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BiS2C: Lecture 12: Acquiring Novelty

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Slides for BIs2C at UC Davis Spring 2016.
Lecture by Jonathan Eisen.
Topic: Microbial Growth and Functions

Publicado en: Ciencias
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BiS2C: Lecture 12: Acquiring Novelty

  1. 1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Lecture 12: Acquiring Novelty BIS 002C Biodiversity & the Tree of Life Spring 2016 Prof. Jonathan Eisen 1
  2. 2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Office Hours and Midterm • Eisen: Today ~2:15 - 3:15 • Moore: Today 4:00 - 5:00 • Review Session !Sunday !1001 Geidt Hall !6:00 - 7:30 PM 2
  3. 3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Where we are going and where we have been • Previous Lecture: !11: Function • Current Lecture: !12: Novelty and Acquiring Functions • Next Lecture: !13: Human Microbiome 3
  4. 4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Thought Questions & Main Topics • How do organisms get new functions? • How can we classify the ways organisms live together? 4
  5. 5. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Key Concepts • Lateral gene transfer • Symbiosis !Mutualism !Commensalism !Parasitism • Phylogenetic applications 5
  6. 6. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Origin of Novelty • How do organisms get new functions? 6
  7. 7. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Origin of Novelty • How do organisms get new functions? • Intrinsic (changes on the inside) 7
  8. 8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Origin of Novelty • How do organisms get new functions • Intrinsic (changes on the inside) • Extrinsic (acquired from the outside) 8
  9. 9. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Extrinsic Origin of Novelty Extrinsic acquisition of novelty • Sexual recombination • Lateral gene transfer • Interactions w/ Other Organisms 9
  10. 10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Extrinsic Origin of Novelty Extrinsic acquisition of novelty • Sexual recombination • Lateral gene transfer • Interactions w/ Other Organisms 10
  11. 11. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 11 Sexual Recombination In eukaryotes, the variants produced by mutation can “recombine” via sex meiosismeiosis fertilization
  12. 12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Extrinsic Origin of Novelty Extrinsic acquisition of novelty • Sexual recombination • Lateral gene transfer • Interactions w/ Other Organisms 12
  13. 13. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Lateral gene transfer model 13 A CB D E F G Note Slides Compared to Those Used in Section A
  14. 14. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 14 A CB D E F G Gene Transfer Lateral gene transfer model
  15. 15. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 15 A CB D E F G Lateral gene transfer model Suppose this was EFG Gene Transfer
  16. 16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 16 A CB D E F G Lateral gene transfer model Suppose this was EFG Now D will have 2 EFGs EFG transfer
  17. 17. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 17 A CB D E F G Lateral gene transfer model EFG transfer
  18. 18. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 18 A1 CA2 D1 E F G1D2B G2 Lateral gene transfer model EFG transfer
  19. 19. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 19 Suppose we built phylogenetic trees with EFGs form these species A1 CA2 D1 E F G1D2B G2 Lateral gene transfer model EFG transfer
  20. 20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 20 A1 CA2 D1 E F G1D2B G2 EFG Set #1 ‘Normal” EFGs from D1, D2
  21. 21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 21 A1 CA2 D1 E F G1D2B G2 EFG Set #1 Also any other non- transferred genes
  22. 22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 EFG Set #2 22 A1 CA2 D1 E F G1D2B G2 ‘Transferred” EFGs for D1, D2
  23. 23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 All EFGs 23 A1 CA2 D1 E F G1D2B G2D1 D2 All EFGs
  24. 24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Clicker 24
  25. 25. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 25 A1 CA2 D1 E F G1D2B G2 Double Lateral Transfer of EFGs If we built a tree of all the EFGs in these organisms, which of the following would not be seen as a monophyletic grouping? A: D1, D2 B. D1, D2, E C. D1, D2, B D. G1, G2, F E. A1, A2 EFG
  26. 26. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 26 A CA2 D1 E F G1D2B G2 If we built a tree of all the EFGs in these organisms, which of the following would not be seen as a monophyletic grouping? A: D1, D2 B. D1, D2, E C. D1, D2, B D. G1, G2, F E. A1, A2 EFG Double Lateral Transfer of EFGs
  27. 27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 27 A CA2 D1 E F G1D2B G2 If we built a tree of all the EFGs in these organisms, which of the following would not be seen as a monophyletic grouping? A: D1, D2 B. D1, D2, E C. D1, D2, B D. G1, G2, F E. A1, A2 EFG Double Lateral Transfer of EFGs
  28. 28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 28 A CA2 D2 E F G1D2B G2D1 D1 B If we built a tree of all the EFGs in these organisms, which of the following would not be seen as a monophyletic grouping? A: D1, D2 B. D1, D2, E C. D1, D2, B D. G1, G2, F E. A1, A2 Double Lateral Transfer of EFGs
  29. 29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Antibiotic Resistance Can Transfer Between Species • http://www.niaid.nih.gov/ SiteCollectionImages/topics/ antimicrobialresistance/3geneTransfer.gif 29
  30. 30. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Extrinsic Origin of Novelty Extrinsic acquisition of novelty • Sexual recombination • Lateral gene transfer • Interactions w/ Other Organisms 30
  31. 31. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Symbioss • Symbiosis is an intimate association between at least two different organisms in which at least one of them benefits • Endosymbiosis is a symbiosis in which one of the organisms live inside the cells of the other 32
  32. 32. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Classes of symbiosis Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - 33
  33. 33. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Classes of symbiosis Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - 34
  34. 34. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Mutualistic Symbioses of Bacteria in Eukaryotes • Digestive ! Ruminants ! Cellulolytic insects • Defensive • Behavioral ! Squid light organs • Autotrophic ! Photosynthetic (many) ! Chemosynthetic in deep sea • Nutritional ! Aphids ! Nitrogen fixation in legumes 35
  35. 35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Mutualistic Symbioses of Bacteria in Eukaryotes • Digestive ! Ruminants ! Cellulolytic insects • Defensive • Behavioral ! Squid light organs • Autotrophic ! Photosynthetic (many) ! Chemosynthetic in deep sea • Nutritional ! Aphids ! Nitrogen fixation in legumes 36 More When We Discuss PAF (Plants, Animals, Fungi)
  36. 36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Classes of symbiosis Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - 37
  37. 37. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Classes of symbiosis Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - 38 More in Lecture 13 The Human Microbiome
  38. 38. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Classes of symbiosis Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - 39
  39. 39. II. Some terms • Pathogens are infectious agents that cause a disease (can be considered a subclass of parasites) • Pathogenicity = ability to enter a host and cause disease • Virulence = degree of pathogenicity • Note - not all parasites are pathogens but all pathogens are parasites !40
  40. 40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 The Following is a Brief Tour 41
  41. 41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Spirochetes • Gram-negative • Motile • Chemoheterotrophic • Unique rotating, axial filaments (modified flagella) • Many are pathogens: !Syphilis !Lyme disease • Others free-living 42
  42. 42. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Chlamydias • Gram-negative • Cocci or rod-shaped • Extremely small • Live only as parasites inside cells of eukaryotes & cause various diseases !Trachoma !Multiple sexually transmitted diseases !Pneumonia 43 C. trachomatis
  43. 43. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 High-GC Gram Positives (Actinobacteria) • High G+C/A+T ratio in DNA • Elaborate branching • Some reproduce by forming chains of spores at tips of filaments • Most antibiotics are from this group • Causative agents of many diseases such as tuberculosis and leprosy • Many originally misclassified as fungi 44
  44. 44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Low-GC Gram Positives (Firmicutes) • Low G+C/A+T ratio in DNA • Some produce endospores which are resistant “seeds” that germinate when conditions are good • Many agents of diseases (e.g., anthrax, MRSA, Streptococcus, botulism, tetanus) • Many of agricultural and industrial use (e.g., Lactic acid bacteria) • Some (Mycoplasmas) have no cell wall and are extremely small 45 Mycoplasmas
  45. 45. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Proteobacteria • Gram-negative • Escherichia coli: model organism and human gut commensal and pathogen • Mitochondria evolved from this group • Includes many human and animal pathogens: plague, cholera, typhoid 46
  46. 46. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Alveolates: Apicomplexans • All parasitic • Have a mass of organelles at one tip —the apical complex that help the parasite enter the host’s cells. 47 Apical complex • Plasmodium falciparum- Malaria kills 700,000-2,000,000 people per year—75% of them are African children
  47. 47. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Alveolates: Ciliates 48 Movement in a ciliate from the gut of a termite • All have numerous cilia, the structure is identical to flagella. • Most are heterotrophic; very diverse group. • Have complex body forms and two types of nuclei. • Some pathogens (e.g., Ick)
  48. 48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Stramenopiles: Oomcyetes Phytophthora Potato Late Blight • Non-photosynthetic. • Are absorptive heterotrophs • Once were classed as fungi, but are unrelated. 49 Sudden Oak Death
  49. 49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Excavates: Diplomonads and Parabisalids • Unicellular • Lack mitochondria and most are anaerobic. This is a derived condition • Giardia lamblia - a diplomonad - is a human parasite • Trichomonas vaginalis - parabasalid - STD 50
  50. 50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Excavates: Kinetoplastids • Unicellular parasites with two flagella and a single mitochondrion. • Mitochondrion contains a kinetoplast - structure with multiple, circular DNA molecules • Includes trypanosomes and agents of chagas, sleeping sickness, Leishmaniasis Trypanosoma sp. mixed with blood cells 51
  51. 51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Excavates: Heteroloboseans • Amoeboid body form. • Naegleria can enter humans and cause a fatal nervous system disease - “brain eating” • Some can transform between amoeboid and flagellated stages. 52
  52. 52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 • Not colonial; live as single cells • Some secrete shells or glue sand grains together to form a casing. • Many pathogens 53 Amoebozoans: Loboseans
  53. 53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 No archaeal pathogens • Lots of types of pathogens ! Bacteria that infect eukaryotes ! Viruses that infect eukaryotes, archaea and bacteria ! Eukaryotes that infect other eukaryotes • No known archaeal pathogens of any organism ! No clear explanation of why ! If you discover one, you will become famous (well, among scientists) 54
  54. 54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Case Study: Anthrax 55
  55. 55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 56 Slide by Brian Moore for BIS2C at UC Davis Spring 2016
  56. 56. Anthrax letters - 9/18/2001 !57
  57. 57. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Bacillus anthracis • A member of the Firmicutes (low GC Gram positive) phylum • Sporulates • Animal and human pathogen • Highly invasive • “Weoponized” by multiple countries 58
  58. 58. Anthrax forensics • Question - How do you figure out where the Anthrax in the letters came from? • Answer came from phylogenetics !60
  59. 59. Anthrax Diversity Figure 3. Worldwide distribution of B. anthracis clonal lineages:Phylogenetic and geographic relationships among 1,033 B. anthracis isolates. doi:10.1371/journal.pone.0000461.g002 !61
  60. 60. Anthrax Diversity Figure 3. Worldwide distribution of B. anthracis clonal lineages:Phylogenetic and geographic relationships among 1,033 B. anthracis isolates. doi:10.1371/journal.pone.0000461.g002 !61
  61. 61. Anthrax Diversity Figure 3. Worldwide distribution of B. anthracis clonal lineages:Phylogenetic and geographic relationships among 1,033 B. anthracis isolates. doi:10.1371/journal.pone.0000461.g002 !61
  62. 62. Anthrax Diversity Figure 3. Worldwide distribution of B. anthracis clonal lineages:Phylogenetic and geographic relationships among 1,033 B. anthracis isolates. doi:10.1371/journal.pone.0000461.g002 !61
  63. 63. VNTR Tree by Paul Keim et al Figure 2. UPGMA dendrogram of VNTR data from worldwide B. anthracis isolates: Fifteen VNTR loci and UPGMA cluster analysis were used to establish genetic relationships among the 1,033 B. anthracis isolates.!62
  64. 64. VNTR Tree by Paul Keim et al Figure 2. UPGMA dendrogram of VNTR data from worldwide B. anthracis isolates: Fifteen VNTR loci and UPGMA cluster analysis were used to establish genetic relationships among the 1,033 B. anthracis isolates.!63
  65. 65. VNTR Tree by Paul Keim et al Figure 2. UPGMA dendrogram of VNTR data from worldwide B. anthracis isolates: Fifteen VNTR loci and UPGMA cluster analysis were used to establish genetic relationships among the 1,033 B. anthracis isolates.!63 • The “AMES” strain of anthrax • Used in labs throughout world
  66. 66. Anthrax Letters !64
  67. 67. !65
  68. 68. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Case Study: Viruses and the Tree of Life 66
  69. 69. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Viruses Viruses are obligate parasites of other organisms and cannot live on their own 67
  70. 70. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 68 Viral Diversity
  71. 71. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Phage 69 A double-stranded DNA virus: Bacteriophage T4. Viruses that infect bacteria are referred to as bacteriophage (or simply phage). T4 attaches leglike fibers to the outside of its host cell and injects its DNA into the cytoplasm through its “tail” (pink structure in this rendition). A double-stranded DNA mimivirus: This Acanthamoeba polyphaga mimivirus (APMV) has the largest diameter of all known viruses and a genome larger than some prokaryote genomes. It is named for its host, an amoeba. Cutaway view. 150 nm60 nm • Phage are DNA viruses that infect bacteria and archaea • Phage therapy involves using phage to attack bacterial infections • Repopularize w/ spread of antibiotic resistance
  72. 72. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 CRISPR is an Adaptive Immune System for Bacteria/Archaea 71 doi:10.1016/j.biochi.2015.03.025 2015 Breakthrough Prize Jennifer Doudna Emmanuelle Charpentier
  73. 73. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2016 Mimivirus 72 A double-stranded DNA virus: Bacteriophage T4. Viruses that infect bacteria are referred to as bacteriophage (or simply phage). T4 attaches leglike fibers to the outside of its host cell and injects its DNA into the cytoplasm through its “tail” (pink structure in this rendition). A double-stranded DNA mimivirus: This Acanthamoeba polyphaga mimivirus (APMV) has the largest diameter of all known viruses and a genome larger than some prokaryote genomes. It is named for its host, an amoeba. Cutaway view. 150 nm60 nm • Mimivirus is a DNA virus w/ giant genome • It is infected by its own viruses • Incredibly diverse functional content
  74. 74. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Mimiviruses Genomes Similar in Size to Those of Many Parasitic 73
  75. 75. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Where do viruses sit on the tree of life? Viruses are obligate parasites of other organisms and cannot live on their own 74
  76. 76. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 76 Bacteria Archaea Eukaryotes Virus Evolution Model 1: The Fourth Domain Viruses
  77. 77. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 77 Bacteria Archaea Eukaryotes Virus Evolution Model 2: Separate Origin Viruses
  78. 78. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 78 Bacteria Archaea EukaryotesViruses Viruses Virus Evolution Model 3: From Within Other Groups
  79. 79. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Probably a Little of Each 79
  80. 80. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Where do viruses sit on the tree of life? • Viruses are obligate parasites of other organisms and cannot live on their own • Three main theories about viruses and where they sit on the tree of life • 1. Viruses are relics from a pre-cellular world • 2. Viruses are escaped portions of cellular organisms • 3. Viruses are extremely derived and reduced cellular organisms 80
  81. 81. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Case Study: Influenza Virus 81
  82. 82. Influenza virus !82 A negative-sense single-stranded RNA virus: Influenza virus H5N1, the “bird flu” virus. Surface view. A positive-sense single-stranded RNA virus: Coronavirus of a type thought to be responsible for severe acute respiratory syndrome (SARS). Surface view. 50 nm50 nm • “Influenza” – term dates from 15th century Italy when epidemics were attributed to the influence of the stars • Negative strand RNA viruses • 8 single strand chromosomes • Two key proteins for antigenicity ! H = Hemagglutanin ! N = Neuraminadase
  83. 83. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Flu Phylogeny PLoS Currents Influenza. 2009 Sep 3:RRN1031. 83 Different segments of the flu genome can have very different histories
  84. 84. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Flu Recombination 84
  85. 85. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Recent work of Prof. Brian Moore … 85 Viruses 2015, 7, 3310-3328; doi:10.3390/v7062773

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