1.
Genetic Characterization Of Pakistani Wild Quails Using Mitochondrial Coi Gene
by Wajiha Shakil (2012-VA-817) | Dr. Ali Raza Awan | Dr. Muhammad Yasir Zahoor | Prof. Dr. Tahir Yaqub.
Material type: ; Literary form:
not fiction
Publisher: 2015Dissertation note: A latest taxonomic tool termed as DNA barcoding is being used to genetically characterize animals. DNA barcoding is helpful in determining evolutionary relationship among species. Being a small sized genome and agile enough to show rapid mutation, mtDNA has been used as a pertinent marker of molecular biodiversity. DNA barcode works as an efficient tool in food manufacturing industry, diet investigation, forensics analysis, preventing unlawful trade and felonious poaching. The aim of this study was to develop DNA barcode for genetic characterization of Pakistani wild quail. Pakistani wild quail is important due to its demand for eggs, meat production, experimental purposes and gaming as well. Japanese quail was also included in this study because this quail is excessively produced in Pakistani farms. Japanese quail is present throughout the year and is comparatively bigger in size than wild quail. It has longer lifespan; farmers can easily breed this species in farms. It is suitable in poultry due to better meat yield.
COI gene (500bp) was used as a molecular marker for identification at species level. DNA was extracted from blood samples of ten wild quails (Coturnix coturnix and fifteen japanese quails (Coturnix japonica). Reported bird universal primers were used to amplify COI region from the extracted mtDNA samples using PCR. Amplicon were then sequenced by Sanger sequencing method (Sanger et al. 1977). Forward and reverse DNA Sequences were aligned with the reference sequence using nucleotide BLAST on NCBI to observe the dissimilarity among the sequences. Consensus sequences generated were used to construct their phylogenetic tree to see their evolutionary relationship with other bird species. Japanese quail which is thought to be domesticated from Japan, its Pakistani population showed close relation with sequences
Summary
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generated in Japan for this particular species. Pakistani wild quail species showed its closest linkage with C. coturnix.
In conclusion, COI barcode proved as an authentic tool for species identification and phylogenetic inference of Pakistani wild and farm grown quails. Wild quail species has been characterized using partial COI gene sequences. This study has provided a specific genetic marker which can differentiate Japanese quail from wild quail at molecular level as most of the time both species are confused with each other. It can be helpful to the farmers and bird fanciers because they can select the birds of their choice correctly. This is the first study reporting DNA barcode of this Pakistani quail species. It would help researchers to study about phylogenetic and taxonomic status and also assist quail fanciers and quail farmers to unaffectedly identify their species of interest in farming. Identification of quail species is also important for conservation of biodiversity as it helps in preservation and identification of endangered species by generating their barcodes from even minimal evidence available. Availability: Items available for loan: UVAS Library [Call number: 2311-T] (1).
2.
Analysis Of Genetic Polymorphism In Exon 6 & 11 Of Glucosidase Beta Acid (Gba) Gene In Gaucher Diseased Patients From Punjab, Pakistan
by Aysha Arshad (2009-VA-571) | Dr. Muhammad Yasir Zahoor | Dr. Muhammad Imran | Dr. Imran Altaf.
Material type: ; Format:
print
; Literary form:
not fiction
Publisher: 2015Dissertation note: Gaucher disease (GD) is amajor predominant heterogenic, inherited and metabolic lysosomal storage disorder. It is prompted by an alteration in glucosidase acid beta (GBA) gene. GBA gene encodes a 497 amino acid glucocerebrosidase enzyme. It is a lysosomal hydrolase, present in all mammalian cells membrane that carries the catalysis of complex ubiquitous sphingolipids called glucocerebrosides (GlcCer) into smaller and simpler molecules of sugar and ceramide. The human glucocereborside (GBA) gene is present in highly gene dense area on q arm of 21 chromosome and its fragment length is 7.8kb comprising of 11 exons. A pseudogene is also present in vicinity of GBA gene which shares 96% homology of sequence with functional gene. Genetic recombination and gene conversion among these two GBA genes are responsible for 10-20% GD mutations. >300 mutations of GBA have been described till 2014. GD has three different clinical forms depend on its heterogeneity. These are characterized by the age of onset and with or without the participation of CNS.
In this study, 10 blood samples were collected of GD patients from repository at Molecular and Genomic Laboratory located at IBBT department, UVAS Lahore and from Children Hospital Lahore. DNA extraction was done by using organic method from blood samples. Amplification of GBA gene exons 1, 6 and 11 was performed using PCR. PCR products were sequenced using Sanger di-deoxy sequencing method. Different bioinformatics tools were applied for the sequence analysis of exon 1, 6 and 11. We found two variants of GBA gene. A deletion of CT nucleotide repeat in intron 1 was found. We also found a substitutional change of nucleotide T>A in intron 8. Availability: Items available for loan: UVAS Library [Call number: 2334-T] (1).
3.
The Variability Analysis of The Gene Encoding HCV Non-Structural Protein NS2
by Abdul Rehman (2009-VA-546) | Dr. M. Imran | Dr. Muhammad Yasir Zahoor | Ms. Faiza Masood.
Material type: ; Literary form:
not fiction
Publisher: 2015Dissertation note: Theses submitted with blank cd. Availability: Items available for loan: UVAS Library [Call number: 2337-T] (1).
4.
Mutational Analysis of CaSR in Calcium Nephrolithiasis Affected Pakistani Families
by Asad Tufail (2013-VA-558) | Dr. Muhammad Yasir Zahoor.
Material type: ; Literary form:
not fiction
Publisher: 2015Dissertation note: Thesis submitted with blank cd. Availability: Items available for loan: UVAS Library [Call number: 2343-T] (1).
5.
Genetic Polymorphism Of Prss12 Gene Responsible For Cognitive Dysfunction And Its Homology Analysis With Canine
by Hafsa Amjad (2014-VA-776) | Dr. Muhammad Yasir Zahoor | Dr. Muhammad Imran | Mr. Shahid Abass.
Material type: ; Literary form:
not fiction
Publisher: 2016Dissertation note: Neurotrypsin a multi domain serine protease predominantly expressed in brain is considered to be involved in cognition by the establishment and maintenance of synapses in mammals. Mutations in PRSS12 gene have been reported for cognitive disability in Algerian family.
In present study, DNA of 10 enrolled non-relative cognitive dysfunctioned patients was extracted through organic method. The normal individual samples of siblings and parents of relevant families was also included in this study as control. This amplification exon 7 of PRSS12 was done after designing primer by using Primer3 software. Exons was sequenced by using BigDye Terminator Cycle Sequencing Ready Kit(Perkin Elmer/ABI) and read in automated sequener, ABI Prism model 3730 (Perkin Elmer). No significant mutation was identified in affected individuals.
Computational comparative sequence analysis tools were used for the nucleotide and amino acid sequences to predict the homology in PRSS12 gene among mammals of well-developed cognition. PROSITE domain database search was performed to determine domain organization and Phyre software was used to develop secondary structural features and 3D protein models and ReptroX for multiple sequence alignment of tertiary structures. Using the generated alignments highly conserved regions in primary and secondary structures of neurotrypsin in mammals were identified. Phylogenetic analysis indicated highest similarity of human PRSS12 with non-human primates (chimpanzee, orangutan and monkey) followed by Catecians, Felis, and Canine evolving from the same ancestor. The predicted domain architecture shows the neurotrypsin consisting of kringle domain, four scavenger receptor cysteine-rich
CHAPTER 6
SUMMARY
Summary
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domains and a serine protease domain named trypsin. Whereas mouse consists of only three scavenger receptor cysteine-rich domain. Prediction and comparison of domains in mammals indicated that primates and catecians protein domains have high similarity with humans. Computational analysis by using animal models can aid in evolutionary studies and. understanding the role of neurotrypsin in cognition. Availability: Items available for loan: UVAS Library [Call number: 2498-T] (1).
6.
Identification Of Genetic Variants In The Low Density Lipoprotein Receptor Gene Causing Familial Hypercholesterolemia And Its Sequence Homology With Mus Musculus
by Ameer Hassan (2014-VA-504) | Dr. Wasim Shehzad | Dr. Muhammad Yasir Zahoor | Dr. Muhammad Tayyab.
Material type: ; Literary form:
not fiction
Publisher: 2016Dissertation note: Familial hypercholesterolemia (FH) is caused by mutations in the genes coding for the low-density lipoprotein receptor (LDLR), apolipoprotein B-100, or proprotein convertase subtilisin/kexin type 9 (PCSK9). In this study, a molecular analysis of LDLR gene was performed in 20 unrelated patients from Pakistan. All patients were clinically diagnosed with definite or possible hypercholesterolemia according to a uniform protocol and internationally accepted WHO criteria. Preferable study was made to highlight the Genetic variation in Exon 4 of LDLR gene associated with defective catabolism of cholesterol effecting lipid metabolism which results in Familial Hypercholesterolemia. The extraction of genomic DNA was done from all selected blood samples. By selecting primers they were synthesized and optimized on extracted DNA samples. PCR product was sequenced and aligned. Mutations in the LDLR gene and its sequenced homology with Mus musculus were analyzed. We didn’t found any polymorphisms in the LDLR gene exon 4. So we concluded that there is no association between SNPs and increased levels of cholesterol in Pakistani population. More research should be carried out in Pakistan by increasing the sample size and considering the other regions of LDLR gene. This study will help the early detection and treatment of such cases and may ultimately reduce the incidence of mortality due to myocardial infarction. Apart from diagnosis, we also suggest it will be a potential therapeutic strategy to manage FH. Availability: Items available for loan: UVAS Library [Call number: 2538-T] (1).
7.
Homology & Polymorphism Analysis Of Cc2d1a Gene In Human And Canine For Cognitive Function
by Hafiz Qamar Abbas (2014-VA-214) | Dr. Muhammad Yasir Zahoor | Dr. Wasim Shehzad | Dr. Saadat Ali.
Material type: ; Literary form:
not fiction
Publisher: 2016Dissertation note: Cognitive disability is a group of genetically heterogeneous abnormality that leads to variable degrees of cognition deficits. It has been shown that inherited disorders can be caused by mutations in large number of different genes and there is evidence for the presence of as yet unknown genes in a significant proportion of patients. This disease can affect 1-3% of overall population and higher in consanguineous families. We aimed to identifying the homology and polymorphism of the gene CC2D1A between human and canines. The present research work was carried out in four phases. The first phase was including enrolment of 10 affected non relevant families with disease history and consent was taken on consent forms as approved by IRB, UVAS. Secondly DNA extraction was done by using standard lab protocols. Thirdly amplification of the selected domains of selected gene (CC2D1A) was done through PCR amplification after designing primers of the selected domains. Sequencing of the amplified products has to be done through Sanger method and mutation analysis was conducted for variants We found two new asynonymous mutation one is deletion of c. 1664_1664delA which lead to the change in the normal function of protein (88%) and other is heterozygous mutation c.1921A/T that result in amino acid change from R to W (12%). Whereas homology analysis shows that deletion region is partially conserved as it code different amino acid but some key domains are conserved. This homology shows that deletion in this region can change the protein expression which can relate to unconscious condition like behavioral or mental retardation. This will be helpful in providing genetic counseling services to indigenous population for intellectual disability cases. Availability: Items available for loan: UVAS Library [Call number: 2627-T] (1).
8.
Study On Polymorphism Of Promoter Region Of Bovine Lactoferrin Gene And Its Relation With Mastitis In Nili Ravi Buffalo
by Muhammad Asim (2012-VA-636) | Dr. Sehrish Firyal | Dr. Muhammad Yasir Zahoor | Dr. Muhammad Tayyab.
Material type: ; Literary form:
not fiction
Publisher: 2017Dissertation note: Dairy animals in Pakistan and worldwide are facing most persistent and economically affecting
disease mastitis. Only a healthy buffalo can produce good quality milk of physiologically normal
composition. Mammary gland inflammation due to mastitis badly affects the quantity and quality
of milk and this causes big loss to dairy industry. Even province Punjab bears economic losses of
240 million per annum due to mastitis.
Susceptibility and resistance to mastitis is affected by the variation in immunity genes. Among
immunity genes Lactoferrin (LF) have important role in immune defense system and perform
antibacterial, antiviral and anti-inflammatory function. LF is found in most of body fluids like,
milk, blood, tear, saliva, bile and mucous. Polymorphism in promoter region of Lactoferrin gene
is associated with mastitis susceptibility and resistance. For screening of the mastitis
susceptibility and resistance of dairy buffaloes, LF is a potential candidate gene.
The present study was designed for the identification of polymorphism in LF gene associated
with mastitis. Blood samples from 20 Nili Ravi buffalos having clinical and subclinical mastitis
were selected. Blood samples of normal Nili Ravi buffalos were also collected. DNA was
extracted; specific primers for amplification of LF gene were designed with Primer-3 software
by using already reported sequence on NCBI.
Amplification of LF gene performed by PCR and sequenced the amplicon. A comparative
analysis of sequence result was performed by using NCBI BLAST. BioEdit software was used to
perform multiple sequence alignment. Comparison analysis of LF gene promoter region shows
multiple mutations in in clinical and subclinical as compare to reported sequence (accession no.
EF650854) at NCBI. While normal samples sequence results are similar to reference data. These
results show LF is a candidate gene for mastitis resistance. Availability: Items available for loan: UVAS Library [Call number: 2923-T] (1).
9.
Identification Of Pkhd1 Gene Mutation In Polycystic Kidney Disease And In-Silico Molecular Characterization In Different Mammals
by Taslim Un Nisa (2015-VA-1105) | Dr. Wasim Shehzad | Dr Muhammad Yasir Zahoor | Prof.Dr. Aftab Ahmad Anjum.
Material type: ; Literary form:
not fiction
Publisher: 2017Dissertation note: Fibrocystin is a large, receptor-like protein that is involved in the tubulogenisis and maintenance of duct-lumen architecture of epithelium. Fibrocystin has a combination with the primary cilia of epithelial cell. Renal tubules (small tube) of kidney where urine is formed lined by tiny hair like projection.
Twenty five suspected patient was selected and DNA extracted through organic extraction method from the suspected patient blood. Primers were designed PKHD1gene’s coding sequence located at 6p12.2 in human. The coding region sequenced using the ready mate terminator Sequencing Reaction Kit by Perkin Elmer/ABI and read in an automated sequencer. The allele’s variants have been only reported for Fibrocystin protein in human.
All of the sequences are evaluated by using Chromas and Bioedit software for sequence analysis. The in-silico protein analysis is done for normal and mutated alleles through UCSC and RAPTROX. Homology analysis was also done between human and mammals DNA sequence.
We found mutations which are associated with ARPKD disease and these variants are most common in other population whereas we also found some new variants. There are some reported mutations which we found in our study such as (c3790C>T),(c3891G>T),(c3790C>T). We found three new mutations in PKHD1 gene. The new mutations which we found are (c3681G>A),(c3804C>T),(c3931A>C).These mutations (c3790C>T) and (c3931A>C) in the exon 32 show significant effect on the gene and protein function. Geneticanalysis of PKHD1gene show thatPakistanifamilies have mutations as compared to other population along with some common exonic regions such as exon 32 whichisalsodescribed by others in two different studies.We also analyze the pedigrees of these patients which are consanguineous families and autosomal recessive polycystic disease.
We found total six mutations in this gene including missense/ synonymous mutations. In which, three novel mutations and others are reported mutations. These variations from the results are due to the population and consanguineous families’ pattern.In our study, we also found that Mouse and Chickencan preferably be used as a modal organisms in pathology.This study will also help us in the development of molecular genetic testing for their detection in Pakistani families and population.
Availability: Items available for loan: UVAS Library [Call number: 2941-T] (1).
