intro L1-11 Flashcards
1
Q
light microscope res and mag
A
200nm res
*1000 mag
2
Q
types of light microscopy
A
brightfield (standard)
darkfield (^contrast no stain)
phase contrast (refraction/ interference)
DIC (differential interference contrast)
fluorescence
3
Q
types of scanning electron microscopy
A
confocal (laser to scan multiple z-planes)
2 photon (long wavelength light)
4
Q
gram-staining process
A
- add primary crystal violet stain
- iodine application (mordant)
- wash w alcohol (decolorizer)
- safranin application (counterstain)
5
Q
gram negative
A
outer-membrane
less peptidoglycan
e.g. e.coli
6
Q
gram pos
A
thin peptidoglycan layers
no outer membrane
7
Q
bacterial cell wall functions
A
protection
target
cell division
cell shape
8
Q
GFP
A
green fluorescent protein
good for live imaging, simultaneous visualization of various,
misleading malfunction
9
Q
bacterial S layer
A
outermost layer
crystalline lattice of single protein
protective selective sieve
lost in lab strains often
10
Q
capsules
A
polysaccharide
sometimes covalently attached to cell wall
biofilms importance > can be immunogenic
immune response avoidance
11
Q
pili and fimbriae
A
protein polymers
attachment/ adhesion
pathogenesis / immunogenic
support conjugation
“twitching” motility
pili longer and fewer
12
Q
chemotaxis
A
directionality
13
Q
flagella
A
bio nanomachine w rotary motor
14
Q
endospores
A
starvation triggered
v resistant
germinate under conditions
survival mechanisms
15
Q
biofilms
A
communities
held by matrix
often differentiate
promote adhesion and resistance
16
Q
phases of batch growth
A
lag
expon
stationary
death
17
Q
lag phase
A
condition adjustment
metabolic enzyme/ metabolite synthesis
18
Q
expon phase
A
optimal growth
19
Q
stationary phase
A
rate of cell production = rate of cell death
growth limit by nutrient depletion/ toxin accumulation
20
Q
death phase
A
complex viability loss w some cell turnover
21
Q
growth measurement methods
A
plating
turbidity
direct microscopic counting
flow cytometry
22
Q
plating methods
A
“colony forming units” extrapolated for cell numbers
23
Q
:) of plating methods
A
v sensitive
customization for species of interest
only viable cells
24
Q
:( of plating methods
A
underestimates for cells in chains/ clusters
no. dependent on growth conditions
25
turbidity method
measures light scattering by cells
26
:)/ :( of turbidity method
:)simple
convenient/ continuous
non-destructive
:(measures dead cells
decreasing sensitivity
accuracy affected by culture turbidity
27
:) direct counting method
direct
clumping/ chaining accomodation
28
:(
laborious
can't distinguish live/dead
29
flow cytometry
measures particles in a microfluidic flow
30
:) flow cytometry
automated
measures fluorescence at multiple wave-lengths
cell sorting
31
FACS
Fluorescence Activated Cell Sorting
:( equipment required
32
cell splitting in binary fission
septum forms at mid-cell as Z-ring constricts
33
replisome
DNA replication machinery
34
replication fork
structure formed as DNA is replicated
35
chromosomes replication
replisomes bind to oriC
bidirectional replication to 'terC'
chromosomes segregate and cells divide
36
bacterial chromosome replication time
~40 mins
1000bpm
37
why do b.subtilis and e.coli divide every 20 mins?
as they initiate replication in previous cell cycle
38
daughter oriC's location on chromosome
1/4 or 3/4 distance along cell
39
divisome
governs septum formation/ cell division
assembles into Z-ring
40
cyanobacteria differentiations
heterocysts > N2 fixation
akinetes > survival
41
B. dellovibrio
grows inside other bacteria
42
myxococcus
eats other bacteria and complex fruiting bodies
43
catabolic vs anabolic
energy releasing/ energy building into food
44
macronutrients
proteins
lipids
carbohydrates
nucelic acids
45
two types of nutrient media
chemically defined
undefined 'complex'
46
bacterial monitoring measurement and calculations
measures population density and number
calculates growth rate and generation time
47
cell count formulae
N=N(0)2^n
final cell number= initial cell number*2^(no. generations)
g=t/n
generation time= expon growth duration/ no. generations
48
factors affecting growth of bacteria
temp
pH
osmolarity
O2 availability
49
chemostats
bioreactors
open system in which fresh media is added whilst spent media removed
50
chemostats advantages
growth at "steady state"
important in bioprocessing
51
dilution rate
flow rate/ volume
52
mu
growth rate relating to slope
53
flow rate and growth rate relation
if flow> growth rate - wash-out
if flow < growth - stationary phase/ wash out
54
microfluidics
agar pad w tracks whilst SEM observes individuals
silicon master
55
bacterial DNA
v condensed
4.6 mbp
3 micrometers
not double-membrane bound
56
E.Coli chromosome
circular
operons
gene clusters transcribed together
densely-packed genes
57
bacterial DNA mobile elements
plasmids
antibiotic resistance genes
transposable elements
conjugation plasmid
small extrasomal DNA strand
58
shigella
E.Coli related
causes dyssentry
plasmid pINV encodes key virulence genes
59
types of bacteriophage
lytic
lysogenic
transduction
60
transposons
jumping genes
often resistance
61
integrons
accumulate 'useful' genes
62
bacterial genome variation
core > "housekeeping" genes
accessory > mobile elements inc
63
pangenome
totality of genes across all strains of a species
64
implications of genome sequencing
epidemiology of infectious disease
comparative genomics
understanding bacterial genetic
uncovering unsampled diversity
changing classification of organisms
metagenomics
art
65
illumina genome sequencing
highly scalable
short DNA fragments
66
sanger genome sequencing
slow / expensive
accurate
67
sequence assembly
overlapping sequences aligned
complete genome assembly
68
oxford nanopore
v long reads
:( less accurate
69
bioremediation
use of microorganisms, plants or enzymes to detoxify soil contaminants (as xenobiotic pollutants resistant to natural degradation)
70
biotechnology
cellular factories
organisms producing medically/ commercially useful biomolecules
quick/ cheap
71
genetic modification of bacteria
clone gene of interest into expression vector > linearise > ligate > transform> multiplication> lysis and purification and induction
72
recomb therapeutics + enzymes
small-scale, high value products or high volume, low-cost commodities
73
synthetic bio and bio engineering
design/ construction of new bio parts/ redesign of existing, natural bio systems for useful purposes
74
bio components
modular
non-chronological assembly
predictable outputs and complexity w symbols
75
optogenetics
bacterial gene expression induction via small molecule signalling
potential therapeutic delivery tool
76
metabolic engineering
gene circuits and engineered proteins combined for metabolic processes
complex, multi-enzyme cascades
^efficiency
77
transcriptomics
measures gene expression of all genes at specific condition
infers bacterial cell function systemically
78
CRISPR
Clustered-Regularly Interspaced Short Palindromic Repeats
79
microbe detection
culturing
DNA/RNA sequencing
80
NGS microbiome profiling applications
metabolomics
roteomics
81
culturomics
identifying unknown microbes
:) reference database/ phenotypic and mechanistic studies/ culture collections/ therapy development
:( expensive/ labour-intensive
82
functions of gut microbiota
complex sugar breakdown
breast-milk oligosaccharides
immune programming
83
life factors influencing microbiome during pregnancy
intra-uterine environment (amniotic)
maternal exposures
gestation length
weight at birth
84
life factors influencing microbiome during birth
delivery mode
mother/ healthcare professional contact
environment
85
life factors influencing microbiome after birth
feeding modality
weaning/ antibiotics/ food supplementation
home/ family setting
home structure
86
immune programing
mucosal and systemic immune compartments stimulate 'tolerance'
87
causes of microbiota disturbances
diet
antibiotics
infection
genetics
88
microbiota diseases
autoimmune
brain-linked
intestinal
metabolic
immune
89
colonisation
microbe growth after gaining access to host tissue
90
pathogenicity
pathogen ability to inflict host damage
91
virulence
degree of pathogenicity of an invading pathogen
92
mechanisms of microbial pathogenesis
exposure> adherence> invasion> colonisation/growth
93
bacterial abundance in upper vs lower respiratory tract
upper respiratory tract v abundant and lower is devoid
94
where does TB survive?
in immune cells
95
legionella pneumophila growth environment
stagnant water at ~35 degrees
96
legionella pneumophila survival
lives in immune cells with protective vacuole
97
what type of bacteria is legionella pneumophila
amino acid auxotroph (proteasomal degradation for nutrients)
98
types of gastroenteritis
viral
bacterial
parasitic
// chronic
acute
99
E.coli
gram negative rod bacterium in gut
100
types of E.coli
extra-intestinal pathogenic
intestinal pathogenic (most common)
101
burger bug
intestinal pathogenic E.coli encoding shiga toxin causing HUS
102
vibrio cholerae
motile, gram neg
phage-encoded CTX > fluid loss
103
helicobacter pylori
gram neg
motile
etiological agent of gastric/peptic ulcers
104
types of immunity
innate (immediate response)
adaptive (exposure w targeted defence mechanisms)
105
inflammation
non-specific
driven by neutrophil accumulation
106
acute infection signs
calor
rubor (redness) /vasodilation
tumor / ^plasma movement to tissue
dalor (pain)
change in function
107
adaptive immunity methods
specificity and memory
humoral
cellular
108
specificity and memory mechanism
host-mediated
repeated
rapid
intense
109
humoral immunity
B cell antibody production
110
cellular immunity
T-cells attack intracellular pathogens
111
ADCC
antibody dependent cell-mediated cytotoxicity
112
bacteriaemia
bacteria present in bloodstream
113
sepsis
extreme response to blood poisoning
114
systemic shock
systemic decrease in bp
mass organ failure
115
pathogen reservoirs
human / UPEC
zoonotic / EHEC
environmental
116
diagnostic media
general
enrichment
selective
differential
117
general media
non-selective
establishes growth
usually LB agar
118
enrichment media
selective
certain species
119
differential media
selects between 2 species
chromogenic substrate additive
e.g. MacConkey agar detects bacilli and enteric
120
selective media process
blood-based antimicrobial mixed w mixed bac sample
incubated at 42 degrees
uses media/ growth conditions to select
121
pathogenicity/ virulence factors
structures, molecules or regulatory systems enabling the disease process
122
drive of virulence factors
adhesion to epithelial surface/ underlying tissue invasion
123
what is a bacterial capsule?
polymer encasing gram -
excludes hydrophobic detergents
precursor to biofilm formation
resistance against immune recog/ phagocytosis
124
cell surface appendage examples
physical defence
niche maintenance
nutrition
intercellular communication
genetic material exchange
125
infection stages
adsorption
irreversible attachment
growth and division
mature macrocolony
dispersion
126
fimbrial-mediated adhesion
sugar-binding, lectin-like protein caps
T1 > CUP adhesion of gram neg
fimH> higher affin for mannose
127
pili
longer
fewer
genetic exchange
128
catch-bond theory
binding strength dictated by allosteric switch in FimH-sugar interaction
*chemical inhibition possible
129
2 pathways across IM
TAT
SEC
130
SEC
common
unfolded
131
virulence systems
T3SS (epithelial attachment/ EHEC)
T4SS (involved in genetic exchange)
T6SS (inter-bacterial warfare)
132
types of toxins
exotoxins
endotoxins
Stx
133
exotoxins
encoded on PAIs
site-specific
134
exotoxin mechanisms of action
stimulatory
disruptive
cytolytic
135
Stx
EHEC T3SS
colonisation essential
stress-triggered
136
Stx-phage
repressive effect on T3SS, stimulating cell receptor host expression
137
endotoxins
cell-bound lipopolysaccharides
released in lysis
less toxic than exotoxins
138
pathogenic islands
accessory DNA on islands from pathogenic bacterial strains
phage-mediated transfer
ecological selective advantage
139
latex agglutination
antibody-antigen interaction explorations for rapid diagnostics > isolate identity
> pathogen-associated identity of pathogens
140
serology
diagnostic identification of antibodies in serum
141
serotyping
determination of subtype of organism
142
biochemical assay pros
metabolic capabilities
rapid
accurate
143
oxidase enzyme tests
Pseudomonas spp +
E.coli -
144
catalase enzyme tests
gram + bacteria
145
urease enzyme tests
helicobacter pylori
146
advantages of molecular diagnosis of infections
unique bacterial genomes
genetic material extraction from infected specimens
DNA easy to detect and quantify
sensitive 1-10 CFU reaction
147
disadvantages of molecular diagnosis of infections
tech still developing
some tests require isolation first
too sensitive
standardisation issues
148
DNA sequence detection
detection + ID gel electrophoresis = gene specific
fluorescent DNA intercalating agent
real time detection of PCR production w dyes
149
meningitis RT-PCR
pre-emptive treatment before antibiotics
rapid correct treatment
150
whooping cough RT-PCR
3-12 day incubation culture growth
diagnoses within hours
prophylaxis of contacts/ correct treatment
151
major classes of protein synthesis-inhibitting antibacterials
tetracyclines
aminoglycosides
chloramphenicol/ macrolides/ lincosamides
152
tetracyclines
bind to 30S ribosomal unit
block tRNA binding
153
aminoglycosides
bind to 30S ribosomal subunits
impair proof-reading > faulty protein production
154
chloramphenicol/ macrolides/ lincosamides
bind to 50S ribosomal subunit
prevent peptide bond formation
stop protein synthesis
155
modifying approaches for treating infection
antibiotic use limiting
last resort antibiotics
combination therapy
phage therapy
faecal transplant
156
source of outbreak parameters
who
where
outbreak type
those at risk
157
global monitoring functions
limit spread
epidemic prevention
in-field diagnostics
158
phylogeny
evolutionary history of group of organisms
nucleotide/ amino acid sequence data
most common marker > SSUrRNA
159
SSUrRNA
found in all life domains 16S in pro/ 18S in eu/12S in plastids
functionally constant
sufficiently conserved
protein coding genes increasingly used to complement
160
mitochondria, chloroplasts and plastids genome
encode rRNA's and some proteins
machinery for protein synthesis
161
universal SSUrRNA tree of life
bacteria
archaea (prokaryotes)
eukarya
162
archezoa hypothesis
nucleus came first prior mitochondrion acquisition via endosymbiosis
163
hydrogenosomes
produce hydrogen/ ASTP via substrate-level phosphorylation
some have genome
164
mitosomes
reduce in size
no genome/ ATP production
165
extracellular parasites
thrive on/ in tissues without entering host cells
166
ntracellular parasites
penetrate host cells to complete life cycle
167
apicomplexan
apical organ orchestrating moving junction-mediated entry
168
kinetoplastids
lysosome-mediated entry
phagocytosis
169
microsporidia
polar tube mediated entry
in combo w endocytosis/ phagocytosis
170
animals/ metazoa
host many microbial species
niches for microbes
171
choanoflagellates/ ichthyosporea
mostly marine species
172
fungi/ microsporidia
important decomposers of dead animals/ plants
mutualistic interactions
173
microsporidia infecting humans
opportunistic pathogens (e.g. AIDs)
bienusi/ intestinalis
oral-faecal route has zoonotic origin
have mitosomes
174
microsporidia life cycle
no proliferative extracellular forms
depend on 1+ host
175
stramenopiles
free-living species
prasites
176
discovery of apicoplast in plasmodium
molecular data
genome organisation
ultrastructural studies
177
apicomplexa jinfecting humans examples
p. falciparum
toxoplasma gondii
c. hominis
178
t., gondii
cause benign disease in immuno-competent adults (congenital/ AIDs transmission)
tissue cyst forming coccidia
feline definitive host / birds/ mammals intermediate hosts
mitochondria/ apicoplast w organellar genome
179
cryptosporidium
c. parvum (cattle) c.hominis (only human)
self-limiting diarrhea in immuno-competent persons
180
t. vaginalis
STI
associated w HIV and mycoplasma
prenatal/ postnatal complications
