Dina El-Khishin (Ph.D.)

Deputy director of AGERI &

Head of the Genomics, Proteomics&

Bioinformatics Research Facility

Agricultural Genetic Engineering Research Institute (AGERI)

Giza

EGYPT

Genomics is the molecular

characterization of whole

genomes.

Genomics is the molecular

characterization of whole

genomes.

GGenomics Integrates Five enomics Integrates Five Traditional Areas of GeneticsTraditional Areas of Genetics

MENDELIAN MENDELIAN GENETICSGENETICS CytogeneticsCytogenetics Molecular Molecular

GeneticsGenetics

Population Population GeneticsGenetics

Quantitative Quantitative GeneticsGenetics

GENOMICSGENOMICS

DNA DNA Sequence Sequence AnalysisAnalysisSSequence equence AssemblyAssemblySSequence equence AlignmentAlignmentSSequence equence ComparisonComparison

Classical Classical GenomicsGenomics

GGenetic Markersenetic MarkersLLinkage Analysisinkage AnalysisGGene Orderingene OrderingMMultipoint ultipoint AnalysisAnalysisGGenetic Mappingenetic MappingQQTL MappingTL Mapping

Genome Genome InformaticsInformatics

DData bases ata bases

SSequence equence ComparisonComparisonDData ata CommunicationCommunication

AAutomationutomation

• Typed in 10-pitch font, one human sequence would stretch for more than 5,000 miles.

One Human Sequence

• Biologically encoded, it fits easily within a single cell.

• Digitally formatted, it could be stored on one CD-ROM.

GENOMICSGENOMICS

COMPARATIVECOMPARATIVEGENOMICSGENOMICS

STRUCTURALSTRUCTURALGENOMICSGENOMICS

FUNCTIONALFUNCTIONALGENOMICSGENOMICS

Characterizes the physical nature of whole genomes.

Includes the genetic mapping, physical mapping and sequencing of entire genomes.

STRUCTURAL GENOMICS

Overview of the general approaches of structural

genomics

Overview of the general approaches of structural

genomics

Sequence organization.

Assigning loci to specific chromosomes.

High-resolution chromosome maps.

Physical mapping of genomes.

Genome sequencing.

Using genome maps in genetic analysis.

Sequence organization.

Assigning loci to specific chromosomes.

High-resolution chromosome maps.

Physical mapping of genomes.

Genome sequencing.

Using genome maps in genetic analysis.

STRUCTURAL GENOMICSSTRUCTURAL GENOMICS

Complete Published Genome Projects

Feb., 2007

Archaeal 35Bacterial 421Eukaryal 47Organelle 1089Phage 346Plasmid 480Viroid 39Virus 1260

Comparative Genomics

Meaning information gained in one organism can have applications in other even distantly related organisms.

Circle of genes Syntenic relationships

The genomes of several grasses arranged so that regions carrying similar genes are aligned

Functional Genomics

Attempts to understand the broad sweep of genome function at different developmental stages and under different environmental conditions using different techniques.

stuvwxyzattemptsmnopqrstoasdhfjfunderstandabcdethentdfbroadbcdelsweepfghijklofghjfgenomeijklmnsdtyjtfunctioncdefghatasrtdifferentijklmndevelopmentalijklmnstagesijklmanddefgunderdefgdifferentopqrsdikjjldenvironmentaldefgconditionsghijklmnopqrstusingfhgjgjkldifferentopqrstuvwxyztechniquescvbfffmdkgjgdlldm

Which genes are turned off then on ?

TGT AAT AGT TAT ATT TTCATT ATA AAT TGT GTT TGT AGA CAT CAT AAA TTT AAAACA TGG CTT TTT AAC CTGATA AAT CCT ACG AAT ATTTGT AAT AGT TAT GTT ATTGCA GTA AGT ACC GTT TGT ATT ATA AAT TGT GTT CTG

TGT AAT AGT TAT ATT TTCATT ATA AAT TGT GTT TGT AGA CAT CAT AAA TTT AAAACA TGG CTT TTT AAC CTGATA AAT CCT ACG AAT ATTTGT AAT AGT TAT GTT ATTGCA GTA AGT ACC GTT TGT ATT ATA AAT TGT GTT CTG

Young Moo Lee, 2000

IIn ORF analysis, genomic DNA n ORF analysis, genomic DNA sequence is fed into a computer, and sequence is fed into a computer, and analyzed for function by searching the analyzed for function by searching the data bases, looking for full or partial data bases, looking for full or partial homology to known genes homology to known genes characterized in other organisms.characterized in other organisms.

CCharacterization of the proteome haracterization of the proteome by ORF analysisby ORF analysis

OORF function can be RF function can be investigated by knocking out investigated by knocking out the gene by in vitro the gene by in vitro mutagenesis, and looking for mutagenesis, and looking for possible mutant phenotypes possible mutant phenotypes that may provide a clue about that may provide a clue about the function.the function.

GGene disruption (Knockouts)ene disruption (Knockouts)

AA mutant allele of a gene can often mutant allele of a gene can often be suppressed or modified by a be suppressed or modified by a range of mutations in other genes.range of mutations in other genes.

EElucidation of such patterns of lucidation of such patterns of suppression and epistasis generates suppression and epistasis generates networks of interacting proteins.networks of interacting proteins.

SStudy of gene interactions by tudy of gene interactions by Suppressor analysisSuppressor analysis

SStudy of gene interactions tudy of gene interactions by Yeast Twoby Yeast Two--Hybrid Hybrid

systemsystem

TThe basis for this test is the he basis for this test is the yeast GAL4 transcriptional yeast GAL4 transcriptional activator.activator.

Yeast twoYeast two--hybrid system for detecting gene hybrid system for detecting gene interaction. The system uses the binding of two interaction. The system uses the binding of two proteins under test to restore the function of the proteins under test to restore the function of the GAL4 protein which activates a reporter gene.GAL4 protein which activates a reporter gene.

A Genetic markerRepresents variation at a particular site on the genome which is heritable, easy to assay and can be followed over generations.

Types of genetic markers:

Morphological

Biochemical

Molecular

Morphological markers

Biochemical Markers

a. Isozymes

b. Protein Banding Pattern

Molecular Markers

Reflect heritable differences in homologous DNA sequences among individuals.

They may be due to:

-Base pair changes.

-Rearrangements (translocation or inversion).

-Insertions or deletions.

A wide array of different molecular techniques are used to detect polymorphism at the DNA level.

Most Molecular Markers fall into 3 basic categories:

-Hybridization-based (non-PCR) techniques

-Arbitrarily-primed PCR techniques

-Sequence targeted and single locus PCR

Hybridization based (non-PCR) techniques

Restriction Fragment Length Polymorphism (RFLP) analysis.

Botstein et al. (1980)

BDNA Isolation

Restriction

A

C

B

A

CHybridization-based fingerprinting

1-

2-

3- Agarose

RFLP technology II

-

+A B C Hybridization with

labelled probe

A B C

5-

4- Transfer to membrane

6- Wash

7- Autoradiography

(A)(A)(B)(B)

RFLP analysis(A) Polymorphism revealed by different probe/enzyme combinations in three varieties.

(B) Polymorphism among 13 different accessions.

RFLP analysis is used for genetic analyses where the number of samples is moderately low (<300-400).

Strengths•All alleles are seen simultaneously.•The DNA polymorphisms act as codominant genetic markers.•No prior information on DNA sequence is needed.•Relatively simple technique.•Easily reproducible.

Weaknesses•Has relatively low throughput•High labor and materials costs. •Requires relatively large amounts of high quality DNA•Gel based and thus not easily automatable.

Arbitrarily-primed PCR techniques

Development of PCR removed the necessity for probe hybridization steps.

A common feature of these techniques is the lack of requirement for sequence information from the genome under investigation.

The range of different approaches in this category differ in the length and sequence of the primers used, the stringency of the PCR conditions and the method of fragment separation and detection.

This includes:

1- Random Amplified Polymorphic DNA (RAPD) analysis in which the amplification products are separated on agarose gels in the presence of ethidium bromide and visualized under ultraviolet light.

2- Arbitrarily Primed PCR (AP-PCR).

3- DNA Amplification Fingerprinting (DAF) in which the products are separated on polyacrylamide gels.

RAPD technology

AB

C

Arbitrary Primers

Thermostable Polymerase

Nucleotides & Buffers

I

Thermocycling

Williams et al. (1990)&

Welsh and Mcllelland (1990)

Electrophoresis

A B C

RAPD technology II

RAPD technology III

-520 bp

-360 bp

-260 bp

-

+ B CA

RAPD analysis

M 2 3 4 5 6 7 8 9 10 11 12 13 14 15

Strengths•Non-radioactive detection•No prior DNA sequence information •Universal primers work in any genome•Very small amounts of genomic DNA •Experimental simplicity•No need for expensive equipment•Automation

Weaknesses•Reproducibility of RAPD profiles. •Dominant markers •Underestimation of genetic distances

In a second subgroup, primers used are semi-arbitrary in that they are based upon restriction enzyme sites or sequences interspersed in the genome such as repetitive elements, transposable elementsand microsatellites.

1-Selective Restriction FragmentAmplification (SRFA).

2-Amplified Fragment Length Polymorphism (AFLP).

AFLP Analysis

AAmplified mplified FFragment ragment LLength ength PPolymorphismolymorphism

An arbitrarily amplified DNA technique that uses ligation of adapters to the ends of restricted DNA and amplification with hemi-specific primers.

Amplification products are generally visualized by polyacrylamide gel electrophoresis, and silver staining.

AFLP Analysis Vos et al., 1995

1- genomic DNA2- RestrictionA

C

B

5- Selective amplification

3-Adapter ligation- -- --- ---- ----- - - - -- ---- -- -- - -- -- -- -- -- --- ---------- ---- -- -- ---- --- ------ ---

4- Preamplification-- --- - - -- - -- ---- -- - -- - ---- -- -- - --

AFLP ProcessGenomic DNA is digested with a frequent and a rare cutting enzyme (Mse1 and EcoR1).

Mse1 adapter

EcoR1 adapterSpecific adapters to restriction sites are then ligated to generate fragments.

Three types of restriction fragments:

EcoR1 cuts at both ends.

EcoR1 cut at one end, Mse1 cut at the other end.

Mse1 cuts at both ends.

Mse1 cut EcoR1 cut

PCR

+1 Selective primers(EcoR1 adapter + selective base A)(Mse1 adapter + selective base C)

Preselective amplification step achieves a 16-fold reduction of the complexity of the restriction-ligation products.

AC

C

A

+2 selective primers(EcoR1 adapter + selective base AC)(Mse1 adapter + selective base CA)

PCRselective amplification step reduces the complexity of the PCR product mixture by 256 fold.

A C

C A

A C

C A

The +2 products are then run on denaturing polyacrylamide gels and DNA fingerprints are visualized by silver staining.

analyses of gene expression from 2 to 10 weeks after emergenceanalyses of gene expression from 2 to 10 weeks after emergencecDNAcDNA--AFLPAFLP

EcoRIEcoRI+AAG +AAG MseIMseI+GG+GG

22 33 44 55 66 77 88 99 1010 2 3 4 5 6 7 8 9 10

offoff

onon

1,55

8 po

lymor

phic f

ragm

ents

AFLP analysis, using different primer combinations.

Strengths

•PCR-based

•Requires minimal amounts of DNA

•Automatable

•Robust, Reliable & reproducible

•No prior sequence knowledge

•High marker density

Sequence targeted and single locus PCR

A series of very short (2-10), tandemly arranged, highly variable DNA sequences dispersed throughout the genome.

If SSR loci are cloned and sequenced, primers to the flanking regions can be designed to produce a sequence-tagged microsatellite site (STMS), or SSR marker.

SSRs are highly attractive markers because each primer pair (typically) identifies a single locus.

SSR loci may have many alleles because of their high mutability.

Minisatellites are generally very difficult to clone by virtue of their size but if they can be isolated with sufficient flanking sequence for primer design, they provide single locus markers similar to STMS.

(1-10 bp) microsatellite

(10-60 bp)minisatellite

(100-300 bp)satellite

I Length

Senior et al. 1998

tandem arrays(head - to - tail)

II Distribution

interspersed

repetitive unit

SSR analysis in 20 different lines.

M 1 2 3 4 5 6 7 8 9 10 11 12 1314 15 16 171819 20 M

Strengths

•Highly abundant & evenly distributed in the genome

•Highly polymorphic

•Codominant

•Rapidly typed

•Easy to automate

Weaknesses

•Prior sequence Knowledge

•Difficult & time consuming

Differential Expression

• Yields fragments of expressed genes for analysis• Reverse transcribe mRNA• Restriction digest• Add adapters• PCR subsets of genes using PCR primers similar

to AFLP• Separate gene fragments• Silver stain

ATG TAAA

ATG

ATG

CAAA

GAAA

ATG TAAA

ATG

ATG

CAAA

GAAA

ATG TAAA

ATG

ATG

CAAA

GAAA

Salt Treatment After 1h

Control

Salt Treatment After 10h

Rt-PCR

Rt-PCR

A C G

A C G

Rt-PCR

A C G

PCR

PCR

A C G

A C G

PCR

A C G

A C GC T C T G T

A C GC T C T G T

DNA Extraction& Seq.

ATGCGTCGACVTGCGTACGTGGGGCTTACCAAAA……………….

ATGCGTCGACVTGCGTACGTGGGGCTTACCAAAA……………….

Blast Against Gene Bank

DD-Gels showing the differentially displayed bandsDD-Gels showing the differentially displayed bands

Score E Sequences producing significant alignments: (bits) Valuegi|37497095|dbj|AP004790.2| Oryza sativa (japonica cultivar... 252 2e-64 gi|10130005|gb|AF223412.1|AF223412 Zea mays kinesin-like ca... 46 0.025gi|27905022|gb|AC128674.3| Homo sapiens BAC clone RP11-1390... 40 1.5 gi|4826471|emb|AL022240.8|HS328E19 Human DNA sequence from ... 40 1.5 gi|25809666|emb|AL954711.3| Human DNA sequence from clone R... 40 1.5gi|27228812|gb|AC112187.2| Homo sapiens chromosome 5 clone ... 40 1.5gi|33636254|emb|BX546487.5| Human DNA sequence from clone R... 40 1.5gi|24158580|gb|AC127384.4| Homo sapiens BAC clone RP11-1390... 40 1.5 gi|30962461|emb|AL451058.16| Human DNA sequence from clone ... 40 1.5 gi|30230949|emb|BX248398.9| Human DNA sequence from clone R... 40 1.5 gi|18614049|emb|AL592492.10| Human DNA sequence from clone ... 40 1.5 gi|21738486|emb|AL671858.6| Mouse DNA sequence from clone R... 40 1.5gi|38175833|gb|AC079218.5| Mus musculus chromosome 6 clone ... 38 6.0gi|34419749|gb|AC146104.3| Pan troglodytes BAC clone RP43-2... 38 6.0gi|31746709|gb|AC145217.1| Homo sapiens BAC clone RP11-527C... 38 6.0 gi|14596392|emb|AL589963.7| Human DNA sequence from clone R... 38 6.0gi|34327996|dbj|AP004566.2| Oryza sativa (japonica cultivar... 38 6.0gi|17736863|dbj|AP004496.1| Lotus corniculatus var. japonic... 38 6.0 gi|7417381|gb|AF245226.1|AF245226 Homo sapiens chromosome 2... 38 6.0gi|7768666|dbj|AP001674.1| Homo sapiens genomic DNA, chromo... 38 6.0 gi|7362968|emb|AL121826.11|HS1010E17 Human DNA sequence fro... 38 6.0 gi|7262576|dbj|AP001345.2| Homo sapiens genomic DNA, chromo... 38 6.0

Score E Sequences producing significant alignments: (bits) Valuegi|37497095|dbj|AP004790.2| Oryza sativa (japonica cultivar... 252 2e-64 gi|10130005|gb|AF223412.1|AF223412 Zea mays kinesin-like ca... 46 0.025gi|27905022|gb|AC128674.3| Homo sapiens BAC clone RP11-1390... 40 1.5 gi|4826471|emb|AL022240.8|HS328E19 Human DNA sequence from ... 40 1.5 gi|25809666|emb|AL954711.3| Human DNA sequence from clone R... 40 1.5gi|27228812|gb|AC112187.2| Homo sapiens chromosome 5 clone ... 40 1.5gi|33636254|emb|BX546487.5| Human DNA sequence from clone R... 40 1.5gi|24158580|gb|AC127384.4| Homo sapiens BAC clone RP11-1390... 40 1.5 gi|30962461|emb|AL451058.16| Human DNA sequence from clone ... 40 1.5 gi|30230949|emb|BX248398.9| Human DNA sequence from clone R... 40 1.5 gi|18614049|emb|AL592492.10| Human DNA sequence from clone ... 40 1.5 gi|21738486|emb|AL671858.6| Mouse DNA sequence from clone R... 40 1.5gi|38175833|gb|AC079218.5| Mus musculus chromosome 6 clone ... 38 6.0gi|34419749|gb|AC146104.3| Pan troglodytes BAC clone RP43-2... 38 6.0gi|31746709|gb|AC145217.1| Homo sapiens BAC clone RP11-527C... 38 6.0 gi|14596392|emb|AL589963.7| Human DNA sequence from clone R... 38 6.0gi|34327996|dbj|AP004566.2| Oryza sativa (japonica cultivar... 38 6.0gi|17736863|dbj|AP004496.1| Lotus corniculatus var. japonic... 38 6.0 gi|7417381|gb|AF245226.1|AF245226 Homo sapiens chromosome 2... 38 6.0gi|7768666|dbj|AP001674.1| Homo sapiens genomic DNA, chromo... 38 6.0 gi|7362968|emb|AL121826.11|HS1010E17 Human DNA sequence fro... 38 6.0 gi|7262576|dbj|AP001345.2| Homo sapiens genomic DNA, chromo... 38 6.0

CCGAAGATATCATGATTGTCATGCAGCGATGCCGCTACCTAACTTTATCTTTTATGCACCTAAACTGGCATGCCTAACATGACAAACACATAGTATAACCTATNGNATGTGAGATGCATATTAGACCACTGAAATTCTCCAAGAAAAGGGCCTNNCCTACCCTCATTGGATAGTTAGTATCAGCAAATTGTCTAGNATTCCAAAAAAAAGCAGCTTAA

CCGAAGATATCATGATTGTCATGCAGCGATGCCGCTACCTAACTTTATCTTTTATGCACCTAAACTGGCATGCCTAACATGACAAACACATAGTATAACCTATNGNATGTGAGATGCATATTAGACCACTGAAATTCTCCAAGAAAAGGGCCTNNCCTACCCTCATTGGATAGTTAGTATCAGCAAATTGTCTAGNATTCCAAAAAAAAGCAGCTTAA

Sequences from DD or cDNA-AFLP

C lo n e S iz e b p T is s u e H o u r sA f te rI n o c .

S im i la r T o

B 5 .3 4 2 3 r o o t 6 p e r o x ida s e

A 5 .3 4 8 5 r o o t 6 A T Ps y n th a s e

B 3 .2 4 6 3 r o o t 6 N A D H -u b iq u in -o x id o -r e d u c ta s

DATA ANALYSIS

765432000110011000111101100111111111011000111111100111111111000111111111

Scoring of bands

653742١٠٠2

١٠٠94.14١٠٠87.593.37

١٠٠80.094.187.53١٠٠53.371.462.566.75

١٠٠92.357.161.553.357.16

Genetic Similarity matrix calculated according to Jaccard’s coefficient based

on marker data.

0.50

0.70

0.80

0.90

1.00

2

3

4

55

6

7

Dendrogram constructed with UPGMA cluster analysis of marker data showing the genetic relationships among the different samples.

DDNA chips are revolutionizing genetics NA chips are revolutionizing genetics in the same way that silicone chips in the same way that silicone chips revolutionized the computer industry.revolutionized the computer industry.

DDNA chips are samples of DNA laid NA chips are samples of DNA laid out in regimented arrays bound to a out in regimented arrays bound to a glass glass ““chipchip”” the size of a microscope the size of a microscope cover slip.cover slip.

SStudy of developmental tudy of developmental regulation by using DNA chipsregulation by using DNA chips

•The array, which contains immobilized nucleic acid sequences, or “targets”

Key concepts of Microarray systems

•A detection system that quantitates the hybridization signal

•One or more labelled samples or “probes”, that are hybridized with the microarray

Overview of Microarray Process

0

100000

200000

300000

400000

500000

600000

700000

800000

900000

1000000

0 100000 200000 300000 400000 500000 600000 700000 800000 900000 1000000

Target Preparation& Deposition

Probe Preparation & Hybridization

Scanning & Data Analysis

Array Array

ScannerScanner

Array SpotterArray Spotter

ID

Target preparation

TEST (Altered) CELLCONTROL (Normal) CELL

Labelled target

from RNA

Probe Preparation & Hybridization

Cy3Cy3

Cy3

Cy3

Cy3

Cy5Cy5

Cy5

Cy5

Cy5

HybridizeHybridize

Gene 3

Probe printedonto slide

Gene 1 Gene 2 Gene 4 Gene 5

TEST (Altered) CELLCONTROL (Normal) CELL

Cyanine3

Cyanine5 Gene

GREEN, Control DNA where either DNA or cDNA derived from normal tissue is hybridized to the target DNA.

RED, Sample DNA where either DNA or cDNA is derived from diseased tissue hybridized to the target DNA.

YELLOW, a combination of Control and Sample DNA where both hybridized equally to the target DNA.

BLACK, areas where neither the Control nor Sample DNA hybridized to the target DNA

NoDifference

Higher expressionin control

Higher expressionin test

NoDifference

NoDifference

Gene 1 Gene 2 Gene 3 Gene 4 Gene 5

Slide Scanned

Spot intensitiesanalysed

TEST (Altered) CELLCONTROL (Normal) CELLLabelled target Cy3

Cy3

Cy3

Cy3

Cy3

Cy5Cy5

Cy5

Cy5

Cy5

Probe printedonto slide

Hybridize

Gene 1 Gene 2 Gene 3 Gene 4 Gene 5

Microarraysubstrates

Filled spottingplates

Microarrayspotting

Rawspottedmicroarrays

Blockingkit

Washkit

Attach/block / wash/

dry

Finishedspottedmicroarrays

Treated source “A”

RNAextraction

Purified extraction

“A”

Probelabeling

Fluorophore kit “A”

Labeled probe “A”

Hybridize& wash

Hybridizationwash kit

Hybridizationbuffer kit

Scanning Images

ImageQuantification

Quantitated Data

Labeling kit

Spottingplate prep.

Spottingbuffer kit

Purified PCR products

PCR &purify genes

Target genes,on plasmids inbacteria colony

PCR kit

DNApurificationkit

Audit /query exp.variables

Datamining,

visualization

RNA isolation kit

RNA purification kit

PCR plates

Spotting plates

Gelelectro-

phoresis

QC’ed PCR products

Gelelectrophoresiskit

RNAextraction

Purified extraction

“B”

Probelabeling

Fluorophore kit “B”

Labeled probe “B”

Labeling kit

RNA isolation kit

RNA purification kit

Hybridizedmicroarray

Treated source “B”

Treatment“A”

Tissue or cell line “A”

Treatment“B”

Tissue or cell line “B”

QC Stain QC ScanQC Quant

Stainedmicroarrays

Stainingkit QC Images

QC’edMicroarrays

QC Quant Data

The Gene Expression Microarray

Process

GENE EXPRESSION: A COMPLEX PROCESS………...

SOMEDNA Microarray Applications

SOMEDNA Microarray Applications

• Quantitative Gene Expression• Mutation detection • Genotyping / Mapping• Library screening prior to DNA sequencing • Disease Profiling• Patient monitoring• Others to come!

• Quantitative Gene Expression• Mutation detection • Genotyping / Mapping• Library screening prior to DNA sequencing • Disease Profiling• Patient monitoring• Others to come!

Bioinformatics of microarrays

• 20,000 genes x 10 time points x 3 replications x 2 probes =– 1,200,000 data points per experiment

• Merge with EST database• Quantification software• Biodiscovery software• Using Oracle software

– share relational data through laboratories– built in Web capabilities

cDNA library

Prep Plasmids PCR inserts Print microarrayChip reader

Identify interesting clonesfor sequencing and analysis

DNA sequence

Computer DatabaseSearch

Store sequencesIdentify homologues

Computer analysisGene expression patterns

Store array

Microarray Analysis

ConstructcDNA library

array

Sample 2Sample 1

Hybridize

Relational Database Design

• Data storage is a critical and often underestimated step

• Two main types, repositories and local databases

• Microarray database design should incorporate MIAME and MAGE-ML www.mged.org/index.html

• Serve as an analysis tool

SGMD – ER diagram

FFunctional genomics, will lead unctional genomics, will lead to development of a robust to development of a robust genetic engineering discipline genetic engineering discipline in which rational changes can in which rational changes can be designed and modeled.be designed and modeled.

Omics would provide answers to some Omics would provide answers to some of the basic questions of biology like:of the basic questions of biology like:

WWhy is an organism the way it is and hy is an organism the way it is and different from other organismsdifferent from other organisms??

HHow were genomes assembled through ow were genomes assembled through the processes of evolutionthe processes of evolution??

AAre the precise positions of genes re the precise positions of genes on chromosomes unimportanton chromosomes unimportant?? Or Or must genes be in specific locations must genes be in specific locations to ensure proper functionto ensure proper function??

WWhat are the numbers and types hat are the numbers and types of genes needed to specify an of genes needed to specify an individual species and how do they individual species and how do they differ between taxadiffer between taxa??

The ultimate goal of Omicsresearch is to find all the genes

in the DNA sequence and to develop tools for using this

information in serving mankind.

NOT ONLY GENOMICS…

METABOLOMICSPATHOGENOMICS

PHARMACOGENOMICS

OPEROMICS

PHENOMICSTRANSCRIPTOMICS

PROTEOMICS

GENOMICS

COMPARATIVEGENOMICS

STRUCTURALGENOMICS

FUNCTIONALGENOMICS

……OMICS

Thanks

DNA SEQUENCERMICROARRAY SPOTTERQ-PIX COLONIES PICKING SYSTEM392 ABI DNA SYNTHESIZER1- D GEL ELECTROPHORESIS SYSTEM2-D GEL ELECTROPHORESIS SYSTEM

MULTI PROBE ROBOT

UPGRADE OF FACILITIESGenomics & Proteomics

Facility

The Genomics, Proteomics & Bioinformatics facility at AGERI provides the following services.

•DNA oligonucleotide synthesis• DNA sequencing• DNA Fingerprinting• GMO testing• 2D gel electrophoresis• SDS-PAGE• PCR• Real-time PCR• Colony picking and gridding• Microarray printing• Laser scanning for fluorescent labelled DNA and Protein• Spot picking from 2D gels• Primer design (DNA Star)• Cloning and Vectors design (NT Suite)• Genome assembly (Sequencher)• Diversity database fingerprinting software• Genes cloning and proteins expression•Analyzing microarray, AFLP, SSR and RAPD experiments.

This presentation has been combined from personal, colleagues and web based presentations.