Geomics proteomics

applications

1. Application of genomics Identity comparison for new nucleic acid sequences. Analysis of gene expression profile. Database of model organism. Hunting for disease related genes. Analysis of the genes related to drug action. Screening of poisonous side effect genes.

2. Applications of genomics Genomics has provided applications in many fields, including medicine , biotechnology , anthropology and other social sciences .

3. Genomic medicine Next-generation genomic technologies allow clinicians and biomedical researchers to drastically increase the amount of genomic data collected on large study populations . When combined with new informatics approaches that integrate many kinds of data with genomic data in disease research, this allows researchers to better understand the genetic bases of drug response and disease.

4. Synthetic biology and bioengineering The growth of genomic knowledge has enabled increasingly sophisticated applications of synthetic biology . In 2010 researchers at the J. Craig Venter Institute announced the creation of a partially synthetic species of bacterium , Mycoplasma laboratorium , derived from the genome of Mycoplasma genitalium .

5. Others… The immediate impact of genomics is being seen on diagnosis; Identifying genetic abnormalities. Identifying victims by their remains Distinguishing between naturally occurring and intentional outbreaks of infections

6. Proteomics The entire protein component of a given organism is called ‘proteome ’ the term coined by Wasinger in 1995 . A proteome is a quantitatively expressed protein of a genome that provides information on the gene products that are translated, amount of products and any post translational modifications . Proteomics is an emerging area of research in the post-genomic era, which involves identifying the structures and functions of all proteins of a proteome. It is sometimes also treated as structural based functional genomics.

7. Application:

8. Biomarker The National Institutes of Health has defined a biomarker as “a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention. For example, proteomics is highly useful in identification of candidate biomarkers (proteins in body fluids that are of value for diagnosis), identification of the bacterial antigens that are targeted by the immune response, and identification of possible immunohistochemistry markers of infectious or neoplastic diseases.

9. Post-Translational Modifications: Proteomics studies involve certain unique features as the ability to analyze post- translational modifications of proteins. These modifications can be phosphorylation, glycosylation and sulphation as well as some other modifications involved in the maintenance of the structure of a protein. These modifications are very important for the activity, solubility and localization of proteins in the cell. Determination of protein modification is much more difficult rather than the identification of proteins. As for identification purpose, only few peptides are required for protease cleavages followed by database alignment of a known sequence of a peptide. But for determination of modification in a protein, much more material is needed as all the peptides do not have the expected molecular mass need to be analyzed further .

10. Continue… For example, during protein phosphorylation events, phosphopeptides are 80 Da heavier than their unmodified counterparts. Therefore, it gives, rise to a specific fragment (PO 3-  mass 79) bind to metal resins, get recognized by specific antibodies and later phosphate group can be removed by phosphatases ( Clauser et al. 1999; Colledge and Scott, 1999). So protein of interest (post-translationally modified protein) can be detected by Western blotting with the help of antibodies or  32 P-labelling that recognize only the active state of molecules. Later, these spots can be identified by mass spectrometry.

11. Importance of PTMs Play a crucial role in generating the heterogeneity in proteins Help in utilizing identical proteins for different cellular functions in different cell types. Regulation of particular protein sequence behaviour in most of the eukaryotic organisms.

12. Interaction proteomics and protein networks Interaction proteomics is the analysis of protein interactions from scales of binary interactions to proteome- or network-wide. Most proteins function via protein–protein interactions , and one goal of interaction proteomics is to identify binary protein interactions , protein complexes , and interactomes .

13. Expression proteomics Expression proteomics includes the analysis of protein expression at larger scale. It helps identify main proteins in a particular sample, and those proteins differentially expressed in related samples—such as diseased vs. healthy tissue. If a protein is found only in a diseased. There are technologies such as 2D-PAGE and mass spectrometry that are used in expression proteomics

14. Proteogenomics In proteogenomics , proteomic technologies such as mass spectrometry are used for improving gene annotations. Parallel analysis of the genome and the proteome facilitates discovery of post-translational modifications and proteolytic events, especially when comparing multiple species (comparative proteogenomics ).

15. Structural proteomics Structural proteomics includes the analysis of protein structures at large-scale. It compares protein structures and helps identify functions of newly discovered genes. The structural analysis also helps to understand that where drugs bind to proteins and also show where proteins interact with each other. This understanding is achieved using different technologies such as X-ray crystallography and NMR spectroscopy

16. Bioinformatics for proteomics (proteome informatics) Protein identification Mass spectrometry and microarray produce peptide fragmentation information but do not give identification of specific proteins present in the original sample UniProt and PROSITE to predict what proteins are in the sample with a degree of certainty. Protein structure The biomolecular structure forms the 3D configuration of the protein . the 3D structure of proteins could only be determined using X-ray crystallography and NMR spectroscopy

17. Protein Expression Profiling: The largest application of proteomics continues to be protein expression profiling. The expression levels of a protein sample could be measured by 2-DE or other novel technique such as isotope coded affinity tag (ICAT). Using these approaches the varying levels of expression of two different protein samples can also be analyzed . This application of proteomics would be helpful in identifying the signaling mechanisms as well as disease specific proteins. With the help of 2-DE several proteins have been identified that are responsible for heart diseases and cancer ( Celis et al. 1999). Proteomics helps in identifying the cancer cells from the non-cancerous cells due to the presence of differentially expressed proteins.

18. In future…