Genetics Flashcards
Heredity
the transmission of traits from one generation to the next
Genetics
the scientific study of heredity and variation in heredity
What did Gregor Mendel use to discover heritable units
Pea plants
What are heritable units
Genes
What is applied Molecular genetics
using genetic information for research, conservation and management
How does Classical Genetics work
The use of crosses to breed new strains of organisms and to understand how traits are transmitted
What is An important tool of classical genetics
Isolation of mutants affecting particular traits which are then compared to normal strains
What is the roadmap of classical genetics
Pheno–> Geno
Biological process–Identify mutants–find the gene–biochemical function
What is modern genetics
the study of genes at the molecular level
Roadmap of modern genetics
Gene in hand–create mutants–phenotype–biological process
geno–>pheno
Law of segregation
Inherited characteristics are determined by indivisible factors adn alternative versions account for variations
For each characteristics, a diploid organism inherits two alleles, one from each parent
Dominant is phenotype
recessive is not visible
Law of Independent assortment
Each gene segregates independently during gamete formation
Cystic fibrosis DOM Or REC
Recessive
Sickle cell anemia, DOM or REC
Recessive
Tay-sachs disease DOM or REC
Recessive
Phenylketonuria DOM or REC
Recessive
Hemophilia DOM or REC
Sex-linked recessive
Huntington’s disease DOM or REC
Dominant
Muscular Dystrophy DOM or REC
Sex-linked recessive
Congenital Hypothyroidism DOM or REC
Recessive
Hypercholesterolemia DOM or REC
Dominant
Two findings that became known as Chargaff’s rules
The base composition of DNA varies between species
In any species the number of A and T bases are equal and the number of G and C bases
Purines
Adenine and guanine
Pyrimidine
Cytosine and thymine
Why did they find out that A and T only pair and C and G only pair
Because when they paired like with like there was no uniform width
What are three sources of genetic variation
Mutations
Recombination and crossing over
Random fertilization
What is a mutation
change in genetic material
What is recombination or crossing over
exchange of chromosomal material between homologous chromosomes at meiosis
What is random fertilization
sperm fuses with any unfertilized egg
Germline mutations
occur in gametes
significant because they can be transmitted to offspring
mostly from parental line
Somatic mutations
May have little efect on organism because they are confined to just one cell and its daughter cells
Cannot be passed to offspring
What is the order of replication and variation in SARS COV2
1 Spike protein on the virion binds to ACE2 a cell surface protein
2 The Virion releases its RNA
3 Some RNA is translated into proteins by the cell’s machinery
4 Some of these proteins form a replication complex to make more RNA
5 Proteins and RNA are assembled into a new virion in the GOLGI
6 Released
Is the transmission of SARS COV2 mendelian
No
What year did chargaff report that DNA composition varies from one species to the next
1950
What year did franklin produce a picture of the DNA molecules using X-ray Crystallography
1952
What year did Watson and crick introduce an elegant double helical model for the structure of DNA
1953
When was protein electrophoresis invented
Mid 1960s
When was the law of segregation first elucidated
1856-1863
Gene
Any region of the genome
Allele
Variation of a gene
Genotype
A combination of alleles
Haplotype
Combination of linked alleles
What did studies reveal inearly protein electrophoresis
that the extent of genetic variation is much higher than previously thought
RFLP
Restriction Fragment Length Polymorphisms
AFLP
Amplified Fragment Length Polymorphisms
VNTR
Variable Number of Tandem Repeats
STR
Short Tandem Repeats
What do restriction enzymes do
Recognize sequence motifs and cut DNA at the motif
Restriction enzymes in an idealized genome:
RE cuts every 4^length of the motif
RE that has a 4bp motif cuts every 4^4
how were RFLPs detected
by hybridizing radioactively labelled probes to DNA, transferred from a gel to a filter (“Southern Blotting”)
Minisatallite info
Repeat unit usually 30bp
Among the first markers to be used for DNA fingerprinting
What is replication slippage
Dissociation and subsequent mispairing gives change in number of repeats
Some problems using microsatellites as genetic markers
Time and labour consuming to develop primers for non-model species
Often do not transfer well between species - i.e. may amplify or may not be variable
Null alleles or PCR-induced mutations can cause problems
Difficulties in modeling the mutation process poses problems for population genetics
Exclusion
No match
Non-exlusion
Match or inclusion
Inconclusive
No result
Why are SNPs popular as genetic markers
they are abundant
They can be genotyped in a high-throughput manner
the mutation mechanism is well established
Why might SNPS not Replace STRs
Large databases containing STR informations - would need to replace data on existing platforms
Mixture detection and interpretation benefits from marker systems with many alleles; SNPs only have two to three genotype possibilities
Degraded DNA can be successfully analyzed in many cases thus removing a primary motivation in using SNPs
Sanger Sequencing
Chain termination with ddNTP
produces good quality sequences up to 1kb
Costly and not high-throughput
Automated Sanger Sequencing
ddNTPs are labelled with florescent dyes
Hit with a laser and photographed
Only one lane needed in gel
Next Gen sequencing
aka massively parallel sequencing
Shorter time
Illumina - produces shorter reads + lower quality at each base than fro sanger
Ex. Roche 454
Illumina
PacBio
Ion Torrent
Hydrogen ions released when nucleotide added
Pacbio
Start with high quality double stranded DNA
Ligate SMRTBELL adapters and size sleet
Anneal primers and bind DNA polymerase
Circularized DNA is sequenced in repeated passes
Difference between sanger and HTS
Sequencing volume
Sanger only sequences a single DNA fragment at a time
HTS is massively parallel, sequencing millions of fragments simultaneously
Applications of Massively parallel sequencing techniques
Genome sequencing
Expression analysis
Pros and cons of HTS/NGS
pros
Sequence millions of fragments simultaneously per run
Cons
Computational challenge in putting together millions of short reads into meaningful sequence
require bioinformatics & significant computational abilities
What markers are wildlife conservation analysis based on
Microsatellites and mtDNA
When was the first case of wildlife DNA that was used in court get submitted to the NRDPFC
1987
Why do we need wildlife forensics
Poaching investigations
Illegal movement of animals
Track source of spread of disease
Animal cruelty cases
CITES
Convention on International Trade in Endangered Species of Wildlife Flora and Fauna
WAPPRIITA
Wild Animal and Plant protection and Regulation of Interprovincial and International Trade Act
Appendix I species
Speces are rare or endangered and trade will not be permitted for primarily commercial purposes
Appendix II species
Species are not rare or endangered at present but could become so if trade is not regulated
Appendix III species
Species are not endangered but are managed within the listing nation
Pangolin facts
most trafficked animal in the world
For scales
Appendix I in CITES
Ivory Trade Facts
Genetic test to track illegal ivory trade - determine where animals are coming from
Key drivers - Law enforcement, china GDP
Rhino Trade Facts
Horns are used for medicine
DNA tests track rhino poachers; track daggers or powdered medicines back to source populations
RHODIS
What does RHODIS do
Has over 15,000 animals in the database
Links carcass or tool to animal
What DNA did they use in the Chilean Sea Bass case to link the carcass to fishery
mtDNA
Some issues in wildlife profiling
Development of species-specific markers
Low genetic variation
The need to establish databases for each species
Main difference between human and animal forensics
need to distinguish between variety of species (mtDNA and cpDNA)
also: sex, individual identification, population identification, parentage
Some properties that make microorganisms potentially harmful for cultivation and outbreaks
Accessability
Culturability
Capability for large scale production
Stability during preparation
Incubation period
Toxicity
How many microsatellite loci are usually relied on for human identification
~20
What are Acinetobacter Baumannii
Opportunistic pathogens in humans, affecting people with compromised immune systems
What are Carbapenem-Resistant K. pneumoniae
Bacterial pathogen responsible for roughly 15% of Gram negative infections in ICU
Primarily affects immuno-compromised patients
SARS COV2
Corona virus
cause mild to moderate upper respiratory tract diseases in humans
by identifying spike protein we can find out what the variants are and see how we can discriminate between them
Different Molecular techniques for tracking SARS CoV2
What form of omics involves DNA?
Genomics & epigenomics
Linear regression of microbiomes
Automates variable selection and address multi-collinearity
Shrinks and minimizes (very crude)
Genomics & epigenomics role in forensic science
-Cause of death
- Age at death
- sex, ancestry, phenotype
What does an R^2 value of 0 mean
Your regression explains none fo the variation
What does and R^2 value of 1 mean
Your regression explains all of the variation
What form of omics involves mRNA?
Transcriptomics
Why does soil serve as powerful contact trace evidence
It is highly individualistic and has a high transfer and retention rate
Transcriptomics role in forensic science
Post-mortem interval
What is the study of proteins?
Proteomics
Proteomics role in forensic science
- Cause of death
- Age at death
- Sex, ancestry, phenotype
- PMI
What does standard analysis of soil examine
Minerology, geophysics, tecture and colour
What is the study of metabolites
Metabolomics is & lipidomics
Metabolomics & lipidomics role in forensic science
- Cause of death
- PMI
What is Sorenson’s similarity index
a statistical measure used to quantify the similarity between two samples,
What is the study of microbes
Microbiomics
Limitations of DGGE
There is a strong bias for dominant populations
Biases generated by differential DNA extraction and PCR amplification and bands can migrate to the same gel positions
Microbiomics role in forensic science
- Cause of death
- Age at death
- PMI
How does High-throughput sequencing benefit soil analysis
Offers a means to improve discrimination between forensic soil samples by identifying individual taxa and exploring non-culurable species
Less than 1% of bacteria grow in lab
Provides the ability to generate a detailed picture of soil microbial BUT requires bioinformatics and significant computational abilities
Limitations to forensic soil analysis
temporal effects
Storage conditions
Transfer of soil to objects
Concerns related to microbiome and PMI
surrogates decompose differently and have different microbiomes
Predictive models need to be developed for each region
Appreciate and understand the mean absolute error
What has species monitoring traditionally relied on
physical identification by visual surveys and counting of individuals
What is eDNA
Environmental DNA can be defined as trace DNA released from skin, mucous, saliva, sperm, secretions
mixture of potentially degraded DNA from many different organisms
eDNA studies have predominantly focused on:
THE METHOD
IDENTIFYING SPECIES
RECONTRUCTION OF DIETS AND ANCIENT COMMUNITIES
Limitations of eDNA
Assay development & bioinformatics not straightforward
no information can be collected on life stages, demography, fecundity or health of the target species – all critical to management
eDNA is not homogeneously distributed throughout a water body
Why use cow blood in studies
easier to work with than human blood
Species specific attributes
What does the top panel on gel electrophoresis show
how big any detectable fragments are
What does the bottom panel of gel electrophoresis show
How much DNA is quantified at each size
How long is eDNA detectable in freshwater
36 hours
how long is eDNA detectable in saltwater
84 hours
First generation sequencing
Sanger & Maxam-Gilbert
Second generation sequencing
-Illumina
-Roche 454
- SOLiD
- Ion torrent
- DNA Nanoball
Third generation sequencing
- PacBio
-Helicos - Oxford nanopore
Fourth generation sequencing
-Massively parallel spatially resolved
- Single cell in situ Transcriptomics
4 steps of illumina sequencing
- Fragment DNA and bridge amplification
- cluster generation
- Sequencing by synthesis
- Sequence alignment and compare
What affects DNA’s persistence in the environment?
Environmental conditions
pH levels
UV radiation
Habitat
What species do the CITES Appendices cover
What is required for identifying transmission events
Why the different molecular techniques are used in tracking SARS CoV 2
Sequencing was used to understand transmission genetics (genome and mutations)
Diagnostic purposes
qPCR for presence or absence of COVID
How is genetic variation generated
mutations, Recombination and gene flow
Why was the specific pairing - i. E. the observation of Watson and Crick - so important
showed genetic stability of DNA, basis of Gene code
What is a “genomic” data set
large data set that includes genes of one or multiple organisms
Describe sequencing by synthesis
Illumina all colours at once
ion torrent
What species do the CITES Appendices cover
Appendix 1-3
What is required for identifying transmission events
high-quality genomic data
What genetic marker was among the first to be used for fingerprinting?
Mini satellites - VNTR
