Block 1 - global influences of microbes Flashcards
(286 cards)
1
Q
list some applications of microbes
A
drugs vaccines food bioterrorism genetic engineering decontamination
2
Q
list some cellular biological entities
A
fungi
protist
bacteria
archaea
3
Q
list some acellular biology entities
A
viruses
viroids
prions
4
Q
what are kochs postulates
A
isolation and confirmation of a particular organism with a specific disease
4 criteria reliant on pure culture of microbes
5
Q
what is a windogradsky column
A
used to stratify microbial communities in a sample
6
Q
what developments have allowed us to isolate and culture many more bacteria
A
development of agar
identification of different media
growth temperatures
oxygenation etc
7
Q
from which kind of bacteria are antibiotics mainly isolated from
A
soil bacteria
8
Q
list some roles of the microbiome
A
availability and uptake of nutrients
resistance to disease
regulation of immune response
generation and uptake of key dietary factors
9
Q
what can be a consequence of losing a microbial population in our gut
A
we may not be able to attain all the required nutrients
10
Q
what is the purpose of the earth microbiome project
A
seeks to understand patterns in microbial ecology across the biomes and habitats of the planet
11
Q
what is the iCHIP
A
allows culturing of microbes that are difficult to grow
- currently being used to culture bacteria capable of making new antibiotics e.g. against c. difficile
12
Q
what are the characteristics of prokaryotes
A
no nucleus
DNA in cytoplasm
only ribosomes
no bacterial wall
13
Q
what are the two categories that allow us to classify microbes by action
A
saprotroph
pathogen
14
Q
what is a saprotroph
A
feeds on dead organic material
useful in digestion and manufacture of food products
15
Q
what is a pathogen
A
feeds on plants and animals - causes diseases e.g. TB, pneumonia
16
Q
what are the 4 ways we classify microbe shape
A
coccus - spherical
bacillus - rod
spirillum - spiral
vibrio - comma
17
Q
what are the 2 ways we can classify microbes by their reproduction
A
sexual - DNA exchange
asexual - by bipartition - upon reaching a certain size the stem cell divides originating 2 offspring
18
Q
what is 16S
A
a bacterial ribosome protein which is highly conserved and functionally very consistent
it is essential for translation of bacterial proteins but undergoes small changes over time
conserved and variable regions are used for bacterial identification
19
Q
16S can be used as a ………… …………. to determine evolutionary relatedness
A
molecular clock
20
Q
how do we identify a bacteria using 16S
A
primers have been created to hybridise to variable 16S regions and PCR analysis is carried out
21
Q
using 16S sequencing we can estimate divergence by looking at similarity of sequences using …………. …………….
A
phylogenetic trees
22
Q
what are the 3 domains of life
A
eukaryotes
archaea
bacteria
23
Q
list some common traits between archaea and eukarya
A
have introns between genes
RNA pol/TFs more similar to eukaryotes than prokaryotes
translation initiator - methionine (bacteria - formylmethionine)
24
Q
what are some unique features to archaea
A
methanogenesis
non pathogenic
thermophilic
25
give evidence of archaea being diverse colonisers
they colonise hydrothermal vents, high pressure environments, cold and dark marine environments, high salt concentrated areas, wetlands, sediment, GI tract
26
describe vent thermophiles
- chemoautotrophs
- survive extreme temperature and pressure
- black smokers formed by precipitation of inorganic compounds
- microbes generate energy by reducing sulphur to H2S which is used as an electron acceptor for the energy source
- water drains --> heated by magma --> steam rises --> water emerges and cools, precipitating FeS and other minerals
27
describe the symbiotic relationship of the Hoff crab (kiwa tylari) and bacteria
- survives by eating bacteria it farms on hairs on claws
- bacteria proliferate as chemoautotrophs and utilize inorganic chemicals released from the vent (carbon source)
- crab provides shelter and protection from extreme temperature which allows persistence
28
why does culturing of some microbes require specialist equipment from NASA
because the extreme conditions of their natural environment need to be maintained
29
what is P.abyssi
a microbe that forms single cell biofilms on rocks and pass nutrients in order to persist in the community
cell grow as flat discs with cannulae (cytoplasmic extensions) that link the organisms together
30
give an example of archaea that don't prefer extreme conditions
methanogens in the gut
31
why do we know so much about true bacteria
it is because of their ability to cause disease
they are good models for understanding fundamental mechanisms
true bacteria offer solutions to many problems
32
what is the order of classification
```
domain
phylum
class
order
family
genus
species
strain
```
33
why is it common to find antibiotic producing microbes in the soil and sediment
find gram positive due to their peptidoglycan coat and endospore formation which generate chemicals to kill competitors e.g. antibiotics form streptomyces
34
what are the 2 types of bacteria
archaebacteria and eubacteria
35
describe bacillaes
firmicutes recovered from soil samples grown aerobically and survive at high temperature
they are a model for spore production (sporulation triggered by starvation
36
describe actinomycetes
they are actinobacteria
aerobic spore forming bacteria that form hyphae (fungi also produce these projections)
they make antibiotics in their secondary metabolism
they include Streptomyces
they produce anti-cancer/fungal/helminth drugs
37
explain how microbes have a dual role in climate change
they are sometimes the cause of increased greenhouse gases due to the products of their metabolism but they can also be the solution to many of the climate problems
38
which organisms can fix CO2 by photosynthesis
plants
algae
cyanobacteria
39
describe marine bacteria/algae
- responsible for 50% global CO2 fixation
- live in the top 200m water column
- absorb light using pigments and have a gas vesicle for depth adjustment to maximise light capture
40
describe phytoplankton
- they are photoautotrophic cyanobacteria that fix CO2 similarly to plants
- light harvesting apparatus in thylakoid membranes and rubisco in carboxysomes
- all O2 derived from plants or cyanobacteria containing chloroplasts (water used as an electron donor, releasing CO2)
41
cyanobacterial blooms fix CO2 but also have negative effects, what are these
- changes is nutrients, temp and light intensity
- loss of stratification of water
- organic material dies due to lack of light and organisms that utilize this material deplete the O2 and the water becomes anoxic which attracts anaerobic organisms and can support most marine life
- bacteria can produce metabolites/by products that affect water quality and can be toxic
42
what is a dead zone and how do they result
run off --> algal blooms that crash and are consumed by heterotrophic bacteria --> O2 depletion --> kills fish and invertebrates
43
describe the carbon cycling chained events
phytoplankton fix CO2 --> phytoplankton consumed (carbon oxidised by respiration --> CO2 and water) --> small crustacea consumed and more complex molecules assimilated
heteroorganotrophs cannot generate their own food but breakdown what they consume for energy
44
what are carbon sinks and how do they form
CO2 return occurs by respiration but the bottom of the ocean is low in O2 so not many microbes can return CO2 from the dead material
C compounds like methane and alcohols compress at the bottom of the ocean --> fossil fuels
45
what is the problem with burning fossil fuels
lots of CO2 release which was fixed millions of years ago
46
what are methanogens
obligate anaerobe chemoautotrophic archaea that use H2 as a terminal electron acceptor during anaerobic respiration
- fix CO2 through reduction of chemicals like H2S to methane
- they also produce methane from short chain FA produce by other gut bacteria
47
gut microbe energy harvest depends on ………..
symbiosis
48
what do gut microbe primary degraders do
attack bonds --> initial breakdown
49
what do gut microbe secondary fermenters do
they result in further breakdown - produce by products including CO2 and H2 which can be useful e.g. butyrate for gut health
50
what is one of the endpoints of gut microbial activity
methane
51
what are gut metabolism short chain FA by products used for
as a C source for by enterocytes
52
methanogens thrive on carbohydrates broken into ….. ….. ....
short chain FA
53
describe termite gut symbiosis
- termites produce CO2 and CH4 during wood digestion
- wood digesting bacteria in gut, mixotricha paradoxa (eukaryotic protist) contain bacterial endosymbionts which digest lignin in wood to generate acetate which is further broken down
- polysaccharides --> acetic acid + organic acids are utilized by termites. H2 and CO2 generated in conversion are used by methanogens to make methane
54
why is permafrost thawing
due to CO2/methane release due to increasing accessibility of microbes to organic material
55
how are changes in population resulting in increased methane in the environment
intensified farming for food --> more animals and organic material --> higher levels of methane in the environment
56
how can we reduce cattle emissions
by changing the cellulose (hay) diet to a grain diet which has more starch and so is more digestible and results in faster growth
this diet has also shown decreased FA and methane through 16S sequencing
however there appears to be an increased risk on pathogenic e. coli colonising due to the microbiome change
57
which greenhouse gas is 100x more harmful than CO2 and how is it produced
N2O - produced due to microbial activity in nitrogen cycling
58
what happens to N fixation in some bacteria when other N sources are available
it is turned off
59
what is the haber process
N2 + H2 under extreme temp/pressure = NO3 for fertilizers etc
60
what are the steps in Nitrogen fixation
1. N2 --> NH3 : N2 fixed by clostridial sp in soil and cyanobacteria in marine environments (anaerobic organisms as nitrogenase enzyme is O2 sensitive). Energy dependent - needs 16 ATP
2. Nitrification NO3 (ate) --> NO2 (ite). Nitrates are accessible by plants. non utilised nitrates or nitrites are used by microbes for energy under anaerobic conditions
3. denitrification : Reduce back to atmospheric N2.
61
what is the rate determining step for plant growth and which greenhouse gas does this influence the production of
NO3 soil availability is the rate determining step for plant growth and influences N2O production
62
what does runoff of fertilizer result in
denitrification in marine environments
| lots of excess nitrate which undergoes denitrification in the environment
63
give examples of bioremediation
detoxification of pollutants and environmental contaminants
| combinations of landfill microbes breakdown and use complex carbohydrates as a carbon source
64
how are biofuels made and why are they good
many methods
fungi ferment sugars and produce ethanol as a by-product
biofuels are good because they are carbon neutral - CO2 release of CO2 that was fixed by plants used to make it (not from pre-existing sources)
renewable source of energy
can be used in isolation or mixed with other fuels
65
what are disadvantages of biofuels
biofuels are currently made of food - not so good - should use non food crops
use of land that could be used for food
requires energy
damaging in non compatible fuel systems
66
what are the options for feedstocks for biofuels
easiest - sugar crops - ferment, distil
harder - starch crops - hydrolysis, ferment, distil
hardest - lignocellulose material - pre treatment, hydrolysis, ferment, distil
as it gets harder it is because they require greater processing and energy
67
……..……. …………. to express enzymes involved in simultaneous saccharification (………….) and fermentation of lignocellulosic material --> implications for cellulose and ethanol industry e.g. ……… ………….. ……….. …….. ………...
genetic engineering
hydrolysis
efficiency and waste material usage
68
give some reasons for the importance of plants
the provide O2, food, maintain biosphere and carbon storage, use for biofuel, use for vaccines/antimicrobials
69
describe the plant immune system
no specialised circulating immune cells
every cell can amount an immune response
non circulatory vascular system transports immune cells from infection site to uninfected tissues
PAMPs and PRRs are sued
they have memory and acquired immunity
memory is transmitted to subsequent generations i.e. in an epigenetic manner
70
describe the process of plant pathogen detection and coevolution
pathogen type recognised --> PAMP triggered immunity --> cellular signalling --> immune response --> pathogen evolution --> effector triggered susceptibility --> immune response impaired --> plant evolves counter measures --> effector triggered immunity --> immune response
this is an example of coevolution of plants and the pathogen
71
coevolution is more controllable in plants than animals - true or false
false - coevolution in plants is not as controlled as in animals
72
what are phytohormones and give 3 examples
```
they are plant hormones with central roles in signalling to each other and other plants in response to disease
3 examples
- Jasmonic acid
- ethylene
- salicylic acid
```
73
do plants encode pathogenesis related proteins
yes they act as defence proteins
74
give an example of how Jasmonic acid can defend the plant
it defends against caterpillars
| caterpillar saliva + leaves --> JA --> wasps (parasitoid)
75
what is aspirin in relation to phytohormones
it is acetylated salicylic acid
76
what are some plant defences against insect attack
hard waxy surfaces
toxins
recruitment of parasitoid insects
77
what are some plant defences against grazing
thorns
silical granules in leaves - grasses
toxins such as alkaloids in foliage, fruits, seeds
proteins such as ricin, lectins and proteinase inhibitors
78
what are parasitoid insects
they are insects that are attracted by emergency compound e.g. JA in response to damage
79
why must certain microbes be tolerated by plants and give some examples
e.g. Mycorrhiza - roles in plant nutrient exchange, communication, growth, productivity
80
what are the 2 types of mycorrhiza
ecto-mycorrhizae (outside roots)
| endo-mycorrhizae (inside roots)
81
what is the rhizobium
a genus of gram negative soil bacteria that fix nitrogen and colonize plant cells within root nodules
they convert N --> NH3 --> organic nitrogenous compounds
the plant provides organic compounds from photosynthesis to bacteria
MUTUALISM
82
the rhizobium is in …… with plants
synergy
83
give examples of each of the 5 plant pathogen types
virus - TMV
bacteria - agrobacterium tumefaciens
oomycete - potato blight
fungus - dutch elm disease and ash dieback disease
nematode - potato cyst nematode and pine wilt nematode
84
describe TMV in plants
- it is a +ve ss RNA virus with helical symmetry. it infects the tobacco plant and other members of the solanacaea. it causes mosaic mottling of leaves
- spread: infects wounds --> replicates --> spreads via plasmodesmata - seed borne spreading by contaminated hands/tools
- structure: rod form of delicate spiral with RNA in centre and the protein coat surrounding the RNA self assembles
85
what was the first identified filterable virus
TMV
86
which plant virus is useful for making vaccines
TMV
87
describe agrobacterium infection of plants
tumour galls caused by TDNA in the T plasmid
88
how can agrobacterium be used in research
replace TDNA with gene of interest to create transgenic plants
1. cut TDNA with restriction enzyme and insert DNA of interest to make a recombinant plasmid
2. introduce plasmid to plant cells and culture
3. grow plant expressing new trait
89
what pathogen causes potato blight
phytophthora infestans - oomycete
90
describe potato blight infection
phytophthora infestans grows in plant tissues initially as a biotroph (depending on living cells) then hyphae emerge from stomata once the plant is dead - the spores that emerge are windborne and spread
91
what is unexpected about the potato blight pathogen
unusually large genome
92
describe the irish potato famine
successive phytophthora infestans epidemics --> mass starvation
monocultures are very susceptible to infection - diversity in plants is important
93
describe dutch elm disease
it is caused by fungi ophiostoma ulmi and ophiostoma novo-ulmi
they block water conduction channels (xylem) causing wilt and host response also plugs vessels
shoots die back from the tip
cell wall degrading enzymes help the fungus invade the xylem and hyphae grow between xylem cells and the whole plant dies
spread - elm bark beetles burrow in trees and lay eggs, larvae then burrow sideways and pupate, transmitting as adults
94
describe ash dies back disease
caused by chalara fraxinea and its sexual stage - hymenoscyphis pseudoalbidus
it is tree borne beetlw transmitted and the spores are windborne
95
what are nematodes
they eukaryotic organisms and most of them are sexually reproducing
moult 4 times during development
developmental arrest when the environment is poor
plant parasitic nematodes cause lesion/gall formation
most cause non specific symptoms
most are parasite of roots
they have protrusible stylets or mouth spears connected to secretory apparatus
96
nematodes have internal ………… …………. to antagonize muscle
turgor pressure
97
what is the difference between endo and ecto nematodes
endo migrate into the tissues and ecto use the roots
98
give an example of how nematodes can re-differentiate host tissue
giant cells - stylet penetrates cell wall and gland secretors are deposited which interact with cells making them giant for feeding
other examples include:
stationary cells
non muscular cells
99
what are potato cyst nematodes caused by
heterodera and globodera spp
100
why are cyst nematodes especially bad for farmers fields
because they can survive for up to 20y and contaminate fields for up to 30y
101
how do cycst nematodes infect plants
they invade the root tip until they reach the inner cortex --> moult to J2 in egg --> J2 inserts stylet --> induce cell to become syncytial cell --> nematode moults to adult --> males revert to vermiform and leave roots in search of females --> females grow and break through the root surface --> female death --> cyst forms containing eggs and lasts for 20+ years
102
what factors do nematodes have that help them infect plants
cell wall modifying enzymes
suppression of host defences
auxin pathway interruption (high concentration at feed site)
effectors that target plant cell nucleus
103
describe infection by the pine wilt nematode
caused by burcaphelenchus xylophilus which invades the tree, kills it, feeds on fungi then consume it
104
describe the large scale HGT seen in pine wilt disease
transfer of information from fungi to nematode (get cellulases - cell wall modifying genes
105
in terms of cattle what are the costs in terms of health and economic risks
```
health risk -
animal health and transmission
poorly developed animals --> starvation
foodborne disease
endemic disease
economic risk -
diagnostics need to be efficient
vaccines/medicines need to be effective
market disruptions/productivity loss/costly
```
106
what causes TB in cattle
Mycobacterium bovis but it can jump species
107
how is there a one health aspect of zoonotic infections
because animal health influences human health and human health influences animal health
108
name 3 diseases of cattle: one of each category
bacteria
parasite
virus
bacteria - bovine TB
parasite - Nagana
virus - rinderpest
109
what agents cause TB in cattle, humans and birds
cattle - M bovis
humans - M TB
birds - M avium
110
as well as being an agent for bird TB what is another roe of TB avium
opportunistic pathogen in AIDS patients
111
what are the phylum, genus and species of the TB pathogen in cattle
phylum - actinobacteria
genus - mycobacterium
species - bovis
112
is mycobacterium bovis in extracellular or intracellular bacteria
also describe its structure
intracellular
| curved rod shape gram +ve with a high lipid content
113
what is meant by M TB being acid fast
have mycolic acid in cell wall so retain carbol fuschin colour because decolouriser doesn't enter
114
what are the symptoms of TB in cattle
weakness, coughing, weight loss
head lymph nodes affected first then tubercles form on surface of chest cavity and lungs
long replication rate --> can take years to develop
115
when does testing for TB in cattle occur
evey 1-4y and before movement
116
how do farmers deal with cattle infected with M TB
immediate slaughter
117
how does M TB evade the immune system
macrophages usually take up bacteria and contain them in a vacuole (phagosome). this fuses with the lysosome forming a phagolysosome resulting in low pH and ROS. HOWEVER M TB PERSISTS
they block phagosome maturation and prevent phagolysosome fusion by secreting protein and lipid factors. they have enzymes that make them resistant to low pH and ROS. immune cells engulf M TB but can't kill it --> tubercles
long term evasion --> granuloma
118
what is needed to kill mycobacteria
activated macrophages (e.g. by IFNg) will kill them effectively
119
what is a granuloma
build up of immune cells
120
how do we ensure that farmers are treated fairly for losing cattle to TB
they are compensated with the amount depending on the quality of the cow
121
how does the UK ensure that humans are no infected with TB by cattle
all milk is now pasteurised and screened
122
how is TB spread
it is spread by aerosol and from wildlife reservoirs e.g. badgers
123
how are vaccines implemented in TB prevention
- humans are vaccinated with an attenuated BCG strain
- there has been investment in badger and cattle
vaccines
- badger vaccines reduce the risk of TB in the badger vaccinated and its cubs too
124
what are the problems with TB vaccines
- no effect in already infected badgers
- costly and time consuming to vaccinate wildlife
- an oral vaccine is difficult to develop
- the cattle vaccine has shown mixed results and we can't tell the difference between vaccinated and infected cattle
125
what kind approach will be required to eradicate TB and what will be required for this
a combinatorial approach - would involve vaccination, culling, monitoring, proper animal husbandry
126
what is another name for nagana
African animal trypanosomiasis
127
how is nagana spread
it is caused by trypanosomes and spread through tsetse flies
128
what are the symptoms of nagana
swelling, fever, reduced milk, fertility issues, weight loss, malnutrition
129
where is the tsetse belt
central africa
130
which 3 trypanosomes cause nagana
congolense - common, resides in blood vessels --> anaemia
virax - can spread independent of tsetse flies and are also found outside the tsetse belt
brucei - only causes disease in animals, gambiense and rhodesiense cause African sleeping sickness in human s
131
how do trypanosomes evade the immune system
antigenic variation - variant surface glycoprotein switching
altering the immune response is costly and is what leads to symptoms of nagana
132
how do we treat and prevent nagana
vector control
drugs exist e.g. berenil
only breed trypanotolerant cattle
no vaccine exists yet
133
what is rinderpest
highly contagious viral disease of water buffalo, cattle and other wildlife
It is caused by paramyxoviridae a morbillivirus
134
what is the structure of paramyxoviridae
ss -ve sense RNA
multiplies in host cell
similar to measles virus
135
the mass starvation and lack of grazing animals once caused by rinderpest lead to thickets - what is the result of this
tsetse flies increase
136
how is rinderpest spread
close contact (breath, secretions, excretions)
137
what are the symptoms of rinderpest
fever, diarrhoea, oral lesions
138
rinderpest had a high/low mortality and high/low morbidity
high
| high
139
how does the paramyxoviridae suppress the immune system
- infected individuals have long lasting morbillivirus immunity but suffer from transient generalised suppression of immune responses to other pathogens
- reduced B cells, monocytes, neutrophils, some T cell types
140
how was rinderpest eradicated
attempts: slaughter, movement restrictions, vaccinations
| eradication campaign: cattle vaccination, diagnostic test, tissue culture rinderpest vaccine
141
what is ringworm
trichophyton verrucosum fungal infection off hair and keratinised layers of the skin also known as dermatophytosis which has economic consequences to farmers
zoonotic - direct contact and bites - largely occupational
142
ringworm has high/low morbidity and high/low mortality
high morbidity
| low mortality
143
how do we prevent and treat ringworm
vaccination reduces the level of outbreaks
treatment shortens the period of clinical signs although the infection is generally only self limiting
the environment must be disinfected because the chlamydospores persist in the environment
144
what is FMD
highly contagious virus of hoofed animals which is difficult to control with large economic threats to agriculture
incubation period of up to 2 weeks and transmission period can occur before culling
caused by picornavirus
145
what is the structure of the picornavirus that causes FMD
non enveloped ss +ve sense RNA with 7 serotypes
146
how does having multiple serotypes in FMD complicate treatment
there are 7 serotypes and it is difficult to make a treatment for them all
only get immunity to the serotype infected with
it also complicates diagnosis
147
FMD has high/low morbidity and high/low mortality
high
| high
148
what are the symptoms of FMD
fever, blister on feet and mouth, temporary immunosuppression, reduced milk production and lameness (has quite a bad effect on productivity)
149
how is FMD transmitted
direct contact or fomites and can survive in the environment for months
recovery is rare and it remains latent and can resurface
150
what is the preferred way to deal with animals with FMD
culling
151
what controls have been put in place in previous FMD outbreaks
culling
surveillance zones
ban on movement
152
how do we diagnose FMD
it is only detectable 2 days before clinical symptoms
ELISA is the quickest method - detection of antibody/antigen in serum and can be serotype specific
qPCR takes longer
genome sequencing takes even longer and requires expertise
virus isolation takes even longer and you need a cell line
153
what controls are used for FMD when a cow is infected
ring culling
disinfection of premises
restriction of movement
154
how is vaccination used for FMD
- the vaccine only gives short term immunity and the virus has high mutation rate
- it is generally given to limit infection in an outbreak but culling more common
- infected and vaccinated cattle can develop a carrier status (latent in lymph nodes)
- the vaccine is live and chemically attenuated so production is risky
- it is challenging to produce a vaccine against all strains
- subunit vaccines are in development which are safer but not as effective
155
how are domestic cats a threat to wildcats
infections of domestic cats can infect wildcats which are endangered
156
name 2 feline retroviruses
feline leukaemia virus
| feline immunodeficiency virus
157
how can cats be a threat to pregnant women
they can get toxoplasmosis which is transmissible to pregnant females
158
what are retroviruses
enveloped + ss RNA viruses that use RT for replication. DNA integrates into the host genome. they are classed as proviruses - they remain latent and resurface
159
what are the steps in the retrovirus cycle
1. RT converts RNA --> DNA once RNA enters host
2. DNA integrated to host chromosomes
3. viral particle assembly and exit
160
what is FIV
- Feline immunodeficiency virus
- the cat equivalent of HIV
- vaccine available - fel-o-vax - chemically inactivated but underused do to lack of differentiation
- infects Th cells and impairs the immune system
- spread by scratches and bites
161
what is FLV
- feline leukaemia virus
- transmitted from saliva in bites
- causes anaemia and lymphoma in cats
- some cats remain viraemic but will die in 2-3 years
- originally thought to be cancer but it is transmissible (horizontal transfer)
- may be possible to make a vaccine against lymphosarcoma and other FLV associated diseases
- there are vaccines currently but they need to be given soon after birth and they don't differentiate
- supportive therapies - keep indoors, treat secondary infections, maintain vaccinations
- diagnostics - ELISA but false +ves common - PCR and virus culture culture are more time consuming
162
describe H5N1
```
bird flu
bird to human transmission
no human to human transmission
60% mortality
easier to track n
```
163
describe H7N9
```
less deadly - 30% mortality
difficult to track
bird to human transmission
human to human transmission
Tamiflu resistance (drug)
```
164
what is the family and genus of avian influenza
family - orthomyxoviridae
| genus - alphianfluenzevirus
165
how do we get different influenza subtypes
based on N and H antigenic variation
166
what is H (hemagglutinin)
causes aggregation of rbcs, glutination of heme - recognises host - 18 types
167
what is N (neuraminidase)
controls release of new viral flu particles - 11 types
168
what is trichomonas
trichomonas gallinae is a protozoan parasite and causes yellow deposits/lesions on the oral cavity and can restrict diet leading to death by malnourishment
the lesions break down the mandible bone in the mouth
169
how are trichomonas spread
they don't survive long outside
they spread through unwashed birdfeeders
it can also infect domestic birds but there is no zoonosis
170
how do we prevent trichomonas
clean your bird feeders
171
what is eimeria
causes coccidosis in poultry and goats
caused by many different species (one affects one type of animal)
caused by an intracellular protist and is an apicomplex parasite
eimeria tenella is a major pathogen of intensively farmed chickens in close proximity
172
how is emieria transmitted
fecal oral - introduced on farmers boots or new infected stock
173
what causes the pathology of emeria
apical complex used to enter host - replicates in the intestinal epithelial cells and causes tissue change and sometimes bloody diarrhoea
174
what is the life cycle of emeria
1. oocyst excreted - contains 4 sporocysts which each contain 2 sporozoites
2. sporulation - sporozoites released - humidity/temp dependent
3. sporozoites invade gut epithelium (symptoms appear) and undergo asexual replication
4. sporozoites --> merozoites and invade new cells (if they don't they develop into male/female gametes)
5. sexual replication produces new oocysts which are excreted
(see diagram)
175
how do we control eimeria
chemo (anti coccidial drugs) but emerging AMR
live attenuated vaccine available but not very effective
improve the environment - less crowded - free range effective
176
what is the only human retrovirus that causes cancer
HTLV1 - causes ATL
177
how does HIV indirectly lead to cancer
via immunosuppression
178
what are the 3 mechanisms for retroviral transformation
transducing (animals only)
cis-activating (animals only)
trans-activating (humans e.g. HTLV1)
179
what does a normal retrovirus genome contain
promoter - controls viral gene transcription
gag - codes proteins that make up the capsid - structure
pol - important for coding RNA --> DNA, also makes other enzymes
env - encodes glycoproteins on surface of virus particles - help bind/enter cells
180
describe transducing reteroviruses
- usually replication deficient without helper virus
- has v-onc - oncogenes that encode proteins for cell growth - cause MAPK that leads to cell proliferation they are acquired form infected cells and altered to be hyperactive. some normal genes are lost when the v-onc gained
181
give an example of a transducing retrovirus
rous sarcoma virus - got all the replication machinery + viral oncogene (tyrosine kinase-v-sarc) - causes sarcomas in chickens
182
give examples of some retroviral oncogenes
```
sis
src
abl
ras
jun
myc
```
183
describe cis activating retroviruses and give an example
no viral oncogenes but everything they need to replicate
integrate into the host chromosomes close to normal cellular oncogene and disrupt its function (upregulate -> proliferation)
e.g. avian leukosis, mouse mammary tumour, murine leukaemia virus
184
describe trans activating retroviruses and give an example
viral protein regulates transcription of the virus and cellular genes
tax - binds onto LTR and controls viral and cellular gene transcription (transcriptional regulator e.g. if it binds to T cell, causes upregulation of IL-2 genes causing T cell to proliferate continuously --> cancer
e.g. HTLV1
185
describe the tumour formation efficiency of the transducing, cis activating and trans activating retroviruses
transducing - high
cis activating - high/intermediate
trans activating - very low
186
describe the tumour latency of the transducing, cis activating and trans activating retroviruses
transducing - short (days)
cis activating - weeks/months
trans activating - months/years
187
describe the replication of the transducing, cis activating and trans activating retroviruses
transducing - defective
cis activating - competent
trans activating - competent
188
describe the oncogenic element of the transducing, cis activating and trans activating retroviruses
transducing - cell derived oncogene
cis activating - cellular oncogene activated
trans activating - regulatory protein controlling transcription
189
are there any transducing retroviruses in humans
no
190
viruses associated with malignancy …………. in the host after primary infection
persist
191
what is the time interval for retroviral malignancy development usually like
long
192
describe HPV
- family - papovaviridae, tumour - cervical cancer
- there are 14 high risk types
- 16 and 18 cause most cervical cancers and precancerous lesions
- also associated with anus/vulva/vagina/penis cancers
- HVP E6 and E7 genes are expressed in tumour cells and interact with p53 and pRb (tumour suppressor proteins)
193
what parts of the world is HPV cancer most common
less developed regions that lack screening
194
describe the structure of the cervix in relation to HPV
- ectocervix - stratified epithelium. basal layer - cells capable of dividing. towards the top layer cells differentiate and are less capable of dividing
- endocervical canal - single layer of cells - glandular cells transform into squamous cells - most prone to HPV infection - these cells are sampled in screening
- endocervix - soft columnar glandular cells
195
how does HPV infection occur
- abrasion on the cervix - straight to basal cells
| - infects columnar cells in the canal to get to basal cells
196
describe the HPV genome
```
8 genes
E genes (early expression)
L genes (late expression)
```
197
what part of the HPV genome does the immune system target
targets L1 proteins but they are not recognised due to the immune system being more active at the basal level (layer where L1 isn't expressed)
198
what are the basic steps from HPV infection to cancer
infection (progression) precancerous lesion (invasion) cancer
199
what happens to most people when they are infected with HPV
they will clear the virus within 2 years but if not they are at risk of progression
200
how do the epithelial cells change after HPV infection to become cancerous
epithelial cells --> basal cells (continual replication) --> fully malignant
201
what is the role of HPV E7
when pRB is bound to the E2F (TF) the cell cycle is held in the G1 phase. when not bound to E2F, it drives the cell through the cell cycle
E7 binds to pRB leading to degradation so E2F drives the cell cycle --> cancer
202
what is the role of p53 (along with E6 and 7) in HPV infection
when activated by stress p53 induces transcription of genes that mediate either growth arrest (p21WAFI/CIPI) or apoptosis (Bax). p53 level is regulated through interaction with mdm-2 protein which signals p53 degradation. expression of E7 increases p53 levels causing cell cycle arrest. E6 binds to p53 and causes degradation so cell cycle resumes --> cancer
203
what is involved in HPV screening
if HPV infected cells are detected in a smear test we check for abnormal cells (cytology) and if abnormal cell are detected we refer for a colposcopy. if abnormal cells are not identified then you are just screened more frequently
204
what is available for HPV in terms of vaccination
the current vaccine protects against HPV 6, 11, 16, 18and a new version is looking to protect against 9 types
it used to only be given to teenage girls but not it will also be give to teenage boys as they can be carriers
205
what is Epstein barr virus
- family - herpesviridae
- tumour - BL, HL, NPC, B/T/NK cell lymphomas, PTLD
- most primary infections occur in childhood and remain latent in B cells and cancer development is uncommon
- infection in adolescence or adulthood is associated with glandular fever
- EBV immortalises in B cells in vitro creating a lymphoblastic cell line - 9 proteins cause immortalisation
206
what are the 3 latency patterns of EBV
I. EBNA1 - BL
II. EBNA1, LMP1, 2a, 2b - HL, NPC
III. EBNA1, 2, 3a/b/c, LMP1, 2a, 2b - IM, PTLD, AIDs lymphoma
207
what is the significance of EBNA 3a/b/c in the third EBV latency pattern
they are CTL targets - they are not recognised if immunosuppressed and will lead to cancer
208
where is Burkitt lymphoma endemic
malarial areas
209
what causes Burkitt lymphoma
it is sporadic and caused by EBV infection
it involves ch8 of c-myc TF gene and ch14 where immunoglobin heavy chain Ch locus is. a translocation occurs: c-myc --> ch14 causing proliferation as c-myc is upregulated
(can also get 8-2, 8-22 translocation)
210
what is the Ch locus (involved in BL)
it is highly expressed in B cells in BL to make their surface immunoglobins
211
describe the role of EBV and malaria in progression to BL
malaria diminishes T cell control of EBV infected cells - those with malaria are slightly immunosuppressed. malarial Ag induce polyclonal B cell proliferation causing induced EBV replication and increased EBV infected B cell pool and thus an increased chance of c-myc translocation. cells that express high levels of c-myc undergo apoptosis but EBNA1 of EBV prevents this --> cancer
212
describe HBV
- family - hepadnaviridae
- tumour - HCC
- attacks the liver and can cause acute and chronic disease
- the older one is infected the less likely they are to develop chronic infection
- 20-30% adults infected develop cirrhosis and/or liver cancer
213
describe HCV
- family - flaviviridae
- tumour - HCC
- can cause acute and chronic hepatitis - those who don't clear it develop chronic HCV infection
214
what is HCC
hepatocellular carcinoma - liver cancer
215
what is the leading cause of HCC
HBV and HCV infections
216
what is the indirect mechanism of HCV/HBV infection causing cancer
the viruses continually replicate in hepatocytes and need to be killed
the continual regeneration and proliferation increases the chance of a mutation and development of cancer
217
what is the direct mechanism of HCV/HBV infection causing cancer
HBV: HBV integrates into host chromosomes and alters oncogene expression. HBx regulates genes involved in signal transduction/cell cycle control
HVC: HCV core protein induces mitochondrial damage/oxidative stress, a trigger of HCC. HCV N55B protein interacts with pRB leading to degradation
218
what are the treatments and prevention mechanisms for HBV and HCV
HBV prevention/treatment - increase vaccination, antiviral drugs available for long term therapy but only reduce HCC risk, rather than eliminating it
HCV treatment - new antivirals can cure chronic infection but are expensive and have the best effect when treated before cirrhosis development
219
what is industrial microbiology
use of microbes to produce commercial products or carry our important chemical transformations (usually large scale)
can include enhancement of metabolic reactions
often use yeast/mold/bacteria
220
what is the difference between industrial microbiology and biotechnology
biotechnology involves genetic modification but industrial microbiology does not
221
are pharmaceutical products like antibiotics and steroids primary or secondary metabolites
secondary metabolites
222
name 2 speciality chemicals and food additives
vitamins and amino acids
223
describe commodity chemicals and give an example
inexpensive chemicals produced in bulk e.g. ethanol
| generally primary metabolites
224
what is the basic chemical equation of vinegar production
ethanol --> acetaldehyde --> acetic acid
| oxidation reactions
225
what is a rate limiting factor of vinegar production
high oxygen demand
226
name and describe 2 acetic acid bacteria
acetobacter, gluconobacter
| they are pH tolerant, aerobic and don't fully oxidise acetic acid to CO2
227
what are the 3 methods of producing vinegar
open vat/orleans -traditional, surface culture, needs mixed
trickle - continuous culture (new ethanol constantly fed in), media constantly turned over
bubble - stirred tank reactor, constant mixing, O2 pumped in from bottom, efficient (no wood taste :((…)
228
describe the trickle method of vinegar production
alcohol trickled through woodshavings aerated from below and bacteria coated on shavings (biofilm) - continuous culture --> efficiency
229
describe the bubble method of vinegar production
large scale, sparging (inject O2), attached to computer to monitor pH, temperature, O2 demand etc to make efficient
230
describe batch culture and its advantages and disadvantages
- closed system
- growth declines to diminishing nutrients or accumulation of toxic waste products
- they are more common because the product may only be required in small amounts intermittently, high product concentration may be required, certain product sonly made in the stationary page, strain instability may require culture renewal, technically easier
- vessel productivity is not increased
231
describe continuous culture and its advantages and disadvantages
open system, fittest bacteria survive, nutrients added and culture removed continuously, organisms grow under steady conditions
advantages - productivity for given sized vessel increased, growth rate can be maintained at optimum
disadvantages - limited uses, technically difficult
232
what is a primary metabolite
a metabolite that forms during exponential growth e.g. alcohol
233
what is a secondary metabolite
a metabolite that forms in the stationary phase - more complex, not essential for growth, dependent on conditions, closely related bacteria produce closely related metabolites, highly overproduced, often by spore
234
can we get interaction between primary and secondary metabolite pathways
yes e.g. antibiotics
235
what are some difficulties with scaling up a reaction
```
choosing an appropriate vessel
O2 availability
mixing
scaling up volume
media (e.g. clostridium only grows on solid media)
```
236
what are the stages of scaling up
```
lab flask (get commercial interest)
lab fermenter (alter growth conditions)
pilot stage plant (introduce instruments and computer control)
commercial fermenter (1000-5000000L)
```
237
describe the different types of downstream processing of products
separation - filtration, centrifugation, disruption of cells (if product intracellular)
concentration - extraction, ultrafiltration, precipitation
purification - chromatography, crystallisation
drying
238
list some properties of a useful microbe
```
large scale growth
spore or reproductive cell form
grow and produce product rapidly
cheap
non-pathogenic
genetically able to manipulate
```
239
what is brewing
the manufacture of alcohol from malted grains
240
how is most alcohol produced
by yeast production of ethanol
241
what is gasohol and what are its advantages and disadvantages
alternative energy made by yeast
| it reduces reliance on fossil fuels and increases fuel efficiency but there are food ethics
242
what yeast is commonly used to make alcohol
saccharomyces cerevisiae
243
what types of yeasts are required to make ales and lagers
ales - top fermenting
| lagers - bottom fermenting
244
how do we make distilled alcohol beverages
heat previously fermented liquid to a temperature that volatizes most of the alcohol
245
what is the process of malting
Barley (raw material - high C, low N) --> Malt (germination - enzymes convert starch to maltose)
246
yeast use the enzymes from dried ………...
malt
247
what is the process of mashing
malt (crush)--> grist (water)--> wort
248
what are adjuncts
they added to malt to increase the carbohydrate content of wort for fermentation e.g. wheat, maize, rice
249
what happens to the wort produced
hops are added to it and it is filter and boiled to produce clarified hopped wort
250
what can spare wort be used for
cattle feed
251
what can spare clarified hopped wort be used for
fertilizer
252
what are the function of hops
they have antiseptic properties and prevent spoiling
253
describe the fermentation of ale
batch, open vat, top fermenting, s.cerevisiae, pitched with large inoculum, rapid growth --> may need aerated, yeast skimmed off to use again, 5-6 days, 14-23 C, pH 5.2-4.1
254
describe the fermentation of lager
batch, bottom fermenting yeast, s.carisbergensis, 8-14 days, 6-12 C
255
describe the maturation process in brewing
fresh beer is filtered and centrifuged and stored in storage tanks for a few days for natural conditioning at 4-8 C
256
what is any surplus yeast from beer brewing used for
food products
257
what is the difference between beer, lager and ale
beer is an umbrella term covering ale and lager
| ale and lager differ in taste and are brewed differently
258
in maturation what is the difference in the storage of lager and ale
lager is stored for weeks at -1 C
| ale is stored for a few days at 4-8 C
259
what is involved in the finishing process
pasteurisation and bottling
260
what is the chemical equation for going from maltose to ethanol
maltose --> glucose --> pyruvate --> acetaldehyde --> CO2 --> ethanol
261
which chemical process makes the alcohol taste good
sugars, proteins, fats --> ethanol + higher alcohols, organic acids --> ester (maturation)
262
what is spoilage caused by in brewing
contaminants after boiling wort, from air, water, or pitching yeast
263
why can only certain bacteria/yeast cause food spoilage
because of the harsh conditions of the beer (pH, low temp, hops, anaerobic etc)
264
how do we prevent beer spoilage
aseptic technique and hygiene
using pure strains
pasteurisation
265
what is the story of the ale conner
if trousers stick to the bench the beer is not fermented enough and there is too much sugar
266
what type of organism are the majority of biowarfare agents
bacteria and some are viruses
267
what is anthrax
a disease caused by bacillus anthracis
268
what about BA makes in good for BW
its spores
269
what are characteristics of a good BW agent
infectivity, casualty effectiveness, resistance, availability and means of transmission
270
what is LD50
lethal does 50 - the lethal dose to kill 50% of the population
the lower the LD50 the more virulent the organism
271
what is more virulent - streptococcus or salmonella
streptococcus
272
what is the BA life cycle
- spores taken in (ingested/inhaled)
- spread to bloodstream and germinate into non spore forming form, generating large numbers
- spread to different species by biting fly/meat/inhalation
273
what is cutaneous anthrax
occurs when the BA has entered a wound
it causes blackened lesions on skin (tissue necrosis)
it is self limiting and is treatable
274
what is inhalation anthrax
caused by inhalation of BA spores in the lungs which travel to the blood stream by passing through alveoli
it produces 2-3 toxins and causes haemorrhagic meningitis
it has high mortality and is effective for BW
275
what did Pasteur do
made a vaccine administered to livestock which was effective
BA became a standard organism but needed to be produced locally - the spread of knowledge increased the chance of it being used maliciously
(availability + means of transmission = good BW)
276
what is Glanders
- it is a disease cause by burkholedera and is given to horses by germans
- it can also affect other animals and sometimes humans
- it is difficult to diagnose and often fatal
it is multifactorial - infection types - localised, pus forming cutaneous infections, pulmonary infections, bloodstream infections and chronic supportive infections on the skin
- no vaccine, no diagnostic, no antibiotic
277
why did none of the horses infected with burkholedera by the germans die
because they only developed a cutaneous infection
278
describe the French BA bombs
they failed to develop effective inhalation formulations and relied on cuts and lesions for cutaneous infection
planes weren't sophisticated enough and there were difficulties making vapour clouds
279
what is woolsorter's disease
it occurs when wool sorters inhale BA
the wool contained the spores and there were vapour clouds in the factories due to poor ventilation which lead to inhalation anthrax
people either got flu like or severe symptoms (death)
280
what is the british BW programme
they developed new strains and aerosol testing apparatus was developed
they could deliver fixed amounts of spores (not clumps) of different sizes and volumes and test using the new apparatus
many workers died from anthrax
281
what is the softer version of BA
Bacillus subtilis
282
what is the human LD50 for BA
based on primate data
| 2500 --> 55000 spores inhaled to be lethal
283
viruses have poor transmission as a BW agent without a ……..….. …………...…
carrying agent
284
what is salmonella typhimurium and how was it used in BW
gram -ve bacteria that spreads in contaminated food e.g. contaminated salad bars in Dallas - could've been more effective with more potent strain
285
describe the amerithrax situation
letters sent from Washington contained dried spores of anthrax and had code in them likely to be from a scientist
it was a homegrown attack by a forensic scientist
it was an ames strain - radiocarbon dating established it was cultured <2y before mailings
north east water source used
sequencing showed mutations and they found the flask
suspect worked at government biodefense lab and killed himself
286
is BW as dangerous as nuclear weapons
just as dangerous if not more
