A mutation-sensitive, multiplexed and amplification-free detection of nucleic acids by stretching single-molecule tandem hairpin probes.

The detection of nucleic acid sequences in parallel with the discrimination of single nucleotide variations (SNVs) is critical for research and clinical applications. A few limitations make the detection technically challenging, such as too small variation in probe-hybridization energy caused by SNVs, the non-specific amplification of false nucleic acid fragments and the few options of dyes limited by spectral overlaps. To circumvent these limitations, we developed a single-molecule nucleic acid detection assay without amplification or fluorescence termed THREF (hybridization-induced tandem DNA hairpin refolding failure) based on multiplexed magnetic tweezers. THREF can detect DNA and RNA sequences at femtomolar concentrations within 30 min, monitor multiple probes in parallel, quantify the expression level of miR-122 in patient tissues, discriminate SNVs including the hard-to-detect G-U or T-G wobble mutations and reuse the probes to save the cost. In our demonstrative detections using mock clinic samples, we profiled the let-7 family microRNAs in serum and genotyped SARS-CoV-2 strains in saliva. Overall, the THREF assay can discriminate SNVs with the advantages of high sensitivity, ultra-specificity, multiplexing, reusability, sample hands-free and robustness.

Proper RPA acetylation promotes accurate DNA replication and repair.

The single-stranded DNA (ssDNA) binding protein complex RPA plays a critical role in promoting DNA replication and multiple DNA repair pathways. However, how RPA is regulated to achieve its functions precisely in these processes remains elusive. Here, we found that proper acetylation and deacetylation of RPA are required to regulate RPA function in promoting high-fidelity DNA replication and repair. We show that yeast RPA is acetylated on multiple conserved lysines by the acetyltransferase NuA4 upon DNA damage. Mimicking constitutive RPA acetylation or blocking its acetylation causes spontaneous mutations with the signature of micro-homology-mediated large deletions or insertions. In parallel, improper RPA acetylation/deacetylation impairs DNA double-strand break (DSB) repair by the accurate gene conversion or break-induced replication while increasing the error-prone repair by single-strand annealing or alternative end joining. Mechanistically, we show that proper acetylation and deacetylation of RPA ensure its normal nuclear localization and ssDNA binding ability. Importantly, mutation of the equivalent residues in human RPA1 also impairs RPA binding on ssDNA, leading to attenuated RAD51 loading and homologous recombination repair. Thus, timely RPA acetylation and deacetylation likely represent a conserved mechanism promoting high-fidelity replication and repair while discriminating the error-prone repair mechanisms in eukaryotes.

Intuitionistic fuzzy-based entropy weight method-TOPSIS for multi-attribute group decision-making in drilling fluid waste treatment technology selection.

Drilling fluid waste is produced by oil and gas industry operations and can potentially cause serious environmental pollution and energy consumption if not properly treated. Currently, there are several treatment methods available for drilling fluid waste such as bioremediation, thermal treatment, solidification/stabilization treatment, electrochemical remediation, physiochemical treatment, and supercritical fluid treatment. However, selecting an adequate method to treat drilling fluid waste is a critical consideration. The objective of this work is to analyze the problem of drilling fluid waste pollution and treatment methods, establish a drilling fluid waste treatment decision index system that takes into account various factors, and apply the intuitionistic fuzzy-based entropy weight method (EWM)-technique for order of preference by similarity to ideal solution (TOPSIS) method to make a multi-attribute group decision on drilling fluid waste treatment methods. The method is then applied to the WBQ004-1-H1 drilling project as an example for comprehensive analysis. The final decision results show that A3 (0.566) > A1 (0.537) > A6 (0.526) > A5 (0.485) > A4 (0.478) > A2 (0.447), so the solidification/stabilization treatment is the most suitable method for this project, providing new insights into selecting drilling fluid waste treatment methods in actual projects.

Ecological evaluation of heavy metal pollution in the soil of Pb-Zn mines.

Soil heavy metal pollution evaluations are a necessary measure for mine ecological control projects. In this study, the heavy metals Pb, Zn and Cd were studied in mining areas, tailings areas, sewage plant areas, residential areas, reclamation areas, and farmland areas. Soil pollution assessments of lead-zinc ore mine soils in the countryside of China are performed based on the index of geoaccumulation (Igeo) and the improved analytic hierarchy process (AHP). Finally, the pollution sources were analyzed by positive matrix factorization (PMF). The Igeo for the heavy metals Pb, Zn and Cd in the mining area reached 5.20, 3.34, and 5.66, respectively. In addition, 80 and 65% of the mining area and tailings area reached extremely strong pollution, respectively. The numerical simulation predicts that the pollution hazard in the southeast of the mine is high and that the pollution is concentrated. The severity of soil pollution in mines derived by the index of improved analytic hierarchy process (PAHP) was as follows: mining area (70.80) > sewage plant area (35.57) > tailings area (30.64) > farmland area (28.40) > residential area (21.11) > reclamation area (10.06). Among the three categories of pollution sources, one includes reclamation area, farmland area and tailings area; one includes sewage plant area and residential area; and one includes mining area. The source contribution of Pb by the phenomenon of indiscriminate discharge of wastewater after ore smelting was as high as 90.4%; The contribution of the blind mining and tailings piling phenomenon of mines to the source of heavy metals Zn and Cd was 81.4 and 90.2%, respectively. This study proposes a reliable scientific method and technical method for evaluating mine soil pollution and provides a guiding basis for mine development and protection.

Intelligent mine safety risk based on knowledge graph: hotspots and frontiers.

The safety of mining has always been a concern. The occurrence of safety accidents not only endangers human health, but also causes serious damage to the ecological environment. With the continuous upgrade and improvement of mining technology, most mines are undergoing intelligent construction and transformation. In order to analyze security risks that should be focused on the construction of intelligent mines and the technical challenges that will be faced, we used the Web of Science (WOS) Core Collection to identify 283 publications on the field of security risks in intelligent mines from 2013 to 2022. We combined the Vosviewer, CiteSpace, and Bibliometrix R software packages to conduct an in-depth analysis and exquisite visualization of the literature, including the authors, journals, countries, hot topics, and research frontiers. This paper can help scholars comprehensively and quickly understand the research status and hotspots in the field of intelligent mine safety and risk, and it provides theoretical support for further research and exploration in the future.

[Temporal variability of the isotope compositions of plum rain in Nanjing from event to interannual time scales]. / å—äº¬æ¢ é›¨é™æ°´åŒä½ç´ ç»„æˆä»Žäº‹ä»¶åˆ°å¹´é™ å°ºåº¦çš„å˜åŒ–ç‰¹å¾.

Precipitation in the plum rain period accounts for 40%-50% of annual precipitation in the monsoon region. To clarify the temporal variability of the isotopic composition of precipitation during the plum rain period from event to interannual time scale and identify the influencing factors, we analyzed the isotopic composition of precipitation and its influencing factors in Nanjing from 2015 to 2022. By using the Hybrid Single-particle Lagran-gian Integrated Trajectory (HYSPLIT) model with specific humidity analysis, we investigated the water vapor source and influencing factors. The results showed that 1) the isotopic abundance of atmospheric precipitation was depleted in the summer and enriched in winter. dx was lower in summer and higher in winter. The isotopic abundance of precipitation from the plum rain was depleted compared to mean value of the whole-year. 2) There was no significant correlation between δ2H and δ18O of the plum rain (precipitation) with local meteorological factors. However, dx was lower in light rain, reflecting the effect of sub-cloud evaporation. The average dx was higher during plum rain period in years with more total plum rain precipitation. 3) The low-latitude South China Sea and the western Pacific Ocean source area provided water vapor for the plum rain. The shift of moisture source region led to abrupt changes in precipitation isotopes. Our results could provide data support for studies on precipitation isotopes in the monsoon region, as well as a reference point for further understanding the precipitation mechanism of the plum rain and stu-dying the seasonal variability of atmospheric circulation in the East Asian monsoon region.

Quantifying the contribution of evaporation from Lake Taihu to precipitation with an isotope-based method.

Moisture recycling plays a crucial role in regional hydrological budgets. The isotopic composition of precipitation has long been considered as a good tracer to investigate moisture recycling. This study quantifies the moisture recycling fractions (fr) in the Lake Taihu region using spatial variations of deuterium excess in precipitation (dP) and surface water vapour flux (dE). Results show that dP at a site downwind of the lake was higher than that at an upwind site, indicating the influence of lake moisture recycling. Spatial variations in dP after sub-cloud evaporation corrections were 2.3, 1.4 and 3.2 ‰, and dE values were 27.4, 32.3 and 31.4 ‰ for the first winter monsoon, the summer monsoon and the second winter monsoon, respectively. Moisture recycling fractions were 0.48 ± 0.13, 0.07 ± 0.03 and 0.38 ± 0.05 for the three monsoon periods, respectively. Both using the lake parameterization kinetic fractionation factors or neglecting sub-cloud evaporation would decrease fr, and the former has a larger influence on the fr calculation. The larger fr in the winter monsoon periods was mainly caused by lower specific humidity of airmasses but comparable moisture uptake along their trajectories compared to the summer monsoon period.

Changes in the Structures and Directions of Heavy Metal-Contaminated Soil Remediation Research from 1999 to 2020: A Bibliometric & Scientometric Study.

The pollution of heavy metals in soil is a problem of great concern to international scholars today. This research investigates the current research activities in the field of soil heavy metal pollution remediation and discusses the current areas of research focus and development trends. We conducted a bibliometric analysis of the literature on soil heavy metal pollution remediation from 1999 to 2020. CiteSpace and Vosviewer were used to conduct document co-citation and cluster analyses on the collected data. The research was mainly carried out based on the following factors: chronological distribution, country and institution distribution, source journal analysis, keyword co-occurrence analysis, and reference co-citation analysis. China (2173, 28.64%) and the United States (946, 12.47%) are the top two countries in terms of the number of articles published, and Environmental Science and Pollution Research (384, 5.06%) and Science of the Total Environment (345, 4.55%) published the most articles. The Chinese Academy of Science (485) is the organization that has contributed the most to the total number of publications. Furthermore, based on a keyword co-word analysis with Vosviewer and CitesSpace, it was concluded that the applications of phytoremediation and biochar in the remediation of heavy metals in soil are current research hotspots. Additionally, future research should focus on repair mechanisms, the development of new repair technology and joint repair systems.

Substance P enhances wound closure in nitric oxide synthase knockout mice.

INTRODUCTION: The neuropeptide, substance P (SP), up-regulates nitric oxide production (NO). The purpose of this study was to determine whether SP enhances response to cutaneous injury in nitric oxide synthase knockout (NOS null) mice. METHODS: We studied mice with targeted deletions of the 3 NOS genes, neuronal NOS, inducible NOS, or endothelial NOS. Full thickness dorsal wounds were treated daily (d 0-6) with topical SP or normal saline (NaCl). Wounds were analyzed by flow cytometry for macrophage, leukocyte, endothelial, and dendritic cells. Healing time and wound epithelialization were compared using analysis of variance. RESULTS: Wound closure in the 3 NOS null mice was slower than the control mice (P < 0.05). SP treatment enhanced wound closure in NOS null mice (P < 0.02). NOS null wounds exhibited reduced inflammation. SP increased macrophage, leukocyte, and dendritic cell densities at d 3 and d 7 (P < 0.05) in all NOS null mice. SP increased endothelial cell number in neuronal NOS and inducible NOS null mice, but not in endothelial NOS null mice (P > 0.05). CONCLUSIONS: SP ameliorated the impaired wound healing response observed in NOS null mice by enhancing wound closure kinetics and epithelialization. SP increased inflammatory cell density in the wounds supporting the essential role of inflammatory cells, especially macrophages, in wound repair.

[Effects of Water Vapor Source and Local Evaporation on the Stable Hydrogen and Oxygen Isotopic Compositions of Precipitation].

Stable hydrogen and oxygen isotopic compositions in precipitation are good tracers and can provide unique information about the water cycle. Precipitation samples were collected at the Nanjing, Liyang, Yixing, and Dongshan sites in 2016, and the HDO and H218O compositions of precipitation were measured. The temporal variability of HDO and H218O compositions and deuterium-excess of precipitation were analyzed, and the influence of the water vapor source and local evaporation on stable isotopic composition of precipitation were discussed. The results indicated that:① Seasonal variations in the HDO composition, H218O composition, and deuterium-excess of precipitation occurred due to different water vapor sources during the summer and winter monsoon seasons. The HDO and H218O compositions were depleted during the summer monsoon season and enriched during the winter monsoon season. The deuterium-excess during the summer monsoon season was lower compared to the winter monsoon season. ② During the summer monsoon, the evaporation of Lake Taihu made the deuterium-excess of downwind precipitation and the downwind intercept of the local meteoric water line higher. During the winter monsoon season, local evaporation had little influence on HDO and H218O components in precipitation. ③ Both of the intercepts and slopes of the local meteoric water line were higher than those of the global meteoric water line, due to moisture recycling during the winter monsoon season and different water vapor sources between the summer and winter monsoon seasons.

Topical substance P increases inflammatory cell density in genetically diabetic murine wounds.

The neuropeptide substance P (SP) is a known inflammatory mediator released from cutaneous peripheral nerve terminals. SP effects on cellular composition in the cutaneous response to injury remain unclear. Based on our previous observations about SP effects on wound repair, we hypothesized that topical SP increases inflammatory cell density infiltration early after injury. A full-thickness 1.5 x 1.5 cm(2) wound was created on the dorsum of 8-9-week-old C57BL/6J-m+Lepr(db) mice (db/db). Wounds were treated daily with 300 muL of either normal saline (0.9% NaCl) or 10(-9) M SP for 7 days. Three wounds from each group were harvested at 2, 3, 7, 14, and 28 days. Samples underwent enzymatic digestion and were incubated with fluorescent-labeled antibodies. Using flow cytometry, cellular content and density for each sample was derived. Masson Trichrome stained histology specimens were prepared to confirm results. Cell density in the SP-treated wounds (11.3 x 10(7) cells/g tissue, standard deviation [SD]+/-1.5 x 10(7)) was greater than in NaCl-treated wounds (7 x 10(7) cells/g tissue, SD+/-2.3 x 10(7), p<0.05) at day 7 postwounding. SP significantly increased the density of leukocytes (2.1 x 10(7), SD +/-3.6 x 10(6) vs. 1.8 x 10(7), SD+/-4.9 x 10(5), p<0.02) 3 days after wounding and the density of macrophages (2.9 x 10(7), SD+/-7.5 x 10(6) vs. 1.3 x 10(7), SD+/-1.4 x 10(6), p<0.05) 7 days after wounding. There were no significant differences in endothelial cell, leukocyte, or macrophage density at later time points. Topical SP treatment increases early inflammatory density in the healing wounds of db/db mice. These data support a role for nerve-mediated inflammation in cutaneous wound repair.

[Quantification of Methane Ebullition Flux from Small Ponds Using the Inverted-Funnel Method].

To quantify the ratio of CH4 ebullition to total flux in subtropical shallow ponds, the CH4 flux at the water-air interface was measured using the inverted-funnel and water equilibrium methods in two small ponds in Quanjiao, Anhui Province from July 28 to August 13, 2016. The average CH4 ebullition fluxes were 121.78 and 161.08 mg·(m2·d)-1 and the average diffusion fluxes were 3.38 and 3.79 mg·(m2·d)-1 over pond A and pond B, respectively. The ebullition flux accounted for 97.5% and 96.4% of the total flux over pond A and pond B, respectively. Methane ebullition ranged from 0.11 to 446.90 mg·(m2·d)-1 over pond A and from 0.05 to 607.51 mg·(m2·d)-1 over pond B. Gas ebullition rate during the day was higher than that at night and was controlled by wind speed. Methane ebullition flux was influenced by wind speed over the shallow pond at hourly scale and by water depth and wind speed at daily scale, with positive correlation with wind speed and negative correlation with water depth. Varying with latitude, methane ebullition flux was higher for the water bodies in the mid-latitude region compared to those in the high-latitude region. Direct observations of the methane ebullition flux over small ponds provide data support and theoretical reference to precisely estimate the contribution of inland water bodies to regional and global carbon cycle.

Boron deficiency decreases growth and photosynthesis, and increases starch and hexoses in leaves of citrus seedlings.

Seedlings of sweet orange (Citrus sinensis) were fertilized for 14 weeks with boron (B)-free or B-sufficient (2.5 or 10 microM H(3)BO(3)) nutrient solution every other day. Boron deficiency resulted in an overall inhibition of plant growth, with a reduction in root, stem and leaf dry weight (DW). Boron-starved leaves showed decreased CO(2) assimilation and stomatal conductance, but increased intercellular CO(2) concentrations. Activities of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), NADP-glyceraldehyde-3-phosphate dehydrogenase (NADP-GAPDH) and stromal fructose-1,6-bisphosphatase (FBPase) were lower in B-deficient leaves than in controls. Contents of glucose, fructose and starch were increased in B-deficient leaves while sucrose was decreased. Boron-deficient leaves displayed higher or similar superoxide dismutase (SOD), ascorbate peroxidase (APX), monodehydroascorbate reductase (MDAR) and glutathione reductase (GR) activities, while dehydroascorbate reductase (DHAR) and catalase (CAT) activities were lower. Expressed on a leaf area or protein basis, B-deficient leaves showed a higher ascorbate (AsA) concentration, but a similar AsA concentration on a DW basis. For reduced glutathione (GSH), we found a similar GSH concentration on a leaf area or protein basis and an even lower content on a DW basis. Superoxide anion (O(2)(-)) generation, malondialdehyde (MDA) concentration and electrolyte leakage were higher in B-deficient than in control leaves. In conclusion, CO(2) assimilation may be feedback-regulated by the excessive accumulation of starch and hexoses in B-deficient leaves via direct interference with chloroplast function and/or indirect repression of photosynthetic enzymes. Although B-deficient leaves remain high in activity of antioxidant enzymes, their antioxidant system as a whole does not provide sufficient protection from oxidative damage.

[Pathomorphological observation of the hypertrophic scar induced by injury to conical structure in female red Duroc pig].

UNLABELLED: To further explore the relationship between hypertrophic scar and injury to conical structure of skin and the pathogenesis of hypertrophic scar, and to reproduce an optimal animal model of hypertrophic scar. METHODS: The back of two FRDP pigs were shaved, and a piece of normal skin was harvested for the observation of conical structure of skin. Skin wounds with depth of 0.38 mm, 0.76 mm, 1.14 mm and 1.52 mm, respectively, were created by gas-driven dermatome. Eight wounds measuring 7.0 cm x 7.0 cm were created on each pig. The wounds were divided into 4 groups according to the wound depth with 4 wounds in each group, i.e. 0.38 mm group, 0.76 mm group, 1.14 mm group and 1.52 mm group. The 0.38 mm and 0.76 mm groups were designated as superficial wound groups and 1.14 mm and 1.52 mm groups as deep wound groups. The wounds were allowed to heal without treatment. Tissue samples from the wound were harvested on 0, 10, 30, 60, 90 and 150 post injury day (PID) , and they were sectioned for HE staining and staining for elastic fibers (VVG). The wound healing and the scar formation were observed with naked eye. The skin conical structures in normal and injured skin were also observed. The morphology of hypertrophic scar was observed, and the thickness of the scar tissue was determined and scored. RESULTS: The wounds in superficial wound groups healed within 3 weeks with flat surface without scar formation. The wounds in deep wound groups healed later than 4 weeks with thick, hairless, hard in texture, with depigmentation or pigmentation, finally forming contracture. The skin conical structure could be found on the back of FRDP with HE and VVG staining, and it was similar to that of human in terms of the structure. In superficial wound groups, the upper part of the skin conical structure was injured, but fat fornix and glands were intact. In deep wound groups, the lower part of the skin cone, together with the fat fornix and gland were all injured. On the 150th post injury day, the histological picture of the tissue in superficial wound groups was similar to that of normal skin. But the skin conical structure could not be found in deep wound groups, and the wounds were filled by a large accumulation of disarrayed and irregularly arranged collagen fibers. With passage of time, the scar became thicker and thicker, and the scar hypertrophy reached the zenith in 150th PID. CONCLUSION: The injury of skin conical structure can lead to the formation of hypertrophic scar. FRDP can be used to reproduce and ideal model of hypertrophic scar.