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Item In silico interaction studies of spike protein from different SARS-COV-2 variants with its angiotensin-converting ENZYME-2 receptor with respect to geographical regions(UMT, Lhr, 2023) Ayesha AminThe emergence of SARS-CoV-2 in late 2019 resulted in the global pandemic of Coronavirus disease 2019 (COVID-19), causing significant disruptions in various aspects of society. SARSCoV-2 belongs to the beta Coronavirus family and is highly infectious, primarily spreading through respiratory droplets. Its genome consists of a single-stranded RNA encoding structural and nonstructural proteins. The spike protein plays a crucial role in viral attachment to host cells through interaction with the ACE2 receptor. Other structural proteins include the envelope, nucleocapsid, and membrane proteins. The virus also encodes 16 nonstructural proteins involved in various aspects of its life cycle, serving as potential targets for drug development. Understanding the structural and nonstructural proteins of SARS-CoV-2 is essential for comprehending its lifecycle and developing effective therapeutic strategies. This study provides an overview of the viral proteins, their functions, and the lifecycle of SARS-CoV-2, offering valuable insights for further research and the development of antiviral interventions.Item In-silico analysis to identify pathogenicity of mutations in CBS gene(UMT, Lhr, 2023) Maliha NoorHomocystinuria is an autosomal recessive disease related with neurological and physical abnormalities. It is associated with facial deformities, skeletal deformation, ocular disorders, cardiac problems and intellectual disability. Homocystinuria is mainly caused due to mutations in CBS gene which encodes Cystathionine betasynthase enzyme which, catalyzes methionine into homocysteine. In-silico approach was used to predict the pathogenicity associated with CBS gene known to be involved in Homocystinuria. The study’s goal was to emphasize the importance of CBS gene as well as to uncover pathogenic variants related to CBS gene for aiding in the diagnosis and treatment of homocystinurai. The variants were retrieved from gnomAD and analyzed by multiple bioinformatics tools and databases i.e., missense variation analysis, Stability, function, conservation and PTM mechanism analysis and also for splice site affecting variations were also analyzed. A total of 54 missense variants in CBS gene were predicted to be pathogenic by CADD and meta-SNP. These mutations were analyzed by Cupsat, Dynamut and Duet for their effect on stability and 9 of 54 variations were predicted pathogenic overall. 51 of the 54 variations were predicted to be effecting the function of the gene by Mutpred and 42% of the gene structure was predicted to be conserved by Consurf. 3 variations G134E, G134R and G388N were predicted by Scan prosite and netsurf to effecting the PTM mechanism of the protein. These 54 missense variants were visualized by Chimera. CADD predicted 751 splice site variants out or which 20 were pathogenic and further analyzed for their effect by SPiCE v2.1, Splice AI and Mutation Taster. None of variations with uncertain significance found in splice site were predicted to effecting the splicing mechanism of the gene. data can be used for he early detection of mutations in Cystathionine beta-synthase enzyme by cloning the mutation individually and determining their effect in vectors by mutagenesis.These findings contribute to our understanding of CBS gene representing complex disease features. This study demonstrated the importance of bioinformatics in determining highly pathogenic variants associated with the functional and structural relationship of Cystathionine beta-synthase protein.Item Computational analysis predicting deleterious variants in fbxo31 gene(UMT, Lhr, 2023) Amina KhawarIntellectual developmental disorder is an autosomal recessive disorder characterized by severely below overall intellectual functioning together with abnormalities in adaptive behavior. It is often associated with depression, autism, hyperactivity disorder, and attention deficit. It is mainly caused due to mutations in the FBXO31 gene. The FBXO31 gene is located on chromosome 16 contains nine exons and encodes for 539 amino acid proteins and works as a centrosomal E3 ubiquitin ligase together with SKP1 and Cullin-1. The complex of FBXO31, SKP1 and Cullin-1 is significant for axonal identity and neuronal morphogenesis. Mutations in the FBXO31 gene lead to the deregulation of this complex and its subunits resulting in intellectual disability. In this study, bioinformatic approach has been used to predict the highly pathogenic missense and splice site variants of the FBXO31 gene that caused the deregulation of Skp/Cullin/F-box (SCF) ubiquitin E3 ligase complex. For the screening of pathogenic variants of FBXO31 gene multiple analysis such as missense, stability, post translational modification, conservation, and splice site analysis was done. The pathogenic variants were retrieved from gnomAD and analyzed by missense and splice site variation analysis. For missense analysis, CADD, CAPICE and metaSNP tools were used. Pathogenicity and stability of the variants analyzed by web tools predicted 89 highly pathogenic missense variants and among these 89 variants, 8 were highly destabilizing on the basis of Gibbs Free energy predicted by Duet and DynaMut. The functional analysis of deleterious variants done by Mutpred tool and it was predicted that 85 pathogenic variants disturbing the function of the protein. Moreover, UCSF chimera utilized to check the clashes and 21 deleterious variants clashing with their surrounding residues in the structure of protein. Furthermore, Consurf tool utilized to check the impact of the pathogenic variants on the conserved regions of the protein and 42% gene predicted as conserved. PTM analysis done by utilizing Scan Prosite and NetSurf2.0 and it was predicted that 4/89 pathogenic variants are disturbing the post translational modification sites of FBXO31 gene. Moreover, splice sites analysis was also done by SPiCE v2.1, Splice AI and Mutation Taster and 6 pathogenic variants predicted to affect the splicing mechanism of the FBXO31 gene. This study proved that these variations have a significant role in the deregulation of FBXO31 complex that leads to intellectual disability. FBXO31 deleterious variants predicted in this study can be further analyzed on cell assays.Item In-silico tripartite interaction analysis of bacterium, insect and plant in citrus greening or huanglongbing disease(UMT, Lhr, 2023) Muhammad AwaisCitrus greening disease which is also known as Huanglongbing (HLB), it caused serious threat to the citrus industry across the globe due to its rapid spread. it is caused when tripartite association occur between psyllid, bacteria and hots plant. it infects the citrus plants through vector Asian citrus psyllid (ACP) also known as Diaphorina citri Kuwayama (D. citri) which carry the infectious bacterium Candidatus Liberibacter asiaticus (CLas), which is gramnegative bacterium. During infection the fruits become smaller, taste sour, and bitter and sometime cause the death of plant. The aim of this study was to access the potential treatment of HLB, for this approach we conducted the in-silico experiment. Where we docked the maximum number of proteins of D.citri and CLas with citus plant’s phytochemicals, Density functional theory (DFT) of phytochemicals was performed to check the reactivity of those phytochemicals which showed best binging energies with maximum number of proteins of psyllid and CLas. Three phytochemicals, Eriocitrin, Rhoifolin and Narirutin showed beast binging affinities as compare to the restItem Comparison between microarray and rna seq data of rheumatoid arthritis patients from both blood and synovial fluid(UMT, Lhr, 2023) Laiba TahirThe joints are largely affected by the chronic inflammatory illness known as rheumatoid arthritis (RA). Asymmetrically attacking the exact same joints on both sides of the body, it is characterized by swelling, stiffness, discomfort, and inflammation in the joints. However, rheumatoid arthritis can also impact the body's various organs and functions. In our study we aimed to identify hub genes that have a role to play in the occurrence of rheumatoid arthritis from microarray and RNA seq data from both blood and synovial fluid. To those means we used a microarray blood sample dataset GSE15573 (18 RA patients and 15 controls), a microarray synovial fluid sample dataset GSE10500 (5 RA patients and 3 controls) and a RNA seq dataset GSE154474 (3 blood neutrophil RA patients and 3 synovial fluid neutrophil RA patients). By taking a bioinformatics approach we were able to identify ten hub genes (HBB, RGMB, AXIN2, LEF1, TCF7, DMTN, HBA1, HBA2, KRT5, NOG). We were able to conclude that the identified hub genes all have potential to act as biomarkers for rheumatoid arthritis.Item Binning and annotation of saline soil metagenome(UMT, Lhr, 2023) Zain AbbasThere are about 10 million to 14 million estimated number of earth’s current species. Of them, reporting of 1.2 million has been done and 86% of them have not yet been described. To establish a tree of life and to get a comprehensive idea of all types of species existing on this planet and their phylogenetic relation, genome sequencing of all forms of life has to be done. Extreme environments are fascinating regions on Earth where organisms have adapted to survive and thrive under extreme conditions that are generally inhospitable to most life forms. It is estimate that 1 gram of soil contains billions of microbial species and reporting of only 1-2% will have been done. Modern NGS technologies with their exploitation in microbial field has discovered enormous number of species. The term metagenomics discovered to study the diversity of microbes present in different habitat. In this study, hypersaline soil samples were collected from the Khewra region. The samples were pooled together and total DNA was extracted using MO BIO's PowerSoil DNA Isolation Kit. The sample was sequenced from University of Minnesota, Genomics Center using PacBio SMRT sequencing technology. The reads obtained were further processed for quality control and trimming. There were 965 contigs found out with 65 percent GC content. The structural and functional annotation was done through IMG JGI database system. The binning and phylogenetic analysis was done through Busybee Web for comprehensive and differential composition-based metagenomic binning. It was found out that there were 186 RNA genes and 19909 protein coding genes. Functional annotation showed a fraction of protein coding genes that have function in inorganic ions transport and metabolism, cell wall/envelope biogenesis making the microbes able to survive in extreme saline conditions. The distribution of halophiles such as Haloterrigena, Halorubrum, Streptomyces, Paraoceanicella, Mesorhizobium, and Natronomonas across the saline habitat suggesting their important role in this environment. Further pathway analysis output showed involvement of genes in different pathways such as energy metabolism, amino acid metabolism, xenobiotics degradation, motility. We successfully characterized the saline soil microbial community of khewra mines using PacBio SMRT sequencing technology.Item Revalence and risk factors of postpartum depression in pakistani women.(UMT, Lhr, 2023) Farwa DaarBackground: According to the International Classification Disease (ICD-10), the start of depressive symptoms during the six weeks after child birth is called postpartum depression. It may occur soon after delivery or up to a year later. Most of the time, it occurs within the first 3 months after delivery. Worldwide about 15% of mothers are affected by the postpartum depression yearly. Symptoms of postpartum depression include overwhelmed feeling, continuous crying , lack of attachment with her new born baby and feeling that she is not able to care for yourself and baby. In this study, we aim to find out the prevalence of postpartum depression among the population of a specific region of Pakistan where this is not studies before. Methodology: This study was a hospital based study to collect the data randomly from 250 women who was going through the second day of their cesarean after baby birth. The data is collected by visiting my patients personally to fill up my questionnaire based on patient history regarding pregnancy complications and other medical complications in association with their social life stability and its combine effect on their mental health. By personally contacting each patient on phone call after 6 weeks of their baby birth to screen them for postpartum depression. This screening test is performed by using EPDS scale which is pre structured questionnaire with 10 questions. The study has been conducted in a specific area of Punjab Pakistan the city Sheikhupura children complex hospital and Nimrah hospital Sheikhupura. This area is selected to know the risk factors causing postpartum depression because of the difference in culture from the other areas and provinces. Results: Total 250 mothers participated in the survey. The average of age (standard deviation) was 26.18 (5.53) years that ranked between 18 to 50 years. Over 61.6% women did not receive any formal education, constituting the majority of the study population And only 46% of population has high income status. About 53.2 % of females support facing more PPD and 60.8% with high social support having fewer chances PPD. Formula milk feeding, low social support, gender of the baby and family type of the newborn was significantly associated with increased frequency of postpartum depression. In this study according to EPDS the incidence of postpartum depression in the current study population was 17.5%. Conclusion: There is great need of social support to newly born babies mothers in their emotions and also in their handling of baby and to give them the time to recover themselves and their body conditions to the normal.Item Knowledge, attitude and practices of general population of punjab, pakistan regarding to obesity, a cross sectional study.(UMT, Lhr, 2023) UMER AMINBackground: Obesity is a condition of body with overload of fat in the body, which is due to the genetic and environmental factors and is difficult to overcome through dieting. Over weight and obesity are different from each other. Basically, overweight is the weight of body more than normal weight. And obesity is the excess of body fat. It is mandatory that all obese persons are overweight, but not all overweight people are obese. The well-known and the most used method to measure obesity are calculating BMI of a person. It is actually the ratio of weight to height multiplied by number 703. The weight is usually measured in (Kg) and height in (m2). There is also many other methods are available to measure the obesity. Major types of obesity are: Physical obesity and Pathological obesity.According to global disease calculation in 2014 it is howed that Pakistan becomes 8th number country in the list of countries which are dealing with obese people of the half of the 693 million in the world. Methodology: This study was a cross-sectional study. An initial survey form has been designed by using Google-forms to collect the information about the knowledge, attitude and practices regarding obesity. The survey was sent both electronically as well as survey was conducted physically and interviews have been taken. The data has been obtained from the students, employers, un-employers, (male, female) of age groups (18 to 50years). The study has been conducted in a specific area of Punjab Pakistan the city Sheikhupura Nutrition clinics, Gyms, Private and public health care facilities, Public parks, Community and Pharmacies. This area is selected to collect the Knowledge, attitude and practices of general population of this area in regard to obesity. Results: According to the results the knowledge of people about obesity is’nt enough. Only 37% people kmows that obesity can be assesed by an entitiy called BMI. And about 38% people know that obesity is associated with cardiac diseases and the main reason of it is more sugar consumption. The attitude of the people towards obesity is not much beneficial. From the total population being studied only 14% people consider themselves obese and 46% people think they are not obese definitely. About 55% people think that regular breakfast is good for health and only 4% people respond negative on this question. Attitude of the people in controlling their obesity is also about 50% positive. Almost 25% are very confident that they prefer salad or healthy food on fried foods and 16% are slightly confident in it. If we talk about the practices of people to control the obesity or their overweight only 18% people do excercises regularly and 13% do once in a week and 23% people never do exercise. About 18% people use helpers for their household activities and 23% rarely use helpers. Coclusion: However, the results of our study is suggesting that the transformation of positive attitudes into practice still requires further work. Because unless or until we wouldn't accept about our extreme level of dependency on modern technology inventions rapidly changing our lifestyle from physically active to sedentary.Item Prevalence of dengue fever in adolescents and adults in lahore, pakistan.(UMT, Lhr, 2023) AQSA AHSANDengue is a mosquito-borne viral disease that is caused by female Aedes Mosquito. Severe form of this infectious disease is deadly which is known as DHF or DSS. This disease has become a topic of interest for the whole world as it is affecting large number of people around the world. There is no any proper treatment, medicine or vaccination for this disease. The Aim of our study was to determine the prevalence of Dengue fever among adolescents and adults in Lahore region. Total of 400 individuals were selected for study. Blood samples were extracted from patients, collected, centrifuged and stored in test tubes. ELISA was performed to determine the presence of IgM in sera sample of patients. Hematology analyzer was used for CBC, with the help of which number of RBCs, WBCs, Hb, Platelet count etc. was determined. Data of all the subjects was collected on Excel sheet and SPSS software was used to determine the descriptive statistics of Data. The results of our study revealed that dengue affects males more than females. Out of 400 total subjects, 182 (45%) were females and 218 (55%) were males. Age group 21-40 was found to be mostly affected by dengue. Among all the cities included in our study, Lahore was found to be at risk of spreading Dengue infection. It was also found that dengue also causes changes in all the hematological parameters like Hb, WBCs, RBCs and hematocrit. Moreover, it also causes changes in liver enzymes and its severe form can even damage the liver. As, Lahore is at risk of developing this disease, there must be awareness spreading programs among people of all over Punjab to take precautionary measures strictly.Item Biochemical characterization of naringenin producing yeast (saccharomyces cerevisiae) strain(UMT, Lhr, 2023) WAJEEHA UROOJExtensive research has been carried out during the last few decades, providing a detailed account of thousands of discovered phytochemicals and their biological activities that have the potential to be exploited for a wide variety of medicinal purposes. These phytochemicals, which are pharmacologically important for clinical use, primarily consist of polyphenols, followed by terpenoids and alkaloids. Numerous published reports indicate the primary role of phytochemicals proven to possess therapeutic potential against several diseases. However, not all phytochemicals possess significant medicinal properties, and only some of them exhibit viable biological effects. Naringenin, a flavanone found in citrus fruits, is known to improve immunity, repair DNA damage, and scavenge free radicals. Despite the very low bioavailability of naringenin, it is known to exhibit various promising biological properties of medicinal importance, including anti-inflammatory and antioxidant activities. It focuses on various aspects related to naringenin, particularly its physicochemical properties. Furthermore, various pharmacological activites of naringenin, such as anticancer, antidiabetic, hepatoprotective, neuroprotective, cardioprotective, nephroprotective and gastroprotective effects, have been discussed along with their mechanisms of action. In our research, yeast was engineered with naringenin pathway genes (TAL, 4CL, CHS, CHI). The production of desired product increased by using different biochemical parameters. I explored various permutations of essential parameters such as pH, temperature, inoculum size, carbon source, nitrogen source, and substrate concentration using Response Surface Methodology (RSM) software. Naringenin compound was extracted from the fermented broth by using ethyl acetate. The extracted compounds was first analyzed by using highthroughput chemicals (sodium Hydroxide, folin, potassium hydroxide, magnesium sulfate, lead oxide and ammonium hydroxide) and subsequently, conducted confirmation test using HPLC. This comprehensive analysis sought to determine the concentration at which our yeast exhibited the highest production of the desired flavonoid, Naringenin. The engineered strain produced naringenin compound which was further optimized with different biochemical parameters. The engineered strain produce maximum compounds when use inoculum size 4%, carbon source 8%, nitrogen 3%, pH 6, temperature 30 oC and subtrate concentration 0.30%. These conditions were confirmed by chemical methods. Among all chemical sodium hydroxide oxide maximally bind with the naringenin compounds and give bright yellow colour. Other methods which need to be add to increase the desired compounds by adding malonyl-CoA and overexpression of pathway genes. As one molecule of naringenin requires three molecules of malonyl-CoA, and malonyl-CoA availability represents a bottleneck in the biosynthesis pathway. The recombinant yeast strain was fed with phenylpropanoid acids and produced naringenin. In conclusion, the production of naringenin using microbial cell factories, including yeast strains such as Saccharomyces cerevisiae, has shown promise. However, yields remain low, and further optimization is needed to increase production. There is no specific study on the biochemical characterization of a naringenin -producing S. cerevisiae strain, studies on naringenin biosynthesis in S. cerevisiae therefore it is the first study to consider biochemical characterization of S. cerevisiae to produce naringenin.Item computational analysis of potential repellents against economically important insects(UMT, Lhr, 2023) SANA NASIMMosquitoes are vectors for multiple diseases caused by bacteria, viruses, and protozoa. Because mosquitoes convey a variety of illnesses, the exponential population growth of mosquitoes poses a serious threat to many countries. Because of the lactic acid found in human sweat, mosquitoes are attracted to humans. A chemical that works locally or remotely to keep insects from biting people or animals' skin is known as an insect repellent. The use of plant-based repellents has gained popularity again recently due to their abundance of bioactive phytochemicals that are safe and biodegradable into byproducts that are not harmful and can be tested for insecticidal and repellent properties. Most plants create a variety of chemicals to stave against attacks by insects that consume plants, or phytophagous insects. In this study, main focus is on domain of computational analysis in the pursuit of potential repellent compounds against economically important mosquito species. Specifically, we delve into the intricate molecular world of mosquitoes and their interaction with twoprominent plant species, Mari Gold (Tagetes spp.) and English Lavender (Lavandula angustifolia). These plants, due to their aromatic properties, hint at the presence of chemical constituents that may possess the ability to repel mosquitoes and provide a novel avenue for pest management. This study is designed to: investigate the interactions between mosquito proteins and specific compounds present in the plant repellents, i.e., Mari Gold and English Lavender. Various bioinformatics tools including PDB, Dr. Duke, modeler 10.1, chimera 1.15, PubChem, Server NCBI, and MOE are used in the research. The docking process showed the interactions between proteins of mosquitoes and the phytochemicals. DFT confirmed the energy gapsand verified the results. After screening selecting phytochemicals, the lowest energy gap is of antheraxanthin which is 0.08144 kcal/mol. So this phytochemical has high reactivity with protein and low binding energy gap So, Antheraxanthin proved to be the best phytochemical to repel insects.Item Prevalence of deviated nasal septum (DNS) among patients having nasal symptoms in lahore pakistan(UMT, Lhr, 2023) Muhammad Nauman AzizWhen the bone and cartilage septum that divides the nasal cavity is misaligned, it is said to have a deviated septum. Some people are born with a deviated septum. Others develop it as a result of a nasal injury. A highly deviated septum may result in headaches, congestion, and breathing problems. A deviated septum may be surgically corrected. The purpose of this study is to ascertain the frequency of Deviated Nasal Septum (DNS) among patients in the city of Lahore who have nasal symptoms. On 260 patients from various hospitals in Lahore, a cross-sectional study was randomly conducted. The Beckman Depression Inventory Scale (BDI) and the Nasal Obstruction Symptom Evaluation (NOSE) scales were used to collect the data. The data was analyzed using (SPSS 24.0). Ages between 20 to 40 years, both sexes, patients who have been diagnosed already, those without a history of trauma, and those who have had nasal symptoms (such as congestion) for more than a month were included. Out of 260 patients the mean age was 35.91± 8.64. The male to female ratio was same (n=130) and the mean BMI was 28.6 ± 4.55. Out of 260 patients the mean NOSE scoring was 70.2 ± 13.2 and BDI scoring was 33.61± 4.18. There was a significant association of gender with level of depression, nasal congestion or stuffiness, nasal blockage or obstruction, trouble breathing , trouble sleeping and unable to get enough air of patients as p = 0.003, 0.013, 0.24, 0.005, 0.032 and 0.003 (< 0.005). DNS was present in approximately 75% of cases among patients with nasal symptoms. However, the study suggests that DNS is more prevalent in males and may be associated with an increased risk of depression.Item Prevalence of asthma associated with deviated nasal septum in lahore, pakistan.(UMT, Lhr, 2023) MaryamDeviated nasal septum (DNS) is a common nasal abnormality that can causes persistent upper airway obstructions. Asthma was linked to the incidence of DNS with an obstructive symptom. This study was conducted to ascertain the prevalence of asthma among the Deviated Nasal Septum patients in Lahore city. This was an observational cross-sectional study and was conducted at the Lahore population among 250 randomly selected patients. Age between 20 to 50 years, both genders diagnosed with asthma and nasal septal defect and having symptoms from the last 3 or more months along with no history of surgery or injury or having septal defect by heredity or dentition were included. The data was collected from standardized Nasal Obstruction Symptom Evaluation, Patient Health Questionnaire (PHQ) and the Asthma Control Questionnaire. The data was computed through (SPSS-25.0v). For categorical data, frequency and percentages were used, and the chi-square test to establish the relationship between the various variables, with a p-value of > 0.05 considered significant. For the association of the data correlation was evaluated and standard deviation was used to measure the spread of values in a sample. According to the results, out of 250 patients Mean ± SD age was 35.35 ± 8.815, the male and female ratio was the same n=125) and BMI was 28.49 ± 4.495. Out of 250 patients, the Mean ± SD value of Nasal obstruction and septoplasty effectiveness scale and total scoring was 70.92 ± 13.20, Asthma Control Questionnaire total scoring was 17.99±3.17 and Patient Health Questionnaire (PHQ-9) total scoring was 2.26 ± 0.749.Out of 250 patients there was significant association between Nasal Obstruction and Septoplasty Effectiveness Scale Total Scoring and asthma total scoring as p=0.038 (<0.05), asthma total scoring and PHQ-9 total scoring as p=0.028 (<0.05).The one sample t test shows significant association as p=0.000 (<0.05). In conclusion, the study found a significant association between deviated nasal septum and asthma. This suggests that patients with DNS may be at a higher risk of developing asthma. As well found mostly males are more prevalent in suffering from DNS.Item Plant growth promoting purple non-sulfur bacteria isolated from local pond in lahore(UMT, Lhr, 2023) NimraPurple non-sulfur bacteria (PNSB) belong to the phylum Proteobacteria and give reddish brown to purple color when grown in anaerobic conditions and incandescent light. PNSB are of outstanding biotechnological interest because of their recognized variety of metabolic activities. Purple nonsulfur bacteria were recovered from ponds close to the Kot Lakhpat prison, Model Town Park, and Arfa Kareem Park, Lahore. PNSB were tested for resistance against different concentrations of arsenic, cadmium, mercury and chromium. PNSB were characterized using a combination of molecular, morphological, and physiological techniques. PNSB are also known for the production of clean, renewable hydrogen gas. All PNSB isolates were analyzed for the gas production. Except for MNP2, MNP4, and MNP7, all strains showed positive results. Plant-promoting activities of PNSB were analyzed such as phosphate solubilization, auxin production, nitrogen fixation, and hydrogen cyanide production. All strains had the ability to solubilize the phosphates. MP2 showed maximum auxin production. In the nitrogen fixation experiment, all isolates demonstrated positive results with the exception of MNP1 and MNP4. In case of HCN production, MNP2 and MNP6 exhibited positive results. Different combinations of Vigna radiata seeds, arsenic, PNSB strains, and pteris vittata were tested. It was found that metal repressed the growth of the plants, however, the presence of PNSB enhanced the plant growth. Moreover, the presence of both PNSB strains and pteris vittata showed maximum plant growth promotion in the presence of arsenic. Using PCR, 16S rRNA gene was amplified and sequencing was performed from Macrogen, South Korea. Arsenic-resistant PNSB can help plants grow better in arsenic contaminated sites in combination with Pteris vitatta.Item Comparative analysis of factors associated with initiation and progression of CVST(UMT, Lhr, 2023) Aun RazaCerebral venous sinus thrombosis is a posterior and cavities condition that forms due to the formation of clots in the veins of the bloodstream, specifically in the area of the paranasal sinuses. It can be diagnosed in several ways, including a physical examination and medical history. Various symptoms such as headaches, seizures, vision disturbances, etc. They appear when the effects of caffeine are related to an inadequate metabolism and the cause of this disease increases due to the constriction of the veins that facilitate the increase in blood pressure and the faster formation of clots in them. areas. In this research, different computational methods were used to identify structural and functional changes associated with a change in the wild-type sequence. 38 of 176 nsSNPs in the human CYP1A2 gene were predicted by a combination of computational methods. As functional variables. To look for possible connections with pathogenicity, functional nsSNPs were further examined. The result was that 18 nsSNPs were predicted as pathogenic, among which variants G73R, G73W, R108Q, R108W, E168K, E346K, R431W, F432S, and R456H were also found to be associated with pathogenicity. These results provide new insights into the structure-function association in CYP1A2, CVST and other CYPs and can be taken into account when planning experimental investigations. To fully understand the links and causes of diseases, it is necessary to use more sophisticated methods.Item Identification of hub genes associated with fanconi anemia via integrated bioinformatic analysis(UMT, Lhr, 2023) Salman HaiderThe Genetic disease FA or Fanconi Anemia is a disorder that is very rare and that cause different genetic changes and different chemical and physical abnormalities in children. The prevalence of the disease is 1 out of 1600000 and present in all ethnic groups and populations but the high ratio of prevalence is present in Jewish, Afrikaans and Spanish communities. The disease symptoms have been confused for a long time with aplastic anemia and different other types of cancers due to its effectiveness on the organs, organ system, skeletal bones, hematological effects including low blood number for platelets, white blood cells and red blood cells. The most reliable treatment is bone marrow transplant although research and advancement are being made on gene therapy and drug therapy. The age expectancy despite of research and treatment being in progress is not more than 30 years. The genetic mutation in one of the 22 genes was considered responsible for the cause of disease in early researches. The scientists later on grouped 23 genes called FANC genes which were mainly affected by mutation causing the Fanocni Anemia disorder. My work and research in the BioGRID project show a total 69 genes obtained from the database and after a very careful analysis of the literature, the gene number increased to 71. All the genes were set in a table with their gene symbol, name and characteristics. The PPI (ProteinProtein Interaction) network was made using STRING, visualized using Cytohubba, a plugin of Cytoscape to find out the main responsible top 10 hub genes of Fanconi Anemia. The GO and KEGG pathway analysis were also made using the DAVID bioinformatics. The obtained results of top 10 hub genes and all components of biological, cellcular, pathway nature could help researchers for designing effective drugs in the treatment of Fanconi Anemia and better understanding of the disease genetics.Item In-silico analysis of coding and non-coding variants in mettl5 gene(UMT, Lhr, 2023) Muhammad Haris Ali KhanIts relationship to intellectual impairment (ID) in people with METTL5 gene. Mutations in METTL5 have been linked to mild to severe forms of ID, which can manifest as deformities, seizures, microcephaly, short stature, and muscular hypotonia. The METTL5 gene is present on chromosome no 2. The METTL5 gene form a complex with TRMT112 and work normally. Due to knockdown of TRMT112 molecule the METTL5 gene expression is low in the body. In this study, bioinformatics approach has been used to predicted the coding and noncoding variants that effect the function, stability, splice site and non-coding region of METTL5 gene. A total of 66 missense variants in METTL5 gene were predicted to be pathogenic by CADD and Meta-SNP. These mutations were analyzed by CUPSAT, DynaMut and DUET for their effect on stability and variations were predicted pathogenic overall. 60 of the 61 variations were predicted to be affecting the function of the gene by Mutpred .4 variations p.Asp49Tyr, p.Asp103Gly, p.Leu76Trp and p.Gly130Glu were predicted by ScanProsite and NetSurfP 2.0 to affecting the PTM mechanism of the protein. These 61 missense variants were visualized by UCSF Chimera. There were no clashes found in protein structure after mutation. CADD predicted 15splice site variants, out of 15 variants 10 variants were pathogenic and further analyzed for their effect by SPiCE v2.1, Splice AI and Mutation Taster. None of variations with uncertain significance found in splice site were predicted by Splice AI, 4 out of 9 variants were predicted pathogenic by SPiCE v2.1 and 2 out of 9 variants were predicted deleterious by Mutation Taster to affecting the splicing site of the gene. The Regulome DB 2.2 was used for the analysis of non-coding variants and predicted that less effect on the TF binding site of METTL5 gene. The protein plus ligand analysis showed that 2 out of 5 mutated residues show no interaction with the ligand and 3 out of 5 mutated residues show the interaction with ligand structure. Data can be used for the early detection of mutations in METTL5 by cloning the mutation individually and determining their effect in vectors by mutagenesis. These findings contribute to our understanding of METTL5 gene representing complex disease features. This study demonstrated the importance of bioinformatics in determining highly pathogenic variants associated with the functional and structural relationship of METTL5Item Biochemical characterization of pinocembrin producing yeast (saccharomyces cerevisiae) strain(UMT, Lhr, 2023) SAULAT NAWAZ SHAHFlavonoids are a wide-ranging class of naturally occurring compounds with different phenolic structures that can be found in many different places, such as fruits, vegetables, cereals, tea, wine, tree bark, roots, stems, and flowers. Because of their strong antioxidant qualities and ability to reduce inflammation-related symptoms, these substances provide a wide range of health advantages and are simple to include in a diet. The possibilities are bright even though researchers have only begun to explore flavonoids' potential as a medicine. Flavonoids are found throughout the kingdom of plants, where they perform a variety of roles. Pinocembrin is unique among these substances due to its diverse biological properties, which include antiinflammatory, antioxidative, and neuroprotective actions. The synthesis of pinocembrin using microbial cell factories specifically, yeast strains like Saccharomyces cerevisiae has attracted attention recently. We thoroughly investigated primer design, oligonucleotide synthesis, yeast transformation techniques, and yeast genomic DNA extraction in our study. Then, we designed a cassette to facilitate the insertion of plant genes into the S. cerevisiae strain and expedite the manufacture of flavonoids. In order to conduct our study, we genetically altered yeast by adding genes (PAL, 4CL, CHS, CHI) related to the pinocembrin pathway. Through the optimization of several important biochemical parameters, this genetic modification led to an increase in the production of the targeted product. Using Response Surface Methodology (RSM) software, we carefully investigated various combinations of important parameters, such as pH, temperature, inoculum size, carbon supply, nitrogen source, and substrate concentration. Ethyl acetate was utilized to extract pinocembrin from the fermenting broth. A complete study of the extracted substances was carried out, using a range of chemicals (sodium hydroxide, Folin, potassium hydroxide, magnesium sulfate, lead oxide, and ammonium hydroxide). High-Performance Liquid Chromatography (HPLC) was then used to confirm these findings. The goal of this thorough investigation was to ascertain the circumstances in which our yeast strain produced the most pinocembrin, the desired flavonoid. Under particular conditions, our engineered yeast strain showed optimum synthesis of pinocembrin 4% inoculum size, 8% carbon source, 3% nitrogen source, pH 6, 30 °C temperature, and 0.30% substrate concentration. These parameters were confirmed by means of chemical analysis, where in sodium hydroxide was found to have the highest binding affinity with pinocembrin compounds, resulting in brownish color. In order to maximize the yield of the desired compound, extra steps were taken, including the addition of malonyl-CoA and the overexpression of pathway genes. This was required because each molecule of pinocembrin requires three molecules of malonyl-CoA, and the availability of malonyl-CoA represents a bottleneck in the biosynthesis pathway. Ultimately, the production of pinocembrin using microbial cell factories—specifically yeast strains like Saccharomyces cerevisiae shows great promise; however, the yields are still relatively low and require additional optimization. Our research is the first to address the biochemical characterization of S. cerevisiae for pinocembrin synthesis, as there are notably few publications that focus specifically on this topic.Item Heavy Metal Resistant Purple Non-Sulfur Bacteria Isolated from Local Pond in Lahore(UMT, Lhr, 2023) MahnoorPurple non sulfur bacteria are phototrophic bacteria belonging to the group Proteobacteria. PNSB give reddish brown to purple color when grown in anaerobic conditions and incandescent light. PNSB are known to possess diverse metabolic activities and hence are of great biotechnological interest. Heavy metals such as arsenic, mercury, cadmium, chromium and nickel are toxic for the environment and can cause many health-related problems. PNSB can help in the detoxification of heavy metals from the environment. In this study, PNSB were isolated from different ponds located in Model town park and from a pond located near Kot Lakhpat jail in Quaid-e-Azam industrial state, Lahore. PNSB were screened for resistance against different toxic metals. The process of characterizing and identifying PNSB combined morphological, biochemical, physiological, and molecular methods. These PNSB isolates were gram negative. To better define PNSB, several physiological tests can be carried out. When PNSB growth was investigated at various pH values and temperatures, all isolates were able to grow at 25 to 40℃, however, maximum growth occurred at 30 and 37℃. PNSB generate pigments including bacteriochlorophylls and carotenoids, which gives them their purple shade. The pigmentation of all PNSB isolates was reddish brown to purple shade. The hydrogen gas generated by PNSB photosynthesis is a clean and renewable energy. For every PNSB isolate, the gas generation experiment was carried out. With the exception of MNP2, MNP4, and MNP7, all outcomes were positive. PNSB were analyzed for resistance against different concentrations of arsenic, cadmium, mercury, chromium and nickel. The maximum concentration of arsenate, arsenite, chromium, cadmium, mercury and nickel resisted by PNSB were 40mM for arsenate, 10mM for arsenite, 5mM for chromium, 2.5mM for cadmium, 2.5 mM for mercury and 5mM for nickel. Growth curve pattern of PNSB was analyzed both in absence and presence of arsenic. The phylogenetic connection of PNSB species is frequently ascertained using 16S rRNA gene sequencing. Genomic DNA was isolated and 16S rRNA gene was amplified using PCR. The amplicons were sequenced from Macrogen, Korea. These PNSB can be utilized to detoxify arsenic along with production of hydrogen.Item A Meta-Analysis of GWAS and Random effect model to detect novel loci in Atriai Fibrillation(UMT, Lhr, 2023-10) Zunara ArshadTo find novel loci with atrial fibrillation risk variants, we undertake a large-scale metaanalysis of atrial fibrillation genome-wide association studies with over 19,166 atrial fibrillation cases and over 2,62,516 control people of European and Japanese ancestry Using the GWAS summary statistics we performed meta-analysis and applied random effect model over million SNPs and find out 1718 novel SNPs from which 15 SNPsarestrongly linked with Atrial Fibrillation (AF) . Risk loci of these 15 novel SNPs are KCNN3, SPATS2L, PHLDB2, PITX2, HNRNPAO, RNU1-18P, CAVl, AOPEP, NEURLl, KCNJ5, TBX5, SYNE2, HCN4, and ZFHX3 identified by using NCBI database. The novel SNPs located at 2q33.1, 4q25, 7q31.2, 10q24.33, 12q24.21 and 16q22.3 have p<5E-8 and shows highest peaks in the Manhattan plot indicating those risk variants that are most susceptible to AF in European and Japsinese population. The variants identified needs to be verified in independent case controls studied across different ethnicities