Suggested web readings etc :(in blue is the syllabus title, print is available for brown)
ADM.sem4
UNIT-I
1. Introduction, Methods, strategies and applications DNA markers,
dna-analysis:
http://aboutforensics.co.uk/dna-analysis/
Advanced/Reference material: DNA profiling
https://en.wikipedia.org/wiki/DNA_profiling
2. Mitochondrial, DNA the hypervariable regions and control region V,
An Introduction to Forensic DNA Analysis by Keith Inman, Norah Rudin pp56-60
other:
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,
An Introduction to Forensic DNA Analysis by Keith Inman, Norah Rudin pp41-56
Forensic Biology by Richard Li: pp. 287-308
other:
Forensic Biology by Richard Li: pp.269-283 Advanced/Reference material:
Minisatellite
https://en.wikipedia.org/wiki/Minisatellite
dna-analysis:
http://aboutforensics.co.uk/dna-analysis/
Advanced/Reference material: DNA profiling
https://en.wikipedia.org/wiki/DNA_profiling
2. Mitochondrial, DNA the hypervariable regions and control region V,
An Introduction to Forensic DNA Analysis by Keith Inman, Norah Rudin pp56-60
other:
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,
An Introduction to Forensic DNA Analysis by Keith Inman, Norah Rudin pp41-56
Forensic Biology by Richard Li: pp. 287-308
other:
Forensic Biology by Richard Li: pp.269-283 Advanced/Reference material:
Minisatellite
https://en.wikipedia.org/wiki/Minisatellite
6. Single Nucleotide Polymorphism (SNP’s)
UNIT-II
1. DNA Extraction, Organic and Inorganic extraction, Comparison of Extraction
methods, Commercial kits
Forensic Biology by Richard Li: pp.199-207
other:
An Introduction to Forensic DNA Analysis by Keith Inman, Norah Rudin pp65-70
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
other:
An Introduction to Forensic DNA Analysis by Keith Inman, Norah Rudin pp76-78
5.Primer dimmer and Hairpins, Mismatch primers,
Forensic Biology by Richard Li: pp.223-234
idt guidelines for primer design
https://www.youtube.com/watch?v=bJab6IG2KeQ
http://projects.nfstc.org/pdi/
New UNIT-III
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
https://store.nanoporetech.com/catalog/product/view/id/219/s/rapid-sequencing-kit/category/28/
https://www.youtube.com/watch?v=APxaiRaZMfQ
3. Application of NGS in forensics
Next generation sequencing and its applications in forensic genetics:
https://ac.els-cdn.com/S1872497315000319/1-s2.0-S1872497315000319-main.pdf?_tid=a502dd86-d576-401b-8614-1c40e10a06ec&acdnat=1550467091_84048d0ae20d2e22b7a3d50668359245
4. Automation in DNA profilling: robotics
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580997/pdf/rstb20140252.pdf
5. Miniaturisation in DNA profilling: microfluidics
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580997/pdf/rstb20140252.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
UNIT-III
http://projects.nfstc.org/pdi/
1. Introduction to Fragment analysis, Automated Fragment Length Determination, Sequence analysis.
other:
An Introduction to Forensic DNA Analysis by Keith Inman, Norah Rudin pp71-76
An Introduction to Forensic DNA Analysis by Keith Inman, Norah Rudin pp41-56
2. Automated Genetic Analyzer Operation theory
http://projects.nfstc.org/pdi/Subject09/pdi_s09_m03_02.htm
http://projects.nfstc.org/pdi/Subject09/pdi_s09_m03_03.htm
Advanced/Reference material: on automation and miniaturization
https://www.fbi.gov/about-us/lab/forensic-science-communications/fsc/oct2004/index.htm/research/2004_10_research04.htm
Fluent™ Laboratory Automation Solution
https://www.youtube.com/watch?v=xO1QihN900k
Mastering the Volumes Through Lab Automation
https://www.youtube.com/watch?v=9l7nXG6iu2g
3. Biology of STRs, Forensic Issues
Forensic Biology by Richard Li: pp. 287-308
Forensic Biology by Richard Li: pp. 373-381
Forensic Biology by Richard Li: pp. 385-401 (better and simpler: http://dna-view.com/profile.htm)
other:
http://projects.nfstc.org/pdi/
4. mtDNA Biology and Analysis
other:
Forensic Biology by Richard Li: pp.351-364
An Introduction to Forensic DNA Analysis by Keith Inman, Norah Rudin pp56-60
5. DNA Sequencing applications in Forensics
BigDye Direct Cycle Sequencing Kit
https://www.youtube.com/watch?v=iTBTHmhNNbE
Advanced/Reference material:
Generating forensic DNA profiles (HD version)
https://www.youtube.com/watch?v=xt3gRO8nfeY
Genetic Analyzer: ABI Theory and Description
https://users.stlcc.edu/departments/fvbio/Genetic_Analyzer_ABI_Theory_Description.pdf
canada parliamentary.pdf
http://www.parl.gc.ca/Content/LOP/researchpublications/bp443-e.pdf
Dr. John Butler - Forensic DNA & DNA Databases- an Introduction to the Use & Iss
https://www.youtube.com/watch?v=dhqEEAl-g34
www.bioforensics.com/app/download/5285103/Steelman1.ppt
www.bioforensics.com/app/download/5285024/DNAStats-1.ppt
UNIT-IV
Forensically relevant SNP classes
http://www.biotechniques.com/multimedia/archive/00003/BTN_A_000112806_O_3727a.pdf
Advanced/Reference material:
Developing a SNP panel for forensic identification
of individuals
http://www.sciencedirect.com/science/article/pii/S0379073805006134http://www.biotechniques.com/multimedia/archive/00003/BTN_A_000112806_O_3727a.pdf
Advanced/Reference material:
Developing a SNP panel for forensic identification
of individuals
UNIT-II
1. DNA Extraction, Organic and Inorganic extraction, Comparison of Extraction
methods, Commercial kits
Forensic Biology by Richard Li: pp.199-207
other:
An Introduction to Forensic DNA Analysis by Keith Inman, Norah Rudin pp65-70
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
other:
An Introduction to Forensic DNA Analysis by Keith Inman, Norah Rudin pp76-78
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/
http://projects.nfstc.org/pdi/
Forensic Biology by Richard Li: pp. 287-308
7. DNA degradation, Inhibition, DNA overload and Cycling.
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
http://projects.nfstc.org/pdi/
New UNIT-III
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
https://store.nanoporetech.com/catalog/product/view/id/219/s/rapid-sequencing-kit/category/28/
https://www.youtube.com/watch?v=APxaiRaZMfQ
3. Application of NGS in forensics
Next generation sequencing and its applications in forensic genetics:
https://ac.els-cdn.com/S1872497315000319/1-s2.0-S1872497315000319-main.pdf?_tid=a502dd86-d576-401b-8614-1c40e10a06ec&acdnat=1550467091_84048d0ae20d2e22b7a3d50668359245
4. Automation in DNA profilling: robotics
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580997/pdf/rstb20140252.pdf
5. Miniaturisation in DNA profilling: microfluidics
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580997/pdf/rstb20140252.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
UNIT-III
http://projects.nfstc.org/pdi/
1. Introduction to Fragment analysis, Automated Fragment Length Determination, Sequence analysis.
other:
An Introduction to Forensic DNA Analysis by Keith Inman, Norah Rudin pp71-76
An Introduction to Forensic DNA Analysis by Keith Inman, Norah Rudin pp41-56
2. Automated Genetic Analyzer Operation theory
http://projects.nfstc.org/pdi/Subject09/pdi_s09_m03_02.htm
http://projects.nfstc.org/pdi/Subject09/pdi_s09_m03_03.htm
Advanced/Reference material: on automation and miniaturization
https://www.fbi.gov/about-us/lab/forensic-science-communications/fsc/oct2004/index.htm/research/2004_10_research04.htm
Fluent™ Laboratory Automation Solution
https://www.youtube.com/watch?v=xO1QihN900k
Mastering the Volumes Through Lab Automation
https://www.youtube.com/watch?v=9l7nXG6iu2g
An integrated CMOS quantitative-polymerase-chain-reaction lab-on-chip for point-of-care diagnostics
https://www.youtube.com/watch?v=7Rjc5DdRt7o
Beckman Coulter BioMek FX Workstation
https://www.youtube.com/watch?v=y8Fl8AJSasU
Sandia Digital Microfluidic Hub
https://www.youtube.com/watch?v=9GInRQYzSJg
Biomek 4000
https://www.youtube.com/watch?v=jSskLzJZ9hc
Forensic Biology by Richard Li: pp. 287-308
Forensic Biology by Richard Li: pp. 373-381
Forensic Biology by Richard Li: pp. 385-401 (better and simpler: http://dna-view.com/profile.htm)
other:
http://projects.nfstc.org/pdi/
4. mtDNA Biology and Analysis
other:
Forensic Biology by Richard Li: pp.351-364
An Introduction to Forensic DNA Analysis by Keith Inman, Norah Rudin pp56-60
5. DNA Sequencing applications in Forensics
BigDye Direct Cycle Sequencing Kit
https://www.youtube.com/watch?v=cqFTGQ_JO1c
Sanger sequencing animation
Advanced/Reference material:
Generating forensic DNA profiles (HD version)
https://www.youtube.com/watch?v=xt3gRO8nfeY
Forensic DNA Mixups | Greg Hampikian | TEDxBoise
https://www.youtube.com/watch?v=Lw-zyoYlIsA
https://users.stlcc.edu/departments/fvbio/Genetic_Analyzer_ABI_Theory_Description.pdf
canada parliamentary.pdf
http://www.parl.gc.ca/Content/LOP/researchpublications/bp443-e.pdf
Dr. John Butler - Forensic DNA & DNA Databases- an Introduction to the Use & Iss
https://www.youtube.com/watch?v=dhqEEAl-g34
www.bioforensics.com/app/download/5285103/Steelman1.ppt
www.bioforensics.com/app/download/5285024/DNAStats-1.ppt
UNIT-IV
1. Eukaryotic genome structure and concepts of genomic analysis
Eukaryotic Genome Complexity
http://www.nature.com/scitable/topicpage/eukaryotic-genome-complexity-437
2. Public sequence databases: DNA, RNA, proteins, whole genomes
http://www.nature.com/scitable/topicpage/genomic-data-resources-challenges-and-promises-743721
UCSC Genome Browser An Introduction tutorial movie
http://www.openhelix.com/showMovie2.cgi?id=27
3. Data mining for homologous sequences
http://www.ncbi.nlm.nih.gov/books/NBK1734/
Eukaryotic Genome Complexity
http://www.nature.com/scitable/topicpage/eukaryotic-genome-complexity-437
2. Public sequence databases: DNA, RNA, proteins, whole genomes
http://www.nature.com/scitable/topicpage/genomic-data-resources-challenges-and-promises-743721
UCSC Genome Browser An Introduction tutorial movie
http://www.openhelix.com/showMovie2.cgi?id=27
3. Data mining for homologous sequences
http://www.ncbi.nlm.nih.gov/books/NBK1734/
http://www.ncbi.nlm.nih.gov/books/NBK2590/
How to: Find a homolog for a gene in another organism:
http://www.ncbi.nlm.nih.gov/guide/howto/find-homolog-gene/
BLAST Results- Expect Values, part 1
https://www.youtube.com/watch?v=Z7ek7UoP7Bg
4. Multiple sequence alignment algorithms
https://en.wikipedia.org/wiki/Multiple_sequence_alignment
6. Phylogenetic trees and molecular evolution
Molecular phylogenetic analysis using ribosomal RNA (rRNA)
https://www.researchgate.net/file.PostFileLoader.html?id=55c2206660614b37738b4585&assetKey=AS%3A273825759989760%401442296556699
Molecular Phylogenetics:
http://www.ncbi.nlm.nih.gov/books/NBK21122/
7. Microarrays and transcriptome analysis
http://projects.nfstc.org/pdi/Subject09/pdi_s09_m03_01_b.htm
How Does a DNA Microarray Work.mp4
https://www.youtube.com/watch?v=pWk_zBpKt_w
8. The proteome, metabolome, glycome, lipidome, and interactome
http://www.nature.com/scitable/topicpage/transcriptome-connecting-the-genome-to-gene-function-605
http://www.nature.com/scitable/topicpage/the-proteome-discovering-the-structure-and-function-613
9. Human genes and genetic disorders
Online Mendelian Inheritance in Man (OMIM): A Directory of Human Genes and Genetic Disorders:
http://citeseerx.ist.psu.edu/viewdoc/download?rep=rep1&type=pdf&doi=10.1.1.220.1899
10. Ethics in human bioinformatics and genomics
Bioethics in Genetics:
http://www.nature.com/scitable/topicpage/bioethics-in-genetics-42093
11. Y Chromosome testing
Forensic Biology by Richard Li: pp.317-326
12 Non-Human, medical, and research applications
Genetic Inequality: Human Genetic Engineering:
http://www.nature.com/scitable/topicpage/genetic-inequality-human-genetic-engineering-768
Genetically Modified Organisms (GMOs): Transgenic Crops and
Recombinant DNA Technology:
http://www.nature.com/scitable/topicpage/genetically-modified-organisms-gmos-transgenic-crops-and-732
Practicals:
How to: Find a homolog for a gene in another organism:
http://www.ncbi.nlm.nih.gov/guide/howto/find-homolog-gene/
BLAST Results- Expect Values, part 1
https://www.youtube.com/watch?v=nO0wJgZRZJs
BLAST Results: Expect Values, part 2
4. Multiple sequence alignment algorithms
https://en.wikipedia.org/wiki/Multiple_sequence_alignment
6. Phylogenetic trees and molecular evolution
Molecular phylogenetic analysis using ribosomal RNA (rRNA)
https://www.researchgate.net/file.PostFileLoader.html?id=55c2206660614b37738b4585&assetKey=AS%3A273825759989760%401442296556699
Molecular Phylogenetics:
http://www.ncbi.nlm.nih.gov/books/NBK21122/
7. Microarrays and transcriptome analysis
http://projects.nfstc.org/pdi/Subject09/pdi_s09_m03_01_b.htm
How Does a DNA Microarray Work.mp4
https://www.youtube.com/watch?v=pWk_zBpKt_w
8. The proteome, metabolome, glycome, lipidome, and interactome
http://www.nature.com/scitable/topicpage/transcriptome-connecting-the-genome-to-gene-function-605
http://www.nature.com/scitable/topicpage/the-proteome-discovering-the-structure-and-function-613
9. Human genes and genetic disorders
Online Mendelian Inheritance in Man (OMIM): A Directory of Human Genes and Genetic Disorders:
http://citeseerx.ist.psu.edu/viewdoc/download?rep=rep1&type=pdf&doi=10.1.1.220.1899
10. Ethics in human bioinformatics and genomics
Bioethics in Genetics:
http://www.nature.com/scitable/topicpage/bioethics-in-genetics-42093
11. Y Chromosome testing
Forensic Biology by Richard Li: pp.317-326
12 Non-Human, medical, and research applications
Genetic Inequality: Human Genetic Engineering:
http://www.nature.com/scitable/topicpage/genetic-inequality-human-genetic-engineering-768
Genetically Modified Organisms (GMOs): Transgenic Crops and
Recombinant DNA Technology:
http://www.nature.com/scitable/topicpage/genetically-modified-organisms-gmos-transgenic-crops-and-732
Practicals:
ESPM 150: A brief tutorial on BLAST
nature.berkeley.edu/garbelotto/downloads/BLASTtutorial2010.doc
http://tools.thermofisher.com/content/sfs/manuals/chargeswitch_forensicdna_man.pdf
idt guidelines for primer design and ncbi primer design
primer design tutorial
MBIBM.sem4
Unit 1:Molecular Biology
Chemistry of Nucleotides, Structure of DNA/RNA
http://www.nature.com/scitable/topicpage/discovery-of-dna-structure-and-function-watson-397
DNA Replication: Eukaryotic and Prokaryotic
Helicases, Topoisomerases and other DNA replicating Enzymes
http://www.nature.com/scitable/topicpage/major-molecular-events-of-dna-replication-413
DNA Denaturation, Cot-Rot curves,
http://faculty.tru.ca/dnelson/courses/biol335/335notes/3recdna/4-hybrization/recDNA3b.html
DNA Repair mechanisms
http://www.nature.com/scitable/topicpage/dna-damage-repair-mechanisms-for-maintaining-dna-344
DNA Epigenetics
http://www.nature.com/scitable/topicpage/epigenetic-influences-and-disease-895
Eukaryotic and Prokaryotic Transcription.
http://www.nature.com/scitable/topicpage/dna-transcription-426RNA Processing and Editing
Protein synthesis and Gene Regulation
http://www.nature.com/scitable/topicpage/nucleic-acids-to-amino-acids-dna-specifies-935
Practicals.
Detection, Isolation and Staining methods for different microorganisms of forensic
application
2. Isolation of DNA RNA from biological material. Isolation of Plasmid DNA,
Restriction enzyme digestion - ligation of plasmid DNA
3. Study (observation) of some pathogenic Fungi and bacteria, (permanent slides)
4. Microbiological examination of water (Coli form test Microbiological examination of
milk
idt guidelines for primer design and ncbi primer design
primer design tutorial
MBIBM.sem4
Unit 1:Molecular Biology
Chemistry of Nucleotides, Structure of DNA/RNA
http://www.nature.com/scitable/topicpage/discovery-of-dna-structure-and-function-watson-397
DNA Replication: Eukaryotic and Prokaryotic
Helicases, Topoisomerases and other DNA replicating Enzymes
http://www.nature.com/scitable/topicpage/major-molecular-events-of-dna-replication-413
DNA Denaturation, Cot-Rot curves,
http://faculty.tru.ca/dnelson/courses/biol335/335notes/3recdna/4-hybrization/recDNA3b.html
DNA Repair mechanisms
http://www.nature.com/scitable/topicpage/dna-damage-repair-mechanisms-for-maintaining-dna-344
DNA Epigenetics
http://www.nature.com/scitable/topicpage/epigenetic-influences-and-disease-895
Eukaryotic and Prokaryotic Transcription.
http://www.nature.com/scitable/topicpage/dna-transcription-426RNA Processing and Editing
Protein synthesis and Gene Regulation
http://www.nature.com/scitable/topicpage/nucleic-acids-to-amino-acids-dna-specifies-935
Practicals.
Detection, Isolation and Staining methods for different microorganisms of forensic
application
2. Isolation of DNA RNA from biological material. Isolation of Plasmid DNA,
Restriction enzyme digestion - ligation of plasmid DNA
3. Study (observation) of some pathogenic Fungi and bacteria, (permanent slides)
4. Microbiological examination of water (Coli form test Microbiological examination of
milk
