FISH510 Lec 1

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Overview of FISH510: Seminar, NGS in SAFS

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FISH510 Lec 1

  1. 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. 2. Today• Evolution of the class• Personal Learning Environment• Sharing what you know• Biology• What is new sequencing technology?
  3. 3. Evolution of this class
  4. 4. me
  5. 5. Evolution
  6. 6. Evolution
  7. 7. Evolution
  8. 8. Evolution
  9. 9. Evolution
  10. 10. This class• Focus on application of large-scale sequencing data to address issues in ecology and natural resource management
  11. 11. Large scale sequence data•Large•Technologies are constantly changing*•Bioinformatics is not trivial
  12. 12. Today• Evolution of the class• Personal Learning Environment• Sharing what you know• Biology• What is new sequencing technology?
  13. 13. Large scale sequence data•Large•Technologies are constantly changing*•Bioinformatics is not trivial
  14. 14. Teaching you to teach yourself
  15. 15. PLE
  16. 16. PLE
  17. 17. PLE
  18. 18. PLEme
  19. 19. Networks
  20. 20. Directionality• Push• Pull (~passive)• Pull (active) eg ask question
  21. 21. Where would you pull from?
  22. 22. Databases
  23. 23. other aquaticy databases
  24. 24. other aquaticy databases
  25. 25. what (where) else ?
  26. 26. how could you push?
  27. 27. how could you push without and effort?
  28. 28. Evolution
  29. 29. Today• Evolution of the class• Personal Learning Environment• Sharing what you know• Biology• What is new sequencing technology?
  30. 30. Evolution
  31. 31. CLE
  32. 32. Today• Evolution of the class• Personal Learning Environment• Sharing what you know• Biology• What is new sequencing technology?
  33. 33. Why do nucleotides even matter?
  34. 34. Biology Genetics Transcriptomics Has temperature stress compromised immune function?Are these populationsreproductively isolated What makes a parasiteor is there successfully virulent?interbreeding? How are growth processes controlled?
  35. 35. Biology Gene Expression is a Dynamic ProcessGenes are the expressed •Different proteins perform a wide variety of biologicalportion of the genome functions.Genomic DNA • enzymes, which catalyze chemical reactionsMessenger RNA (mRNA) • structural or mechanical roles, • immune responsemRNA codes for proteins • storage and transport of chemical signals • cell communication
  36. 36. Biology What can influence gene expression… Environment (Temperature, Salinity, Oxygen) Pollution (Environmental Estrogens, Pesticides) Development and Everyday Biology Gene Expression is a Dynamic ProcessGenes are the expressed •Different proteins perform a wide variety of biologicalportion of the genome functions.Genomic DNA • enzymes, which catalyze chemical reactionsMessenger RNA (mRNA) • structural or mechanical roles, • immune responsemRNA codes for proteins • storage and transport of chemical signals • cell communication
  37. 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 ProcessGenes are the expressed •Different proteins perform a wide variety of biologicalportion of the genome functions.Genomic DNA • enzymes, which catalyze chemical reactionsMessenger RNA (mRNA) • structural or mechanical roles, • immune responsemRNA codes for proteins • storage and transport of chemical signals • cell communication
  38. 38. Biologylink
  39. 39. Biology
  40. 40. Biology
  41. 41. BiologyStructure of DNA Purines Pyrimidines
  42. 42. Biology Sense Strand Antisense Strand
  43. 43. Biology Working with RNA Transcription changes over time RNA is less stable than DNA1. 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. 44. Today• Evolution of the class• Personal Learning Environment• Sharing what you know• Biology• What is new sequencing technology?
  45. 45. NGS
  46. 46. NGS
  47. 47. NGS• template prep• sequencing and imaging• data analysis
  48. 48. template prep• clonal amplification of single DNA molecules• single DNA molecule template
  49. 49. clonally amplified• emulsion PCR• solid-phase amplification
  50. 50. emulsion PCR
  51. 51. solid phase
  52. 52. single molecule
  53. 53. Sequencing and imaging • Cyclic reversible termination • Sequencing by ligation • Pyrosequencing
  54. 54. CRT
  55. 55. CRT
  56. 56. Sequencing and imaging • Cyclic reversible termination • Sequencing by ligation • Pyrosequencing
  57. 57. SBL
  58. 58. Sequencing and imaging • Cyclic reversible termination • Sequencing by ligation • Pyrosequencing
  59. 59. pyrosequencing
  60. 60. Genome Enrichment What? Why?
  61. 61. some ngs applications•variant discovery by resequencing targeted regions ofinterest or whole genomes,• de novo assemblies of bacterial and lower eukaryoticgenomes,•cataloguing the transcriptomes of cells,•tissues and organisms (RNA–seq)5,•genome-wide profiling of epigenetic marks and chromatinstructure using other seq-based methods (ChIP–seq,methyl–seq and DNase–seq)4,•species classification and/or gene discovery bymetagenomics studies7
  62. 62. videos
  63. 63. You should know• know what this class is going to be• how you are going to participate• what you can learn

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