1.
Polymorphisms Of Bovine Tumor Necrosis Factor Alpha Gene And Its Association With Mastitis In Sahiwal Cows
by Huma Sattar (2013-VA-03) | Dr. Sehrish Firyal | Dr. Ali Raza Awan | Dr. Muhammad Tayyab.
Material type: ; Literary form:
not fiction
Publisher: 2015Dissertation note: Mastitis is one of the shocking maladies of milch animals causing high production losses to livestock industry of Pakistan (Kenyanjui et al. 2011). It is an inflammatory condition of udder; represent a major problem in dairy cow management. It is one of the most common and frequent disease of dairy industry. Producers suffer a huge loss due to veterinary treatment costs and necessary culling of the infected animals. It negatively affects the milk production, quality of milk, and farm economics (Fourichon et al. 2005). Increasing the disease resistance among dairy cattle is therefore desirable because without controlling mastitis, the national goals of developing dairy farming on commercial and scientific lines and production of wholesome milk which conforms to the standards of WTO Accord would remain elusive.
Mastitis is inflammation of udder that caused by physiological and metabolical changes (Schalm and Noorlander 1957). There are two main types of mastitis; clinical mastitis (characterized by classical symptoms i.e., swelling of udder, redness, clumps and clots in milk etc) and sub-clinical mastitis (not show any symptoms, Milk appear normal, udder appear normal) (Schrick et al. 2001). Mastitis is ranked as a top disease of dairy herds (Rinaldi et al. 2010). This mammary gland infection caused by pathogenic micro organisms such as Staphylococcus aureus, Streptococcus uberis, and Esherichia coli in the mammary gland (Heringstad et al. 2000).
India, China and United States are the larger producer of milk and Pakistan is on forth number in milk yield. Pakistan almost produces 36.5 million tons of milk yeild per year (Cady et al. 1983).The Sahiwal breed is well known among for its superior dairy qualities (Barker et al. 1998). Both cross and pure breed Sahiwal cows have high milk production rate (Khan et al. 2013).
It is very difficult to comprehend this disease because numerous environmental and genetic factors are involved in the origin and development of mastitis (Bradley 2002; Carvajal et al. 2013). Susceptibility and resistance to mastitis is a complex trait influenced by genetic variation of animals. Among these variations, the polymorphisms in immunity genes are principal key factors in defensive mechanism of mammary gland (Ibeagha-Awemu et al. 2008).
The mammary gland tissue is protected by immune system by two defense system; innate and acquired immunity. Innate immunity response by the host is a quick response of bacterial defense system (Mesquita et al. 2012). Innate system is a rapid and effective mechanism that activated on recognition of antigen (Akira et al. 2006). Innate immune system is activated when specific pattern recognition receptors (PRR) that are present on the surfaces which are attach to the specific pathogen (Shuster et al. 1996). PRR are presnt on leucocytes in milk and on the epithelial cells lining of udder. It is reported that T- lymphocyte subset i.e., CD4+, CD8+ and ɤδT are present in infected bovine mammary glands. (Goldammer et al. 2004; Strandberg et al. 2005).
Innate defense (nonspecific) of the mammary gland is stimulated by the physical barrier such as teat end, natural killer (NK) cells, neutrophils, macrophages and certain other soluble factors. The teat cannals are considering the main line of defense. Microorganisms enter from teat canal in milk. The main roles of teat sphincter muscles are to remain orifice close so that bacteria cannot enter. This teat canal also lined with keratin, whose estrified and non estified fatty acid function as bacteriostatics that provide protection and play role to eliminate bacteria causing mastitis (Oviedo-Boyso et al. 2007).
If a pathogen is not eliminated by the physical barrier, the acquired immune system is triggered. In comparison, this system is much faster than other immune response. The memory response is significantly stronger, long durable and more efficient to kill the pathogen. The acquired immune system (memory response) have ability to differentiate self or nonself cells and produce antibodies only against antigens through membrane bound protein called major histocompatibility complex (MHC) molecules. Specific immune system activate only when antigens bind with an MHC that is present on the surface of certain cells, this process is referred as antigen presentation. Recognition of pathogenic factors for elimination is mediated by macrophages, several lymphoid, and immunoglobulins (Ig) or antibodies (Sordillo and Streicher 2002).
The most acute responding macrophages and T-cell cytokines are TNF-α, LTF, IL1, IL6, IL8, and IFN-ɤ present in intramammary infection in cows. These genes play important role in improvement of immunity to mastitis (Burton and Erskine 2003).
Tumor necrosis factor alpha is main pro-inflammatory adipokine that is part of systematic immune defense. The main function of TNF-α gene is responsible for proliferation, differentiation and activity of many immune system cells; B lymphocytes, NK (natural killer). It also induces the production and release of many other cytokines (Wojdak Maksymiec et al. 2013) and also enhances the chemotactic and phagocytic effects of immune response. TNF-α gene contains four exons and three introns that are present on chromosome BTA23q22 (Bannerman 2009; Moyes et al. 2009).
TNF-α is a member of a group of cytokines that stimulate the specific immune system. TNF consist of 212 amino acid arranged in stable homotrimers (Kriegler et al. 1988; Tang et al. 1996). The 17-kilodalton (kDa) TNF protomers are composed of two β-pleated sheets and β-strands, joined together antiparallel (Tang et al. 1996).
TNF-α is a component of natural protection systems of humans and animals. Milk gives nourishment and disease resistance to the new born. Various cellular and soluble immune components are important for protecting the mammary gland from infectious diseases like mastitis. Mastitis affects one third of all dairy cows and cost the dairy industry about 2 million dollars annually (National Mastitis Council (1996). Dairy cattle are especially susceptible to mastitis due to diminished mammary gland defense mechanisms (Sordillo and Streicher 2002).
TNF-α is not only produced by activation of macrophages, but also other cell types such as CD4+ lymphocytes, NK cells, neutrophils, mast cells, eosinophils, and neurons. Large amounts of TNF are released in response to lipopolysaccharide, other bacterial products, and Interleukin-1 (IL-1).TNF-α stimulates the proliferation, differentiation and activity of many immune system cells; B lymphocytes, NK (natural killer). TNF-α induces the release of many other cytokines (Wojdak-Maksymiec and Mikolajczyk 2012). TNF-α also enhance the chemotactic and phagocytic effects of immune response.
. The present study is designed to determine the genetic polymorphism in exon 4 of TNF-α gene of mastitic cows and its association resistance and susceptibility towards mastitis.
Availability: Items available for loan: UVAS Library [Call number: 2224-T] (1).
2.
DNA Based Characterization of Xylanase Gene From Hyperthermophilic Archeon
by Saima Zulfiqar (2012-VA-539) | Dr. Muhammad Tayyab | Dr. Faiza Masood | Dr.Sehrish Firyal.
Material type: ; Literary form:
not fiction
Publisher: 2014Dissertation note: Blank CD Availability: Items available for loan: UVAS Library [Call number: 2233-T] (1).
3.
Sequence Analysis Of Mitochondrial Atpase 8/6 Gene Variants In Equine
by Kashif Hameed Anjum (2012-VA-905) | Dr. Asif Nadeem | Mr.Maryam Javed | Dr. Muhammad Tayyab.
Material type: ; Literary form:
not fiction
Publisher: 2014Dissertation note: Human has been using horses for doing different jobs like transportation, hunts, carrying loads, warfare and sports (Zhang et al. 2012). In Pakistan, horses and donkeys are mostly used for transportation whilehorses are also used for racing and playing games like polo.There are two main types of horses:Equuscaballusare domesticated horses and Equusferus are the wild horses. There are more than 300 breeds of horses in the world today (Barbara and Dafydd, 2007). The horse population is estimated as 0.32 million and has been decreasing over the years in Pakistan. Main breeds of horses that are found all over the Pakistan are Kajlan, Kakka, Balochi, Morna, Shien, Anmol, Makra, Pak-thoroughbred,Heerzaiand Waziri (Khan, 2004).
Seventy percent of the population earns living from the land. Agriculture contributes nearly 21% to gross domestic product and generates 43% of all jobs. Over 30 million people in rural areas derive their livelihood from livestock production. The number of impoverished communities moving from the country to find work in Pakistan’s towns and cities is rising. Many of these people rely on working equine animals to earn a living.
Nuclear and mitochondrial genomes are frequently used in animal genetic research. Nuclear genomeis generally a huge and complicated molecule and is not well studied in many species. However mitochondrial DNA being small sized and having high mutation rate is used frequently for the purpose of genetic research (Stanley et al. 1994). Characteristic of having fast evolution rate as compared to nuclear DNA makes mitochondrial genes a good tool for genetic studies (Avise, 1994).
Several studies have investigated the genetic relationship among horse and donkey breeds using mitochondrial sequences as a marker for breed characterization and phylogenetic. Each mitochondrion contains its own circular DNA, replication, transcription and translation machinery and serves as semi-autonomous organelle. Mitochondria perform so many important functions in our body like metabolism(oxidative phosphorylation), apoptosis and aging(Weinberg, 2007).
The advent ofpolymerase chain reaction and direct sequencing techniques with the use of mtDNA as a phylogenetic marker has been extended to much greater levels of phylogenetic inclusiveness (Zardoya and Meyer,1996). The special features of mtDNAi-e,lack of introns, maternal inheritance, absence of recombination events and haploidy have made it the most common type of sequence information used to estimate phylogenies among both closely and distantly related texa(Meyer, 1993).
Four of the five mitochondrial respiratory chain complexes, namely C1, C3, C4 and C5 (ATP synthase) contain subunits encoded by mitochondrial DNA (Kadenbach, 2012). ATP synthase (Complex5) functions to make ATP that is used by the cell (Von et al. 2009). ATP synthasecomprisesan integral membrane cylindrical, the F0 particle and a peripheral matrix-facing F1 particle, the catalytic ATP synthase domain (Boyer, 1997). All aerobically respiring organisms possess ATP synthase enzymes and are located inthe cell membrane in prokaryotes, the mitochondrial inner membrane in eukaryotes and the chloroplast thylakoid membrane (Ackerman and Tzagoloff, 2005). This enzyme is responsible for the final step of oxidative phosphorylation. The protons move down their concentration gradient from inter membrane space to matrix through F0 particle while F1particleuses the energy provided by influx of these protons and converts ADP molecule into ATP. ATPase 6 and ATPase 8 proteins are components of F0 particle where they play direct role in maintaining the structure and function of ATP synthase (complex 5). All five subunits of F1 and most of the F0 subunits are nuclear encoded(Collinson et al. 1996). Only two proteins i-e, ATPase 6 and ATPase 8 are encoded by mtDNA (Boyer, 1993).
The present study is designed to investigate the diversity and phylogenetic analysis of Thoroughbred Pakistani horse and donkey breeds on the basis of ATPase 6 and ATPase 8 genes.
Availability: Items available for loan: UVAS Library [Call number: 2236-T] (1).
4.
DNA Based Characterization Of Arginase Gene From Geobacillus Sp. SBS-4s
by Raabia Bibi (2012-VA-537) | Dr. Muhammad Tayyab | Dr. Abu Saeed Hashmi | Dr. Muhammad Imran.
Material type: ; Literary form:
not fiction
Publisher: 2015Dissertation note: Geobacillus is a group gram-positive, rod-shaped, aerobic, endospore-forming and obligate thermophilic bacteria, isolated from the diverse habitats, hot springs, thermal environments, terrestrial soils, deep sea sediments (Zeigler, 2014), petroleum and soil of desserts (Claus and Berkeley 1986). It grows at a wide range of temperature from 45 to 75°C and pH ranging from 6.2 to 7.8 (Nazina et al. 2001). These bacteria survives at higher temperature where most of other living species fail to survive (Claus and Berkeley 1986). Geobacillus have achieved a significant population with a worldwide distribution, probably in large part due to adaptive features of their spores (Zeigler, 2014). These can be found singly or in short chains and motile by means of peritrichous flagella and is capable of secreting a wide variety of extracellular and intracellular enzymes i.e amylase, lipase, carboxypeptidase, cellulase, xylanase, protease and galactosidase (Fogarth et al. 1974; Obeidat et al. 2012).
Geobacillus sp. SBS-4S was isolated from hot spring located in Gilgit, Northern areas of Pakistan. It was found to be an aerobic, gram-positive and rod-shaped bacteria having ability to hydrolyze a variety of sugars, carboxylic acids and hydrocarbons at elevated temperatures from 45 to 75°C. SBS-4S was found to be involved in the production of various intra and extra cellular enzymes (Tayyab et al. 2011).
Arginase is the enzyme responsible for the degradation of arginine resulting in the production of urea and ornithine (Kaur et al. 2009). It is accomplished by the cleaving of the guanidinium group from arginine which yields urea (Turras et al. 2008). Arginase present in many mammals (Homo sapiens), Bacilli (cyanobacteria), protozoa (Entamoeba histolytica), yeast (Saccharomyces cerevisiae), fungi (Neurospora crassa) and plants (Lathyrus sativus) etc (Kaur et al. 2009). The crystal structure of arginases have been determined by X ray crystallographic studies. This is a manganese dependent enzyme. The enzyme shows its activity through the metal ion. Metal ion is actively responsible for the incorporation of water molecules essential for the activity of the enzyme. A second proposed mechanism, based on electron paramagnetic resonance (EPR) studies postulates direct coordination of the substrate to manganese and disruption of the aqua bridge. Arginases are homo-oligomers, with a typical subunit mass of 32 to 36 kDa (Bewley et al. 1999).
There are two types of arginases, arginase-I and arginase-II, located in the cytoplasm and mitochondria, respectively. The principal ureagenic enzyme activity arginase-I is most abundant in normal mammalian liver and acts in coordination with the other enzymes of the urea cycle to sequester and eliminate excess nitrogen from the body. The second form arginase-II can be found in many organs, with the highest levels found in kidney and prostate where as lower levels in macrophages and lactating mammary glands (Iyer et al. 2002).
Important role of arginase in controlling the cellular levels of arginine and ornithine, which are required for various critical metabolic processes, including protein synthesis and the production of creatine, polyamines, proline and nitric oxide (NO). Type II arginase is found in a variety of different tissues and have a key role in the regulation of urea cycle arginine metabolism by regulating levels of arginine in the cell (Bewley et al. 1999). The enzyme arginase plays key role in the pathogenesis of pulmonary disorders such as asthma through dysregulation of L-arginine metabolism and modulation of nitric oxide (NO) homeostasis and it also play role in the development of chronic airway remodeling through formation of ornithine with downstream production of polyamines and L-proline, which are involved in processes of cellular proliferation and collagen deposition (Benson et al. 2011). Arginase involved in tissue repair processes by the synthesis of L-ornithine, which is the precursor of polyamines and proline that are involved in cell proliferation and collagen synthesis (Maarsingh et al. 2009).
Genetically engineered arginase as fusion protein with prolonged half-life and increased efficacy are used to treat different tumor lines that inhibit cell proliferation and impaired cellular migration in vitro and in vivo (Li et al. 2013). This is a arginine-degrading and ornithine producing enzyme and is used to treat arginine-dependent cancers (Yu et al. 2013). Chemically modified arginase-II has been employed for the treatment of taper liver tumor and L5178Y murine leukemia (Kaur et al. 2009). The enzyme was cloned and expressed in E. coli and subsequently conjugated to polyethylene glycol to increase the circulating half-life and decrease the immunogenicity of the recombinant mycoplasma enzyme. The human hepatocellular carcinoma, melanoma cell lines and tissue samples do not express argininosuccinate synthetase (ASS), making them auxotrophic for arginine and thus reasonable candidates for arginine deprivation (Yang et al. 2010).
Arginase is induced in murine myeloid cells mainly by T-helper 2 cells cytokines and inflammatory agents and participates in a variety of inflammatory diseases by down-regulation of nitric oxide synthesis, induction of fibrosis and tissue regeneration. In humans, arginase I is constitutively expressed in polymorphonuclear neutrophils and is liberated during inflammation. Myeloid cell arginase-mediated L-arginine depletion profoundly suppresses T cell immune responses and this is a fundamental mechanism of inflammation-associated immunosuppression. Pharmacological interference with L-arginine metabolism is a novel promising strategy in the treatment of cancer, autoimmunity or unwanted immune deviation (Munder, 2009).
Arginase has very important role in nitrogen fixation and fruit ripening (Yu et al. 2013). Putrescine (1,4-butanediamine) is the product obtained from arginine with the highest market value and it is used as an intermediate in a large number of industries, including the pharmaceutical industry, agrochemical industry and textile industry (Turras et al. 2008).
Arginine is a semi-essential amino acid and is the precursor for the formation of nitric oxide (NO) by nitric oxide synthases (Getz and Reardon, 2006). One of the major functions of arginine within the body is as an intermediate in the urea cycle. In the cytosol of hepatocytes, arginase-I removes the guanidine group from arginine to produce urea and ornithine. Urea is then transported from the hepatocyte into the bloodstream and ornithine is used to regenerate arginine within the hepatocyte. Arginine deficiency causes several disorder like, hyper cholesterolemia, hypertension, diabetes mellitus, kidney failure, hyper homo-cysteinemia, smoking, and aging (Alvares et al. 2012). Arginine is used to modulate the cellular immune response during infection. The generation of nitric oxide from arginine is responsible for efficient immune response (Das et al. 2010).
Arginine is synthesised in humans and other mammals from citrulline in two steps through the urea cycle enzymes, argininosuccinate synthetase (ASS) and argininosuccinate lyase (ASL). ASS catalyses the conversion of citrulline and aspartic acid to argininosuccinate, which is then converted to arginine and fumaric acid by ASL (Yang et al. 2010).
Ararinase play important role in conversion of arginine to 1,4–butanediamine (a building block for nylon-4,6), through two main transformations: the hydrolysis of arginine to ornithine and urea; and the decarboxylation of ornithine to 1,4–butanediamine and carbon dioxide. Both steps can be catalyzed chemically or enzymatically (Turras et al. 2008).
The present study deals with the characterization of arginase gene.
Availability: Items available for loan: UVAS Library [Call number: 2244-T] (1).
5.
Assessment Of Evolutionary Rate In Different Serotypes Of Foot & Mouth Disease Virus
by Muhammad Farooq (2011-va-823) | Dr. Ali Raza Awan | Prof. Dr. Thair Yaqub | Dr. Muhammad Tayyab.
Material type: ; Literary form:
not fiction
Publisher: 2015Dissertation note: FMDV belongs to the family Picornaviridae with seven serotypes around the world. Nevertheless, serotypes prevalent in Asia includes A, O and Asia-1. Because of evolution in genomic sequence of FMDV, it is becoming difficult to control the problem through conventional methods. Changes in the genome can be detected using software through sequence analysis. In the software, evolutionary models are used to measure the evolutionary change for the identification of new sub lineages.
In current study genomes sequence data (1998 - 2011) of bovine FMD serotypes (A, O and Asia 1) was collected through NCBI in FASTA format. This data was converted into PHYLIP format. On Dell workstation, with Microsoft Windows 8.1 operating system, BioEdit, TipDate V.1.2 was deployed. Sequence data was aligned through CLUSTAL W algorithm of Multiple Sequence Alignment using BioEdit. Using TipDate, genome sequence data was analyzed using three evolutionary models (F84, HKY and REV) and phylogenetic trees were produced showing evolutionary rate and likelihood ratio of FMDV serotypes O, A and Asia-1..
Results of the current study showed higher values of evolutionary rate in bovine FMD virus which was estimated 7.49 x 10-4 with likelihood value -1429.507680 in serotype A, 2.418 x 10-3 with likelihood -3707.168484 in serotype O and2.16 x 10-3 with likelihood value -3723.344884 in serotype Asia-1, respectively. Markove Reversible Model showed higher rates of evolution in all three serotype with best likelihood values. Phylogenetic results showed higher rate of evolution or substitution in viruses. Furthermore serotypes A, O and Asia-1are mutating with passage of time and new variants are being observed. It was also observed that this evolutionary process is continued in these three serotypes during 1998-2011.
This study confirmed the evolutionary changes in FMDV serotypes prevalent in Pakistan during the period 1998 – 2011. This study showed that isolate are evolving with increasing rate. High rate of mutation in Asia-1 was observed than serotype A and serotype O. F84 and HKY85 models produced close results
but these models are not identical works on equal and unequal base frequencies. Markove model estimated average base substitution with mutation and depicts good phylogenetic trees of sequence data. Availability: Items available for loan: UVAS Library [Call number: 2372-T] (1).
6.
Physical, Chemical and Biological Treatment of Rice Husk to Improve Its Nutrative Value
by Rahat Naseer (2003-VA-196) | Dr. Abu Saeed Hashmi | Dr. Muhammad Tayyab | Prof. Dr. Habib ur Rehman.
Material type: ; Literary form:
not fiction
Publisher: 2015Dissertation note: Thesis submitted without CD. Availability: Items available for loan: UVAS Library [Call number: 2450-T] (1).
7.
Molecular Phylogeny And Diversity Analysis Of Bovidae (Boselaphus Tragocamelus, Antilope Cervicapra) And Cervidae (Axis Axis, Axis Porcinus) In Pakistan
by Ghulam Abbas (2011-VA-748) | Dr. Asif Nadeem | Prof. Dr. Mansoor Ellahi Babar | Dr. Muhammad Tayyab.
Material type: ; Literary form:
not fiction
Publisher: 2016Dissertation note: Many species of mammals have declined within the past two centuries due to human
caused disturbances and the unsustainable use of natural resources. Molecular methods have an
important role in phylogeny and diversity analysis. The present study was designed for diversity
analysis of Boselaphus tragocamelus & Antelope cervicapra (Bovidae) and Axis axis & Axis
porcinus (Cervidae) family in Pakistan. A total of 25 samples from each of the four species were
collected from different parks, zoos and natural habitats. DNA was extracted, PCR primers were
designed and cytochrome-b, cytochrome-c gene and d-loop regions were amplified by PCR.
PCR products were sequenced bi-directionally by Big DyeTM Terminator. Bioinformatics tools,
Blast 2 sequences, Clustal-W, MEGA-6, Bioconductor in “R” were applied for analysis. The
clustering of the samples indicates that each species contains less within-population genetic
variability. Same pattern was observed when sequence of three genes was combined and MDS
plot was constructed. Phylogenetic analysis of the gene sequences revealed that each species
comprised a clade that is clearly distinct from the clade comprised of other species of deer
selected for this study. Finding of this study indicated that these species of deer have significant
genetic variations among-species that differentiate them from each other. This is the first report
from our region. The information of selected species of deer is prerequisite for designing
effective strategy in future conservation practices. However further genomic investigations
should be carried out at larger scale. Availability: Items available for loan: UVAS Library [Call number: 2560-T] (1).
