1.
Detection And Analysis Of Improvised Explosive Devices Used In Terrorism Activities In Pakistan
by Arslan Nazar (2012-VA-630) | Dr. Sehrish Firyal | Dr. Muhammad Sarwar | Dr. Muhammad Wasim | FaizaMasood.
Material type: ; Literary form:
not fiction
Publisher: 2014Dissertation note: Defence and security organizations are in steadyrequirement of finding new options for the detection of explosives. Fundamental applied research in this area focuses on uncovering of highly energetic substances as well as home-basedexplosives that could be a weapon of mass devastation (Marshal and oxley, 2009 yinon and Zitrin 1996, Scubert and Rimiski-Korsakove, 2006). Current methods of detection for explosives or highly energetic materials are based on a wide variety of technologies that focus on either massexplosives or little portions of explosives. Mass explosives can be distinguishedin some way by imaging features,character of the explosives charge, wires and detonators or unswervingly by spotting the chemistry and dielectric characteristics of the explosive substance. Trace recognition method relay on revealing of vapours given off by the explosives or on explosive’sconstituent part that are set down on nearbyexteriors (national Academy of sciences Committee, 2004). Even though, numerous published material is available about methods of sensing of explosives present in air,water, clothing,soiletc and these put forward the benefit of providing traceconfines of sensation at ppb intensities (Caron et al,. 2010; Hilimi and Luonge). Inthe bulk of the criminal acts, sampling is done at the scene trailed by a sample preparationmove, to be shortly processed by a particular technique for analysis. Sampling and samples preparation are amidmajor, shortcomings in explosive uncovering in many cases frightening the physical condition and life of examiner and the responding officer.
Improvised explosive devices are widely used by military in wars and police to keep up regulation and command. Gush of terrorist activities and increase in criminal conduct have been a matter of great concern worldwide and particularly for Pakistan. There have been motiveless
annihilation of private and community properties as well as industrial centres, causing irretrievabledamages to state and local markets and imperillinghumanexistence(Shen et al. 2005). Potentially perilous explosives like dynamite, varied military explosives havingnitroglycerine (NG), Cyclotrimethylenetrinitramine commonly known as RDX, Cyclotetramethylenetetranitramine and alternativehome-produced low explosives and provocative devices are now currently promptly obtainable to scandalous and terrorists. The haphazard and deliberate uses of these explosives consist ofextortion of cash and taking vengeance, unlawful transportation of prohibited substances, assassinations, terrorist and delinquent activities in numerous regions of the country (Sharma and Lahiri 2005).
Recognition of detonating method, estimating the path ways taken by explosive transportation andarresting the anti-social charactersconnected with unstable materials and explosions is primary aim of explosive analysis. For this purpose various explosive substances and explosive remains are to be examined qualitatively and the ingredients are to be approximated quantitatively using primarily by thin layer chromatography (TLC). TLC is a technique employed for the screening of organic constituents at hand in the post blast samples. The identification of explosives containing alkylammonium nitrate is done by TLC. Secondly Gas chromatography with mass spectrometry (GC-MS) technique with the benefit of anelevated resolving supremacy is avitalapparatus for the analysis of chemical composition of explosives. The extremelyproficient GC analysis withcapillary columns authorizes the examination of explosive hydrocarbons, identical substances of nitroaromatics, hexogen (RDX) and the high explosive pentaerythritoltetranitrate (PETN) in a single run. The spectroscopic identification of explosive materials by FTIR is striking due to the intrinsicpotential of real-time detection, non-vicious analysis, and nominal sample preparation, thirdly the scanning electron microscope (SEM) produces an increased image of the sample based on the contact of an electron beam with the sample’s exterior. Finding of minutemasses of explosive remains play an important part in forces, inhabitant, and counter terrorism requests(Pacheco-Londono et al. 2005). To press on explosives sensor methods, present methods need to become affordable and transportable without disturbing the integrity of the devices. The uncovering of ordinary explosives as well as trinitrotoluene (TNT), RDX, HMX, 2,4,6 Trinitrophenyl-N-methylnitramine (TETRYL)Pentaerythritoltetranitrate (PENT), and NG were carried out using diverseprocedures(Sanchez et al. 2007).
Detection of explosives is anparticularly relevant analytical concern for law enforcement personals and for the environmental protection agencies. As the use of explosive substances have been increased by the terrorists, problems have increased for law enforcement and environment and security agencies regarding the detection ofexplosives residues in baggage, parcels vehicles, aeroplane, on travellers, etc. In bomb scene investigations, it is important to find debris that includes detection of explosive residues. Mobile and hand held explosives detectors, similar to those used for detecting hidden explosives, can be of great help in detecting such residues. Several methods i.e. GC/MS, SEM, FTIR were used in Punjab Forensic Science Agency (PFSA) to analyze residues of explosives. The detection of landmines is an acute, urgent worldwide problem that needs specific and effective detection methods (Yinon 2002). Keeping in mind the above said situations, the project was designed with following objectives
Availability: Items available for loan: UVAS Library [Call number: 2235-T] (1).
2.
Antiviral Effect Of Human Saliva Against Avian Influenza Virus Strain H9n2
by Maryam Riaz (2008-VA-340) | Prof. Dr. Tahir Yaqub | Dr. Sehrish Firyal | Prof. Dr. Kamran Ashraf.
Material type: ; Literary form:
not fiction
Publisher: 2015Dissertation note: Saliva is an important body fluid that contains a complex array of proteins, peptides and various substances that help in maintaining the health of the oral cavity. Saliva exhibits a broad-spectrum of antiviral activity against enveloped viruses as it disrupts the viral membrane. Influenza is a common virus that has been diagnosed in humans and avian species due to AIV. This study has demonstrated the naturally occurring antiviral activity of human saliva against the H9N2 influenza virus that serves as a serious threat to poultry and has been shown to possess high zoonotic potential which can cause a new pandemic.
In this study saliva samples from healthy individuals were taken and the natural antiviral ability of saliva was observed against AIV (Pk-UDL/01/08 H9N2) of calculated EID50 106.66. Inoculum prepared from saliva and H9N2 virus was injected in 9 days old embryonated eggs using CAS route and incubated at 37°C for 48 hours. A negative control (only saliva) and positive control (only virus inoculum) was also determined in the current study. The antiviral activity of saliva was observed through haemagglutination test. The HA test of harvested fluid showed that human saliva indeed possesses antiviral activity against H9N2 virus and can be used as a natural antiviral agent in medicine.
Furthermore, the genomic DNA was extracted from the blood samples. HTN3 gene responsible for histatin production, was amplified using gene specific oligonucleotides. The obtained HTN3 gene sequences were analyzed using Chromas software. The sequence alignment showed 99% similarity to the available sequences in NCBI database and 100% similarity to each individual sample. To conclude, this study has demonstrated that human saliva possesses antiviral activity against H9N2 virus. The nucleotide sequence analysis from each sample
CHAPTER 6
SUMMARY
Summary
47
showed no particular change which shows that antiviral activity of glycoproteins present in saliva does not vary at a genetic level. This innate antiviral activity can open a new frontier when it comes to combating viral infections that have grown resistant to conventional drugs in both human and animal subjects. Availability: Items available for loan: UVAS Library [Call number: 2336-T] (1).
3.
Genetic Identification And Molecular Classification Of Sub-Family Phasianinae Of Pakistani Bird Species Through Dna Barcoding
by Maryem Hussain (2008-VA-349) | Dr. Ali Raza Awan | Dr. Sehrish Firyal | Dr. Muhammad Tayyab.
Material type: ; Literary form:
not fiction
Publisher: 2015Dissertation note: DNA barcoding is a precise technique that uses molecular genetics tools for accurate identification, categorizing, relating and separating the phylogenies of species. Being a small sized genome and agile enough to show rapid mutation, mtDNA has been used as a pertinent marker of molecular biodiversity.The aim of this study was to develop DNA barcode for genetic characterization and classification of Sub-family Phasianinaeof Pakistani bird species. Theyhave not been genetically identified yet in Pakistan. It includes birds like domestic chicken(Gallus gallusdomesticus), aseel chicken(Gallus gallusdomesticus strain),blue peafowl(Pavo cristatus), green peafowl (Pavo muticus), white peafowl (Pavo cristatus leuticus), Kalij pheasant (Lophura leucomelanos),monal pheasant (Lophophorus impejanus),koklass pheasant(Purcrasia macrolopha), ring necked pheasant (Phasianus colchicus), Tragopan (Tragopan melanocepals) andred junglefowl (Gallus gallus). These birds are considered an important part of an ecosystembecause they play a significant role in seed dissemination, pollination of plants and disease spread which are the basic constituents of an ecosystem. They are used for food, hunting and entertainment purposes.
Mitochondrial geneCytochrome c oxidase subunit 1 (CO1)of 500bps was used as a marker for identification at specie level.Genomic DNA was extracted by each blood and tissue sample of eleven bird species (33 samples). Amplification of CO1 gene was a done by using a universal set of primers (BIRDF1 and BIRDR1)containing region of almost 750 bps (Hebert et al. 2003).Amplicons were purified and sequenced Sanger sequencing method (Sanger et al. 1977). Forward and reverse sequences were analyzed using softwaresEMBOSS merger,ClustalW, BioEdit and nBLAST. Phylogenetic analysis of selected bird species was done. Each sequence was aligned
with its reference sequences of CO1 gene present on NCBI. Every nucleotide position which did not align with the reference sequence was studied to identify SNPs. Fixation index (FST) were used to measure species diversity within a same sub population relative to that found in the entire population. Consensus sequences (500bps) generated was used to construct their phylogenetic tree to see their evolutionary relationship with other bird species. All species showed their closest linkage with their respective species. Pakistani population of peafowl and chicken species showed the close relation with same sequences generated in China. Tranopans showed its closest linkage with T. temminckii.
In conclusion, seven species ofPhasianinaesub-family of Pakistani bird species was genetically characterized first time in Pakistan by using CO1 as a barcode. It proves that DNA barcoding is an efficient and accurate molecular tool for species identifica¬tion and phylogenetic implication. This study leads to establish a DNA Data Bank that helped scientists to investigate the biodiversity, taxonomic classification, specie identification, in forensic purposes and to study the genetic and phenotypic evolution of these species. DNA barcoding through CO1 gene works as a functional tool for detectingmeat mislabeling and preventing illegitimate trade. This study has established foundations for molecular biologists to study taxonomic uncertainties at sub species level using SNP based identifying marker. 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: 2376-T] (1).
4.
Molecular Characterization of Pakistani Common Leopard
by Muhammad Usman Ijaz (2012-VA-908) | Dr. Sehrish Firyal | Dr. Ali Raza Awan | Dr. Muhammad Tayyab.
Material type: ; Literary form:
not fiction
Publisher: 2015Dissertation note: CD not available. Availability: Items available for loan: UVAS Library [Call number: 2379-T] (1).
5.
Determination Of Comparative Effect Of Two Eeg Yolk Based Extenders On Post Thaw Semen Quality Of Sahiwal Bull
by Shahid Ali (2010-VA-05) | Prof. Dr. Main Abdul Sattar | Prof. Dr. manzoor Ahamd | Dr. Sehrish Firyal.
Material type: ; Literary form:
not fiction
Publisher: 2017Dissertation note: Cryopreservation of semen is the principal step for its usage in artificial insemination. Freezing of semen leads to reduction in post thaw semen quality. Glycerol has the cryoprotective properties that led to preserve spermatozoa. Egg yolk is also a basic constituent of semen extenders. Beneficial effect of egg yolk on sperm cryopreservation is plasma membrane protector. Tris based extenders are commonly used for semen cryopreservation of bulls, rams and bucks. Based on the economics and beneficial effects of extenders on bovine post thaw semen quality, tris based commercial as well as custom made semen extenders requiring egg yolk addition, needs to be considered for further studies. This study had been designed to determine the comparative effect of two egg yolk based extenders on post-thaw semen quality (Triladyl™and TCEY) on Sahiwal bulls. Semen was collected using an artificial vagina having temperature of 42 ºC from five adult Sahiwal regular donor bulls, raised at Center of Excellenc for Bovine Genetics (CEBG) Renalakhurd, Okara.Seven replicates of the experiment were performed. Volume, concentration and motility of ejaculates was evaluated. Semen samples having motility >60% and sperm/ml >500x106 were included in study. After evaluation, semen samples were pooled, divided into two aliquots of equal volume and kept in water bath at 37ºC. One aliquot was extended with tris citric acid egg yolk extender (TCEY) and other was extended with commercially available extender (Triladyl™). Pre-freeze CASA sperm motility parameters and kinematics of these extended aliquots were assessedat CEBG. After that, extended semen was cooled to 4 ºC for 4hr, equilibrated for 2hrs at 4ºC and packaged into 0.5 ml French straws (20 x 106 spermatozoa/straw). All semen straws were placed into automatic programmable freezer having liquid nitrogen vapors for 10 min. Afterward, shifted to liquid nitrogen for freezing and were stored until post-thaw semen evaluation carried out. The experiment was
repeated for seven times (replicates, n=seven). For post-thaw semen evaluation, four semen straws per treatment group were thawed (30 seconds) in water bath at 37ºC and post-thaw CASA sperm motility parameters and kinematics were checked. Post-thaw motility (PTM%) , Plasma Membrane Integrity (PMI %) , acrosome integrity (AI %) , live Sperm Percentage (LSP % )and sperm abnormalities (SA %) were checked by phase contrast microscope. Similarly AI (%), PMI (%), mitochondrial integrity (MI%) and DNA integrity (%) were checked by fluorescence microscope at Department of Theriogenology, University of Veterinary and Animal Sciences, Lahore.
Pre-freeze CASA sperm motility parameters;progressive %, rapid %and kinematics;average path velocity (VAP um/s), straight line velocity (VSLum/s), linearity (LIN %) were significantly better in Triladyl thanTCEY.Post thaw CASA sperm motility parameters; motile %, progressive %, rapid % and kinematics; VAP (um/s),VSL (um/s), straightness (STR %) and LIN (%) were also significantly better in Triladyl than TCEY. Post thaw semen quality parameters containing PTM (%), PMI (%), LSP (%), DI (%) andMI (%) were significantly better in Triladyl as compared to TCEY.
Availability: Items available for loan: UVAS Library [Call number: 2785-T] (1).
6.
Prevalance And Distribution Of Soil-Borne Escherichia Coli O157:H7 In District Lahore Of Punjab Province, Pakistan
by Hiba Tabassum (2011-VA-421) | Prof. Dr. Masood Rabbani | Dr. Ali Ahmed Sheikh | Dr. Sehrish Faryal.
Material type: ; Literary form:
not fiction
Publisher: 2017Dissertation note: Salmonella spp. and Campylobacter spp. (Campylobacter coli and Campylobacter jejuni) are
recognized as the leading causes of bacterial gastroenteritis, followed by Shigella spp. and
Shiga toxin-encoding Escherichia coli (STEC).(Control and Prevention 2010).Shigatoxigenic
Escherichia coli (STEC) include Escherichia coli serotypes whose genomes
contain one or more Shiga toxin genes. STEC infections in humans can range from mild selflimiting
diarrhea to more severe disease, including hemorrhagic colitis and hemolytic uremic
syndrome (HUS).
Real-time PCR allows for quantification of the target. Real-time PCR perform better
than the standard culture-based assays to detect pathogenic organisms. In summary, work
load and work flow issues may dictate which system is best for different-sized laboratories
and test volumes.PCR assays to perceive the stx1 and stx2 genes are utilized by several
public health laboratories for identification and confirmation of STEC infection. Depending
on the primers used, these assays will distinguish between stx1 and stx2 (Zaki and El-Adrosy
2007). Assays even have been developed that verify the specific O group of an organism,
detect virulence factors such as intimin and enterohemolysin, and can differentiate among the
subtypes of Shiga toxins.
So there was need to analyze soil of to check the presence of Escherichia coli
O157:H7 for avoiding fatal diseases caused by it and there was also monitored soil chemistry
and its relation with bacterial growth specifically Escherichia coli O157:H7 because
Different soil composition and different environmental risk factors promoted presence of
Escherichia coli O157:H7 in soil.
Real Time-PCR technique was opted to detect Escherichia coli O157:H7 in the soil
from distant areas of district Lahore of Punjab, Pakistan. Soil samples from 10 per cent
Summary
53
villages were collected from this district and handled for genome extraction using
commercially available soil DNA extraction kit. After genome extraction, the samples were
keep running for Real Time-PCR at optimized conditions. The reaction was improved by
variations in standard concentrations of primers, probes, DNA, Taq-polymerase and sequence
of primers.
The dissemination of soil borne Escherichia coli O157:H7 was mapped in mentioned
district of Punjab, Pakistan using geographical co-ordinates recorded by GPS beneficiary.
Relationship of Escherichia coli O157:H7 with environmental factors,soil chemistry and
source of land irrigation (Canal, tubewell and rain or in combination), was resolved. Results of
present project were analyzed through SPSS.
The purpose of the research work was the understanding of occurrence and
distribution of Escherichia coli O157:H7 in district Lahore of Punjab province .It also threw
light on role of soil as a reservoir of Escherichia coli O157:H7, and association of this
infectious agent with various risk factors.
In this study depending upon the statistical analysis data, it was depicted that
Escherichia coli o157 H7 is present in soil although it can’t persist or survive. The prevalence
rate of Escherichia coli O157 h7 is 3.1% in 129 soil samples of Lahore. In case of villages it
is present in 2 villages of of 29.that shows it is 6.8% prevalent in villages.
The presence or absence of pathogen in relation to soil chemistry and seven potential
risk factors was determined through student t distribution (T-test). By observing p value of
variables of positive and negative sites it comes to know that there is no significant
association of these factors to the survival of Escherichia coli O157:H7 in soil.
Remaining all other analytes has not significant association with soil. But it can be
seen Escherichia coli O157 H7 has significant association with organic matters, phosphorus,
Summary
54
copper, cobalt, calcium, sodium, ferrous ion, potassium and sand form of soil ranging from
(0.86-1.97), (9.7-22.5), (24.18-41.12), (0.048-0.51), (0.39-0.96), (0.08-0.16), (41.84-59.14),
(51.02-69.56), (83-86) respectively. Remaining all other analytes has not significant
association with soil.
For further investigations it is necessary that find out those factors which cause
hindrance in survival of Escherichia coli o157 h7 in soil specifically and also search out
those factors which support Escherichia coli O157 h7 persistence in soil. Availability: Items available for loan: UVAS Library [Call number: 2935-T] (1).
7.
Polymorphism Analysis Of Bovine Tumor Necrosis Factor Alpha Gene And Its Association With Mastitis In Nili Ravi Buffaloes
by Samia Tanveer (2011-VA-362) | Dr. Sehrish Firyal | Dr. Muhammad Wasim | Dr. Muhammad Nawaz.
Material type: ; Literary form:
not fiction
Publisher: 2017Dissertation note: Various number of factors cause hindrance in the milk production potential of buffalos. Mastitis is the costly and most prevalent disease causing production losses of dairy herds in Pakistan and elsewhere in the world. Susceptibility and resistance to mastitis is complex trait influenced by genetic variation of animals. Among these immunity gene variations, the polymorphism in tumor necrosis factor alpha gene (TNF-α) play important role in immune response to virus. Polymorphism in TNF-α gene is associated with mastitis susceptibility and resistance. It would be a potential candidate gene for imparting resistance mastitis in dairy buffalos. Blood sample were taken from the 20 Nili Ravi buffalos having clinical and subclinical mastitis. Extraction of DNA was done from frozen blood after thawing, using organic extraction method & also kit method followed by DNA quantification (i.e. gel electrophoresis and nanodrop). Total 5 primers were designed using Primer3 bioinformatics tool. All these primers were optimized using different protocols and a set recipe was obtained for each primer. The amplification of DNA samples was done one by one using all these five primers on optimized protocol. The amplicons obtained were subjected to agarose gel electrophoresis to check whether we have the required product or not using 100 kb ladder and then amplicones were send for the sequencing.
Summary
110
The sequencing analysis of resulted amplicon sequence was done using Bioinformatics software Finch TV. Total of 6 mutations were found while 5 were same in all the samples whereas 6th mutation was found only in clinical samples. It is valuable in accomplishing genetic progress for resistance and to improve the immune response. This study will paved the way for animal breeder for selection of Nili Ravi mastitis resistant buffalos for breeding. TNF-α gene polymorphism based marker is now available for screening of resistant bulls as well. Availability: Items available for loan: UVAS Library [Call number: 2936-T] (1).
