Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

7BBFM128: Forensic Biology > Non-human DNA > Flashcards

Non-human DNA Flashcards

You may prefer our related Brainscape-certified flashcards:
AP® Biology flashcards Biology 101 flashcards
1
Q

LO

A

*** How can animal DNA be useful in a forensic context?
* How can we apply forensic techniques for DNA identification in the field of wildlife forensics?
* What non-human DNA research is Kings forensics undertaking?
**

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Most DNA evidence collected from crime scenes is human, but sometimes the crimes directly involve non-human DNA, in what instance is this the case?

A

Wildlife poaching

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Some evidence that can be left at a crime scene that is non-human can be what?

A

Animal, plant, microbial: Hairs, blood, tissue, fluid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Why is it important to distinguish between human and non-human DNA?

A

 Exclude irrelevant samples
 Link: scene- suspect- victim
 Analyse non-human DNA which is relevant to case

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What do we consider when talking about non-human DNA?

A

o Animal DNA
o Plant DNA
o Microbial DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

When may plant DNA play a part in forensics?

A
  • Identification of illegal plant material (plant DNA)
    o Cannabis
    o Timber: Ebony, rosewood, satinwood- illegal trading and logging
  • Pollen and other plant material at crime scenes- sticks to clothing so can help link forensically
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

When may microbial DNA play a part in forensics?

A

Microbial DNA
o Anthrax- on mail

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

It what areas is animal DNA important in forensics?

A
  • Food fraud
  • Post-mortem interval
  • Wildlife forensics
  • Another animal DNA
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Whats meant by a DNA barcode?

A

Short, homologous sequences of DNA (vary between species but remains conserved within a species)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

In what circumstances is considered ‘food fraud’?

A
  • Charging a premium price
    o Olive oil
    o Caviar
    o Mozzarella
  • Using cheaper ingredients
    o Horsemeat rather than beef
  • Food adulteration
  • GM crops
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

With the horsemeat scandal, what did eurofins offer?

A
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

When have blowflys typically been used in forensics?
Whats the method behind this?

A

Entomology has traditionally been used to establish PM interval of the deceased

Method:
o Collection of insects (e.g., maggots)
o Incubation of insects until species can be identified by microscopy
o Insects collected can be compared to its species’ life cycle
o Extrapolate age of insect at time of collection and PMI

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Whats the limitations to blowfly entomology?

A

o Incubation of insects take time- need facilities and expertise
o Species identification by microscopy can be subjective

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is a molecular genetic tests thats being done on blowflies?

A

Sensitive methods to identify insect species

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is some research going on into blowflies?

A

DNA profiles from the deceased can be obtained from the gut of the insect

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Tell me about DNA barcoding and some target markers
What do you want from your DNA barcodes?

A
  • Method used for identifying species using a short, standardised sequence that varies between species but remains conserved within a species

**Target markers with DNA barcoding: **
o Cytochrome c oxidase I (COI or COX1) gene found in mtDNA genome- generally what is used for animals
o Internal transcribed spacer (ITS) rRNA, often used for fungi
o RuBisCO, often for plants
o 16S rRNA and 18s rRNA, often used for micro-organisms

*** What you want for DNA barcodes: **High taxonomic resolution, specific conservation between species

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What is the process behind DNA barcoding?

A
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

With a blowfly species ID, what are most of the markers (and example) and where are they found?

A
  • Most markers are mitochondrial markers
  • Within the coding and non-coding regions of mtDNA
  • Popular markers
    o COI and COII
    o Cyt b
    o 12S
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is wildlife forensics?
What does this field use scientific procedures to do?

A
  • Wildlife forensics is the application of science to legal cases involving wildlife
  • This field uses scientific procedures to investigate wildlife- related crimes involving the exotic pet trade, poaching, other illegal hunting activities
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What are endangered species at risk to?

A

* Trophies: tusks, horn, pelts, skins
* Food: illegal whale hunting, bush meat, caviar shark fin soup
* Medicines: bears gall bladder, rhino horn, tiger parts
* Sport: fox hunting, illegal killing of birds of prey
* Exotic pets: African grey parrots, marmosets, meerkats, poison dart frogs
* Fashions: furs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Wildlife forensics

A

International wildlife trafficking, or “wildlife and forest crime” (INTERPOL designation)
o Generates between $7 and $23 billion annually
o Grows at approximately x3 the growth rate of the global economy (between 5-7% a year)
o Typically defined as the smuggling, poaching, capture, and/or collection of protected or managed species, and products or derivatives thereof

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What are some biosecurity threats?

A
23
Q

Whats CITES?

A
  • Convention on international trade in endangered species of wild fauna and flora
  • An international agreement between governments. Its aims is to ensure that international trade in specimens of wild animals and plants does not threaten their survival
  • More than 38,700 species of flora and fauna are categorised as endangered
24
Q

Can you enforce legal action against poachers if the animal part/ remains found are beyond recognition?
e.g., carcass, meat, horn

A

No
Over 1/3 of IWT crimes do not result in prosecution due to improper identification of species

25
Q

What can be done in order to identify the species?

A
  • Microscopy of hair
    o Classification of hair features under magnification
  • Immunological testing of blood
    o HPLC
    o Electrospray ionisation mass spectrometric analysis
26
Q

What are the requirements for CITES to investigate?

A

The investigative questions to address the identification of animals and plants, or their parts and derivatives, can generally be categorised into 5 groups:
1. The species involved
2. The geographic origin of a specimen
3. The wild or captive/ cultivates source of a specimen
4. The individual origin of a specimen
5. The age of a specimen

27
Q

Tell me about the Rhodis database

A
  • Poaching is soaring
    o Rumour that a former politician in Vietnam was cured of cancer using a rhino horn remedy

*** RhODIS- Rhino DNA Index System **

  • Contains DNA profiles of individual rhinos
    o 3,968 individual rhinoceros DNA in database
    o 22 STRs + sex marker
    o Enables the linking of rhino remains to a particular rhino
28
Q

What are the stages to STR profiling in non-humans?

A
  • Same concepts as standards (human) STR profiling:
    o DNA extraction
    o Amplification
    o CE
29
Q

How is Rhino DNA obtained?

A
30
Q

Tell me about the Ursaplex database

A
  • STR and sex determining panel for individual genetic identification of North American Black bears
  • Human-wildlife conflict and poaching applications
31
Q

Birds of prey

A
32
Q

Why have MPS multiplexes been developed?

A
  • Conservation genetics
  • Wildlife crime forensics
  • Leverage MPS technology (paralleling human forensics)
  • Exploit newly emerging whole genome reference sequences
  • Improve on existing markers
33
Q

How were markers for non-humans discovered and whats the filtering criteria?

A

*** STR finding tools **
o RepeatMasker
o Msatcommander
o GMATA

*** Filtering criteria **
o Amplicon length: 100-400 bps
o Appropriate flank and primer design sites
o Repeat motif length: 4-6 inclusive
o Number of repeats: optimum 11-16

34
Q

MPS data analysis

A
35
Q

Birds of prey

A

Historical case investigating a falconer who sold allegedly captive-bred young
o Applies 14 STR multiplex
o 49 birds tested
o CE and MPS: additional 8 alleles were observed with MPS
o Relationship testing to compare genotypes to the breeding pairs owned by the accused
o 23 young birds were clearly excluded as being the offspring of any of his breeding pairs

36
Q

Tell me what the source for taxonomic ID is

A
  • Taxonomic source= species, genus, etc
  • Regions from the mitochondrial genome are the primary choice for forensic taxonomic identification
37
Q

What did taxonomic ID from ivory tell us?

A
  • Cartier at al., 2020
    o 21 specimens submitted for testing
  • Morphological analysis revealed it was impossible to determine where the ivory was elephant or mammoth
  • Next generation sequencing:
    o Higher throughout and increased sensitivity means better recovery of full target sequence from poor sample
    o Better for mixed samples as individual reads can be assigned to separate taxa
38
Q

Traditional medicines

A
  • Global annual market of $83 billion (WHO, 2013)
  • Often contain multiple species
  • DNA identification is challenging due to presence of PCR inhibitors (protein, lipids, etc) and degradation through processing
    o Extraction protocol important
    o Arulandu et al 2019
39
Q

Whats Metabarcoding?
What method does it use and what does this enable?

A
  • Target several barcodes for simultaneous detection of multiple species in complex samples

*** Massively parallel sequencing enables this: **
o Reads aligned
o Sequences BLAST searched against NCBI for taxonomic classification
o “Mini-barcodes” useful for degraded samples

40
Q

Whats the minion sequencer and what are the benefits and limitations?

A
  • Portable NGS solution
  • Benefits:
    o Long-read output
    o Low initial start-up cost ($1000)
    o Simple, rapid library preparation protocols
  • Limitations
    o High error rate: 5-25% compared to 0.01% on MiSeq
41
Q

What are the challenges to non-human DNA?

A

Reference samples and database
Quality control
Cost and availability of testing

42
Q

Tell me about the challenge with **Reference samples and database **

A
  • Human forensic genetics
    o Databases e.g., NCBI, EMBL, 1000 genome project
    o Reference genomes e.g., rCRS
  • Wildlife forensics genetics
    o Many different species
    o Mostly only have databases for “appealing” animals
  • EarthBioGenome Project and ForCytDNA
43
Q

Tell me about the challenge with quality control

A
  • Human forensic genetics
    o Accreditation and ISO standards
    o Rigorous and curated databases lie EMPOP or THRD
  • Wildlife forensic genetics
    o Adhered to international quality standards often not priority
  • OSAC wildlife forensic biology subcommittee and society for wildlife forensic science
44
Q

Tell me about the challenge with cost and availability of testing

A
  • Sending samples off-site= expensive and complicated
  • MPS remains out of reach for many labs doing wildlife forensics
  • African Wildlife Forensics Network: network of wildlife forensics stakeholders for the implementation of forensic science and crime scene services across Africa
  • MinION protable technology?
45
Q

DNA evidence can also be utilised in relation to other types of forensic evidence collected from a scene, give two examples

A

*** Ballistics **
o DNA profiles can be obtained from touch DNA or biological evidence recovered from cartridge casings and weapons

*** Fingerprints **
o DNA profiles can be obtained from touch DNA

46
Q

Tell me about obtaining fingerprints from ivory,
whats the aim, a probelm encountered and the outcome

A
  • Low tech equipment needs at police departments, ports and in the field
  • AIM: to recover finger-mark friction ridge detail from seized wildlife items using effective, cheap and easily deployable technology
  • Partnership: The metropolitan police and the international Fund for Animal Welfare (IFAW)
  • Together delivered a fingerprinting kit that works on ivory and horn
47
Q

Fingerprints on ivory continued…

A
48
Q

How can domestic animals be involved in forensics?

A
  • Cats and dogs most common
  • Crimes can take place in settings where animals are present
  • Crimes can directly involve animals:
    o Animal attacks e.g., badger baiting, fox hunting
    o Dog fighting
49
Q

How can Domestic pets be analysed?

A
  • Sample concepts as standard (human) STR profiling
    o DNA extraction
    o Amplification
    o CE
  • Examples “MeowPlex”
    o 11 polymorphic tetranucleotide loci
    o Identify cats
50
Q

When barcoding for mixtures what is used and what are the advantages of MPS here?

A
  • 16S rRNA
  • Advantages of MPS:
    1. Short PCR amplicons
    2. Universal PCR-primers i.e., no need for prior species information
    3. High capacity for sample multiplexing
    4. Deep sequencing
51
Q

When using metabarcoding and trying to identify multiple species from mixed sources, what are the three mtDNA targets used?

A
  • Three mtDNA targets:
    **o 16S rRNA
    o Cytochrome b
    o Cytochrome c oxidase I **
  • In silico studies show they can differentiate vast majority of species (4500 tested)
  • Tested on real cases: bite marks in murder case identified to be from a dog
52
Q

Whats are the limitations to next-generation signalling?

A
  • With great sensitivity comes **great contamination **
    o Validations must address acceptable contamination levels
  • Inhibitors commonly co-extracted with forensic samples can negatively impact ligation of indices or adaptors during library prep
  • Substantial **cost **investment to bring NGS into casework
  • Storage and analysis of large amount of sequence data
    o One illumine MiSeq v3 run generates up to 15GB of data
53
Q

With Forensic genetic identification of Sharks involved in human attacks what two genetic approaches are used?

A

o Barcoding to identify shark species
o Micro satellite testing to confirm species and for individual identification

54
Q

**Conclusions **

A
  • Animals can be perpetrators e.g., animal attacks
  • Animals can be victims e.g., wildlife forensics, animal abuse
  • Animals as evidence: e.g., food fraud, blowflies for PMI, hairs at a crime scene
  • Depending on case we must be able to:
    o Identify specific animal: STR and mrDNA testing
    o Identify species of animal(s): Barcoding and metabarcoding

7BBFM128: Forensic Biology (19 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions