Food Safety: Surveillance 2

Front 1

How is DNA converted to RNA?

Back 1

Transcription

Front 2

How is RNA converted to protein?

Back 2

Translation

Front 3

What 5 methods are used to investigate DNA?

Back 3

Molecular Hybridisation: southern blotting, DNA sequencing, PCR, DNA fingerprinting, Microarrays

Front 4

What 3 things does genomics discover?

Back 4

Identification of specific DNA signatures, prediction of restriction sites, DNA microarrays

Front 5

What 5 methods investigate RNA?

Back 5

Molecular hybridisation: northern blotting, in situ analysis (FISH), RNA sequencing, microarrays, RT-PCR

Front 6

What 4 things does transcriptomics investigate?

Back 6

Prediction of open reading frames, culture media design, prediction of virulence, gene expression in response to the environment

Front 7

What 4 methods are used to investigate proteins?

Back 7

Molecular Hybridisation: western blotting, protein sequencing, mass spectrum, analysis

Front 8

What 3 things are proteomics used for?

Back 8

Identification of antigenic epitopes, MAb production, vaccine design

Front 9

What 4 things is genotyping useful for?

Back 9

quality control, description of laboratory cross-contamination, authentication of re-infection / relapse, investigation of infectious disease outbreak

Front 10

What 3 approaches can be used for genotyping?

Back 10

pulsed-field gel electrophoresis, multi-locus sequence typing, whole genome mapping / sequencing

Front 11

What does sub-typing discriminate?

Back 11

food-borne pathogens below species level

Front 12

Why do sub-typing methods need to be reliable, sensitive and informative?

Back 12

match isolates with cases, discriminate between case isolates and unrelated isolates

Front 13

Why is surveillance needed? 4

Back 13

Identify new or emergent strains / clones, identify potential reservoirs of strains that cause disease, identify routes of transmission, improve knowledge of epidemiology of foodborne disease

Front 14

What is the standardized approach to data acquisition and interpretation?

Back 14

PulseNet

Front 15

What is bacterial sub-typing 1?

Back 15

identification to species or sub-species level, for some bacteria typing is part of identification

Front 16

What is bacterial sub-typing 2?

Back 16

subtyping allows discrimination below species, subspecies

Front 17

What is molecular sub-typing bacteria?

Back 17

characterization of DNA, RNA or protein of bacteria to discriminate below species, subspecies and types

Front 18

HOw many subtypes of S. typhimurium are catalogued in PulseNet?

Back 18

over 1800

Front 19

Why is subtyping needed? 3

Back 19

QC of fermented foods and pro/prebiotics, food processing applications, food-borne disease tracking

Front 20

What are 3 sub-typing methods?

Back 20

Restriction fragment length polymorphism (RFLP) methods, PCR-based methods and DNA sequencing

Front 21

What are the 4 types of RFLP based methods used to sub-type?

Back 21

Whole genome RFLP, ribotyping, pulsed field gel electrophoresis, whole genome mapping

Front 22

What are the 3 PCR-based methods used for sub-typing?

Back 22

RAPD, REP and ERIC and multi-locus variable number of tandem repeats analysis (MLVA)

Front 23

What are the 2 types of DNA sequencing used to sub-type?

Back 23

Multi-locus sequence typing (MLST) and whole genome sequencing

Front 24

How can complexity of a DNA fingerprint be reduced?

Back 24

Pulsed-field gel electrophoresis (PFGE)

Front 25

What does REA produce?

Back 25

large number of overlapping, poorly resolved DNA fragments

Front 26

What is DNA macrorestriction analysis by PFGE?

Back 26

RFLP-based method that uses rare cutting restriction endonucleases to cut chromosomal DNA

Front 27

Why are agarose plugs used in PFGE?

Back 27

DNA is digested in agarose plugs to prevent shearing

Front 28

How are DNA fragments separated in PGFE?

Back 28

agarose gel

Front 29

How is electricity involved in PGFE?

Back 29

Orientation of an electric field changes in a pulsed manner

Front 30

What are macrorestricted profiles composed of?

Back 30

5-30 well resolved bands

Front 31

What size are macrorestricted profiles?

Back 31

10-800kbp

Front 32

What is the gold standard technique of sub-typing?

Back 32

PGFE

Front 33

What restriction enzymes are used for E. coli?

Back 33

Xbal, Blnl, NotI

Front 34

What are the 4 limitations of PGFE?

Back 34

specialized and expensive equipment, laborious and time consuming, not amenable to automation, interpretation of results can be difficult

Front 35

What is likely to supersede conventional sub-typing?

Back 35

Whole genome sequencing

Front 36

What happens during whole genome sequencing?

Back 36

Bacterial genome preparation is fragmented then sequenced using a suitable method

Front 37

How is the genome assembled in WGS?

Back 37

Bioinformatic programs used, development of contigs first, then closure of remaining gaps

Front 38

What is the genome used for?

Back 38

comparative studies to further characterize the bacterium, link genetic structure to phenotype

Front 39

What are the 3 steps of traditional sequencing?

Back 39

Cloning, sanger sequencing-chain termination mechanism, electrophoresis with laser readout

Front 40

What does NGS produce?

Back 40

shorter reads and more reads in shorter time

Front 41

What does NGS sequence?

Back 41

individual clonally amplified DNA molecules

Front 42

Does sanger or NGS have higher error rate?

Back 42

NGS

Front 43

What does NGS provide?

Back 43

window to view real-time bacterial evolution

Front 44

What is pyrosequencing?

Back 44

sequencing by synthesis methods, dNTP is incorporated and detected by photon emission

Front 45

What does photon emission depend on?

Back 45

series of enzymatic reactions

Front 46

How is ATP produced in pyrosequencing?

Back 46

PPi combines with adenosine phosphosulphate, catalysed by ATP sulphurylase

Front 47

What produces light in pyrosequencing?

Back 47

luciferase, D-luciferin and O2 combine to make light

Front 48

What does apyrase do in pyrosequencing?

Back 48

degrades any unincorporated dNTPs

Front 49

What is important about E. coli's genome

Back 49

it is dynamic

Front 50

What is S. agona's genome devoid of?

Back 50

plasmids

Front 51

What type of antibiotics is E. coli O104 resistant to?

Back 51

b-lactam antibiotics

Front 52

In what type of sells is there an epigenetic role of methylated bases?

Back 52

eukaryotic

Front 53

What can methylate bases?

Back 53

bacteria as a function of their restriction modification systems

Front 54

What do RM systems in bacteria do?

Back 54

Protect against deterious effects of partner restriction enzymes which act on transmissible DNA molecules, including phage

Front 55

What are known to play a role in virulence?

Back 55

Methyl-transferases (MTases)

Front 56

What detects methylated bases?

Back 56

SMRT sequencing

Front 57

What is PFGE used for?

Back 57

tracking pathogens and identifying hot-spots of contamination

Front 58

What can be identified by sub-typing in food industry?

Back 58

persistent clones that contaminate processing environment and the food production chain and may infect consumers

Front 59

What 4 factors facilitate pathogen survival?

Back 59

growth rate in food matrices, heat resistance, resistance to biocides, virulence

Front 60

What are the 9 characteristics of an idea sub-typing method?

Back 60

wide applicability, rapid results, high discrimination, reproducible, easy, automatable, inexpensive, ease of result interpretation, easy and automated comparison of patterns

Front 61

What is the problem with genetic diversity?

Back 61

isolates differing by 1 DNA band may be very different

Front 62

Can sub-typing prove or disprove a connection?

Back 62

multiple genotypes from food, co-infection

Front 63

When are high clock speeds used?

Back 63

outbreak investigations

Front 64

When are low clock speeds used?

Back 64

longitudinal studies

Front 65

what is a standardized method?

Back 65

PFGE