Unravelling of the genetic diversity, population structure, and phylogenetic relationships of the indigenous horse breeds of Pakistan.

The current study aimed to evaluate the genetic diversity, level of admixture, and phylogenetic relationship, of the Pakistani horse breeds, along with their morphological characterization. Data for the body measurements showed that Morna horses had the highest values of body height, body length, chest girth, leg length, and head length, whereas the Baluchi horses had the lowest values for these traits. For the genetic diversity 64 animals, 15/breed except for Baluchi(14) and Topras(05), were genotyped by using the 17-plex equine genotyping kit. The AMOVA results showed that 13% of genetic diversity was explained by breed differences, whereas 27% and 60% came from among and within individuals respectively. The highest values of genetic diversity parameters including Na(7.29±0.29), Ne(5.73±0.28), Ho(0.74±0.05) and He(0.82±0.01) were observed for Morna, whereas their lowest values were found for Topras. However, the highest value of inbreeding coefficient (Fis) was found for Baluchi and the lowest for KB horses. Among the markers, CA425 was found as the most polymorphic and ASB23 as the least polymorphic and highly fixed marker. Results of structure analysis revealed that, except Topras, each local horse breed had very admixed genetic structure perhaps due to their continuous crossing with other breeds in the past. Moreover, the structure analysis also showed that Morna and Shiean breeds had mixing of each other which was also confirmed by the lowest value of their pairwise Fst values and likewise the phylogenetic analysis also showed their close genetic relationship with each other. The phylogenetic analysis also revealed that Shiean breed had close genetic relationship with Arabian horses. Collectively, our data showed that Morna is the largest and genetically most diverse horse breed of Pakistan, whereas Baluchi horses are the smallest in size and have the highest values of inbreeding coefficient. And the phylogeny analysis showed that Shiean breed had close genetic relationship with the Arabian.

Genomic architecture and evolutionary relationship of BA.2.75: A Centaurus subvariant of Omicron SARS-CoV-2.

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.

Identification of polymorphisms in the MSTN and ADRB3 genes associated with growth and ultrasound carcass traits in Kajli sheep.

The aim of this investigation was to find single nucleotide polymorphisms (SNPs) in the myostatin (MSTN) and the beta-3 adrenergic receptor (ADRB3) genes associated with growth and ultrasound carcass traits in Kajli sheep. The five growth traits were birth weight (BWT-EBV), 120-day weight (120DWT-EBV), 180-day weight (180DWT-EBV), 270-day weight (270DWT-EBV), and 365-day weight (365DWT-EBV). The three ultrasound carcass traits were width (WLD) and depth of longissimus dorsi (DLD) and back fat thickness (BFT). The analysis of the MSTN sequence revealed one non-synonymous substitution (c.197T > A) in exon 1, one single nucleotide substitution (c.373 + 18G > T) in intron 1, and one synonymous substitution (c.861T > A) in exon 3. However, there were four single nucleotide synonymous substitutions (c.130C > T, c.294C > G, c.579G > T, and c.654C > G) in exon 1 of the ADRB3 gene. All the SNPs in the MSTN gene, except for c.373 + 18G > T, were in Hardy-Weinberg Equilibrium (HWE). Conversely, none of the SNPs found in ADRB3 were in HWE. Two of the MSTN SNPs (c.197T > A and c.373 + 18G > T) had significant associations with all evaluated growth and ultrasound carcass traits. The SNPs c.130C > T and c.294C > G in ADRB3 were significantly associated with 180DWT-EBV. Collectively, these findings indicate that several SNPs in the studied genes were significantly related to growth and carcass traits in Kajli sheep.

Genomic landscape of alpha-variant of SARS-CoV-2 circulated in Pakistan.

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.

Exogenous progesterone-dependent modulation in the follicular dynamics of Bos indicus cattle undergoing repeated ovum pick-up sessions.

The objective of the present study was to evaluate the role of serum progesterone (P4) in follicular dynamics, oocytes' recovery and quality and their in vitro developmental competence during consecutive ovum pick-up (OPU) sessions in Bos indicus dairy cows. Wave-synchronized Sahiwal cattle (n = 20) were randomly divided into treatment (n = 10) and control (n = 10) groups. CIDR was used as a source of external progesterone in the treatment group. Four consecutive OPU sessions at 96-hr intervals were conducted and repeated ultrasonography at 12-hr intervals was done to monitor follicular dynamics. The viable oocytes were processed for IVC following IVM and IVF until day 7. The serum P4 concentrations in the P4 and control groups were recorded as 2.31 ± 0.059 versus.0.32 ± 0.065 ng/ml, respectively (p < .05). In the treatment group, the total number of recorded follicles was higher (p < .05; 12.05 ± 0.37 versus. 10.87 ± 0.40), whilst the growth rate (mm/day) of follicles was lower (p > .05). Per session recovered oocytes (5.31 ± 0.19 versus. 3.58 ± 0.21; p < .0001) and recovery rate (54.23 versus. 42.53%; p < .05) were also higher in the treatment group compared to control. Similarly, the viable oocytes (4.54 ± 0.187 versus. 3.06 ± 0.199) and the number of grade I and II oocytes per session (3.37 ± 0.196 versus. 2.06 ± 0.21) were higher (p < .05) in the treatment group compared with the control group. However, the nuclear maturation, cleavage, and blastocyst rate did not differ (p > .05) between the groups. Taken together, during OPU sessions, serum P4 improves oocytes' recovery and quality, whilst does not affect the in vitro developmental competence of recovered oocytes.

Genomic Epidemiology of SARS-CoV-2 Divulge B.1, B.1.36, and B.1.1.7 as the Most Dominant Lineages in First, Second, and Third Wave of SARS-CoV-2 Infections in Pakistan.

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.

Genetics and genomics of susceptibility and immune response to necrotic enteritis in chicken: a review.

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.

Transcriptional profile of breast muscle in heat stressed layers is similar to that of broiler chickens at control temperature.

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 Express3D 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.

Validity of early parathyroid hormone assay as a diagnostic tool for sub-total thyroidectomy related hypocalcaemia.

OBJECTIVE: To determine the validity of early (one hour postoperatively) parathyroid hormone (PTH) assay (² 10 pg/ml), keeping gold standard as the serum ionic calcium level, for predicting sub-total thyroidectomy-related hypocalcaemia and to calculate the sensitivity and specificity of latent signs of tetany. STUDY DESIGN: Cross-sectional validation study. PLACE AND DURATION OF STUDY: Department of General Surgery, Pakistan Institute of Medical Sciences, Islamabad from August 2008 to August 2010. METHODOLOGY: Patients undergoing sub-total thyroidectomy were included by convenience sampling. PTH assay was performed 1 hour post sub-total thyroidectomy. Serum calcium levels were performed at 24 and 48 hours, 5th day and 2 weeks after surgery. Cases that developed hypocalcaemia were followed-up for a period of 6 months with monthly calcium level estimation to identify cases of permanent hypocalcaemia. Symptoms and signs of hypocalcaemia manifesting in our patients were recorded. Data was analyzed through SPSS version 10. 2 x 2 tables were used to calculate sensitivity and specificity of PTH in detecting post-thyroidectomy hypocalcaemia. RESULTS: Out of a total of 110 patients included in the study, 16.36% (n=18) developed hypocalcaemia including 1.81% (n=2) cases of permanent hypoparathyroidism. The sensitivity of one hour postoperative PTH assay as a predictive tool for post-thyroidectomy related hypocalcaemia was 94.4% while its specificity was 83.6% with 53% positive predictive value and 98.7% negative predictive value. CONCLUSION: One hour post sub-total thyroidectomy PTH assay can be helpful in predicting post sub-total thyroidectomy hypocalcaemia. Moreover, it can be useful in safe discharge of day-care thyroidectomy patients.

Carcinoma multiplex.

Multiple primaries in a single patient are uncommon, though not very rare. The existence of such cancers in two un-related, non-paired organs is even more un-common. Here, we present a case of 55 years old male who presented to us with a mucoepidermoid carcinoma of the parotid gland and was operated. Later on, he presented with a large cystic swelling in the pelvis which turned out to be pseudomyxoma peritonei. A review of slides and immunohistochemistry indicated it to be adenocarcinoma colon. He presented again with recurrent mucoepidermoid carcinoma of the parotid which was operated successfully with the use of myocutaneous flap for wound closure. He is currently undergoing chemotherapy. In order to establish a separate mono-clonal etiology of both tumours, immunohistochemistry was performed. To the best of our knowledge, carcinoma multiplex in the colon and the parotid has never been reported before.