1.
Molecular Basis Of Antibiotic Resistanc In E. Coli Isolates From Poultry Drinking Water
by Hira Naseer | Ms. Sehrish Firyal | Prof. Dr. Masroor Ellahi Babar.
Material type: ; Format:
print
; Literary form:
drama
Publisher: 2012Dissertation note: Back Ground:
E. coli is a single-celled organism belonging to the large bacterial family Enterobacteriaceae, the enteric bacteria. Most of the E. coli strains are harmless but there are some serotypes of it that are pathogenic and cause serious food poisoning in human and major economic losses in both chicken and turkeys. Poultry, the second largest industry in Pakistan is supplied by lots of antibiotics like streptomycin, sulfamethoxazole and tetracycline, streptomycin and ampicillin etc, either through feed or water. Use of antibiotics at large scale is resulting in the development of antibiotic resistance in poultry and human.
Hypothesis:
To check the molecular basis of antibiotic resistance in E.coli and to find out the genotypic and phenotypic correlation between resistant E.coli from poultry drinking water.
Methodology/Parameters:
In this study, drinking water samples from poultry water were collected and cultured on MacConkey agar. Standard disk diffusion method will be used to check antibiotic susceptibility. Plasmid DNA was extracted from colonies showing antibiotic resistance by mini-prep protocol. Using universal set of primers, antibiotic resistant genes was amplified and then sequenced. The sequence thus obtained was compared in the database with previously reported sequences of antibiotic resistant gene in E. coli strains.
Statistical Design:
Prevalence of tetA and tetB genes was shown by a Column chart.
Outcomes:
This study helped to find out prevalence of these antibiotic resistance gene in E. coli isolated from poultry drinking water, which are potential threats to human being.
Availability: Items available for loan: UVAS Library [Call number: 1497,T] (1).
2.
Linkage And Mutational Analysis Of Gene Lebercilin (Lca5) In Families With Leber Congenital Amaurosis
by Adeel Ahmad | Prof. Dr. Masroor Ellahi Babar | Dr. Abu Saeed | Mrs. Saeeda Kalsoom.
Material type: ; Format:
print
Publisher: 2012Dissertation note: Leber congenital amaurosis (LCA, MIM #204000) accounts for at least 5% of all retinal dystrophies and approximately 20% of children attending schools for the blind. LCA is the most severe retinal dystrophy causing blindness or severe visual impairment before the age of 1 year. Inheritance is autosomal recessive in most cases. Clinically, LCA is characterized by the presence of four key features, namely severe and early visual loss (usually around the age of 6 weeks), sensory nystagmus, amaurotic pupils, and minimal or absent responses on the electroretinogram (ERG).
A total of five families (LA01-LA05) were enrolled, blood samples were collected and processed for DNA extraction. During linkage and genome scan, single family showed linkage to LCA5 locus. The diagnosis was established in all affected individuals by medical history, funduscopy, and standard ERG. We performed genome-wide linkage analysis for mapping the disease locus in this family.
Congenitally severely reduced visual acuity and nystagmus were reported for all patients. LCA in the family cosegregated with homozygosity for a single nucleotide polymorphism (SNP) haplotype on chromosome 6p14.1. The respective candidate region contained Leber congenital amaurosis 5 (LCA5), a gene previously reported to underlie LCA; subsequently identified a novel truncating mutation in exon 4 of LCA5, c.642delC, in homozygous state in all affected persons of the family LA01. Here, a novel LCA5 mutation causing LCA in a Pakistani family is reported.
Availability: Items available for loan: UVAS Library [Call number: 1518,T] (1).
3.
Identification Of Polymorphism Of Cyp2D6 Gene In Pakistani Patients Of Epilepsy
by Sana Kulsoom | Prof. Dr. Masroor Ellahi Babar | Dr. Ali Raza Awan | Mr. Zahid.
Material type: ; Format:
print
; Literary form:
drama
Publisher: 2011Dissertation note: Epilepsy is a neurological disorder which causes seizures by sudden burst of hyperactivity in the brain. It is a global health problem and 50 million people have epilepsy all over the world. The majority of epilepsy patients can pass a good life if they receive proper treatment. Various types of epilepsy are present in Pakistan but Generalized tonic-clonic seizure (GTCS) is the most frequent type of epilepsy present in Pakistani patients. GTCS is a type of seizers involving the entire brain. It is also called a grand mal seizure. CYP2D6 is a gene associated with GTCS.
CYP2D6 is a 4.6 kb gene which encodes the protein cytochrome P450, a metabolizing enzyme. CYP2D6 is a highly polymorphic gene with 09 exons. Patient data and blood samples of different epilepsy patient were collected. DNA was isolated by Organic method. PCR amplification was performed for CYP2D6 gene (exon 6-9) and sequencing was performed on ABI 3130 XL Genetic analyzer and the results were analyzed. In this way the mutations, 2850 C>T in exon 6 of CYP2D6 gene have been caricaturized in Pakistani patients of GTCS encoding Cyctine in place of Argine at 296 in CYP2D6 enzyme. This change may be associated with GTCS in Pakistani Patients. Above study will help medical scientists in Molecular diagnosis, Genetic counseling and Gene therapy.
Availability: Items available for loan: UVAS Library [Call number: 1519,T] (1).
4.
Designing Of Oligo Pool All For The Selection Of Superior Dairy Animals In Pakistan
by Kamran Abbas | Prof. Dr. Masroor Ellahi Babar | Dr. Aftab | Mr. Muhammad Asif.
Material type: ; Format:
print
Publisher: 2011Dissertation note: Livestock has an important role in an agriculture based country like Pakistan with a large number of dairy animals. However the average daily milk yield of dairy animals is very low. There is need to improve milk yield by the selection of superior dairy animals using latest genomic selection procedures. Selection of superior animals on the basis of genetic markers has a tremendous potential for breed improvement across the globe. Substantial advances have been made over the past decades through the application of molecular genetics used in industry programs for several decades and is growing, the extent of use has not lived up to initial expectations. Most applications to date have been integrated in existing programs on temporary basis.
Among various molecular markers the Single Nucleotide Polymorphism (SNP) is one of the major genetic marker used worldwide. Through SNP genotyping selection of phenotypic superior animals can be done. There are many techniques used for SNP genotyping but the most advanced technique is Veracode GoldenGate Assay by Illumina. Illumina's VeraCode technology with the BeadXpress (BX) Reader is ideal for high-throughput small to mid-scale genotyping studies and SNP validation. BX leverages the power of digital holographic codes and the robust GoldenGate Genotyping Assay to provide a detection method for multiplex assays requiring high precision, accuracy, and speed. A custom assay of 48, 96, 144,192 and up to 384-SNPs OPA (Oligos Pool All) is designed using Illumina's Assay Design Tool and manufactured by Illumina.
As a first step for designing of Veracode GoldenGate Assay the development of Oligo Pool All (OPA) is necessary. The OPA was designed by using the genes for milk production, growth, fertility, health and other performance traits. The SNP's in these genes was searched from different gene banks and after proper arrangement the files were sent to Illumina for scoring. After scoring the OPA was finalized for the Veracode GoldenGate Assay for the selection of superior dairy animals in the country using the highly robust BeadXpress technology. The development of OPA for the selection of superior dairy animals was done for the very first of its kind based on modern technology, Veracode GoldenGate Assay in Pakistan. This will greatly help the livestock and dairy development departments, livestock owners, breeders, forensic agencies and researchers to use this unique panel of molecular markers for the selection of superior animals on the basis of marker assisted selection.
Availability: Items available for loan: UVAS Library [Call number: 1528,T] (1).
5.
Identification Of Single Nucleotide Potymorphisms In Atp Synthase F0 Subunit 6 And Synthase 8 Genes
by Rizwan Ali | Mr.Tanveer Hussain | Prof. Dr. Masroor Ellahi Babar.
Material type: ; Format:
print
; Literary form:
not fiction
Publisher: 2013Dissertation note: Pakistan is a fertile country regarding Animal Genetic Resource (AnGR), which have more than 1 million camel population belonging to 21 breeds of one humped camel i.e. Camelus dromedarius. Pakistan is the third major camel raising county in the world after Somalia and Sudan. All camel breeds of Pakistan has unique phenotypic traits, however, genetic data is inadequate for their evolutionary and phylogentic study. So to explore and use the genetic potential of dromedary camel, this research work was done.
ATP 6 and ATP 8 genes
ATP synthase is an enzyme in which oxidative phosphorylation occurs in prokaryotic and eukaryotic cells. The objective of this research was to examine the sequence of ATP 6 and ATP 8 genes in eight camel breeds of Pakistan (Marceeha, Barela, Kachhi, Pahari, Thari, Watni, Kharani, and mix-bred) to find SNPs and to see phylogenetic relationship among them as well as their position while considering already reported camel breeds from all over the world along with other mammalian species in GenBank NCBI.
A total of 79 blood samples from eight selected camel breeds of Pakistan, were collected from different government livestock farms and private owners in respective breeding areas of each breed by travelling throughout the country. DNA was extracted and quantified using standard protocols. Specific primers for the selected ATP 6 and ATP 8 genes was designed using primer fox software from reported sequences from the NCBI GenBank (Accession number, JN632608). Primers were optimized and PCR amplification was done on all camel DNA samples. Then all PCR products were processed for sequencing using ABI Prism Genetic Analyzer 3130 xl following standard protocols.
Sequence and Phylogenetic analyses
All sequences were aligned and analyzed using blast2sequence available on NCBI and CodonCode Aligner. Twenty nine Single Nucleotide Polymorphisms (SNPs) were identified from the aligned 842 bp coding region of ATP 6 and ATP 8 genes. Consensus sequences for eight breeds of Pakistan were used for construction of phylogenetic tree (Neighbor-Joining method) among them using MEGA5.1 software package. The tree indicated high genetic similarity between Mareecha and Pahari camel breeds of Punjab. The Thari, Watni, Kharani and Kachhi breeds of Balochistan province grouped close to each other indicating genetic relatedness among them. Further the phylogenetic trees were constructed for the comparison of Pakistani camel sequences with reported sequences of other camel breeds of the world and different species/ mammals available on GenBank, NCBI. The UPGMA Phylogenetic tree showed the high similarity of all Pakistani camels with Arabian dromedarius camel confirming the dromedarius genetic architecture of Pakistani camels. The two humped (Camelus bactrianus) grouped separately like llama, alpaca (the biological cousins of camel), However both types of camel and llamas were clustered together in one clade while all other mammalian species were grouped together in another clade. However cattle, yak and American bison grouped together, buffalo remained close to cattle. Sheep and goat were also grouped together. Conclusively the phylogenetic tree based on ATP 6 and ATP 8 genes reconfirmed not only the genetic position of Pakistani camel but also the biological/ taxonomic classification of other mammals and species.
Significance of research work
This work provided the genetic information on eight selected camel breeds of Pakistan and contributed in the existing information in Animal Genetic Resources of Pakistan and helped in exploring the rich genetic structure of our local camel breeds for their effective and meaningful conservation for future generations of Pakistan. This study was just an initial step to explore the genetic worth of Pakistani camel and data produced may act as base line information for other researcher planning to do more research work on camel to get maximum benefits from genetic potential of camel with its unique characteristics. This may also be helpful in designing proper breeding and conservation policies for camel in Pakistan.
Availability: Items available for loan: UVAS Library [Call number: 1570,T] (1).
6.
Develoopment Of A Reliable Microsatellites Maarkers Panel For Parentage Analysis In Cattle Breeds Of Pakistan and Its Validatio Through Cytochrome B Gene Sequencing
by Tanveer Hussain | Prof. Dr. Masroor Ellahi Babar | Dr. Ahmad Ali | Dr. Muhammad Wasim.
Material type: ; Format:
print
Publisher: 2013Dissertation note: Pakistan posseses enormous Animal Genetic Resource (AnGR) with 36.9 millions of cattle population. The data on genetic fabric of these breed is yet to be documented for their genetic characterization and identification. This work reports first country wide microsatellite markers and cytochrome b gene based genetic characterization of 10 famous cattle breeds of Pakistan. A total of 352 blood samples from unrelated and phenotypically representative of ten native cattle breeds including Bos indicus; Sahiwal, Cholistani, Red Sindhi, Tharparker, Dhanni, Dajal, Lohai, Bhagnari, Achai and Bos indicus x Bos taurus; Nari Master, and an exotic Bos taurus; Holstein Friesian breeds were collected from their respective home tracts, institutional herds and private livestock farms located throughtout the country. These samples were subject to DNA extraction using inorganic method caliberated to same concentration in Molecular Biology and Genomics Laboratory of the Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore Pakistan. A total of 21 microsatellite markers recommended by the programme for the global management of genetic resources (MoDAD) for breed characterization of Food and Agriculture Organization (FAO) of the United Nations and International Society for Animal Genetics (ISAG) were applied. Multiplex PCR were optimized for amplification and were genotyped using ABI Genetic Analyzer 3130 xl using LIZ as size standard. Genotyping results were analyzed using POPGENE and Arlequin ver 3.5 software. The observed and effective number of alleles ranged from 10 (INRA32) to 43 (TGLA126) and 2.3574 (CSSM66) to 15.0019 (BM6526) respectively in all breeds? The observed and expected heterozygosity estimates ranged from 0.0638 (INRA32) to 0.7101 (BM2113) and 0.6510 (INRA32) to 0.9347 (BM6526) respectively in the experimental samples. Mean values for observed and expected heterozygosity was 0.4943 ± 0.1647 and 0.8164 ± 0.0930 respectively. Mean values for Fis, Fit and Fst in all cattle breeds were calculated as 0.2819, 0.3864 and 0.1456 respectively. Average polymorphic information content (PIC) of all microsatellite loci was 0.81 indicating a high degree of informativeness of all microsatellite markers used. It implies that the same set of markers is equally good and could reliably be used for parentage confirmation in Pakistani cattle breeds. The data produced, also showed least degree of genetic difference between Red Sindhi and Tharparker breeds. This may due to mixing of the two breeds for being in close proximity of their home tracts.
Fragment mitochondrial cytochrome b gene was also amplified using specific primers through PCR of 130 individuals representing all selected breeds and sequencing was done using ABI Genetic Analyzer 3130 xl. The sequences were aligned and analyzed with CodonCode Alligner 4.0.4 software. The analysis revealed highly degree of sequence conservation in all the Pakistani cattle while documenting changes in only 9 nucleotides from 26 individuals whereas multiple nucleotide changes in 5 locations were shown by more than one individual in the data presented. One polymorphic site was found in nucleotide 318 (T?C) in several breeds of indicine cattle while 2 Lohani and 5 Nari Master individuals showed nucleotide changes specific to taurine cattle. Of all the changes found, only three of them caused changes in the amino acid sequence. The UPGMA tree using MEGA 5.1 showed a clear differentiation between taurine and indicine cattle, except for Nari Master Pakistani cattle showing mitochondrial taurine sequences because it's a cross between Bhagnari (Bos indicus) and Australian Draught Master (Bos taurrus). The estimates of divergence among breeds were also low for most breed pairs, except for Nari Master and Dhanni whereas the overall divergence within Bos indicus or within Bos taurus were also very low (0.002 and 0.003, respectively) but the differences between Bos indicus and Bos taurus were significantly higher (0.014) as should be the case.
These results of microsatellite markers have produced a set of information that can be recommended as a reliable marker panel for studies on genetic diversity analysis, parentage confirmation. The cytochrome b data on the other hand not only substantiated genetic diversity analyses but it also proved to be equally good for comparative Phylogenetic analysis of Pakistani cattle breeds and exotic breeds. This work provides most authenticated data and adds a great deal, to already existing information on Pakistani AnGR. This information coupled with prospective data using next generation genetic technologies will assist designing breed improvement focused breeding policies and conservation activities in future.
Availability: Items available for loan: UVAS Library [Call number: 1597,T] (1).
7.
Identification Of Polymorphisms In 6Th & 7Th Exons Of "Parkin Gene" And Their Relationship With Parkinson'S Disease.
by Sadaf Niaz | Prof. Dr. Masroor Ellahi Babar | Dr. Abu Saeed Hashmi | Dr. Aif Nadeem.
Material type: ; Format:
print
Publisher: 2013Dissertation note: Abstract Availability: Items available for loan: UVAS Library [Call number: 1638,T] (1).
8.
Mutational Analysis Of Parkin Gene And Its Association Eith Parkinson'S Disease
by Misbah Hussain | Prof. Dr. Masroor Ellahi Babar | Miss. Asma | Miss. Saeeda Kalsoom.
Material type: ; Format:
print
; Literary form:
drama
Publisher: 2013Dissertation note: Parkinson's disease (PD) is a neurodegenerative disease in which dopamine neurons are lost in sabstantia nigra. It is second most prevalent disorder after Alzheimer's disease. PD is also referred as movement disorder because its main characteristics are movement related like rigidity, slowness of movement and resting tremors which are caused by the loss of dopamine in putamen specially its caudal portion
Lots of work has been done on PD but still actual mechanism of its progression is unknown. Scientists have declared genetic mutations, oxidative stress, pesticide exposure, high caloric food etc as causative agents for PD. There are 6 genes which are responsible for PD. Mutations in the parkin gene produce Early Onset Parkinson's disease (EOPD) in 50-60% of patients. parkin gene encodes for Parkin protein which consist of 4 domains (UBL, RING1, IBR, RING2). UBL domain is involved in the interaction with substrates. While the other 3 domains helps in interaction with E2 Ubiquitin- conjugating enzyme.
Most frequent mutations in this gene are the point mutations. 2nd exon of parkin gene is considered as one of the hotspot for mutations. First three exons code for Ubiquitin-like (UBL) domain, which help in the attachment with substrates like Rpn10 subunit of 26S proteasome. Rpn10 subunit of 26S proteasome binds with Arginine at position 42 located in UBL domain of parkin. This 26S proteasome degrade the unfolded proteins into short peptides of 7-8 amino acids in length, which are then further degraded in shorter fragments which are then used in the formation of new proteins.
In current study, I have done mutational analysis of parkin gene and found one very important noval point mutation which is a transition C'T mutation in UBL domain, which results in the amino acid substitution Arginine' Cysteine at position 42 (location where Rpn10 subunit of 26S proteasome binds). Arginine and Cysteine are biochemically different in nature and in the classification based on R group they belongs to different groups. Arginine is a polar positive amino acid while Cysteine is polar uncharged and contain sulfur molecule. So, this amino acid change could result in the decreased or no attachment of 26S proteasome (catalyzes protein degradation) via its Rpn10 subunit which selectively binds with the poly-ubiquitin chain of damaged proteins.
So, this decreased attachment inhibits the degradation of misfolded and defected protein in the cytosol. In result of this inhibition these defected proteins will start gathering and form aggregates within the cytosol of cell it will eventually decrease cell's function and cell will start dying.
Availability: Items available for loan: UVAS Library [Call number: 1643,T] (1).
9.
Molecular Charaterization Of Ampk Gene Of Pakistan Buffalo
by Waqas Ahmed Khan | Prof. Dr. Masroor Ellahi Babar | Dr. Aftab | Dr. Ali Raza Awan.
Material type: ; Format:
print
; Literary form:
not fiction
Publisher: 2011Dissertation note: Pakistan is an agriculture country and its economy is mainly dependent on agriculture, agriculture products. Livestock has been playing an important role in the economy of the country. Livestock sector contributed approximately 51.8 percent of the agriculture value added and 11.3 percent to national GDP. Buffalo which is known as black gold of Pakistan is famous for its largest milk production in the world. A better understanding of the genetic control of energy metabolism in farm animals can have far-reaching implications for molecular breeding programs. It can allow the implementation of knowledge-based breeding to increase feed efficiency and to improve meat quality. In addition, because of the high degree of evolutionary conservation of these genes, the information gained about the genetic control of animal nutrition can be extrapolated back to questions about human nutritional genomics and disease. This study was performed to discover the single nucleotide polymorphism at AMP-activated protein kinase (AMPK) gene in Nilli Ravi and Kundi Buffalo and their possible association with milk production. As AMPK is a sensor of energy metabolism so genetic variations in AMPK gene may also have effect the feed utilizing efficiency of animals. Buffalo is popular for utilizing low quality roughages in a better way. Buffaloes are popular in the world for high fat content and low cholesterol content as compare to cattle. A total of 128 single nucleotide polymorphisms were discovered at AMPK gene in Nilli-Ravi and Kundi Buffalo. Out of which 10 are in exonic region and 118 are in Intronic region. Most of the SNPs are Intronic it also shows that AMPK is highly conserved as it has been shown by many studies. The Intronic SNPs may have role in regulation of AMPK gene. Forty-six SNPs were discovered in Intronic region of A1 subunit of AMPK gene. Out of these 46 SNPs. Forty-four SNPs are same in both Nilli-Ravi&Kundi buffalo.
Two SNPs found at position 11908 and 12217 was present only in Kundi buffalo. These two SNPs can be used for breed characterization of Nilli-Ravi&Kundi buffalo. The numbers of SNPs discovered in exonic region are 6. These all SNPs are non-synonymous mutations and changes amino acids at position 23333 from Histidine>Tyrosine, at 23387 from Glutamic acid>Lysine, at 23402 from Valine>Isoleucine, at 23426 from Ser>Pro, at 23489 from Stop codon>Arg and at 23612 from Ala>Thr. Forty SNPs were discovered in Intronic region of A2 subunit of AMPK gene. Out of these 43 SNPs 28 are same in both Nilli-Ravi & Kundi buffalo. SNPs at positions 71371, 71382, 71383, 71396, 71558, 42736, 42766, 42881, 41661, 41900 and 42021 are only present in Kundi buffalo while SNPs at position 70900, 71613, 42935 and 42944 are present only in Nilli-Ravi buffalo. These SNPs can also be used for breed characterization of Nilli-Ravi and Kundi buffalo. The B1 subunit of AMPK gene has 21 SNPs in Intronic region, which is common, both in Nilli-Ravi and Kundi buffalo. These polymorphisms may have role in regulation of AMPK gene. The SNPs found in exonic region are 3 which are all non-synonymous mutations and changes amino acids at position 4362 from Histidine>Tyrosine and at positions 8193, 8195 from Glycine>Serine. All exonic SNPs are non-synonymous mutations, which show that it will change the function of protein and might be associated with milk production and feeding efficiency in Nilli-Ravi & Kundi buffalo. This study is an example of candidate gene approach to find some novel variations at population level. It is the first study conducted for Molecular Characterization of AMPK gene in Buffalo. The only way to associate these polymorphisms to the trait under consideration (energy metabolism) by back tracing the sampling groups. This study is first in finding some molecular markers for energy metabolism in Nilli-Ravi and Kundi buffalo that can be used for future selection and breeding programs. More the population will be diversified for the trait and showing trends of heterozygosity, better will be the chances of selection of animals with suitable genetic makeup.
Availability: Items available for loan: UVAS Library [Call number: 1796,T] (1).
10.
Molecular Genetic Study Of Oculocutaneous Albinism In Pakistani Population
by Sajjad ali shah | Prof. Dr. Masroor ellahi babar | Dr. Asif nadeem | Dr. Muhammad Tayyeb.
Material type: ; Format:
print
Publisher: 2014Dissertation note: Abstract Availability: Items available for loan: UVAS Library [Call number: 2080,T] (1).
11.
Study Of Candidate Genes Involved In Milk Production Traits For Identification Of Probable Biomarkers In Nili-Ravi Buffalo
by Maryam Javed | Prof. Dr. Masroor Ellahi Babar | Dr. Abu Saeed | Dr. Muhammad Wasim.
Material type: ; Format:
print
; Literary form:
not fiction
Publisher: 2014Dissertation note: Abstract Availability: Items available for loan: UVAS Library [Call number: 2120,T] (1).
12.
Lvistmsa: Interactive Visual Tools For Multiple Sequence Alignments
by Muhammad Tariq Pervez | Dr. Asif Nadeem | Prof. Dr. Masroor Ellahi Babar.
Material type: ; Format:
print
; Literary form:
not fiction
Publisher: 2014Dissertation note: Abstract Availability: Items available for loan: UVAS Library [Call number: 2140,T] (1).
