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AIN US SABA 15
BASIC PRINCIPLE OF ALL OMICs GENOMICS TRANSCRIPTOMICS PROTEOMICS METABLOMICS APPLICATIONS CONCLUSION
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 .
The first free-living organism to be sequenced was that of Haemophilus influenzae (1. The first genomes to be sequenced. and were done by Fred Sanger. a virus and a mitochondrion. In 1972. 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 . Walter Fiers and his team were the first to determine the gene for Bacteriophage MS2 coat protein.8 Mb) in 1995 As of September 2007.
GENOMICS NITROGENOMICS PERSONAL GENOMICS METAGENOMICS .
WHOLE GENOME SEQUENCING BAC to BAC Sequencing Whole Genome Shotgun Sequencing .
Making M13 library &sequencing These sequences are fed into PHRAP that looks for common sequences that join two fragments together.000 bp plasmid libraries are sequenced.000 and 10. .000 and the 10. Computer algorithms assemble the millions of sequenced fragments into a continuous stretch resembling each chromosome. These pieces are fingerprinted to give each piece a unique identification tag that determines the order of the fragments.000 bp fragment is inserted into a plasmid Both the 2. Multiple copies of the genome are randomly shredded into pieces Each 2.physical mapping Several copies of the genome are randomly cut into pieces Each fragments is inserted into a BAC-a bacterial artificial chromosome.BAC to BAC Sequencing Shotgun Sequencing cutting the chromosomes into large pieces.
rRNA. Techniques Expression profiling DNA microarrays SAGE(serial analysis of gene expression) . The transcriptome is the set of all RNA molecules. tRNA. Study of transcriptome is called transcriptomics. and other non-coding RNA produced in one or a population of cells. including mRNA.
. 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.
. that a cell or organism undergoes. Theproteome ◦ 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.
PTM . 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. 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. proteomics is considered the next step in the study of biological systems. done by mRNA analysis.
Gel Electrophoresis ◦ Isoelectric point ◦ Molecular weight Affinity capture ◦ Phosphorylation Protein Binding ◦ Receptors ◦ Complexes Liquid Chromatography Fluorescence Staining Mass Spectrometry ◦ Accurate molecular weight 19 .
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.
Protein separation ◦ Molecular weight (Mw) ◦ Isoelectric point (pI) Staining Birds-eye view of protein abundance 23 .
. ◦ 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. left to right). 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.to Cterminus.
Sample + _ Ionizer MALDI Electro-Spray Ionization (ESI) Mass Analyzer Time-Of-Flight (TOF) Quadrapole Ion-Trap Detector Electron Multiplier (EM) 27 .
Enzymatic Digest and Fractionation 28 .
Liquid Chromatography Mass Spectrometry LC/MS: 1 MS spectrum every 1-2 seconds 29 .
=> 30 .
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. which are the end products of cellular processes ◦ metabolic profiling can give an instantaneous snapshot of the physiology of that cell. organ or organism.
first metabolite database(called METLIN) In January 2007. In 2005. They catalogued approximately ◦ 2500 metabolites.ca This information.000 metabolites have been characterized from the plant kingdom . ◦ 1200 drugs ◦ 3500 food components ◦ www.hmdb. available at the Human Metabolome Database over 50. scientists at the University of Alberta and the University of Calgary completed the first draft of the human metabolome.
TECHNIQUES GC MS NMR HPLC RHPLC .
Toxicology Nutrition Medical profiling Pharmacology Diagnostics………. .
. This term refers to the study of entities in aggregate. 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. . The two major advances that have made HDB possible are technological breakthroughs that allow simultaneous examination of thousands of genes. transcripts. with high-throughput techniques and analytical tools to extract information. Such complexity can become tractable with the use of "omics" research. etc. and proteins.