Search

There have been 6,566,610 fatalities and 626,337,158 reported cases of COVID-19 worldwide. Pakistan presently has over 1,573,922 confirmed cases and 30,625 deaths. A survey-based study was performed from January to September 2022 among different university communities to find out their KAP level. Data was collected in Google Forms through a questionnaire. The Independent t-test, Multinomial regressions, and Non-parametric Mann-Whitney test were used to assess the level of significance (p-value ≤0.05). 317 out of 605 participants were male (52.5 %), the majority of participants were 15-29 years old (72.7 %), unmarried/divorced (71.6 %), have no children (82.1 %), residing in the urban area (54.9 %) and possess a college/university degree (59.5 %). The majority of participants correctly answered five out of six knowledge questions (M = 4.96, SD = 1.03) and correctly identified the primary symptoms of COVID-19 (94.4 %) along with the proper identification of mode of transmission (95.2 %) while 1.8% wrongly replied and 2.1 % did not reply. A knowledge test revealed the significant frequency of misconception, with nearly half of the respondents (46.3 %) assuming that illness might be contracted by eating or coming into touch with wild animals. Wearing a facial mask is highly practiced (M = 3.59, SD = 0.91), followed by avoiding crowded places (M = 3.44, SD = 0.95) and practicing hand hygiene (M = 3.36, SD = 1.04). Females, the elderly, and the less educated, on the other hand, have less understanding of COVID-19, making them especially susceptible to the pandemic. It is proposed that further awareness might contribute to a favorable attitude and practice.

Aim: To characterize and analyze polymorphism of the MPT64 gene and evaluate AgMPT64-based immunochromatographic assay (ICA) specificity associated with polymorphism. Materials & methods: A total of 1449 suspected samples were tested for tuberculosis (TB), and the MPT64/ rv1980c gene was sequenced using next-generation sequencing for polymorphism analysis. Results: Of the TB-positive individuals, 200 (13.80%), 186 (12.84%) and 129 (8.90%) were positive using the liquid culture, GeneXpert and fluorescence microscopy assays, respectively. Liquid culture medium-based samples were confirmed using ICA, in which 193 (96.5%) were positive while seven (3.5%) were negative. Out of 14 sequenced samples, seven were positive and seven negative; 13 were identical to the reference and just one (ICA positive) showed a C477A point mutation (F159L). Conclusion: The results indicate that AgMPT64 can be considered as a potent vaccine candidate.

This research study focused on the economic impact of covid-19 on small and medium entrepreneurs. This research study was conducted in seven districts of Khyber Pakhtunkhwa. A total of 350 samples were randomly selected from seven districts. From each district 50 samples were selected including 25 small and 25 medium entrepreneurs. All the samples were taken from auto, hoteling, grocery, fresh food and garments industries. The results showed that stay-at-home policy inflicted huge economic cost both on small and medium entrepreneurs in Khyber Pakhtunkhwa. On average a small entrepreneur in Khyber Pakhtunkhwa lost US $1552.8 per day while every medium entrepreneur lost US $13084.2 per day in the garments industry during covid-19 lock down. Similarly, per day average cost of a small entrepreneur in Khyber Pakhtunkhwa was US $898.7 while that of the medium entrepreneur was US $6140.65 during covid-19 lock down. This financial lost/cost did not include any past or current liabilities rather it was derived from the sale and purchase data collected from the local entrepreneurs in Khyber Pakhtunkhwa.

The recent COVID-19 pandemic has brought attention to the strategies of quarantine and other governmental measures, such as lockdown, media coverage on social isolation, strengthening of public safety, etc. All these strategies are because to manage the disease as there is no vaccine and appropriate medicine for treatment. The mathematical model can assist to determine whether these intervention options are the most effective ones for illness control and how they might impact the dynamics of the disease. Motivated by this, in this manuscript, a classical order nonlinear mathematical model has been proposed to analyze the pandemic COVID-19. The model has been analyzed numerically. The suggested mathematical model is classified into susceptible, exposed, recovered, and infected classes. The non-standard finite difference scheme (NSFDS) is used to achieve the approximate results for each compartment. The graphical presentations for various compartments of the systems that correspond to some real facts are given via MATLAB.

Background: Genetic studies play a significant role in understanding the underlying risk factors of breast cancer. Polymorphism in the tumor suppressor gene TP 53, CDH1 and ATM genes are found to increase susceptibility for breast cancer globally. Objective: This study aimed to identify/analyze the contribution of genetic polymorphisms in the breast cancer candidate genes ATM, TP53 and CDH1 that may be associated with familial breast cancer risk in the Khyber Pakhtunkhwa population. Subjects and Methods: In the present case-control study, Whole Exome Sequencing (WES) of the 100 breast cancer patients and 100 ethnic controls were performed for the selected genes in the target population. Results: Of the studied variants rs3743674 of the CDH1 gene (crude P=0.014 and adjusted p=0.000) evident significant association with breast cancer in Pakistani Pashtun population. Whereas TP53rs1042522 (crude P=0.251 and adjusted P=0.851) and ATM rs659243 (crude p=0.256 and adjusted p=0.975) showed no or negative association with breast cancer in study population.Conclusion: The present study demonstrates that CDH1rs3743674 polymorphism is associated with elevated breast cancer risk in the Pashtun ethic population of Khyber Pakhtunkhwa. Keywords: Breast cancer; TP53; CDH1; ATM; Risk Allele; Genotype.

COVID-19 disease caused by the SARS-CoV-2 virus has shaken our health and wealth foundations. Although COVID-19 vaccines will become available allowing for attenuation of disease progression rates, distribution of vaccines can create other challenges and delays. Hence repurposed drugs against SARS-CoV-2 can be an attractive parallel strategy that can be integrated into routine clinical practice even in poorly-resourced countries. The present study was designed using knowledge of viral pathogenesis and pharmacodynamics of broad-spectrum antiviral agents (BSAAs). We carried out the virtual screening of BSAAs against the SARS-CoV-2 spike glycoprotein, RNA dependent RNA polymerase (RdRp), the main protease (Mpro) and the helicase enzyme of SARS-CoV-2. Imatinib (a tyrosine kinase inhibitor), Suramin (an anti-parasitic), Glycyrrhizin (an anti-inflammatory) and Bromocriptine (a dopamine agonist) showed higher binding affinity to multiple targets. Further through molecular dynamics simulation, critical conformational changes in the target protein molecules were revealed upon drug binding which illustrates the favorable binding conformations of antiviral drugs against SARS-CoV-2 target proteins. The resulting drugs from the present study in combination and in cocktails from the arsenal of existing drugs could reduce the translational distance and could offer substantial clinical benefit to decrease the burden of COVID-19 illness. This also creates a roadmap for subsequent viral diseases that emerge. Communicated by Ramaswamy H. Sarma

The publication of the first draft of human genome, has led to the explosion of high throughput technologies including genomics, epigenomics, transcriptomic, proteomics, and metabolomics aiming to characterize the various biological molecules (DNA, RNA, proteins, and metabolites). These high throughput technologies collectively called as omics revolutionized medical research in the last two decades. The advent of next generation sequencing (NGS) reduced the time and economic cost of traditional sequencing and has led to the emergence of genomics as the first discipline of omics. Following the emergence of genomics, a number of projects such as The Cancer Genome Atlas (TCGA), 1000 Genome Project (1KGP), and the International Cancer Genome Consortium have been accomplished. These projects contributed significantly to the understanding of genetic variations in different cancers, for instance, TCGA produced over 2.5 petabytes of big data. Furthermore, the big data produced by these mega projects has been made publicly available to the clinicians and researchers to fast-track the diagnosis and prognosis of complex rare diseases. In developed countries, a multi-omics approach has been applied holistically to the clinical practice for the diagnosis and prognosis of various cancers and rare Mendelian diseases.

Non-synonymous missense SNPs (nsSNPs) in CPE and GNAS genes were investigated computationally. In silico identified nsSNPs were experimentally validated in type II diabetes mellitus (T2DM) in Pakistani Pathan population using next generation sequencing (NGS). Sixty two high-risk nsSNPs in CPE and 44 in GNAS were identified. Only 12 in GNAS were clinically significant. Thirty six high-risk nsSNPs in CPE and 08 clinically significant nsSNPs in GNAS lies in the most conserved regions. I-mutant predicted that nsSNPs decrease the proteins stability and ModPred predicted 20 and 12 post-translational modification sites in CPE and GNAS proteins respectively. Ramachandran plot showed 88.7% residues are in the most favored region of protein models. By experimentation, none of the nsSNPs were found to be associated with T2DM. In conclusion, this study differentiates the deleterious nsSNPs from the neutral ones. Although nsSNPs are not associated with T2DM, they can be targeted in other CPE and GNAS genes related disorders.

More than 200 countries across the globe, including Pakistan, have closed educational institutions (schools, colleges, universities and madrassas) to contain the spread of coronavirus (COVID-19 pan...

In this paper, the depositional environment, age, and tectonic context of the Sub-Himalayan Kuldana Formation are discussed in detail. To determine the Kuldana Formation’s depositional environment, age, and tectonic setting, sedimentological, palaeontological, and petrographic investigations have been conducted accordingly. The Kuldana Formation lithologically consists of both siliciclastic and carbonate rocks. Petrographically, the Kuldana Formation’s sandstone is divided into litharenite and feldspathic litharenite petrofacies. The sandstone plots on the QtFL and QmFLt suggest that the sandstone of the Kuldana Formation derived from a recycled orogen provenance field that developed during the collision of the Indian and Eurasian plates in the Lesser and Higher Himalayas. The plots in the diamond diagram further demonstrate that the detritus of the Kuldana Formation was derived from low and middle-to-upper rank metamorphic rocks of the Himalayas. Throughout the deposition of sandstone, paleo-climate conditions were semi-humid to semiarid. Dolostone and limestone are the two main types of carbonate rocks found in the Kuldana Formation. According to Dunham’s Classification, the Kuldana Formation limestone is classified as mudstone, wackstone, and packstone. These petrofacies suggest that the limestone was deposited in an inner-outer ramp setting. The bioclasts include bivalves, brachiopods, crinoid, gastropods, Globigerinoides spp., Lockhartia pustulosa, miliolids, Nummulites atacicus, Nummulites discorbina, Nummulites mamillatus, Nummulites djodjokartae, Nummulites vascus, and ostracods suggesting that the age of Kuldana Formation is Middle Eocene-early Oligocene. The Kuldana Formation was deposited during the initial stages of the Himalayan Orogeny as a result of the Ceno-Tethys Ocean’s regression and transgression, as revealed by a succession of siliciclastic and non-clastic rocks.

β-Thalassemia (β-thal) is a common monogenic disease with ethnic-specific mutations on the HBB gene throughout the world. The reported mutations either reduce the expression or completely inactivate the HBB gene. In Pakistan, the prevalence of β-thal is high due to consanguineous marriages. Accurate identification of mutations in carriers is imperative for prevention of β-thal in subsequent generations. To overcome the limitations of traditional testing methods for β-thal, a next-generation sequencing (NGS)-based diagnostic test was designed and validated by sequencing the entire HBB gene. The primer set covering the entire HBB gene was designed and validated in a Pashtun β-thalassemic family. The polymerase chain reaction (PCR) product was sequenced using an Illumina MiSeq platform. A homozygous pathogenic insertion of A>AC/AC (rs35699606) was detected in an affected member of the family, while unaffected members were heterozygous for it. In addition, all family members were homozygous for the synonymous variant, A>G/G (rs713040), except the father who was heterozygous for it. We sequenced the entire HBB gene using the NGS-based test, which is highly sensitive, robust and specific for the diagnosis and screening of β-thal in Pakistan, especially for families practicing consanguineous marriages.

This study focuses on suicidal ideation in victims of sexual abuse. Drawing upon semi-structured interviews of thirty victims of sexual abuse in Khyber Pukhtunkhwah, Pakistan, this paper discusses the theme, i.e. domestic violence, including indiscriminate sexual abuse and the abhorring crime of incest, which remains hidden due to aggressively upheld patriarchal norms of women exploitation. The interviews conducted at six different locations, present women's narratives of their untold plight for the first time. The findings of this research show that among the respondents, only those women had strong suicidal ideations who were the victims of incest. Irritation, aggression and self-deprecating behaviour were strong symptoms of their suicidal temptations. Pain, physical and emotional, caused by overwhelming stress in the form of familial and social hatred, social disconnectedness, burdensomeness and the previous history of violence were the main factors that highly escalated their risk factor in committing suicide

Chronic Myeloid Leukaemia (CML) is characterized by BCR-ABL1 mutation. A number of research studies have published reports of concomitant JAK2-V617F mutation in BCR-ABL positive Chronic Myeloid Leukaemia. This study aims to investigate the frequency of JAK2-V617F mutation in BCR-ABL positive CML cases. After approval from ethical committee, participants were enrolled in the study. A total of 103 samples from CML patients were analysed for the presence of JAK2-V617F mutation using real-time polymerase chain reaction. Patients were monitored for treatment response using real-time quantitative PCR for BCR-ABL1 mutation. Out of 103 samples analysed, 2 patients tested positive for JAK2-V617F mutation. These two patients when treated with standard Tyrosine Kinase Inhibitors (TKI) therapy achieved molecular response and normalized the haemoglobin and white cell counts. However, one patient has sustained thrombocytosis. JAK2 remained positive throughout the treatment course. We could not follow the second patient till the end of the study. JAK2 mutation in BCR-ABL1 mutated CML appears to be rare. Treatment with TKI does not appear to reduce JAK2 mutation burden despite a decrease in BCR-ABL1 copy numbers.

This study aimed to characterize the whole genome of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) isolated from an oropharyngeal swab specimen of a Pashtun Pakistani patient using next-generation sequencing. Upon comparing the SARS-CoV2 genome to the reference genome, a total of 10 genetic variants were identified. Among the 10 genetic variants, 1 missense mutation (c.1139A > G, p.Lys292Glu) in the Open Reading Frame 1ab (ORF1ab) positioned at 112 in the non-structural protein 2 (NSP2) was found to be unique. Phylogenetic analysis (n = 84) revealed that the current SARS-CoV2 genome was closely clustered with 8 Pakistani strains belonging to Punjab, Federal Capital, Azad Jammu and Kashmir (AJK), and Khyber Pakhtunkhwa (KP). In addition, the current SARS-CoV2 genome was very similar to the genome of SARS-CoV2 reported from Guam, Taiwan, India, the USA, and France. Overall, this study reports a slight mismatch in the SARS-CoV2 genome, indicating the presence of a single unique missense mutation. However, phylogenetic analysis revealed that the current SARS-CoV2 genome was closely clustered with 8 other Pakistani strains. Supplementary Information The online version contains supplementary material available at 10.1007/s00284-021-02743-y.

Background: Coronavirus disease 2019 (COVID-19) is a global health threat and caused a universal psychosocial impact on the general population. Therefore, the knowledge, attitude, and perceptions (KAPs) of the general population are critical for the development and effective implementation of standard operating procedures (SOP) to contain the contagion and minimize the losses. Therefore, the current study was conducted to understand and evaluate the KAPs of Pakistani populations toward the COVID-19.Methods: An online cross-sectional study was carried out among participants from 1 May to 30 July 2020 in different areas of Pakistan. The respondents of the study were the general population with age ≥ 18 years. The poll URL was posted on several channels after a call for participation. Other social media platforms such as WeChat, WhatsApp, Facebook, Twitter, Instagram, Messenger, and LinkedIn were engaged to maximize general population engagement. The questionnaire included details about sociodemographic, knowledge about COVID-19, perceptions toward universal safety precautions of COVID-19, and beliefs attitude toward the COVID-19. The obtained data were exported into a Microsoft Excel spreadsheet and SPSS software version 21 for windows. The descriptive statistics values were presented in frequencies and percentages. Binary logistic regression, Chi-square test, and one-way ANOVA were applied to analyze the participants' socio-demographic characteristics and variables related to KAPs. P-value < 0.05 was recorded as significant.Results: A total of 1,000 participants were invited of which 734 participated in this study. The response rate was 73.4% (734/1,000). The gender, marital status, education, and residence showed a significant association with the knowledge score. The majority of the study participants were thinking that COVID-19 may be more dangerous in elderly individuals 94.5% (n = 700), and individuals with chronic diseases or severe complications 96.7% (n = 710) (p = 0.00). More than half of the participants 52.5% (n = 385) showed their concern that either they or their family members might get the infection. More than 98% (n = 703), (P-value = 0.00) of the participants held that COVID-19 would be successfully controlled in Pakistan by following the standard SOPs and government guidelines.Conclusion: This study showed that the general population of Pakistan has good awareness and reasonable attitudes and perceptions toward the full features of the COVID-19. The current study suggests that mass-level effective health education programs are necessary for developing countries to improve and limit the gap between KAP toward COVID-19.

A high prevalence of multidrug-resistant (MDR) pathogens has been reported in adult and pediatric populations of Pakistan. However, data describing the effect of MDR microbes on the gut microbiota is scarce. We designed a cross-sectional pediatric study to investigate the effect of MDR microbes’ infection on the gut microbiome and its resistome of children using high-throughput next-generation sequencing (NGS). A cross-sectional study was conducted at a tertiary health care hospital in Peshawar Pakistan, between 5 September 2019 to 15 February 2020. Pediatric patients with acute gastroenteritis (n = 200) were enrolled. All the enrolled pediatric patients underwent initial antimicrobial resistance (AMR) screening using the disk diffusion method. Children with MDR infections were identified and selected for gut microbiome and its resistome profiling using NGS. Out of 200 enrolled pediatric patients, 80 (40%) were found infected with MDR diarrheagenic Enterobacteriaceae consisting of 50 (62.5%) infections caused by extended-spectrum beta-lactamase (ESBL) producing E. coli while 30 (37.5%) by MDR Enterobacter specie. A total of 63 and 17 antibiotic-resistant genes (ARGs) conferring resistance to 7 and 5 classes of antibiotics were identified in the resistomes of MDR diarrheagenic Enterobacteriaceae infected and healthy children, respectively. NGS-based gut microbial profiling of MDR Enterobacter spp., ESBL producing E. coli infected pediatric patients and healthy controls revealed the predominance of Proteobacteria and Actinobacteria, respectively. An increased abundance of several pathogenic gram-negative bacteria namely E. coli, Enterobacter cloacae, and Salmonella enterica was observed in the gut microbiota of children infected with MDR bacterial infections than that of the healthy controls. This work indicates that children with MDR infections have reduced microbial diversity and enriched ARGs than healthy controls. The emergence of MDR bacterial strains and their association with gut dysbiosis needs immediate attention to regulate antibiotics usage in Pakistani children.

OBJECTIVE: To find out the self-motivated cadence of intestinal microbiota by zinc obtainability with help of next generation sequencing. METHODS: This cross-sectional study was conducted on infants aging 1-4 months from Peshawar, Pakistan. Out of 50 infants enrolled in study, data of 46 healthy infants [23 breast-fed (BF) and 23 formula-fed (FF)] were available for final analysis. Their blood and stool samples were collected and analyzed for zinc and fecal DNA extraction, for metagenomic shot gun sequencing using next generation. RESULTS: Mean age of infants was 78.40±35.88 days. Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria are the four dominating major phyla found in the gut microbiota of the sample population. In breast-fed infants, mean plasma zinc was 0.138 ± 0.118 mg/L whereas, in formula-fed infants it was 0.120±0. 026 mg/L. Correlation of zinc levels with gut microbes revealed that Phylum Bacteroidetes was very low in breast-fed while in formula-fed infants it was negligible to an extent that cannot be correlated with zinc. It was also observed that there is abundance of Proteobacteria (BF: r=-0.276, p=0.264) and (FF: r= -0.043, p= 0.873) in both the zinc deficient groups whereas, Firmicutes content was (BF: r= 0.392, p=0.207) and (FF: r= -0.030, p= 0.905). CONCLUSION: Both breast-fed and formula-fed infants had low gut microbial diversity due to low zinc levels emphasizing the need to address and rectify this problem. The improved zinc status of the infants will enable the researchers to establish and ascertain the association of zinc status with the diversity of microbiome.

In this paper, we aimed to characterize the fecal microbiome and its resistomes of healthy and diseased subjects infected with multidrug-resistant Escherichia coli using next-generation sequencing (NGS). After initial screening, 26 stools samples belonging to healthy (n = 13) and diseased subjects (n = 13) were selected and subjected to NGS. A total of 23 and 42 antibiotic-resistant genes (ARGs) conferring resistance to 6 and 9 classes of antibiotics were identified in the resistomes of healthy and diseased subjects, respectively. Bacteroidetes were found to be the major phylum in both healthy and diseased subjects, however, Proteobacteria was predominantly present in the diseased subjects only. Microbial dysbiosis and predominance of various ARGs in the resistome of diseased subjects reflect the excessive usage of antibiotics in Pakistan and warrants immediate attention to regulate the use of various antimicrobials.

The study was designed to investigate the fecal microbiome and resistome of broiler chickens infected with multidrug-resistant (MDR) Escherichia coli (E. coli). Fecal samples (n = 410) from broiler chickens were collected from thirteen randomly selected sites of Khyber Pakhtunkhwa and screened for the presence of MDR E. coli. Upon initial screening, thirteen (13) MDR E. coli isolates were then subjected to shotgun metagenome next-generation sequencing (NGS). NGS based resistome analysis identified the multidrug efflux pump system-related genes at the highest prevalence (36%) followed by aminoglycoside (26.1%), tetracycline (15.9%), macrolide-lincosamide-streptogramin (9.6%), beta-lactam (6.6%), rifampin (2%), sulphonamide (1.3%), phenicol (0.91%), vancomycin (0.62%), trimethoprim (0.34%), colistin (0.30%), and quinolone (0.33%). The most abundant virulence-associated genes (VAGs) identified were iroN, iutA, iss, and iucA. NGS based taxonomic profiling at the phylum level revealed the predominance of Proteobacteria (38.9%) followed by Firmicutes (36.4%), Bacteroidetes (15.8%), and Tenericutes (8.9%). Furthermore, pathobionts such as E. coli, Salmonella enterica, Klebsiella pneumoniae, and Shigella flexneri belonging to the family Enterobacteriaceae were predominantly found. This study revealed the widespread presence of MDR genes, diverse VAGs, and a dysbiotic gut in the broiler chickens infected with MDR E. coli of Khyber Pakhtunkhwa for the first time using NGS.

Simple Summary Antimicrobial resistance acquired an endemic status in the Pakistan poultry sector. A cross-sectional study was designed to investigate the fecal microbiome and resistome of broiler chickens infected with multidrug-resistant Escherichia coli using next-generation sequencing. Results show the widespread presence of diverse antibiotic resistance genes, virulence-associated genes, plasmid replicon types, and dysbiotic fecal microbial communities. Results indicate that antibiotic resistance altered the fecal microbial community structure of broiler chickens. The use of next-generation sequencing in this study documents a robust and cost-effective approach to study the fecal microbiome and resistome diversities of broiler chickens. Abstract The study was designed to investigate the fecal microbiome and resistome of broiler chickens infected with multidrug-resistant (MDR) Escherichia coli (E. coli). Fecal samples (n = 410) from broiler chickens were collected from thirteen randomly selected sites of Khyber Pakhtunkhwa and screened for the presence of MDR E. coli. Upon initial screening, thirteen (13) MDR E. coli isolates were then subjected to shotgun metagenome next-generation sequencing (NGS). NGS based resistome analysis identified the multidrug efflux pump system-related genes at the highest prevalence (36%) followed by aminoglycoside (26.1%), tetracycline (15.9%), macrolide-lincosamide-streptogramin (9.6%), beta-lactam (6.6%), rifampin (2%), sulphonamide (1.3%), phenicol (0.91%), vancomycin (0.62%), trimethoprim (0.34%), colistin (0.30%), and quinolone (0.33%). The most abundant virulence-associated genes (VAGs) identified were iroN, iutA, iss, and iucA. NGS based taxonomic profiling at the phylum level revealed the predominance of Proteobacteria (38.9%) followed by Firmicutes (36.4%), Bacteroidetes (15.8%), and Tenericutes (8.9%). Furthermore, pathobionts such as E. coli, Salmonella enterica, Klebsiella pneumoniae, and Shigella flexneri belonging to the family Enterobacteriaceae were predominantly found. This study revealed the widespread presence of MDR genes, diverse VAGs, and a dysbiotic gut in the broiler chickens infected with MDR E. coli of Khyber Pakhtunkhwa for the first time using NGS.

The rapid breakout of the coronavirus disease of 2019 (COVID-19) has been declared pandemic with serious global concern due to high morbidity and mortality. As we enter the phase beyond limitations there is an urgent need for explicit treatment against COVID-19. To face this immediate global challenge, drug development from scratch is a lengthy process and unrealistic to conquer this battle. Drug repurposing is an emerging and practical approach where existing drugs, safe for humans, are redeployed to fight this harder to treat disease. A number of multi clinical studies have repurposed combined cocktail (remdesivir + chloroquine and favipiravir + chloroquine) to be effective against COVID-19. However, the exact mechanistic aspect has not yet been revealed. In the present study, we have tried to decipher the mechanistic aspects of existing medicines at the viral entry and replication stage via the structural viroinformatics approach. Here we implied the molecular docking and dynamic simulations with emphasis on the unique structural properties of host receptor angiotensin-converting enzyme 2 (ACE2), SARS-CoV2 spike protein and RNA dependent RNA polymerase enzyme (RdRp) of the SARS-CoV2. Deep structural analysis of target molecules exposed key binding residues and structural twists involved in binding with important pharmacophore features of existing drugs [(7-chloro-N-[5-(diethylamino)pentan-2-yl]quinolin-4-amine (chloroquine),N-[[4-(4-methylpiperazin-1-yl)phenyl]methyl]-1,2-oxazole-5-carboxamide N-[[4-(4-methylpiperazin-1-yl)phenyl]methyl]-1,2-oxazole-5-carboxamide) (SSAA09E2), 2-ethylbutyl (2S)-2-{[(S)-{[(2R,3S,4R,5R)-5-{4-aminopyrrolo[2,1-f][1,2,4]triazin-7-yl}-5-cyano-3 (remdesivir) and 6-Fluor-3-oxo-3,4-dihydro-2-pyrazincarboxamid (favipiravir)]. It is evident from this structural informatics study that combo of chloroquine + SSAA09E2 with remdesivir or favipiravir could significantly restrain the virus at the entry and replication stage. Thus, drug repurposition is an attractive approach with reduced time and cost to treat COVID-19, we don't have enough time as the whole world is lockdown and we are in urgent need of an obvious therapeutics' measures.

Genome-wide association studies (GWAS) have identified multiple type 2 diabetes (T2D) loci, mostly among populations of European descent. There is a high prevalence of T2D among Pakistanis. Both genetic and environmental factors may be responsible for this high prevalence. In order to understand the shared genetic basis of T2D among Pakistanis and Europeans, we examined 77 genome-wide significant variants previously implicated among European populations. We genotyped 77 single-nucleotide polymorphisms (SNPs) by iPLEX® Gold or TaqMan® assays in a case-control sample of 1,683 individuals. Association analysis was performed using logistic regression. A total of 16 SNPs (TCF7L2/rs7903146, GLIS3/rs7041847, CHCHD9/rs13292136, PLEKHA1/rs2292626, FTO/rs9936385, CDKAL1/rs7756992, KCNJ11/rs5215, LOC105372155/rs12970134, KCNQ1/rs163182, CTRB1/rs7202877, ST6GAL1/rs16861329, ADAMTS9-AS2/rs6795735, LOC105370275/rs1359790, C5orf67/rs459193, ZBED3-AS1/rs6878122 and UBE2E2/rs7612463) showed statistically significant associations after controlling for the false discovery rate. While KCNQ1/rs163182 and ZBED3-AS1/rs6878122 showed opposite allelic effects, the remaining significant SNPs had the same allelic effects as reported previously. Our data indicate that a selected number of T2D loci previously identified among populations of European descent also affect the risk of T2D in the Pakistani population.

BackgroundThe ongoing COVID-19 pandemic caused by SARs-CoV-2 was transmitted person to person via droplet infections and fecal-oral transmission. This illustrates the probability of environmentally facilitated transmission, mainly the sewage.MethodWe used existing Pakistan polio environment surveillance network to investigate presence of SARs-CoV-2 using three commercially available kits and E-Gene detection published assay for surety and confirmatory of positivity. A Two-phase separation method is used for sample clarification and concentration. An additional high-speed centrifugation (14000Xg for 30 min) step was introduced, prior RNA extraction, to increase viral RNA yield resulting a decrease in Cq value.ResultsA total of 78 wastewater samples collected from 38 districts across Pakistan, 74 wastewater samples from existing polio environment surveillance sites, 3 from drains of COVID-19 infected areas and 1 from COVID 19 quarantine center drainage, were tested for presence of SARs-CoV-2. 21 wastewater samples (27%) from 13 districts turned to be positive on RT-qPCR. SARs-COV-2 RNA positive samples from areas with COVID patients and COVID 19 patient quarantine center drainage strengthen the findings and use of wastewater surveillance in future. Furthermore, sequence data of partial ORF 1a generated from COVID 19 patient quarantine center drainage sample also reinforce our findings that SARs-CoV-2 can be detected in wastewater.DiscussionThis study finding indicates that SARs-CoV-2 detection through wastewater surveillance has an epidemiologic potential that can be used as early warning system to monitor viral tracking and circulation in cities with lower COVID-19 disease burden or heavily populated areas where door-to-door tracing may not be possible. However, attention needed on virus concentration and detection assay to increase the sensitivity. Development of highly sensitive assay will be an indicator for virus monitoring and to provide early warning signs.

Aim: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a pernicious viral disease, causes acute respiratory distress responsible for mortality and morbidity worldwide. To screen different immunomodulatory medicinal compounds to unravel their interaction with SARS-CoV-2 viral proteins. Materials & methods: A library of immunomodulatory medicinal compounds with antiviral capability were analyzed against SARS proteases, spike protein and nonstructural proteins (NSP-9, 15) using Autodock vina. Results: Out of more than 300 medicinal compounds, only six compounds: arzanol, ferulic acid, genistein, resveratrol, rosmanol and thymohydroquinone showed significant interaction with the SARS viral proteins by forming hydrogen bonds with the active site residues with low binding energy. Further ADMET (absorption, distribution, metabolism, excretion and toxicity) analysis showed good pharmacokinetic properties and low acute toxicity of these compounds. Conclusion: The current study provides convincing evidence that these medicinal compounds exert antiviral activity against the SARS-CoV-2 virus and could be further exploited for the treatment of this disease.

Background: Microbiota plays an important role in food safety and its alteration poses a serious threat to humans. Comparative microbiome profiling using next-generation sequencing (NGS) enabled the understanding of microbial diversity and similarity between different species. In this study, we used NGS to profile the fecal microbiota of sick human and broiler chickens. A total of 26 fecal samples were collected from severely sick human subjects (n= 13) and broiler chickens (n=13) with similar symptoms. Results: The total number of microbial species detected in broiler chickens fecal microbiota was higher than that of humans. Phylum Proteobacteria was the most abundant in both human and broiler chickens fecal microbiota while Tenericutes was found to be least abundant in both species. Phylum Actinobacteria was found only in the human fecal microbiota. In both humans and broiler chickens, E.coli was found to be phylogenetically related suggesting a microbial association between both species. Conclusion: NGS based taxonomic profiling revealed the association of microbial dysbiosis with extreme sickness in both humans and broiler chickens. The dominance of phylum Proteobacteria in both the species ascertains their altered gut microbiota. Both human and broiler chickens microbial communities were found to be genetically related indicating horizontal transfer of microbes between the two species.

Soil organic carbon (SOC) sequestration is one of the major agronomic measures to mitigate green house gas emission, enhance food security, and improve agriculture sustainability. The study, theref...

Soon after its emergence in Wuhan, China in late December, the novel coronavirus (SARS-CoV-2) spread rapidly to the other parts of the world and acquired a pandemic status. Pakistan reported its first case of SARS-CoV-2 on February 26, 2020, in Karachi. Since then, a higher prevalence of COVID-19 was reported from almost all major cities of Pakistan. Owing to the high rate of COVID-19, Pakistan enforced a lockdown across the whole country on March 24, 2020. This lockdown controlled the SARS-CoV-2 successfully; however, severe economic losses were observed in the lockdown Standard Operating Procedure (SOP) guidelines. We, therefore, proposed an alternative plan termed as “regulated reverse lockdown” which will help decrease the burden of COVID-19 without having a negative effect on the economy. The present editorial will address the potential flaws in the already imposed lockdown and will propose an alternative plan to make the lockdown more effective in terms of COVID-19 prevalence and economic growth of Pakistan.

Objective: In Pakistan, 74% of consanguineous marriages are among the first cousins. Continuity of consanguineous marriages over generations increases the risk of recessive diseases such as deafness. The objective of this study was to investigate genetic origin of Pakistani deaf brothers with parents of consanguineous marriage. Methods: DNA was extracted from the blood through Qiagen kit. Paired-end sequencing library was prepared according to protocol of Illumina’s TruSight Rapid Capture kit and TruSight Inherited Disease Panel. Library was normalized and used for Next Generation Sequencing through MiSeq. NGS data were analyzed using various bioinformatics tools. Results: Both brothers were found to have novel deleterious mutation in MYO7A (c.2476G>A) while the younger brother had additional novel deleterious mutation in TH (c.43C>T) and EVC2 (c.2614C>T) genes. Conclusion: It is concluded that in addition to novel mutations in MYO7A, TH and EVC2, the CDH23 and GJB2 can also be responsible for deafness in the family with consanguineous marriages. How to cite this:Sabiha B, Ali J, Yousafzai YM, Haider SA. Novel deleterious mutation in MYO7A, TH and EVC2 in two Pakistani brothers with familial deafness. Pak J Med Sci. 2019;35(1):17-22. doi: https://doi.org/10.12669/pjms.35.1.98 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

The occurrence of microbial communities harboring antibiotic resistance bacteria and antibiotic resistance genes in the drinking water distribution system pose a significant threat to the aquatic ecosystem and to public health, especially in developing countries. In this study, we have used next-generation sequencing technology to explore bacterial community diversity and the abundance of antibiotic resistance genes in biofilms collected from the drinking water distribution system of Peshawar, the capital city of the Khyber Pakhtunkhwa province of Pakistan. The results showed that Proteobacteria were the most abundant phyla (89.79%) in all biofilm samples, followed by Bacteroidetes (3.48%) and Actinobacteria (2.79%). At genus level, Pseudomonas was the most common (22.45%) in all biofilm samples. Overall, bacterial diversity and richness was higher in biofilm samples collected from the consumer end than the source site. Bacterial diversity was also dependent on the piping material (GI vs. PVC) and water supply (direct vs. indirect). Functional annotation reveals a differential abundance of common metabolic pathways at source and consumer end. Resistome analysis revealed a prevalence of resistance genes against 12 classes of antibiotics in all samples with macrolides resistance being the commonest at the consumer end (42.1%) and fluoroquinolone resistance at the source end (24%). To our knowledge, this is the first study that provides new insight and evidence into the microbial community diversity and antibiotic resistance in the drinking water supply system of Peshawar. These findings may ultimately help the authorities to design and implement effective strategies for controlling biofilms and ensuring a continuous supply of safe drinking water to the community.

Objectives: To assess the role of double J stent in management of renal andureteric calculi measuring 1.5 to 2.5 cm size prior to ESWL. Period: 1st January 2015 to 30thDecember 2015. Study Design: Retrospective study. Methods: We included 120 patientswhich were divided in two groups. In group A we took 40 patients in whom double J stentswere inserted before ESWL while in group B, 80 patients underwent ESWL without stenting. Weincluded patients of both sex having radio-opaque stones in kidney or proximal ureter measuring1.5cm to 2.5cm in size in adults (age > 18) years where stone fragmentation resulted afterESWL. The average stone size in both groups was comparable (p > 0.05). Patients with urinarytract infections, pregnancy, radiolucent stones, bleeding disorders, larger or small stones,anatomical abnormality, nonfunctioning kidney and where ESWL was not successful after thirdsession were excluded from study. The patients were randomized on basis of their choice foreither procedure and majority 80 patients (66 %) refused stenting before ESWL due to fearof invasive procedure and socioeconomic reasons. Patient’s pre-operative investigations likecomplete blood count, urea/creatinine, X-ray & ultrasound KUB and IVU were done. ESWL wasdone without anesthesia and after complete clearance of fragments stents were removed withinthree months. Results: Out of 120 patients 70 were male (58.33 %) and 50 were female (41.66%). In group A (with ureteric stenting) there was no ureteric obstruction noticed after ESWLand fragments clearance resulted with mild pain or discomfort in 12(10%) patients. There wasdelayed clearance of the fragments in patients but that had no impact on patient daily activities.While in group B (without ureteric stenting) 30 (37.5%) patients developed complications likesevere colicky pain for which they were hospitalized whereas remaining 50(62.5%) patientshad mild to moderate pain with stein-stresse appearance which was managed using oral andsystemic analgesics, increase oral fluids and reassurance to the patients. The time of stonefragments clearance was delayed in group A as compared to group B (p < 0.05). Conclusion:We conclude that double J stent should be passed prior to ESWL in cases of large renal andureteric calculi to avoid severe colicky pain.

Objective To investigate the prevalence of Staphylococcus aureus ( S. aureus ) isolated from skin wards of the hospitals of Khyber Pakhtunkhwa, its resistance against various commonly and commercially available antibiotics, as well as different genetic traits of resistance and their correlations with the phenotypic visible resistance. Methods In the present study a simple PCR technique were used to investigate the genetic traits of resistance in S. aureus isolated from skin wards of two major hospitals of Khyber Pakhtunkhwa, Pakistan. A total of 100 samples were collected from both the male and female, of which 50 were from patient's site of infection and 50 from ward environment. Results These results demonstrated that the total prevalence of S. aureus both in ward as well as in patients was 48%. The S. aureus prevalence was the highest in female patients (50%) followed by ward environment (29%) and then male patients (21%). The antibiotic sensitivity tests revealed that the highest (91.6% isolates) sensitivity was shown to imipenem. However, the highest resistance was found to be against penicillin (100% isolates) followed by cefotaxime (75% isolates). In addition, only 29% of the isolates were found to be resistant to methicillin. PCR technique based on the previously designed primers targeting different genetic traits of resistance revealed that 13 out of the 14 isolates resistant to methicillin were positive for mecA gene. blaZ Genetic traits were found in all isolates resistant to penicillin. The multi-drug resistance traits, vgaA and vgaB each was detected only in 12.5% of S. aureus isolates. The phenotypic character of antibiotic resistance is highly correlated to different genetic traits of resistance. Conclusions Based on our findings, it is concluded that antibiotic resistance in S. aureus strains is increasing day by day due to self-medications and medication by non-registered medical practitioners. Therefore, for quick and fast detection, we propose next-generation sequencing be utilized to screen for antibiotic resistance.

The role of different growth media and chemical enhancer on synthesis of secondary metabolites Cladosporium resinae (NRL-6437) was investigated for their in vitro biological activities. Cladosporium resinae (NRL-6437) were grown in various nutrient media (Czapeak-dox Broth (CB), Czapeak Yeast-extract Broth (CYB), Yeast Extract Sucrose (YES), Potato Dextrose Broth (PDB) and Czapeak-dox (supplemented with glucose and starch) Broth (CGSB) for the production of metabolites. Two chemical epigenetic modifiers (suberoyl-anilide hydroxamic acid (SAHA) and 5-azacytidine (5-AZA) were also used for the expression of silent genes for secondary metabolite production. Our results indicated that among different media, Czapeak yeast extract broth produced more secondary metabolites. Application of 15mM of both modifiers was effective for the expressions of silent genes resulting in an increased metabolites production. Secondary metabolites extracted in ethyl acetate and fractionized in n-Hexane were also tested for their biological activity. The secondary metabolites revealed varying degrees of growth inhibitions of the tested organisms. Similarly, these metabolites were also active against brine shrimps and Lemna.

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide. It accounts for 2.5% of all new cancer cases and 1.9% of all cancer deaths annually. More than 90% of oral cancers (occurring in the mouth, lip, and tongue) are oral squamous cell carcinoma. The incidence rate of oral cancer varies widely throughout the world, with an evident prevalence in South Asian countries. This high incidence occurs in correlation with oral cancer-associated behaviors such as alcohol, tobacco use. Researchers have reported that these behaviors lead to genetic variations in tumor suppressor genes (APC, p53), proto-oncogenes (Myc), oncogene (Ras) and genes controlling normal cellular processes (EIF3E, GSTM1). Processes such as segregation of chromosomes, genomic copy number, loss of heterozygosity, telomere stabilities, regulations of cell-cycle checkpoints, DNA damage repairs and defects in notch signaling pathways are involved in causing oral cancer. In order to develop preventive and therapeutic options, it is necessary to comprehend the basic molecular mechanisms forcing oral tumorigenesis. This review examines, in detail, the mechanisms of genetic alteration which are considered to be responsible for the initiation of oral cancer.

Objective: I. To determine the frequency of malignancy in multi nodular goiter. II. To determine the histopathological types.Design: This is a prospective study. Setting: Surgical department of Foundation Hospital Rawalpindi and associated Teaching Hospital ofFrontier Medical College Abbottabad. Period: Aug. 2002 to Aug. 2007. Patients and Methods. One hundred patients with Multi nodular wereincluded in this study. Patient with diffuse goiter, solitary nodules, patient operated somewhere else and suspected cases of malignancy wereexcluded from the study. Tissue were sent to Armed Force Institute for histopathological examination. Patients were followed for 2 weeks aftersurgery with histopathological report, all the preoperative and postoperative findings were recorded in detail. Data was analyzed byusingSPSS 14. Results. Majority of patients studied, belonged to Azad Kashmir and Gilgit which are among the known endemic regions for goitrein Pakistan and other from Chakwal and Jhelum. Histopathology revealed 96 (96%) patients with multi nodular goiter, 3 (3%) papillary carcinomaand 1 (1 %) Follicular carcinoma. Conclusions: Multinodularity of the goitre should not be considered as low risk of malignancy and delay forsurgical intervention. Changes in the size of gland, the appearance of new and hard nodules or cervical lymphadenopathy may indicatemalignant change and prompt indication for surgery.

B a c k g r o u n d : Lump breast is a fairly common presenting complaint for which patient seeks medical advice and becomesanxious about the diagnosis. Fine needle aspiration cytology (FNAC) for the diagnosis of lump breast has been proved as a simple, rapidand economical Procedure. The present study was done to evaluate the diagnostic accuracy of fine lump breast in our set-up comparedwith open biopsy. M e t h o d s : The study was conducted in surgical department of Nishtar Hospital Multan and Frontier Medical CollegeAbbottabad. One hundred female patients with lump breast were selected for the study and their medical history was recorded. The agerange was 15- 65 years. All of the patients under went FNAC of the lump breast followed by open biopsy for comparison. R e s u l t s : Theresults reveal that this study shows a sensitivity of 87.5% for FNAC to pick malignant lesions and specificity of 82.4% while over all diagnosticaccuracy 84%. C o n c l u s i o n s : Fine needle aspiration cytology is safe, easy, cheap and accurate procedure. Its sensitivity and specificityis fairly high and is a good alternative to open biopsy. FNAC should be routinely used and open biopsy should be performed in doubtfulcases only.

Objective: To study the frequency of complications of central venous pressure line. S t u d y d e s i g n . Descriptiveobservational study. S e t t i n g : This study was carried out in surgical ward and intensive care unit of Fauji Foundation hospital Rawalpindiand Frontier Medical College Abbottabad. P e r i o d : From 2003-2007. M e t h o d s a n d Materials: One hundred consecutive surgical patientsneeding central venous line insertion above 14 years of age were included in the study. Patients under 14 years of age, with central venousline in situ at the time of admission, with thoracic trauma, chronic obstructive pulmonary disease, burns involving upper chest and neck areas,cardiovascular disease and bleeding disorders were excluded from this study. R e s u l t s : 100 cases were included in the study with the rangeof age between 16-82 years. There were 76% female and 24% male. Out of these 100 cases 40 were suffering from malignancy, 20 weresuffering from intestinal obstruction, 10 were with peritonitis and 30 cases were having miscellaneous disorders. Rate of complications ofcentral venous line was 30% in this study. Rate of infection was 20%, rate of misplacement of catheter was 8% and rate of pneumothoraxwas 2% C o n c l u s i o n : infection is the most common complication of the central venous line insertion followed by misplacement of catheterand pneumothorax, so it is important to take specific measures to minimize these complications

Diabetic foot is one of the most common complications of diabetes mellitus. The management and out come is very much dependent on proper assessment of foot ulcer severity. Objectives: To asses severity of diabetic foot and to find a correlation between Ankle Brachial Pressure Index (ABPI) and foot ulcer grades. Study design: Prospective study. Period: Jan 2001 to Dec 2003. Patients & Methods and Setting: Patients with diabetic foot ulcers from all the medical and surgical units of Ayub teaching hospital Abbottabad were enrolled in the study. Results: Ankle Brachial Pressure Index (ABPI) levels revealed 5 (5.8%) with ABPI < 0.5 for grade V, 8 patients (9.3%) ABPI 0.5 – 0.89 for grade IV, 18 patients (20.9%) ABPI 0.9-1 for grade III, 44 (51.2%) ABPI 0.9-1 for grade II, and 9 patients (10.5%) ABPI > 1 for grade I diabetic foot ulcer. This data was analyzed via SPSS version 8.0. Conclusions: Ankle brachial pressure index is a good diagnostic tool to assess the lower extremity arterial disease in diabetic foot patients. ABPI readings should be cautiously interpreted as these may be falsely elevated in atherosclerotic patients.

Objective: To assess the body mass index in patients withdiabetes mellitus type 2 in a tertiary care hospital. Study design: Analytical (cross-sectional) study. Place and durationof study: The outpatient clinic at Shahina Jamil Trust Hospital Abbottabad from November 2006 to April 2007. Patientsand methods: One hundred patients seen in the outpatient clinic were enrolled in the study. All patients were 30 yearsof age or above, diagnosed as a case of diabetes mellitus were included. Patients with diabetes mellitus type 1 andpregnant diabetic women were excluded. Results: Sixty-seven percent were females and thirty three percent weremales. Mean age of the patients was 53.4±11.0 years (F: 51.9±12.0, M: 56.5±7.8) and mean duration of diabetesmellitus type 2 was 7.1±6.5 years (F: 7.1±6.4, M: 7.9±6.8), mean height of patients with DM type 2 was 1.5±.09 m (F:1.5±.08, M: 1.6±.08), mean weight was 71.4±14.3 kg (F: 70.1±15.0, M: 74.2±12.6), and mean BMI was 28.3±6.4 (F:28.7±6.9, M: 27.5±5.2). Among all patients, 34% (F: 23, M: 11) had normal weight, 28% (F: 17, M: 11) were overweight,32% (F: 23, M: 9) were obese and 6% (F: 4, M: 2) had morbid obesity. Conclusion: There was strong association ofobesity with type 2 diabetes mellitus with no significant difference of mean BMIs among male and female patients.

*† Summary As part of a larger project to sequence the Populus genome and generate genomic resources for this emerging model tree, we constructed a physical map of the Populus genome, representing one of the few such maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2802 contigs, was constructed from fingerprinted bacterial artificial chromosome (BAC) clones. The map represents approximately 9.4-fold coverage of the Populus genome, which has been estimated from the genome sequence assembly to be 485 10 Mb in size. BAC ends were sequenced to assist long-range assembly of wholegenome shotgun sequence scaffolds and to anchor the physical map to the genome sequence. Simple sequence repeat-based markers were derived from the end sequences and used to initiate integration of the BAC and genetic maps. A total of 2411 physical map contigs, representing 97% of all clones assigned to contigs, were aligned to the sequence assembly (JGI Populus trichocarpa, version 1.0). These alignments represent a total coverage of 384 Mb (79%) of the entire poplar sequence assembly and 295 Mb (96%) of linkage group sequence assemblies. A striking result of the physical map contig alignments to the sequence assembly was the co-localization of multiple contigs across numerous regions of the 19 linkage groups. Targeted sequencing of BAC clones and genetic analysis in a small number of representative regions showed that these co-aligning contigs represent distinct haplotypes in the heterozygous individual sequenced, and revealed the nature of these haplotype sequence differences.

Human chromosome 7 has historically received prominent attention in the human genetics community, primarily related to the search for the cystic fibrosis gene and the frequent cytogenetic changes associated with various forms of cancer. Here we present more than 153 million base pairs representing 99.4% of the euchromatic sequence of chromosome 7, the first metacentric chromosome completed so far. The sequence has excellent concordance with previously established physical and genetic maps, and it exhibits an unusual amount of segmentally duplicated sequence (8.2%), with marked differences between the two arms. Our initial analyses have identified 1,150 protein-coding genes, 605 of which have been confirmed by complementary DNA sequences, and an additional 941 pseudogenes. Of genes confirmed by transcript sequences, some are polymorphic for mutations that disrupt the reading frame.

Salmonella enterica subspecies I, serovar Typhimurium (S. typhimurium), is a leading cause of human gastroenteritis, and is used as a mouse model of human typhoid fever. The incidence of non-typhoid salmonellosis is increasing worldwide, causing millions of infections and many deaths in the human population each year. Here we sequenced the 4,857-kilobase (kb) chromosome and 94-kb virulence plasmid of S. typhimurium strain LT2. The distribution of close homologues of S. typhimurium LT2 genes in eight related enterobacteria was determined using previously completed genomes of three related bacteria, sample sequencing of both S. enterica serovar Paratyphi A (S. paratyphi A) and Klebsiella pneumoniae, and hybridization of three unsequenced genomes to a microarray of S. typhimurium LT2 genes. Lateral transfer of genes is frequent, with 11% of the S. typhimurium LT2 genes missing from S. enterica serovar Typhi (S. typhi), and 29% missing from Escherichia coli K12. The 352 gene homologues of S. typhimurium LT2 confined to subspecies I of S. enterica-containing most mammalian and bird pathogens-are useful for studies of epidemiology, host specificity and pathogenesis. Most of these homologues were previously unknown, and 50 may be exported to the periplasm or outer membrane, rendering them accessible as therapeutic or vaccine targets.

The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins.

Motivation: Copy number variations (CNVs) are a major source of genomic variability and are especially significant in cancer. Until recently microarray technologies have been used to characterize CNVs in genomes. However, advances in next-generation sequencing technology offer significant opportunities to deduce copy number directly from genome sequencing data. Unfortunately cancer genomes differ from normal genomes in several aspects that make them far less amenable to copy number detection. For example, cancer genomes are often aneuploid and an admixture of diploid/non-tumor cell fractions. Also patient-derived xenograft models can be laden with mouse contamination that strongly affects accurate assignment of copy number. Hence, there is a need to develop analytical tools that can take into account cancer-specific parameters for detecting CNVs directly from genome sequencing data. Results: We have developed WaveCNV, a software package to identify copy number alterations by detecting breakpoints of CNVs using translation-invariant discrete wavelet transforms and assign digitized copy numbers to each event using next-generation sequencing data. We also assign alleles specifying the chromosomal ratio following duplication/loss. We verified copy number calls using both microarray (correlation coefficient 0.97) and quantitative polymerase chain reaction (correlation coefficient 0.94) and found them to be highly concordant. We demonstrate its utility in pancreatic primary and xenograft sequencing data. Availability and implementation: Source code and executables are available at https://github.com/WaveCNV. The segmentation algorithm is implemented in MATLAB, and copy number assignment is implemented Perl. Contact: lakshmi.muthuswamy@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.

The Pleiades Promoter Project integrates genomewide bioinformatics with large-scale knockin mouse production and histological examination of expression patterns to develop MiniPromoters and related tools designed to study and treat the brain by directed gene expression. Genes with brain expression patterns of interest are subjected to bioinformatic analysis to delineate candidate regulatory regions, which are then incorporated into a panel of compact human MiniPromoters to drive expression to brain regions and cell types of interest. Using single-copy, homologous-recombination “knockins” in embryonic stem cells, each MiniPromoter reporter is integrated immediately 5′ of the Hprt locus in the mouse genome. MiniPromoter expression profiles are characterized in differentiation assays of the transgenic cells or in mouse brains following transgenic mouse production. Histological examination of adult brains, eyes, and spinal cords for reporter gene activity is coupled to costaining with cell-type–specific markers to define expression. The publicly available Pleiades MiniPromoter Project is a key resource to facilitate research on brain development and therapies.

Primary Vaginal Hydrocoele of Testis is a common condition which is primarily treated surgically. Many patients with Hydrocoele of testis are either not willing or are unfit for surgery. This study was done to know the safety, efficacy and out come of tetracycline induced sclerotherapy of Primary Vaginal Hydrocoele of Testis in adults.This quasi experimental study was done in Shahina Jamil Hospital, attached with Frontier Medical College and Ayub Teaching Hospital, Abbottabad from March 2006 to April, 2007. Thirty-seven patients with primary vaginal hydrocoele were included in the study. Aspiration and instillation of Tetracycline was done after spermatic cord block with 2% lignocaine. Procedure time, Peri and Post-procedure complications, number of injections for cure and patients' satisfaction with the procedure were recorded. Patients were discharged home 3 to 4 hours after the procedure and followed up after one week, one month, three months and six months. Direct admission and re-admissions were recorded.The mean age of patients was 47 years. Mean procedure time was 45 minutes. All patients were cured. Mild postoprocedure pain occurred in 12 (40%), moderate pain in 14 (46%) patients and severe pain in 4 (13.3%) patients. No patient developed haematoma or local infection. One patient (3.3%) had micturition problem. Two (6.6%) patients had minimal recurrence. One injection was sufficient for cure in all patients. 28 (93%) patients were satisfied while 2 (6.6%) patients were not satisfied with this procedure. No patient was admitted in the hospital after the procedure.Aspiration and injection of tetracycline in Primary vaginal Hydrocoele of Testis in adults is safe, effective and very economical procedure.

Cancellation of operations in hospitals is a significant problem with far reaching consequences. This study was planned to evaluate reasons for cancellation of elective surgical operation on the day of surgery in Ayub Teaching Hospital, Abbottabad.From July 2006 to June 2007 the medical records of all the patients who had their operations cancelled on the day of surgery in all the three General Surgical units of Ayub Teaching Hospital, Abbottabad were audited prospectively. The number of operation cancelled and reasons for cancellations were documented.3756 patients were scheduled for surgery during the study period. 2820 (75%) patients were operated upon. 936 (25%) operations were cancelled out of which 338 (36%) were cancelled due to shortage of time, 296 (31.6%) were cancelled due to medical reasons, 152 (16.2%) were cancelled due to shortage of beds while 55 (5.8%) were cancelled due to shortage of anaesthetists. Three operation lists were lost completely. The Anaesthetist cancelled 43%, Surgeon 39% while 18% of operations were cancelled due organizational reasons.Cancellation of patients on operation lists occupy a substantial population (25%) of cases. Majority of cancellation were due to reasons other than patients medical conditions. Better management could have avoided most of these cancellations.

As part of a larger project to sequence the Populus genome and generate genomic resources for this emerging model tree, we constructed a physical map of the Populus genome, representing one of the few such maps of an undomesticated, highly heterozygous plant species. The physical map, consisting of 2802 contigs, was constructed from fingerprinted bacterial artificial chromosome (BAC) clones. The map represents approximately 9.4-fold coverage of the Populus genome, which has been estimated from the genome sequence assembly to be 485 +/- 10 Mb in size. BAC ends were sequenced to assist long-range assembly of whole-genome shotgun sequence scaffolds and to anchor the physical map to the genome sequence. Simple sequence repeat-based markers were derived from the end sequences and used to initiate integration of the BAC and genetic maps. A total of 2411 physical map contigs, representing 97% of all clones assigned to contigs, were aligned to the sequence assembly (JGI Populus trichocarpa, version 1.0). These alignments represent a total coverage of 384 Mb (79%) of the entire poplar sequence assembly and 295 Mb (96%) of linkage group sequence assemblies. A striking result of the physical map contig alignments to the sequence assembly was the co-localization of multiple contigs across numerous regions of the 19 linkage groups. Targeted sequencing of BAC clones and genetic analysis in a small number of representative regions showed that these co-aligning contigs represent distinct haplotypes in the heterozygous individual sequenced, and revealed the nature of these haplotype sequence differences.