Parasite genomics

Question 1

Prokaryotic genome description (4)

Answer 1

1) Nearly all coding (no-nonsense)
2) Few repetitive
3) Rapid evolve
4) Large population sizes

Question 2

Eukaryotic genome description

Answer 2

1) Lots of noncoding
2) Lots repetitive element
3) Conserved mode of evolution
4) Smaller population sizes

Question 3

Prokaryotic genome shape

Answer 3

-circular
-plasmids

Question 4

Eukaryotic genome shape

Answer 4

linear chromosomes

Question 5

Parasite genome description

Answer 5

-Larger genome
-different arrangements and structures
-low abundance
-complex life cycles and host interactions

Question 6

What processes lag when it comes to treating parasites

Answer 6

-prioritisation methods
-pipeline development
-applications of public health

Question 7

what does toxoplasma gondii cause

Answer 7

Toxoplasmosis

Question 8

What does severe toxoplasmosis cause

Answer 8

-brain and eye damage

Question 9

What does congenital toxoplasmosis cause

Answer 9

-miscarriage/still birth
-hydrocephaly
-microcephaly
-brain/eye damage later

Question 10

What protein is most abundant on toxoplasma gondii

Answer 10

SAG1 on cell surface

Question 11

What gene plays a major role in reducing Toxoplasma gondii

Answer 11

-1 gene
-SRS29C

Question 12

What is lymphatic filariasis

Answer 12

-neglected tropical disease
-causes damage to lymphatic system
-mosquito borne
-Eosinophillia

Question 13

What damage does lymphatic filariasis cause

Answer 13

-lymphedema
-bacterial infections of skin and lymph
-hardening and thickening of skin

Question 14

What is Elephantiasis

Answer 14

hardening and thickening of skin

Question 15

Novel lymphatic filariasis treatment discovery

Answer 15

-genome of Brugia Malayi explored
-essential metabolic enzymes identified
-compared with US FDA approved

Question 16

What is VEuPathDB

Answer 16

-14 databases
-over 709 organisms
-can be non-pathogenic and host

Question 17

what is cryptosporidium

Answer 17

an apicomplexan gastro-intestinal protozoan parasite

Question 18

Treatments for cryptosporidium

Answer 18

-none in EU and UK
-US = Nitazoxanide

Question 19

Acute cryptosporidiosis in UK

Answer 19

-especially common in young children
-8 cases for every case reported
-multiple outbreaks a year

Question 20

Diagnosing cryptosporidium

Answer 20

-ICLF dipstick
-Ziehl-Neesen stained microscopy
-Auramine phenol stained microscopy
-Enzyme immune assay
-PCR

Question 21

How to improve cryptosporidium treatments

Answer 21

-better detection
-identify; mechanisms, new target sites, virulence factors, clinical impact

Question 22

Cryptosporidium genome factors

Answer 22

-8 chromosomes
-highly compact coding genes (75%)
-AT rich
-Introns in 11% genes
-low complexity
-high repeats

Question 23

How is sample prep for cryptosporidium challenging

Answer 23

-oocytes shed into faeces
-may be low density
-hard to isolate from background material
-DNA extraction could cause dilution

Question 24

DNA mix in a faecal sample from someone with cryptosporidium

Answer 24

-Host DNA with small % cryptosporidium

Question 25

Pre-extraction process for high quality DNA

Answer 25

1)oocytes harvested by flotation (semi purified) 2)concentrated and purified by IMS 3)oocytes sterilised by 0.6% NaClO

Question 26

how can genome be amplified

Answer 26

Multiple displacement amplification (MDA)

Question 27

benefits of using multiple displacement amplification

Answer 27

-no need for IMS -extends sample to be analysed

Question 28

genomic diversity of a parasite population was shown how

Answer 28

-Tests of children in Bangladesh -aliquots of fecal material from same child showed genomic diversity -high recombination rates

Question 29

where does C. Hominis infect

Answer 29

almost exclusively low-middle income countries

Question 30

where does C. Aquapotensis infect

Answer 30

high-income countries with improved sanitation

Question 31

how is gp60 gene useful

Answer 31

-hypervariable for diversity -shows different types of cryptosporidium

Question 32

what was the initial focus for Multilocus Genotyping (MLG) scheme

Answer 32

C. Parvum

Question 33

advantages of fragment sizing to identify tandem repeats (C. Parvum)

Answer 33

-cost effective -rapid automated -samples can contain >1 allele -indicate how often multiple infections occur

Question 34

MVLA subtyping scheme for C. Parvum

Answer 34

7 locus subtypes

Question 35

Subtype of C. Parvum in December 2020

Answer 35

gp60 subtype llaA16G1R1 MVLA profile 4-14-5-7-18-25-17

Question 36

common MVLA in animal contact outbreaks

Answer 36

gp60 = IIaA17G2R1

Question 37

What does MVLA help to identify

Answer 37

-indicate unrecognised outbreaks or cases missed by surveillance alone