2. TECHNIQUES INVOVED IN PROTEOMICS,GENOMICS,TRANSCRIPTOMICS…….
AIN US SABA 15

3. OUTLINE BASIC PRINCIPLE OF ALL OMICs GENOMICS TRANSCRIPTOMICS
PROTEOMICS
METABLOMICS
APPLICATIONS
CONCLUSION

4. BASIC PRINCIPLE OF OMICS

5. GENOMICS
The actual term 'genomics' is thought to have been coined by Dr. Tom Roderick
Genomics is
study of the genomes of organisms.
determine
the entire DNA sequence of organisms
fine-scale genetic mapping
studies of intragenomic phenomena
aim of this genetic
pathway
functional information analysis response to the entire genome's networks

6. HISTORY
The first genomes to be sequenced, a virus and a mitochondrion, and were done by Fred Sanger.
In 1972, Walter Fiers and his team were the first to determine the gene for Bacteriophage MS2 coat protein.
The first free-living organism to be sequenced was that of Haemophilus influenzae (1.8 Mb) in 1995
As of September 2007, the complete sequence was known of about
1879 viruses
577 bacterial
23 eukaryote
A rough draft of the human genome was completed by the Human Genome Project in early 2001

7. GENOMICS
NITROGENOMICS
PERSONAL GENOMICS
METAGENOMICS

8. WHOLE GENOME SEQUENCING BAC to BAC Sequencing
Whole Genome Shotgun Sequencing

9. Whole genome sequencing
BAC to BAC Sequencing
Shotgun Sequencing
Multiple copies of the genome are randomly shredded into pieces
Each 2,000 and 10,000 bp fragment is inserted into a plasmid
Both the 2,000 and the 10,000 bp plasmid libraries are sequenced.
Computer algorithms assemble the millions of sequenced fragments into a continuous stretch resembling each chromosome.
cutting the chromosomes into large pieces,physical mapping
Several copies of the genome are randomly cut into pieces
Each fragments is inserted into a BAC-a bacterial artificial chromosome.
These pieces are fingerprinted to give each piece a unique identification tag that determines the order of the fragments.
Making M13 library &sequencing
These sequences are fed into PHRAP that looks for common sequences that join two fragments together.

14. Trancriptomics
The transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA produced in one or a population of cells.
Study of transcriptome is called transcriptomics.
Techniques
Expression profiling
DNA microarrays
SAGE(serial analysis of gene expression)

16. PROTEOMICS The term "proteomics“ was first coined in 1997
to make an analogy with genomics
"proteome" is a blend of "protein" and "genome“
coined by Marc Wilkins in 1994
Proteomics is the large-scale study of proteins
 structures 
functions.

17. PROTEOME Theproteome This will vary with
is the entire complement of proteins
 including the modifications made to a particular set of proteins
This will vary with
time
distinct requirements
or stresses, that a cell or organism undergoes.

18. COMPLEXITY OF PROBLEM
proteomics is considered the next step in the study of biological systems.
It is much more complicated than genomics
organism's genome is more or less constant
 proteome differs from cell to cell and from time to time.
done by mRNA analysis,
correlate with protein content
now known that mRNA is not always translated into protein
SO,Proteomics confirms the presence of the protein and provides a direct measure of the quantity present.
PTM

19. Protein Chemistry Assay Techniques
Gel Electrophoresis
Isoelectric point
Molecular weight
Liquid Chromatography
Fluorescence
Staining
Affinity capture
Phosphorylation
Protein Binding
Receptors
Complexes
Mass Spectrometry
Accurate molecular weight

20. TECHNIQUES develop an antibody which is specific to that modification.
For glycosylation lectins 
two-dimensional gel electrophoresis“
 PROTOMAP which combines
 SDS-PAGE with shotgun proteomics

21. AFFINITY CAPTURE Antibodies are adding to the protein mixture
Antibodies bind to proteins that have modified
Proteins of interest can be separated based on the modification.

23. 2D Gel-Electrophoresis
Protein separation
Molecular weight (Mw)
Isoelectric point (pI)
Staining
Birds-eye view of protein abundance

25. PROTOMAP PRotein TOpography and Migration Analysis Platform
Is combination of
SDS-PAGE with shotgun proteomics
is performed by
resolving control and experimental samples in separate lanes of a 1D SDS-PAGE gel
proteins in these bands are sequenced using shotgun proteomics.
Sequence information from all of these bands are bioinformatically integrated into a visual format called a peptograph 
which plots gel-migration in the vertical dimension (high- to low-molecular weight, top to bottom)
sequence coverage in the horizontal dimension (N- to C- terminus, left to right).

27. Mass Spectrometer Ionizer Sample Mass Analyzer Detector MALDI+ _
Mass Analyzer
Detector
MALDI
Electro-Spray Ionization (ESI)
Time-Of-Flight (TOF)
Quadrapole
Ion-Trap
Electron Multiplier (EM)

28. LC/MS for Peptide Abundance
Enzymatic Digest
and
Fractionation

29. LC/MS for Peptide Abundance
Liquid Chromatography
Mass
Spectrometry
LC/MS: 1 MS spectrum every 1-2 seconds

30. The NMR Spectrometer
=>

31. METABLOMICS Newborn cousin to genomics and proteomics
study of chemical processes involving metabolites.
"systematic study of the unique chemical fingerprints that specific cellular processes leave behind
The metabolome
represents the collection of all metabolites in a biological cell, tissue, organ or organism, which are the end products of cellular processes
metabolic profiling can give an instantaneous snapshot of the physiology of that cell.

32. HISTORY In 2005, first metabolite database(called METLIN)
In January 2007, scientists at the University of Alberta and the University of Calgary completed the first draft of the human metabolome.
They catalogued approximately
2500 metabolites,
1200 drugs
3500 food components
This information, available at the Human Metabolome Database
over 50,000 metabolites have been characterized from the plant kingdom

33. TECHNIQUES GC MS
NMR
HPLC
RHPLC

35. APPLICATIONS Toxicology Nutrition Medical profiling Pharmacology
Diagnostics……….

36. CONCLUSION
High-dimensional biology (HDB) refers to the simultaneous study in health and disease
The fundamental premise is that the evolutionary complexity of biological systems renders them difficult to comprehensively understand using only a reductionist approach.
Such complexity can become tractable with the use of "omics" research.
This term refers to the study of entities in aggregate.
The two major advances that have made HDB possible are technological breakthroughs that allow simultaneous examination of thousands of genes, transcripts, and proteins, etc., with high-throughput techniques and analytical tools to extract information.