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Eye Color Prediction Using Snps Of Oca2 And Herc2 Genes In Different Eye Color Groups From Pakistani Population

by Iqra Baig (2015-VA-813) | Dr. Muhammad Yasir Zahoor | Dr. Saadat Ali | Dr. Amjad Riaz.

Material type: book Book; Format: print ; Literary form: not fiction Publisher: 2017Dissertation note: The outward appearance of living organism that can be visualized is known as External visible characteristic (EVCs). These are related to the interaction of different genes among themselves and with their environment. Through this technique police investigators or other forensic investigators determine perpetrators which are completely unknown to investigating authourities or to pinpoint missing persons utilizing biological samples in those situations where all other evidences of query, along with conventional DNA profiling give non-uniformities. Eye color is a multiplex trait controlled by many genes but the two major genes which play crucial role to determine eye color are OCA2 and HERC2 genes. 74% eye color of human is under the control of OCA2 gene and its function is influenced by HERC2 gene. These are present on chromosome 15. Eye color trait has miscellaneous inheritance pattern which does not obey simple pattern of Mendelian inheritance. Blood samples of 40 volunteers along with photographs of iris collected from local population of Pakistan by categorizing different eye colors. DNA was extracted using organic extraction method. Then amplified using PCR with primers of SNP rs1800401 of OCA2 gene and SNP rs12913832 of HERC2 gene. Primers were designed through primer 3 software. Amplicons were analyzed by gel electrophoresis. Samples were sequenced by Sanger sequencing and chromatograms were analyzed by pairwise and multiple alignment tools. We mapped five polymorphic sites in OCA2 gene including SNPs rs1800401 and rs10300271. Polymorphic sites of OCA2 are 89406 C>T, 89401 G>T, 894019 A>T, 89422 A>C and 89435 C>A. Six polymorphic sites of HERC2 also analyzed including SNP rs12913832 at 206678 T>C and other polymorphic sites are 206617delA, 206631delA, 206683 T>A, 206688delA and 206713delA. These polymorphic sites were further analyzed by applying t-test which shows no significant association between retrieved polymorphic sites and eye color except polymorphic site 89422 with genotype A>C in OCA2 gene (novel) and polymorphic site 206678 with genotype T>C in HERC2 gene (already reported) both are associated with non-brown eye color variation in our study. In conclusion, more research to DNA based human appearance prediction is recommended using large sample size as there are more SNPs also involve that would be very useful for identification or investigative leads in forensic future aspects. Availability: Items available for loan: UVAS Library [Call number: 2902-T] (1).

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2.
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Sequence Analysis Of Comt Gene As Suceptibility Factor For Aggression In Domestic And Wild Cats

by Maham Nawaz (2011-VA-455) | Dr. Asif Nadeem | Dr. Saadat Ali | Dr. Amjad Riaz.

Material type: book Book; Literary form: not fiction Publisher: 2017Dissertation note: Behavior that is directed to injure living beings and damage their neuroconductual processes without any incitement, represents the aggressive behavior. COMT gene is of much importance in determining violent act in both animal and human.The present study is designed to molecular characterize the gene with following objective: to screen out polymorphism (SNPs) in exonic region of COMT gene in cats and tiger and to associate the identified polymorphism in cats and tiger. Aggression questionnaire was filled by honors of all domestic and wild cats included in our study.Blood sample of 5 Stray cat, 5 Persian cat and 5 Siamese cat and 5 Bengal tigers were collected from Lahore Zoo, UVAS PET Centre, Private Pet Clinics and Safari Zoo Lahore for SNP analysis. DNA were extracted from blood by organic method, 5 sets of primers were designed by primer 3 software for the amplification of the COMT genes. The amplified PCR products were precipitated and sequenced bi-directionally on ABI 3130XL Genetic analyzer, for the identification of SNPs.Alignment of sequences were done with the help of blast2 sequences. For sequence data analysis, Bioedit and Clustal W were used to complete the study.Results of sequencing were analyzed using BioEdit software. Sequence alignment tool like Clustal W was used for SNPs identification. 3 intronic and 1 exonic SNPs were observed and confirmed by Clustal W. Exonic SNP was linked to aggression. However, intronic SNPs were not found to be associated with self-reported aggression. SNP observed in exon 2 is reported to be involved in psychiatric and depressive disorders.Our study highlighted the role of COMTgene polymorphisms in aggression in animals (Cats and tiger). Different breeding Policies and Pet plains are now working and we can screen out the susceptibility of aggression in cats and tiger. Availability: Items available for loan: UVAS Library [Call number: 2901-T] (1).

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Development Of Novel MTDNA Metbarcodes For Species Differentiation Of Class Pisces

by Hira (2010-VA-476) | Dr. Muhammad Imran | Dr. Saadat Ali | Dr. Amjad Riaz.

Material type: book Book; Literary form: not fiction Publisher: 2017Dissertation note: The Folmer COI mtDNA universal primers that are considered standard for DNA barcoding of life contain so many mismatches against the target sequences of vertebrate origin that they often end in failure to amplify many of vertebrate DNA extractions. This discrepancy favors for the selection and designing of new metabarcode primers that can be used to identify all individuals of vertebrates or at least all individuals represented in a class of Vertebrata such as Class Pisces. The current study embarks on such an endeavor. In this study development of new mtDNA metabarcode (16SrRNA) that can be used as universal primers to amplify almost all species of Class Aves for different forensic and molecular biodiversity analyses. Fins/tissue samples were collected from Class Pisces (one specimen from every order reported to be present in Pakistan). DNA was extracted from the collected specimens through standard organic method, qualified and quantified and then PCR-amplified using novel universal primers selected from aligned mtDNA sequences originating from all Pisces mitochondrial DNA genomes submitted to different online sequence databases such as NCBI nucleotide database. The sensitivity of PCR also be assessed using a range of DNA concentrations. The amplified products were sequenced on ABI Genetic Analyzer following Sanger’s dideoxy method of sequencing. The correctness of obtained mtDNA sequences were examined visually in Chromas Lite 2.1 software and then alignment of these sequences were performed against highly similar DNA sequences in NCBI nucleotide databases using BLAST in order to identify origin of unknown mtDNA sequences. With the help of sequencing and phylogenetic studies specificity of the universal primer set confirmed and presented as a novel metabarcode (16SrRNA) for species level identification of large number of Piscean species In summary, we present universal method for species classification of Pisces using a targeted parallel sequencing approach. Both sequencing and phylogenetic studies experiments confirm specificity of universal primer set. Although promising results were obtained with current settings, rapid improvement of bench top instruments will further develop method with less hands-on, fewer sequencing errors and lower detection limit. So, in future, this barcode can be used for species identification in various fields of study such as meat adulteration, illegal trade, food mislabeling and molecular estimation of biodiversity. Availability: Items available for loan: UVAS Library [Call number: 2899-T] (1).

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