Transcript proteomicsx - 123SeminarsOnly.com

AIN US SABA
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BASIC PRINCIPLE OF ALL OMICs
GENOMICS
TRANSCRIPTOMICS
PROTEOMICS
METABLOMICS
APPLICATIONS
CONCLUSION
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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
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aim of this genetic
◦ pathway
◦ functional information analysis response to the entire
genome's networks
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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
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A rough draft of the human genome was completed
by the Human Genome Project in early 2001
GENOMICS
NITROGENOMICS
PERSONAL
GENOMICS
METAGENOMICS
WHOLE GENOME
SEQUENCING
BAC to BAC
Sequencing
Whole Genome
Shotgun Sequencing
BAC to BAC Sequencing
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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.
Shotgun Sequencing
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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.
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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)
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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.
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Theproteome
◦ is the entire complement of proteins
◦ including the modifications made to a particular
set of proteins
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This will vary with
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time
distinct requirements
or stresses, that a cell or organism undergoes.
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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
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Gel
Electrophoresis
◦ Isoelectric point
◦ Molecular weight
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Liquid
Chromatography
Fluorescence
Staining
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Affinity capture
◦ Phosphorylation
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Protein Binding
◦ Receptors
◦ Complexes
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Mass
Spectrometry
◦ Accurate molecular
weight
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develop an antibody which is specific to that
modification.
For glycosylation
lectins
two-dimensional gel electrophoresis“
PROTOMAP which combines
SDS-PAGE with shotgun proteomics
1) Antibodies are adding to the protein mixture
2) Antibodies bind to proteins that have modified
3) Proteins of interest can be separated based on the
modification.
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Protein separation
◦ Molecular weight
(Mw)
◦ Isoelectric point (pI)
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Staining
Birds-eye view of
protein abundance
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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 (highto low-molecular weight, top to bottom)
◦ sequence coverage in the horizontal dimension (N- to Cterminus, left to right).
Sample
+
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Ionizer
MALDI
Electro-Spray
Ionization (ESI)
Mass Analyzer
Time-Of-Flight (TOF)
Quadrapole
Ion-Trap
Detector
Electron
Multiplier
(EM)
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Enzymatic Digest
and
Fractionation
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Liquid Chromatography
Mass
Spectrometry
LC/MS: 1 MS spectrum every 1-2 seconds
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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.
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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
◦ www.hmdb.ca
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over 50,000 metabolites have been characterized
from the plant kingdom
TECHNIQUES
GC
MS
NMR
HPLC
RHPLC
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Toxicology
Nutrition
Medical profiling
Pharmacology
Diagnostics……….
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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.