Lecture 18 Flashcards
(29 cards)
what is referred to Omics technology?
a new era of systems biology generated by the complete sequencing of species genomes
what is omics?
the comprehensive analysis of biological systems
what is systems biology?
‘biology’ that focuses on complex systems of life
what does omics look at?
- first biological responses of organisms to stressors
- used to better understand and predict changes at the protein, cellular, and individual levels
- biological molecules that translate into the structure and function of an organism
what is a brief history of omics?
- derived from the term genome
- ‘ome’ signifies the ‘collectivity’ of things
- genomics first appeared in the 1980s and became widely used in the 1990s
- genome is the most fundamental part of many omics
what is the genome?
- all the genetic information of an organism
what is transcriptome?
- constructed by the process of transcription, in which individual genes are copied into RNA molecules
- the first product of genome expression
- RNA copies of the active protein-coding genes
what is proteome?
- involves the translation of these RNA molecules into protein
- the cell’s repertoire of proteins
what is metabolome?
- small molecule substrates, intermediates, and products of cell metabolism
- represents the complete set of metabolites in a biological cell, tissue, organ, or organism, which are end products of cellular processes
- snapshot of the physiology of a cell
what are ‘omes’?
- each -ome addresses the object of study
- genome = genomics
- transcriptome = transcriptomics
- proteome = proteomics
- metabolome = metabolomics
what are the types of omics?
- genomics
- transcriptomics
- proteomics
- glycomics
- metabolomics -> lipodomics
which of the omics are related to marine mammal toxicology?
- genomics
- transcriptomics
- proteomics
- metabolomics -> lipidomics
what analytical methods are used for omics?
- transcriptomics: qPCR, RNA sequencing
- proteomics: liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS)
- metabolomics: LC-MS/MS
what is qPCR?
- useful for quantifying the expression of a few genes
- can only detect known sequences
what is RNA sequencing (RNA-seq)?
- RNA-seq using Next Generation Sequencing can detect both known and novel transcripts
- RNA-seq does not require pre-designed probes, the data sets are unbiased, allowing for the hypothesis-free experimental design
when can you use qPCR?
- analyze the expression of a few genes with a known sequence ~ maximum of 30
- qPCR has the widest dynamic range, the lowest quantification limits, and the least biased results in comparison to microarrays or RNA-seq
- amount of starting material can be very low and running 30 reactions per sample will still be cheaper than RNA-seq
what is the purpose of RNA-seq?
in comparison to microarrays, RNA-seq enables you to look at differential expressions at a much broader dynamic range
what are the negatives of RNA-seq?
- more expensive than microarrays and presents a bigger challenge in the planning stage:
1) select technologies
2) select library prep (strand specific or not)
3) what kind of sequencing you want (read length, single or paired end)
4) how many reads you want to sequence, which can impact detecting weakly expressed genes
what are 5 applications of omics?
- biomarkers of disease
- toxicology
- newborn screening
- food safety
- drug discovery
what is the future of omics?
- disease
- contaminant exposure
- immune response
- reproductive effects
what can you look at with marine mammal skin? feces? blubber?
- skin: Hg, omics (years)
- feces: POPs, hormones, omics (hours to days)
- blubber: POPs, hormones, omics (years)
what are transcriptomics?
targeted gene transcripts that play an important role in immune function, endocrine function, and chemical detoxification
how were new health biomarkers (gene targets) for PCBs found in seals?
- assembled the transcriptome for ring seal blubber
- found altered metabolism in PCB exposed seals
- identified 5 new biomarkers for seals
what were the results of measuring metabolites in ringed seals?
- metabolite patterns varied with PCB exposure, driven by energy metabolism, amino acid, and bile acid metabolites
- consistent with the transcriptomics study that showed altered energy metabolism with increasing PCBs in seals
