-178. New York. Garland Publishing. 2004.

Campbell,A. Malcom. Microarray Animation. Davidson College. 2001. www.bio.davidson.edu/courses/genomics/chip/chip.html

http://cmgm.stanford.edu http://www.gene-chips.com/