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BEGR 424 Molecular Biology William Terzaghi Spring, 2017

BEGR 424 Molecular Biology William Terzaghi Spring, 2017. BEGR424- Resource and Policy Information Instructor: Dr. William Terzaghi Office: SLC 363 / CSC228 Office hours: MWF 11:00-12:00 in SLC 363, TR 1-2 in CSC228 or by appointment Phone: (570) 408-4762 Email: terzaghi@wilkes.edu.

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BEGR 424 Molecular Biology William Terzaghi Spring, 2017

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  1. BEGR 424 Molecular Biology William Terzaghi Spring, 2017

  2. BEGR424- Resource and Policy Information Instructor: Dr. William Terzaghi Office: SLC 363/CSC228 Office hours: MWF 11:00-12:00 in SLC 363, TR 1-2 in CSC228 or by appointment Phone: (570) 408-4762 Email: terzaghi@wilkes.edu

  3. BEGR424- Resource and Policy Information Instructor: Dr. William Terzaghi Office: SLC 363/CSC228 Office hours: MWF 11:00-12:00 in SLC 363, TR 1-2 in CSC228 or by appointment Phone: (570) 408-4762 Email: terzaghi@wilkes.edu Course webpage: http://staffweb.wilkes.edu/william.terzaghi/BEGR424.html

  4. General considerations • Graduate courses • learning about current literature

  5. General considerations • Graduate courses • learning about current literature • Learning how to give presentations

  6. General considerations • Graduate courses • learning about current literature • Learning current techniques

  7. General considerations • Graduate courses • learning about current literature • Learning current techniques • Using them!

  8. Provide a genuine experience in using cell and molecular biology to learn about a fundamental problem in biology.

  9. Provide a genuine experience in using cell and molecular biology to learn about a fundamental problem in biology. • Rather than following a set series of lectures, study a problem and see where it leads us.

  10. Provide a genuine experience in using cell and molecular biology to learn about a fundamental problem in biology. • Rather than following a set series of lectures, study a problem and see where it leads us. • Lectures & presentations will relate to current status

  11. Provide a genuine experience in using cell and molecular biology to learn about a fundamental problem in biology. • Rather than following a set series of lectures, study a problem and see where it leads us. • Lectures & presentations will relate to current status • Some class time will be spent in lab & vice-versa • we may need to come in at other times as well

  12. Pick a problem

  13. Pick a problem Design some experiments

  14. Pick a problem Design some experiments See where they lead us

  15. Pick a problem Design some experiments See where they lead us Grading? Combination of papers and presentations

  16. GRADING? • Combination of papers and presentations • First presentation: 5 points • Research presentation: 10 points • Final presentation: 15 points • Assignments: 5 points each • Poster: 10 points • Intermediate report 10 points • Final report: 30 points • Alternatives • Paper(s) instead of 1 or two presentations • Research proposal instead of a presentation • One or two exams?

  17. Topics? • Studying ncRNA • Making Crispr/CAS9 proteins • Mutate/replace specific genes • Bind specific DNA sequences • Color code with fluorescent proteins • Repress expression • Make transcriptional activators by fusing with activation domains • Adding aptamers to Bryant’s or Mikey’s ncRNAs

  18. Topics? • Studying ncRNA • Studying sugar signaling • Comparing expression of genes in Bryant’s mutants vs wt under various conditions

  19. Topics? • Studying ncRNA • Studying sugar signaling • Comparing expression of genes in Bryant’s mutants vs wt under various conditions • Studying Gibberellic Acid signaling • Comparing expression of genes in Mikey’s mutants vs wt under various conditions

  20. Topics? • Studying ncRNA • Studying sugar signaling • Comparing expression of genes in Bryant’s mutants vs wt under various conditions • Studying Gibberellic Acid signaling • Comparing expression of genes in Mikey’s mutants vs wt under various conditions • Bioremediation

  21. Topics? • Studying ncRNA • Studying sugar signaling • Studying GA signaling • Bioremediation • Atrazine • Enhancing expression of TrzN • Adding AtzB, AtzC etc to the constructs • making an atrazine-inducible construct

  22. Topics? • Studying ncRNA • Studying sugar signaling • Studying GA signaling • Bioremediation • Atrazine • Neonicotinoid pesticides (e.g. imidacloprid) • Bind nicotinic acetylcholine receptors • Used on most crops: 95% of corn, > 50% of soy • Cause bee colony collapse?

  23. Topics? • Studying ncRNA • Studying sugar signaling • Studying GA signaling • Bioremediation • Atrazine • Neonicotinoid pesticides • Metals, other mine or fracking waste?

  24. Topics? • Studying ncRNA • Studying sugar signaling • Studying GA signaling • Bioremediation • Atrazine • Neonicotinoid pesticides • Metals, other mine or fracking waste? • Something else??

  25. Topics? Studying ncRNA Studying sugar signaling Studying GA signaling Bioremediation Making plants/algae that bypass Rubisco to fix CO2

  26. Topics? • Studying ncRNA • Studying sugar signaling • Studying GA signaling • Bioremediation • Making plants/algae that bypass Rubisco to fix CO2 • Making novel biofuels • blue-green algae that generate electricity • Plants/algae that make methane or hydrogen • Biodiesel • Other ideas???

  27. Topics? • Studying ncRNA • Studying sugar signaling • Studying GA signaling • Bioremediation • Making plants/algae that bypass Rubisco to fix CO2 • Making novel biofuels • Enhancing resveratrol production • In J. knotweed • In Arabidopsis • In black rice

  28. Topics? Studying ncRNA Studying sugar signaling Studying GA signaling Bioremediation Making plants/algae that bypass Rubisco to fix CO2 Making novel biofuels Enhancing resveratrol production Studying proteins that regulate telomere length Something else?

  29. Assignments? identify a gene and design primers presentation on new sequencing tech designing a protocol to verify your clone presentations on gene regulation presentation on applying mol bio Other work draft of report on cloning & sequencing poster for symposium final gene report draft of formal report formal report

  30. Genome Projects Studying structure & function of genomes

  31. Genome Projects • Studying structure & function of genomes • Sequence first

  32. Genome Projects • Studying structure & function of genomes • Sequence first • Then location and function of every part

  33. Genome Projects How much DNA is there? SV40 has 5000 base pairs

  34. Genome Projects How much DNA is there? SV40 has 5000 base pairs E. coli has 5 x 106

  35. Genome Projects • How much DNA is there? • SV40 has 5000 base pairs • E. coli has 5 x 106 • Yeast has 2 x 107

  36. Genome Projects • How much DNA is there? • SV40 has 5000 base pairs • E. coli has 5 x 106 • Yeast has 2 x 107 • Arabidopsishas 108 • Ricehas 5 x 108 • Humans have 3 x 109 • Soybeans have 3 x 109 • Toads have 3 x 109 • Salamanders have 8 x 1010 • Lilies have 1011

  37. C-value paradox • C-value paradox: DNA content/haploid genome varies widely

  38. Genome Projects • C-value paradox: DNA content/haploid genome varies widely • Some phyla show little variation: birds all have ~109bp

  39. Genome Projects • C-value paradox: DNA content/haploid genome varies widely • Some phyla show little variation: birds all have ~109bp • mammals all have ~ 3 x 109 bp

  40. Genome Projects • C-value paradox: DNA content/haploid genome varies widely • Some phyla show little variation: birds all have ~109bp • mammals all have ~ 3 x 109 bp • Other phyla are all over • Insects vary 100 x

  41. Genome Projects • C-value paradox: DNA content/haploid genome varies widely • Some phyla show little variation: birds all have ~109bp • mammals all have ~ 3 x 109 bp • Other phyla are all over • Insects vary 100 x • flowering plants • vary 1000x

  42. C-value paradox • One cause = variations in chromosome # • 2C chromosome numbers vary widely • Haplopappus gracilis has 4

  43. C-value paradox • One cause = variations in chromosome # • 2C chromosome numbers vary widely • Haplopappus has 2 • Arabidopsis has 10

  44. C-value paradox • One cause = variations in chromosome numbers and ploidy • 2C chromosome numbers vary widely • Haplopappus has 2 • Arabidopsis has 10 • Rice has 24 • Humans have 46 • Tobacco (hexaploid) has 72 • Kiwifruit (octaploid) have 196

  45. C-value paradox • One cause = variations in chromosome numbers and ploidy • 2C chromosome numbers vary widely • Haplopappus has 2 • Arabidopsis has 10 • Rice has 24 • Humans have 46 • Tobacco (hexaploid) has 72 • Kiwifruit (octaploid) have 196

  46. C-value paradox Chromosome numbers vary So does chromosome size!

  47. C-value paradox Chromosome numbers vary So does chromosome size! Reason = variation in amounts of repetitive DNA

  48. C-value paradox Chromosome numbers vary So does chromosome size! Reason = variation in amounts of repetitive DNA first demonstrated using Cot curves

  49. Cot curves • denature (melt) DNA by heating

  50. Cot curves • denature (melt) DNA by heating • dissociates into two single strands

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