GDB 103 Final Review Flashcards
(118 cards)
1
Q
quorum sensing
A
genetic switch that allows traits within a bacterium to be activated based on the density of bacteria in the environment
2
Q
low cell densities
A
low concentration of cells
3
Q
high cell densities
A
high concentration of cells
4
Q
cells reach threshold
A
receptors in or on cells are activated, resulting in new gene expression and a switch in bacterial behavior
5
Q
diffusible signal factor (DSF)
A
lipid based
6
Q
DSF- high cell density
A
high DSF
- virulence off, biofilm on
7
Q
DSF- low cell density
A
low DSF
- virulence on, biofilm off
8
Q
DSF- high cell density explanation
A
suppression of virulence and motility. activation of attachment and biofilm formation
9
Q
DSF- low cell density explanation
A
expression of virulence and motility gene. no expression of attachment and biofilm formation genes
10
Q
low cell densities of Homoserine lactone (HSL)
A
HSL regulated genes off
11
Q
high cell densities of Homoserine lactone (HSL)
A
HSL regulated genes on
12
Q
DSF and HSL
A
both activate new gene expression and traits in a density dependent manner
13
Q
xyllela fastidiosa and pierce’s grapes
A
induces water stress by plugging the water conducting xylem vessels
14
Q
vibrio fastidiosa and bobtail squid
A
symbiotic relationship
- bioluminescent properties, heterotrophic, moves in means of flagella, survive on decaying matter
15
Q
What makes xyllela fastidiosa worse?
A
environmental drought and water limitation to improve berry quality
16
Q
benefit to bobtail squid
A
bioluminescence to find mates. avoid predators, attract prey, communicate with other organisms
17
Q
benefit to bacterium
A
nutrient rich environment, active release of progeny to increase fitness
18
Q
pseudomonas fluorescens and mycoparasitism
A
builds up in soils and colonizes plant root. parasitic to G. gramminis
production of broad spectrum antibiotic to kill fungal pathogen
19
Q
agrobacterium tumefaciens
A
sharing of metabolic capacities. plants make opines, rich sources of C and N.
20
Q
How does opines work
A
individual strains utilize specific opines, but not others.
- share necessary gene with other members of the community through horizontal gene transfer
therefore, optimize metabolic capacity of larger agrobacterium community
21
Q
rhizobium nodulation genes
A
rhizobium bacteria exhibit high degree of host specificity
22
Q
how does rhizobium nodulation work?
A
all bacteria that fix nitrogen with legumes share a common set of genes “nod genes”
- acquired by horizontal gene transfer
23
Q
how does rhizobium nodulation work cont
A
encode bacterial signal that triggers development of nodule organ on the plant root
24
Q
Nod factor
A
signal molecule made by the bacterium and perceived by the plant
25
endophytes
within a plant (inside)
low alpha diversity, high selectivity
26
epiphytes
on the plant surface
27
peripheral communities
nearby in the soil
28
what do plant breeders do
routinely manipulate host genes to create resistant crops
29
plant immune system
controlled by host and pathogen genetics. plant pathogen behavior often host dependent
30
Number of taxa changes
decreases significantly from soil, to root surface to plant interior
31
changes in microbial communities
reproducible among plants and between locations, indicating a high degree of selectivity
32
What does selectivity suggest
co-evolution between plants and microbes. functional relevance to such associations
33
Koch causality 1
organism must always be present
34
koch causality 2
organism isolated from host and grown in pure culture
35
koch causality 3
sample of the organism taken from pure culture must cause same disease when inoculated into healthy, susceptible animal in the lab
36
koch causality 4
organism must be isolated from the inoculated animal and must be identified as same organism first isolated from the originally diseased host
37
16S DNA sequencing
for prokaryotes. amplicon based and not very deep. specific region (PCR and amplify)
38
18S DNA sequencing
for fungi and other eukaryotes
39
microbiome experiment
each sequence is a separate observation of a particular microbe. data can be used in statistical tests for enrichment of microbial taxa in diseased plants
40
pseudomonas fluorescens
builds up in the soils and colonizes plant roots and is parasitic to G. gramminis
41
parasitism and G. gramminis
involves production of a broad spectrum antibiotic to kill the fungal pathogen
42
p. fluorescens and quorum sensing
P. fluorescens antibiotic production is regulated by quorum sensing
43
trichoderma virens
produces enzymes that degrade fungal cell walls and anti fungal compounds
44
biological control of trichoderma virens
activate immune systems in plants to better defend themselves
45
bacillus subtilis
targets a wide range of fungal and bacterial pathogens
46
reductionist science
frequently hypothesis driven
47
features of reductionist science
manipulate only one aspect
- gnotobiotic systems
- modify host status or genetics
- antibiotic treatment
48
discovery science
not hypothesis driven, usually discovery
49
features of discovery science
focuses on features, patterns and statistical correlations
- 16S sequencing
- metagenomics
- whole genome sequencing
50
16S sequencing
targeted portion of a genome
51
metagenomics
bulk sequencing of environmental DNA
- sacrifices sequencing depth and therefore sensitivity
52
whole genome sequencing
sequencing of pure strain isolates
53
proper experimental design
system appropriate to the question
- choosing subjects
- selecting landscape
- designing experiment
design lend power and suitable for statistical analysis
- replication
- nature of manipulation
- types of analyses
54
Surfer example
discovery science. characterizing/ describing and not manipulating
55
NY subway
microbiome of inanimate geographical space. lots of human DNA (skin and bodily fluids) match back to ethnicity and origins
56
measuring data from NY subway
ability compare sequences back to taxa and what we know. single nucleotide difference can identify human ancestry. human ancestry predictions mirror census data
57
Yersinia pestis and humans
looking at short read data for evidence of a pathogenicity gene from the black plague pathogen
58
yersinia pests effect on humans
responsible for deep tissue invasion
59
sampling arctic microbiome
largely inaccessible area of the planet, spacial issues- among fastest changing ecosystems on the planet and strongly impacted by climate change
60
microorganisms in arctic microbiome
microorganisms found within and below the sea ice form the foundation of the marine food web
61
where to collect data via levels
biological, geological, atmospheric, chemical
62
replication
sampling multiple times in same environment and same area
63
seasonality/ frequency
multiple times during year and times a day
64
mice and arabidopsis for model systems
extremely well characterized biology. extensive genetic resources in public domain
- traditional genetic stocks
- mutant collections
- full genome
- mutant tools
65
plant immune signaling pathways
in plants:
- jasmonic acid
- salicylic acid
- ethylene
66
controls in mouse vs human studies
multiple inoculations with fecal bacteria. use of twins to control genetic factors. replication with 4 pairs of twins
67
significance of co-housing mice
converts obese to lean mice.
conversion of Bacteroidales from lean to obese mice
68
observation of phylogeny with families of gut bacteria
phylogeny of two major families of gut bacteria has the same topology at the homind host
69
How would this arise
isolation (genetic drift) or selection and co-evolution
70
What does this relationship indicate
very long standing (stable) interactions
71
gyrB gene
better for closer relationships
encodes an enzyme involved in regulating DNA structure
72
chloroplast phylogenies in plants
the phylogeny of established endosymbionts mirror the phylogeny of their host genome
73
resiliency
rate of recovery after disturbance
74
resistance
intensity to disturbance
75
stability
a function of resilience and resistance
76
ecological resistance
many stable states in which a community may reside
77
Human gut microbiome and ciproflaxin treatment
huge drop in alpha diversity. drug has huge effect on microbiome. patient specific differences
78
control and amoixicilin
similar shift, immediate shift in frequency
79
tylosin
delay in maturation in the microbiome
80
children with sever malnutrition
microbiome does not mature with children with severe malnutrition
81
antibiotic use: spontaneous recovery
slower, typically complete recovery of microbiome
82
probiotics
recovery of microbiome delayed and incomplete
83
FMT
fast and complete recovery of microbiome
84
alpha diversity for antibiotics
control: steady amount
sp: took a little longer but still complete
pro: incomplete and declined
FMT: bounded back quickest
85
beta diversity (unifrac, distance to baseline)
control: closest
sp: mid
pro: far from baseline
FMT: joined
86
role of appendix
acts as a "house" for healthy gut commensals. possible reservoir of healthy gut microbiome
87
removal of appendix
correlated with gut dysbiosis
88
effect of gut dysbiosis
correlated with increased risk of colorectal cancer. immediately after appendectomy, there is a shift in the gut microbiome
89
clearing gut of dominant microbes
can lead to dominance of C. Dif as gut is recolonized. C Dif can cause ineffective diarrhea
90
phosphatidyl choline
promotes cardiovascular disease
91
trimethylamine-n-oxide
gut microbiota linked to CVD risk and other human outcomes
92
maternal immune activation
epidemiological studies suggest that activation of the material immune system during pregnancy increases risk of ASD
93
bacteroides fragilis
normal component of the human gut microbiome. can suppress 4EPS levels
94
treatment of MIA ASD mice with human Bacteroides fragilis corrects
ASD related behaviors
restores gut permability
alters the microbiome to a new state
95
4EPS
can induce ASD like behaviors in normal mice
96
What does the data suggest
a gut microbiome brain connection and may lead to pharmacological therapies for ASD
97
Belgian and Dutch subjects
two genera of bacteria, Coprococcus and Dialister were missing from the microbiome of the depressed subjects
98
lactobacillus rhamnosus
decreases production of stress hormone. regulates emotional behavior and central GABA receptor expression
99
GABA
naturally occurring amino acid, works as a neurotransmitter in your brain, can boost mood, having calming/ relaxing effect on the nervous system,
100
GABA acronym
gamma aminobutyric acid
101
Vagus nerve
main proposed gut-brain connection. food satiation and reward
102
zombie ants and Ophiocordyceps
fungus produce different chemicals that grow on brains of different ant species. fungus erupts from ant's head to produce spores that fall to forest floor
103
Toxoplasma gondii
aggregate neuorticism (anxiety, fear, moodiness). cat odor activates sexual arousal pathways in brains of toxoplasma gondii infected rodents
104
toxoplasma and humans
tend to show long terms personality changes
- women: more intelligent, affectionate, social
- mean: less intelligent, more loyal, frugal and mild tempered
105
both genders
higher level of neuroticism: more prone to guilt, self doubt and insecurity
106
The Force analogy
microscopic organisms that exist symbiotically in all living cells. enhance natural, physical and mental abilities
107
mealworms and styrofoam
antibiotic treatment resulted in reduction in bacterial numbers in the gut and less depolymerization and mineralization of styrofoam
108
sheep developing "staggers"
many cool season grasses are infected by "endophyte" fungi that produce toxic alkaloids
109
alkaloid examples
LSD: halucinogenic
morphine: pain control
opium: psychoactive
nicotine: stimulant
vinblastine: anti tumor
110
mosquitos and humans
A. gambiae: highly attracted to humans based on olfactory cues derived from human skin
111
individuals attraction to A. gambiae
higher abundance but lower diversity of bacteria on their skin
112
Japanese population and seaweed
transfer of enzymes from marine bacteria to Japanese gut microbiota
113
microbes alter scents of hosts
scents correlated with sex, species and reproductive status. can attract pollinators and repel pests. removal of floral microbiota reduces floral terpene emissions
114
dr Domingues bello
urbanization, new diseases, processed foods, medicine influences the microbiome structure
115
health issues
obesity, asthma, celiac disease
less hunter gatherer and gardening
116
yanomami
in direct content with western civilization. competition against soil bacteria
117
informed consent
full knowledge of procedure and risk. free will without any coercion. understand what they're consenting to
118
