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In this study, we explored the genomic architecture and phylogenomic relationship of BA.2.75, a subvariant of Omicron SARS-CoV-2. A set of 1468 whole-genome sequences of BA.2.75, submitted by 28 countries worldwide were retrieved from GISAID and used for finding genomic mutations. Moreover, the phylogenetic analysis of BA.2.75 was performed by using 2948 whole-genome sequences of all sub-variants of Omicron along with the Delta variant of SAS-CoV-2. We detected 1885 mutations, which were further grouped into 1025 missense mutations, 740 silent mutations, 72 mutations in non-coding regions, 16 in-frame deletions, 02 in-frame insertions, 8 frameshift deletions, 8 frameshift insertions and 14 stop-gained variants. Additionally, we also found 11 characteristic mutations having a prevalence of 81–99% and were not observed in any of the previously reported variant of SARS-CoV-2. Out of these mutations K147E, W152R, F157L, E210V, V213G, G339H were found in the NTD, and G446S & N460K in the RBD region of the Spike protein, whereas S403L and T11A were present in the NSP3, and E protein respectively. The phylogenetic relationship of this variant revealed that BA.2.75 is descended from the Omicron sub-variant BA.5. This evolutionary relationship suggests that the surge of BA.5 infections can reduce the severity of the infections accredited to BA.2.75. These findings would also improve our knowledge and understanding that how genetic similarities in different variants of SARS-CoV-2 can prime the immune system to fight off the infection caused by one subvariant, after defeating the other.

In this study, we investigated the genomic variability of alpha-VOC of SARS-CoV-2 in Pakistan, in context of the global population of this variant. A set of 461 whole-genome sequences of Pakistani samples of alpha-variant, retrieved from GISAID, were aligned in MAFFT and used as an input to the Coronapp web-application. Phylogenetic tree was constructed through maximum-likelihood method by downloading the 100 whole-genome sequences of alpha-variant for each of the 12 countries having the largest number of Pakistani diasporas. We detected 1725 mutations, which were further categorized into 899 missense mutations, 654 silent mutations, 52 mutations in non-coding regions, 25 in-frame deletions, 01 in-frame insertion, 51 frameshift deletions, 21 frameshift insertions, 21 stop-gained variants, and 1 stop-gained deletion. We found NSP3 and Spike as the most variable proteins with 355 and 233 mutations respectively. However, some characteristic mutations like Δ144(S), G204R(N), and T1001I, I2230T, del3675–3677(ORF1ab) were missing in the Pakistani population of alpha-variant. Likewise, R1518K(NSP3), P83L(NSP9), and A52V, H164Y(NSP13) were found for the first time in this study. Interestingly, Y145 deletion(S) had 99% prevalence in Pakistan but globally it was just 4.2% prevalent. Likewise, R68S substitution (ORF3a), F120 frameshift deletion, L120 insertion, L118V substitution (ORF8), and N280Y(NSP2) had 20.4%, 14.3%, 14.8%, 9.1%, 13.9% prevalence locally but globally they were just 0.1%, 0.2%, 0.04%, 1.5%, and 2.4% prevalent respectively. The phylogeny analysis revealed that majority of Pakistani samples were grouped together in the same clusters with Italian, and Spanish samples suggesting the transmission of alpha-variant to Pakistan from these western European countries.

The present study aims to investigate the genomic variability and epidemiology of SARS-CoV-2 in Pakistan along with its role in the spread and severity of infection during the three waves of COVID-19. A total of 453 genomic sequences of Pakistani SARS-CoV-2 were retrieved from GISAID and subjected to MAFFT-based alignment and QC check which resulted in removal of 53 samples. The remaining 400 samples were subjected to Pangolin-based genomic lineage identification. And to infer our SARS-CoV-2 time-scaled and divergence phylogenetic trees, 3804 selected global reference sequences plus 400 Pakistani samples were used for the Nextstrain analysis with Wuhan/Hu-1/2019, as reference genome. Finally, maximum likelihood based phylogenetic tree was built by using the Nextstrain and coverage map was created by employing Nextclade. By using the amino acid substitutions, the maximum likelihood phylogenetic trees were developed for each wave, separately. Our results reveal the circulation of 29 lineages, belonging to following seven clades G, GH, GR, GRY, L, O, and S in the three waves. From first wave, 16 genomic lineages of SARS-CoV-2 were identified with B.1(24.7%), B.1.36(18.8%), and B.1.471(18.8%) as the most prevalent lineages respectively. The second wave data showed 18 lineages, 10 of which were overlapping with the first wave suggesting that those variants could not be contained during the first wave. In this wave, a new lineage, AE.4, was reported from Pakistan for the very first time in the world. However, B.1.36 (17.8%), B.1.36.31 (11.9%), B.1.1.7 (8.5%), and B.1.1.1 (5.9%) were the major lineages in second wave. Third wave data showed the presence of nine lineages with Alpha/B.1.1.7 (72.7%), Beta/B.1.351 (12.99%), and Delta/B.1.617.2 (10.39%) as the most predominant variants. It is suggested that these VOCs should be contained at the earliest in order to prevent any devastating outbreak of SARS-CoV-2 in the country.

The present study is aimed to analyze and assess the critical quality parameters of ground water in district Srinagar spread over distinct seasons of the year 2020. The analysis was carried out on 15 Physio-Chemical quality parameters and 6 trace element concentrations (Lead, Zinc, Cadmium, Chromium, Nickel & Copper). Primary data was collected from 6 distinct sites of the district and subjected to methodical analysis. It was revealed that the mean values of various physio- chemical parameters are within the prescribed permissible levels while as heavy metal concentrations exhibit an escalating tendency across all selected sites especially GW1 (Pb 329, Cu 86, Ar 61, Zn 191), GW2 (Zn 132) and GW3 (Zn 144, Ar 67). The results indicate that waste disposal mechanism in hospitals of Srinagar is not environmental conducive and there is necessity to prevent further denigration of ground water sources in the region. Not denying that the present work is not the panacea for ground water contamination but the methodology adopted for this study is expected to pave way for further hydro-geological analysis in the region to identify the critical quality issues and also to explore remedial strategy to conserve the qualitative characteristics of ground water in the region.

Background In recent years, the commercial importance of changes in muscle function of broiler chickens and of the corresponding effects on meat quality has increased. Furthermore, broilers are more sensitive to heat stress during transport and at high ambient temperatures than smaller egg-laying chickens. We hypothesised that heat stress would amplify muscle damage and expression of genes that are involved in such changes and, thus, lead to the identification of pathways and networks associated with broiler muscle and meat quality traits. Broiler and layer chickens were exposed to control or high ambient temperatures to characterise differences in gene expression between the two genotypes and the two environments. Results Whole-genome expression studies in breast muscles of broiler and layer chickens were conducted before and after heat stress; 2213 differentially-expressed genes were detected based on a significant ( P  < 0.05) genotype × treatment interaction. This gene set was analysed with the BioLayout Express 3D and Ingenuity Pathway Analysis software and relevant biological pathways and networks were identified. Genes involved in functions related to inflammatory reactions, cell death, oxidative stress and tissue damage were upregulated in control broilers compared with control and heat-stressed layers. Expression of these genes was further increased in heat-stressed broilers. Conclusions Differences in gene expression between broiler and layer chickens under control and heat stress conditions suggest that damage of breast muscles in broilers at normal ambient temperatures is similar to that in heat-stressed layers and is amplified when broilers are exposed to heat stress. The patterns of gene expression of the two genotypes under heat stress were almost the polar opposite of each other, which is consistent with the conclusion that broiler chickens were not able to cope with heat stress by dissipating their body heat. The differentially expressed gene networks and pathways were consistent with the pathological changes that are observed in the breast muscle of heat-stressed broilers.

Global poultry production is facing many challenges and is currently under pressure due to the presence of several diseases like Necrotic Enteritis (NE). It is estimated that NE-caused global economic losses has increased from 2 billion to 6 billion US$ in 2015 because it is not easy to diagnose and control disease at the earlier stage of occurrence. Additionally, ban on the in-feed antibiotics and some other genetic and non-genetic predisposing factors affect the occurrence of the disease. Though the incidence of the disease can be reduced by minimizing the predisposing factors and through immunization of birds but there is no single remedy to control the disease. Therefore, we suggest that there is need to find out the genetic variants that could help to select the birds resistant to NE. The current review details the pertinent features about the genetic and genomics of susceptibility and immune response of birds to Necrotic Enteritis. We report here the list of candidate gene reported for their involvement with the susceptibility and/or resistance to the disease. However, most of these genes are involved in immune-related functions. For better understanding of the role of Clostridium perfringens and its toxins in the pathogenesis of disease there is need to unveil the association between any specific genetic variation and clinical status of NE. However, the presence of substantial genetic variations among different breeds/strains of chicken shows that it is possible to develop broiler strain with genetic resistant against NE. It would help in the cost-effective and sustainable production of safe broiler meat.

The current study aimed to construct the growth curve and find the best-fitting non-linear model for the Nili-Ravi buffalo calves. The pedigree and monthly body weight data for 6644 calves born between 2010 and 2020 (inclusive) in six herds, maintained in different geographical regions of Punjab were collected. The study was performed under a longitudinal design and various non-linear models were used to associate the age with weight by using the easyreg package in R studio. Finally, the genetic parameters of growth curve were estimated through the bi-variate sire model in ASReml (v4.2). The model with the highest value of coefficient of determination and the lowest values of Akaike’s information criterion, Bayesian information criterion, and root-mean-square error was considered as the best fit for defining the growth curve. The Brody model was found as the best fitted model with the values of 0.6648, 627871.80, 627908.10, and 30.793 for the R2adj, AIC, BIC, & RMSE respectively, for the combined dataset. The values of growth curve parameters for the Brody model were 943.99 ± 101.38Kg (A), 0.96 ± 0.004Kg (B), and 0.0005 ± 0.00Kg (K) for all animals. A higher K-value of females indicates their early maturity compared with male animals in this breed. The heritability estimates for the growth curve traits were low, while the values of genetic correlations were higher than those of phenotypic correlations. The data revealed that Asymptotic weight (A) and birth weight (B) were positively correlated with each other, while the rate of maturity (K) was negatively correlated with initial and final body weights.

ABSTRACT The objectives of this study were to evaluate non-genetic and genetic effects as well as heritabilities and repeatabilities for seven reproductive traits using phenotypic records from an experimental Kajli flock in Punjab, Pakistan. Phenotypic data comprised 2501 records of litter size at birth (LSB), cumulative litter weight at birth (LWB), and mean litter weight at birth/ lamb born (LMWB), 1657 records of litter size at weaning (LSW), cumulative litter weight at weaning (LWW), and mean litter weight at weaning/ lamb weaned (LMWW), and 1674 records of lambing interval (LI) from Kajli sheep housed at the Livestock experiment station Khushab from 2007 to 2018. Least squares procedures (SAS, 9.1) were used to assess the effect year of service (YOS), season of service (SOS), parity of dam, and breeding ram on the expression of all reproductive traits. A derivative free REML algorithm was used to estimate heritabilities and repeatabilities with software WOMBAT®. The overall least squares means ± standard error for LSB, LWB, LMWB, LSW, LWW, LMWW and LI were 1.19±0.03, 5.75±0.17 kg, 4.88±0.06 kg, 1.17±0.05, 20.77±0.91 kg, 17.87±0.57 kg, 330.69±20.48 days, respectively. The YOS had significant (p≤0.01) impact on LSB, LWB, LMWB, LWW and LMWW. However, SOS did not affect any reproductive trait except for LI (p≤0.01). Parity significantly affected LMWB (p<0.05) as well as LSB, LWB, LSW and LWW (p≤0.01), but not LMWW and LI. Breeding ram influenced LSB, LSW and LWW significantly (p≤0.01). Genetic parameter estimates were very low due to large values of environmental variances for all reproductive traits. Estimates of heritability were low for all traits (0.08±0.05, 0.01±0.02, 0.02±0.02, 0.01±0.01, 0.04±0.03, 0.07±0.05 for LSB, LWB, LMWB, LSW, LWW and LMWW, respectively). The heritability for LI was zero. Repeatability estimates were also low for all traits (0.09±0.05, 0.02±0.02, 0.06±0.03, 0.02±0.01, 0.04±0.02, 0.09±0.06, 0.01±0.01 for LSB, LWB, LMWB, LSW, LWW, LMWW and LI, respectively). Regression of estimated breeding values for all reproductive traits on year of breeding yielded no significant genetic trends during the 12 years of the study.

Background: Vesicovaginal fistula (VVF) is a debilitating condition leaving the effected female incontinent of urine. There has been a shift in the etiology of VVF in developing nations where hysterectomy is becoming a leading cause of VVF. Objective: To share our experience of transvaginal repair of VVF using a modified Latzko technique and evaluate various factors for a successful repair. Study type, settings & duration: This retrospective study was carried out at the Department of Urology and Kidney Transplantation, Fauji Foundation Hospital, Rawalpindi from March 2010, to August 2020.   Methodology: Data were collected from patients who underwent transvaginal repair of VVF by a modified Latzko technique. Data consisting of multiple variables was analyzed using SPSS version 21. For qualitative data, percentages and frequencies were given and for quantitative data mean±SD were used. A comparison of two quantitative variables was done by using an independent t-test. For categorical variables, the chi-Square test was used. The p value ≤0.05 was taken as statistically significant. Results: A record of 144 patients was analyzed. Multivariate analysis revealed a statistically significant relationship between etiology (p-value 0.000), location (p-value 0.002) and size of VVF (p-value 0.000) and a successful repair, while number (p-value = 0.71) and VVF with a previous history of repair (p-value = 0.83) were insignificant factors. Success was observed in 98.6% while recurrence occurred in 1.4%. Conclusion: Transvaginal repair of Vesicovaginal fistula using a modified Latzko technique can be carried out in all vesicovaginal fistulae whether ...

Background: Vesicovaginal fistula (VVF) is a debilitating condition leaving the effected female incontinent of urine. There has been a shift in the etiology of VVF in developing nations where hysterectomy is becoming a leading cause of VVF. Objective: To share our experience of transvaginal repair of VVF using a modified Latzko technique and evaluate various factors for a successful repair. Study type, settings & duration: This retrospective study was carried out at the Department of Urology and Kidney Transplantation, Fauji Foundation Hospital, Rawalpindi from March 2010, to August 2020.   Methodology: Data were collected from patients who underwent transvaginal repair of VVF by a modified Latzko technique. Data consisting of multiple variables was analyzed using SPSS version 21. For qualitative data, percentages and frequencies were given and for quantitative data mean±SD were used. A comparison of two quantitative variables was done by using an independent t-test. For categorical variables, the chi-Square test was used. The p value ≤0.05 was taken as statistically significant. Results: A record of 144 patients was analyzed. Multivariate analysis revealed a statistically significant relationship between etiology (p-value 0.000), location (p-value 0.002) and size of VVF (p-value 0.000) and a successful repair, while number (p-value = 0.71) and VVF with a previous history of repair (p-value = 0.83) were insignificant factors. Success was observed in 98.6% while recurrence occurred in 1.4%. Conclusion: Transvaginal repair of Vesicovaginal fistula using a modified Latzko technique can be carried out in all vesicovaginal fistulae whether ...