Molecular Genetics 7-12 Flashcards
What is forensic science?
The application of science to criminal and civil laws, mainly on the criminal side during criminal investigation, as governed by the legal standards or admissible evidence and criminal procedure
What are the three fundamental principles that fingerprinting follows?
1) A fingerprint is an individual characteristic - no two people have been found to have the same fingerprint pattern.
2) A fingerprint pattern remains unchanged for life, however the print itself may change due to permanent scars and skin diseases.
3) Fingerprints have general characteristic ridge patterns that allow them to be systematically identified.
When was fingerprinting first used?
1892
What are the three specific classes for all fingerprints based upon their visual pattern?
Arch
Loop
Whorl
What is the arch fingerprint class subdivided into?
Plain arch
Tented arch
What is the loop fingerprint class subdivided into?
Radial loop
Ulnar loop
What is the whorl fingerprint class subdivided into?
Plain whorl
Central pocket whorl
Double loop whorl
Accidental
When was blood typing discovered and by whom?
1901
Karl Landsteiner
Who invented DNA fingerprinting and what had they actually been researching?
Alec Jeffreys
He was researching the myoglobin gene, but discovered simple tandem-repeat regions of DNA
What are simple tandem-repeat regions of DNA?
Short repeated DNA sequences within introns. There is a polymorphism of repeat lengths among individuals which arises from unequal pairing and crossing over between repeats.
When was the first DNA fingerprint produced?
September 1984 in Leicester University
When was the first immigration case solved by DNA fingerprinting?
1985 - proved child belonged to certain parents entering the country
When was the first paternity case solved by DNA fingerprinting?
1985
When was the first identification of identical twins solved by DNA fingerprinting?
1985
When was the first criminal investigation solved by DNA fingerprinting?
1986
What are simple tandem-repeats also known as?
Minisatellites
What are the features of minisatellite DNA sequences?
1) Highly polymorphic
2) Stable within a lifetime
3) Inherited by offspring
4) Measurable by gel-based techniques
What size are minisatellites compared to microsatellites?
Larger
What is DNA fingerprinting?
A forensic technique used to identify individuals by characteristics of their DNA
How do minisatellites vary within individuals?
DNA sequence
Length of repeats
How is DNA fingerprinting used in criminal investigations?
To match DNA obtained from a crime scene to suspects
Multiple minisatellites will be used in actual criminal investigations to increase accuracy
What is the downside of DJA fingerprinting?
Relatively large amount of DNA needed - 50-250ng (several thousand cells)
Not ideal for forensic evidence with small degraded samples
The four steps of minisatellites typing:
1) Extract and purify DNA
2) Carry our PCR
3) Run PCR product on genetic analyser
4) Assign genotypes
What is multiplex PCR?
Amplifies multiple pieces of DNA in one PCR mixture using multiple sets of forward and reverse primers, one for each DNA template
Advantages of minisatellite typing
Less than 1ng of DNA required to type 13-15 loci
Can be processed within 24 hours
Relatively degraded DNA samples can be used
What is the issue with whole genome amplification (WGA)?
As screens become more sensitive the possibility of contamination becomes greater
What is clonal identity?
Small samples of crops are taken and tested in labs to ensure they are what they are being sold as
What is distinctness, uniformity and stability (DUS) testing?
A way of determining whether a newly bred variety differs from existing varieties within the same species (distinctness), whether the characteristics used to establish distinctness are expressed uniformly (uniformity) and that these characteristics do not change over subsequent generations (stability)
Why does DUS testing exist?
So that new varieties can legally gain access to their market via the U.K. National List and the granting of Plant Breeders Rights (intellectual rights)
Where is a DUS test normally conducted?
In the field or glasshouse over two consecutive growing seasons, and over this time a number of mainly morphological characteristics are measured and established.
What is marker-assisted selection (MAS)?
The use of DNA markers that are tightly linked to target loci as a substitute for or to assist genetic screening
What is the assumption made during marker-assisted selection (MAS)?
That DNA markers can reliably predict phenotype
What is the process of marker-assisted selection?
Cross parents with desirable characteristics, screen offspring of F2 generation for even better desirable characteristics e.g. resistance to high salinity, bacterial blight or phosphorus deficiency
Advantages of marker-assisted selection (MAS):
1) Simpler method compared to phenotypic screening
2) Selection at seedling stage
3) Increased reliability
4) More accurate and efficient at selection of specific genotypes
5) More efficient use of resources
How far is the maximum distance markers should be from the selected gene?
5 cM
What is the best way to use markers to increase reliability to 99.5%?
Use a pair of flanking markers (one on each side of the gene)
What is the shortcoming of using flanking markers?
Increases time and cost
What must the markers be to differentiate between different alleles?
Polymorphic
What happens to the number of phenotypic categories as the number of trait loci increases?
It also increases
The number of phenotypic categories =
(number of gene pairs x 2) + 1
What is a multifactorial or quantitative trait?
A characteristic that is both polygenic and influenced by environmental factors e.g. weight, height, heart disease
How many genes have been found so far that influence blood pressure?
29 as of 2009
What can high blood pressure lead to?
Heart disease, stroke, kidney failure
What is genomic selection?
A technology for increasing the accuracy with which the genetic merit of potential breeding stock (animals and plants) can be determined
What are the two steps of genomic selection?
1) Estimate the effects of markers in a reference (training) population (phenotyped and genotyped)
2) This information is utilised to predict the breeding value of candidates to selection in a testing (evaluation) population (genotyped)
Differences between MAS and genomic selection
- MAS concentrates on a few genes having association with markers
- Genomic section uses a genome-wide panel of very dense markers
What is genomic selection especially useful for?
Traits with low heritability (fitness traits)
Traits difficult/expensive to measure
Disease susceptibility / resistance traits
Traits that take a lifetime to measure (longevity)
What are some future challenges to breeding?
Global warming
Food/feed shortage
Energy, water, land and other shortages
Reducing environmental footprint
What are the two main evolutionary theories?
1) Out of Africa Theory (OOA)
2) Multi-regional Evolution Theory
When did the first Homo species evolve and what was it called?
In Africa 2 million years ago
Homo habilis
What was the next Homo species to evolve?
Homo erectus (spread out of Africa)
When did Homo erectus give rise to Homo sapiens?
100,000-200,000 years ago
What is the Out of Africa Theory (OOA)?
Suggests Homo erectus evolved into Homo sapiens in Africa, then ventured out of Africa and dispersed to all round the world
What is the Multi-regional Evolution Theory?
Suggests that Homo erectus ventures out of Africa and then evolved into modern man in several different locations throughout the world .
Also suggests Neanderthals evolved from European Homo erectus, and then evolved into Homo sapiens later
What types of DNA are used to determine which evolutionary theory is true?
-Mitochondrial DNA
-Y chromosome DNA
-Microsatellite DNA
All suggest Out of Africa Theory is correct
Did Homo sapiens interact with Neanderthals? mtDNA answer
No Neanderthal mitochondria in modern Europeans - potentially a high interbreeding rate but sterility of offspring?
How did Neanderthal Y chromosome potentially prevent interbreeding with humans?
The chromosome may have created conditions that frequently led to miscarriages - three mutations on their Y chromosome would have produced molecules that can trigger immune responses from women during pregnancy
How much of human DNA might Neanderthals have contributed to?
1-4%
In what area did Neanderthals not contribute to the DNA of humans?
Africa - Neanderthals never lived there
What is the alternative to Neanderthals dying out?
They may have been assimilated into the human population
What is CCR5?
C-C chemokine receptor 5
A protein on the surface of white blood cells that is involved in the immune system as it acts as a receptor for chemokines
What is CCR5 involved in?
The process by which T cells are attracted to specific tissue and organ targets
What initially uses CCR5 to enter and infect cells?
Many forms of HIV
What mutation must individuals carry to be protected against HIV?
CCR5-🔼32 (they must be homozygotes)
Why is the CCR5-🔼32 mutation so frequent in Northern Europe when HIV is recent?
It may have provided resistance to previous epidemics including bubonic plague and smallpox
What are the possibilities of protection from HIV with the CCR5 gene mutation?
If pharmaceuticals could mimic the mutation then the attachment of HIV could be blocked
What do For-Profit Personal Genome Companies use to determine which alleles you have?
SNPs, not sequencing
What does large scale genotyping look at?
1,000,000 bases (0.03% of human genome)
What does whole exome sequencing look at?
60,000,000 bases (2% of human genome)
What does whole genome sequencing look at?
300,000,000 bases (100% of human genome)
How much more computer time does it take to analyse DNA sequences as opposed to analysing genotyping data?
1000 times more computer time
What is a pro-drug?
It is activated once inside the body
What does Tamoxifen do?
Can be used to prevent / treat breast cancer
How many women do not activate Tamoxifen once it is inside their body?
7-10%
What is the alternative to Tamoxifen?
Aromatase inhibitors
What is targeted therapy?
It is where testing using biomarkers is carried out prior to treatment, to ensure only a treatment that will work for the individual is carried out
What is the heritability of human height?
0.8 - 80% of variation in height is due to genetic factors
What are types of disease which interact very strongly with the environment and as a result are very unpredictable?
Complex, polygenic and multifactorial disease
Advantages of mtDNA
- Can be amplified from old or degraded samples
- Maternal relatives will have the same sequence
Disadvantages of mtDNA
- Not specific to an individual
- Maternal relatives will have the same sequence
- Random individuals may have the same sequence
Other names for microsatellite?
Simple sequence repeats (SSRs)
Sequence tagged simple sequence repeats (STSSRs)
What are microsatellites?
Single-locus, multi-allelic PCR based molecular markers which are used in mapping and diversity studies. They can be multiplexed
What is a co-dominant marker?
A marker than can distinguish between homozygotes and heterozygotes
How many alleles can SNPs distinguish between?
2
They are bi-allelic
How many alleles can SSRs distinguish between?
Multiple
They are multi-allelic
