Developing the script “degenerate primer 111” to enhance the coverage of universal primers for the small subunit rRNA gene on target microorganisms

Amplifying small subunit (SSU) rRNA genes with universal primers in assessing microbial populations diversity, but target microorganisms are sometimes omitted due to inadequate primer coverage. Adding degenerate bases to primers can help, but existing methods are complex and time-consuming. This study introduces a user-friendly tool called “Degenerate primer 111” for adding degenerate bases to existing universal primers. By aligning one universal primer with one uncovered target microorganism’s SSU rRNA gene, this tool iteratively generates a new primer, maximizing coverage for the target microorganisms. The tool was used to modify eight pairs of universal primers (515F Parada–806R Apprill, S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21, OP_F114-KP_R013, 27F-1492R, 341F-806R, OP_F066-KP_R013, 515F Parada–926R Quince, 616*F-1132R), and generated 29 new universal primers with increased coverage of specific target microorganisms without increasing coverage of non-target microorganisms. To verify the effectiveness of the improved primers, one set of original and improved primers (BA-515F-806R and BA-515F-806R-M1) was used to amplify DNA from the same sample, and high-throughput sequencing of the amplicons confirmed that the improved primers detected more microbial species compared to the original primers. Future researchers can use this tool to develop more personalized primers to meet their diverse microorganism detection needs

Genetic diversities of cytochrome B in Xinjiang Uyghur unveiled its origin and migration history

Abstract Background Uyghurs are one of the many populations of Central Eurasia that is considered to be genetically related to Eastern and Western Eurasian populations. However, there are some different opinions on the relative importance of the degree of Eastern and Western Eurasian genetic influence. In addition, the genetic diversity of the Uyghur in different geographic locations has not been clearly studied. Results In this study, we are the first to report on the DNA polymorphism of cytochrome B in the Uyghur population located in Xinjiang in northwest China. We observed a total of 102 mutant sites in the 240 samples that were studied. The average number of mutated nucleotides in the samples was 5.126. A total of 93 different haplotypes were observed. The gene diversity and discrimination power were 0.9480 and 0.9440, respectively. There were founder and bottleneck haplotypes observed in Xinjiang Uyghurs. Xinjiang Uyghurs are more genetically related to Chinese population in genetics than to Caucasians. Moreover, there was genetic diversity between Uyghurs from the southern and northern regions. There was significance in genetic distance between the southern Xinjiang Uyghurs and Chinese population, but not between the northern Xinjiang Uyghurs and Chinese. The European vs. East Asian contribution to the ten regional Uyghur groups varies among the groups and the European contribution to the Uyghur increases from north to south geographically. Conclusion This study is the first report on DNA polymorphisms of cytochrome B in the Uyghur population. The study also further confirms that there are significant genetic differences among the Uyghurs in different geographical locations. </jats:sec

Global, regional, national burden and trends of unintentional injuries from 1990 to 2021 and projections to 2035: a systematic analysis of the Global Burden of Disease study 2021

BackgroundUnintentional injuries, including drowning, falls, and heat-related incidents, constitute a substantial challenge to global health. The present study utilizes data from t the Global Burden of Disease (GBD) database to investigate the burden of unintentional injuries spanning the period from 1990 to 2021. It integrates these findings with future projections and advanced analytical approaches.MethodsEpidemiological data pertaining to unintentional injuries, sourced from the Global Burden of Disease (GBD) database covering the period 1990–2021, were subjected to analysis. This study centered on three core indicators: age-standardised incidence rate (ASIR), age-standardised mortality rate (ASDR), and age-standardised disability-adjusted life years (DALYs). The data were stratified by geographical region and classified in accordance with the Sociodemographic Index (SDI). The analytical approaches employed encompassed the computation of key metrics, trend evaluation, determination of relative variations, as well as the application of sophisticated methodologies for frontier analysis and projections, with all analyses conducted using R software.ResultsFrom 1990 to 2021, the global number of new cases of unintentional injuries rose, while both mortality figures and DALYs cases associated with such injuries trended downward. Age-standardized rates for incidence, mortality, and DALYs also decreased to varying extents. Among level 3 classifications of unintentional injuries based on age-standardized rates, falls imposed the heaviest burden. A robust positive association was identified between ASIR and SDI, in contrast to the strong inverse correlations observed between SDI and both ASDR and age-standardized DALYs rate. Frontier analysis encompassing 204 countries and territories further indicated that age-standardized DALYs rates generally diminished as SDI levels climbed. Projections extending to 2035 suggest that the global downward trajectory will persist for age-standardized indicators, including ASIR, ASDR, and age-standardized DALYs rate.ConclusionAlthough ASIR of unintentional injuries decreased between 1990 and 2021, and the burden of such injuries is relatively lighter in regions with a high SDI, notable disparities remain across countries. Sustained scholarly inquiry and innovative healthcare policies are imperative to further alleviate the burden imposed by unintentional injuries

The sugar and energy in non-carbonated sugar-sweetened beverages: a cross-sectional study.

BACKGROUND: The consumption of non-carbonated sugar-sweetened beverages (NCSSBs) has many adverse health effects. However, the sugar and energy content in NCSSBs sold in China remain unknown. We aimed to investigate the sugar and energy content of NCSSBs in China and how these contents were labelled. METHODS: A cross-sectional survey was conducted in 15 supermarkets in Haidian District, Beijing from July to October 2017. The product packaging and nutrient information panels of NCSSBs were recorded to obtain type of products (local/imported), serving size, nutrient contents of carbohydrate, sugar and energy. For those NCSSBs without sugar content information, we used carbohydrate content as a replacement. RESULTS: A total of 463 NCSSBs met the inclusion criteria and were included in our analysis. The median of sugar content and energy content was 9.6 [interquartile range (IQR): 7.1-11.3] g/100 ml and 176 (IQR: 121-201) kJ/100 ml. The median of sugar contents in juice drinks, tea-based beverages, sports drinks and energy drinks were 10.4, 8.5, 5.0 and 7.4 g/100 ml. Imported products had higher sugar and energy content than local products. There were 95.2% products of NCSSBs receiving a 'red'(high) label for sugars per portion according to the UK criteria, and 81.6% products exceeding the daily free sugar intake recommendation from the World Health Organization (25 g). There were 82 (17.7%) products with sugar content on the nutrition labels and 60.2% of them were imported products. CONCLUSIONS: NCSSBs had high sugar and energy content, and few of them provided sugar content information on their nutrition labels especially in local products. Measures including developing better regulation of labelling, reducing sugar content and restricting the serving size are needed for reducing sugar intakes in China

Myosin Light Chain Kinase Mediates Intestinal Barrier Disruption following Burn Injury

Background: Severe burn injury results in the loss of intestinal barrier function, however, the underlying mechanism remains unclear. Myosin light chain (MLC) phosphorylation mediated by MLC kinase (MLCK) is critical to the pathophysiological regulation of intestinal barrier function. We hypothesized that the MLCK-dependent MLC phosphorylation mediates the regulation of intestinal barrier function following burn injury, and that MLCK inhibition attenuates the burn-induced intestinal barrier disfunction. Methodology/Principal Findings: Male balb/c mice were assigned randomly to either sham burn (control) or 30 % total body surface area (TBSA) full thickness burn without or with intraperitoneal injection of ML-9 (2 mg/kg), an MLCK inhibitor. In vivo intestinal permeability to fluorescein isothiocyanate (FITC)-dextran was measured. Intestinal mucosa injury was assessed histologically. Tight junction proteins ZO-1, occludin and claudin-1 was analyzed by immunofluorescent assay. Expression of MLCK and phosphorylated MLC in ileal mucosa was assessed by Western blot. Intestinal permeability was increased significantly after burn injury, which was accompanied by mucosa injury, tight junction protein alterations, and increase of both MLCK and MLC phosphorylation. Treatment with ML-9 attenuated the burn-caused increase of intestinal permeability, mucosa injury, tight junction protein alterations, and decreased MLC phosphorylation, but not MLCK expression

Mineralogy and Geochemistry of High-Sulfur Coals from the M8 Coal Seam, Shihao Mine, Songzao Coalfield, Chongqing, Southwestern China

Mineral matter, including minerals and non-mineral elements, in coal is of great significance for geological evolution, high-value coal utilization, and environment protection. The minerals and elemental geochemistry of Late Permian coals from the M8 coal seam, Shihao mine, Songzao coalfield in Chongqing, were analyzed to evaluate the sediment source, sedimentary environment, hydrothermal fluids, and utilization prospects of critical metals. The average total sulfur (4.21%) was high in coals, which mainly exists in the forms of pyritic sulfur. Kaolinite, pyrite, calcite, quartz, illite and illite/smectite (I/S) mixed layers, and anatase predominated in coals, with trace amounts of chlorite, ankerite, and siderite. Epigenetic cell- and fracture-filling pyrite, veined calcite, and ankerite were related to hydrothermal fluids and/or pore water after the diagenesis stage. Compared to the world&rsquo;s hard coals, As and Cd are enriched in the Shihao M8 coals, and Li, Cr, Co, Zr, Mo, Pb, and Tb are slightly enriched. These high contents of sulfophile elements may be related to seawater intrusion. The terrigenous clastics of the Shihao M8 coals originated from the felsic&ndash;intermediate rocks atop the Emeishan Large Igneous Provinces (ELIP) (Kangdian Upland), while the roof and floor samples were derived from Emeishan high-Ti basalt. Through the combination of sulfur contents and indicator parameters of Fe2O3 + CaO + MgO/SiO2 + Al2O3, Sr/Ba and Y/Ho, the depositional environment of peat swamp was found to be influenced by seawater. Although the critical elements in coal or coal ash did not reach the cut-off grade for beneficial recovery, the concentration of Li and Zr were high enough in coal ash

Study on the Mechanism of Gas Ignition by Friction Effect of Hard Quartz Sandstone Instability

When the upper part of a high gas coal seam has hard and thick sandstone roof, the gas explosion accident in goaf is even caused by roof collapse. Taking the mining of 1007 working face of 10 coal seam under Xia KuoTan Coal Mine as the engineering background, using the method of indoor experiment and theoretical analysis, the possibility of rock friction effect igniting gas is studied. Under the engineering geological conditions, the results show that the heat produced by the friction process of hard sandstone can ignite gas. According to the 3DEC numerical simulation, the instability characteristics of the overburden hard rock are studied. The results show that the size of the slab instability area is not changed when the length of the working face increases. When the thickness of the roof is increased, the area of sliding instability is increased and the degree of sliding instability is more intense. At the boundary of the tunnel, the overlying strata are subjected to the largest shear stress, and it tends to form a friction surface with greater slip instability.</jats:p