BEGR 424 Molecular Biology William Terzaghi Spring, 2016

1. BEGR 424 Molecular Biology William Terzaghi Spring, 2016

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

4. General considerations What do you hope to learn?

5. General considerations • What do you hope to learn? • Graduate courses • learning about current literature

6. General considerations • What do you hope to learn? • Graduate courses • learning about current literature • Learning how to give presentations

7. General considerations • What do you hope to learn? • Graduate courses • learning about current literature • Learning current techniques

8. General considerations • What do you hope to learn? • Graduate courses • learning about current literature • Learning current techniques • Using them!

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

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.

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

12. 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

13. Pick a problem

14. Pick a problem Design some experiments

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

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

17. 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?

18. Trying to find another way to remove oxalate

19. Topics? • Trying to find another way to remove oxalate • Making a probiotic bacterium that removes oxalate • Identifying best candidates • Figuring out how to engineer them • Add oxalate transporter? • Add more/different oxalate altering enzymes? • Target them to different locations?

20. Topics? • Trying to find another way to remove oxalate • Making a probiotic bacterium that removes oxalate • Engineering magnetosomes to express novel proteins • Membrane-bound single-domain iron-oxide crystals made by magnetotic bacteria to help find correct pO2

21. Topics? • Trying to find another way to remove oxalate • Making a probiotic bacterium that removes oxalate • Engineering magnetosomes to express novel proteins • Membrane-bound single-domain iron-oxide crystals made by magnetotic bacteria to help find correct pO2 • Can engineer Mms13-fusion proteins

22. Topics? • Trying to find another way to remove oxalate • Making a probiotic bacterium that removes oxalate • Engineering magnetosomes to express novel proteins • 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

23. Topics? • Trying to find another way to remove oxalate • Making a probiotic bacterium that removes oxalate • Engineering magnetosomes to express novel proteins • Studying ncRNA • Studying sugar signaling

24. Topics? • Trying to find another way to remove oxalate • Making a probiotic bacterium that removes oxalate • Engineering magnetosomes to express novel proteins • Studying ncRNA • Studying sugar signaling • Bioremediation • Atrazine • Neonicotinoid pesticides • Something else??

25. Topics? Trying to find another way to remove oxalate Making a probiotic bacterium that removes oxalate Engineering magnetosomes to express novel proteins Studying ncRNA Studying sugar signaling Bioremediation Making plants/algae that bypass Rubisco to fix CO2

26. Topics? • Trying to find another way to remove oxalate • Making a probiotic bacterium that removes oxalate • Engineering magnetosomes to express novel proteins • Studying ncRNA • Studying sugar 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? Trying to find another way to remove oxalate Making a probiotic bacterium that removes oxalate Engineering magnetosomes to express novel proteins Studying ncRNA Studying sugar signaling Bioremediation Making plants/algae that bypass Rubisco to fix CO2 Making novel biofuels Making vectors for Dr. Harms Something else?

28. 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

29. Genome Projects Studying structure & function of genomes

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

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

32. 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

33. Genome Projects • C-value paradox: DNA content/haploid genome varies widely

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

35. 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

36. 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 and amphibians vary 100 x

37. 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 and amphibians vary 100 x • flowering plants vary 1000x

38. C-value paradox • One cause = variations in chromosome numbers and ploidy • 2C chromosome numbers vary widely • Haplopappus has 2

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

40. 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

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

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

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

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

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

46. Cot curves • denature (melt) DNA by heating • Cool DNA

47. Cot curves • denature (melt) DNA by heating • Cool DNA:complementary strands find each other &anneal

48. Cot curves • denature (melt) DNA by heating • Cool DNA:complementary strands find each other &anneal • hybridize

49. Cot curves • denature (melt) DNA by heating • Cool DNA:complementary strands find each other &anneal • Hybridize: don't have to be the same strands

50. Cot curves • denature (melt) DNA by heating • Cool DNA:complementary strands find each other &anneal • Hybridize: don't have to be the same strands • Rate depends on [complementary strands]