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BIS2C2020 - Lecture 10 - Parasites and Pathogens

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Lecture for UC Davis Class BIS2C - Biodiversity and the Tree of Life

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BIS2C2020 - Lecture 10 - Parasites and Pathogens

  1. 1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 BIS2C Biodiversity & the Tree of Life Spring 2020 Lecture 10: Parasites and Pathogens Prof. Jonathan Eisen
  2. 2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Pics
  3. 3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  4. 4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  5. 5. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  6. 6. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Learning Goals • Understand and define “symbiosis” and its different forms and also “pathogen” • Know examples of diseases caused by pathogens and which type of organism the pathogen is • Understand approaches to fighting pathogens and examples for each approach • Understand examples of resistance to anti- pathogen drugs
  7. 7. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 9: Diversity of form and function 10: Parasites and pathogens 11: Viruses and gene transfer Lecture 10 Context
  8. 8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 10 Outline • Background and Context • Parasites and Pathogens Symbioses Pathogen Examples Fighting Pathogens Resistance
  9. 9. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 10 Outline • Background and Context • Parasites and Pathogens Symbioses Pathogen Examples Fighting Pathogens Resistance
  10. 10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Background: Lab Connections • Lab 2: Station A on pathogenicity over tree • Lab 2 Station E on classes of symbiosis • Lab 3: Life Cycle of Plasmodium
  11. 11. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Background: Review Lecture 9
  12. 12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 9 Outline • Background and Context • Diversity of Form and Function Form Trophy Extremophily
  13. 13. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Unicellularity & Multicellularity continuum • Unicellular: one cell does everything R • Colonial: collections of many attached cells (usually of the same genotype); no differentiation or division of labor or reproduction capabilities • Multicellular: collection of many attached cells (usually of same genotype); differentiation and division of labor and reproductive capabilities
  14. 14. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Bacteria & “Prokaryotic Archaea” : Major Cell Forms Cocci = Spheres Bacilli = Rods Spirilla = Curved
  15. 15. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Bacteria & “Prokaryotic Archaea” : Major Cell Forms • Among the Bacteria and Archaea, three shapes are common: Sphere or coccus (plural cocci), occur singly or in plates, blocks, or clusters. Rod—bacillus (plural bacilli) Helical • Rods and helical shapes may form chains or clusters. Cocci = Spheres Bacilli = Rods Spirilla = Curved Tours
  16. 16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • More than just cocci, bacilli, and spirals but these are common • Most are single celled but some are colonial and a few may be multicellular • Many are motile • Some can be identified from morphology • In most cases morphology does not match phylogeny and is more related to ecology or functions • Most phylogenetic studies are based on Diversity of Form in Bacteria and “Prokaryotic Archaea”
  17. 17. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • Range from single celled to colonial to multicellular • Incredible diversity in form & motility among Eukaryotes • For many, but not all taxa, morphology (aka form) is a valuable trait for identification and phylogeny Eukaryotic Diversity of Form (Need to Know This)
  18. 18. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Fungal Hyphae
  19. 19. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 9 Outline • Background and Context • Diversity of Form and Function Form Trophy Extremophily
  20. 20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Component Different Forms Energy source Light Photo Chemical Chemo Electron source (reducing equivalent) Inorganic Litho Organic Organo Carbon source Carbon from inorganic Auto Carbon from organics Hetero Trophy • Three main components to “trophy” Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  21. 21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 9 Outline • Background and Context • Diversity of Form and Function Form Trophy Extremophily
  22. 22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Set up some flasks with growth media 60° 70° 80° 90° 1 2 3 4 Use different flasks for different conditions 1 2 3 4 60° 70° 80° 90° 1h 1h 1h 1h 1 2 3 4 60° 70° 80° 90° 2h 2h 2h 2h 1 2 3 4 60° 70° 80° 90° 3h 3h 3h 3h Determining Optimal Growth Temperature Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 33 Grow starter culture Add a small portion of the starter culture to flasks Monitor growth over time
  23. 23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Hug et al 2016 Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Thermophiles Across the Tree Hug et al. Nature Microbiology. A new view of the tree of life. http://dx.doi.org/10.1038/nmicrobiol.2016.48 41 - 80 °C Thermophiles Across Tree of Life
  24. 24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Hug et al 2016 Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Hyperthermophiles Across the Tree Hug et al. Nature Microbiology. A new view of the tree of life. http://dx.doi.org/10.1038/nmicrobiol.2016.48 Hyperthermophiles Across Tree of Life No Eukaryotes Only a few Bacteria 81 - 122 °C
  25. 25. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Hug et al 2016 Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Extreme Halophiles Across the Tree Hug et al. Nature Microbiology. A new view of the tree of life. http://dx.doi.org/10.1038/nmicrobiol.2016.48 Most extreme halophiles are from a single clade of “prokaryotic Archaea”
  26. 26. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 10 Outline • Background and Context • Parasites and Pathogens Symbioses Pathogen Examples Fighting Pathogens Resistance
  27. 27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 10 Outline • Background and Context • Parasites and Pathogens Symbioses Pathogen Examples Fighting Pathogens Resistance
  28. 28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Symbiosis Symbiosis: an intimate association between at least two organism
  29. 29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Symbiosis Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - Symbiosis: an intimate association between at least two organism
  30. 30. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Organism Class of symbiosis A B Mutualism + + Symbiosis: Mutualism Symbiosis: an intimate association between at least two organism
  31. 31. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Organism Class of symbiosis A B Mutualism + + Lecture 12 and many other parts Symbiosis: an intimate association between at least two organism Symbiosis: Mutualism
  32. 32. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Symbiosis: Commensalism Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Symbiosis: an intimate association between at least two organism
  33. 33. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Lecture 12 Symbiosis: an intimate association between at least two organism Symbiosis: Commensalism
  34. 34. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Organism Class of symbiosis A B Mutualism + + Commensalism + 0 Parasitism + - Today Symbiosis: an intimate association between at least two organism Symbiosis: Parasitism
  35. 35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Parasitism: an intimate association between at least two different organisms in which one of them benefits and one of them is negatively affected. Host: the organism that is harmed. Parasite: the organism that benefits. Symbiosis: Parasitism
  36. 36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Parasitism: an intimate association between at least two different organisms in which one of them benefits and one of them is negatively affected. Host: the organism that is harmed. Parasite: the organism that benefits. Pathogen: infectious agent that causes a disease. This is a major subclass of parasites. Symbiosis: Parasitism
  37. 37. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Thought question Which of the following is a true statement? A: All parasites are cellular B: All symbioses are mutualisms C: All parasitisms are symbioses D: All mutualisms are microbial E: None of the above
  38. 38. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Thought question Which of the following is a true statement? A: All parasites are cellular B: All symbioses are mutualisms C: All parasitisms are symbioses D: All mutualisms are microbial E: None of the above
  39. 39. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 10 Outline • Background and Context • Parasites and Pathogens Symbioses Pathogen Examples Fighting Pathogens Resistance
  40. 40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Pathogen Examples • What follows is a tour • For this tour you need to know for underlined and bolded diseases: which are caused by bacteria which are caused by “prokaryotic archaea” which are caused eukaryotes which are caused by viruses • For the ones caused by bacteria, you need to know: which are caused by Gram-positives which are caused by Gram-negatives
  41. 41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Pathogenic Bacteria Examples
  42. 42. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Bacteria: Spirochetes • Gram-negative • Motile • Chemoheterotrophic • Unique rotating, axial filaments (modified flagella) • Includes causes of: Syphilis Lyme disease
  43. 43. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Bacteria: Chlamydias • Gram-negative • Cocci or rod-shaped • Extremely small • Live only as parasites inside cells of eukaryotes • Includes causes of: Chlamydia Trachoma Multiple sexually transmitted diseases Pneumonia C. trachomatis
  44. 44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Bacteria: Proteobacteria • Gram-negative • Includes Escherichia coli • Mitochondria from this group • Incredible diversity within group • Includes many human and animal pathogens including causes of • Plague • Cholera • Typhoid
  45. 45. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Bacteria: Actinobacteria • Gram positive • Elaborate branching • Many originally misclassified as fungi • Many antibiotics come from species in this group • Includes causes of: • Tuberculosis • Leprosy
  46. 46. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Bacteria: Firmicutes • Gram positive • Some produce endospores • Many of agricultural and industrial use • Some have no cell wall and are extremely small • Includes causes of: • Anthrax • MRSA • Botulism • Tetanus Mycoplasmas
  47. 47. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Pathogenic Eukarya Examples
  48. 48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Eukaryotes: Alveolates: Apicomplexans • All parasitic • Have a mass of organelles at one tip—the apical complex that help the parasite enter the host’s cells. • Includes cause of malaria Apical complex More in Lab 3
  49. 49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Eukaryotes: Alveolates: Ciliates Movement in a ciliate from the gut of a termite • All have numerous cilia • Most are heterotrophic; very diverse group. • Have complex body forms and two types of nuclei. • Includes cause of Ick
  50. 50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Eukaryotes: Stramenopiles: Oomcyetes Phytophthora • Absorptive heterotrophs • Once were classed as fungi • Includes causes of potato blight and sudden oak death Sudden Oak Death Potato Late Blight
  51. 51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Eukaryotes: Excavates: Diplomonads and Parabisalids • Unicellular • Lack mitochondria • Most are anaerobic • Includes causes of giardia and trichomoniasis
  52. 52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Eukaryotes: Excavates: Kinetoplastids • Unicellular parasites • Mitochondrion contains a kinetoplast - structure with multiple, circular DNA molecules • Includes causes of • chagas • sleeping sickness • Leishmaniasis Trypanosoma sp. mixed with blood cells
  53. 53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Pathogenic Viruses Too Viruses Too
  54. 54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 All viruses are parasites, many are pathogens Lecture 11 Diseases caused by viruses include • AIDS • Polio • COVID19 • Flu • Rabies
  55. 55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Pathogen Examples What’s Missing? “Prokaryotic Archaea"
  56. 56. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 No “Prokaryotic Archaea” Parasites or Pathogens • Note - there are no known archaeal pathogens or parasites • No clear explanation of why • If you discover a reason and can prove it, you will become famous
  57. 57. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 No “Prokaryotic Archaea” Parasites or Pathogens • Note - there are no known archaeal pathogens or parasites • No clear explanation of why • If you discover a reason and can prove it, you will become famous • (Among scientists)
  58. 58. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 No “Prokaryotic Archaea” Parasites or Pathogens • Note - there are no known archaeal pathogens or parasites • No clear explanation of why • If you discover a reason and can prove it, you will become famous • (Among scientists) • (Or, at least among microbiologists)
  59. 59. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Knowing Where Pathogen is on Tree of Life Matters
  60. 60. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 10 Outline • Background and Context • Pathogens and Parasites Symbiosis Pathogen Examples Fighting Pathogens Resistance
  61. 61. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Approach 1: Limit Transmission Attack Vectors Hygiene Physical Barriers Building Practices Behavioral Changes https:// doi.org/10.1128/mSystems.00245-20.
  62. 62. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Approach 2: Boost Immune Response
  63. 63. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Approach 3: Treat Symptoms
  64. 64. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Approach 4: Attack the pathogen • Antibiotics, also known as antibacterials: inhibit or kill bacteria • Antifungals: inhibit or kill fungi • Antivirals: inhibit or kill viruses • Some are broad in their targets and some are narrower
  65. 65. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Attacking pathogens
  66. 66. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Thought question Peptidoglycan is found in which organisms A. Bacteria B. "Prokaryotic archaea” C. Eukaryotes D. A and B E. A, B and C
  67. 67. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Thought question Peptidoglycan is found in which organisms A. Bacteria B. “Prokaryotic archaea” C. Eukaryotes D. A and B E. A, B and C
  68. 68. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • Many antibiotics kill or inhibit bacteria by interfering with peptidoglycan • Drugs that target peptidoglycan sometimes have different effects on Gram negatives vs. Gram positives • Why? Attacking pathogens
  69. 69. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • Many antibiotics kill or inhibit bacteria by interfering with peptidoglycan • Drugs that target peptidoglycan sometimes have different effects on Gram negatives vs. Gram positives • Why? Attacking pathogens
  70. 70. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Attacking pathogens Binds to, and inhibits the function of protein (PBP) involved in peptidoglycan polymerization
  71. 71. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Thought Question Gram + Gram - Gram - Gram negative and positive groups of bacteria are labelled in this tree. Which of the following is a true statement? A. Gram positives are monophyletic, Gram negatives are not monophyletic. B. Gram positives are monophyletic, Gram negatives are monophyletic. C. Gram positives are not monophyletic, Gram negatives are not monophyletic. D. Gram positives are not monophyletic, Gram negatives are monophyletic.
  72. 72. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Thought Question Gram + Gram - Gram - Gram negative and positive groups of bacteria are labelled in this tree. Which of the following is a true statement? A. Gram positives are monophyletic, Gram negatives are not monophyletic. B. Gram positives are monophyletic, Gram negatives are monophyletic. C. Gram positives are not monophyletic, Gram negatives are not monophyletic. D. Gram positives are not monophyletic, Gram negatives are monophyletic.
  73. 73. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Lecture 10 Outline • Background and Context • Pathogens and Parasites Symbiosis Pathogen Examples Fighting Pathogens Resistance
  74. 74. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 • Many possible reasons that an antibiotic treatment would not work. Resistance
  75. 75. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Example 1: Form special structures Some bacteria in the Firmicutes phylum can enter a resting state known as an endospore or spore. These are incredibly resistant to just about any attempt to kill them. Examples includes causes of tetanus, anthrax, botulism.
  76. 76. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Example 2: Form biofilms
  77. 77. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Example 3: Resistance Binds to, and inhibits the function of protein (PBP) involved in peptidoglycan polymerization Acquire a new version of PBP protein that methicillin does not bind to or inhibit
  78. 78. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Example 3: Resistance • Use of antibiotics leads to the spread and evolution of “resistance” • Resistance is becoming a MASSIVE problem due to overuse and misuse of antimicrobials • Resistance can evolve remarkably rapidly even without gene transfer (see video …)
  79. 79. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
  80. 80. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Solutions to Resistance?
  81. 81. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Solution 1: New Antibiotics • New Ab
  82. 82. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Solution 2: Phage therapy (viruses that kill bacteria) Lecture 11
  83. 83. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 Solution 3: Fecal transplants • Probiotics Lecture 12
  84. 84. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020 9: Diversity of form and function 10: Parasites and pathogens 11: Viruses and gene transfer Lecture 10 Context

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