BIS2C2020 - Lecture 10 - Parasites and Pathogens

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

Pics

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

9: Diversity of form and function
10: Parasites and pathogens
11: Viruses and gene transfer
Lecture 10 Context

Lecture 10 Outline
• Background and Context
• Parasites and Pathogens
Symbioses
Pathogen Examples
Fighting Pathogens
Resistance

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

Background: Review Lecture 9

Lecture 9 Outline
• Diversity of Form and Function
Form
Trophy
Extremophily

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

Bacteria & “Prokaryotic Archaea” : Major Cell Forms
Cocci = Spheres Bacilli = Rods Spirilla = Curved

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

• 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”

• 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)

Fungal Hyphae

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”

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

Hug et al 2016
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

Hug et al 2016
Hyperthermophiles Across the Tree
Hyperthermophiles
Across Tree of Life
No Eukaryotes
Only a few Bacteria
81 - 122 °C

Hug et al 2016
Extreme Halophiles Across the Tree
Most extreme
halophiles are from a
single clade of
“prokaryotic
Archaea”

Symbiosis
Symbiosis: an intimate association between at least two organism

Symbiosis
Organism
Class of symbiosis A B
Mutualism + +
Commensalism + 0
Parasitism + -

Organism
Mutualism + +
Symbiosis: Mutualism

Organism
Mutualism + +
Lecture 12 and many other parts
Symbiosis: Mutualism

Symbiosis: Commensalism
Organism
Mutualism + +
Commensalism + 0

Organism
Mutualism + +
Commensalism + 0
Lecture 12
Symbiosis: Commensalism

Organism
Mutualism + +
Commensalism + 0
Parasitism + -
Today
Symbiosis: Parasitism

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.

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.

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

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

Pathogenic Bacteria Examples

Bacteria: Spirochetes
• Gram-negative
• Motile
• Chemoheterotrophic
• Unique rotating, axial
filaments (modified flagella)
• Includes causes of:
Syphilis
Lyme disease

Bacteria: Chlamydias
• Gram-negative
• Cocci or rod-shaped
• Extremely small
• Live only as parasites
inside cells of eukaryotes
Chlamydia
Trachoma
Multiple sexually
transmitted diseases
Pneumonia
C. trachomatis

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

Bacteria: Actinobacteria
• Gram positive
• Elaborate branching
• Many originally
misclassified as fungi
• Many antibiotics come
from species in this group
• Tuberculosis
• Leprosy

Bacteria: Firmicutes
• Gram positive
• Some produce endospores
• Many of agricultural and
industrial use
• Some have no cell wall
and are extremely small
• Anthrax
• MRSA
• Botulism
• Tetanus
Mycoplasmas

Pathogenic Eukarya Examples

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

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

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

Eukaryotes: Excavates: Diplomonads and Parabisalids
• Unicellular
• Lack mitochondria
• Most are anaerobic
• Includes causes of giardia and
trichomoniasis

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

Pathogenic Viruses Too
Viruses Too

All viruses are parasites, many are pathogens
Lecture 11
Diseases
caused by
viruses
include
• AIDS
• Polio
• COVID19
• Flu
• Rabies

Pathogen Examples
What’s
Missing?
“Prokaryotic
Archaea"

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)

• (Among scientists)
• (Or, at least among microbiologists)

Knowing Where Pathogen is on Tree of Life Matters

Lecture 10 Outline
• Pathogens and Parasites
Symbiosis
Pathogen Examples
Fighting Pathogens
Resistance

Approach 1: Limit Transmission
Attack Vectors Hygiene Physical Barriers
Building Practices
Behavioral Changes
https:// doi.org/10.1128/mSystems.00245-20.

Approach 2: Boost Immune Response

Approach 3: Treat Symptoms

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

Attacking pathogens

Thought question
Peptidoglycan is found in which organisms
A. Bacteria
B. "Prokaryotic archaea”
C. Eukaryotes
D. A and B
E. A, B and C

Thought question
Peptidoglycan is found in which organisms
A. Bacteria
B. “Prokaryotic archaea”
C. Eukaryotes
D. A and B
E. A, B and C

• 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

Attacking pathogens
Binds to, and inhibits the
function of protein (PBP)
involved in peptidoglycan
polymerization

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.

• Many possible reasons that an antibiotic
treatment would not work.
Resistance

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.

Example 2: Form biofilms

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

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 …)

Solutions to Resistance?

Solution 1: New Antibiotics
• New Ab

Solution 2: Phage therapy (viruses that kill bacteria)
Lecture 11

Solution 3: Fecal transplants
• Probiotics
Lecture 12

BIS2C2020 - Lecture 10 - Parasites and Pathogens

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