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Genomics > Paleomicrobiology > Flashcards

Paleomicrobiology Flashcards

1
Q

Y. pestis

  • disease
  • 3 major human pandemics
  • acquired via
  • most common form
A

plague

Justinian
Black death
Modern

flea bites
- host = rodents

Bubonic plague

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2
Q

Y. pestis biovars

  • define
  • differentiated how?
A

= variant prokaryotic strain that differs physiologically or biochemically from other strains

sub lineage attributed as the cause of major pandemics

metabolic traits

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3
Q

Where did Y.pestis originate from?

Where did it spread to?

A

Justinian
- from E/C Africa
via Egypt to Med

Black death
- central Asia
via Caspian se to Europe
via silk routes

Modern
- China
via Hong King through shipping globally

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4
Q

Pneumonic plague

- process

A
  1. enters via eyes, nose, mouth
  2. pneumonia in lungs
    (usually 100% mortality)
  3. exit via eyes, nose, mouth
    (v contagious)
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5
Q

Bubonic plague

- process

A
  1. enters via rat flea bite
  2. spreads via lymphatic system
  3. buboes
    pneumonia
    internal organ haemorrhage
  4. exit via eyes, nose, mouth
    (v contagious)
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6
Q

how does plague spread?

where do bacteria multiply?

overwhelming infection can lead to?

A

via lymphatics within macrophages

extracellularly
- cell lysis in lymph nodes, liver + spleen

multi-organ failure

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7
Q

pseudogene

A

where sequence suggests a gene in non-functional

e.g. STOP codon in middle of sequence

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8
Q

Who sequenced the Y. pestis genome?

A

Parkhill et al

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9
Q

What were the findings of the Y. pestis sequence?

- in terms of ancestry?

A

loss of many genes associated w/ ancestral enteropathogenic niche
- enterotoxins + adhesins
- many present as pseudogenes
(150 found in total)

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10
Q

What were the findings of the Y. pestis sequence?

  • IS elements
  • acquisition
  • plasmids
A

large no.s of IS elements
- contribute to gene loss/activation

acquisition of insect toxin homologues
- adaptation to insect vector host?

several plasmids

  • some common to genus
  • some specific to pestis carrying virulence determinants
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11
Q

Y. pestis evolution

A

acquires series of plasmids
-> improve efficiency and virulence

e.g. virulence plasmid + phospholipase D plasmid for flea survival
+
chromosomal genes for biofilm formation + insect toxins from bacteria in soil or gut

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12
Q

Y. pestis paper by?

A

Prentice et al (2007)

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13
Q

black death

  • killed..?
  • entered country via?
  • caused by?
A

killed ~50% of population in 1948-1949

port in Weymouth

Y. pestis

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14
Q

Controversy surrounding Y.pestis, Justinian + black death plagues

A

high mortality rates + clinical manifestation differ from modern Y. pestis
- if same pathogen, why don’t we see modern pandemics?

inconsistent PCR-based detections in ancient samples

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15
Q

Y. pestis

- genomic make up

A

chromosome + pCD1
- shared with non-pestis ancestors

pMT + PCP1 plasmids
- Y. pestis-specific plasmids

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16
Q

PCP1 plasmid

- features (ideal for things to look for in an ancient sample)

A

Y. pestis specific

high copy number (100x more than chromosome)

17
Q

paleomicrobiology

- what is it

A

studying the genomes of ancient samples

18
Q

paleomicrobiology

- major technical issues

A

DNA degraded into short fragments

pathogen DNA = tiny proportion of total

direct sequencing of pathogen DNA not possible

19
Q

DNA extraction from ancient samples

A

extract pulp from molar

-> extract DNA

20
Q

why are molars favoured samples?

A

large
often intact
enamel used for radiodating

21
Q

preventing contamination

  • contamination sources
  • preventative measures
A
  • microbial flora from burial site
  • from lab
  • cross-contamination

> gloves
UV irradiation
run 1 -ve control for 3 samples

22
Q

techniques for detecting ancient pathogens

A

electron or optical microscope

imumunodetection

isolation + culture

PCR-based detection + sequencing

23
Q

extracting out pathogen DNA (Y. pestis) from sample

A
  1. cut PCP1 plasmid sequence up into fragments
  2. PCP1 backbone synthesised ‘bait’ DNA
    (sequences stuck to beads)
  3. hybridise bait w/ extracted DNA
  4. samples eluted + sequenced using net gene sequencing
24
Q

black death sequence

  • techniques used
  • findings
A

used array-based capture
- sequence using next gen

almost identical to Y.pestis strains that cause bubonic strains today
- no unique traits obvious

  • perceived increased virulence of disease may not have been du to bacterial phenotype
25
Q

black death

- phylogenetics

A

Black death strain sits at root of evolutionary tree (17 contemporary strains of Y. pestis)

-> black death strain = progenitor of present Y. pests is strains

26
Q

what caused the high mortality of black death?

A

> malnutrition + host susceptibility
- poor weather + subsequent crop failures in years before

> pneumonic vs bubonic plague
- pneumonic ~95% fatality rate transmitted via sneezing (human-human transmission)
- bubonic ~ 45% fatality
transmitted via flea bites

> no treatments available

27
Q

Justinian plague

  • when?
  • where?
  • deaths?
A

AD 541-542

Eastern Roman Empire affected

no reliable no. of fatalities

28
Q

Justinian plague

- sequence

A

tooth pulp from 2 skeletons

generated Y. pestis genome

compared to 131 sequenced Y. pestis strains from later pandemics
- construct phylogenetic tree

lineages that cause Justinian plague + black death were independent emergences from rodents into humans

29
Q

Tuberculosis (TB) in a mummy

A

extracted lung tissue

sequenced in a single Illumia MiSeq run

<1% of reads aligned to human genome
8% aligned to M. tuberculosis reference strain

30
Q

comparative genomics

A

identify SNPs that describe genetic variation among population

use only common DNA

use SNPS to infer phylogenetic tree
-> depicts evolutionary relationships among samples

31
Q

molecular clock

A

DNA + protein sequences evolve at rate relatively constant over time + among different orgs

can be calibrated using temporal info from aDNA (as samples can be dated)

Genomics (6 decks)

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