27. Omics cascade

Question 1

what is the omics cascade?

Answer 1

• genomics
  – DNA
• transcriptomics
  – RNA
• proteomics
  – proteins
• metabolomics
  – metabolites

Question 2

what are transcriptomics?

Answer 2

• study of transcriptome
  – set of all RNA transcripts produces by genomes at point in time
  – including non-coding in individual or population of cells

Question 3

what are the two main techniques of transcriptomics?

Answer 3

• microarray assay
• RNA sequencing

– both extract and convert mRNA to complementary DNA or cDNA

Question 4

what are the applications of transriptomics?

Answer 4

• medical biosciences
• agriculture
• bioprocesses
• marine biology
• reduce complexity seen on metagenomicswh

Question 5

what are the challenges of transcriptomics?

Answer 5

• low recovery of high quality RNA
  – from environmental samples
• short half life of mRNA
• difficulties enriching mRNA

Question 6

what are proteomics?

Answer 6

• study of composition, structure, function, interactions of proteins
  – directing cell activity
• proteome
  – entire set of proteins produces/modified by organism or system
• proteome differes from cell to cell
  – constantly changes through biochemical interactions with genome and environment
• transcription of gene gives only rough estimate of level of expression of protein
• proteins experience post translational modification
  – profoundly affect activities

Question 7

what are proteins?

Answer 7

• large complex molecules
  – composed of sequence amino acids
• made of long chains of amino acids
  – peptides

Question 8

what is 2D sodium dodecyl sulfate polyacrylamide gel electrophoresis?

Answer 8

• 1st dimension
  – pH gradient, proteins separated based on isoelectric point (PI)
  – PI is pH with no net charge in protein
• 2nd dimension
  – separate proteins based on molecular weights
• when comparing protein expression across different experimental samples
  – gells typically stained with silver/coomassie blue for total protein
• various image analysis platforms used to scan and compare

Question 9

what is the proteomics workflow?

Answer 9

• protein mixture
  – proteolytic digestion using trypsin
• intact protein
• peptide mixture
• LC-MS/MS
• thousands of MS/MS spectra
• protein database search
• computational analysis with various search algorithm
• protein identification

Question 10

proteomics

Answer 10

• 3D structure prediction of protein
• determine time of protein synthesis
• rates of production, degradation, steady-state abundance of protein
• protein modifications
  – post-translational modifications
• protein transport between subcellular compartments
• involvement of proteins in metabollic pathways
• interactio of proteins with one another

Question 11

what are the applications of proteomics?

Answer 11

• bioprocesses
• medical microbiology
• discovery of new drugs
• study of diease mechanisms
• agriculture
• study complex microbial communities in biofil
  – or symbiotic interactions of microorganisms in environment

Question 12

what are metabolomics?

Answer 12

• qualitative and quantitative measures of low molecular-weight molecules
  – involved in metabolic reactions required for maintenance, growth, normal fxn of microbial community
• metabolite
  – organic molecule with M<1500 Da
  – sugars, AAs, ketones, organic acids, amines, lipids, steroids, alkaloids, pollutants, drugs

Question 13

what is the metabolomics workflow?

Answer 13

• sample preparation
• sample analysis
  – by HPLC
  – MS
  – NMR
• pre processing data analysis
• metabolite identification
• pathway analysis

Question 14

why are metabolomics important?

Answer 14

• diagnostic clinical assays
  – test small moleculess
• medical drugs are small molecules
  – derived from pre-existing metabolites
• several genetic disorders
  – involve disease of metabolising small molecules
• metabolites serve as cofactors
  – and signaling of molecules and proteins

Question 15

how is the omics cascade compared?

Answer 15

• coverage
  – 1: chemicals
  – 2: protein
  – 3: genes
• chemistry diversity
  – 1: 2x10^5 chemicals
  – 2: 20 AAs
  – 3: 4 bases