Identification of Two Species of the Family Sparidae for eDNA Sequences using a Representative 16SrRNA Reference Library for Omani Fish

Identification of fish species accurately is required to support efforts for conserving fishery biodiversity assessment and sustainable management. Recently, environmental DNA (eDNA) was suggested for regular monitoring of species for effective management of biodiversity. In Oman, molecular reference library representing fish species from the Omani coastline can support such potential approaches. In this communication, we used a local mtDNA-16SrRNA reference library representing Sparidae fish species from the Omani coastlines to identify two Sparidae eDNA sequences (zotu24 and zotu85, from Muscat and Dhofar, respectively) from Acanthopagrus and Diplodus genera reported by a recent eDNA study from Oman.  The two species are found to be Acanthopagrus berda and Diplodus cervinus and their sampling sites matches the locations range of the reference specimens. The results indicate the utility and importance for DNA markers’ reference library representing fish species from the Omani coastline to effectively sustain the marine resources using emerging technologies. Keywords: Sparidae, eDNA; 16SrRNA; Acanthopagrus berda; Diplodus cervinus; Oman. &nbsp

Detection of Unlabeled Genetically Modified Soybean in the Omani Market

This study aimed to screen for products containing Genetically Modified (GM) food in the Omani market using detection methods for the presence of Roundup Ready Soybean, Bt176 and MON810 maize in food products and to quantify it in positive samples using real time Polymerase Chain Reaction (PCR). A total of 100 food samples were collected randomly from markets in Oman. Out of 59 samples, 8  (13.5%) were successfully amplified with the maize plant specific PCR. GM screening showed negative for all samples, which indicated low or no GM maize in the samples tested. Out of 57 soy containing samples, 40 (70%) were successfully amplified by the soybean plant specific PCR. Six samples out of the 40 (15%) were found positive for GM using P35S-cf3/P35S-cr4 and HA-nos118-f/HA-nos118-r, primer pairs and using GMO5/GMO9 and GMO7/GMO8 primer pairs for specific detection of Roundup Ready Soybean. Real time PCR (TaqMan™ system) was carried out for the positive Roundup Ready Soybean samples and results showed that 2 out of the positive GM soy samples contained more than 5%; a Soy Formula for Infants (imported) sample contained 21% GM soybean and raw soybean seeds (imported in bulk amounts and packed in Oman)  contained 88% GM soybean. The results demonstrate for the first time the presence of GM-soy in food products in the Omani market, reinforcing the need for the use of qualitative and quantitative methods for GM detection in food products

The Identification of Pompe Disease Mutations in Archival Tissues and Development of a Rapid Molecular-based Test

Objectives: Pompe disease (glycogen storage disease type II) is a rare autosomal recessive lysosomal storage disease that is caused by acid alpha-glucosidase deficiency. Early enzyme replacement therapy can benefit infants with the disease but the diagnosis is complicated by the rarity of the disease and the heterogeneity of the clinical manifestations. In this study, DNA extracted from archival postmortem formalin-fixed paraffin-embedded tissues was used to identify Pompe disease mutations in Oman and develop a rapid molecular-based test. Methods: Intronic primers were designed to amplify short fragments (193–454 base pairs [bp]) from coding exons (2–20) and screen for mutations using direct sequencing (DS). Results: Two mutations known to cause severe disease were identified in two infants. One was a coding mutation, c.2560C>T (p.Arg854X), and the second was found at a splice acceptor site, c.1327-2A>G. Polymerase chain reaction- and restriction fragment length polymorphism-based tests were designed for the rapid genotyping of the identified mutations. Conclusion: These tests can facilitate prenatal diagnosis and help in identifying carriers in families with the identified mutations

The use of high throughput DNA sequence analysis to assess the endophytic microbiome of date palm roots grown under different levels of salt stress

Date palms are able to grow under diverse abiotic stress conditions including in saline soils, where microbial communities may be help in the plant’s salinity tolerance. These communities able to produce specific growth promoting substances can enhance date palm growth in a saline environment. However, these communities are poorly defined. In the work reported here, the date palm endophytic bacterial and fungal communities were identified using the pyrosequencing method, and the microbial differential abundance in the root upon exposure to salinity stress was estimated. Approximately 150,061 reads were produced from the analysis of six ribosomal DNA libraries, which were prepared from endophytic microorganisms colonizing date palm root tissues. DNA sequence analysis of these libraries predicted the presence of a variety of bacterial and fungal endophytic species, some known and others unknown. The microbial community compositions of 30% and 8% of the bacterial and fungal species, respectively, were significantly (p ≤ 0.05) altered in response to salinity stress. Differential enrichment analysis showed that microbe diversity indicated by the Chao, Shannon and Simpson indices were slightly reduced, however, the overall microbial community structures were not significantly affected as a consequence of salinity. This may reflect a buffering effect by the host plant on the internal environments that these communities are colonizing. Some of the endophytes identified in this study were strains that were previously isolated from saline and marine environments. This suggests possible interactions with the plant that are favorable to salinity tolerance in date palm. [Int Microbiol 19(3):143-155 (2016)]Keywords: Phoenix dactylifera · endophytes · salt stres

Detection of Unlabeled Genetically Modified Soybean in the Omani Market

This study aimed to screen for products containing Genetically Modified (GM) food in the Omani market using detection methods for the presence of Roundup Ready Soybean, Bt176 and MON810 maize in food products and to quantify it in positive samples using real time Polymerase Chain Reaction (PCR). A total of 100 food samples were collected randomly from markets in Oman. Out of 59 samples, 8  (13.5%) were successfully amplified with the maize plant specific PCR. GM screening showed negative for all samples, which indicated low or no GM maize in the samples tested. Out of 57 soy containing samples, 40 (70%) were successfully amplified by the soybean plant specific PCR. Six samples out of the 40 (15%) were found positive for GM using P35S-cf3/P35S-cr4 and HA-nos118-f/HA-nos118-r, primer pairs and using GMO5/GMO9 and GMO7/GMO8 primer pairs for specific detection of Roundup Ready Soybean. Real time PCR (TaqMan™ system) was carried out for the positive Roundup Ready Soybean samples and results showed that 2 out of the positive GM soy samples contained more than 5%; a Soy Formula for Infants (imported) sample contained 21% GM soybean and raw soybean seeds (imported in bulk amounts and packed in Oman)  contained 88% GM soybean. The results demonstrate for the first time the presence of GM-soy in food products in the Omani market, reinforcing the need for the use of qualitative and quantitative methods for GM detection in food products

Fc receptor gamma subunit polymorphisms and systemic lupus erythematosus

Objective: To investigate the possible association between Fc receptor (FcR) gamma polymorphisms and systemic lupus erythernatosus (SLE)

Effects of pre-operative isolation on postoperative pulmonary complications after elective surgery: an international prospective cohort study an international prospective cohort study

We aimed to determine the impact of pre-operative isolation on postoperative pulmonary complications after elective surgery during the global SARS-CoV-2 pandemic. We performed an international prospective cohort study including patients undergoing elective surgery in October 2020. Isolation was defined as the period before surgery during which patients did not leave their house or receive visitors from outside their household. The primary outcome was postoperative pulmonary complications, adjusted in multivariable models for measured confounders. Pre-defined sub-group analyses were performed for the primary outcome. A total of 96,454 patients from 114 countries were included and overall, 26,948 (27.9%) patients isolated before surgery. Postoperative pulmonary complications were recorded in 1947 (2.0%) patients of which 227 (11.7%) were associated with SARS-CoV-2 infection. Patients who isolated pre-operatively were older, had more respiratory comorbidities and were more commonly from areas of high SARS-CoV-2 incidence and high-income countries. Although the overall rates of postoperative pulmonary complications were similar in those that isolated and those that did not (2.1% vs 2.0%, respectively), isolation was associated with higher rates of postoperative pulmonary complications after adjustment (adjusted OR 1.20, 95%CI 1.05–1.36, p = 0.005). Sensitivity analyses revealed no further differences when patients were categorised by: pre-operative testing; use of COVID-19-free pathways; or community SARS-CoV-2 prevalence. The rate of postoperative pulmonary complications increased with periods of isolation longer than 3 days, with an OR (95%CI) at 4–7 days or ≥ 8 days of 1.25 (1.04–1.48), p = 0.015 and 1.31 (1.11–1.55), p = 0.001, respectively. Isolation before elective surgery might be associated with a small but clinically important increased risk of postoperative pulmonary complications. Longer periods of isolation showed no reduction in the risk of postoperative pulmonary complications. These findings have significant implications for global provision of elective surgical care. We aimed to determine the impact of pre-operative isolation on postoperative pulmonary complications after elective surgery during the global SARS-CoV-2 pandemic. We performed an international prospective cohort study including patients undergoing elective surgery in October 2020. Isolation was defined as the period before surgery during which patients did not leave their house or receive visitors from outside their household. The primary outcome was postoperative pulmonary complications, adjusted in multivariable models for measured confounders. Pre-defined sub-group analyses were performed for the primary outcome. A total of 96,454 patients from 114 countries were included and overall, 26,948 (27.9%) patients isolated before surgery. Postoperative pulmonary complications were recorded in 1947 (2.0%) patients of which 227 (11.7%) were associated with SARS-CoV-2 infection. Patients who isolated pre-operatively were older, had more respiratory comorbidities and were more commonly from areas of high SARS-CoV-2 incidence and high-income countries. Although the overall rates of postoperative pulmonary complications were similar in those that isolated and those that did not (2.1% vs 2.0%, respectively), isolation was associated with higher rates of postoperative pulmonary complications after adjustment (adjusted OR 1.20, 95%CI 1.05–1.36, p = 0.005). Sensitivity analyses revealed no further differences when patients were categorised by: pre-operative testing; use of COVID-19-free pathways; or community SARS-CoV-2 prevalence. The rate of postoperative pulmonary complications increased with periods of isolation longer than 3 days, with an OR (95%CI) at 4–7 days or ≥ 8 days of 1.25 (1.04–1.48), p = 0.015 and 1.31 (1.11–1.55), p = 0.001, respectively. Isolation before elective surgery might be associated with a small but clinically important increased risk of postoperative pulmonary complications. Longer periods of isolation showed no reduction in the risk of postoperative pulmonary complications. These findings have significant implications for global provision of elective surgical care