MFS-T4-DES-B

Suggested web readings etc :(in blue is the syllabus title, print is available for brown)
 UNIT-I
1. Introduction, Methods, strategies and applications DNA markers,
 Forensic Biology by Richard Li: pp.185-195, (in detail: 287-364)
Advanced/Reference material:
 dna-analysis:
http://aboutforensics.co.uk/dna-analysis
 DNA profiling
 https://en.wikipedia.org/wiki/DNA_profiling
2. Mitochondrial, DNA the hypervariable regions and control region V,
Forensic Biology by Richard Li: pp.351-364
3. Cytochrome b, Chloroplast DNA,
http://www.dnabarcoding101.org/introduction.html
4. Chromosomal DNA Amelogenin, Autosomal STRs, Y Chromosomal STRs, X
chromosomal STRs,
Forensic Biology by Richard Li: pp.317-326
extra:
Forensics, DNA Fingerprinting, and CODIS:
 http://www.nature.com/scitable/topicpage/forensics-dna-fingerprinting-and-codis-736
 5. Variable Number Tandem Repeat (VNTR’s) and Short Tandem Repeat (STR’s)
markers,
Forensic Biology by Richard Li: pp. 287-308
Advanced/Reference material:
Minisatellite
 https://en.wikipedia.org/wiki/Minisatellite
6. Single Nucleotide Polymorphism (SNP’s)
Forensic Biology by Richard Li: pp 333-350
https://doi.org/10.1016/j.forsciint.2004.10.020
 UNIT-II
1. DNA Extraction, Organic and Inorganic extraction, Comparison of Extraction
methods, Commercial kits

Forensic Biology by Richard Li: pp.199-207

2. DNA Quantitation, Importance of quantitation, Spectrophotometric analysis,
Agarose Gel Electrophoresis, Slot Blot Hybridization, Real Time PCR.
Forensic Biology by Richard Li: pp. 211-219
3.Polymerase Chain Reaction
Forensic Biology by Richard Li: pp.223-234
4. Basic PCR mechanism, Real time PCR, Primer designing

5.Primer dimmer and Hairpins, Mismatch primers,Forensic Biology by Richard Li: pp.223-234 
idt guidelines  for primer design
6. Software’s packages, Multiplex PCR, PCR failures,
 http://projects.nfstc.org/pdi/
Forensic Biology by Richard Li: pp. 287-308
7. DNA degradation, Inhibition, DNA overload and Cycling.
Forensic Biology by Richard Li: pp. 287-308

GeneMarker® HID Software - Introduction Part 1
https://www.youtube.com/watch?v=_Heupu3n8v0


GeneMarker® HID Software - Introduction Part 2
https://www.youtube.com/watch?v=bJab6IG2KeQ


http://projects.nfstc.org/pdi/
 
 
UNIT-III
1. DNA barcoding for Species identification
2. DNA barcoding of Plant, fungi and animals
3. Challenges in DNA barcoding of forensic samples and their solution
4. Databases of DNA barcodes
5. International missions/facilities/projects on DNA barcoding
6. Applications of DNA barcoding in forensics: drug adulteration, wild life crime,
associative evidence at crime scene (wood leaf, pollen, spores, diatoms)
 
 http://www.dnabarcoding101.org/

http://www.dnabarcoding101.org/files/using-dna-barcodes.pdf
http://www.dnabarcoding101.org/resources/index.html
http://www.ibol.org/phase1/about-us/what-is-dna-barcoding/
http://www.ibol.org/phase1/about-us/what-is-ibol/
http://www.ibol.org/phase1/about-us/campaigns/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4909793/
https://www.boldsystems.org/index.php/Resources/whatIsBOLD
http://www.sciencedirect.com/science/article/pii/S1875176815301037 
 
https://eol.org/docs/what-is-eol
https://ibol.org/site/wp-content/uploads/2019/07/BIOSCAN-overviewJuly9.pdf
https://dnabarcoding101.org/files/DNA-Barcoding.pptx

7. Aptamers and affibody: forensic applications
http://www.sciencedirect.com/science/article/pii/S0165993610003110
8. Protein engineering and invitro evolution for making proteins for forensic
application
http://scs.illinois.edu/~zhaogrp/publications/HZ38.pdf
9. Concept of antigen- antibody reaction and application to species identification

 Forensic Biology by Richard Li: pp. 101-112
10. Monoclonal and polyclonal antibodies

 Forensic Biology by Richard Li: pp. 53-66, 69-81
 
UNIT-IV
1. NGS (next generation sequencing techniques of DNA): principles
 Illumina Sequencing by Synthesis
https://www.youtube.com/watch?v=fCd6B5HRaZ8
SMRT technique
www.youtube.com/watch?v=WMZmG00uhwU#action=share
Oxford Nanopore
https://www.youtube.com/watch?v=GUb1TZvMWsw
https://www.youtube.com/watch?v=hs0FdiTHMbc
https://nanoporetech.com/how-it-works
 Next Generation Sequencing (NGS) - An Introduction
https://www.youtube.com/watch?v=jFCD8Q6qSTM
2. Protocols in NGS
 Next Generation Sequencing (NGS) - Sample Preparation
https://www.youtube.com/watch?v=-kTcFZxP6kM&t=308s

protocol for SMRTbell Library prepration
http://smrt.med.cornell.edu/Services.html

http://files.pacb.com/Training/IntroductiontoSMRTbellTemplatePreparation/story_content/external_files/Introduction%20to%20SMRTbell%E2%84%A2%20Template%20Preparation.pdf
(Page 7 is most important)

VolTRAX – a small device designed to perform library preparation automatically


https://youtu.be/RJ2IMSYiCiw

3. Application of NGS in forensics
Next generation sequencing and its applications in forensic genetics:
https://www.ncbi.nlm.nih.gov/pubmed/25704953



4. Automation in DNA profilling: robotics

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580997/pdf/rstb20140252.pdf


5. Miniaturisation in DNA profilling: microfluidics
http://www.avensonline.org/wp-content/uploads/JFI-2330-0396-02-0012.pdf



6. Recent developments in DNA profilling and databases
The future of forensic DNA analysis
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580997/pdf/rstb20140252.pdf



PRACTICALS

 INSTAcard fta card

The buffer composition is not mentioned in himedia manual(https://drive.google.com/file/d/1DQJ50fnNStKmqYh1zSIhJzYp-oJAbXb_/view?usp=sharing ), so the sigma protocol (https://www.sigmaaldrich.com/IN/en/technical-documents/protocol/genomics/dna-and-rna-purification/genomic-dna-purification-from-sample-applied-to-fta-cards) will be followed in sigma protocol:

FTA purification reagent = 5ul (20mg/ml)Proteinase k + 150uul TE-1

TE-1 buffer (10 mM Tris-HCl, 0.1 mM EDTA, pH 8.0)* * Note that this buffer contains 0.1 mM EDTA, not 1 mM EDTA

Searching Barcode database for identification of insects: click for example

Sequence analysis, BLAST Search, troubleshooting: see example







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