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Item Immunoinformatic-based screening of immunogenic fragments from the pathogenic proteins of NAEGLERIA FOWLERI against the HLA-alleles of majorly affected population(UMT Lahore, 2020) Mehwish AndleebNaegleria fowleri is a unicellular pathogenic amoeboid flagellate. The trophozoite phase is responsible for causing primary amoebic meningoencephalitis, with the 98% fatality rate. Considering the complex pathogenicity, as well as the resistance towards most of the antifungal drugs, present study aimed to propose a multi-epitope ensemble against N. fowleri restricted to targeted populations. The significant B-cell and T-cell epitopes from all five immunogenic surface proteins, such as Mp2CL5 (181), HSP70 (659), Naegleria Pore A (307), Naegleria Pore B (484), and NF23 (229), were selected. The immunogenicity and allergenicity of selected epitopes were analyzed using VaxiJen and AllerTop v. 2.0. The binding affinities of selected T-cell epitopes with the South Asian, USA, and Australian specific HLA alleles, retrieved through AFND, were evaluated through the IEDB server. The antigenic fragments with the highest binding affinity towards these alleles were analyzed. The nominated epitopes were covering 94.53% for the USA, 84.27% for Australia, and 73.77% for the South Asian region. The structural modeling through I-TASSER and validation via SAVES server v.5.0 suggested all these proteins were stable. The common T-cell epitopes from all these populations were labeled using the PyMol graphic tool. The immunogenicity, non-allergenicity, and maximum population coverage of short-listed epitopes marked them as efficient candidates for vaccine designing.Item Organization: Paktex group of industries(UMT Lahore, 2020) UZAIR ISHTIAQItem City pharmaceuticals PVT, Limited(UMT Lahore, 2019-10-15) SAQIB ABBASItem Isolation and optimization of efficient bacteria during mesophilic phase of municipal solid waste composting(UMT Lahore, 2020) SABAHAT MAHNOORComposting is an environment friendly and most economical method to decompose the organic waste by biologically active degraders which are naturally present in the municipal solid waste. Due to increase in world population the rate of pollution has also been increased. Compost also produce essential components (K, P, N) which help in amendment of soil. Composting carried out under the ideal conditions of temperature, pH, nutrients level and lignin content. Soil plays a crucial role to produce microorganism (Bacteria, Fungi) which help in decomposition of waste. This study is designed to isolate and identify the efficient bacteria at mesophilic stage of composting which works best on optimum temperature of 35°C. Bacterial strain “X” isolated from mesophilic stage of composting and optimised. Activity of bacterial strain “X” was observed on blood agar and three different carbohydrate media. Optimization was carried out by using spectrophotometry and electrical impedance techniques. Literature revealed that bacterial species present in compost pile always show best degradation capabilities. This study is designed to isolate the most efficient bacillus strain. This strain has best potential and it is able to degrade more efficiently in a very short duration of time.Item Comparison of three different DNA extraction methods for betel quid spits and gutka spits collected from ten different surfaces(UMT Lahore, 2020) Ameer HamzaBetel quid and Gutka chewing is habit of a mass population mainly consist of Asian countries and is also spread to other world through immigrants. Chewing of Betel quid and Gutka induce some chemical changes in the saliva of consumers due to the presence of a number of carcinogenic and other substances present in them which cause inhibition in the isolation of DNA from their chewer’s saliva. Saliva is an important examined biological fluid in forensic analysis. It is a significant evidence that can help to investigate a rape case, assault and homicide cases. This study was designed to make an evaluation and compare three manual methods consisting of Phenol Chloroform isoamyl alcohol (PCI) test, Trehalose test and Alkaline lysis test for DNA isolation from Betel quid and Gutka samples collected from ten different surfaces. The aim of this study was to find a most suitable method for DNA isolation to face these kind of challenging samples in the field of Forensic science. The surfaces which were supposed in this study were more susceptible as a part of crime scene where evidential saliva might be found. soil, marble, glass, cloth, wood, plastic, cardboard, paper, metal and plant material were the surfaces selected in this study. The isolated DNA was checked for concentration and purity through spectrophotometer method in order to evaluate the most favorable method for DNA isolation. In this study Phenol Chloroform Isoamyl Alcohol was found to be the most favorable and efficient method from two other methods for both Betel quid and Gutka spit samples. However, it was observed in this study that it is difficult to recover DNA from these kind of Forensic samples.Item Isolation and growth optimization of bacteria at suitable pH and temperature from maturation phase of aerobic composting with different waste composition(UMT Lahore, 2020) Ali RazaComposting is an aerobic microbiological method that is persuaded by microorganisms such as bacteria and fungi. Microorganisms perform degradation by the use of water and oxygen and result in the production of compost, carbon dioxide, heat, and water. It enriches the soil and reduces the need for chemical fertilizers by recycling various organic material and nutrients to the soil. The maturation phase is responsible for determining the final quality of the mature compost. To order to identify the optimal composting decomposition conditions, this study is designed to optimize the parameters for isolated bacteria from the maturation stage of the compost. An important similarity of the isolated bacteria from the maturation stage of composting process was also observed between temperature, pH, OD and EC. It was observed that optimizing the parameters of the compost promotes the rate of decomposition, product stability, and humification process. In this phase, therefore, further research is required to improve the aerobic composting process and reduce the composting time.Item Isolation and growth optimization of fungus from thermophilic phase of composting(UMT Lahore, 2020) Aqsa ShehzadiStimulated by exponential growth population and increase consumption proportionality, organic waste has become a crucial environmental issue. Composting is the simplest method of reducing the organic waste encourages the production of beneficial bacteria and fungi that break down organic matter to create humus or compost. It is a self-heating biological conversion, which generates a suitable end product such as biofertilizer. Thermophilic phase accelerates the degradation of organic waste or complex carbohydrate, because temperatures above 400C. Thermophilic fungi are of wide interest due to their potential to produce heat-tolerant enzymes for industrial and biotechnological processes. This study is designed to optimize the parameters for isolated fungi from thermophilic phase of compost in order to determine best composting decomposition condition. Various parameters such as pH, temperature, EC, biomass were investigated to evaluate the effect on growth rate of fungus and for the production of lipase enzyme and α-amylase enzyme. To determine the suitable conditions, fungus was grown at different temperature and pH. Isolated fungus was active in acidic pH of 5.5 and 450C temperature. It was rapidly determined that the optimization of compost’s parameter promotes the decomposition rate, stability of the final product and better humification process. Therefore, more research ought to be done on this phase, in order to further optimize the composting process and reduce the time of composting process.Item Quantification of touch DNA from mobile surfaces using three manual DNA extraction methods(UMT Lahore, 2020) AMINA MUNIRApplications of forensic science resolve legal matters that are in physical, natural, and social discipline. Offenders are getting up to date with innovative technology, where the use of the mobile phone is very common, nowadays. A big leap is to overcome cold cases with inexpensive, finer, and less time taking ways. The purpose of this study was Quantification of touch DNA from mobile surfaces using three manual DNA extraction methods towards. The genuine idea of touch DNA and contact DNA proof has stayed difficult to track down, where three protocols further process the shed cells to get better yield; Phenol Chloroform, Alkaline Lysis, and Trehalose. In this study, DNA extracted by the results of these manual organic methods and spectrophotometer used for quantification of male and female DNA samples from different mobile surfaces; Glass, Plastic, Metal, and Rubber. Where the plastic and glass surfaces were showing more fine extracted quantity than metal and rubber. This research was to evaluate the best DNA extraction method for contact DNA, having better quantification. Overall, Alkaline lysis showed distinguishable results for DNA concentration than Trehalose and PCI. Whereas PCI is more, appropriate for purification. Hence, it was the Alkaline lysis method observed with a higher concentration of DNA mark for a DNA profile.Item Isolation and growth optimization of most fungus from mesophilic stage of municipal solid waste composting(UMT Lahore, 2020) RIDA ASHFAQThe rate of waste production, waste components and the amount of waste increases with industrialization and urbanization day by day. Composting is a major and sustainable process in waste management due to recycling of waste into beneficial products that can based in soil improvement. In microbial decomposition process, tolerate the dynamics of various microbial genera. It is impact due to microbial population and their physical activities. The factors of composting like temperature, pH, moisture level, oxygen level and carbon oxygen ratio effected the decomposition of organic waste and performance. These parameters are major issues for sustainable waste management, in which high rate of compost prepared to improve the methods applied in soil recycling. According to the optimum condition to the culture for the growth on an increase or decrease its growth by assistance to it with changing temperature and pH. The study supports the composting can be useful for the wide range of organic compounds such as food processing, household waste and yard trimming discards. Furthermore, knowledge regarding species composition of the microorganism of different compost help to optimize the compost quality standards.Item In silico analysis of functional nonsynonymous SNP in human INSR gene associated with polycystic ovarian syndrome(UMT Lahore, 2020) KHIZRA BANOPolycystic ovarian syndrome (PCOS) is a very complicated condition having many risk factors behind it, which in turn lead to other diseases. According to Rotterdam criteria, three factors are necessary for its diagnosis such as hyperandrogenism, irregular menstruation and polycystic ovaries on ultrasound. It also results in increased chances of obesity, type two diabetes and cardiovascular diseases. We compared various factors between PCOS women and healthy women after signing written consent by them, which revealed that PCOS women were more prone to Obesity, diabetes and irregular menstruation as compared to healthy women. In order to study genetic factors behind PCOS, we analyzed role of INSR gene polymorphism with the help of various bioinformatics tools showing role of non-synonymous SNP in causing damage to protein function. Structural comparison between wild type and mutant strain of protein showed no interaction between protein and ligand but having impact on protein stability predicted by I-mutant server showed that SNP at position 1161 where alanine changes to threonine resulting in decreased protein stability. The protein 3D structure was further validate by Ramachandran plot.Item Isolaion and optimization of efficient bacteria during thermophillic phase of municipal solid waste composting(UMT Lahore, 2020) KHADIJA TARIQComposting is biological decomposition of organic waste into more stable humus like compound carried by microbial population. The complex organic matter into simpler form by the help of microbial activity of bacteria and fungi. Different physical and chemical parameter like pH, moisture content of substrate, oxygen concentration, carbon-nitrogen ratio, particle size play important factors in supporting stability of the final product. Thermophilic stage is the most active stage of composting starts by replacing microphillic flora and continues until 62℃ is reached. The optimum temperature for thermophilic stage is 35 to 55 °C. Thermophiles plays an important role and have a huge diversity, thermophilic phase was found to be dominant by Bacillus. On the other hand degree of humification and maturation process in composting is improved by microbial inoculants. This study is designed to isolate and identify most efficient degrading bacteria at thermophilic stage of composting. Growth of strain ‘X’ on different carbohydrates media and blood agar media was observed and evaluated. Optimization of Bacterial ‘X’ strain at different temperature and pH was also evaluated by spectrophotometry and electrical impedance. The most suitable temperature for better growth of bacteria ‘X’ was 450C and 5.5 pH.Item Isolation and growth optimization of most prevalent bacteria on different pH, temperature and growth media from maturation phase of composting(UMT Lahore, 2020) Faisal HanifProper management of waste is a major problem in most parts of the world. Composting is one of the oldest and simplest methods of organic waste recycling. It is a self-heating biological conversion, which generates suitable end products such as bio-fertilizers. The maturation phase is a very idle one where slow microbial activity leads to moderate (at best) degradation of organic matter. This phase is responsible for determining the final quality of the mature compost. This study is designed to optimize the parameters for isolated bacteria from the maturation stage of compost, in order to determine the best composting decomposition conditions. A significant correlation was also found between temperature, pH, OD and EC of the isolated bacteria from maturation stage of composting process. It was rapidly determined that the optimization of compost’s parameters promotes the decomposition rate, stability of the final product and humification process. While there has been considerable study of optimization of parameters during the mesophilic and thermophilic phase, there is much less research on the optimization of such parameters at the maturation phase. Therefore, more research ought to be done on this phase, in order to further optimize the composting process and reduce the time of composting process.Item Effect of water and detergent washings on detection of saliva stains from commonly used natural and synthetic clothes(UMT Lahore, 2020) FATIMA ARSHADForensic science plays main role in criminal justice system. Mainly, homicide, sexual assault and burglary, permit the assembly of biological evidence. Blood, semen and saliva commonly obtain from the crime scene. Culprit often tries to remove these biological stains through washing out the crime scene or the items but previously it has demonstrated that DNA can still recover from laundered clothes. The purpose of this study was to observe the effect of water and detergent wash on clothes and to extract, detect and quantify the amount DNA from these clothes. In this study, natural and synthetic clothes gave positive results under various presumptive tests. Both types of clothes gave different ranges of mean diameter after water wash till three washings. Saliva was found retain from laundered natural clothes till ten washings after processing with detergent while the laundered synthetic clothes could not efficiently retain saliva after treatment with detergent. DNA extracted from clothes analyzed under UV spectrophotometer demonstrated that both natural and synthetic clothes could give the good amount of DNA that was enough to generate the DNA profile. Overall terry, cotton, linen, khaddar, denim and spandex clothes showed the efficient results for saliva detection while wool, polyester and nylon exhibited the poor results.Item In silico analysis of LR34 gene resistance to leaf rust in wheat TRITICUM AESTIVUM L(UMT Lahore, 2020) Muhammad Usama YaqoobLr34 is a leaf rust resistance gene of hexaploid wheat Triticum aestivum L. This wheat is also known as the bread wheat as it is the source of food for humans and also feeding stuff for the animals. 95% of the world wheat cultivated constitutes hexaploid wheat which is Triticum aestivum L. It is the main host of leaf rust pathogen called Puccinia triticina. Lr34 gene provides resistance against the urediniospore's life stage of Pt. Some studies show that the locus of LR34 is on 7D chromosomes while other homologs are present on other chromosomes. This study involves various in silico techniques to carry out the analysis, characterization, structural and functional predictions, and the phylogenetic and evolutionary relationship of the LR34 protein encoded by the Lr34 gene. Various computational tools were used for the predictions and verification of the results. NCBI was used for the data and the sequence retrieval which showed that the protein contains 1402 amino acids and has an accession ID ADK62371. Other tools that were used in this study include Scanprosite, InterPro, NCBI CDD, SOPMA, DNAssist, I-TASSER, SWISS MODEL, SAVES 5.0, and MEGAX. PyMOL and Chimera were used for visualization. From different domain search tools, it was found that LR34 contains the domains of the ABC transporter family. Out of three NCBI, CDD predicted the conserved domain region from amino acod#43 onward. While the sequence homology and the phylogenetic analysis confirmed hypothetical protein CFC21_054641 [Triticum aestivum] as the nearest neighbor and homolog of LR34 in the evolutionary history. I- TASSER predicted the model which had only 6% residues in the disallowed region in the Ramachandran plot while the rest were in the most favored, additional allowed, and generously allowed regions. To make the model more favorable the model was further energy minimized. It was found that the protein is involved in oxidoreductase reaction more specifically in fatty acid catalysis and is an obsolete intracellular part.Item City pharmaceuticals PVT, Limited(UMT Lahore, 2020) SAQIB ABBASItem In silico structural and functionalcharacterization of hypothetical proteinsof candida auris(UMT Lahore, 2020) Qamar AbbasCandida auris is a fungal pathogen, which provokes a wide array of infections in humans including, bloodstream, wound, and ear infection. Due to its resistivity to all types of antifungal drugs, the treatment of infections caused by this pathogen has become very challenging. Previous studies revealed that some of its proteins are involved in causing the pathogenicity in the host but these proteins are not structurally and functionally annotated, and, therefore, are hypothetical. So, the present study is designed to use multiple in silico strategies to characterize the hypothetical proteins of C.auris to get a structural and functional insight about this deadly microorganism. The study started initially with the 50 proteins, selected randomly from NCBI. The homolog screening via BLAST based on percentage identity and E-value reduced the number of proteins from 50 to 12. All these 12 hypothetical proteins were then characterized using multiple computational tools, including physicochemical characterization via ExPASY ProtParam, conserved domain search through CDD, Pfam and, InterProScan. The analysis of the subcellular localization of these proteins via CELLO and SecretomeP v 2.0 marked all these proteins to be present in the cytoplasm. The structural modeling of these hypothetical proteins was performed using I-TASSER, followed by the model validations via SAVES V.5.0. Finally, the functional annotations revealed that these proteins are likely to have diverse functions, including, transposition, transmembrane transporter activity, DNA directed DNA polymerase activity, and hydrolase and peptidase activity. The results of this study may help in understanding the function of uncharacterized proteins from C.auris. After the screening of virulent factors from this pathogen, it would be easy to identify ligand-binding sites and drug targets through docking analysis.Item In silico screening of the putative epitopes from the surface proteins of streptococcus pneumoniae against south asians specific human leukocyte antigens(UMT Lahore, 2020) Anosha LiaqatStreptococcus pneumoniae is a causative agent of sinusitis, bacteremia, pneumococcal pneumonia, and other pneumococcal infections, most commonly in children under five years. Two serotype-based vaccines, polysaccharide vaccines (PPV) and protein conjugated polysaccharide vaccine (PCV), have provided some protection against this organism, but serotype specificity, and low immunogenicity of these conventional vaccines, have driven the research toward the designing of more efficient treatment strategy against this organism. This study attempted to design the population-specific and highly immunogenic vaccine candidates that can evoke both cell-mediated and humoral immune responses against S. pneumoniae. Consequently, both B and T-cell epitopes from the four pathogenic surface proteins of S. pneumoniae, including PspC, PvaA, PhtD, and Pneumolysin, were identified. Following the epitope prediction, the antigenicity and allergenicity assessments of these epitopes were done by using VaxiJen and AllerTOP. Binding restrictions of selected T-cell epitopes with South Asian specific alleles, retrieved through AFND, were determined using IEDB MHC-binding prediction tools, with the selection of best binder epitopes based on IC50 values of less than 50nM. Population coverage analysis revealed that these epitopes were covering 83.75% of the South Asian population. Finally, after the structural modeling and validations through I-TASSER and SAVES v5.0, the identified epitopes were labeled on their respective protein models using PyMOL. The identified epitopes were not only immunogenic and non-allergenic but also show restriction to the majority of the HLA alleles of the South Asian populations, the identified epitopes might therefore be the probable vaccine candidates for these populations.Item Prevalence of various Gynacological cancer in patients admitted at Lahore general hospital, Pakistan(UMT Lahore, 2020) AUN RAZAUterus cancer is a disease spread due to different factors but the most common one is due to sexual activities, genetic mutation and HPV. The cancer spread on the different site of the uterus and classified according to the site i.e. cervical, endometrial, ovarian etc. majority of the risk factors are similar among all types and their symptoms are also close enough. But by the help of screening and other analysis methods the exact type can be identified. There are number of treatments available for all the different types including surgeries, chemotherapies, radiation therapies and also much prevention to reduce the risk of having uterus cancer. According to the WHO, uterus cancer is the second most common cancer type in the female that cause more deaths per year. As a rough figure indicated that more than 500000 patients are diagnosed with the uterus cancer and about half of them die due to this disease. The infected ration is more in developing countries. The incidence and spread of uterus cancer in Pakistan is not known precisely because it is a neglected disease in terms of detection and prevention. Epidemiological information on inconsistencies can be accessed in many tests in the light of some considerations, population restriction and only the management of registered cases. More than 1000 patients are reported in a single hospital in the area of Lahore in one and half year. Out of which about 70% are diagnosed with the Benin tumors and 30% with any one of the uterus cancer type. Out of the 30% of the uterus cancer, 32.5% are cervical cancer, 41% are ovarian cancer, 22% are endometrial cancer etc. This number of cases also highlighted the issue of increasing uterus cancer. The statistical analysis showed the non-significant relationship between the age group of the patients and the number of patients. It is most common among the women of 40 years plus, this is the belief that women have concluded that this final cancer means expected death, in this way that they believe it is better to refrain from screening and not have absolutely no information on wellness.Item In silico characterization of hypothetical proteins of vibrio parahaemolyticus(UMT Lahore, 2020) Rabia AkhtarVibrio parahaemolyticus is a gram-negative, rod-shaped, halophilic bacterium that lives in warm aquatic environments and is involved in causing acute gastrointestinal infections among humans, due to the consumption of contaminated, raw, or uncooked seafood. It was first reported in 1950, in Japan, and in the early 1996 it disseminated throughout the world and was declared as a pandemic. This seafood-borne pathogen contains several virulence factors, including adhesion molecules, hemolysins, and secretion systems, however, many of its proteins are still uncharacterized. The pandemic of this pathogen demands the characterization of all of its proteins to trace the virulent factors and their effect on humans. In this study, 23 hypothetical proteins of V. parahaemolyticus have been targeted for functional and structural annotation. The selected proteins were first subjected to homology screening to check the templates accessibility. After filtering, the 11 hypothetical proteins were evaluated further for the conserved domain analysis via CDD, Pfam, Interproscan, and scanprosite, physicochemical characterization via ExPASy ProtParam, subcellular localization via CELLO v2.5 and PSORTb v3.0, and structural modeling via I-TASSER and SAVES server (v.5.0). The pathogenicity assessment, using VirulentPred and functional annotation through CATH v4.2 and Argot v2.5 revealed that 7 out of 11 hypothetical proteins, could act as the potential virulent factors. The finding of this study could assist in confirming the functions and pathogenic involvement of these proteins and may, therefore, help in target identification for drug discovery and vaccine designing for V. parahaemolyticus.Item Prevalence of various breast cancer in patients admitted at Lahore general hospital, Pakistan(UMT Lahore, 2020) MUHAMMAD SHAHBAZBreast cancer is a disease spread due to different factors but the most common one is due to, genetic mutation and menstrual cycle, breast feeding. Majority of the risk factors are similar among all types and their symptoms are also close enough. But by the help of screening and other analysis methods the exact type can be identified. There are number of treatments available for all the different types including surgeries, chemotherapies, radiation therapies and also much prevention to reduce the risk of having breast cancer. According to the WHO, breast cancer is the second most common cancer type after lungs cancer in the female that cause more deaths per year. As a rough figure indicated that more than 2.1 million patients are diagnosed with the breast cancer, and it also cause the greatest number of cancer related death among women. The ratio of cancer incidence is more in developing nation. The incidence and spread of breast cancer in Pakistan are higher due to lack of awareness among women’s not known precisely because it is a neglected disease in terms of detection and prevention. Epidemiological information on inconsistencies can be accessed in many tests in the light of some considerations, population restriction and only the management of registered cases. More than 300 patients are reported in a single hospital in the area of Lahore in one and half year. Out of which about 65% are diagnosed with the Benin tumors and 35% with any one of the breast cancer type. Out of the 35% of the breast cancer, 60% are ductal carcinoma, 40% are lobular carcinoma. This number of cases also highlighted the issue of increasing breast cancer. The statistical analysis showed the non-significant relationship between the age group of the patients and the number of patients. It is most common among the women of 40 years plus.