1. FISH510: Applications of New Sequencing Technologies in Aquatic Sciences
This course will provide students (both field and lab-centric) a forum to discuss innovations in
sequencing technologies that have recently evolved to play major roles in physiology, ecology,
and population genetics. The format will include presentations from researchers using the
technologies, discussions of challenges unique to working with non-model organisms, and a
survey of tools available for data analysis.
2. Today
• Evolution of the class
• Personal Learning Environment
• Sharing what you know
• Biology
• What is new sequencing technology?
34. Biology
Genetics
Transcriptomics
Has temperature stress
compromised immune
function?
Are these populations
reproductively isolated What makes a parasite
or is there successfully virulent?
interbreeding?
How are growth
processes controlled?
35. Biology
Gene Expression is a Dynamic Process
Genes are the expressed •Different proteins perform a
wide variety of biological
portion of the genome
functions.
Genomic DNA • enzymes, which catalyze
chemical reactions
Messenger RNA (mRNA) • structural or mechanical roles,
• immune response
mRNA codes for proteins • storage and transport of
chemical signals
• cell communication
36. Biology
What can influence gene expression…
Environment (Temperature, Salinity, Oxygen)
Pollution (Environmental Estrogens, Pesticides)
Development and Everyday Biology
Gene Expression is a Dynamic Process
Genes are the expressed •Different proteins perform a
wide variety of biological
portion of the genome
functions.
Genomic DNA • enzymes, which catalyze
chemical reactions
Messenger RNA (mRNA) • structural or mechanical roles,
• immune response
mRNA codes for proteins • storage and transport of
chemical signals
• cell communication
37. Biology
What can influence gene expression… EVERYTHING
Environment (Temperature, Salinity, Oxygen)
Pollution (Environmental Estrogens, Pesticides)
Development and Everyday Biology
Gene Expression is a Dynamic Process
Genes are the expressed •Different proteins perform a
wide variety of biological
portion of the genome
functions.
Genomic DNA • enzymes, which catalyze
chemical reactions
Messenger RNA (mRNA) • structural or mechanical roles,
• immune response
mRNA codes for proteins • storage and transport of
chemical signals
• cell communication
43. Biology
Working with RNA
Transcription changes over time
RNA is less stable than DNA
1. RNA Isolation 2. Reverse Transcribe
Process immediately RNA into
Preserve it complementary DNA
Disrupt sample to release RNA This allows PCR to be
Extract and purify performed on RNA
acid phenol/choloroform
glass filter
oligo dT binding
Store
44. Today
• Evolution of the class
• Personal Learning Environment
• Sharing what you know
• Biology
• What is new sequencing technology?
61. some ngs applications
•variant discovery by resequencing targeted regions of
interest or whole genomes,
• de novo assemblies of bacterial and lower eukaryotic
genomes,
•cataloguing the transcriptomes of cells,
•tissues and organisms (RNA–seq)5,
•genome-wide profiling of epigenetic marks and chromatin
structure using other seq-based methods (ChIP–seq,
methyl–seq and DNase–seq)4,
•species classification and/or gene discovery by
metagenomics studies7