OMICS tecnology


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OMICS tecnology

  1. 1. Omics Technology Trishita Issar I M.Sc.Foods, Nutrition &Dietetics Roll no. 26 Andhra University
  2. 2. Contents <ul><li>Introduction – </li></ul><ul><li>What is OMICS technology? </li></ul><ul><li>History of Omics </li></ul><ul><li>Omes and Omics </li></ul><ul><li>Types of Omics </li></ul>
  3. 3. <ul><li>Omics related to Nutrition Field </li></ul><ul><ul><li>Nutrigenomics </li></ul></ul><ul><ul><ul><li>Genomics </li></ul></ul></ul><ul><ul><ul><li>Proteomics </li></ul></ul></ul><ul><ul><ul><li>Transcriptomics </li></ul></ul></ul><ul><ul><ul><li>Metabolomics </li></ul></ul></ul><ul><li>Nutrigenomics: the effect of food on genes </li></ul><ul><li>Genetic effects of Food </li></ul><ul><li>Conclusion </li></ul>Contents…..
  4. 4. Introduction <ul><li>The complete sequencing of the human genome has ushered in a new era of systems biology referred to as Omics technology . </li></ul>
  5. 5. <ul><li>The term omics refers to the comprehensive analysis of biological systems . </li></ul><ul><li>Systems biology is “biology” that focuses on complex systems of life. </li></ul>
  6. 6. History of OMICS <ul><li>Modern uses of the term &quot;omics&quot; derive from the term genome (hence genomics), a term invented by Hans Winkler in 1920, although the use of -ome is older, signifying the ‘‘collectivity’’ of a set of things. </li></ul>
  7. 7. <ul><li>The word genomics is said to be appeared in the 1980s and became widely used in the 1990s.  </li></ul><ul><li>The first genome was completely sequenced by Sanger in Cambridge, UK, in the 1970s. Genome is the most fundamental part of many omics. </li></ul>
  8. 8. <ul><li>The suffix “ -om- ” originated as a  back-formation  from “ gen ome”, a word formed in analogy with “chromos ome ”. </li></ul><ul><li>The word “ chromosome” comes from the Greek stems meaning colour and body . </li></ul>
  9. 9. <ul><li>The word GENOMICS implies some hidden network among genetic elements. This network is regulated by many other omics such as proteomics, transcriptomics , metabolomics and physiomics. </li></ul>
  10. 10. Omes & Omics <ul><li>The word  ’omics’  refers to a field of study in biology ending in the suffix  -omics  such as genomics, metabolomics, or proteomics. </li></ul>
  11. 11. <ul><li>The related  ome  addresses the objects of study of such fields, such as the genome, metabolome, or proteome respectively. </li></ul>
  12. 12. Types of OMICS <ul><li>Antibodyome & Antibodyomics </li></ul><ul><li>Bacteriome </li></ul><ul><li>Cardiogenomics </li></ul><ul><li>Cellome & Cellomics </li></ul><ul><li>Diseaseome & Diseaseomics </li></ul><ul><li>Epigenome & Epigenomics </li></ul><ul><li>Foodome &Foodomics </li></ul>
  13. 13. <ul><li>Genome & Genomics </li></ul><ul><li>Glycome & Glycomics </li></ul><ul><li>Healthome & Healthomics </li></ul><ul><li>Herbome  & Herbomics </li></ul><ul><li>Hygienome &Hygienomics </li></ul><ul><li>Immunolome & Immunolomics </li></ul><ul><li>Lipidome & Lipidomics </li></ul><ul><li>Lipoproteome & Lipoproteomics </li></ul>Types of OMICS ….
  14. 14. <ul><li>Metabolome & Metabolomics </li></ul><ul><li>Neurogenome </li></ul><ul><li>Nucleome </li></ul><ul><li>Nutrigenomics </li></ul><ul><li>Proteome & Proteomics </li></ul><ul><li>Sequenceome </li></ul><ul><li>Transcriptomics </li></ul><ul><li>Virusomics AND MANY MORE….. </li></ul>Types of OMICS ….
  15. 15. Research in… <ul><li>The omics technology has driven new areas of research: </li></ul><ul><ul><li>DNA and protein micro arrays </li></ul></ul><ul><ul><li>Mass spectrometry </li></ul></ul><ul><ul><li>A number of other instruments that enable high-throughput analysis. </li></ul></ul>
  16. 16. Omics related to Nutrition <ul><li>NUTRIGENOMICS & its related technologies : </li></ul><ul><ul><li>Genomics </li></ul></ul><ul><ul><li>Transcriptomics </li></ul></ul><ul><ul><li>Proteomics </li></ul></ul><ul><ul><li>Metabolomics </li></ul></ul>
  17. 17. <ul><li>The science that studies the effect of dietary bioactive compounds on gene expression is called nutrigenomics. </li></ul>
  18. 19. <ul><li>Nutrigenomics is a modern discipline at the interface between genetics , molecular nutrition, molecular biology, pharmacogenomics and molecular medicine. </li></ul>
  20. 22. Nutrigenomics <ul><li>Nutrigenomics is the science that examines the response of individuals to food compounds using post-genomic and related technologies. (e.g. genomics, Transcriptomics, proteomics, metabolomics etc.). </li></ul>
  21. 23. <ul><li>The long-term aim of Nutrigenomics is to understand how the whole body responds to real foods . </li></ul><ul><li>The huge advantage in this approach is that the studies can examine people (i.e. populations, sub-populations - based on genes or disease - and individuals), food, life-stage and life-style without preconceived ideas. </li></ul>
  22. 24. <ul><li>Nutrigenomics focuses on the relationship between dietary nutrients and gene expression using state-of-the-art technology. </li></ul>
  23. 26. <ul><li>Nutrigenomics applies high –throughput molecular biology techniques including sequencing and genotyping (genomics), Transcriptomics, proteomics and metabolomics. </li></ul>
  24. 27. Analytical tools in molecular nutrition : mRNA Protein NUTRIGENOMICS GENOMICS TRANSCRIPTOMICS PROTEOMICS METABOLOMICS DNA Metabolites
  25. 28. <ul><li>Transcriptomics determines patterns of gene expression in response to a nutrient </li></ul><ul><li>Proteomics studies the effect of nutrients on protein synthesis, protein structure and patterns of protein expression. </li></ul><ul><li>The profile and function of metabolites are analyzed by Metabolomics techniques, </li></ul><ul><li>The comprehensive data handling is finally accomplished by bioinformatic tools </li></ul>
  26. 29. Genomics <ul><li>Genomics may be described as the comprehensive analysis of DNA structure and function. </li></ul><ul><li>Understanding biological diversity at the whole genome level will yield insight into the origins of individual traits and disease susceptibility. </li></ul>
  27. 30. <ul><li>Though organisms such as humans are quite similar at the genetic level, differences exist at a frequency of about 1 in every 1000 nucleotide bases. This translates into approximately 3 million base differences between each individual. Such changes are referred to as single nucleotide polymorphisms (SNPs) </li></ul>
  28. 31. <ul><li>A polymorphism is distinct from a mutation. The latter is considered rare; affecting less than one percent of the species, whereas a polymorphism is relatively common and its prevalence is no different to what is considered normal. </li></ul>
  29. 32. GENETIC TESTING <ul><li>Genetic testing involves the direct examination of the DNA molecule itself. A scientist scans a patient’s DNA sample for mutated sequences. </li></ul>
  30. 33. GENE THERAPY <ul><li>Gene therapy may be used for treating, or even curing, genetic and acquired diseases like cancer and AIDS by using normal genes to supplement or replace defective genes or to bolster a normal function such as immunity. </li></ul>
  31. 34. APPLICATIONS OF GENOMICS: <ul><li>Diagnose a disease. </li></ul><ul><li>Confirm a diagnosis. </li></ul><ul><li>Confirm the existence of a disease in individuals. </li></ul><ul><li>predict the risk of future disease in healthy individuals. Genetic testing is now used for: </li></ul><ul><li>Carrier screening, or the identification of unaffected individuals who carry one copy of a gene for a disease that requires two copies for the disease to manifest. </li></ul><ul><li>Prenatal diagnostic screening </li></ul><ul><li>Newborn screening </li></ul><ul><li>Presymptomatic testing for predicting adult-onset disorders </li></ul><ul><li>Presymptomatic testing for estimating the risk of developing adult-onset cancers </li></ul><ul><li>Confirmational diagnosis of symptomatic individuals </li></ul><ul><li>Forensic/identity testing </li></ul>
  32. 35. GENOMICS AND PROTEOMICS <ul><li>Genomics focuses on an organism's genetic makeup, while proteomics focuses on gene products.  </li></ul><ul><li>Both are interrelated .   </li></ul>
  33. 37. Proteomics <ul><li>The focus of proteomics is a biological group called the proteome. </li></ul><ul><li>The proteome is dynamic, defined as the set of proteins expressed in a specific cell, given a particular set of conditions. Within a given human proteome, the number of proteins can be as large as 2 million. </li></ul>
  34. 38. <ul><li>Proteins themselves are macromolecules: long chains of amino acids. This amino acid chain is constructed when the cellular machinery of the ribosome translates RNA transcripts from DNA in the cell's nucleus. The transfer of information within cells commonly follows this path, from DNA to RNA to protein. </li></ul>
  35. 40. Techniques in Proteomics <ul><li>Gel electrophoresis </li></ul><ul><li>X-ray crystallography </li></ul>
  36. 41. <ul><li>Nuclear Magnetic Resonance spectroscopy </li></ul><ul><li>Mass spectrometry etc... </li></ul>
  37. 42. Applications of Proteomics <ul><li>HIV </li></ul><ul><li>Biomarkers Eg: ELISA & immunohistochemical staining etc.. </li></ul><ul><li>Alzheimer's disease </li></ul><ul><li>Heart disease </li></ul><ul><li>Cancerous cells </li></ul>
  38. 43. Transcriptomics <ul><li>The transcriptome is the set of all messenger RNA (mRNA) molecules, or &quot;transcripts,&quot; produced in one or a population of cells. The term can be applied to the total set of transcripts in a given organism, or to the specific subset of transcripts present in a particular cell type. </li></ul>
  39. 44. <ul><li>The study of  transcriptomics , also referred to as  Expression Profiling , examines the expression level of mRNAs in a given cell population, often using high-throughput techniques based on DNA micro array technology. </li></ul><ul><li>The use of next-generation sequencing technology to study the transcriptome at the nucleotide level is known as RNA-Seq. </li></ul>
  40. 46. Applications of Transcriptomics <ul><li>The transcriptomes of stem cells and cancer cells are of particular interest to researchers who seek to understand the processes of Cellular differentiation and carcinogenesis. </li></ul>
  41. 47. METABOLOMICS <ul><li>The development of metabolomics began in 1970 by Arthur Robinson. </li></ul><ul><li>Metabolomics is the &quot;systematic study of the unique chemical fingerprints that specific cellular processes leave behind&quot; - specifically, the study of their small-molecule metabolite profiles. </li></ul>
  42. 48. <ul><li>Metabolome refers to the complete set of small-molecule metabolites (such as metabolic intermediates, hormones and other signaling molecules, and secondary metabolites) to be found within a biological sample, such as a single organism. </li></ul><ul><li>Metabolites are the intermediates and products of metabolism. The term  metabolite  is usually restricted to small molecules. </li></ul><ul><li>Techniques in metabolomics: </li></ul><ul><li>Mass spectrometry is mostly used in metabolomics </li></ul>
  43. 49. Applications of Metabolomics <ul><li>Toxicity assessment/toxicology </li></ul><ul><ul><li>Urine or blood plasma samples can be used to detect the physiological changes caused by toxic insult of a chemical (or mixture of chemicals) </li></ul></ul><ul><li>Functional genomics. </li></ul><ul><ul><li>Metabolomics can be an excellent tool for determining the phenotype caused by a genetic manipulation, such as gene deletion or insertion. More exciting is the prospect of predicting the function of unknown genes by comparison with the metabolic perturbations caused by deletion/insertion of known genes. </li></ul></ul>
  44. 50. Nutrigenomics <ul><li>The science that studies the effect of dietary bioactive compounds on gene expression is called nutrigenomics. </li></ul><ul><li>Nutrigenomics—understanding how nutrients —affect genes—will enable foods to be developed that can be used to prevent and treat disease. </li></ul>
  45. 52. <ul><li>In 1996, Ghai and coworkers filed a seminal patent which highlighted the potential for development of foods or supplements that could alter the expression of genes associated with human diseases (Ghai et al., 1999). They demonstrated that certain flavonoids found in citrus peel enhanced expression of a gene involved in the human body’s natural defense against cancer. </li></ul>
  46. 53. Genetic Effects of Food <ul><li>Chemicals found in food interact with biochemical pathways at the molecular level—for example, to elicit allergic reactions alter (potentially increase or decrease) the levels of biomarkers, such as blood/sugar, cholesterol, and various proteins. </li></ul>
  47. 54. <ul><li>While researchers are exploring methods to identify bioactives that alter gene expression in humans, the food we eat is already altering expression of our genes. </li></ul>
  48. 55. Table 1: How nutrients regulate genes Arthritis Decrease mRNA synthesis Theaflavins Cancer Increase mRNA synthesis Flavones Kidney disease mRNA stability Vitamin D Obesity Bind to transcription factors Fatty acids Cancer DNA methylation Folic acid Potential Disease Gene impact Nutrient
  49. 56. <ul><li>Ordovas et al. (2002) demonstrated how a </li></ul><ul><li>single-point mutation in the APOA1 gene alters how an individual responds to the effect of polyunsaturated fatty acids on HDL cholesterol levels. </li></ul>
  50. 57. <ul><li>Several genes directly involved in inflammation include COX-2, </li></ul><ul><li>tumor necrosis factor: </li></ul><ul><li>α (TNF-α), interleukin-1 (IL-1), phospholipase A2, 5-lipoxygenase (LOX), and inducible nitric oxide synthase (iNOS). </li></ul>TARGETING INFLAMMATION
  51. 58. <ul><li>Omega-3s, on the other hand, such as </li></ul><ul><li>EPA and DHA, are competitive inhibitors of both COX and LOX, thereby having anti-inflammatory effects. </li></ul>
  52. 59. <ul><li>Another study done by V.Mohan “ Gene Environment interactions and the Diabetes epidemic in India ” at Madras Diabetes Research Foundation & Dr. Mohan’s Diabetes Specialties Center, Chennai.(2007) </li></ul>
  53. 60. <ul><li>They carried out gene-diet interaction studies, which revealed that the Adiponectin Gene polymorphism contributed to insulin resistance and Diabetes. </li></ul><ul><li>These subjects were at an increased risk for Hypoadiponectinemia . </li></ul>
  54. 61. <ul><li>Similarly, the Ala54Thr polymorphism of the fatty acid-binding protein 2 gene showed a synergistic effect with a high glycemic load increasing the risk for Hypertriglceridemia . </li></ul><ul><li>These studies indicate that the gene-diet interactions could play a major role in increasing the risk of Diabetes. </li></ul>
  55. 62. Conclusion <ul><li>Routine use of Nutrigenomics in clinical labs, in turn, will demand a new brand of dietitians, genetic counselors and nutritional scientists . </li></ul>
  56. 63. Thank You