final!!! Flashcards
1
Q
biological signaling can be broken down into 3 parts:
A
input, signal transduction, output
2
Q
signaling systems can control many different
A
genes/operons at the same time
3
Q
the set of genes/operons controlled by a single signaling system is called a
A
regulon
4
Q
regulons can induce and repress
A
different genes/operons at the same time
5
Q
anti-sigma factors
A
control sigma factor availability
6
Q
sigma factors
A
proteins that bind to promoters and control gene expression
7
Q
promoter
A
region of dna where rna polymerase binds to initiate transcription
8
Q
ecf sigma factors activated by
A
degradation of the anti-sigma factor
9
Q
input signal activates
A
protease
10
Q
protease
A
enzyme that degrades proteins
11
Q
misfolded proteins
A
stress response
12
Q
spoll ab
A
anti-sigma factor in bacillus sporulation
13
Q
spoll aa
A
anti anti-sigma factor in bacillus sporulation
14
Q
activity of spoll ab is regulated by
A
activity of spoll aa
15
Q
spoll e
A
protein removes phosphate from spoll ab
16
Q
spoll aa is inactivated by
A
phosphorylation
17
Q
sporulation signal induces
A
spoll e to remove P
18
Q
two component signaling
A
major bacterial signaling mechanism with two protein components: sensor histidine kinase and response regulator
19
Q
histidine kinase
A
protein that senses extracellular signals and transfers phosphate to response regulator
20
Q
signal transduction
A
based on phosphate transfer
21
Q
response regulator
A
protein that receives phosphate from histidine kinase and activates output domain
22
Q
binding of the signal
A
induces a conformation change inside the cell
23
Q
what is caused by binding of signal?
A
the HATPase C domain cleaves ATP and place a phosphoric group on a histidine in the HisKA domain
24
Q
phosphorelay
A
longer two-component system with histidine phosphotransfer protein (Hpt)
25
phosphorylation of receiver causes conformation change that activates
the output domain, the output domain then performs its function
26
most common output domain
helix-turn-helix dna binding domain, phosphorylation activates dna binding
27
diguanylate cyclases
output domain that synthesizes cyclic-di-GMP, a second messenger
28
initial signal
first messenger
29
small molecule signal affected by first messenger, transmit signals and modulate cellular responses
second messenger
30
second messengers exist as
intracellular pools
31
pseudomonas aeruginosa has
41 different c-di-GMP metabolizing proteins
32
almost all pools have
some sort of sensory domain (not just two component kind)
33
different kinds of sensory domains
Small molecules
Redox potential
Light
Voltage
Oxygen
Nutrients
Osmolarity
Antibiotics
34
second messengers can modulate
large cellular responses
35
many different proteins sense second messengers
respond in different ways
36
response ways after sensing second messengers
gene expression
post-transcriptional/post-translational regulation
allosteric enzyme control
37
in bacteria, c-di-GMP generally governs
surface attachment lifestyle
38
low c-di-GMP
motile
39
high c-di-GMP
sessile
40
the strident response- the ribosome has an associated protein
RelA
41
when an uncharged tRNA enters and leaves the A-site,
RelA catalyzes the production of (p)ppGpp
42
the more uncharged tRNA, the more (p)ppGpp
- inhibits rRNA transcription
- inhibits tRNA transcription
- reduces mRNA transcription
- increases proteolysis
SLOWS CELL GROWTH
43
quorum sensing
population sensing mechanism in bacteria
44
quorum sensing- gram negative
acylated homoserine lactone autoinducers
45
autoinducer
small molecule used in quorum sensing to communicate between bacteria
46
quorum sensing- gram positive
small peptide autoinducers
47
what do bacteria do with quorum sensing?
pathogenesis and marine bioluminescent symbionts
48
pathogenesis
ability to cause diseases, some pathogens don't express virulence factors until signficant population density
49
marine bioluminenscent symbionts
- in fish and squid
50
hawaiian obtain squid- vibrio fischeri
quorum sensing timing mechanism so luminescent only at night
- counterilluminiation
51
catabolite repression
regulation of gene expression based on carbon/energy source availability
52
e. coli prefers glucose over
lactose
53
genes encoding enzymes that metabolize non-preferred carbon sources
may require transcriptional activation by CAP
54
CAP
protein that activates transcription of genes involved in metabolizing non-preferred carbon sources
55
transcriptional activation by CAP requires
binding by cyclic AMP (cAMP)
56
cAMP is made by
adenylate cyclase
57
a protein involved in glucose uptake
stimulates adenylate cyclase
58
cAMP with glucose
that protein is unavailable, no adenylate cyclase activity
59
cAMP without glucose
the protein is available, adenylate cyclase activity
60
cAMP
cyclic AMP, molecule that binds to CAP and activates transcription
61
adenylate cyclase
enzyme that synthesizes cAMP
62
diauxic growth
growth pattern with two distinct growth phases on different carbon sources
63
catabolite repression leads to
diauxic growth
64
d. growth chart (media with glucose and lactose)
lag, growth on glucose (catabolite repression) ON FIRST RISE, cAMP levels increase (catabolite enzymes induced) SECOND LAG, growth on lactose SECOND RISE, stationary
65
quorum sensing mechanism
by which bacteria communicate with each other
66
(p)ppGpp
molecule that inhibits various cellular processes and slows cell growth
67
firmicutes in the tree of life
second largest phylum in terms of cultured organisms (proteobacteria largest)
68
firmicutes originally grouped with
acintobacteria- both gram positive
69
firmicutes were separated based on GC content of chromosome
firmicutes- low GC
actinobacteria- high GC
70
16s rRNA sequencing show they are
different phyla, probably had a common ancestor
71
firmicutes all <50% GC content of
chromosome
72
most firmicutes have
no cell wall
73
firmicutes can subdivided based on
whether they make spores or not. FUNCTIONAL DEFINITION
74
bacillus is very common in
soils
75
bacillus is
aerobic or facultative anaerobes, often capable of using complex organic substrates (starch)
76
bacillus produce
extracellular lytic enzymes
77
some bacillus produce
antibiotics or other secondary metabolites
78
bacillus is genetically
facile (easy to use)
model for prokaryotic molecular/cell biology
79
bacillus subtitles endospore formation is
the third major model developmental system
80
how does bacillus decide when to sporulate?
through modulation of a complex phosphorelay
81
starvation induces
sporulation
82
kinA may respond to
ATP or redox levels
83
spo in sporulation (1)
spo0F transfers phosphate to Response Spo0B
84
spo in sporulation (2)
spo0B transfers phosphate to response regulator spo0A
85
spo0A turns on
sporulation
86
phosphates RapA and RapB dephosphorylate Spo0F,
preventing sporulation even though the signaling system is active
87
three other phosphates act on system,
Spo0F, Spo0B, Spo0A
88
same signals that induce sporulation also induce
competence (DNA uptake)
89
part of competence regulon is secretion of
pentapeptide outside cell
90
when pentapeptide builds up,
re-enters cell, shuts down phosphatases, sporulation starts
91
pseudo quorum
sensing system
92
sporulation is a time and energy
expensive process
93
sporulation is terminal
for the cell
94
sporulation is the last response to
starvation, worst case scenario
95
competence system inhibiting sporulation=
maybe there's some DNA out there that can help
96
pseudo quorum sensing system allowing sporulation=
im not just in trouble, everyone around me is in trouble, time to bail
97
mother cell compartment
E then K
98
forespore compartment
F then G
99
parallel sigma cascades control
separate expression programs
100
initiation
H
101
B. anthracis causes
anthrax
102
cutaneous anthrax
large, black skin lesions
103
b. anthracis was the first bacterium
conclusively linked with a disease (ROBERT KOCH 1876)
104
b. cereus almost indistinguable from
b. anthracis
105
b. cereus can cause
food poisoning (fried rice syndrome)
106
b. cereus common soil organism
coating seeds with spores increases germination
107
b. thuringiensis
insect pathogen
108
b. thuringiensis genes for
Bt toxin cloned into plants (corn)
109
b. thuringiensis (bt toxin)
-insect pests eat cropland die, no effect on people
-transgenic crop hysteria
110
clostridium
obligate anaerobes- anoxic part of soil, intestinal microflora
111
some clostridium are capable fermenting amino acids/proteins
produce foul smells
putrefying meat/flesh
112
clostridium mostly known
for the famous pathogens
113
c. tetani causes tetanus
spores enter wound and germinate
114
tetanus toxin one of the strongest on earth
- 175 nanograms cal kill 150 lb human
- despite vaccine, 700k-1 million cases per year
115
toxin produced during
sporulation, released when mother cell lyses
116
toxins of c. tetani cause
motor neurons to continuously fire
117
risus sardonicus (c. tetani)
rigid smile
118
trismus (c. tetani)
lockjaw
119
opisthotonus (c. tetani)
rigid, arched back
120
c. difficile natural intestinal microflora in part of population
nosocomial
121
c. difficile can take over
intestine after it's cleared of normal flora
- antibiotic
122
c. difficile causes pseudomembranous colitis
- bloating, diarrhea, abdominal pain
- can lead to toxic megacolon
123
c. perfringens natural intestinal microflora in part of population
nosocomial
124
c. perfringens can cause
some food poisoning, but that's not the claim to fame
125
c. perfringens causes
gas gangrene
126
gas gangrene
- infects wounds, big in war
- necrotized muscle tissue, releases gas
- causes corpses to swell up
127
c. botulinum first isolated in 1895
by emile van ermengem from home cured ham
128
botulinus- latin for sausage
apparently "sausage poisoning" was common in 18th century germany
129
botulism spores survive
canning/jarring
130
botulinum toxin causes flaccid muscle paralysis
- muscles can't contract
- good: can treat cross-eyes, excessive blinking, excessive sweating, chronic migraine
131
questionable: botox
paralyzes expression muscles to prevent wrinkles
132
staphylococci commonly found on
skin and mucous membranes of some animals
- monkeys, birds, humans
- most ae harmless
133
staph. grow in the presence of
bile salts or 7.5% NaCl
134
high salt can be used as a selective agent
mannitol salt agar
135
staph. epidermidis is one of the most common
skin microflora (everyone has this, which is good)
136
staph. epi.
- crowds out pathogens from skin niches
- teichoic acids suppress inflammation response during wound repair
137
staph. epi. most common detected in lab culturing-
contamination
138
staph. epi. is practically non-pathogenic, except for...
biofilms on plastic devices
- catheters--blockage
- heart valves-- endocarditis, sepsis
139
s. epi. biofilms very antibiotic resistant
generally have to replace the device
140
s. aureus
- forms yellow colonies
- 20% population are carriers
- mostly known for MRSA
141
virulence factors staphyloxanthin
golden pigment, antioxidant, survives reactive oxygen species generated by immune system
142
virulence factors coagulase
surface enzyme causes blood-clotting, leads to fibrin coating cell, thought to aid in phagocytosis resistance
143
virulence factors capsule
extracellular polysaccharide that prevents phagocytosis, makes biofilm
144
s. aureus diseases (localized skin infection)
- styes
- boils
- carbunkles- huge boils that leak pus
145
s. aureus diseases- diffuse skin infection
impetigo- large sores over skin surface
- break and leak pus or fluid to form scab
- most common among pre-school children or contact-sports athletes
146
s. aureus diseases non-cutaneous infections
- septicemia
- acute endocarditis
- necrotizing pneumonia
147
septicemia
whole body inflammation
- septic arthritis
148
acute endocarditis
inflammation of heart valve
149
necrotizing pneumonia
lung infection causing death of the tissue
150
styes
infected glands around the eye
151
boils
infected, pus-filled hair follicle
152
carbunkles
huge boils that leak pus
153
toxinoses- reactions to S. aureus toxins
- bacteriostatic antibiotics
- scalded skin syndrome
- toxic shock syndrome
154
scalded skin syndrome
fluid leakage through skin, causing inflammation, peeling, scaly, scabby skin
155
toxic shock syndrome
total body shock, can lead to coma, multiple organ failure, death
156
1978- proctor and gamble produces the rely long-lasting tampon
made of carboxymethylcellulose and compressed polyester beads
- absorbs 20x own weight
- also expands in width, so prevents leaks
157
1980- toxic shock syndrome defined, cases skyrocket
95% cases menstruating women using tampons
158
1982- tss linked to use of long-lasting tampons
- synthetic materials and menstrual chemistry promote s. aureus growth
159
bacteremia
removal of tampons left in too long cause tears/wound
160
tampon materials themselves inert/non-toxic
- only bacterial reaction to situation caused disease
161
tss led to legal definition of tampons as medical devices
more robust testing
162
s. saprophyticus
- part of the normal vaginal microflora
- causes 10-20% of urinary tract infections
- particularly in sexually active young women
163
s. sap. can bind specifically to urothelium
surface tissue of urinary tract
164
spermicides and candid (fungal) infection
increase risk of disease
- perturb vaginal microflora
165
streptococcus
commensal- skin, mouth, intestine, upper respiratory tract
166
strep. divided into three groups based on reaction on blood agar
alpha-hemolytic
beta-hemolytic
gamma-hemolytic
167
alpha-hemolytic
h202 produced oxidizes iron in hemoglobin, turns green
168
beta-hemolytic
hemolysis lyses blood cells, clearing
169
gamma-hemolytic
does nothing to blood cells
170
(alpha) s. pneumoniae
aerotolerant anaerobe
leading cause of bacterial pneumonia
- also causes sinusitis, meningitis, otitis (ear infection)
171
(alpha) s. pneumoniae thought to cause disease through inflammation
inflammation illness- septicemia, septic arthritis, etc
172
(alpha) s. mutans- major contributor to dental cavities
- ferment sugar to lactic acid
173
(alpha) s. mitis- insides of cheeks
- may have survived in the surveyor 3 camera on the moon for 2 years
- or someone sneezed on the camera after they brought it back
174
(alpha) s. salivarius
dorsal side of tongue
175
(beta) s. pyogenes
streptococcal pharyngitis
scarlet fever
rheumatic fever
necrotizing fascilitis
176
streptococcal pharyngitis
strep throat
177
scarlet fever
- fever, sore throat, bright red tongue, rash
- reaction to toxin produced by strains carrying t12 phage
178
rheumatic fever
inflammation involving heart, skin, joints, brain
- cross-reactivity of antibodies to streptococci with myocardium and joints
179
necrotizing fasciitis- "flesh-eating bacteria"
toxins cause destruction of muscle/skin
180
(beta) s. agalactiae
-pneumonia, meningitis in children/elderly
- colonize female reproductive tract
- can cause premature rupture of membrane during pregnancy
- transfer to infant
181
(gamma) enterococci
originally classified as strep. since they are very similar
- dna analysis indicated different genus
182
enterococci commensal in intestine
- e. faecalis (90-95%), e. faecium (5-10%) clinical isolates
183
enterococci can cause disease
uti, endocarditis, meningitis
- emerging nosocomial infection
- naturally very antibiotic resistant, gaining more
184
due to high salt tolerance, enterococci has become standard for
fecal coliform testing at saltwater
- e. coli used for freshwater
185
staph and strep inhabit similar niches,
cause similar diseases
186
after culturing patient, staph and strep can be easily distinguished by growth pattern
growth pattern
187
staphylococcus
staph- greek for grape
188
streptococcus
strepto- greek for easily twisted, chain
189
staph divide sequentially along each axis
each division leaves a thick peptidoglycan rib
190
the peptidoglycan rib directs
which axis will be used next
191
lactic acid bacteria ferments sugars to lactic acid
make own acid-tolerate low pH
192
lactic acid bacteria generally require
many amino acids and vitamins
193
lactic acid bacteria divided phenotypically on other fermentation products
- homofermentative
- heterofermmentative
194
homofermentative
streptococci, lactococcus, lactobacillus, etc.
- only make lactic acid-- emden-meyerhoff fermentation
195
heterofermmentative
leuconostoc, oenococcus, etc.
- make lactic acid, ethanol, and O2- pentose phosphate fermentation
196
sauerkraut, pickles
principally leuconostoc, mesenteries, others
197
kimchi
lactobacillus kimchii
198
salami
weissella, lactobacilli
199
beer (lambics)
yeast with 80 other bacteria, principally pediococcus
200
wine
yeast with other bacteria, oenococcus performs malolactic fermentation, creating rounder mouthfeel
201
listeria monocytogenes
- 10% of human intestines, but also a lot in food products
- most deadly food born pathogen (20-30% fatality in clinical cases)
202
listeriosis
septicemia, meningitis, encephalitis, pneumonia, and spontaneous abortion/stillbirth in pregnant women
203
(listeriosis) women advised to
avoid soft cheeses during pregnancy, good reason for everyone to avoid raw milk products
204
(listeria) moderately psychophilic- can grow in refrigerated meats
fda has approved cocktail of six bacteriophages as food additives
205
live, attenuated L. monocytogenes being developed as
cervical cancer vaccine
206
l. monocytogenes flagella inactive at 37ºC,
move in eukaryotic cells by polymerizing actin behind them, pushed like rocket
207
mollicutes- "soft/pilable skin"
- lack cell wall
- animal pathogens
- plant pathogens
- parasitic lifestyle
- basis for the first artificial life forms
208
mollicutes- animal pathogens
mycoplasma, ureaplasma
- lungs, urinary tract
209
mollicutes- plant pathogens
phytoplasma, spiroplasma
210
mollicutes- parasitic lifestyle- degraded genome
- require host for many biological molecules
- m. genitalium genome 580 kbp, 482 genes
- smallest known Buchner aphidicola, 357 genes
- some candidate organisms estimated between 169- 242 genes
211
mycoplasma, minimal genome project started with M. genitalium genome (482 genes)
and deleted genes until they found the fewest that could support life (382 genes)
212
mycoplasma, minimal genome project: 2008
synthetically synthesized genome with 382 genes and included watermarks
213
watermarks
small sequences that make peptides coded peptides
214
mycoplasma as artificial life
-synthetically made the M. mycoses 1.2m genome from computer file
- put into m. capricolum cell with original dna removed
- new cell was viable and behaved like M. mycoses (synthia)
215
july 2012- made computer simulation of m. genitalium
doubles in computer every 10 hrs, like in real life
- can now do experiments in M. genital without having to work with organism
216
protein export
moving a protein across a membrane
217
protein secretion
moving a protein into the extracellular medium
218
bacteria have multiple destinations proteins can go- gram positive
Cytoplasm
Membrane
Cell wall
Medium
219
bacteria have multiple destinations proteins can go- gram neg
Cytoplasm
Inner Membrane
Periplasm
Cell Wall (rare)
Outer membrane
Medium
220
getting proteins across the membrane- general protein export
- the sec system (or general secretory pathway)
- major protein export system in all bacteria
221
general protein export functions to
-translocate proteins across the cytoplasmic membrane
-embed integral membrane proteins into the cytoplasmic membrane
222
protein export is determined by a signal (leader) sequence
-found at n-terminus of protein
- NOT A SPECIFIC PROTEIN SEQUENCE
223
three general regions of signal sequence
- a basic region (1-3 positive amino acids)
- hydrophobic regions (about 15 aminos acids, inserts into membrane)
- signal peptidase recognition region (site where signal peptide is cut, removed from rest of protein if necessary)
224
signal peptidase cleave site
site where signal peptide is cut, removed from rest of protein if necessary
225
protein + signal=
preprotein
226
secB (chaperone) binds newly translated protein,
prevent secondary/tertiary structure protein folding would interfere with export
227
secB hands protein off to SecA,
protein associated with SecY/SecE transmembrane pore
228
basic region of signal sequence associated with phosphate head group
of phospholipid
229
hydrophobic region of signal peptide begins
inserting into membrane core
230
carboxy terminus of signal sequence flips to
periplasmic side
231
pre protein enters the
translocate channel
232
secA disassociates
requires atp, small amount of protein translocated
233
proton motive force
drives rest of protein translocation
234
signal peptidase cleaves
protein off membrane (optional)
235
integral membrane proteins, exported proteins can have
stop transfer signals
- protein sequences that stop transfer, enter membrane
236
integral membrane proteins can also have
secondary export sequences
- reinitiate export at a second site
237
integral membrane proteins- combination of these signals lead to
membrane proteins of varying topologies
238
targeting of many integral inner membrane proteins is performed by the signal recognition particle
- SRP recognizes signal peptide as ribosome translates
- Pauses translation and brings signal peptide to Sec system
239
second export method- TAT Export (twin arginine translocation)
found throughout all bacteria, archaea, plant chloroplasts and mitochondria
240
TAT Export translocates folded proteins across cytoplasmic membrane
- Extracellular/periplasmic space harsher environment for folding
- Some proteins may required cytoplasmic chaperones for proper folding
- May require cofactors found in cytoplasm
- Translocates multiprotein complexes, including those without export signals (hitchhikers)
241
TAT signal peptide-sec
both have general features, but TAT has specific sequence
242
TAT signal peptide- n-region
positively charged
243
TAT signal peptide- h-region
hydrophobic
244
TAT signal peptide- C-region
signal peptide recognition
245
what about the other destinations? periplasmic proteins
already in periplasm, no direction necessary
246
what about the other destinations? cell wall proteins
- In appropriate compartment after export
- Covalently attached to peptidoglycan by sortases
- Recognize C-terminal sortase sequence
247
what about the other destinations? outer membrane proteins
- No specialized membrane-embedding system
- Self assemble into outer membrane
248
what about the other destinations? outside the cell- secretion systems
a gram negative problem
249
type 2 secretion
- major secretion pathway
- related to type iv pilus assembly
- requires proteins to be transported to periplasm by sec/tat pathway first
- secretion signal not well-understood
- large multiprotein complex
250
type 2 secretion- large multiprotein complex
- inner membrane/cytoplasmic platform powered by ATP
- pseudopilus used as piston to push folded proteins through outer membrane pore
251
type 1 secretion
- one family of efflux pumps
252
efflux pumps
protein-based transporters
-- Toxins
--Antibiotics
--Heavy metals
253
all families of efflux pumps have
same basic organization
254
type 1 secretion uses atp to
translocate proteins
255
type 1 secretion recognizes c-terminal
motif on exported protein (not cleaved)
256
type 1 secretion often has 1
transporter for 1 protein
257
type 3 secretion
-used for pathogenesis
-related to flagellum structure
258
type 3 secretion- related to flagellum structure
- Share basal body structure
- Flagellum has built in protein secretion mechanism to form structure
259
type 3 secretion proteins secreted:
- Probably uses ATP
- Recognized by N-terminal signal (not cleaved)
260
needle
tube that connects bacterial cell to eukaryotic target cell
261
type IV secretion used for
- pathogenesis
- translocation of oncogenic DNA/effectors
- bacterial conjugation
- competence
262
type IV secretion structure
pilus structure with macromolecules passing through pilus tube
263
type IV secretion proteins secreted
- c-terminal secretion signal and accessory factors/chaperones
- likely powered by ATP
- cytoplasm to outside, some examples of periplasm to outside
264
type V secretion
- autotransporters or two-partner secretion
- secreted to periplasm by Sec/Tat
265
type V secretion- autotransporter
- C-terminal region of protein forms beta-barrel in outer membrane
- N-terminal portion passes through barrel
- Either stay as is, or be released from barrel by proteolysis (autoproteolysis or dedicated protease)
266
type V secretion- two partner secretion
same as auto transporters except beta barrel is separate protein
267
type VI secretion
- found in about 1/4 of sequenced gram negative genomes
- similar to tail/spike of T4 phage
- symbiosis, pathogenesis, intermicrobial interaction/competition
268
flagellar motility is based on
rotation of the flagellum filaments
269
the helical structure of flagellum filaments/ bundles provides
propulsion
270
e. coli has peritrichous flagella that form a helical
bundle when swimming smoothly (running)
271
when e coli wants to change direction,
it changes the rotation of its flagella
272
this rotational change causes the flagella to fly apart from the bundle and
rotate separately, reorienting the cell (TUMBLE)
273
changing the rotation of the flagellum to alter the running/ tumbling behavior is
a generally conserved aspect of swimming motility regardless of the number and placement of the flagella
274
tumbling frequency
general pattern of running and tumbling
275
tumbling frequency can be altered
in response to a chemical stimulus
276
chemotaxis
- chemoattractant
- chemorepellent
277
chemoattractant
increases running, decreases tumbling
278
chemorepellent
decreases running, increases tumbling
279
alteration of tumbling frequency can lead to
net translocation of cells up or down chemical gradients
280
swimming cells
random walkc
281
hemotaxis creates a
biased walk
282
running/tumbling behavior is controlled by the
chemotaxis signaling system (many similarities to two-component signaling systems)
283
CheA
similar to histidine kinase
284
CheW
adaptor protein
285
MCP
methyl-accepting chemotaxis protein
286
CheY- similar to response regulator
induces tumbling (CW or CCW depends on organism)
287
balance of CheY and CheY-P
determines tumbling frequency
288
binding of chemoattractant to MCP shuts off phosphorylation pathway
decreases CheY-P, reduces tumbling
289
chemorepellents induce
more phosphorylation
290
bacteria sense chemoeffectors over time
the adaptation response
291
CheB
removes methyl groups from MCPs when phosphorylated
292
CheR
puts methyl groups on MCPs constitutively
293
CheR- methyl groups
inactivate MCPs
294
explains why cells respond to chemical gradients
Require increasing concentrations of chemicals to overcome adaptation
294
adaptation response necessary so
don’t shoot past areas with desired chemicals
295
Cells sensing/sampling chemical concentration over time, not in space
- Important because cells too small to sense chemical gradients over body length
- Balance of stimulus and adaptation way of comparing chemical concentration between time points
- Chemical Marco Polo
296
the problem of "gain"- chemotaxis can respond to a chemical
at concentrations over 5 orders of magnitude
297
the problem of "gain"- chemotaxis response
- Same behavior response to 50 molecules as to 5,000,000
- MCP’s only have one substrate binding affinity
- Substrate way below affinity, virtually none bound, should get no response induction
298
chemotaxis systems must have a way to generate "gain"
- Amplify low level signals to create as robust a response as a larger signal
- Pumping up the Volume
299
a possible solution to "gain"
binding of chemoeffector to one MCP may affect conformation or those around it such that their signaling state is changed even though they are not bound to a chemoaffector
300
MCPs are found in dimers
dimers binders to groups of three
- trimers of dimers hexagonally pack into chemoreceptor arrays
301
phototaxis
lighta
302
aerotaxis
oxygen- can be o2 directly or redox state of cytochrome pool
303
magnetotaxis
- Some bacteria produce magnetosomes, chains of magnetite crystals in cell
- Cells align along magnetic pole of the Earth
- Northern Hemisphere cells swim to the North Pole, opposite in Southern Hemisphere
- Poles underground, causes cells to move up/down water column
- Magnetotactic bacteria obligate microaerophiles/anaerobes
304
surface motility using flagella- swarming motility
-requires peritrichous flagella
- cells gather together and move as groups
- requires production of a surfactant
305
surface motility using flagella- swarming motility requires p. flagella
- Cells will often swim with one flagellum, but change to multiple flagella to swarm
- Swarming flagella genetically distinct from swimming flagella, e.g. Vibrio parahaemolyticus
306
cells gather and move as groups
"rafts"- swarming cells fall out of rafts and become non-motile
307
surface motility using flagella- swarming motility require production of surfactant
chemical that reduces surface tension, essentially a lubricant
308
twitching motility
Uses polar Type IV pili
Pilus extends and attaches to substrate
Pilus retracts, pulling cell forward
309
Gliding Motility
- work of myxococcus xanthus
- attachment of focal adhesion sites to a substrate
- adhesion sites cycle around the cell proppeling it forward
310
M. xapnthus secretes a polyscarrachride slime
- Likely serves as self-made adhesion substrate
- Analogous to laying down track in front of a moving train
311
Mycoplasma are obligate
pathogens/parasites
312
M. pneumoniae
walking pneumonia
313
Mycoplasma are smallest genomes of all bacteria
- 580-860 kbps (~1/10 of most bacteria)
- Likely genome degraded
- Relies on host for many essential functions
----Cannot make purines
314
mycoplasma lack a cell wall
so they have unusual cell shape
315
mycoplasma UGA codon not to stop,
tyyptophan
316
mycoplasma move by
proteins on their terminal organelle
317
actinobacteria- gram
positive
318
actinobacteria- shape
rods or filamentous
319
actinobacteria- respiration
most respire aerobically, some fermentation
320
actinobacteria- location
common in soils, some pathogens
321
actinobacteria- diversity
large diversity at suborder level
322
actinobacteria- >50%
GC content genome
323
Deinococcus radiodurans
Bacteria – carries 4-10 copies of its chromosome
- Can survive 15,000 Grays ionizing radiation with 37% loss of viability
- 5 Grays will kill a human
324
deinococcus is NOT in
the actinobacteria
325
kineococcus and rubrobacter ARE
in the actinobacteria
326
kineococcus and rubrobacter are as good at radiation resistance as
deinococcus
327
propionic acid bacteria
- aerotolerant anaerobes
- can ferment lactic acid
- unique ability to propionic acid and co2 from fermentation
327
propionic acid bacteria- fermentation
unusual transcacrboxylase enzymes acting on succinate
328
propionic acid bacteria- can ferment lactic acid
fermentation of a fermentation product is "secondary fermentation"
329
propionibacterium acnes
lives on skin, sweat glands, sebaceous glands--> causes acne
330
propionibacterium freudenreichii
- used for swiss cheese, propionic acid flavor, co2 for holes
- same type of organism that causes pimples makes swiss cheese
331
bifidobacteria-anaerobes
- one of the most common commensal bacteria
---- one of the most common probiotic organisms
332
bifidobacteria dominate infant gut microflora
- infant associated bifidobacteria display milk oligasaccharide utilization
- adult-associated bifidobacteria display plant oligosaccharide utilization
333
corynebacteria are
- facultative anaerobes
- common in soil, human commensal
- rods, often club shaped
334
corynebacterium diptheriae
- causes diphtheria
- cells infected with lysogenic B phage-- carries toxin gene
- colonize lesion in upper respiratory tract
- general antibiotic sensitive, easily controlled by vaccination
335
corynebacterium diptheriae- lysogenic B phage
- toxin gene depressed by low iron
336
corynebacterium diptheriae- lesion
- toxin causes necrotic injury to epithelial cells
- platelets leak out, form pseudomembrane of dead cells, fibrin
- c. diphtheria grows in it
- can spread to lungs- suffocation, also toxin illnesses
337
corynebacterium diptheriae- general antibiotic sensitive
- 3 cases in US between 2000-2007
- fall of USSR- vaccination decreased, 200k, 5k deaths in 1998
338
mycobacterium tuberculosis id
1-10 cells
339
mycobacterium tuberculosis- first line treatment
rifampicin and isoniazid
340
mycobacterium tuberculosis (multi-drug resistant)
resistant to first line
341
mycobacterium tuberculosis- extensively drug resistant (XDR)
resistant to first and second line
342
mycobacteria
- Aerobic, mostly aquatic
- Can live in chlorinated tap water
- Some obligate pathogens
343
Mycobacteria tuberculosis
- Causes Tuberculosis (Consumption)
- Infects alveolar macrophages
- 50% mortality if untreated
- One-third of population is infected (nearly 3 billion)
------80% Asia, 5-10% US
344
Mycobacteria leprae
- Causes Hansen’s Disease (Leprosy)
- Divides every 15-20 days
----Never successfully cultured outside of cells
- Transmitted by close, prolonged contact – nasal droplets
------Major source for US is from armadillos (including Mississippi)
345
Mycobacteria leprae 2
- Entry and exit route from humans not known (disease not understood)
- Primarily infects nerve cells – inflammation response kills nerves
-----Numbness --> untended lesions --> necrosis and limb removal
346
mycelia are acid fast
mycobacteria appear weakly gram positive or variable
- acid fast due to their unusual cell wall
347
acid fast staining procedure
- Initial stain taken by cells
- Decolorize with acid/alcohol mixture
- Counterstain
- Acid Fast bacteria retain initial stain
348
myolic acids of m. tuberculosis
- creates outer layer 3-4 times thick as normal membrane
349
actinomyces
- facultive anaerobes, but prefer anaerobic
- similar to nocardia in lifestyle
- grow as branching filaments, fungi-like
350
actinomyces location and characteristics
- very common in soil, normal commensal of gingival area of mouth
- opportunistic pathogen in mouth
- dental procedures
- actinomyces Israelii most common pathogen
351
actinomycetes- streptomyces coelicolor
- model developmental organism
- closest thing to a bacterial fungus
- grows in hyphae
- well-known and utilized for secondary metabolite production
352
streptomyces coelicolor- hyphae
- long, branching filaments
- grow below surface (soil, agar)
- produces aerial hyphae, spores develop at the tip
353
streptomyces coelicolor- secondary metabolite production
- Antibiotics, antifungals, antiparasitics, geosmin, etc
- Two-thirds of clinical antibiotics of natural origin from Actinomycetes
354
coriobacterium
- Anaerobe
- Ferments glucose to acetic acid, lactic acid, ethanol, CO2, H2
- Commensal symbiont in the midgut of Firebugs
355
gut microflora
- huge field of research
- the types of microbes that live in insect guts determine what they can eat
356
gut microflora- lower termites
- Termites ingest wood pulp (cellulose, lignin), can’t metabolize it
- Some bacteria ferment to short chain fatty acids
- Protists metabolize to CO2 + H2
- wood pulp nitrogen poor
-hindgut
357
gut microflora- protists metabolization
- Bacterial exo/endosymbionts with protists
-----Methanogenesis (CO2 + H2 CH4)
------Acetogenesis (CO2 + H2 Acetate)
358
gut microflora- wood pulp nitrogen poor
- bacteria recycle uric acid
- nitrogen fixation
359
hindgut
anaerobic digestor-- up to 1/3 body weight of termite
360
ant agriculture
- ants collect plant material, return to special garden in nest
- pulp material, inoculate with fungus
- ants carry actinobacteria on cuticle
361
ant agriculture- pulp material
- Single cultivar of fungus, cannot live outside nest
- Fungus grows, produces gongylidia
----- Swollen hyphal tips rich in lipids/carbohydrates
----- Ants harvest gongylidia for food
362
ant agriculture- escovopsis
specifically infects fungal gardens
363
ant agriculture- carry actinobacteria (streptomyces, pseudonocardia)
- Bacteria produce antibiotics/antifungals
- Ants use bacteria to “weed” their garden
364
cyanobacteria
oxygenic photosynthesis
365
chloroflexi
an oxygenic photosynthesis, green non-sulfur
366
chlorobi
anoxygenic photosynthesis, green sulfur
367
cyanobacteria
- gram negative
- oxygenic photosynthesis, calvin cycle carbon fixation
- widespread in water (fresh/salt)
- "blue-green algae"
368
cyanobacteria- photosynthesis, carbon fixation
Chlorophyll a and phycobilins (secondary pigments) in thylakoid membranes
369
cyanobacteria- in water
surface soil layer, even in deserts
370
cyanobacteria- "blue-green algae"
- Phycobilins give blue color
- Weren’t considered bacteria
- 16S rRNA sequencing clearly shows prokaryote
371
nitrogen starvation induces
heterocyst formation
372
heterocysts
terminally differentiated cells
373
heterocysts- 3 exterior layers
- Glycolipid
- Compacted polysaccharide
- Un-compacted polysaccharide
374
heterocysts-
degration of photosystem 2
--- ceases oxygenic photosynthesis
scavenging of excess o2
--- production of nitrogenase
cell dedicated to n2 fixation
375
heterocyst cannot fix carbon
need from other cells
376
regular cells need nitrogen
from heterocyst
377
metabolites diffuse
through the filament
378
heterocyst form at regular intervals in filament
Cells starve for nitrogen
Cell turning into heterocyst produces small peptide that inhibits heterocyst formation in adjacent cells
Peptide forms gradient through filament
Where peptide concentration low enough, heterocyst develops
379
why have regular spaced heterocyst?
- Terminally differentiated and energetically costly
- Spaced to have maximum effect with minimum number
380
heterocyst- akinetes
Large granular-looking cells
Induced by starvation
Granules of storage polymers
Glycogen – carbon
Cyanophycin – nitrogen
Metabolically dormant
Cold and desiccation resistant
Not heat resistant
Not a spore, more of a cyst
381
akinetes often form in patterns when heterocysts are present
- pattern dependent on organism
- random when no heterocyst present
382
some genes in cyanobacteria display patterns of gene expression based on
diurnal (light/dark cycle)
383
synechocystis
Hooked a bioluminescent reporter up to a gene encoding part of Photosystem II
Measured luminescence over time
384
64% of all synechocystis genes display "circadian rhythms"
Cyanobacteria circadian rhythm controlled by “molecular clock”
-- KaiA, KaiB, KaiC proteins
-- KaiC phosphorylated on multiple sites
-- Phosphorylation level changes over time
385
circadian rhythm
repeated biological process based on 24 hour light/dark cycle
- Cycle sensitive to light (resetting)
- Found in bacteria, fungi, plants, animals (humans)
386
molecular clock can be reconstituted in vitro
KaiA + KaiB + KaiC + ATP
387
circadian rhythms provide selectable advantage to cyanobacteria
89% of photosynthesis genes circadian regulated
388
Biotechnology with cyanobacteria during day
Photosynthesis, fix carbon, produce ethanol
Ethanol evaporates into headspace of reaction chamber
389
Biotechnology with cyanobacteria- during night
Ethanol condenses on sides of chamber (solar trap/still)
Collected and purified
390
Biotechnology with cyanobacteria- sept 2012
Algenol claims make 7,000 gallons/acre/day
Meet US gas needs by 2025
Require area 1/10 of other bioethanol processes (corn)
Half a county worth of land
Requires only freshwater, minerals
391
prochlorophytes
Subgroup within cyanobacteria
Use Chlorophyll b instead of phycobilins
Can be very small cells
Can be in open ocean
Prochlorococcus
Can be marine invertabrate symbiont
Prochloron (sea squirt)
Nearest common ancestor to chloroplasts
392
chloroflexi
- Green non-sulfur bacteria
- Anoxygenic photosynthesis
- Use organic carbon sources
- Gram Positive cell wall (stain Gram Negative)
- Mostly thermophiles (hot springs)
393
chloroflexi- photosynthesis
Do not use H2S as electron donor
----Some do
394
chloroflexi- gram + cell wall
Different peptidoglycan size/composition
No peptidoglycan, use S-layer
395
chloroflexi- thermophiles
Some mesophilic chemoheterotrophs found
396
Herpetosiphon aurantiacus
- Aerobic heterotroph common in high nutrient environments
- Long filaments, able to glide and prey on other bacteria
397
Herpetosiphon giganteus
16 restriction enzyme
398
Herpetosiphon giganteus – 16 restriction enzyme systems
Dehalococcoides ethenogenes
can metabolize chlorinated industrial solvents
Recent analysis suggests might be distinct lineage from Chloroflexi
399
chlorobi
- green sulfur bacteria
- Anoxygenic photosynthesis
- Fix carbon by reverse TCA, not Calvin Cycle
- contain Chlorosomes
400
chlorobi- photosynthesis
- use H2S as electron donor
- Elemental S waste deposited outside cell
- Not in periplasm, like purple photosynthetic bacteria
401
chlorobi- chromosomes
Efficient light harvesting complexes, use low intensity
Live deeper in water column where H2S concentration higher
----Can live at 100 m depth, few photons/chlorophyll/day
One found living near “black smoker” 2,500 meters ocean depth
----Living off glow of vent, no sunlight gets down that far
402
chlorosomes
Contain huge stacks of pigment – no protein
403
deinococcus- thermus clade
Gram Negative, stain Gram Positive due to thick peptidoglycan layer
Resistant to hazardous environments
404
Deinococcus radiodurans
Bacteria – carries 4-10 copies of its chromosome
Can survive 15,000 Grays ionizing radiation with 37% loss of viability
5 Grays will kill a human
405
Thermus- Thermus aquaticus
- identified from hot spring in yellowstone
- growth range- 50º to 80ºC
- chemolithoautotroph
- source of taq polymerase
406
Thermus- Thermus aquaticus- Taq polymerase
- Thermostable DNA polymerase
- Sparked development of PCR
----Could be heated repeatedly without losing activity
- No 3’ exonuclease
--- More error prone, 1 in 1000 bases
- Puts A’s on the ends of PCR fragments
407
bacterioides
one of two phyla that dominate gut microflora (firmicutes)
---- 10^10-10^11 cells/gram human feces
- digests soluble dietary fiber
---- 18% genome dedicated to polysaccharide utilization
408
bacteroides health risks
Usually harmless, but can act as repository of antibiotic resistance systems that spread to pathogens
B. thetaiotaomicron, B. fragilis
Opportunistic pathogens, common abdominal infection
409
bacteroides fun fact
Bacteroides in guts of native Japanese have special enzyme for degrading seaweed sulfonated-polysaccharides (not found in Westerners)
---Picked it up from marine bacterium Zobellia galactanivorans by horizontal gene transfer
410
spirochetes
- Long, thin, tightly-spiraled cells
- Heterotrophs
- Have flagella in the periplasm (axial filaments)
- Widespread in water
- Several important pathogens
411
leptospira
- causes leptospirosis (canefield fever, fort bragg fever, black jaundice, rat chasers yellows)
- infects most mammals
--- causes disease in dogs
--- transmitted to humans through contact with animal urine
- common among ribal native americans
--- constant contact with infected waters
- outbreaks in ww1
--- pooled water in trenches (gallipoli)
2010- killed british rower andy holmes
412
leptospira symptoms
Phase 1 – flu-like (fever, chills, ache, vomiting), then clears up
Phase 2 – meningitis, renal failure, liver failure (jaundice)
413
Borrelia burgdorferi
Causes Lyme Disease (endemic to North America)
Identified in Lyme, Connecticut
- does not require Fe, uses Mn for all processed
---- works well in pathogenesis
414
Borrelia burgdorferi
transmission
Transmitted by Ixodes ticks
-- Lives in digestive tract tick
-- Transmitted when bacterium travels to salivary gland while tick is feeding
-- Usually only occurs 24 after feeding initiated
415
lyme disease- early localized infection
Bullseye rash at bite, potentially flu-like symptoms, ~20% asymptomatic
416
lyme disease- early disseminated infection
bacteria, rashes at other sites, potentially facial palsy/meningitis
417
lyme disease- Late disseminated infection
shooting pains, numbness, severe joint pain, paraplegia
Psychosis – anxiety, panic attacks, delusions, depersonalization (detachment from reality)
418
Treponema pallidum
causes and transmitted through
- Causes Syphilis
- Transmitted through sexual contact
----- Also mother-to-fetus during pregnancy/birth (congenital syphilis)
419
Treponema pallidum
stages
Stage 1 (3-90 days) – single chancre (firm, painless, non-itchy ulceration) point of infection
Stage 2 (4-10 weeks) – rash (red papules, white pustules, both infectious) over torso/extremities, characteristically on palms and soles
Stage 3 (10 weeks to 3 years) – asymptomatic latency
Stage 4 (3-15 years) – cardiovascular, neurological, gummatous (gummas = soft, tumor-like balls of inflammation on skin/bone/liver)
420
Treponema pallidum
- congenital
Congenital – two-thirds born asymptomatic, develop later
Rash, fever, neurosyphilis, large liver/spleen deformed clavicle, “saber shin”, “saddle nose”
421
Syphilis in History
The Columbian Exchange – exchange plants, animals, people and diseases between Europe and Americas
Evidence indicates Syphilis in Americas, brought back to Europe
First European outbreak recorded in 1495 – French troops besieging Naples, Italy (Spanish mercenaries from Columbus’ trip)
Native Americans gave Europeans syphilis, Europeans gave Native Americans smallpox
Major cause of death during the Renaissance
Much more virulent then than now
422
syphillis name coined by fracastoro
Made Syphilis name of sheepherder in poem that first contracted disease, then used in own medical textbook
423
tuskegee syphilis study
USPHS never told them they had syphilis and didnt get treatment
--- 28 died of syphilis, 100 of related complications, 40 wives contracted disease, 19 children congenital syphilis
424
T. pallidum subspecies cause other diseases
- beiel
arid countries of Mediterranean, West Africa
-- Small mucosal patch in mouth, eroding lesions on body, inflammation of leg bones, gummas on nose/mouth
-- Transmitted by mouth/mouth contact, sharing utensils
425
T. pallidum subspecies cause other diseases
- pinta
Mexico, Central/South America
Papule at contact, flat lesions over body, mixture of hyperpigmentation/depigmentation
Transmitted by skin/skin contact
426
T. pallidum subspecies cause other diseases
- yaws
humid tropical latitudes
Warty nodules, widespread skin ulcers, destruction of joints/soft tissue
Transmitted by skin/lesion contact
Been with homonids 1.5 million years
427
chlamydia
Obligate intracellular pathogens
Humans, mammals, birds, protozoa
Little biosynthetic capability (~600 genes)
Have an unusual cell cycle, two forms
Elementary body – similar to spore
Infectious form, taken into cell by phagocytosis
Turns into reticulate body
Reticulate body – growth form
Grows by binary fission
New cells turn into Elementary bodies
Host cell bursts, releasing Elementary bodies
428
Chlamydia trachomatis
Causes Chlamydia
Most common STD
2.5 million cases/year in US
- eye infection
---- Was a major cause of blindness until ~15 years ago (now 3.6%)
429
Chlamydia trachomatis
- presentation
Men – clear/white discharge from penis
Women – “Silent Epidemic”, 50-70% cases asymptomatic
Pelvic Inflammatory Disease (inflammation of reproductive organs)
Scarring, ectopic pregnancy, spontaneous abortion, sterility
Passed to child during birth
430
Verrucomicrobia
New recognized phylum
Few cultured species
Environment DNA analysis suggests may be one of the most abundant bacteria in water/soil
Verrucamicrobium spinosum was first described
Has small stalks, make cell look “warty”
431
Epixenosomes
Euplotidium is marine unicellular ciliate
Has on surface a zones of epibionts
Bacteria that live on the outside of another organism
Bacteria belong to Verrucomicrobia
Bacteria attach and grow for a while by binary fission
Then differentiate into epixenosomes
Cell have coiled protein filament, surrounded by “basket” of tubulin
432
When Euplotidium is attacked by another ciliate, Litonotus lamella, the “bacteria” sense it
Can be stimulated in lab by adrenaline
Bacteria respond in activation of cyclic-AMP system
433
Bacteria burst, extend 40mm long filament, tipped with compacted DNA
Fights off predator (unknown mechanism)
Similar in concept to jellyfish nematocyst
434
Fusobacteria
Anaerobic, Gram Negative
Rods with tapered ends
Ferment carbohydrates/amino acids
Butyrate, acetic acid products
Commonly found in mouth, other mucus membranes
Cells exceptionally good at sticking to other cells
Colonize established biofilms in mouth (plaque)
Cause disease
435
Disease causing Fusobacteria
Streptobacillus moniliformis
Causes Haverhill Fever (form of Rat-Bite Fever)
Spirochaete-based Rat-Bite Fever – in Japan called Sodoku
Bite or exposure to mucosal secretions/urine from rodents
Flu-like symptoms, rash
Generally not fatal, especially with treatment
436
Disease causing Fusobacteria
-Fusobacterium polymorphum
Found in human gingival crevice
Implicated in various periodontal diseases
437
Disease causing Fusobacteria
- Fusobacterium necrophorum
10% acute sore throats, 21% recurring sore throats, 23% peritonsillar abscesses
Lemierre’s Syndrome
Bacteremia leading to thrombosis (blockage) of jugular vein, then to lungs, brain vessels
Often F. necrophorum secondary infection on primary throat infection (Strep)
438
Caldiserica
Caldisericum exile
Gram Negative, anaerobic thermophile
65oC optimum
10.4 hr doubling time
Non-sulfate sulfur reducer
Multicellular filaments
Single polar flagellum, for some reason
439
Gemmatimonadetes
Gemmatimonas aurantiaca
Gram Negative, facultative anaerobe
Heterotrophic
Common in soil
Produces unusual carotenoids
Grows slowly
2 weeks for colony to arise
440
Elusimicrobia
Elusimicrobium minitum
Only member of Termite Group 1 phylum
Isolated from scarab beetle intestine
Gram Negative anaerobe
Ferments sugars
Takes 4 weeks to form colonies
Only noticed when sealed tubes sitting for 6 months looked contaminated
441
Elusimicrobia
Elusimicrobium minitum
- It is an Ultramicrobacterium
Cell volume <0.1 mm3
E. coli = 0.7 mm3
So small it passes through filter normally used to sterilize solutions
When growing rapidly, total cell size has to elongate to accommodate increased ribosome number
National Academy of Science panel concluded life must have at least 0.2 mm diameter
E. minitum diameter 0.17-0.3 mm
442
Chrysiogenetes
Chrysiogenes arsenatis
Gram Negative anaerobe
Isolated from reed bed enrichments
Heterotroph
When grown on acetate could only use nitrate as electron acceptor
Can grow on other carbon sources, but requires arsenate as electron acceptor
443
What are the Archaea?
Distinct evolutionary lineage – unique from bacteria and eukaryotes
Have characteristics in common with other lineages
444
archaea- similar to bacteria
Unicellular, small cells with no organelles
Circular genome
Genes in operons with no introns
445
archaea- similar to eukaryotes
No peptidoglycan
DNA replication, repair, association with histones
Transcriptional machinery (promoters, Met initiation, polymerase)
446
Unique to Archaea
Cell wall (pseudomurein, sole S-layer)
Ether lipids (found in bacteria but very rare)
Translation (ribosome structure, tRNA sequences)
447
So where are these special bugs?
archaea
Originally thought to be confined to most extreme environments
Hot springs, acidic lakes, etc
DNA sampling indicates much more widespread
Soil, lakes, ocean, etc
No spore-formers
No pathogens
Some are commensal (e.g. intestine)
448
Archaeal Phylogeny- phyla
Two major: Euryarchaeota and Crenarchaeota
“Korarchaeota” deeply branching phylum
Related to Crenarchaeota
“Nanoarcheota” – based on single species found in 2003
Another potential group of ultrasmall archaea found in 2006
“Thaumarcheota” group proposed in 2008
449
Euryarcheota
Largest archaeal group
Found in broad range of environments
Major groups
Halophiles
Methanogens
Thermoplasmas
Hyperthermophiles
450
Halophiles
Require high salt concentration for growth
Most can live in saturated salt solutions
35% NaCl, 10x concentration salt water
Face a unique problem – reversal of osmotic pressure
Accumulate ions in cell to balance osmotic equilibrium
K+
Halorhodopsin
Related to rhodopsin that senses light in human eye
Light-driven Cl- pump, accumulates Cl- in cell against gradient
Bacteriorhodopsin
Light-driven H+ pump
Generates Proton Motive Force, completely different than ETS
Most studied: Halobacterium – found in Great Salt Lake, Dead Sea, etc.
451
Methanogens
Obligate anaerobes
Sensitive to even trace amounts of O2
Generate CH4
Some from carbon substrates
Many from H2 + CO2 (autotrophic)
Most mesophilic, some thermophiles
Common in anoxic environments
Intestines, wetlands, deep subsurface, wastewater plants
Diverse group
452
How Methanogens led to the internal combustion engine
Alessandro Giuseppe Antonio Anastasio Volta
Known for works in electricity
Voltaic Pile – predecessor to the battery
1776 – noticed bubbles rising from disturbed mud in Lake Maggiore
Wanted to experiment with the gas
Voltaic Pistol
Device to capture marsh gas, detonate it
Measured force of explosion
Led to first measurments of O2 in atmosphere
Voltaic Pistol predecessor to internal combustion engine
453
Thermoplasmatales
Hyper-acidophilic (pH <2.0)
Some also thermophilic
454
Thermoplasmatales
Thermoplasma
Facultative anaerobe (O2 or S electron acceptor)
Found originally in coal refuse piles
455
Thermoplasmatales
Ferroplasma
Chemoautotrophs (Fe2+ electron donor)
Found in mine tailings – oxidize pyrite (FeS), produce acid
Tailings = leftovers after ore extraction, very toxic
456
Thermoplasmatales
Picrophilus
Optimal growth pH 0.7 (lowest known, like sulfuric acid)
Found in acid hot springs
This bug lives in boiling acid
457
Hyperthermophilic Euryarchaeota
Small, unrelated groups
Grow at very high temperatures (>85oC)
Branch close to the root of archaeal tree
458
Pyrococcus furiosus
Growth optimum 100oC
Growth maxiumum 103oC
Anaerobic heterotroph
- Produces CO2 + H2, but H2 is toxic to organism
- Uses S to make H2S, gets no energy from reaction
Found in geothermal marine sediments
Enzymes
- DNA polymerase Pfu alternative to Taq
- Some enzymes require tungsten (unique)
459
Crenarchaeota
Cultured: genetically diverse hyperthermophiles
Environmental DNA: may be most abundant Archaea in ocean (all temps)
Phenotypically separated based on environment
Terrestrial (hot springs)
Submarine (hydrothermal vents)
460
Terrestrial Hyperthermophilic Crenarchaeota
Sulfolobus (spherical with lobes)
One of the most studied (easy to culture)
Aerobic chemoautotrophs (Fe2+, H2S, S electron donors)
Can use organic substrates with aerobic respiration
Found in sulfur-rich hot springs (up to 90oC)
461
Terrestrial Hyperthermophilic Crenarchaeota
pyrobaculum
Facultative anaerobes (S, NO3- electron acceptors)
Found in neutral/alkaline hot springs
462
Submarine Hyperthermophilic Crenarchaeota
Includes most thermophilic Archaea
Found around deep sea hydrothermal vents
>100oC, 2,000-5,000 m deep
463
Submarine Hyperthermophilic Crenarchaeota
pyrodictum
(growth optimum 105oC)
Disc-shaped cells growing as mycelium
Obligate anaerobes
Oxidize organics or H2
S electron acceptor
464
Submarine Hyperthermophilic Crenarchaeota
Staphylothermus
(growth optimum 92oC)
Growth pattern resembles Staphylococcus
Ferments proteins
465
Submarine Hyperthermophilic Crenarchaeota
Pyrolobus fumarii
Most thermophilic organism known
Can grow at 113oC, survive at 121oC (autoclave)
Autotroph, H2 donor, NO3-/thiosulfate/low O2 acceptor
466
Korarchaeota
No cultured isolates
Can culture with other organisms
Only been found in hydrothermal environments
Originally sequenced 16S from Obsidian Pool, Yellowstone
Branch very closely to base of Archaea
May be similar to ancient life
467
Nanoarchaeota
Appear to be tiny, parasitic cells on some thermophilic Crenarchaeota
Distinct from other Archaea, but not much else clear about them
Nanoarchaeum equitans (only named species)
Lives on Ignicoccus
1/100 size of E. coli
Very small genome (490 kbp, smaller than Mycoplasma)
Cannot make amino acids, lipids, nucleotides, cofactors
Does have DNA replication/repair machinery
Not clear if it can make it’s own ATP (is this alive?)
468
Thaumarchaeota
Newly-proposed phylum
Four species
- Nitrosopumilus maritimus
- Cenarchaeum symbiosum
- Nitrososphaera viennensis
- Nitrososphaera gargensis
All chemolithoautotrophic ammonia-oxidizers
May be important for biogeochemical cycles
469
Nitrosopumilus maritimus
in open ocean, cultured
470
Cenarchaeum symbiosum
sponge symbiont
471
Nitrososphaera viennensis
soil
472
Nitrososphaera gargensis
46oC hot spring
473
Archaea have a lot of hyperthermophiles
How do they survive at such high temperatures?
lipids
protein
dna
temp limit prob determined by monomer stability
-- ATP breaks down quickly at 120oC, unstable at 150oC
474
lipids- archaea hyperthermophiles
Composition different so more stable (longer chain, ether linkage)
475
protein- archaea hyperthermophiles
Different amino acid composition to make more stable
More densely packed, less floppy parts
More chaperones (aid in folding)
476
dna- archaea hyperthermophiles
Reverse Gyrase adds positive supercoiling
Only found in organisms >70oC
Most genomes negatively supercoiled
May have proteins/salts to prevent denaturing
477
viruses
Genetic elements need host cell to replicate
DNA or RNA
Replicate independently of host chromosome
Have stable, transmissable extracellular form
Different from plasmids
Formation of extracellular form usually destructive to host cell
Classified based on host
Bacteriophage viruses that infect bacteria
478
Where do viruses come from? RT
Regressive theory – were bacteria that degraded
E.g. Nanoarchaeota
479
Where do viruses come from? COT
Cellular origin theory – were plasmids that grew up
Plasmids that transfer are kind of like virus genomes
480
Where do viruses come from? CT
Coevolution theory – independent origin
Ancient; evolved with cells from the beginning
481
virus composition
Extracellular form = virus particle, virion
Nucleic acid surrounded by protein coat (capsid)
Intracellular form = just the genome
Genome comes in variety of flavors
DNA or RNA
Single or double-stranded
Linear or circular
482
Virion structures
Small
Generally 1/100 size bacteria
Small genome
Generally 5,000-200,000 bp
Capsid
Repeating structural protein subunits (capsomers)
Capsomers self-organize
Nucleic acid + capsid = nucleocapsid
Some nucleocapsids surrounded by lipid bilayer
Envelope
483
Virus shapes
Rod-shaped- Helical symmetry
Spherical-shaped- Icosahedral symmetry
Complex- Multiple symmetrical parts
484
virus replication Step 1: Attachment (Adsorption)
Virion has outer proteins that recognize specific host surface protein (receptor)
Virus proteins in capsid or envelope
Receptors usually perform other necessary function
Virus coopts protein for own use
Can have different stages of attachment through different structures
No receptor, no attachment, no infection
Virion receptor recognizing proteins good targets for antibodies
Antibodies physically block receptor binding
485
virus replication Step 2: Penetration
Whole/part of virus enters cell
Chromosome can be injected (e.g. T4 phage)
Particle can be taken in
Envelope fuses with membrane, release particle
Can be multi-stage process
Influenza virus bind receptors, taken in by phagocytosis
Acidification of phagosome alters structure of receptor-binding protein
Hydrophobic portion of receptor-binding protein initiates fusion, escape from phagosome
486
virus replication Step 3: Replication
Host cell machinery hijacked – used for viral replication
Viral mRNA made to produce “early proteins”
Mechanism varies
DNA or RNA, single or double-stranded
“Early proteins” carry out replication of viral genome
“Late proteins” expressed
Mainly for making up virion particle
487
virus replication Step 4: Assembly
“Late proteins” spontaneously assemble into capsomers
Capsomers arrange themselves around nucleic acid to form capsid
Naked virions done here
Enveloped virions derive membrane from host membrane
Virion receptor-binding proteins in envelope must be put in host membrane first
488
vis replication Step 5: Release
Mature virion particles released from host
Usually host cell lyses
Some viruses released from intact cells
489
baltimore classification system
Class I: Double-stranded DNA
Class III: Double-stranded RNA
Class V: Single-stranded RNA (Negative)
Class VI: Single-stranded RNA
(DNA intermediate)
490
Bacteriophage
Identified for many, many bacteria
Most are naked but with complex structure
Why?
Most well-studied: infect enteric bacteria
E. coli, Salmonella typhimurium
Most common: double-stranded DNA (Class I)
T4, Lambda, T7 (infect E. coli)
Also single-stranded DNA, and RNA (double-stranded, both single-stranded varieties)
491
Animal Viruses
Enveloped much more common
Whole virion enter cell
492
Animal Viruses
persistant
Virions continually released without cell death
Common for enveloped
493
Animal Viruses
latent
Delay between infection and replication
DNA not integrated into host genome
Sporadically enters lytic pathway
Herpes simplex virus (cold sores)
494
Common Animal Viruses
Single-stranded RNA (very common)
Rhinovirus
Common cold – respiratory epithelial cells
Rabies virus
Rabies – nerves, brain cells
Influenza viruses
Various
Poliovirus
Poliomyelitis – fecal/oral transmission, infects central nervous system
495
Common Animal Viruses
Double-stranded RNA (very common)
Rotavirus
Gastroenteritis in infants – fecal/oral transmission, small intestine cells
496
Common Animal Viruses
DNA
(often latent)
Herpes Simplex Virus
Genital herpes, cold sores
Varicella Zoster Virus
Chicken Pox (latent resurgence – Shingles)
Poxviruses
Small pox
497
Smallpox
“Great Pox” = syphilis
Double-stranded DNA
Emerged in humans ~10,000 BC
At least 7 deities dedicated to smallpox
End of 1700’s killed 400,000 Europeans a year
5 monarchs
Caused third of all blindness
Two forms
Variola minor – less common, 1% mortality
Variola major – more common, 35% mortality
Airborne transmission most common
1796 – Edward Jenner shows cowpox virus effective vaccine against smallpox
WHO smallpox eradication programs in 1950’s and 1960’s
Last natural case in 1979
Humans are only reservoir – it is now gone from the Earth
Except: two stocks maintained (CDC in Atlanta, VECTOR in Koltsovo, Russia)
One of two eradicated diseases (Rinderpest – cattle virus, 2011)
498
Retroviruses
RNA virus with DNA intermediate
Generally enveloped
Two identical single strands and enzymes in capsid
RNA replicated as DNA by Reverse Transcriptase
Very inaccurate high mutation rate
DNA integrates into host chromosome
Rous Sarcoma Retrovirus (chickens)
First virus shown to cause cancer (oncovirus)
Human Immunodeficiency Virus
Causes AIDS – infects helper T cells
Destroys the immune system secondary infections
499
Ebola Virus
Single-strand negative sense
Enveloped
Persistent
Requires BSL-4 (highest level)
Flu-like onset
Hemorrhagic fever
Blood clots in small vessels
40% bleed from mucous membrane
Death from multiple organ failure
Typical mortality in outbreaks 65-75%
500
Zika Virus
Flaviviridae – similar to Dengue, Yellow Fever, West Nile
Icosohedral, enveloped
10 kB (+)RNA genome
7 non-structural and 3 structural proteins
There is no treatment
There is no vaccine (maybe 10 years out)
501
zika transmission
Day feeding mosquitos
Sexually
Mother-to-fetus
Severe microcephaly where portion of skull has collapsed
Reduced brain growth
Impacted joints
Based on similar viruses unlikely to impact future pregnancies once virus is cleared (immune after)
502
Coronavirus
Positive-sense single strand RNA genome
26-32 kb
5’ methyl cap, poly A tail
Helical symmetry
Enveloped
Club proteins give a “halo” or “corona”appearance under electron microscope
Club proteins function in receptor interaction and membrane fusion
503
Coronavirus epidemiology
4 subfamilies of coronavirus
2 naturally reside in birds
2 naturally reside in bats
Respiratory infections in birds and humans
Digestive infections for everything else
7 coronavirus strains infect humans (through animal intermediates)
4 mild, part of common cold pool (200+ viruses, mostly rhinovirus)
3 serious (SARS-CoV, MERS-CoV, SARS-CoV-2)
504
Mimivirus
Naked, linear double-stranded DNA genome
Infects amoeba
Discovered in 1992 during Gram Stain
Mistaken for Gram Positive microbe
Capsid diameter 390 nm (second largest)
Bigger than some bacteria
1.2 Mbp genome
Bigger than some bacteria
Genome surrounded by lipid bilayer
Genes for tRNA’s, sugar, lipid, amino acid metabolism
mRNA transcripts in nucleocapsid (DNA replicase, tRNA’s)
Missing Link between bacteria and viruses
Sputnik Virophage
“Virus” of amoeba that requires mimivirus infection to replicate
Essentially, a virus of a virus
505
Groups of human-associated microbes
Normal microflora
Indigenous microbiota
Hundreds of species
90% cells on/in human body are microbes
Parasites
Organism living on/in host to detriment of host
Microbial parasites = pathogens
Opportunistic pathogens
Cause disease under unusual situations
Host defenses not present
Likeliness of pathogen causing disease = virulence
506
Terminology
Infection
Microorganism present and growing in host
Does not have to cause harm
Disease
Damage to host that affects it’s function
Virulence
Measure of pathogenicity of organism
Can be expressed as number of cells to trigger host response
Colloquially refer to amount of damage done to host
507
Where bacteria interact with their host
Anywhere there is an surface
Human body is a conglomeration of microenvironments
Each environment has own moisture, temperature, pH, nutrient availability
Conditions of environment dictate microbes present
Body has lots of mucous membranes
Moist areas exposed to external environment
Microorganisms love these
Attach, possibly penetrate and cause disease
Distinct regions
Skin, oral cavity, respiratory tract, intestines, urogenital tract
508
Bacteria on the skin
Skin generally too dry for most bacteria
Most found around sweat or sebaceous glands
Resident vs. Temporary populations
Residents – generally Gram Positive
Staphylococcus (epidermidis)
Propionibacterium (acnes)
Corynebacterium
Acinetobacter (Gram Negative)
Temporary
E. coli and Enterobacter
Common transient from fecal contamination
509
Bacteria in the mouth
Moist, warm, nutrient-rich
Bacteria happy
Saliva dilutes nutrients, contains lysozyme (degrades peptidoglycan) and lactoperoxidase (generates toxic oxygen species)
Bacteria unhappy
Some organisms (including methanogenic Archaea) invade gums
Gingivitis, periodontal disease
Most attached to surface in biofilm
510
Progression of dental plaque formation
Teeth cleaned
Surface rapidly coated with organic film (saliva)
Initially colonized by Streptococcus
Other bacteria colonize as it thickens
Fusobacterium (filamentous), Borrelia, Actinomyces (filamentous)
Anaerobic species become more common as plaque develops
Bacteria in plaque produce organic acids, decalcify tooth enamel
S. mutans, S. sobrinus sugars lactic acid
511
Bacteria in the gastrointestinal tract
Stomach
Acidity prevents ingested bacteria from reaching intestine
Few can live in stomach itself (Helicobacter pylori)
Duodenum
Still acidic, has lower numbers of bacteria
Jejunum and Ilium
Increased numbers Enterococcus and Lactobacillus
Up to 107 bacteria/g content toward end of Ilium
Large Intestine
Some facultative anaerobes (enterics)
Mostly obligate anaerobes (Bacteroides, Clostridium)
1010 bacteria/g content
Also some methanogens (Archaea)
512
We want bacteria in our intestines
Intestinal bacteria:
Produce Vitamin B12 and K
Activate some steroids produced by liver
Produce enzymes that aid digestion
Diet can affect microflora
High meat promotes Bacteroides instead of coliforms and lactic acid bacteria
Bacteroides often protein degraders
Oral antibiotics kill/inhibit gut microflora
Pathogens take over
Clostridium difficile pseudomembranous colitis
513
Bacteria in the respiratory tract
Upper respiratory tract (nose, pharynx/throat)
Whatever is airborne gets trapped in mucous of nasopharynx/throat
Mucous gets shuttled to stomach for disposal
Staphylococcus, Streptococcus common
Lower respiratory tract (trachea, bronchi, lungs)
No resident microflora
Cilia push bacteria up and out
Rest get eaten by alveolar macrophages
514
Bacteria in the urogenital tract
Bladder is sterile
Urethra colonized by facultative anaerobes
Escherichia, Klebsiella, Proteus
Can be pathogenic at high numbers
Vagina colonized by acid-tolerant microbes
Weakly acidic
Lactobacillus acidophilus ferments glycogen to lactic acid
Yeasts common
515
How do pathogens get inside us?
From a surface
Skin, mucous membrane, intestinal epithelia
Often through wound
Usually specifically adhere to these surfaces
Cell surface proteins, polysaccharide, fimbriae, pili
Most penetrate epithelial tissue
Move to other parts of the body through blood/lymph
Initial infection usually localized but can spread
Bacteremia – bacterial growth in blood stream itself
516
Virulence Factors
Bacterial products that help pathogen enter host more efficiently or stay in host longer
Often extracellular enzymes
Hyaluronidase (S. pyogenes, S. aureus, C. perfringens)
Breaks down intercellular matrix between host cells
Streptokinase (S. pyogenes)
Breaks down fibrin clots
Used by host to limit bacterial spread
Coagulase (S. aureus)
Forms fibrin clots
Cloaks/protects cells from host immune response
517
Toxins
Exotoxins
Extracellular proteins released by some pathogens
Cytolytic toxins
Cause host cells to lyse
E.g. beta hemolysins
A-B toxins
Have components that bind and enter host cells
E.g. botulinum toxin, tetanus toxin
Block release of neurotransmitters
E.g. diptheria toxin
Damage heart muscle/neural tissue
Superantigen toxin
Trigger massive immune response
518
Toxins
Enterotoxins
Exotoxins that affect the small intestine
Secretion of huge amounts of fluid
Diarrhea and vomiting
Produced by intestinal pathogens, food poisoning pathogens
Can get food enterotoxins without bacteria being present
Most well-known is Cholera toxin (V. cholerae)
A-B toxin
Cause epithelial cells pump out Cl-, prevent import Na+
High salt buildup outside of cell water efflux out of cell
Benefit isn’t clear, possible the bacteria is screwing up colonization
Increases cAMP which bacteria eats, but also causes water loss
Death by dehydration
519
Toxins
Endotoxins
Shed LPS from Gram Negative bacteria that cause toxic effect
Usually released when cells lyse
Polysaccharide chains make molecule soluble
Lipid portion toxic
Lead to:
Fever (“pyrogenic”, raise host body temp)
Diarrhea
Inflammation
Immune response
Rarely fatal unless in high doses
Non-bacteriolytic antibiotics
520
Cellular differences between Eukarya and Bacteria/Archaea
Eukarya always have membrane bound nucleus
Other organelles vary
Almost all eukaryotes have mitochondria
Where did mitochondria come from?
Photosynthetic eukaryotes have chloroplasts
Where did chloroplasts come from?
A few microscopic eukaryotes have hydrogenosome
Oxidizes pyruvate, produces H2
Only found in organisms that carry out fermentation
Likely derived from mitochondria
521
Types of microbial Eukarya
Traditionally divided in animals, plants, fungi and protists
DNA suggests protists divided into multiple distinct lineages
522
Diplomonads
Most exist as paired cells, each with 4 flagella
Lack mitochondria and Golgi
Giardia lamblia
Causes giardiasis
Ingestion of cysts
Develop into trophozoites
Active, replicating form
Swim around intestine
Causes explosive diarrhea, excessive sulfurous gas, nausea
523
Trichomonads
Anaerobic, flagellated cells
Do not form cysts
Lack mitochondria, have hydrogenosomes
Trichomonas vaginalis
Causes Trichomoniasis
Most common protozoan pathogen in developed countries
5 million cases/yr in US, 160 million worldwide
Sexually transmitted urogenital disease (direct, no cysts)
Men usually asymptomatic
Women have “strawberry cervix” – punctate pattern on surface
Increased susceptibility to HIV, cervical cancer
524
Protozoa
Various separate lineages traditionally grouped together
Single-celled, lack cell walls
Feed by engulfing particles (phagocytosis)
Most motile
Classified by motility method
525
Mastigophora
Flagellates
Many free-living in soil/water
Some parasites
Some have chloroplasts (e.g. Euglena)
Likely most ancient group of protozoa
Trypanosoma brucei – African Sleeping Sickness
Spread by Tsetse Fly
Stage 1 – hugely swollen lymph nodes, fever, ache
Stage 2 – parasite crosses blood-brain barrier
Confusion, fatigue, day-time slumber, night-time insomnia
Parasite produces tryptohol – induces sleepiness in human
526
Mastigophora
Flagellates
2
Trypanosoma cruzi – Chagas Disease
Spread by Reduviid bugs (“Kissing Bugs”)
Hide in crevices during day
Come out at night to feed on peoples faces
Attract to CO2 among other things lips
After feeding, they defecate
People rub feces into bite
Acute stage – fever, rash, diarrhea, etc.
Chronic stage – 60-80% asymptomatic
Rest – life-threatening heart/digestive disorders
13% stillborns in Brazil
Leishmania - Leishmaniasis
Spread by Sand Flies
Huge skin ulcers, spleen/liver damage
527
Ciliophora
Ciliates
Motile with cilia at some stage of life cycle
Cilia – shorter flagella in large numbers
Can use cilia for feeding – sweep food into “oral groove”
Have two kinds of nuclei
Micronucleus
Diploid – used for reproduction
Macronucleus
Polyploid – used for mRNA/protein
Most free-living in soil/water (e.g. Paramecium)
Some anaerobes in rumen
Some invertebrate parasites
528
Sarcodina
Amoeba
Motile through amoeboid motion (crawling)
Extension of pseudopod, cell flows into pseudopod
Exact mechanism unknown
Maintain osmotic balance through Contractile Vacuole
Vesicle fills with water, contraction ejects water into surroundings
Under unfavorable conditions, can form cyst
Common in soil/water
Some parasites (mouth, digestive tract)
Entamoeba histolytica – amebic dysentery
Ingestion of cysts, trophozoites in intestine
Damage intestinal wall – bloody diarrhea, spread to organs
529
Foraminifera
Originally classified with Amoeba, now own phylum
Uses pseudopods for locomotion, feeding
Most less than 1 mm diameter
Largest over 6 cm (2 inches)
Fossils from Cambrian era up to 15 cm
Size due to production of “test” (shell)
Different compositions depending on species
Carbonate, silica, organic material
Test usually chambered, with organism occupying last few chambers
Hole(s) open to ocean for pseudopods
Some anterior chamber can be colonized by algae/cyanobac
530
Apicomplexa
Sporozoans
No motile adult stage
Obligate animal parasites
Form sporozoites (spore-like cells) for transmission
Plasmodium falciparum, Plasmodium vivax
Cause malaria – infect red blood cells
Fever, aches, anemia
Transmitted by mosquitoes
500 million cases/yr (2 million deaths)
Cyclospora
Fecal-oral cyst transmission (contaminated fruits/water)
One of causes for “Traveler’s Diarrhea”
Cryptosporidium
Fecal-oral (water)
Short term diarrhea
Fun fact: rare in that mitochondria don’t have DNA
531
Toxoplasma gondii
Two stage life cycle
Sexual stage – intestines of cats, produce cysts
Asexual stage – warm-blooded animals
Mice (which is eaten by cat), birds, humans
Both stages, organism lives in cellular vacuole
Contracted by cat feces, contaminated food (pork)
Evades immune system
Causes toxoplasmosis in humans
Acute – aches, swollen lymph nodes
Latent – cysts persist in muscle, nerve tissue
Approximately 1/3 world infected (10-12% US)
532
Toxoplasma gondii
2
T. gondii induces behavior changes in mice
More adventurous, less fearful (dopamine)
Some seek out places marked by cat urine
Increases likelihood mouse eaten by cat
T. gondii wants this
T. gondii linked to mental disorders in humans
Anxiety, depression, schizophrenia
Exact reason very unclear
By-product of behavior modification system
Cysts in nervous tissue early in development
Inducing latent human genes
533
Fungi
Chitin cell wall, produce spores
Usually classified on spore/spore-containing structures
Tight lineage
Ascomycetes – e.g. yeasts (Saccharomyces)
Basidomycetes – e.g. mushrooms (Agaricus)
Zygomycetes – e.g. bread molds (Rhizopus)
Multiple cell forms
Single cell – yeast form
Filaments – hyphae (mycelium)
Many can switch between forms
Most terrestrial, some aquatic
Detritivores – aerobic heterotrophs, significant degradation organisms
Some plant/animal/human pathogens
Candida albicans – oral/genital infections (“thrush”, candidiasis)
534
Slime molds
Separate lineage, characteristics of fungi and protozoa
Found on decaying plant matter, mainly feed on bacteria
Two main groups
Acellular (plasmodial) – e.g. Physarum
Cellular – e.g. Dictyostelium
Acellular slime molds
One gigantic, multi-nucleate amoebic cell (can be over meter in diameter)
Cellular slime molds
Separate amoebic cells
When starved, both types form sporangia (spore-containing fruiting bodies)
Cellular slime molds – multiple cells group together to form essentially new organism
Spore germination
Acellular – form swarmer cells that fuse into plasmodium
Cellular – form separate cells
535
Algae
Oxygenic photosynthetic Eukarya
Some capable of heterotrophy in dark
Chloroplasts – chlorophyll a, other pigments
Mainly classified on accessory pigments
Chlorophyta – green algae
Rhodophyta – red algae
Diatoms
Abundant in aquatic/moist environments
Microscopic or macroscopic (seaweed)
Unicellular or colonial
Dinoflagellates – related to Ciliophora
Free-living or symbiotic
Blooms cause Red Tide
