Introduction to Omics Science PDF

Chapter-1: Introduction to omics science  What is –Omics Sciences?  In biological context. the suffice –omics is used to refer study of large set of biological molecules.  The realization of that DNA alone not regulate complex biological process.  as result of triggered rapid development of...

Chapter-1: Introduction to omics science  What is –Omics Sciences?  In biological context. the suffice –omics is used to refer study of large set of biological molecules.  The realization of that DNA alone not regulate complex biological process.  as result of triggered rapid development of several fields in molecular biology that together described with the term OMICs 1 compiled by Tola B, The Omics term is used with suffix -ome to address the study of field in  genomics for genome,  proteomics for proteome,  metabolomics for metabolome, and many more.  Omics reflects the use of diverse technologies to gain an insight into the complexity of biomolecules influencing the structure and function of organisms. 2 compiled by Tola B,  The omics-driven research has led to understanding of complex regulatory networks that controls: gene expression,   protein modification, and  metabolite composition.  Transcriptomics, metabolomics, bioinformatics, and high-throughput DNA sequencing led to the deciphering of diverse regulatory networks in different systems resulting in enhanced understanding for its potential applications in clinical diagnosis, prognosis, and therapeutic purposes 3 compiled by Tola B, 4 compiled by Tola B, 1.2 Types of Omics Sciences  The field of -omics sciences has been divided into the following main categories :  Genomics  Trancriptomics  Proteomics  Metabolomics  Bioinformatics (tool) 5 compiled by Tola B,  Genomics  Genomics : the study of the genome in totality and is further classified into several sub branches: comparative genomics Structural genomics Functional genomics Epigenomics Meta genomics Personal genomics Cogenetve genomics 6 compiled by Tola B, Comparative genomics Comparative genomics: field of omics science in which the genome features of different organisms are compared.  The genomic features may include the:  DNA sequence  Gene  gene order  regulatory sequences and  other genomic structural landmarks  provides an insight into the evolutionary aspects of organisms compared based on the sequences at whole genome level. 7 compiled by Tola B,  useful to understand the variability in terms of functional DNA segments, such as coding exons, noncoding RNAs, and also some gene regulatory regions.  The genome sequences are compared by aligning them to score the match or mismatch between them.  Various softwares and algorithms have been developed for the alignment of several genome sequences simultaneously and elucidate genome evolution and function. 8 compiled by Tola B, 9 compiled by Tola B,  Functional genomics  Functional genomics :is the study of how genes and intergenic regions of the genome contribute to different biological processes.  Uses means of genome-wide analysis through high- throughput methods  Focuses on the functional aspects such as:  regulation of gene expression,  functions and  interaction of different genes, etc 10 compiled by Tola B, 11 compiled by Tola B,  Structural genomics  It aims to decipher the 3D structure of all proteins encoded by a particular genome using either experimental tools or in silico tools or sometimes both.  The structure of the total number of identified protein of particular genome is determined while in traditional structural prediction, structure of only one particular protein is determined. 12 compiled by Tola B,  Through the availability of full genome sequences of number of organisms, structural prediction can be done by using both the experimental and modeling approaches, as well as previously known protein structures. Thesequence-structure–function relationship provides an opportunity to analyze the putative functions of the identified proteins of an organism under purview of structural genomics 13 compiled by Tola B, 14 compiled by Tola B,  Epigenomiics  Epigenomccs :refers to the external modification of DNA.  It alters the physical structure of DNA without altering the DNA sequence. E. g The DNA methylations, that is, the addition of a methyl group, or a “chemical cap,” to part of the DNA molecule and histone modification  focused on the epigenetic regulation of genome expression.  Study of epigenetic process (expression not involving DNA on target (ultimately genome wide scale. 15 compiled by Tola B, 16 compiled by Tola B,  Metagenomics  Metagenomics is emerging as an important discipline to access the biocatalytic potential of uncultivable microorganisms.  Despite very rich microbial diversity of the range of a million species per 1 g of soil, very few microorganisms can be cultured under in vitro conditions.  With the advances made in the field of metagenomics, DNA can be extracted from environmental samples from which genomic library can be prepared. This library can be further explored by screening the clones for biological activity to identify clones possessing desired characteristics.  A number of biocatalysts such as laccase, xylanase, endoglucanase, exoglucanase, and lipase have been recently identified from metagenomic libraries 17 compiled by Tola B, 18 compiled by Tola B,  Cognitive genomics  Cognitive genomics is the sub-field of genomics pertaining to cognitive function in which the genes and non-coding sequences of an organism's genome related to the health and activity of the brains are studied 19 compiled by Tola B, 20 compiled by Tola B,  Personal genomics  Single nucleotide polymorphism (SNP), copy number variation, and complex structural variations can be typed with the help of sequencing data.  initiated to truly understand the genesis of most complex human traits—from deadly diseases to the talents and other features that makes every individual unique.  useful for disease management and understanding of human health. It also deals with the ethical, legal, and social issues (ELSI) related to personal genomics. 21 compiled by Tola B, 22 compiled by Tola B, Trancritomics  Trancriptomics :is the study of total RNAs in particular cell or tissue or organism.  focused on the genome expression  The abundances of specific mRNAs transcripts in a biological samples is reflection of the expression level of the correspondent genes 23 compiled by Tola B,  Is used in gene expression profiling:  The identification and characterization of the mixture of mRNAs that is expressed in specific samples  Applicable :To associate different mRNAs mixture from deferent group of individuals to phenotype differences between the groups.  Challenge: the trancriptoeme in contrast to genome is highly variable over time between cell type s and environmental change. 24 compiled by Tola B,  It deals with the study of the complete set of RNAs/transcriptomes encoded by the genome of a cell or organism at a specific time and under a specific set of conditions.  The techniques that are frequently used for genome-wide analysis for gene expression are:  complementary DNA (cDNA) microarrays and protein microarrays,  cDNA–amplified fragment length polymorphism (AFLP), and  serial analysis of gene expression (SAGE). 25 compiled by Tola B, 26 compiled by Tola B, Proteomics  Proteomics is a comprehensive study of proteins in totality identified in a cell, organ, or organism at a particular time’ Proteomics can categorized into the following categories  Expression proteomics  Structural proteomics  Functional proteomics 27 compiled by Tola B,  Expression proteomics  Expression proteomics is the quantitative comparison of protein expression throughout the entire proteome of different samples. Structural proteomics  Structural proteomics, or cell-map proteomics maps out the structure of the proteins present in a specific cellular organelle.  It allows for the identification of all proteins, determines where they are located and characterizes all of their interactions. In turn, this helps to understand the overall architecture of cells and provides an explanation for why certain proteins result in unique phenotypes.  Functional proteomics is area is aimed at discovering the biological function of unknown proteins and defining cellular mechanisms at the molecular level.  E.g Proteome mining is a functional proteomics approach that is used to extract as much protein information as possible. 28 compiled by Tola B, 29 compiled by Tola B,  Metabolomics  Metabolomics is a branch of omics associated with study of metabolites of an organism in totality. Important in:  pharmacological studies,  functional genomics,  toxicology,  drug discovery,  nutrition,  cancer, and diabetes 30 compiled by Tola B,  Metabolism  The diverse chemical reactions leading to growth and development of an organism is often referred to as metabolism and includes both anabolic and catabolic reactions 31 compiled by Tola B, 32 compiled by Tola B, Bioinformatics  Bioinformatics is the application of information technology to the field of molecular biology.  Bioinformatics is the field of science in which biology and information technology merged into a single discipline.  Bioinformatics is the science of managing, mining, integrating, and interpreting information from biological data at the genomic,metabalomic,proteomic, phylogenetic, cellular, or whole organism levels 33 compiled by Tola B,  Biologist Collect molecular data DNA, RNA, gene & protein etc Bioinformatics Study biological question by analyzing Computer scientist molecular data Mathematics , statistics Develop tools, software, algorithm to store and analyze data. 34 compiled by Tola B, 35 compiled by Tola B, 1.3 Application of sciences of –omics in different fields:  The science of omics has diverse application as discussed in the following  Assessment of genome structure and function: A large volume of information can be generated through high- throughput screening, which in turn can be used for studying structural and functional aspects of genomes. 36 compiled by Tola B, 37 compiled by Tola B, 2. Application in plant metabolomics: Used to interpret plant growth and functions based on metabolite analysis by sophisticated tools influencing the quality of food or plant derived medicines. 3.Toxicogenomics for assessment of environmental pollution: Allows large-scale screening of huge number of biological samples as potential toxicants. 38 compiled by Tola B, 4. Therapeutic application of genomics: Useful for gene- based diagnosis and treatment of individuals. Also helpful to manage epidemics and develop new therapies. 5. Microbial omics and its approaches in biofuel production: Complex microbial communities can be screened by metagenomics for targeted screening of enzymes with industrial applications in biofuel production. 6. In crop improvement: Genomics-based tools for crop improvements are being used with the availability of genome sequences of several crops. Several types of molecular markers have been developed associated with different agronomics traits. 39 compiled by Tola B, 7. Evolution and diversity studies: Useful in studying evolutionary relatedness. 8. Analysis of RNA editing: RNA editing is a post- transcriptional event that recodes hereditary information.  RNA editing is an integral step in generating the diversity and plasticity of cellular RNA signatures. 9. Biomarker for medical research: Disease-related biomarkers are helpful in disease prediction, which may develop over time. Tools for aligning sequences using pairwise and multiple- sequence alignment. 40 compiled by Tola B, 10. Drug discovery: Involved in the drug discovery process ranging from screening hits to its efficacy, stability, and bioavailability 11. Pathological studies: Pathology is the precise study and diagnosis of disease. 12. Clinical toxicology: Involved in the improvement of the drug safety assessment process 41 compiled by Tola B,