27. Omics cascade Flashcards

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1
Q

what is the omics cascade?

A
  • genomics
    – DNA
  • transcriptomics
    – RNA
  • proteomics
    – proteins
  • metabolomics
    – metabolites
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2
Q

what are transcriptomics?

A
  • study of transcriptome
    – set of all RNA transcripts produces by genomes at point in time
    – including non-coding in individual or population of cells
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3
Q

what are the two main techniques of transcriptomics?

A
  • microarray assay
  • RNA sequencing

– both extract and convert mRNA to complementary DNA or cDNA

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4
Q

what are the applications of transriptomics?

A
  • medical biosciences
  • agriculture
  • bioprocesses
  • marine biology
  • reduce complexity seen on metagenomicswh
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5
Q

what are the challenges of transcriptomics?

A
  • low recovery of high quality RNA
    – from environmental samples
  • short half life of mRNA
  • difficulties enriching mRNA
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6
Q

what are proteomics?

A
  • 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
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7
Q

what are proteins?

A
  • large complex molecules
    – composed of sequence amino acids
  • made of long chains of amino acids
    – peptides
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8
Q

what is 2D sodium dodecyl sulfate polyacrylamide gel electrophoresis?

A
  • 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
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9
Q

what is the proteomics workflow?

A
  • 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
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10
Q

proteomics

A
  • 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
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11
Q

what are the applications of proteomics?

A
  • 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
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12
Q

what are metabolomics?

A
  • 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
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13
Q

what is the metabolomics workflow?

A
  • sample preparation
  • sample analysis
    – by HPLC
    – MS
    – NMR
  • pre processing data analysis
  • metabolite identification
  • pathway analysis
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14
Q

why are metabolomics important?

A
  • 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
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15
Q

how is the omics cascade compared?

A
  • coverage
    – 1: chemicals
    – 2: protein
    – 3: genes
  • chemistry diversity
    – 1: 2x10^5 chemicals
    – 2: 20 AAs
    – 3: 4 bases
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16
Q
A