LncRNAway: a web-based sgRNA design tool for precise and effective suppression of long noncoding RNAs.

Thousands of long noncoding RNAs (lncRNAs) have been annotated via high-throughput RNA sequencing, yet only a small fraction have been functionally investigated. Genomic knockout is the mainstream strategy for studying the biological function of protein-coding genes and lncRNAs, whereas the complexity of the lncRNA locus, especially the natural antisense lncRNAs (NAT-lncRNAs), presents great challenges. Knocking out lncRNAs often results in unintended disruptions of neighboring protein-coding genes and small RNAs, leading to ambiguity in observing phenotypes and interpreting biological function. To address this issue, we launched LncRNAway, a user-friendly web tool based on the BESST (branchpoint to 3' splicing site targeting) method, to design sgRNAs for lncRNA knockout. LncRNAway not only provides specific and effective lncRNA knockout guidelines but also integrates genotyping primers and quantitative PCR primers designing, thereby streamlining experimental procedures of lncRNA function study. LncRNAway is freely available at https://www.lncrnaway.com.

Construction and Evaluation of a Degradable Drilling Fluid for Underground Coalbed Methane Extraction Boreholes.

Gas drainage with bedding boreholes is an efficient method for preventing gas and achieving coal and gas comining in underground mining engineering. An underground pressurized drilling method is proposed to maintain the borehole stability. However, the presence of natural fractures in coal seams poses challenges during pressurized drilling. Therefore, it is crucial to establish a low-leadage degradable drilling fluid system that minimizes coal seam damage. In this study, a degradable drilling fluid system was developed based on the characteristics of coal seams. The performance and influencing factors of the drilling fluid and the degrading capability of cellulase were examined. Moreover, the damage of the drilling fluid on fractured coal seams was investigated using core flow test methods. The results showed that additives significantly improved the rheology, filtration, and inhibition of the drilling fluid. The drilling fluid system exhibited excellent stability, rheological properties, low filtration, and sealing performance in coal seam environments. However, drilling fluid invasion and mud cake blockage negatively affected gas flow in fractured coal seams, and a higher content of filtrate reducer hindered the recovery of the gas flow rate. Cellulase was used to degrade polymers and alleviate the challenge of mud cake removal after drilling. Research on the influencing factors of cellulase indicates that the degradation efficiency of cellulase enzymes is influenced by the temperature, pH, salinity, and solid-phase content. For polluted coal samples, the gas flow rate significantly recovered after treatment with a cellulase solution. This study provides insights into a degradable drilling fluid system that can enhance underground pressurized drilling methods and minimize reservoir damage.

OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes.

Advancements in comparative genomics research have led to a growing interest in studying species evolution and genetic diversity. To facilitate this research, OrthoVenn3 has been developed as a powerful, web-based tool that enables users to efficiently identify and annotate orthologous clusters and infer phylogenetic relationships across a range of species. The latest upgrade of OrthoVenn includes several important new features, including enhanced orthologous cluster identification accuracy, improved visualization capabilities for numerous sets of data, and wrapped phylogenetic analysis. Furthermore, OrthoVenn3 now provides gene family contraction and expansion analysis to support researchers better understanding the evolutionary history of gene families, as well as collinearity analysis to detect conserved and variable genomic structures. With its intuitive user interface and robust functionality, OrthoVenn3 is a valuable resource for comparative genomics research. The tool is freely accessible at https://orthovenn3.bioinfotoolkits.net.

A molecular atlas reveals the tri-sectional spinning mechanism of spider dragline silk.

The process of natural silk production in the spider major ampullate (Ma) gland endows dragline silk with extraordinary mechanical properties and the potential for biomimetic applications. However, the precise genetic roles of the Ma gland during this process remain unknown. Here, we performed a systematic molecular atlas of dragline silk production through a high-quality genome assembly for the golden orb-weaving spider Trichonephila clavata and a multiomics approach to defining the Ma gland tri-sectional architecture: Tail, Sac, and Duct. We uncovered a hierarchical biosynthesis of spidroins, organic acids, lipids, and chitin in the sectionalized Ma gland dedicated to fine silk constitution. The ordered secretion of spidroins was achieved by the synergetic regulation of epigenetic and ceRNA signatures for genomic group-distributed spidroin genes. Single-cellular and spatial RNA profiling identified ten cell types with partitioned functional division determining the tri-sectional organization of the Ma gland. Convergence analysis and genetic manipulation further validated that this tri-sectional architecture of the silk gland was analogous across Arthropoda and inextricably linked with silk formation. Collectively, our study provides multidimensional data that significantly expand the knowledge of spider dragline silk generation and ultimately benefit innovation in spider-inspired fibers.

In-vitro evaluation of immunomodulatory activity of sulphation-modified total ginsenosides derivative-3.

Background: Ginseng has been used in biomedicine to prevent and treat decreased physical and mental capacities. Total ginsenosides (TG) from ginseng root which have antitumor and immune-enhancing properties, are the principal active components of Panax ginseng, while the sulphation-modified TG derivative-3 (SMTG-d3) was expected to enhance the anticancer activity in conventional medicinal treatments. Methods: The chlorosulphonic acid-pyridine technique, used for the sulfation modification of TG to improve their biological activity, and the infrared spectroscopic characteristics of TG and SMTG-d3 were investigated, and the effects of SMTG-d3 on immunocytes and cytokines relevant to tumor treatment were assessed. The MTT assay was used to assess the effect of TG and SMTG-d3 on the cytotoxicity and T-lymphocytic proliferation against mouse splenocytes. The LDH method was employed to evaluate NK activity induced by TG or SMTG-d3. The production levels of splenocytes-secreted IL-2 and IFN-γ and peritoneal macrophages-secreted TNF-α were determined using mouse ELISA kits. Results and discussion: It showed that the ideal conditions for the sulfation modification of TG: the volume ratio of chlorosulfonic acid to pyridine lower than 1:2.5; controlled amount of chlorosulfonic acid; and a yield of 51.5% SMTG-d3 (2 h, < 45°C). SMTG-d3 showed two characteristic absorption peaks at 1,230 cm-1 and 810 cm-1, indicating the formation of sulfuric acid esters and the presence of sulfuric acid groups. SMTG-d3 exhibited higher antitumor immunological activity than TG by promoting the proliferation of T lymphocytes and the production of IFN-γ and TNF-α, thus enhancing NK cell activity, and reducing cytotoxicity. The findings imply sulfated modification represents an effective method of enhancing the immunomodulatory activities of TG and could be used as the basis for developing new drug target compounds; SMTG-d3 can serve as an antitumor immunomodulator and can be considered an effective and prospective herbal formulation in clinical applications.

SilkDB 3.0: visualizing and exploring multiple levels of data for silkworm.

SilkDB is an open-accessibility database and powerful platform that provides comprehensive information on the silkworm (Bombyx mori) genome. Since SilkDB 2.0 was released 10 years ago, vast quantities of data about multiple aspects of the silkworm have been generated, including genome, transcriptome, Hi-C and pangenome. To visualize data at these different biological levels, we present SilkDB 3.0 (https://silkdb.bioinfotoolkits.net), a visual analytic tool for exploring silkworm data through an interactive user interface. The database contains a high-quality chromosome-level assembly of the silkworm genome, and its coding sequences and gene sets are more accurate than those in the previous version. SilkDB 3.0 provides a view of the information for each gene at the levels of sequence, protein structure, gene family, orthology, synteny, genome organization and gives access to gene expression information, genetic variation and genome interaction map. A set of visualization tools are available to display the abundant information in the above datasets. With an improved interactive user interface for the integration of large data sets, the updated SilkDB 3.0 database will be a valuable resource for the silkworm and insect research community.

OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species.

OrthoVenn is a powerful web platform for the comparison and analysis of whole-genome orthologous clusters. Here we present an updated version, OrthoVenn2, which provides new features that facilitate the comparative analysis of orthologous clusters among up to 12 species. Additionally, this update offers improvements to data visualization and interpretation, including an occurrence pattern table for interrogating the overlap of each orthologous group for the queried species. Within the occurrence table, the functional annotations and summaries of the disjunctions and intersections of clusters between the chosen species can be displayed through an interactive Venn diagram. To facilitate a broader range of comparisons, a larger number of species, including vertebrates, metazoa, protists, fungi, plants and bacteria, have been added in OrthoVenn2. Finally, a stand-alone version is available to perform large dataset comparisons and to visualize results locally without limitation of species number. In summary, OrthoVenn2 is an efficient and user-friendly web server freely accessible at https://orthovenn2.bioinfotoolkits.net.

Investigation of RC-DTH air hammer performance using CFD approach with dynamic mesh method.

Reverse circulation down-the-hole (RC-DTH) air hammers have been widely used in construction and mining activities owing to their high drilling efficiency and good dust control performance. This paper presents a computational fluid dynamics (CFD) approach with the dynamic mesh method for evaluating the performance of RC-DTH air hammers. Nine stages of operating conditions of the RC-DTH air hammer are described herein to better understand the operating mechanism of the RC-DTH air hammer. Dynamic layering, sliding interfaces, as well as user-defined functions were employed to update the mesh in dynamic mesh modelling. The influences of rebound coefficient, input air pressure, and piston mass on the performance of RC-DTH air hammers were studied. It was found that increasing the rebound coefficient and input air pressure can improve the impact performance of RC-DTH air hammers, whereas increasing input air pressure can reduce energy efficiency and increase energy consumption. In addition, simulation results indicate that increasing the input air pressure may increase the stroke of the piston; the piston mass should be optimally selected to match the designed geometric parameters to avoid a significant drop in performance. The CFD approach with the dynamic mesh method shows superiority in evaluating the performance of RC-DTH air hammers.

Theoretical analysis and design of hydro-hammer with a jet actuator: An engineering application to improve the penetration rate of directional well drilling in hard rock formations.

Rapid horizontal directional well drilling in hard or fractured formations requires efficient drilling technology. The penetration rate of conventional hard rock drilling technology in horizontal directional well excavations is relatively low, resulting in multiple overgrinding of drill cuttings in bottom boreholes. Conventional drilling techniques with reamer or diamond drill bit face difficulties due to the long construction periods, low penetration rates, and high engineering costs in the directional well drilling of hard rock. To improve the impact energy and penetration rate of directional well drilling in hard formations, a new drilling system with a percussive and rotary drilling technology has been proposed, and a hydro-hammer with a jet actuator has also been theoretically designed on the basis of the impulse hydro-turbine pressure model. In addition, the performance parameters of the hydro-hammer with a jet actuator have been numerically and experimentally analyzed, and the influence of impact stroke and pumped flow rate on the motion velocity and impact energy of the hydro-hammer has been obtained. Moreover, the designed hydro-hammer with a jet actuator has been applied to hard rock drilling in a trenchless drilling program. The motion velocity of the hydro-hammer ranges from 1.2 m/s to 3.19 m/s with diverse flow rates and impact strokes, and the motion frequency ranges from 10 Hz to 22 Hz. Moreover, the maximum impact energy of the hydro-hammer is 407 J, and the pumped flow rate is 2.3 m3/min. Thus, the average penetration rate of the optimized hydro-hammer improves by over 30% compared to conventional directional drilling in hard rock formations.

EVALUATION OF THE ACUTE AND SUBCHRONIC TOXICITY OF Aster tataricus L. F.

BACKGROUND: Aster tataricus L. f. is used as a traditional Chinese drug to relieve cough and asthma symptoms and to eliminate phlegm. However, Aster tataricus L. f. possesses toxicity, and little systematic research has been conducted on its toxic effects in the laboratory. METHODS AND MATERIALS: The acute group was administered 75% alcohol extract of Aster tataricus L. f. in a single dose. A subchronic toxicity study was performed via daily oral administration of Aster tataricus L. f. at a dose of 0.34 g/kg body weight in SD rats. The rats were divided into six groups: a petroleum ether extract (PEA) group, an ethyl acetate extract (EEA) group, an n-butyl alcohol extract (NEA) group, a remaining lower aqueous phases (REA) group, a 75% alcohol extract (AEA) group and a control group. Quantitative measurements of cytokines were obtained by fluorescence with a laser scanner using a Cy3 equivalent dye. RESULTS: The LD50 of the 75% alcohol extract of Aster tataricus L. f. was 15.74 g/kg bw. In the subchronic toxicity study, no significant differences were observed among groups in relative organ weights, urine traits, liver antioxidase levels, or cytokine levels. However, significant sporadic differences were observed in body weight gains, haematology indices, biochemistry values, and histopathology features in PEA, EEA group. In addition, sporadic changes in other groups in measures such as WBC, MCHC, CK, ALP, AST, ALT, LDH, T-BIL, LDL-C, HDL-C, and TC were observed. CONCLUSION: The toxicity study showed that Aster tataricus L. f. can produce toxic effects, mainly on the liver; much less on the heart. The LD50 was 15.74 g/kg BW in mice, and the subchronic toxicity study, used a dosage of 0.34 g/kg/d.BW, showed that the toxic components of Aster tataricus L. f. were mainly concentrated in the petroleum ether fraction, followed by the ethyl acetate fraction, the n-butyl alcohol fraction, the lower aqueous phase and the 75% ethanol extracts. Abbreviations: PEA, petroleum ether extract of Aster tataricus L. f.; EEA, ethyl acetate extract of Aster tataricus L. f.; NEA: n-butyl alcohol extract of Aster tataricus L. f.; REA: lower aqueous phases of Aster tataricus L. f.; AEA, 75% alcohol extract of Aster tataricus L. f.; WBC, white blood cell; RBC, red blood cell, PLT, platelet; HCT, haematocrit; MCV, mean corpuscular volume; HGB, haemoglobin; MCH, mean corpuscular haemoglobin; MCHC, mean corpuscular haemoglobin concentration; CREA, creatinine; LDH, lactate dehydrogenase; HDL-C, high-density lipoprotein cholesterol; LDL-C, low-density lipoprotein cholesterol; T-BIL, total bilirubin; ALT, alanine aminotransferase; ALP, alkaline phosphatase; AST, aspartate aminotransferase; TP, total protein; ALB, albumin; Glu, glucose; TC, total cholesterol; TG, triglycerides; CK, creatine kinase; GSH, Glutathione; MDA, malondialdehyde; T-SOD, total superoxide dismutase; TNF, tumour necrosis factor; IFN, interferon; MCP, monocyte chemotactic protein C.

Acute and subacute toxicity of ethanol extracts from Salvia przewalskii Maxim in rodents.

AIM: The present investigation was carried out to evaluate the safety of the lipid-soluble ethanol extracts from rhizome of Salvia przewalskii Maxim (SPM) by determining its potential toxicity after acute and subacute administration in rodents. MATERIALS AND METHODS: For the acute study, SPM extract was administered to mice in single doses given by gavage, intramuscular and intraperitoneal route. General behavior adverse effects and mortality were determined for up to 14 days. In the subacute study, the extract was administered orally at doses of 0, 50 and 250 mg/kg daily for 30 days to rats. Body weight, heart rate, blood pressure, biochemical and hematological parameters were determined at the end of 0, 15 and 30 days of daily administration. RESULTS: In acute study, SPM extract caused dose-dependent general behavior adverse effects and mortality. The no-observed adverse effect levels (NOAEL) of the extract were 1723, 288 and 500 mg/kg, when given by gavage, intramuscular and intraperitoneal routes, respectively, and the lowest-observed adverse effect levels (LOAEL) were 1981, 840 and 781 mg/kg. Mortality increased with increasing doses, with LD(50) of 2547.8, 901.3 and 780.8 mg/kg for the oral, intramuscular and intraperitonal administration. In subacute study, daily oral administration of SPM extract for up to 30 days did not result in death or significant changes in the body weight, heart rate and blood pressure, hematological and mainly biological parameters. In biological analysis, some significant changes occurred, including total protein and albumin, glucose and triglycerides, indicating that SPM extract has lipid-modulating activity. CONCLUSIONS: SPM extract was found to be low or non-toxic when acute toxicities and subacute toxicities in rodents. In view of the doses of the components consumed in traditional medicine, there is a wide margin of safety for the therapeutic use.