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Abstract Background Glucocorticoid-induced osteoporosis (GIOP) is the most common type of secondary osteoporosis. Recently, autophagy has been found to be related with the development of various diseases, including osteoporosis and osteoblast differentiation regulations. BTB and CNC homology 1 (BACH1) was a previously confirmed regulator for osteoblast differentiation, but whether it’s could involve in glucocorticoid-induced human bone mesenchymal stem cells (hBMSCs) differentiation and autophagy regulation remain not been elucidated. Methods hBMSCs were identified by flow cytometry method, and its differentiation ability were measured by ARS staining, oil O red, and Alcian blue staining assays. Gene and proteins were quantified via qRT-PCR and western blot assays, respectively. Autophagy activity was determined using immunofluorescence. ChIP and dual luciferase assay validated the molecular interactions. Results The data revealed that isolated hBMSCs exhibited positive of CD29/CD44 and negative CD45/CD34. Moreover, BACH1 was abated gradually during osteoblast differentiation of hBMSCs, while dexamethasone (Dex) treatment led to BACH1 upregulation. Loss of BACH1 improved osteoblast differentiation and activated autophagy activity in Dex-challenged hBMSCs. Autophagy-related proteins (ATG3, ATG4, ATG5, ATG7, ATG12) were repressed after Dex treatment, while ATG3, ATG7 and BECN1 could be elevated by BACH1 knockdown, especially ATG7. Moreover, BACH1 could interact ATG7 promoter region to inhibit its transcription. Co-inhibition of ATG7 greatly overturned the protective roles of BACH1 loss on osteoblast differentiation and autophagy in Dex-induced hBMSCs. Conclusion Taken together, our results demonstrated that silencing of BACH1 mitigated Dex-triggered osteogenic differentiation inhibition by transcriptionally activating ATG7-mediated autophagy, suggesting that BACH1 may be a therapeutic target for GIOP treatment.

Abstract Acute kidney injury (AKI) is one of the most important lethal factors for patients admitted to intensive care units (ICUs), and timely high-risk prognostic assessment and intervention are essential to improving patient prognosis. In this study, a stacking model using the MIMIC-III dataset with a two-tier feature selection approach was developed to predict the risk of in-hospital mortality in ICU patients admitted for AKI. External validation was performed using separate MIMIC-IV and eICU-CRD. The area under the curve (AUC) was calculated using the stacking model, and features were selected using the Boruta and XGBoost feature selection methods. This study compares the performance of a stacking model using two-tier feature selection with a model using single-tier feature selection (XGBoost: 85; Boruta: 83; two-tier: 0.91). The predictive effectiveness of the stacking model was further validated by using different datasets (Validation 1: 0.83; Validation 2: 0.85) and comparing it with a simpler model and traditional clinical scores (SOFA: 0.65; APACH IV: 0.61). In addition, this study combined interpretable techniques and causal inference to analyze the causal relationship between features and predicted outcomes.

Abstract Objective This study aimed to investigate the clinical features, pathogenic gene variants, and potential genotype–phenotype correlations in Chinese patients with hereditary spherocytosis (HS). Methods Retrospective analysis of clinical data and molecular genetic characteristics was conducted on patients diagnosed with HS at Jiangxi Provincial Children's Hospital, the Second Affiliated Hospital of Nanchang University, Pingxiang People's Hospital and The Third People's Hospital of Jingdezhen between November 2017 and June 2023. Statistical analyses were performed to compare and analyze the red blood cell (RBC), hemoglobin (HB), mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH), and mean corpuscular hemoglobin concentration (MCHC) data between and within groups based on different mutations and age groups (

ObjectiveDespite several observational studies attempting to investigate the potential association between type 1 diabetes mellitus (T1DM) and the risk of digestive cancers, the results remain controversial. The purpose of this study is to examine whether there is a causal relationship between T1DM and the risk of digestive cancers.MethodsWe conducted a Mendelian randomisation (MR) study to systematically investigate the effect of T1DM on six most prevalent types of digestive cancers (oesophageal cancer, stomach cancer, hepatocellular carcinoma, biliary tract cancer, pancreatic cancer, and colorectal cancer). A total of 1,588,872 individuals were enrolled in this analysis, with 372,756 being the highest number for oesophageal cancer and 3,835 being the lowest for pancreatic cancer. Multiple MR methods were performed to evaluate the causal association of T1DM with the risk of six site-specific cancers using genome-wide association study summary data. Sensitivity analyses were also conducted to assess the robustness of the observed associations.ResultsWe selected 35 single nucleotide polymorphisms associated with T1DM as instrumental variables. Our findings indicate no significant effect of T1DM on the overall risk of oesophageal cancer (OR= 0.99992, 95% CI: 0.99979-1.00006, P= 0.2866), stomach cancer (OR=0.9298,95% CI: 0.92065-1.09466, P= 0.9298), hepatocellular carcinoma (OR= 0.99994,95% CI: 0.99987-1.00001, P= 0.1125), biliary tract cancer (OR=0.97348,95% CI: 0.8079-1.1729, P= 0.7775)), or pancreatic cancer (OR =1.01258, 95% CI: 0.96243-1.06533, P= 0.6294). However, we observed a causal association between T1DM and colorectal cancer (OR=1.000, 95% CI: 1.00045-1.0012, P

Abstract Our objective in this study is to determine whether intra-articular injection of miRNA-1 can attenuate the progression of OA in rats by down regulating Ihh. Knee chondrocytes were isolated from male Sprague–Dawley rats aged 2–3 days. Second-generation chondrocytes were transfected with miR-1 mimic and empty vector with lipo3000 for 6 h and then stimulated with 10 ng/mL IL-1β for 24 h. OA-related and cartilage matrix genes were quantified using real-time quantitative polymerase chain reaction (RT-qPCR). Two-month-old male Sprague–Dawley rats were divided into three groups (n = 30?): sham operation group + 50 µL saline, anterior cruciate ligament transection (ACLT) group + 50 µL miR-1 agomir (concentration), and control group ACLT + 50 µL miR-1 agomir. Treatment was started one week after the operation. All animals were euthanized eight weeks after the operation. X-rays and micro-CT were used to detect imaging changes in the knee joints. FMT was used to monitor joint inflammation in vivo. Safranin O staining was used to detect morphological changes in articular cartilage. Immunohistochemistry was used to detect Col2, Col10, metalloproteinase-13 (MMP-13). RT-qPCR was used to detect gene changes includingmiR-1, Col2, Col10, MMP-13, Ihh, Smo, Gli1, Gli2, and Gli3. Overexpression of miR-1 in IL-1β-stimulated chondrocytes reduced the levels of Ihh, MMP-13, and Col10 but increased the levels of Col2 and aggrecan. Intra-articular injection of miR-1 agomir reduced osteophyte formation, inflammation, and prevented cartilage damage. RT-qPCR results indicated that the miR-1 agomir increased articular cartilage anabolism and inhibited cartilage catabonism. miR-1 can attenuate the progression of OA by downregulating Ihh.

The novel deubiquitinase enzyme, motif interacting with ubiquitin-containing novel DUB family-1 (MINDY1), is highly expressed in liver cancer tissues and plays a crucial role in maintaining the stemness of liver cancer cells. Programmed death ligand-1 (PD-L1) is an immunosuppressive molecule overexpressed by tumour cells. The potential role of MINDY1 in inhibiting the stemness of liver cancer cells by deubiquitinating PD-L1 has not yet been reported. To investigate the mechanism by which MINDY1 mediates immune escape in liver cancer through the regulation of PD-L1 ubiquitination, we examined the expression levels of MINDY1 and PD-L1 in liver cancer and adjacent tissues from 50 hepatocellular carcinoma (HCC) patients using protein imprinting and immunohistochemistry. We analyzed the relationship between the expression levels of MINDY1 and PD-L1 in liver cancer tissues and their correlation with the 5-year tumor-free survival rates of patients. Subsequently, MINDY1 expression was knocked down in Huh7 cells using small interfering RNA (siRNA) interference or upregulated through transfection with a MINDY1 overexpression plasmid. The effects of MINDY1 knockdown or overexpression on the proliferation, apoptosis, migration, and invasion of HCC cells, as well as the regulation of PD-L1 binding and ubiquitination, were assessed. The 5-year tumor-free survival rates were significantly lower in both the high MINDY1 expression group and the high PD-L1 expression group (χ2 = 4.919 and 13.158, respectively). A significant difference in survival was observed between the high and low MINDY1 expression groups (χ2= 27.415). MINDY1 was found to directly interact with PD-L1, with MINDY1 gene knockdown promoting PD-L1 ubiquitination and MINDY1 overexpression inhibiting PD-L1 ubiquitination. All comparisons yielded statistically significant results (P < 0.05). In conclusion, MINDY1 inhibits the malignant progression of liver cancer by inhibiting PD-L1 ubiquitination and mediating immune escape.

Abstract In China, circulating tumor DNA analysis is widely used and numerous assays are available. Systematic evaluation to help users make informed selections is needed. Nine circulating tumor DNA assays, including one benchmark assay, were evaluated using 23 contrived reference samples. There were two sample types (cell-free DNA and plasma samples), three circulating tumor DNA inputs (low, 50 ng), two variant allele frequency ranges (low, 0.1–0.5%; intermediate, 0.5–2.5%), and four variant types (single nucleotide, insertion/deletion, structural, and copy number). Sensitivity, specificity, reproducibility, and all processes from cell-free DNA extraction to bioinformatics analysis were assessed. The test assays were generally comparable or superior to the benchmark assay, demonstrating high analytical sensitivity. Variations in circulating tumor DNA extraction and quantification efficiency, sensitivity, and reproducibility were observed, particularly at lower inputs. These findings will guide circulating tumor DNA assay choice for research and clinical studies, allowing consideration of multiple technical parameters.

YTHDC1 (YTH domain containing 1), a crucial reader protein of N6-methyladenosine (m6A) mRNA, plays a critical role in various cellular functions and is considered a promising target for therapeutic intervention in acute myeloid leukemia and other cancers. In this study, we identified orthosteric small-molecule ligands for YTHDC1. Using a molecular docking approach, we screened the eMolecules database and recognized 15 top-ranked ligands. Subsequently, molecular dynamics simulations and MM/PBSA analysis were used to assess the stability and binding free energy of these potential hit compounds in complex with YTHDC1. Notably, five compounds with IDs of ZINC82121447, ZINC02170552, ZINC65274016, ZINC10763862, and ZINC02412146 exhibited high binding affinities and favorable binding free energies. The results also showed that these compounds formed strong hydrogen bonds with residues SER378, ASN363, and ASN367 and interacted with the aromatic cage of the YTHDC1 reader protein through TRP377, TRP428, and hydrophobic residue LEU439. To assess their viability as lead compounds, we conducted absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies to reveal promising features for these identified small molecules, shedding light on their pharmacokinetic and safety profiles.

Abstract Osteoarthritis (OA) is the second-commonest arthritis, but pathogenic and regulatory mechanisms underlying OA remain incompletely understood. Here, we aimed to identify the mechanisms associated with microRNA-1 (miR-1) treatment of OA in rodent OA models using a proteomic approach. First, N = 18 Sprague Dawley (SD) rats underwent sham surgery (n = 6) or ACL transection (n = 12), followed at an interval of one week by randomization of the ACL transection group to intra-articular administration of either 50 µL placebo (control group) or miR-1 agomir, a mimic of endogenous miR-1 (experimental group). After allowing for eight weeks of remodeling, articular cartilage tissue was harvested and immunohistochemically stained for the presence of MMP-13. Second, N = 30 Col2a1-cre-ERT2 /GFPf1/fl -RFP-miR-1 transgenic mice were randomized to intra-articular administration of either placebo (control group, N = 15) or tamoxifen, an inducer of miR-1 expression (experimental group, N = 15), before undergoing surgical disruption of the medial meniscus (DMM) after an interval of five days. After allowing for eight weeks of remodeling, articular cartilage tissue was harvested and underwent differential proteomic analysis. Specifically, tandem mass tagging (TMT) quantitative proteomic analysis was employed to identify inter-group differentially-expressed proteins (DEP), and selected DEPs were validated using real-time quantitative polymerase chain reaction (RT-qPCR) technology. Immunohistochemically-detected MMP-13 expression was significantly lower in the experimental rat group, and proteomic analyses of mouse tissue homogenate demonstrated that of 3526 identified proteins, 345 were differentially expressed (relative up- and down-regulation) in the experimental group. Proteins Fn1, P4ha1, P4ha2, Acan, F2, Col3a1, Fga, Rps29, Rpl34, and Fgg were the *top ten most-connected proteins, implying that miR-1 may regulate an expression network involving these proteins. Of these ten proteins, three were selected for further validation by RT-qPCR: the transcript of Fn1, known to be associated with OA, exhibited relative upregulation in the experimental group, whereas the transcripts of P4ha1 and Acan exhibited relative downregulation. These proteins may thus represent key miR-1 targets during OA-regulatory mechanisms, and may provide additional insights regarding therapeutic mechanisms of miR-1 in context of OA.

Cancer treatment has always been a challenge for humanity. The inadequacies of current technologies underscore the limitations of our efforts against this disease. Nevertheless, the advent of targeted therapy has introduced a promising avenue, furnishing us with more efficacious tools. Consequently, researchers have turned their attention toward epigenetics, offering a novel perspective in this realm. The investigation of epigenetics has brought RNA readers to the forefront, as they play pivotal roles in recognizing and regulating RNA functions. Recently, the development of inhibitors targeting these RNA readers has emerged as a focal point in research and holds promise for further strides in targeted therapy. In this review, we comprehensively summarize various types of inhibitors targeting RNA readers, including non-coding RNA (ncRNA) inhibitors, small-molecule inhibitors, and other potential inhibitors. We systematically elucidate their mechanisms in suppressing cancer progression by inhibiting readers, aiming to present inhibitors of readers at the current stage and provide more insights into the development of anticancer drugs.

In deep-sea mining hydraulic lifting systems, centrifugal pumps are very important as power units. In the process of transportation, the fluid prewhirl phenomenon in the impeller inlet will lead to changes in the state of motion of the particles and fluid and cause the wear of the inlet pipe, which can lead to centrifugal pump failure in serious cases. In this paper, a numerical simulation of the centrifugal pump is carried out based on the CFD-DEM coupling method to analyze the influence of the prewhirl on the wear of the inlet pipe. The results show that the velocity streamline near the impeller inlet position changes significantly. The flow field velocity increases along the radial direction of the inlet pipe, and it has a maximum value at r/R = 0.98. The prewhirl flow pulls the particles to change their original motion direction, and the area where the particles are subjected to high fluid force is concentrated between 0.5 d/D and 1 d/D, about 0.015 to 0.018 N, resulting in the uneven distribution of particles. The high-wear area appears in the bottom-left area (specifically, L4, L9, and L13), and this is also the location of the largest cumulative force; the high-wear area shows a triangle. The collision energy loss of particles increases due to the influence of the prewhirl, which leads to an increase in wear.

Background Polycystic ovary syndrome (PCOS) is the most common endocrine disorder with complex pathophysiological mechanism. It is reported that even a modest weight loss of 5–10% substantially may improve the reproductive and metabolic profile. This study aims to assess the efficacy of the low dose of liraglutide (0.6 mg QD) combined with metformin (0.85 mg BID) in weight loss in Chinese Han women with PCOS.Methods We included clinical data of 102 obese/overweight (≥18 years, body mass index ≥28 kg/m2 or ≥24 kg/m2) women who were diagnosed with PCOS from October 2016 to March 2018 in Wuhan Union Hospital initially. They were treated with dinae-35, low dose of liraglutide (0.6 mg QD) and metformin (0.85 mg BID) for 12 weeks. The demographic and clinical data were retrieved retrospectively, and weight loss was the main outcome measure. Student’s paired t-test and Wilcoxon rank sum test were used to compare the differences before and after therapy, p

The Spike (S) protein of the SARS-CoV-2 virus that causes the COVID-19 disease is considered the most important target for vaccine, drug and therapeutic research as it attaches and binds to the ACE2 receptor of the host cells and allows the entry of this virus. Analysis and classification of newly determined S protein structures for SARS-CoV-2 are critical to properly understand their functional, evolutionary and architectural relatedness to already known protein structures. In this paper, first, the comparative analysis of SARS-CoV-2 S protein structures is performed. Through comparative analysis, the S protein structures in the PDB (protein data bank) database are compared and analyzed not only with each other but with the structures of other viruses for various parameters. Second, the S protein structures in PDB are classified into different variants, and the associated published literature is studied to investigate what kind of therapeutics (antibodies, T-cell receptors and small molecules) are used on the structures. This is the first study that classifies the S protein structures of the SARS-CoV-2 in PDB into various variants, and the obtained comparative analysis results could be beneficial to the research community, in general, and to crystallographers and health workers, in particular.

The mechanism of sex determination and differentiation in animals remains a central focus of reproductive and developmental biology research, and the regulation of sex differentiation in amphioxus remains poorly understood. Cytochrome P450 Family 19 Subfamily A member 1 (CYP19A1) is a crucial sex differentiation gene that catalyzes the conversion of androgens into estrogens. In this study, we identified two aromatase-like genes in amphioxus: cyp19-like1 and cyp19-like2. The cyp19-like1 is more primitive and may represent the ancestral form of cyp19 in zebrafish and other vertebrates, while the cyp19-like2 is likely the result of gene duplication within amphioxus. To gain further insights into the expression level of these two aromatase-like, we examined their expression in different tissues and during different stages of gonad development. While the expression level of the two genes differs in tissues, both are highly expressed in the gonad primordium and are primarily localized to microsomal membrane systems. However, as development proceeds, their expression level decreases significantly. This study enhances our understanding of sex differentiation mechanisms in amphioxus and provides valuable insights into the formation and evolution of sex determination mechanisms in vertebrates.

The phase, mechanical properties, corrosion resistance, hydrophobicity, and interfacial contact resistance of Hastelloy X were investigated to evaluate its performance in proton exchange membrane fuel cells (PEMFCs). For comparison, the corresponding performance of 304 stainless steel (304SS) was also tested. Hastelloy X exhibited a single-phase face-centered cubic structure with a yield strength of 445.5 MPa and a hardness of 262.7 HV. Both Hastelloy X and 304SS exhibited poor hydrophobicity because the water contact angles were all below 80°. In a simulated PEMFC working environment (0.5 M H2SO4 + 2 ppm HF, 80 °C, H2), Hastelloy X exhibited better corrosion resistance than 304SS. At 140 N·cm−2, the interfacial contact resistance of Hastelloy X can reach as low as 7.4 mΩ·cm2. Considering its overall performance, Hastelloy X has better potential application than 304SS as bipolar plate material in PEMFCs.

Manganese (Mn) is a promising positive electrode element for aqueous redox flow batteries (ARFB); however, reversible and stable Mn species are still highly desirable. Herein, an ultra-stable Mn-centered Keggin-type polyoxometalate, viz. (NH4)6[MnW12O40]·9 H2O, is designed for neutral ARFB. The polyoxometalate is extensively characterized by X-ray crystalline diffraction, ultraviolet-visible spectroscopy, X-ray photoelectron spectroscopy, and electrochemical method. It is found that for (NH4)6[MnW12O40], the rigid skeleton and cage-structural coordination yield superior stability in a symmetrical flow battery. Pairing with viologen derivative, 0.50 M (NH4)6[MnW12O40] flow battery delivers a capacity of 10.2 Ah L−1 and a capacity retention ratio of 99.994% per cycle at 20 mA cm−2 over 500 cycles (∼19 days). This work provides new insight into designing stable electroactive materials for ARFB.

Abstract The conversion of CO2 into fuels and valuable chemicals is one of the central topics to combat climate change and meet the growing demand for renewable energy. Herein, we show that the formate dehydrogenase from Clostridium ljungdahlii (ClFDH) adsorbed on electrodes displays clear characteristic voltammetric signals that can be assigned to the reduction and oxidation potential of the [4Fe‐4S]2+/+ cluster under nonturnover conditions. Upon adding substrates, the signals transform into a specific redox center that engages in catalytic electron transport. ClFDH catalyzes rapid and efficient reversible interconversion between CO2 and formate in the presence of substrates. The turnover frequency of electrochemical CO2 reduction is determined as 1210 s−1 at 25 °C and pH 7.0, which can be further enhanced up to 1786 s−1 at 50°C. The Faradaic efficiency at −0.6 V (vs. standard hydrogen electrode) is recorded as 99.3% in a 2‐h reaction. Inhibition experiments and theoretical modeling disclose interesting pathways for CO2 entry, formate exit, and OCN− competition, suggesting an oxidation‐state‐dependent binding mechanism of catalysis. Our results provide a different perspective for understanding the catalytic mechanism of FDH and original insights into the design of synthetic catalysts.

In order to study the composition of volatile aroma components in Fuliang black tea and screen the key aroma components, in this study, headspace-solid phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS) was performed to identify the volatile components of Fuliang black tea, and the key aroma components were selected by the odor activity value (OAV) and principal component analysis (PCA). The 73 kinds of volatile components were isolated and identified in Fuliang black tea, including 16 alcohols, 12 esters, 11 hydrocarbons, 10 ketones, 9 aldehydes, 6 acids, 6 heterocycles and 3 phenols and their derivatives. The kinds and relative contents of alcohols were the highest, among which 44 kinds of volatile components had no significant difference among the three Fuliang black tea samples (P>0.05), and 29 kinds had significant difference (P

Abstract This study aimed to compare MRI quality between conventional fast spin echo T2 weighted imaging (FSE T2WI) with periodically rotated overlapping parallel lines with enhanced reconstruction (PROPELLER) FSE T2WI for patients with various porcelain fused to metal (PFM) crown and analyze the value of PROPELLER technique in reducing metal artifacts. Conventional FSE T2WI and PROPELLER FSE T2WI sequences for axial imaging of head were applied in participants with different PFM crowns: cobalt-chromium (Co–Cr) alloy, pure titanium (Ti), gold–palladium (Au–Pd) alloy. Two radiologists evaluated overall image quality of section in PFM using a 5-point scale qualitatively and measured the maximum artifact area and artifact signal-to-noise ratio (SNR) quantitatively. Fifty-nine participants were evaluated. The metal crown with the least artifacts and the optimum image quality shown in conventional FSE T2WI and PROPELLER FSE T2WI were in Au–Pd alloy, Ti, and Co–Cr alloy order. PROPELLER FSE T2WI was superior to conventional FSE T2WI in improving image quality and reducing artifact area for Co-Cr alloy (17.0 ± 0.2% smaller artifact area, p

In this paper, (1) We show that if there are not enough symmetries and λ-symmetries, some first integrals can still be obtained. And we give two examples to illustrate this theorem. (2) We prove that when X is a λ-symmetry of differential equation field Γ, by multiplying Γ a function μ defineded on Jn−1M, the vector fields μΓ can pass to quotient manifold Q by a group action of λ-symmetry X. (3) If there are some λ-symmetries of equation considered, we show that the vector fields from their linear combination are symmetries of the equation under some conditions. And if we have vector field X defined on Jn−1M with first-order λ-prolongation Y and first-order standard prolongations Z of X defined on JnM, we prove that gY cannot be first-order λ-prolonged vector field of vector field gX if g is not a constant function. (4) We provide a complete set of functionally independent (n−1) order invariants for V(n−1) which are n−1th prolongation of λ-symmetry of V and get an explicit n−1 order reduced equation of explicit n order ordinary equation considered. (5) Assume there is a set of vector fields Xi,i=1,...,n that are in involution, We claim that under some conditions, their λ-prolongations also in involution.

IntroductionOver the past three decades, the view of nutrient limitation has transferred from single-nutrient limitation to multiple-nutrient limitation. On the Qinghai-Tibetan Plateau (QTP), many nitrogen (N) and phosphorus (P) addition experiments have revealed different N- or P-limited patterns at many alpine grassland sites, whereas it is not clear what the general patterns of N and P limitation across the QTP grasslands.MethodsWe performed a meta-analysis, containing 107 publications, to assess how N and P constrained plant biomass and diversity in alpine grasslands across the QTP. We also tested how mean annual precipitation (MAP) and mean annual temperature (MAT) influence N and P limitations.ResultsThe findings show that plant biomass in QTP grasslands is co-limited by N and P. Single N limitation is stronger than single P limitation, and the combined positive effect of N and P addition is stronger than that of single nutrient additions. The response of biomass to N fertilization rate shows an increase firstly and then declines, and peaks at approximately 25 g N·m-2·year-1. MAP promotes the effect of N limitation on plant aboveground biomass and diminishes the effect of N limitation on belowground biomass. Meanwhile, N and P addition generally decline plant diversity. Moreover, the negative response of plant diversity to N and P co-addition is strongest than that of single nutrient additions.DiscussionOur results highlight that N and P co-limitation is more prevalent than N- or P-limitation alone in alpine grasslands on the QTP. Our findings provide a better understanding of nutrient limitation and management for alpine grasslands on the QTP.

This paper presents the design and construction of vacuum preloading incorporated with electroosmosis (VPE) engineering application for the treatment of soft soil on complex terrain for sluice foundation excavation in order to reduce the amount of cement used in construction. Monitoring was conducted during the VPE treatment and laboratory geotechnical tests were carried out once the treatment came to an end. Results show that the electrification mode has a significant influence on electric energy consumption. Stepped-up voltage helped in saving electric energy while electrode conversion consumed a lot of electric energy. The dispersion of soil parameters became larger after VPE treatment. The stability of physical parameters is better than the mechanical parameters, and the latter is better than the deformation parameters. Soil water content has a linear relationship with density and compression coefficient. The given linear fitting equations can help in simplifying the calculation and acquisition of these indexes. Although the mean values of the soil index parameters slightly improved, their coefficient of variation (COV) significantly increased. These locations with improved index parameters scattering in the construction site ensured that the subsequent construction tasks such as pit slope and excavation were successfully realized in this area.

ObjectivesTo observe the elongation of the axial tooth movement in the unopposed rodent molar model with type 1 diabetes mellitus and explore the pathological changes of periodontal ligament and alveolar bone, and their correlation with tooth axial movement.MethodsThe 80 C57BL/6J mice were randomly divided into the streptozotocin(STZ)-injected group (n = 50) and the control group (n = 30). Mice in the streptozotocin(STZ)-injected group were injected intraperitoneal with streptozotocin (STZ), and mice in the control group were given intraperitoneal injection of equal doses of sodium citrate buffer. Thirty mice were randomly selected from the successful models as the T1DM group. The right maxillary molar teeth of mice were extracted under anesthesia, and allowed mandibular molars to super-erupt. Mice were sacrificed at 0, 3, 6,9, and 12 days. Tooth elongation and bone mineral density (BMD) were evaluated by micro-CT analysis(0,and 12 days mice). Conventional HE staining, Masson staining and TRAP staining were used to observe the changes in periodontal tissue(0, 3, 6, 9, and 12 days mice). The expression differences of SPARC, FGF9, BMP4, NOGGIN, and type I collagen were analyzed by RT-qPCR.ResultsAfter 12 days of tooth extraction, our data showed significant super-eruption of mandibular mouse molars of the two groups. The amount of molar super-eruption in the T1DM group was 0.055mm( ± 0.014mm), and in the control group was 0.157( ± 0.017mm). The elongation of the T1DM mice was less than that of the control mice(P

Green entrepreneurial orientation (GEO) and sustainability have been the hot topics in green entrepreneurship research. The GEO integrates market orientation (MO) and environmental orientation (EO), and enterprises need to increase resource investment. However, it is not clear whether this strategic orientation can help new ventures achieve sustainable competitive advantages (SCA). In addition, the integrated role of opportunities and resources in the process of green entrepreneurship cannot be ignored. To fill the gap, we analyzed survey data from 274 emerging green enterprises in China, and we examined the effect of GEO on SCA. Additionally, we proposed the concept of integration of opportunity and resources capabilities (IORC) by integrating the core factors of green entrepreneurship. It can be divided into internal integration (ITI) and external integration (ETI), and the moderating effect of IORC on this relationship was also inspected. The results indicated that GEO significantly affects SCA, and IORC positively moderates the relationships between GEO and SCA. Indeed, compared with the enterprises that adopt a single strategic orientation, enterprises that adopt GEO can obtain greater SCA. In addition, focusing on the internal and external integration of IORC can further enhance the acquisition of SCA. This study not only integrates the theories of entrepreneurship and sustainable development but also compensates for the lack of green entrepreneurship theory while providing practical guidance for new enterprises seeking to engage in green entrepreneurship.

Bone marrow is one of the most important organs in the human body. The evaluation of bone marrow microstructure and gender-related cellular and capillary networks in healthy young adults can help to better understand the process of bone metabolism. Intravoxel incoherent motion (IVIM) provides both diffusion and perfusion quantifications without requiring intravenous contrast agent injection. In this prospective study, 60 healthy young age-matched volunteers (30 men and 30 women) underwent MRI scans at 1.5 T using multi–b-value diffusion-weighted imaging on sagittal planes covering the lumbar bone marrow. The apparent diffusion coefficient (ADC), true ADC (D), pseudo-ADC (D*), and perfusion fraction (f) were calculated from the diffusion-weighted images using the mono- and bi-exponential models. Lumbar cancellous bone (L2–L4) was selected as the region of interest. An independent t-test was used to detect significant differences in ADC values and IVIM parameters between men and women. The differences in IVIM parameters among the L2, L3, and L4 groups were compared with analysis of variance. The D and f values in women were significantly higher than that in men (p = 0.001, 0.026). However, D* was significantly lower in women than that in men (p = 0.001). Furthermore, there was no significant gender difference for the conventional ADC value (p = 0.186). Moreover, there were no significant differences in the D, f, and D* values among the L2, L3, and L4 vertebras of women or men. IVIM parameters can show differences in bone marrow between young women and men. As a non-invasive method, it can assess bone marrow microstructure, such as cellularity and perfusion.

Multiple myeloma (MM) is characterized by clonal expansion of malignant plasma cells in the bone marrow (BM). Despite the significant advances in treatment, relapsed and refractory MM has not yet been completely cured due to the immune dysfunction in the tumor microenvironment (TME). In this study, we analyzed the transcriptome data from patients with newly diagnosed (ND) and relapsed/refractory (R/R) MM to characterize differences in the TME and further decipher the mechanism of tumor progression in MM. We observed highly expressed cancer testis antigens and immune suppressive cell infiltration, such as Th2 and M2 cells, are associated with MM progression. Furthermore, the TGF-β signature contributes to the worse outcome of patients with R/R MM. Moreover, patients with ND MM could be classified into immune-low and immune-high phenotypes. Immune-high patients with higher IFN-g signatures are associated with MHC-II–mediated CD4+ T-cell response through CIITA stimulation. The baseline TME status could potentially inform new therapeutic choices for the ND MM who are ineligible for autologous stem cell transplantation and may help predict the response to CAR-T for patients with R/R MM. Our study demonstrates how integrating tumor transcriptome and clinical information to characterize MM immune microenvironment and elucidate potential mechanisms of tumor progression and immune evasion, which will provide insights into MM treatment selection.

BackgroundMultiple myeloma (MM) remains an incurable malignant tumor of plasma cells. Increasing evidence has reported that hypoxia and immune status contribute to the progression of MM. In this research, the prognostic value of the hypoxia–immune-related gene SLC19A1 in MM was evaluated by bioinformatics analysis.MethodRNA-sequencing (RNA-seq) data along with clinical information on MM were downloaded from the Gene Expression Omnibus (GEO) database. Consistent clustering analysis and ESTIMATE algorithms were performed to establish the MM sample subgroups related to hypoxia and immune status, respectively, based on the GSE24080 dataset. The differentially expressed analysis was performed to identify the hypoxia–immune-related genes. Subsequently, a hypoxia–immune-gene risk signature for MM patients was constructed by univariate and multivariate Cox regression analyses, which was also verified in the GSE4581 dataset. Furthermore, the mRNA expression of SLC19A1 was determined using qRT-PCR in 19 MM patients, and the correlations between the genetic expression of SLC19A1 and clinical features were further analyzed.ResultA total of 47 genes were identified as hypoxia–immune-related genes for MM. Among these genes, SLC19A1 was screened to construct a risk score model that had better predictive power for MM. The constructed prognostic signature based on SLC19A1 was verified in the GSE4581 dataset. All independent prognostic factors (age, β2-microglobulin, LDH, albumin, MRI, and gene risk score) were used to develop a nomogram that showed a better performance for predicting the survival probability of MM patients for 1–5 years. Furthermore, SLC19A1 was highly expressed in newly diagnosed and relapsed MM patients, and high expression of SLC19A1 is correlated with higher bone marrow aspiration plasma cells and β2-microglobulin levels in MM patients.ConclusionIn conclusion, our results suggest that SLC19A1 is aberrantly expressed in MM and highly expressed SLC19A1 might be a biomarker correlated with inferior prognosis. More importantly, we identified SLC19A1 as a hypoxia–immune-related gene in MM. Future functional and mechanistic studies will further clarify the roles of SLC19A1 in MM.

Background: Fourteen meta-analyses reported the individual effects of the GSTM1 and GSTT1 polymorphisms on leukemia risk. However, over 40 studies were not included in previously published meta-analyses. Moreover, one key aspect was that previous meta-analyses did not conduct the false-positive test on the aforementioned issues. Furthermore, previous meta-analyses did not observe the combined effects of GSTM1 present/null and GSTT1 present/null polymorphism with leukemia risk. Therefore, we conducted the current study to further analyze these associations.Objectives: This study aimed to investigate the association between the individual and combined effects of the GSTM1 present/null and GSTT1 present/null polymorphisms and the risk of leukemia.Methods: A meta-analysis was performed applying Meta-analyses of Observational Studies in Epidemiology (MOOSE) guidelines. Moreover, false-positive report probability (FPRP) and Bayesian false discovery probability (BFDP) were applied to investigate the false-positive results.Results: The individual GSTM1 and GSTT1 null genotypes and combined effects of the two genes were associated with a significantly increased leukemia risk in overall and several subgroup analyses, such as Asians, Caucasians, and so on. Then, further analysis was conducted using FPRP and BFDP. Significant associations were considered as “positive” results on the GSTM1 null genotype with leukemia risk in overall populations (FPRP < 0.001 and BFDP = 0.006), Asians (FPRP < 0.001 and BFDP < 0.001), and East Asian population (FPRP < 0.001 and BFDP = 0.002). For the GSTT1 null genotype, significant associations were regarded “positive” results in overall populations, acute myeloid leukemia (AML), Asians, and East Asian population. For the combined effects of the GSTM1 and GSTT1 polymorphisms, significant associations were also considered “positive” results in the overall analysis of Asians, Indians, and East Asian population.Conclusion: This study strongly indicates that the individual GSTM1 and GSTT1 null genotypes and combined effects of the two genes are associated with increased leukemia risk in Asians, especially in the East Asian population; the GSTT1 null genotype is associated with increased AML risk; the combined effects of the two genes are associated with increased leukemia risk in Indians.

MORF-RELATED GENE702 (OsMRG702) regulates flowering time genes in rice, but how it controls transcription is not well known. Here, we found that OsMRGBP can directly interact with OsMRG702. Both Osmrg702 and Osmrgbp mutants show the delayed flowering phenotype with the reduction in the transcription of multiple key flowering time genes, including Ehd1 and RFT1. Chromatin immunoprecipitation study showed that both OsMRG702 and OsMRGBP bind to the Ehd1 and RFT1 loci and the absence of either OsMRG702 or OsMRGBP leads to a decrease of H4K5 acetylation at these loci, indicating OsMRG702 and OsMRGBP cooperatively together to promote the H4K5 acetylation. In addition, whilst Ghd7 are upregulated in both Osmrg702 and Osmrgbp mutants, only OsMRG702 binds to the loci, together with the global increased and Ghd7 locus-specific increased H4K5ac levels in Osmrg702 mutants, suggesting an additional negative effect of OsMRG702 on H4K5 acetylation. In summary, OsMRG702 controls flowering gene regulation by altering H4 acetylation in rice; it works either together with OsMRGBP to enhance transcription by promoting H4 acetylation or with other unknown mechanisms to dampen transcription by preventing H4 acetylation.

Laccase immobilization is a promising method that can be used for the recyclable treatment of refractory phenolic pollutants (e.g., chlorophenols) under mild conditions, but the method is still hindered by the trade-off limits of supports in terms of their high specific surface area and rich functional groups. Herein, confined polymerization was applied to create abundant amino-functionalized polymeric ionic liquids (PILs) featuring a highly specific surface area and mesoporous structure for chemically immobilizing laccase. Benefiting from this strategy, the specific surface area of the as-synthesized PILs was significantly increased by 60-fold, from 5 to 302 m2/g. Further, a maximum activity recovery of 82% towards laccase was recorded. The tolerance and circulation of the immobilized laccase under harsh operating conditions were significantly improved, and the immobilized laccase retained more than 84% of its initial activity after 15 days. After 10 cycles, the immobilized laccase was still able to maintain 80% of its activity. Compared with the free laccase, the immobilized laccase exhibited enhanced stability in the biodegradation of 2,4-dichlorophenol (2,4-DCP), recording around 80% (seven cycles) efficiency. It is proposed that the synergistic effect between PILs and laccase plays an important role in the enhancement of stability and activity in phenolic pollutant degradation. This work provides a strategy for the development of synthetic methods for PILs and the improvement of immobilized laccase stability.

Yersinia pestis, the cause of plague, is a newly evolved Gram-negative bacterium. Through the acquisition of the plasminogen activator (Pla), Y. pestis gained the means to rapidly disseminate throughout its mammalian hosts. It was suggested that Y. pestis utilizes Pla to interact with the DEC-205 (CD205) receptor on antigen-presenting cells (APCs) to initiate host dissemination and infection. However, the evolutionary origin of Pla has not been fully elucidated. The PgtE enzyme of Salmonella enterica, involved in host dissemination, shows sequence similarity with the Y. pestis Pla. In this study, we demonstrated that both Escherichia coli K-12 and Y. pestis bacteria expressing the PgtE-protein were able to interact with primary alveolar macrophages and DEC-205-transfected CHO cells. The interaction between PgtE-expressing bacteria and DEC-205-expressing transfectants could be inhibited by the application of an anti-DEC-205 antibody. Moreover, PgtE-expressing Y. pestis partially re-gained the ability to promote host dissemination and infection. In conclusion, the DEC-205-PgtE interaction plays a role in promoting the dissemination and infection of Y. pestis, suggesting that Pla and the PgtE of S. enterica might share a common evolutionary origin.

Abstract In this paper, we study the Adomian decomposition method (ADM for short) including its iterative scheme and convergence analysis, which is a simple and effective technique in dealing with some nonlinear problems. We take algebraic equations and fractional differential equations as applications to illustrate ADM’s efficiency.

Metachromatic leukodystrophy (MLD) is a rare genetic disease characterised by a dysfunction of the enzyme arylsulphatase A leading to the lysosomal accumulation of cerebroside sulphate (sulphatide) causing subsequent demyelination in patients. The enzyme galactosylceramide (cerebroside) sulphotransferase (CST) catalyses the transfer of a sulphate group from 3′-phosphoadenosine-5'-phosphosulphate (PAPS) to cerebrosides producing sulphatides. Substrate reduction therapy for arylsulphatase A by inhibition of CST was proposed as a promising therapeutic approach. To identify competitive CST inhibitors, we synthesised and investigated analogues of the substrate galactosylceramide with variations at the anomeric position, the acyl substituent and the carbohydrate moiety, and investigated their structure–activity relationships. While most of the compounds behaved as substrates, α-galactosylceramide 16 was identified as the first competitive CST inhibitor. Compound 16 can serve as a new lead structure for the development of drugs for the treatment of this devastating disease, MLD, for which small molecule therapeutics are currently not available.

Organic matter (OM) and carbonate are the important organic and inorganic components, respectively, in the shales of the upper fourth member of the Eocene Shahejie Formation, Dongying Depression, Eastern China. Their enrichment affects the hydrocarbon generation capacity and reservoir development of shales. The development mechanism of sequence stratigraphy and the influence of sequence stratigraphy on OM enrichment and carbonate deposition are investigated in this study. Based on the petrological, mineralogical, and geochemical analyses, a third-order sequence is recognized, including the lowstand systems tract (LST), transgressive systems tract (TST), and highstand systems tract (HST). The total organic carbon (TOC) content is 0.11–9.05 wt% (average 2.2 wt%), and the carbonate content is 3–95 wt% (average 51 wt%). Organic matter and carbonate are enriched in TST and gradually reduced in HST and LST. The decrease in the relative lake level in LST results in the deposition of abundant siltstone, leading to both poor OM preservation and carbonate precipitation. The rapid rise in the relative lake level in TST may be triggered by marine transgression, promoting OM enrichment in terms of both production and preservation. Seawater input brought abundant Ca2+ and Mg2+, which facilitated the precipitation of carbonates. The enrichment of OM and carbonate improves the capacity of hydrocarbon generation and reservoir performance of shales in the TST. The decrease in the relative lake level in HST causes a slight increase in the terrigenous clastic content, which, on the one hand, accelerates the sedimentation rate and OM deposition and, on the other hand, reduces carbonate precipitation. This study not only explains the differential distribution of OM and carbonate but also helps to improve the accuracy of the evaluation of shale oil sweet spots.

In this paper, metallocene polypropylene (mPP) composites filled with carbon nanotubes (CNTs) were prepared using twin-screw extruder. The crystallization behavior, mechanical properties and rheological behavior were characterized by a differential scanning calorimetry (DSC), universal material testing machine and rotational rheometer. The results of DSC indicated that the effect of CNTs on heterogeneous nucleation of mPP was very obvious and the crystallizability of the resin matrix was improved after adding CNTs, especially the initial crystallization temperature ( T _0 ), crystallization temperature ( T _c ) increased by 9.63 °C and 8.28 °C when the CNTs content was 1.25 wt%. The yield stress and elastic modulus increased to 33.98 MPa and 1605.6 MPa as the CNTs concentration increased to 1.0 wt% in contrast to that of the neat mPP. The results of SEM images showed that the better dispersion and adhesion of CNTs into polymer matrix. The results of rotational rheometer proved that interactions increased between CNTs and mPP as the content of CNTs increasing.

Lysyl oxidase-like 2 (LOXL2) is a metalloenzyme that catalyzes the oxidative deamination ε-amino group of lysine. It is found that LOXL2 is a promotor for the metastasis and invasion of cancer cells. Disulfide bonds are important components in LOXL2, and they play a stabilizing role for protein structure or a functional role for regulating protein bioactivity. The redox potential of disulfide bond is one important property to determine the functional role of disulfide bond. In this study, we have calculated the reduction potential of all the disulfide bonds in LOXL2 by non-equilibrium alchemical simulations. Our results show that seven of seventeen disulfide bonds have high redox potentials between −182 and −298 mV and could have a functional role, viz., Cys573–Cys625, Cys579–Cys695, Cys657–Cys673, and Cys663–Cys685 in the catalytic domain, Cys351–Cys414, Cys464–Cys530, and Cys477–Cys543 in the scavenger receptor cysteine-rich (SRCR) domains. The disulfide bond of Cys351–Cys414 is predicted to play an allosteric function role, which could affect the metastasis and invasion of cancer cells. Other functional bonds have a catalytic role related to enzyme activity. The rest of disulfide bonds are predicted to play a structural role. Our study provides an important insight for the classification of disulfide bonds in LOXL2 and can be utilized for the drug design that targets the cysteine residues in LOXL2.

The cell wall of Gram-positive bacteria consists of peptidoglycan modified with other polymers, such as the capsular polysaccharide. Here, the authors reconstitute the biosynthesis of capsular polysaccharide and elucidate its interplay with the cell wall biosynthetic machinery.

The metabolites in the tender shoots of the tea plant are the material basis for the determination of tea quality. The composition and abundance of these metabolites are affected by many key factors, and the tea plant’s age is one of them. However, the effect of plant age on the tender shoot metabolites of tea cultivars of different genotypes is poorly understood. Therefore, we used a combination of untargeted metabolomics and transcriptomics to analyze the differential mechanism behind the differences in the metabolites of the spring tender shoots of 7- and 40-year-old tea plants of two tea cultivars of different genotypes. We found that plant age could significantly change the metabolites in the spring tender shoots of tea plants and that flavonoids, and amino acids and their derivatives, were predominant among the differential metabolites. The quantities of most flavonoids in the aged tea plants of different genotypes were upregulated, which was caused by the upregulated expression of differential genes in the flavonoid biosynthesis pathway. We further discovered that 11 key structural genes play key regulatory roles in the changes in the flavonoid contents of tea plants of different plant ages. However, the influence of plant age on amino acids and their derivatives might be cultivar-specific. By characterizing and evaluating the quality-related metabolites of tea cultivars of two different genotypes at different plant ages, we found that whether an old tea plant (40 years old) can produce high-quality tea is related to the genotype of the tea plant.

Objective: Increasing evidence suggests that microRNA (miRNA) participates in regulating tumor cell apoptosis. We aimed to observe the effect of hsa-miR-33-5p on the apoptosis of breast cancer cells and to explore its regulatory relationship with selenoprotein T (SelT).Methods: RT-qPCR was used to examine the expression of hsa-miR-33-5p and SelT both in breast cancer tissues and cells. MCF-7 and MDA-MB-231 cells were transfected with hsa-miR-33-5p mimics or si-SelT. Then, a flow cytometry assay was carried out to examine the apoptosis of cells. Furthermore, SelT and apoptosis-related proteins including caspase-3, caspase-8, caspase-9, Bax, and Bcl-2 were detected via RT-qPCR and western blot. A luciferase reporter assay was utilized for assessing whether SelT was targeted by hsa-miR-33-5p.Results: Downregulated hsa-miR-33-5p was found both in breast cancer tissues and cells. After its overexpression, MCF-7 cell apoptosis was significantly promoted. Furthermore, our data showed that miR-33-5p elevated apoptosis-related protein expression in MCF-7 cells. Contrary to hsa-miR-33-5p, SelT was upregulated both in breast cancer tissues and cells. SelT expression was significantly inhibited by hsa-miR-33-5p overexpression. The luciferase reporter assay confirmed that SelT was a direct target of hsa-miR-33-5p. SelT overexpression could ameliorate the increase in apoptosis induced by hsa-miR-33-5p mimics.Conclusion: Our findings revealed that hsa-miR-33-5p, as a potential therapeutic target, could accelerate breast cancer cell apoptosis.

Theoretical analyses are valuable for the exploration of the effects of unnatural amino acids on enzyme functions; however, many necessary parameters for unnatural amino acids remain lacking. In this study, we developed and tested force field parameters compatible with Amber ff14SB for 18 phenylalanine and tyrosine derivatives. The charge parameters were derived from ab initio calculations using the RESP fitting approach and then adjusted to reproduce the benchmark relative energies (at the MP2/TZ level) of the α- and β-backbones for each unnatural amino acid dipeptide. The structures optimized under the proposed force field parameters for the 18 unnatural amino acid dipeptides in both the α- and β-backbone forms were in good agreement with their QM structures, as the average RMSD was as small as 0.1 Å. The force field parameters were then tested in their application to seven proteins containing unnatural amino acids. The RMSDs of the simulated configurations of these unnatural amino acids were approximately 1.0 Å compared with those of the crystal structures. The vital interactions between proteins and unnatural amino acids in five protein–ligand complexes were also predicted using MM/PBSA analysis, and they were largely consistent with experimental observations. This work will provide theoretical aid for drug design involving unnatural amino acids.

Trans-acting splicing factors play a pivotal role in modulating alternative splicing by specifically binding to cis-elements in pre-mRNAs. There are approximately 1500 RNA-binding proteins (RBPs) in the human genome, but the activities of these RBPs in alternative splicing are unknown. Since determining RBP activities through experimental methods is expensive and time consuming, the development of an efficient computational method for predicting the activities of RBPs in alternative splicing from their sequences is of great practical importance. Recently, a machine learning model for predicting the activities of splicing factors was built based on features of single and dual amino acid compositions. Here, we explored the role of physicochemical and structural properties in predicting their activities in alternative splicing using machine learning approaches and found that the prediction performance is significantly improved by including these properties. By combining the minimum redundancy–maximum relevance (mRMR) method and forward feature searching strategy, a promising feature subset with 24 features was obtained to predict the activities of RBPs. The feature subset consists of 16 dual amino acid compositions, 5 physicochemical features, and 3 structural features. The physicochemical and structural properties were as important as the sequence composition features for an accurate prediction of the activities of splicing factors. The hydrophobicity and distribution of coil are suggested to be the key physicochemical and structural features, respectively.

The ‘stress-gradient hypothesis’ predicts increasing facilitative interactions with increasing environmental stress, but it remains unclear if the prevailing type of interaction (i.e. facilitative or competitive) between dominant and subordinate plant species occurring in harsh environments is dependent on the plant functional type. In addition, most plant-species removal experiments in grasslands are short-term (1–2 years), which may imprecisely reflect transient effects arising from methodological limitations. We conducted a dominant species removal experiment in a subalpine ecosystem, containing a mosaic of grass-dominated and shrub-dominated community patches, both of which are common in the subalpine zone of the Qinghai-Tibetan Plateau. We examined the direction and magnitude of the effects of three co-dominant grass and a dominant shrub species on subordinate species richness and biomass over a 6-year period. Removal of the dominant grass species alleviated their competitive pressure on subdominant grasses, which resulted in similar total and grass biomass detected in the final year of the study. By contrast, shrub removal showed no effects on its subordinate species biomass. Furthermore, neither the removal of the dominant shrubs nor the grasses altered their respective subordinate species richness. Thus, in subalpine ecosystems that experience harsh environmental conditions, our results showed that the direction of interactive effects of dominant plant species on subordinate species may be dependent on the plant functional type and are not necessarily facilitative. Furthermore, we showed that longer-term plant-removal experiment observations may be required to better determine the effects of species removal for this subalpine and other montane ecosystem(s).

Uropathogenic Escherichia coli (UPEC), a Gram-negative bacterial pathogen, is a major causative agent of urinary tract infections (UTIs). However, the molecular mechanisms of how UPEC causes infections have not been determined. Recent studies indicated that certain enteric Gram-negative bacteria interact with and hijack innate immune receptors DC-SIGN (CD209a) and SIGNR1 (CD209b), often expressed by antigen-presenting cells (APCs), such as macrophages, leading to dissemination and infection. It was not known whether UPEC could utilize DC-SIGN receptors to promote its infection and dissemination similarly to the enteric pathogens. The results of this study reveal that UPEC interacts with CD209-expressing macrophages and transfectants. This interaction is inhibited by anti-CD209 antibody, indicating that CD209s are receptors for UPEC. Additionally, in contrast to the results of previous studies, mice lacking SIGNR1 are more susceptible to infection of this uropathogen, leading to prolonged bacterial persistence. Overall, the results of our study indicate that the innate immune receptor CD209s participate in the clearance of UPEC during UTIs.

Arthrobacter nicotinovorans decomposes nicotine through the pyridine pathway. 6-hydroxypseudooxynicotine 2-oxidoreductase (also named ketone dehydrogenase, Kdh) is an important enzyme in nicotine degradation pathway of A. nicotinovorans, and is responsible for the second hydroxylation of nicotine. Kdh belongs to the molybdenum hydroxylase family, and catalyzes the oxidation of 6-hydroxy-pseudooxynicotine (6-HPON) to 2,6-dihydroxy-pseudooxynicotine (2,6-DHPON). We determined the crystal structure of the Kdh holoenzyme from A. nicotinovorans, with its three subunits KdhL, KdhM, and KdhS, and their associated cofactors molybdopterin cytosine dinucleotide (MCD), two iron-sulfur clusters (Fe2S2), and flavin adenine dinucleotide (FAD), respectively. In addition, we obtained a structural model of the substrate 6-HPON-bound Kdh through molecular docking, and performed molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations to unveil the catalytic mechanism of Kdh. The residues Glu345, Try551, and Glu748 of KdhL were found to participate in substrate binding, and Phe269 and Arg383 of KdhL were found to contribute to stabilize the MCD conformation. Furthermore, site-directed mutagenesis and enzymatic activity assays were performed to support our structural and computational results, which also revealed a trend of increasing catalytic efficiency with the increase in the buffer pH. Lastly, our electrochemical results demonstrated electron transfer among the various cofactors of Kdh. Therefore, our work provides a comprehensive structural, mechanistic, and functional study on the molybdenum hydroxylase Kdh in the nicotine degradation pathway of A. nicotinovorans.

Mycobacterial fatty acid synthase type-I (FAS-I) has an important role in the de novo synthesis of fatty acids, which constitute a major component of the cell wall. The essentiality of FAS-I in the survival and growth of mycobacterium makes it an attractive drug target. However, targeted inhibitors against Mycobacterial FAS-I have not been reported yet. Recently, the structure of FAS-I from Mycobacterium tuberculosis was solved. Therefore, in a quest to find potential inhibitors against FAS-I, molecular docking-based virtual screening and molecular dynamics simulation were done. Subsequently, molecular dynamic simulations based on binding free energy calculations were done to gain insight into the predicted binding mode of putative hits. The detailed analysis resulted in the selection of four putative inhibitors. For compounds BTB14738, RH00608, SPB02705, and CD01000, binding free energy was calculated as −72.27 ± 12.63, −68.06 ± 11.80, −63.57 ± 12.22, and −51.28 ± 13.74 KJ/mol, respectively. These compounds are proposed to be promising pioneer hits.

In China, a new-round marketization reform of electricity industry is in progress, and the electricity transmission and distribution tariff reform is the core and important task. Currently, the electricity transmission and distribution tariff regulation has gone to the second round in China, and the electric power grid enterprises are facing a closed-loop regulatory system and an increasingly strict regulatory environment. Therefore, it is urgent to evaluate the risk of electric power grid enterprise that is related to electricity transmission and distribution tariff regulation, which can aid the electricity regulators and electric power grid enterprise operators to manage risk and promote the sustainable development of electric power industry. In this paper, a hybrid novel multi-criteria decision making (MCDM) method combining the fuzzy Best-Worst method (FBWM) and improved fuzzy comprehensive evaluation method based on a vague set is proposed for the risk evaluation of electric power grid enterprise related to electricity transmission and distribution tariff regulation. The risk evaluation index system is built. Subsequently, the FBWM is utilized to determine the optimal weights of electric power grid enterprise risk criteria, and the improved fuzzy comprehensive evaluation method that is based on vague set is employed to rank the comprehensive risk grade of electric power grid enterprise related to electricity transmission and distribution tariff regulation. The risk of a province-level electric power grid enterprise that is located in Northern China is empirically evaluated using the proposed MCDM method, and the result indicates that the overall risk of this province-level electric power grid enterprise belongs to ‘High’ grade, but it is very close to ‘Very High’ grade. The results indicate that the proposed hybrid novel MCDM method in this paper is effective and practical. Meanwhile, it provides a new view for the risk evaluation of electric power grid enterprise that is related to electricity transmission and distribution tariff regulation.

In the postgenomic age, rapid growth in the number of sequence-known proteins has been accompanied by much slower growth in the number of structure-known proteins (as a result of experimental limitations), and a widening gap between the two is evident. Because protein function is linked to protein structure, successful prediction of protein structure is of significant importance in protein function identification. Foreknowledge of protein structural class can help improve protein structure prediction with significant medical and pharmaceutical implications. Thus, a fast, suitable, reliable, and reasonable computational method for protein structural class prediction has become pivotal in bioinformatics. Here, we review recent efforts in protein structural class prediction from protein sequence, with particular attention paid to new feature descriptors, which extract information from protein sequence, and the use of machine learning algorithms in both feature selection and the construction of new classification models. These new feature descriptors include amino acid composition, sequence order, physicochemical properties, multiprofile Bayes, and secondary structure-based features. Machine learning methods, such as artificial neural networks (ANNs), support vector machine (SVM), K-nearest neighbor (KNN), random forest, deep learning, and examples of their application are discussed in detail. We also present our view on possible future directions, challenges, and opportunities for the applications of machine learning algorithms for prediction of protein structural classes.

Recent studies have identified cyclic GMP-AMP synthase (cGAS) as an important target for treating autoimmune diseases, and several inhibitors of human cGAS (hcGAS) and their structures in complexation with hcGAS have been reported. However, the mechanisms via which these inhibitors interact with hcGAS are not completely understood. Here, we aimed to assess the performance of molecular mechanics/Poisson–Boltzmann solvent-accessible surface area (MM/PBSA) in evaluating the binding affinity of various hcGAS inhibitors and to elucidate their detailed interactions with hcGAS from an energetic viewpoint. Using molecular dynamics (MD) simulation and MM/PBSA approaches, the estimated free energies were in good agreement with the experimental ones, with a Pearson’s correlation coefficient and Spearman’s rank coefficient of 0.67 and 0.46, respectively. In per-residue energy decomposition analysis, four residues, K362, R376, Y436, and K439 in hcGAS were found to contribute significantly to the binding with inhibitors via hydrogen bonding, salt bridges, and various π interactions, such as π· · ·π stacking, cation· · ·π, hydroxyl· · ·π, and alkyl· · ·π interactions. In addition, we discussed other key interactions between specific residues and ligands, in particular, between H363 and JUJ, F379 and 9BY, and H437 and 8ZM. The sandwiched structures of the inhibitor bound to the guanidinium group of R376 and the phenyl ring of Y436 were also consistent with the experimental data. The results indicated that MM/PBSA in combination with other virtual screening methods, could be a reliable approach to discover new hcGAS inhibitors and thus is valuable for potential treatments of cGAS-dependent inflammatory diseases.

Reliable prediction of binding affinities for ligand-receptor complex has been the primary goal of a structure-based drug design process. In this respect, alchemical methods are evolving as a popular choice to predict the binding affinities for biomolecular complexes. However, the highly flexible protein-ligand systems pose a challenge to the accuracy of binding free energy calculations mostly due to insufficient sampling. Herein, integrated computational protocol combining free energy perturbation based absolute binding free energy calculation with free energy landscape method was proposed for improved prediction of binding free energy for flexible protein-ligand complexes. The proposed method is applied to the dataset of various classes of p53-MDM2 (murine double minute 2) inhibitors. The absolute binding free energy calculations for MDMX (murine double minute X) resulted in a mean absolute error value of 0.816 kcal/mol while it is 3.08 kcal/mol for MDM2, a highly flexible protein compared to MDMX. With the integration of the free energy landscape method, the mean absolute error for MDM2 is improved to 1.95 kcal/mol.