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CMB1003- Microbiology and immunology > intro L1-11 > Flashcards

intro L1-11 Flashcards

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1
Q

light microscope res and mag

A

200nm res
*1000 mag

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2
Q

types of light microscopy

A

brightfield (standard)
darkfield (^contrast no stain)
phase contrast (refraction/ interference)
DIC (differential interference contrast)
fluorescence

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3
Q

types of scanning electron microscopy

A

confocal (laser to scan multiple z-planes)
2 photon (long wavelength light)

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4
Q

gram-staining process

A
  1. add primary crystal violet stain
  2. iodine application (mordant)
  3. wash w alcohol (decolorizer)
  4. safranin application (counterstain)
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5
Q

gram negative

A

outer-membrane
less peptidoglycan
e.g. e.coli

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6
Q

gram pos

A

thin peptidoglycan layers
no outer membrane

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7
Q

bacterial cell wall functions

A

protection
target
cell division
cell shape

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8
Q

GFP

A

green fluorescent protein
good for live imaging, simultaneous visualization of various,
misleading malfunction

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9
Q

bacterial S layer

A

outermost layer
crystalline lattice of single protein
protective selective sieve
lost in lab strains often

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10
Q

capsules

A

polysaccharide
sometimes covalently attached to cell wall
biofilms importance > can be immunogenic
immune response avoidance

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11
Q

pili and fimbriae

A

protein polymers
attachment/ adhesion
pathogenesis / immunogenic
support conjugation
“twitching” motility
pili longer and fewer

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12
Q

chemotaxis

A

directionality

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13
Q

flagella

A

bio nanomachine w rotary motor

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14
Q

endospores

A

starvation triggered
v resistant
germinate under conditions
survival mechanisms

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15
Q

biofilms

A

communities
held by matrix
often differentiate
promote adhesion and resistance

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16
Q

phases of batch growth

A

lag
expon
stationary
death

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17
Q

lag phase

A

condition adjustment
metabolic enzyme/ metabolite synthesis

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18
Q

expon phase

A

optimal growth

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19
Q

stationary phase

A

rate of cell production = rate of cell death
growth limit by nutrient depletion/ toxin accumulation

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20
Q

death phase

A

complex viability loss w some cell turnover

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21
Q

growth measurement methods

A

plating
turbidity
direct microscopic counting
flow cytometry

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22
Q

plating methods

A

“colony forming units” extrapolated for cell numbers

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23
Q

:) of plating methods

A

v sensitive
customization for species of interest
only viable cells

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24
Q

:( of plating methods

A

underestimates for cells in chains/ clusters
no. dependent on growth conditions

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25
Q

turbidity method

A

measures light scattering by cells

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26
Q

:)/ :( of turbidity method

A

:)simple
convenient/ continuous
non-destructive
:(measures dead cells
decreasing sensitivity
accuracy affected by culture turbidity

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27
Q

:) direct counting method

A

direct
clumping/ chaining accomodation

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28
Q

:(

A

laborious
can’t distinguish live/dead

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29
Q

flow cytometry

A

measures particles in a microfluidic flow

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30
Q

:) flow cytometry

A

automated
measures fluorescence at multiple wave-lengths
cell sorting

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31
Q

FACS

A

Fluorescence Activated Cell Sorting
:( equipment required

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32
Q

cell splitting in binary fission

A

septum forms at mid-cell as Z-ring constricts

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33
Q

replisome

A

DNA replication machinery

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34
Q

replication fork

A

structure formed as DNA is replicated

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35
Q

chromosomes replication

A

replisomes bind to oriC
bidirectional replication to ‘terC’
chromosomes segregate and cells divide

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36
Q

bacterial chromosome replication time

A

~40 mins
1000bpm

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37
Q

why do b.subtilis and e.coli divide every 20 mins?

A

as they initiate replication in previous cell cycle

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38
Q

daughter oriC’s location on chromosome

A

1/4 or 3/4 distance along cell

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39
Q

divisome

A

governs septum formation/ cell division
assembles into Z-ring

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40
Q

cyanobacteria differentiations

A

heterocysts > N2 fixation
akinetes > survival

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41
Q

B. dellovibrio

A

grows inside other bacteria

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42
Q

myxococcus

A

eats other bacteria and complex fruiting bodies

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43
Q

catabolic vs anabolic

A

energy releasing/ energy building into food

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44
Q

macronutrients

A

proteins
lipids
carbohydrates
nucelic acids

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45
Q

two types of nutrient media

A

chemically defined
undefined ‘complex’

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46
Q

bacterial monitoring measurement and calculations

A

measures population density and number
calculates growth rate and generation time

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47
Q

cell count formulae

A

N=N(0)2^n
final cell number= initial cell number*2^(no. generations)
g=t/n
generation time= expon growth duration/ no. generations

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48
Q

factors affecting growth of bacteria

A

temp
pH
osmolarity
O2 availability

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49
Q

chemostats

A

bioreactors
open system in which fresh media is added whilst spent media removed

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50
Q

chemostats advantages

A

growth at “steady state”
important in bioprocessing

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51
Q

dilution rate

A

flow rate/ volume

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52
Q

mu

A

growth rate relating to slope

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53
Q

flow rate and growth rate relation

A

if flow> growth rate - wash-out
if flow < growth - stationary phase/ wash out

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54
Q

microfluidics

A

agar pad w tracks whilst SEM observes individuals
silicon master

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55
Q

bacterial DNA

A

v condensed
4.6 mbp
3 micrometers
not double-membrane bound

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56
Q

E.Coli chromosome

A

circular
operons
gene clusters transcribed together
densely-packed genes

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57
Q

bacterial DNA mobile elements

A

plasmids
antibiotic resistance genes
transposable elements
conjugation plasmid
small extrasomal DNA strand

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58
Q

shigella

A

E.Coli related
causes dyssentry
plasmid pINV encodes key virulence genes

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59
Q

types of bacteriophage

A

lytic
lysogenic
transduction

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60
Q

transposons

A

jumping genes
often resistance

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61
Q

integrons

A

accumulate ‘useful’ genes

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62
Q

bacterial genome variation

A

core > “housekeeping” genes
accessory > mobile elements inc

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63
Q

pangenome

A

totality of genes across all strains of a species

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64
Q

implications of genome sequencing

A

epidemiology of infectious disease
comparative genomics
understanding bacterial genetic
uncovering unsampled diversity
changing classification of organisms
metagenomics
art

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65
Q

illumina genome sequencing

A

highly scalable
short DNA fragments

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66
Q

sanger genome sequencing

A

slow / expensive
accurate

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67
Q

sequence assembly

A

overlapping sequences aligned
complete genome assembly

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68
Q

oxford nanopore

A

v long reads
:( less accurate

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69
Q

bioremediation

A

use of microorganisms, plants or enzymes to detoxify soil contaminants (as xenobiotic pollutants resistant to natural degradation)

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70
Q

biotechnology

A

cellular factories
organisms producing medically/ commercially useful biomolecules
quick/ cheap

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71
Q

genetic modification of bacteria

A

clone gene of interest into expression vector > linearise > ligate > transform> multiplication> lysis and purification and induction

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72
Q

recomb therapeutics + enzymes

A

small-scale, high value products or high volume, low-cost commodities

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73
Q

synthetic bio and bio engineering

A

design/ construction of new bio parts/ redesign of existing, natural bio systems for useful purposes

74
Q

bio components

A

modular
non-chronological assembly
predictable outputs and complexity w symbols

75
Q

optogenetics

A

bacterial gene expression induction via small molecule signalling
potential therapeutic delivery tool

76
Q

metabolic engineering

A

gene circuits and engineered proteins combined for metabolic processes
complex, multi-enzyme cascades
^efficiency

77
Q

transcriptomics

A

measures gene expression of all genes at specific condition
infers bacterial cell function systemically

78
Q

CRISPR

A

Clustered-Regularly Interspaced Short Palindromic Repeats

79
Q

microbe detection

A

culturing
DNA/RNA sequencing

80
Q

NGS microbiome profiling applications

A

metabolomics
roteomics

81
Q

culturomics

A

identifying unknown microbes
:) reference database/ phenotypic and mechanistic studies/ culture collections/ therapy development
:( expensive/ labour-intensive

82
Q

functions of gut microbiota

A

complex sugar breakdown
breast-milk oligosaccharides
immune programming

83
Q

life factors influencing microbiome during pregnancy

A

intra-uterine environment (amniotic)
maternal exposures
gestation length
weight at birth

84
Q

life factors influencing microbiome during birth

A

delivery mode
mother/ healthcare professional contact
environment

85
Q

life factors influencing microbiome after birth

A

feeding modality
weaning/ antibiotics/ food supplementation
home/ family setting
home structure

86
Q

immune programing

A

mucosal and systemic immune compartments stimulate ‘tolerance’

87
Q

causes of microbiota disturbances

A

diet
antibiotics
infection
genetics

88
Q

microbiota diseases

A

autoimmune
brain-linked
intestinal
metabolic
immune

89
Q

colonisation

A

microbe growth after gaining access to host tissue

90
Q

pathogenicity

A

pathogen ability to inflict host damage

91
Q

virulence

A

degree of pathogenicity of an invading pathogen

92
Q

mechanisms of microbial pathogenesis

A

exposure> adherence> invasion> colonisation/growth

93
Q

bacterial abundance in upper vs lower respiratory tract

A

upper respiratory tract v abundant and lower is devoid

94
Q

where does TB survive?

A

in immune cells

95
Q

legionella pneumophila growth environment

A

stagnant water at ~35 degrees

96
Q

legionella pneumophila survival

A

lives in immune cells with protective vacuole

97
Q

what type of bacteria is legionella pneumophila

A

amino acid auxotroph (proteasomal degradation for nutrients)

98
Q

types of gastroenteritis

A

viral
bacterial
parasitic
// chronic
acute

99
Q

E.coli

A

gram negative rod bacterium in gut

100
Q

types of E.coli

A

extra-intestinal pathogenic
intestinal pathogenic (most common)

101
Q

burger bug

A

intestinal pathogenic E.coli encoding shiga toxin causing HUS

102
Q

vibrio cholerae

A

motile, gram neg
phage-encoded CTX > fluid loss

103
Q

helicobacter pylori

A

gram neg
motile
etiological agent of gastric/peptic ulcers

104
Q

types of immunity

A

innate (immediate response)
adaptive (exposure w targeted defence mechanisms)

105
Q

inflammation

A

non-specific
driven by neutrophil accumulation

106
Q

acute infection signs

A

calor
rubor (redness) /vasodilation
tumor / ^plasma movement to tissue
dalor (pain)
change in function

107
Q

adaptive immunity methods

A

specificity and memory
humoral
cellular

108
Q

specificity and memory mechanism

A

host-mediated
repeated
rapid
intense

109
Q

humoral immunity

A

B cell antibody production

110
Q

cellular immunity

A

T-cells attack intracellular pathogens

111
Q

ADCC

A

antibody dependent cell-mediated cytotoxicity

112
Q

bacteriaemia

A

bacteria present in bloodstream

113
Q

sepsis

A

extreme response to blood poisoning

114
Q

systemic shock

A

systemic decrease in bp
mass organ failure

115
Q

pathogen reservoirs

A

human / UPEC
zoonotic / EHEC
environmental

116
Q

diagnostic media

A

general
enrichment
selective
differential

117
Q

general media

A

non-selective
establishes growth
usually LB agar

118
Q

enrichment media

A

selective
certain species

119
Q

differential media

A

selects between 2 species
chromogenic substrate additive
e.g. MacConkey agar detects bacilli and enteric

120
Q

selective media process

A

blood-based antimicrobial mixed w mixed bac sample
incubated at 42 degrees
uses media/ growth conditions to select

121
Q

pathogenicity/ virulence factors

A

structures, molecules or regulatory systems enabling the disease process

122
Q

drive of virulence factors

A

adhesion to epithelial surface/ underlying tissue invasion

123
Q

what is a bacterial capsule?

A

polymer encasing gram -
excludes hydrophobic detergents
precursor to biofilm formation
resistance against immune recog/ phagocytosis

124
Q

cell surface appendage examples

A

physical defence
niche maintenance
nutrition
intercellular communication
genetic material exchange

125
Q

infection stages

A

adsorption
irreversible attachment
growth and division
mature macrocolony
dispersion

126
Q

fimbrial-mediated adhesion

A

sugar-binding, lectin-like protein caps
T1 > CUP adhesion of gram neg
fimH> higher affin for mannose

127
Q

pili

A

longer
fewer
genetic exchange

128
Q

catch-bond theory

A

binding strength dictated by allosteric switch in FimH-sugar interaction
*chemical inhibition possible

129
Q

2 pathways across IM

A

TAT
SEC

130
Q

SEC

A

common
unfolded

131
Q

virulence systems

A

T3SS (epithelial attachment/ EHEC)
T4SS (involved in genetic exchange)
T6SS (inter-bacterial warfare)

132
Q

types of toxins

A

exotoxins
endotoxins
Stx

133
Q

exotoxins

A

encoded on PAIs
site-specific

134
Q

exotoxin mechanisms of action

A

stimulatory
disruptive
cytolytic

135
Q

Stx

A

EHEC T3SS
colonisation essential
stress-triggered

136
Q

Stx-phage

A

repressive effect on T3SS, stimulating cell receptor host expression

137
Q

endotoxins

A

cell-bound lipopolysaccharides
released in lysis
less toxic than exotoxins

138
Q

pathogenic islands

A

accessory DNA on islands from pathogenic bacterial strains
phage-mediated transfer
ecological selective advantage

139
Q

latex agglutination

A

antibody-antigen interaction explorations for rapid diagnostics > isolate identity
> pathogen-associated identity of pathogens

140
Q

serology

A

diagnostic identification of antibodies in serum

141
Q

serotyping

A

determination of subtype of organism

142
Q

biochemical assay pros

A

metabolic capabilities
rapid
accurate

143
Q

oxidase enzyme tests

A

Pseudomonas spp +
E.coli -

144
Q

catalase enzyme tests

A

gram + bacteria

145
Q

urease enzyme tests

A

helicobacter pylori

146
Q

advantages of molecular diagnosis of infections

A

unique bacterial genomes
genetic material extraction from infected specimens
DNA easy to detect and quantify
sensitive 1-10 CFU reaction

147
Q

disadvantages of molecular diagnosis of infections

A

tech still developing
some tests require isolation first
too sensitive
standardisation issues

148
Q

DNA sequence detection

A

detection + ID gel electrophoresis = gene specific
fluorescent DNA intercalating agent
real time detection of PCR production w dyes

149
Q

meningitis RT-PCR

A

pre-emptive treatment before antibiotics
rapid correct treatment

150
Q

whooping cough RT-PCR

A

3-12 day incubation culture growth
diagnoses within hours
prophylaxis of contacts/ correct treatment

151
Q

major classes of protein synthesis-inhibitting antibacterials

A

tetracyclines
aminoglycosides
chloramphenicol/ macrolides/ lincosamides

152
Q

tetracyclines

A

bind to 30S ribosomal unit
block tRNA binding

153
Q

aminoglycosides

A

bind to 30S ribosomal subunits
impair proof-reading > faulty protein production

154
Q

chloramphenicol/ macrolides/ lincosamides

A

bind to 50S ribosomal subunit
prevent peptide bond formation
stop protein synthesis

155
Q

modifying approaches for treating infection

A

antibiotic use limiting
last resort antibiotics
combination therapy
phage therapy
faecal transplant

156
Q

source of outbreak parameters

A

who
where
outbreak type
those at risk

157
Q

global monitoring functions

A

limit spread
epidemic prevention
in-field diagnostics

158
Q

phylogeny

A

evolutionary history of group of organisms
nucleotide/ amino acid sequence data
most common marker > SSUrRNA

159
Q

SSUrRNA

A

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
Q

mitochondria, chloroplasts and plastids genome

A

encode rRNA’s and some proteins
machinery for protein synthesis

161
Q

universal SSUrRNA tree of life

A

bacteria
archaea (prokaryotes)
eukarya

162
Q

archezoa hypothesis

A

nucleus came first prior mitochondrion acquisition via endosymbiosis

163
Q

hydrogenosomes

A

produce hydrogen/ ASTP via substrate-level phosphorylation
some have genome

164
Q

mitosomes

A

reduce in size
no genome/ ATP production

165
Q

extracellular parasites

A

thrive on/ in tissues without entering host cells

166
Q

ntracellular parasites

A

penetrate host cells to complete life cycle

167
Q

apicomplexan

A

apical organ orchestrating moving junction-mediated entry

168
Q

kinetoplastids

A

lysosome-mediated entry
phagocytosis

169
Q

microsporidia

A

polar tube mediated entry
in combo w endocytosis/ phagocytosis

170
Q

animals/ metazoa

A

host many microbial species
niches for microbes

171
Q

choanoflagellates/ ichthyosporea

A

mostly marine species

172
Q

fungi/ microsporidia

A

important decomposers of dead animals/ plants
mutualistic interactions

173
Q

microsporidia infecting humans

A

opportunistic pathogens (e.g. AIDs)
bienusi/ intestinalis
oral-faecal route has zoonotic origin
have mitosomes

174
Q

microsporidia life cycle

A

no proliferative extracellular forms
depend on 1+ host

175
Q

stramenopiles

A

free-living species
prasites

176
Q

discovery of apicoplast in plasmodium

A

molecular data
genome organisation
ultrastructural studies

177
Q

apicomplexa jinfecting humans examples

A

p. falciparum
toxoplasma gondii
c. hominis

178
Q

t., gondii

A

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
Q

cryptosporidium

A

c. parvum (cattle) c.hominis (only human)
self-limiting diarrhea in immuno-competent persons

180
Q

t. vaginalis

A

STI
associated w HIV and mycoplasma
prenatal/ postnatal complications

CMB1003- Microbiology and immunology (3 decks)

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