14: Genomics and Systems Biology
Imagine that you could identify and quantify every molecule within a cell (Figure 11.1) in a single assay. You could use this ability to better understand almost any aspect of biology. For example, by comparing the molecular profiles of plants that differed in their resistance to drought, you might discover which combination of genes or proteins makes a crop drought tolerant. Although it is not currently possible to study literally every molecule in a cell in a single experiment, recent advances in molecular biology have made it possible to study many genes (or their products) in parallel.
Figure 11.1: An artist’s depiction of part of an E.coli cell, showing many different types of molecules in their typical abundance. mRNA appears as white lines associated with purple ribosomes, while DNA and proteins such as histones are yellow. (Goodsell, Scripps-EDU)
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- 14.1: ‘Omics Technologies
- This page discusses the genome as the complete DNA set of an organism and genomics as the large-scale study of genes. It highlights advancements in technology that improve research efficiency and reduce costs. The term –omics describes high-throughput analyses of biological molecules (transcriptomics, proteomics, metabolomics). It also notes that interpreting this data necessitates bioinformatics expertise, and integrating various –omics forms is referred to as systems biology.
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- 14.2: DNA Sequencing
- This page discusses DNA sequencing and its techniques, including dideoxy sequencing, which uses modified nucleotides to determine sequences, and capillary electrophoresis for fragment analysis. It highlights next-generation sequencing methods like Illumina, which improve speed and cost-effectiveness by sequencing multiple short templates at once but notes the limitation of these short lengths in certain applications.
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- 14.3: Whole Genome Sequencing
- This page explains the necessity of genome assembly in sequencing, due to short read lengths (45bp to 700bp) versus the large size of human genomes (3 billion bp). It describes two main strategies: clone-by-clone sequencing, utilizing mapped DNA fragments, and whole genome shotgun sequencing, which assembles small fragments without a map. While shotgun sequencing is prevalent, it often needs supplementary methods for complete assemblies.
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- 14.4: Functional Genomics – Determining Function(s)
- This page discusses functional genomics and its techniques for determining gene functions post-genome identification, highlighting microarray analysis as a key method. Microarrays measure mRNA abundance across numerous genes, indicating gene activity and expression variations in different tissues and conditions, including development stages and responses to external factors. They visualize transcript levels with fluorescence, revealing patterns of tissue-specific or temporal gene expression.
Contributors
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Dr. Todd Nickle and Isabelle Barrette-Ng (Mount Royal University) The content on this page is licensed under CC SA 3.0 licensing guidelines.