National Symposium : Frontiers in Biotechnology 17th Feb 2011Biotechnology Department, PU, Chandigarh
Invited Talk-Quest of DNA signature of species of animal, plant & microbes :
Can we have a PIN code?
Quest of DNA signature of species of animal, plant & microbes :
Can we have a PIN code?
Invited talk- National symposium - Punjab University Chandigarh, 17th Feb 2011, Biotechnology department
Speeding up sequencing: Sequencing in an hour enables sample to answer in a w...Thermo Fisher Scientific
At this time next generation sequencing (NGS) is hindered by slow and often manual workflow procedures. Decreasing overall workflow times is critical for the widespread adoption of targeted and whole genome sequencing (WGS) for many time-sensitive applications, in particular for infectious disease analysis. To this end, we describe improvements to the four main steps of the NGS workflow: i) library preparation; ii) template preparation, iii) sequencing; iv) and data analysis. Together, these advances dramatically decrease the overall turnaround times.
Ion Torrent semiconductor-based sequencing instruments utilities flow sequencing with speed largely dependent on and the number of nucleotide flows (one flow produces ~0.5 base) and the speed of the flows (Figure 2).
Quest of DNA signature of species of animal, plant & microbes :
Can we have a PIN code?
Invited talk- National symposium - Punjab University Chandigarh, 17th Feb 2011, Biotechnology department
Speeding up sequencing: Sequencing in an hour enables sample to answer in a w...Thermo Fisher Scientific
At this time next generation sequencing (NGS) is hindered by slow and often manual workflow procedures. Decreasing overall workflow times is critical for the widespread adoption of targeted and whole genome sequencing (WGS) for many time-sensitive applications, in particular for infectious disease analysis. To this end, we describe improvements to the four main steps of the NGS workflow: i) library preparation; ii) template preparation, iii) sequencing; iv) and data analysis. Together, these advances dramatically decrease the overall turnaround times.
Ion Torrent semiconductor-based sequencing instruments utilities flow sequencing with speed largely dependent on and the number of nucleotide flows (one flow produces ~0.5 base) and the speed of the flows (Figure 2).
Endosymbiont hunting in the metagenome of Asian citrus psyllid (Diaphorina ci...Surya Saha
The Asian citrus psyllid (D. citri Kuwayama or ACP) is host to 7+ bacterial endosymbionts and is the insect vector of Ca. liberibacter asiaticus (Las), causal agent of citrus greening. To gain a better understanding of endosymbiont and pathogen ecology and develop improved detection strategies for Las, DNA from D. citri was sequenced to 108X coverage. Initial analyses have focused on Wolbachia, an alpha-proteobacterial primary endosymbiont typically found in the reproductive tissues of ACP and other arthropods. The metagenomic sequences were mined for wACP reads using BLAST and 4 sequenced Wolbachia genomes as bait. Putative wACP reads were then assembled using Velvet and MIRA3 assemblers over a range of parameter settings. The resulting wACP contigs were annotated using the RAST pipeline and compared to Wolbachia endosymbiont of Culex quinquefasciatus (wPip). MIRA3 was able to reconstruct a majority of the wPip CDS regions and was selected for scaffolding with Minimus2, SSPACE and SOPRA using large insert mate-pair libraries. The wACP scaffolds were compared to wPip using Abacas and Mauve contig mover to orient and order the contigs. The functional annotation of scaffolds was evaluated by comparing it to wPip genome using RAST. The draft assembly was verified using an OrthoMCL based comparison to the 4 sequenced Wolbachia genomes. We expanded the scope of endosymbiont characterization beyond wACP using 16S rDNA and partial 23S rDNA analysis as a guide. Results will be presented regarding endosymbionts, their potential interactions and their impact on the disease of citrus greening.
The bat genome data can be found at ENA under project ERP006654. Content based on original slides by Jamie Eadie, edited and expanded by David Martin. Photographs are (C) David Martin and may not be used without permission.
Pat Heslop-Harrison presentation for International Chromosome Conference Prague September 2018 Meiosis, recombination, pairing, mitochondria, evolution, genomics, oligonucleotides, in situ hybridization, breeding, genetics, cytogenetics, ICC, ICC22
Targeted T-cell receptor beta immune repertoire sequencing in several FFPE ti...Thermo Fisher Scientific
T-cell receptor beta (TCRβ) immune repertoire analysis by next-generation sequencing is a valuable tool for studies of the tumor microenvironment and potential immune responses to cancer immunotherapy. Here we describe a TCRβ sequencing assay that leverages the low sample input requirements of AmpliSeq library preparation technology to extend the capability of targeted immune repertoire sequencing to include FFPE samples which can often be degraded and in short supply
Introduction to Genetic Material, Physical and Chemical properties of the same and various types of coiling mechanisms as well as information about chromosomal and extra-chromosomal DNA.
This was presented on Mar 11, 2014 at Boyce Thompson Institute, Ithaca, NY at the 3rd BTI Bioinformatics Course http://btiplantbioinfocourse.wordpress.com/
Endosymbiont hunting in the metagenome of Asian citrus psyllid (Diaphorina ci...Surya Saha
The Asian citrus psyllid (D. citri Kuwayama or ACP) is host to 7+ bacterial endosymbionts and is the insect vector of Ca. liberibacter asiaticus (Las), causal agent of citrus greening. To gain a better understanding of endosymbiont and pathogen ecology and develop improved detection strategies for Las, DNA from D. citri was sequenced to 108X coverage. Initial analyses have focused on Wolbachia, an alpha-proteobacterial primary endosymbiont typically found in the reproductive tissues of ACP and other arthropods. The metagenomic sequences were mined for wACP reads using BLAST and 4 sequenced Wolbachia genomes as bait. Putative wACP reads were then assembled using Velvet and MIRA3 assemblers over a range of parameter settings. The resulting wACP contigs were annotated using the RAST pipeline and compared to Wolbachia endosymbiont of Culex quinquefasciatus (wPip). MIRA3 was able to reconstruct a majority of the wPip CDS regions and was selected for scaffolding with Minimus2, SSPACE and SOPRA using large insert mate-pair libraries. The wACP scaffolds were compared to wPip using Abacas and Mauve contig mover to orient and order the contigs. The functional annotation of scaffolds was evaluated by comparing it to wPip genome using RAST. The draft assembly was verified using an OrthoMCL based comparison to the 4 sequenced Wolbachia genomes. We expanded the scope of endosymbiont characterization beyond wACP using 16S rDNA and partial 23S rDNA analysis as a guide. Results will be presented regarding endosymbionts, their potential interactions and their impact on the disease of citrus greening.
The bat genome data can be found at ENA under project ERP006654. Content based on original slides by Jamie Eadie, edited and expanded by David Martin. Photographs are (C) David Martin and may not be used without permission.
Pat Heslop-Harrison presentation for International Chromosome Conference Prague September 2018 Meiosis, recombination, pairing, mitochondria, evolution, genomics, oligonucleotides, in situ hybridization, breeding, genetics, cytogenetics, ICC, ICC22
Targeted T-cell receptor beta immune repertoire sequencing in several FFPE ti...Thermo Fisher Scientific
T-cell receptor beta (TCRβ) immune repertoire analysis by next-generation sequencing is a valuable tool for studies of the tumor microenvironment and potential immune responses to cancer immunotherapy. Here we describe a TCRβ sequencing assay that leverages the low sample input requirements of AmpliSeq library preparation technology to extend the capability of targeted immune repertoire sequencing to include FFPE samples which can often be degraded and in short supply
Introduction to Genetic Material, Physical and Chemical properties of the same and various types of coiling mechanisms as well as information about chromosomal and extra-chromosomal DNA.
This was presented on Mar 11, 2014 at Boyce Thompson Institute, Ithaca, NY at the 3rd BTI Bioinformatics Course http://btiplantbioinfocourse.wordpress.com/
The present PPT discusses following important points:
Aquaculture for affordable animal protein
Hurdles in intensive farming
Vaccinology in Aquaculture industry
DNA vaccines (current status & future prospects)
NCBI has developed a powerful suite of online biomedical and bioinformatics resources, including old friends like PubMed and OMIM and newer resources such as Genome. This collection of databases and tools are widely used by scientists and medical professionals across the world. With such a wealth of information, it is easy to get overwhelmed. Join us for an overview to NCBI resources for the information professional with an emphasis on biodata connectivity. No science degree required!
Metagenomics is the study of genetic material recovered directly from environmental samples. Metagenomics is a molecular tool used to analyse DNA acquired from environmental samples, in order to study the community of microorganisms present, without the necessity of obtaining pure cultures.
Abstract: The focus in this session will be put on the differences between standard DNA mapping and RNAseq-specific transcript mapping: identifying splice variants and isoforms. The issue of transcript quantification and genomic variants that can be identified from RNAseq data will be discussed.
Detection of genomic homology in eukaryotic genomesKlaas Vandepoele
i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets.
Proost S, Fostier J, De Witte D, Dhoedt B, Demeester P, Van de Peer Y, Vandepoele K.
Nucleic Acids Res. 2012 Jan;40(2):e11.
Comparative genomics is a powerful means to gain insight into the evolutionary processes that shape the genomes of related species. As the number of sequenced genomes increases, the development of software to perform accurate cross-species analyses becomes indispensable. However, many implementations that have the ability to compare multiple genomes exhibit unfavorable computational and memory requirements, limiting the number of genomes that can be analyzed in one run. Here, we present a software package to unveil genomic homology based on the identification of conservation of gene content and gene order (collinearity), i-ADHoRe 3.0, and its application to eukaryotic genomes. The use of efficient algorithms and support for parallel computing enable the analysis of large-scale data sets. Unlike other tools, i-ADHoRe can process the Ensembl data set, containing 49 species, in 1 h. Furthermore, the profile search is more sensitive to detect degenerate genomic homology than chaining pairwise collinearity information based on transitive homology. From ultra-conserved collinear regions between mammals and birds, by integrating coexpression information and protein-protein interactions, we identified more than 400 regions in the human genome showing significant functional coherence. The different algorithmical improvements ensure that i-ADHoRe 3.0 will remain a powerful tool to study genome evolution.
Macroeconomics- Movie Location
This will be used as part of your Personal Professional Portfolio once graded.
Objective:
Prepare a presentation or a paper using research, basic comparative analysis, data organization and application of economic information. You will make an informed assessment of an economic climate outside of the United States to accomplish an entertainment industry objective.
Acetabularia Information For Class 9 .docxvaibhavrinwa19
Acetabularia acetabulum is a single-celled green alga that in its vegetative state is morphologically differentiated into a basal rhizoid and an axially elongated stalk, which bears whorls of branching hairs. The single diploid nucleus resides in the rhizoid.
Biological screening of herbal drugs: Introduction and Need for
Phyto-Pharmacological Screening, New Strategies for evaluating
Natural Products, In vitro evaluation techniques for Antioxidants, Antimicrobial and Anticancer drugs. In vivo evaluation techniques
for Anti-inflammatory, Antiulcer, Anticancer, Wound healing, Antidiabetic, Hepatoprotective, Cardio protective, Diuretics and
Antifertility, Toxicity studies as per OECD guidelines
Normal Labour/ Stages of Labour/ Mechanism of LabourWasim Ak
Normal labor is also termed spontaneous labor, defined as the natural physiological process through which the fetus, placenta, and membranes are expelled from the uterus through the birth canal at term (37 to 42 weeks
Operation “Blue Star” is the only event in the history of Independent India where the state went into war with its own people. Even after about 40 years it is not clear if it was culmination of states anger over people of the region, a political game of power or start of dictatorial chapter in the democratic setup.
The people of Punjab felt alienated from main stream due to denial of their just demands during a long democratic struggle since independence. As it happen all over the word, it led to militant struggle with great loss of lives of military, police and civilian personnel. Killing of Indira Gandhi and massacre of innocent Sikhs in Delhi and other India cities was also associated with this movement.
June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...Levi Shapiro
Letter from the Congress of the United States regarding Anti-Semitism sent June 3rd to MIT President Sally Kornbluth, MIT Corp Chair, Mark Gorenberg
Dear Dr. Kornbluth and Mr. Gorenberg,
The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
harassment and intimidation at the Massachusetts Institute of Technology (MIT). Failing to act decisively to ensure a safe learning environment for all students would be a grave dereliction of your responsibilities as President of MIT and Chair of the MIT Corporation.
This Congress will not stand idly by and allow an environment hostile to Jewish students to persist. The House believes that your institution is in violation of Title VI of the Civil Rights Act, and the inability or
unwillingness to rectify this violation through action requires accountability.
Postsecondary education is a unique opportunity for students to learn and have their ideas and beliefs challenged. However, universities receiving hundreds of millions of federal funds annually have denied
students that opportunity and have been hijacked to become venues for the promotion of terrorism, antisemitic harassment and intimidation, unlawful encampments, and in some cases, assaults and riots.
The House of Representatives will not countenance the use of federal funds to indoctrinate students into hateful, antisemitic, anti-American supporters of terrorism. Investigations into campus antisemitism by the Committee on Education and the Workforce and the Committee on Ways and Means have been expanded into a Congress-wide probe across all relevant jurisdictions to address this national crisis. The undersigned Committees will conduct oversight into the use of federal funds at MIT and its learning environment under authorities granted to each Committee.
• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
• The Committee on Oversight and Accountability is investigating the sources of funding and other support flowing to groups espousing pro-Hamas propaganda and engaged in antisemitic harassment and intimidation of students. The Committee on Oversight and Accountability is the principal oversight committee of the US House of Representatives and has broad authority to investigate “any matter” at “any time” under House Rule X.
• The Committee on Ways and Means has been investigating several universities since November 15, 2023, when the Committee held a hearing entitled From Ivory Towers to Dark Corners: Investigating the Nexus Between Antisemitism, Tax-Exempt Universities, and Terror Financing. The Committee followed the hearing with letters to those institutions on January 10, 202
Introduction to AI for Nonprofits with Tapp NetworkTechSoup
Dive into the world of AI! Experts Jon Hill and Tareq Monaur will guide you through AI's role in enhancing nonprofit websites and basic marketing strategies, making it easy to understand and apply.
Unit 8 - Information and Communication Technology (Paper I).pdfThiyagu K
This slides describes the basic concepts of ICT, basics of Email, Emerging Technology and Digital Initiatives in Education. This presentations aligns with the UGC Paper I syllabus.
How to Make a Field invisible in Odoo 17Celine George
It is possible to hide or invisible some fields in odoo. Commonly using “invisible” attribute in the field definition to invisible the fields. This slide will show how to make a field invisible in odoo 17.
2024.06.01 Introducing a competency framework for languag learning materials ...Sandy Millin
http://sandymillin.wordpress.com/iateflwebinar2024
Published classroom materials form the basis of syllabuses, drive teacher professional development, and have a potentially huge influence on learners, teachers and education systems. All teachers also create their own materials, whether a few sentences on a blackboard, a highly-structured fully-realised online course, or anything in between. Despite this, the knowledge and skills needed to create effective language learning materials are rarely part of teacher training, and are mostly learnt by trial and error.
Knowledge and skills frameworks, generally called competency frameworks, for ELT teachers, trainers and managers have existed for a few years now. However, until I created one for my MA dissertation, there wasn’t one drawing together what we need to know and do to be able to effectively produce language learning materials.
This webinar will introduce you to my framework, highlighting the key competencies I identified from my research. It will also show how anybody involved in language teaching (any language, not just English!), teacher training, managing schools or developing language learning materials can benefit from using the framework.
2024.06.01 Introducing a competency framework for languag learning materials ...
DNA signature
1. National Symposium : Frontiers in Biotechnology 17th Feb 2011
Biotechnology Department, PU, Chandigarh
Quest of DNA signature of species of animal, plant & microbes :
Can we have a PIN code?
Dinesh Kumar, B.Sc. Hons Zoo(BHU), M.Sc. Biotechnology(BHU), Ph.D. Biotechnology (BHU), PDF(USA)
Senior Scientist(Animal Biotechnology)
National Bureau of Animal Genetic Resources, Karnal-132 001, Haryana, INDIA
Email: dineshkumarbhu@gmail.com, dinesh@iastate.edu
2. DNA signature- Quest
Genome, some thing identifiable
My single cell, 92 DNA molecule, maternal 46, paternal 46
A part of molecule is unique or combination of these
molecule is unique
Signature in form of DNA marker- SNP or STR
How to tap these signature in genome?
Need bioinformatics tools
Case studies
Domestic Animals , Fish, Microbes, Plant
STR allele-private alleles or private frequencies
SNP- plus and minus assay
Software tools-SNP data and STR data
2/17/2011 Dinesh-PU-Talk-17-02-2011 2
3. How DNA signature is made for each species?
The number of nucleic acid or amino acid differences
between two organisms is proportional to the time since
they diverged from a common ancestor.
1 AAGGCTA 1 2 3
MOLECULAR 2 AAGGGTA 100years
DIFFERENCES 3 AAGGATG
200
Example
years
Rate of Evolution =
1bp per 100 years
TIME
4. Which marker for which purpose?
How long ago did organism A and organism
B last have a common ancestor?
Molecular clock and DNA signature !!!
Very recently - RAPDs/VNTRs/Microsatellites/
resistance genes
10,000s - 100,000s yrs - RNA- ITS, various protein-
coding genes
100,000s - 1,000,000s yrs - ssu rRNA, HSPs,
2/17/2011 Dinesh-PU-Talk-17-02-2011 4
5. DNA barcoding of species
cytochrome c oxidase subunit I gene (COI)
potential 'barcode'.
2/17/2011 Dinesh-PU-Talk-17-02-2011 5
6. Origin of species bar code
Carl Woese used sequence differences in
ribosomal RNA (rRNA) to discover archaea,
which in turn led to the redrawing of the
evolutionary tree, and molecular markers (e.g.,
allozymes, rDNA, and mtDNAvage ) have been
successfully used in molecular systematics for
decades.
In 2003, Paul D.N. Hebert from the University of
Guelph, Ontario, Canada, proposed the
compilation of a public library of DNA barcodes
that would be linked to named specimens.
2/17/2011 Dinesh-PU-Talk-17-02-2011 6
7. Identification of birds by species bar code
Hebert and co-workers sequenced DNA
barcodes of 260 of the 667 bird species that
breed in North America (Hebert et al.
2004).
2/17/2011 Dinesh-PU-Talk-17-02-2011 7
8. Identifying flowering plants by species DNA bar code
Kress et al. (2005) -COI sequence- not appropriate for most
species of plants slower rate of cytochrome c oxidase I gene
evolution in higher plants than in animals”.
A series of experiments was then conducted to find a more
suitable region of the genome for use in the DNA barcoding
of flowering plants.
nuclear internal transcribed spacer region and the plastid
trnH-psbA intergenic spacer as a potential DNA barcode for
flowering plants. Some reports supports MatK
DNA barcoding, no 'master key' may be a 'master keyring',
with different kingdoms of life requiring different keys.
2/17/2011 Dinesh-PU-Talk-17-02-2011 8
9. Microbial species signature
Ribotyping -rRNA database-most used eg 16srDNA
Designing of primer for gene sequencing. Eg HKG,Topoiso II,
Designing of probes for identifications-Eg.real time, microarray
Meta genome analysis- gene prediction
Chip based pyrosequencing and simulation
In silico development of RFLP test for close species
differentiation(our experiences)
MPIDB- functional identification
Miniprimer PCR-a new lens to view microbial world
2/17/2011 Dinesh-PU-Talk-17-02-2011 9
10. rRNA genes - the ideal markers for microbial identification
Small subunit - highest order differences (domains)
Large subunit - medium order differences
ITS - low order differences (species/strains?)
Small Sub-Unit rRNA (16S)
ubiquitous
1.6 - 2.0kb
good molecular chronometer.
some areas conserved (for priming/alignment)
some areas variable (for resolving differences)
2/17/2011 Dinesh-PU-Talk-17-02-2011 10
14. Why we need molecular & bioinformatics tool?
Case study of Ug99-signature search
Stem rust never sleeps- Norman E. Borlaug , 26th April, 2008, New York Times
2/17/2011 Dinesh-PU-Talk-17-02-2011 14
15. Can we have DNA based signatures of Ug99?
National Debate!
Global meet at Delhi, Oct, 2008
Action plan?
2/17/2011 Dinesh-PU-Talk-17-02-2011 15
16. A case study updates-
How to identify Ug99?
Puccinia graminis tritici Ug99
DNA signature is the only answer !
DNA signature of Fungi
– Private alleles of STR(rare)
– STR allele frequency signatures
– SNP based signatures(???)
Where is the signature of Ug99 ??
2/17/2011 Dinesh-PU-Talk-17-02-2011 16
17. What are the available DNA
markers to identify Ug99
SSR
AFLP
Mol Plant
Path
Latest Nov
2008 issue
Dinesh-PU-Talk-17-02-2011 17
2/17/2011
18. SSR data- no DNA signature
Mol Plant Path Nov 2008 issue
2/17/2011 Dinesh-PU-Talk-17-02-2011 18
19. AFLP adapters used to generate signature data
Mol Plant Path
Nov 2008 issue
2/17/2011 Dinesh-PU-Talk-17-02-2011 19
21. No clear signature of Ug55 & 99 by SSR
Mol Plant Path Nov 2008 issue
2/17/2011 Dinesh-PU-Talk-17-02-2011 21
22. AFLP again poor signature b/w Ug99/55
Mol Plant Path Nov 2008 issue
2/17/2011 Dinesh-PU-Talk-17-02-2011 22
23. DNA signature of Ug99 by combining data
of SSR+AFLP
Mol Plant Path Nov 2008 issue
2/17/2011 Dinesh-PU-Talk-17-02-2011 23
24. Clear DNA signature by
Minimum-spanning network analysis
Mol Plant Path Nov 2008 issue
2/17/2011 Dinesh-PU-Talk-17-02-2011 24
25. What bioinformatics can do more in
Ug99 identification?
Allele mining of Puccinia graminis tritici Ug99
– USDA is targeting 400 SNP
STR mining from Puccinia graminis genome data
base
STR based signature search
2/17/2011 Dinesh-PU-Talk-17-02-2011 25
26. Puccinia graminis database
Genome of P. graminis tritici
88.54 Mb, 392 scaffolds, contigs 4557
2/17/2011 Dinesh-PU-Talk-17-02-2011 26
27. Our experiences-DNA based gender
signature using bioinformatics tools
2/17/2011 Dinesh-PU-Talk-17-02-2011 27
28. Our experiences-DNA based microbial species
signature using bioinformatics
House Keeping Genes -CLUSTAL-W-signature with spelling mistake- CLEAVER
KspAI Bsh1236I Mun I
L P P R RR P P R RR P P R RR
KEU1 5'-AAY ATG ATI ACI GGI GCI GCI CAR ATG GA-3'
KEU 2 5'-AYR TTI TCI CCI GGC ATI ACC AT-3'.
KspAI L.paracasei 542,158bp; L.rhamnosa 701bp
Bsh1236I L. paracasei 547,153bp; L. rhamnosa 701bp
Mun I L. paracasei 594,106bp; L. rhamnosa 701bp
New PCR-RFLP test developed for Lactobacillus species differentiation
2/17/2011 Dinesh-PU-Talk-17-02-2011 28
29. DNA based signature of domestic species
Mitochindrial DNA markers
used especially for meat identification,
poaching of wild animals,
adulteration of dairy milk,
dairy products(like cheese) of various
domestic animal species.
2/17/2011 Dinesh-PU-Talk-17-02-2011 29
30. DNA based signature of
domestic animal breeds
Whether a livestock breed can be identified from a sample of blood,
semen, hair, blood spot, carcass etc?
Studies have succeeded in developing a technology for breed
certification and breed-specific genetic/DNA signature
Degree of accuracy of certification of a breed -between 95% to 99%.
STR based three methods viz
(i) Frequency method (Paetkau et al., 1995),
(ii) Bayesian method (Rannala et al, 1997) and
(iii) Distance methods (Goldstein et al 1995)
Use
(i) Development of breed-specific signatures/profiles and
(ii) Development of breed hybrid index.
2/17/2011 Dinesh-PU-Talk-17-02-2011 30
31. STR & breed-specific signatures/profiles
Pig-In UK, Signer et al. (2000) - minisatellite probe pCMS12 -three breeds of pig viz
Chinese, Meishan, Large White and other European breeds. The linear discrimination
analysis revealed that the DNA profiles were breed specific.
Fish-In Finland, Primmer et al. (2000) - disputed fish to a specific population out of 4
suspected fish populations using 7 microsatellite loci by Bayesian method with
confidence limit of 99%.
Sheep-In Spain, Arranz et al. (2001) - Bayesian method with 99.63% accuracy among
five Spanish sheep breed viz. Churra, Latxa, Castellana, Rasa-Aragonesa and Merino
using 18 microsatellite markers.
Horse-In Norway, Bjornstad et al. (2001) -26 microsatellite loci in six breeds of horses,
Fjord, Nordland/ Lyngen, Dole, Trotter, Icelandic horse and Shetland pony with more
than 95% confidence limit.
Cattle-In European countries, Canon et al. (2001) -confidence limit of 99% for 18 local
breeds of cattle of different countries; Alistana, Astruriana, Asturiana Valles,
Sayaguesa, Tudanca, Avilena Negra-Iberica, Bruna del Pirineus, Morucha, Pirenaica,
Retinta of Spain; Alentejana, Barrosa, Maronesa, Mertolenga, Mirandesa of Portugal
and Aubrac, Gasconne, Salers of France
Camel- In Kenya, Mburu et al. (2003) - 4 breeds using 14 microsatellite loci of camel
viz. Somali, Turkana, Rendille, Gabbra) using maximum likelihood method up to 48 %
confidence limit.-weak genetic differentiation and gene flow between populations.
Dog-In Finland, Koskinen (2003) has assigned breeds of domestic dog using
2/17/2011 Dinesh-PU-Talk-17-02-2011 31
microsatellite with 100% accuracy.
32. Development of breed hybrid indices/ profiles
Campton and Utter (1985) -hybrid index, hybrid index for
analyzing hybridization between cut-throat (Oncorhynchus
clarkii , Salmonidae) and rainbow trout ( O. mykiss ,
Salmonidae), and they used allozyme loci for which the two
species were almost fixed for alternate alleles.
Hansen et al. (2000) found that hybrid index statistic is also
useful for microsatellite loci and t- interbreeding between wild
and domesticated brown trout,
Softwares:
ASSIGNMENT CALCULATOR,
GENECLASS or
ARLEQUIN and then importing the data into a spreadsheet where the final calculations can be done.
Relevance in Indian context-
exotic inheritance calculation, Bos indicusx taurus, Alpine x Beetal
cross/admixture populations
2/17/2011 Dinesh-PU-Talk-17-02-2011 32
33. Future breed signature of domestic
animals
Courtesy: Curt & his group USDA
2/17/2011 Dinesh-PU-Talk-17-02-2011 33
35. Few examples: Signature applications
1. Application of polymerase chain reaction to detect adulteration of
sheep's milk with goats: J Dairy Sci (2005) 88: 3115-20.
2. A novel approach to the quantification of bovine milk in ovine cheeses
using a duplex PCR: J Agric Food Chem (2004) 52: 4943-7.
3. Rapid detection of cows' milk in sheeps' and goats' milk by a species-
specific polymerase: J Dairy Sci (2004) 87: 2839-45.
4. Identification of cow's milk in "buffalo" cheese by duplex polymerase
chain reaction. J Food Prot (2002) 65: 362-6.
5. Forensic identification of ungulate species using restriction digests of
PCR-amplified mit J Forensic Sci (1995) 40: 943-51. (15 species)
6. Detection of cows' milk in goats' cheeses inferred from mitochondrial
DNA polymorphism Journal of Dairy Research (2001), 68:229-235
7.Application of polymerase chain reaction for detection of goats' milk
adulteration by milk of cow. Journal of Dairy Research (2001),
68:333-336
2/17/2011 Dinesh-PU-Talk-17-02-2011 35
36. DNA based signature of plant variety, example-
Basmati rice
Basmati rice -aroma compound -2-acetyl-1-
pyrroline.
Fraudulent traders to adulterate traditional basmati.
PCR-based assay similar to DNA fingerprinting in
humans allows for the detection of adulterated and
non-basmati strains. Its detection limit for
adulteration is from
1% upwards with an error rate of ±1.5%.
Exporters of basmati rice use 'purity certificates'
based on DNA tests for their basmati rice
consignments.
It was developed by CDFD, Labindia,
World's First Single-tube, Multiplex(co-amplify
eight microsatellite loci) Microsatellite Assay-based
Kit for Basmati Authentication.
2/17/2011 Dinesh-PU-Talk-17-02-2011 36
37. DNA based bar-coded signature of fish
Ward et al (2005) - cox1 sequencing, or ‘barcoding’, in to
identification of fish species.
207 fish, mostly Australian marine fish, were sequenced
(bar coded) for a 655 bp region of the mitochondrial
cytochrome oxidase subunit I gene (cox1).
Most species were represented by multiple specimens, and
754 sequences were generated.
The GC content of the 143 species of teleosts was higher
than the 61 species of sharks and rays (47.1% versus
42.2%), largely due to a higher GC content of codon
position 3 in the former (41.1% versus 29.9%).
2/17/2011 Dinesh-PU-Talk-17-02-2011 37
38. Few examples of individual DNA signature
and family signature
* Rajiv Gandhi Assassination Case (Chennai,
Tamil Nadu),
* Naina Sahni or the Tandoor case (New Delhi
* Priyadarshini Mattoo (New Delhi),
* Sishu Vihar Child adoption case (Hyderabad,
Andhra Pradesh),
* Black Buck killing case (Jodhpur, Rajasthan)
* Beanth Singh Assassination Case (Punjab)
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40. What is CBOL?
The Consortium for the Barcode of Life (CBOL) is an international initiative devoted
to developing DNA barcoding as a global standard for the identification of biological
species. DNA barcoding is a new technique that uses a short DNA sequence from a
standardized and agreed-upon position in the genome as a molecular diagnostic for
species-level identification. DNA barcode sequences are very short relative to the
entire genome and they can be obtained reasonably quickly and cheaply. The "Folmer
region" at the 5' end of the cytochrome c oxidase subunit 1 mitochondrial region (COI)
is emerging as the standard barcode region for almost all groups of higher animals. This
region is 648 nucleotide base pairs long in most groups and is flanked by regions of
conserved sequences, making it relatively easy to isolate and analyze. A growing
number of studies have shown that COI sequence variability is very low (generally less
than 1-2%) and that the COI sequences of even closely related species differ by several
percent, making it possible to identify species with high confidence. For those groups in
which COI is unable to resolve species-level differences, CBOL recommends the use of
an additional gene region. In some groups, COI is not an effective barcode region and a
different standard region must be identified. In all cases, DNA barcoding is based on the
use of a short, standard region that enables cost-effective species identification.
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58. Conclusion
DNA based species signature is possible
Why to do it?
Who has to do?
What we need?
How to proceed?
Germplasm wealth of “third world” countries
needs protection and pragmatic use!
Biotechnology/Bioinformatics has immense role
Journey of IT & BT !
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59. Acknowledgements
Dr Jagdeep Kaur , Dr Jagtar Singh & team, Biotechnology
Department , Punjab University, Chandigarh
My students- Prashant, Prem, Nishant, Dhiraj (NBAGR)
My UG/PG students- Pooja(NISER) & Uday(GU)
Dr James Reecy & his group, Iowa State University, USA
Dr DK Arora, NBAIM(ICAR)
Dr Rameshwar Singh & Dr SK Tomar, NDRI
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