This course will discuss innovations in sequencing technologies that have become major tools in aquatic sciences. The class will include presentations from researchers using these technologies, discussions of challenges working with non-model organisms, and a survey of available data analysis tools. Students will learn about applications of large-scale sequencing data to address issues in ecology and natural resource management. As technologies continue advancing rapidly, the course will also cover bioinformatics challenges.

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?

3. Evolution of this class

4. me

5. Evolution

6. Evolution

7. Evolution

8. Evolution

9. Evolution

10. This class
• Focus on application of large-scale sequencing data to address issues in
ecology and natural resource management

11. Large scale sequence data
•Large
•Technologies are constantly changing*
•Bioinformatics is not trivial

12. Today
• Evolution of the class
• Personal Learning Environment
• Sharing what you know
• Biology
• What is new sequencing technology?

13. Large scale sequence data
•Large
•Technologies are constantly changing*
•Bioinformatics is not trivial

14. Teaching you to teach yourself

15. PLE

16. PLE

17. PLE

18. PLE
me

19. Networks

20. Directionality
• Push
• Pull (~passive)
• Pull (active) eg ask question

21. Where would you pull from?

22. Databases

23. other aquaticy databases

24. other aquaticy databases

25. what (where) else ?

26. how could you push?

27. how could you push without
and effort?

28. Evolution

29. Today
• Evolution of the class
• Personal Learning Environment
• Sharing what you know
• Biology
• What is new sequencing technology?

30. Evolution

31. CLE

32. Today
• Evolution of the class
• Personal Learning Environment
• Sharing what you know
• Biology
• What is new sequencing technology?

33. Why do nucleotides even matter?

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

38. Biology
link

39. Biology

40. Biology

41. Biology
Structure of DNA
Purines Pyrimidines

42. Biology
Sense Strand
Antisense Strand

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?

45. NGS

46. NGS

47. NGS
• template prep
• sequencing and imaging
• data analysis

48. template prep
• clonal amplification of single DNA molecules
• single DNA molecule template

49. clonally amplified
• emulsion PCR
• solid-phase amplification

50. emulsion PCR

51. solid phase

52. single molecule

53. Sequencing and imaging
• Cyclic reversible termination
• Sequencing by ligation
• Pyrosequencing

54. CRT

55. CRT

56. Sequencing and imaging
• Cyclic reversible termination
• Sequencing by ligation
• Pyrosequencing

57. SBL

58. Sequencing and imaging
• Cyclic reversible termination
• Sequencing by ligation
• Pyrosequencing

59. pyrosequencing

60. Genome Enrichment
What?
Why?

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

62. videos

63. You should know
• know what this class is going to be
• how you are going to participate
• what you can learn