genomics proteomics metbolomics.pptx

genomics
proteomics
metabolomics

1. Aditya bangalore institute of pharmacy department of pharmacology cellular & molecular pharmacology PRESENTATION ON: GENOMICS, PROTEOMICS, METABOLOMICS PREPARED BY: Rajesh yadav DEPARTMENT OF PHARMACOLOGY

2. A. GENOMICS This term genomics was first introduced in 1986 by Tom Roderick ,a geneticist at the Jackson Laboratory in Maine, during a meeting about mapping of the human genome. Genomics is an area within genetics that concerns the sequencing and analysis of an organism’s genome. The genome is the entire DNA content that is present within one cell of an organism. Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble, and analyze the function and structure of genomes.

3. Genomics including genome projects, genome sequencing, and genomic technologies and novel strategies. The promise of genomics is huge. It could someday help us maximize personal health and discover the best medical care for any condition.

4. Types of Genomics Structural genomics : It is used to determine the 3- dimensional structure of every protein encoded by the genome. It is used in drug discovery and in protein engineering on large scale. Functional genomics : It is the branch of genomics that determine the function of genes and their products. Mutational genomics : It is the field of genomics that characterizes mutation associated genes. In this we basically focuses on genomic, epigenomic and transcript alterations in cancer. Comparative genomics : It is the field of genomic research in which the genomic features of different organisms can be compared. The genomic features may include the DNA sequence, genes gene order regulatory sequences.

5. ROLES OF BIOINFORMATICS IN GENOMIC Genomics is a branch of genetics that studies large scale changes in genomes of organisms. • Bioinformatics is a hybrid field that brings together the knowledge of biology and the knowledge of information science, which is a sub-field of computer science. • Genomics and its subfield of transcriptomics, which studies genome-wide changes in the RNA that is transcribed from DNA, studies many genes are once.

6. Genomics may also involve reading and aligning very long sequences of DNA or RNA. Analysing and interpreting such large-scale, complex data requires the help of computers. The human mind, superb as it is, is incapable of handling this much information.

7. Genomes of organisms are very large. The human genome is estimated to have three billion base pairs that contain about 25,000 genes. For comparison, the fruit fly is estimated to have 165 billion base pairs that contain 13,000 genes. Additionally, a subfield of genomics called transcriptomics studies which genes, among the tens of thousands in an organism, are turned on or off at a given time, across multiple time points, and multiple experimental conditions at each time point. In other words, “omics” data contain vast amounts of information that the human mind cannot grasp without the help of computational methods in bioinformatics.

8. Genome analysis DNA Sequencing Annotation

9. DNA Sequencing DNA sequencing approaches fall into two broad categories,  Shotgun high-throughput  (or  next-generation ) sequencing

10. Shotgun sequencing Shotgun sequencing is a sequencing method designed for analysis of DNA sequences longer than 1000 base pairs, up to and including entire chromosomes. Since this method can only be used for fairly short sequences (100 to 1000 base pairs), longer DNA sequences must be broken into random small segments which are then sequenced to obtain  reads.

11. High-throughput sequencing The high demand for low-cost sequencing has driven the development of high-throughput sequencing technologies that  parallelize  the sequencing process, producing thousands or millions of sequences at once.

12. Annotation Genome annotation is the process of attaching biological information to sequences, and consists of three main steps: identifying portions of the genome that do not code for proteins identifying elements on the genome, a process called gene prediction, and attaching biological information to these elements.

13. APPLICATION OF GENOMICS Genetic epidemiology is the study of the role of genetics factors in determining health and disease in families and in populations, and the interplay of such genetic factors with environmental factors. It is closely allied to both molecular epidemiology and statistical genetics but these overlapping fields each have distinct emphases, societies and journals. This traditional approach has proved highly successful in identifying monogenic disorders and locating the genes responsible. These have led to the discovery of many genetic polymorphisms that influence the risk of developing many common disease.

14. B. Proteomics Proteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. Proteomics is a rapidly growing field of that is concerned with the systematic, high-throughput approach to protein expression analysis of a cell or an organism. Typical results of proteomics studies are inventories of the protein content of differentially expressed proteins across multiple conditions.

15. History of proteomics The first protein studies that can be called proteomics began in 1975 with the introduction of the two-dimensional gel and mapping of the proteins from the bacterium Escherichia coli, guinea pig and mouse. Albeit many proteins could be separated and visualized, they could not be identified. The terms “proteome” and “proteomics” were coined in the early 1990s by Marc Wilkins, a student at Australia's Macquarie University, in order to mirror the terms “genomics” and “genome”, which represent the entire collection of genes in an organism

16. PROTEOME Proteome refers to the total sets of proteins expressed in a given cell at a given time. Detailed analysis of the proteome permits the discovery of new protein markers for diagnostic purposes and of novel molecular targets for drug discovery

17. Methods of studying proteins Protein detection with antibodies (immunoassays) Mass spectrometry and protein profiling

18. Protein detection with antibodies (immunoassays) There are several specific techniques and protocols that use antibodies for protein detection. The enzyme-linked immunosorbent assay (ELISA) has been used for decades to detect and quantitatively measure proteins in samples. The Western blot can be used for detection and quantification of individual proteins, where in an initial step a complex protein mixture is separated using SDS-PAGE and then the protein of interest is identified using an antibody.

19. Mass spectrometry and protein profiling There are two mass spectrometry-based methods currently used for protein profiling. The more established and widespread method uses high resolution, two-dimensional electrophoresis to separate proteins from different samples in parallel, followed by selection and staining of differentially expressed proteins to be identified by mass spectrometry

20. Role of proteomics in Bioinformatics Proteomics is a branch of Bioinformatics that deals with the techniques of molecular biology, biochemistry, and genetics to analyze the structure, function, and interactions of the proteins produced by the genes of a particular cell, tissue, or organism. This technology is being improved continuously and new tactics are being introduced. In the current day and age it is possible to acquire the proteome data. Bioinformatics makes it easier to come up with new algorithms to handle large and heterogeneous data sets to improve the processes.

21. Role of proteomics in drug development Proteins are the principal targets of drug discovery. Most large pharmaceutical companies now have a proteomics-oriented biotech or academic partner or have started their own proteomics division. Common applications of proteomics in the drug industry include target identification and validation, identification of efficacy and toxicity biomarkers from readily accessible biological fluids, and investigations into mechanisms of drug action or toxicity. Proteomics technologies may also help identify protein–protein interactions that influence either the disease state or the proposed therapy.

22. Role of proteomics in diseases diagnosis Proteomics is widely envisioned as playing a significant role in the translation of genomics to clinically useful applications, especially in the areas of diagnostics and prognostics. In the diagnosis and treatment of kidney disease, a major priority is the identification of disease- associated biomarkers. Proteomics, with its high- throughput and unbiased approach to the analysis of variations in protein expression patterns, promises to be the most suitable platform for biomarker discovery.

23. C. metabolomics Metabolomics is the systematic study of the metabolome, the unique biochemical fingerprint of all cellular processes Metabolomics is the large-scale study of small molecules, commonly known as metabolites, within cells, biofluids, tissues or organisms. Collectively, these small molecules and their interactions within a biological system are known as the metabolome

24. Small molecules (metabolites) These are the chemical compounds that are vigorously found inside the cell. A small molecule (or metabolite) is a low molecular weight organic compound, typically involved in a biological process as a substrate or product. Metabolomics usually studies small molecules within a mass range of 50 – 1500 daltons (Da). Some examples of small molecules include: sugars, lipids, amino acids, fatty acids, phenolic compounds, alkaloids etc.

25. metabolome The metabolome is the complete set of metabolites within a cell, tissue or biological sample at any given time point. The metabolome is inherently very dynamic: small molecules are continuously absorbed, synthesised, degraded and interact with other molecules, both within and between biological systems, and with the environment. Many reactions take place continuously within cells, so concentrations of metabolites are considered to be very dynamic, and may change rapidly from one time point to the next.

26. Metabolic reactions Metabolic pathways are essentially a series of chemical reactions, catalyzed by enzymes, whereby the product of one reaction becomes the substrate for the next reaction. These reactions can be divided into anabolic and catabolic.

27. Use of metabolomics We benefit from metabolomics on various levels: from product and stress testing in food industries, e.g. control of pesticides and identification of potentially harmful bacterial strains to research in agriculture (crop protection and engineering) medical diagnostics in healthcare future applications in personalized medicine resulting in personliased treatment strategies

28. Analytical technologies Separation methods Gas chromatography High performance liquid chromatography Capillary electrophoresis Detection methods Mass spectrometry (MS) is used to identify and to quantify metabolites after optional separation by GC, HPLC (LC-MS), or CE. 

29. Some applications of metabolomics Toxicology Functional genomics Nutrigenomics Health and medical Environmental metabolomics Biomarker discovery Personalised medicine Agricultural

30. Toxicology Metabolic profiling of the urine or blood could be utilized for the assessment of toxicity. Several techniques are able to detect physiological changes in the physiological sample that result from the presence of a toxin or toxins. The information that is revealed by way of metabolic profiling can also be related to a specific health condition or syndrome, such as a lesion in the liver or kidney.

31. Nutrigenomics Nutrigenomics combines the knowledge obtained from genomics, transcriptomics, proteomics and metabolomics with nutritional principles for humans. A metabolome of any body fluid depends on various endogenous factors including the individual’s age, gender, body composition, genetic susceptibilities, and concurrent health conditions, as well as exogenous factors such as nutrients, other components of food and medications. Metabolomics can be applied in nutrigenomics to determine the metabolic fingerprint of an individual, which portrays the effect of the endogenous and exogenous factors in the body on the metabolism of the individual.

32. Health and medical Metabolomics also promises to help advance the current understanding, diagnosis and treatment of several health conditions, such as endocrine diseases and cancer. The field can help to identify the pathophysiological processes of disease and mechanisms that can be targeted to manage the disease. For example, metabolomics biomarkers in tissue samples or biopsies can be used to categorize and stage the progression of cancers. The information can then be used to guide the appropriate decisions for treatment.

33. Environmental metabolomics Metabolomics can also be applied to characterize the ways in which an organism interacts with its environment. Studying these environmental interactions and assessing the function and health of an organism at a molecule level can reveal useful information about the effect of environment on an organism’s health. This can also be applied to a wider population to provide data for other fields of research, such as ecology.

34. Biomarker discovery Biomarker discovery is another area where metabolomics informs decision making. Biomarkers are "objective indications of medical state observed from outside the patient - which can be measured accurately and reproducibly" In metabolomics, biomarkers are  small molecules  (metabolites) that can be used to distinguish two groups of samples, typically a disease and control group. For example, a metabolite reliably present in disease samples, but not in healthy individuals would be classed as a biomarker. Samples of urine, saliva, bile, or seminal fluid contain highly informative metabolites, and can be readily analysed through metabolomics fingerprinting or profiling, for the purpose of biomarker discovery.

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