Ligand-based virtual screening (LBVS) can be pivotal for identifying potential drug leads, especially when the target protein's structure is unknown. However, current LBVS methods are limited in their ability to consider the ligand conformational flexibility. This study presents AutoDock-SS (Similarity Searching), which adapts protein-ligand docking for use in LBVS. AutoDock-SS integrates novel ligand-based grid maps and AutoDock-GPU into a novel three-dimensional LBVS workflow. Unlike other approaches based on pregenerated conformer libraries, AutoDock-SS's built-in conformational search optimizes conformations dynamically based on the reference ligand, thus providing a more accurate representation of relevant ligand conformations. AutoDock-SS supports two modes: single and multiple ligand queries, allowing for the seamless consideration of multiple reference ligands. When tested on the Directory of Useful DecoysâEnhanced (DUD-E) data set, AutoDock-SS surpassed alternative 3D LBVS methods, achieving a mean AUROC of 0.775 and an EF1% of 25.72 in single-reference mode. The multireference mode, evaluated on the augmented DUD-E+ data set, demonstrated superior accuracy with a mean AUROC of 0.843 and an EF1% of 34.59. This enhanced performance underscores AutoDock-SS's ability to treat compounds as conformationally flexible while considering the ligand's shape, pharmacophore, and electrostatic potential, expanding the potential of LBVS methods.
Molecular Docking Simulation , Ligands , Drug Evaluation, Preclinical/methods , Proteins/chemistry , Proteins/metabolism , User-Computer Interface , Protein Conformation , Molecular Conformation
Groundwater discharge exceeding recharge threatens sustainable aquifer water use internationally. Interest remains high in discovering more hydrologically sustainable and economically affordable measures to protect these aquifers. Previous research has conducted various aquifer assessments. Some work has investigated costs and benefits of various plans that would limit aquifer pumping. Despite notable advances in this kind of analysis, little published work to date has unified these elements into a science-based integrated framework to inform more sustainable aquifer policy design. This work's novel contribution is to integrate analysis of hydrology, economics, institutions, and policy into a unified scientific framework to inform choices on more sustainable pumping strategies while protecting economic activity for agricultural and urban water-using sectors. It does so by conceptualizing, formulating, designing, and applying a mathematical programming framework to replicate historically observed pumping patterns in parts of the Southern and Central High Plains Ogallala Aquifer region in New Mexico, USA. We first calibrated the optimization framework to replicate the historically observed data. We then go on to identify least cost pumping caps that would have partly restored the aquifer to its 2014 level by 2020, while comparing the performance of four other partial aquifer protection policy measures. Findings indicate a surprisingly low cost that could have been incurred to partially protect the aquifer over that period. However, these low costs are complicated by (1) decreasing water quality outside of the irrigated regions and (2) focusing of lateral inputs to a narrower zone of depression around the irrigated regions. These findings carry important implications for identifying more sustainable aquifer management plans internationally. The work's importance comes from its capacity to inform policy debates over a range of water shortage sharing plans, while respecting institutional constraints governing equitable burden sharing.
Objective: The objective of this study was to observe and analyze changes in serum levels of APN, MCP-1, hs-CRP, and SOD in patients with hypertension and diabetes mellitus (DM) and to investigate the correlations among these inflammatory factors. The study aimed to provide insights into disease monitoring and management. Methods: 320 cases were included in this study, including 50 cases in group A (simple diabetes mellitus); 60 cases in group B (simple hypertension); and 90 cases in group C (Hypertension with diabetes). 120 healthy subjects served as the control group. Fasting blood glucose (FPG), glycosylated hemoglobin (GHbA1c) and other biochemical indicators were detected, and ELISA detected the levels of MCP-1, APN and SOD, hs-CRP was detected by immunoenhanced turbidimetric method. Results: Patients with diabetes (group A), hypertension (group B), and hypertension with diabetes (group C) exhibited elevated FPG, GHbA1c, hs-CRP, and MCP-1 levels and decreased APN and SOD levels compared to the control group (P < .05). In patients with hypertension and diabetes (group C), FPG and GHbA1c levels were positively correlated with MCP-1 and hs-CRP, while APN levels showed a negative correlation with these inflammatory markers(P < .05). SOD levels were positively correlated with MCP-1, APN, and hs-CRP levels in group C patients (P < .05). Conclusion: These results suggest that APN, MCP-1, hs-CRP, and SOD are important factors in the development of atherosclerosis in patients with comorbid hypertension and diabetes. Monitoring these biomarkers may guide disease management strategies.
Ultraviolet lithography is a very promising technology used for the batch fabrication of biomedical microswimmers. However, creating microswimmers that can swim at low Reynolds number using biocompatible materials while retaining strong magnetic properties and excellent biomedical functionality is a great challenge. Most of the previously reported biomedical microswimmers possess either strong magnetic properties by using non-biocompatible nickel coating or good biocompatibility by using iron oxide particle-embedded hydrogel with weak magnetism, but not both. Alternatively, iron oxide nanoparticles can be coated on the surface of microswimmers to improve magnetic properties; however, this method limited the usability of the microswimmers' surfaces. To address these shortcomings, this work utilized an in situ synthesis technique to generate high magnetic content inside hydrogel-based achiral planar microswimmers while leaving their surfaces free to be functionalized for SERS detection. The hydrogel matrices of the magnetically actuated hydrogel-based microswimmers were first prepared by ultraviolet lithography. Then, the high concentration of iron oxide was achieved through multiple continuous in situ coprecipitation cycles. Finally, the SERS detection capability of magnetically actuated hydrogel-based microswimmers was enabled by uniformly growing silver nanoparticles on the surface of the microswimmers. In the motion control tests, the microswimmers showed a high swimming efficiency, high step-out frequency, and consistent synchronized motion. Furthermore, the magnetically actuated hydrogel-based microswimmers were able to improve the detection efficiency of analytes under magnetic guidance.
Aberrant expression of circRNAs is closely associated with the progression of gastric cancer; however, the specific mechanisms involved remain unclear. Our aim was to identify new gastric cancer biomarkers and explore the molecular mechanisms of gastric cancer progression. Therefore, we analyzed miRNA and circRNA microarrays of paired early-stage gastric cancer samples. Our study identified a new circRNA called hsa_circ_0069382, that had not been reported before and was expressed at low levels in gastric cancer tissues. Our study also included bioinformatics analyses which determined that the high expression of hsa_circ_0069382 regulated the BTG anti-proliferation factor 2 (BTG2)/ focal adhesion kinase (FAK) axis in gastric cancer lines by sponging for miR-15a-5p. Therefore, proliferation, invasion, and migration of gastric cancer is impacted. miR-15a-5p overexpression partially restored the effects of hsa_circ_0069382. This study provides potential new therapeutic options and a future direction to explore for gastric cancer treatment, and biomarkers.
Magnetically actuated microrobots showed increasing potential in various fields, especially in the biomedical area, such as invasive surgery, targeted cargo delivery, and treatment. However, it remains a challenge to incorporate biocompatible natural polymers that are favorable for practical biomedical applications. In this work, bilayer magnetic microrobots with an achiral planar design were fabricated using a biocompatible natural polymer and Fe3O4 nanoparticles through the photolithography by applying the layer-by-layer method. The microrobots consisted of a magnetic bottom layer and a photo-crosslinked chitosan top layer. The SEM results showed that the microrobot processed the L-shaped planar structure with the average width, length, and thickness of 99.18 ± 5.11 µm, 189.56 ± 11.37 µm, and 23.56 ± 4.08 µm, respectively. Moreover, microrobots actuated using a three-dimensional (3D) Helmholtz coil system was characterized and reached up to an average maximum velocity of 325.30 µm/s and a step-out frequency of 14 Hz. Furthermore, the microrobots exhibited excellent cell biocompatibility towards L929 cells in the CCK-8 assay. Therefore, the development of bi-layered chitosan-based microrobots offers a general solution for using magnetic microrobots in biomedical applications by providing an easy-to-fabricate, highly mobile microrobotic platform with the incorporation of biocompatible natural polymers for enhanced biocompatibility.
Genotype-by-environment interaction (G-by-E) is a common but potentially problematic phenomenon in plant breeding. In this study, we investigated the genotypic performance and two measures of plasticity on a phenotypic and genetic level by assessing 234 maize doubled haploid lines from six populations for 15 traits in seven macro-environments with a focus on varying soil phosphorus levels. It was found intergenic regions contributed the most to the variation of phenotypic linear plasticity. For 15 traits, 124 and 31 quantitative trait loci (QTL) were identified for genotypic performance and phenotypic plasticity, respectively. Further, some genes associated with phosphorus use efficiency, such as Zm00001eb117170, Zm00001eb258520, and Zm00001eb265410, encode small ubiquitin-like modifier E3 ligase were identified. By significantly testing the main effect and G-by-E effect, 38 main QTL and 17 interaction QTL were identified, respectively, in which MQTL38 contained the gene Zm00001eb374120, and its effect was related to phosphorus concentration in the soil, the lower the concentration, the greater the effect. Differences in the size and sign of the QTL effect in multiple environments could account for G-by-E. At last, the superiority of G-by-E in genomic selection was observed. In summary, our findings will provide theoretical guidance for breeding P-efficient and broadly adaptable varieties.
Phosphorus , Zea mays , Zea mays/genetics , Gene-Environment Interaction , Plant Breeding , Soil
The study of tractor ergonomics is both an essential part of public health and a very significant part of the scientific community's focus at the moment. It offers a foundation for the layout design of the tractor cab, making it possible to effectively avoid occupational diseases, minimize the number of safety accidents, and enhance the comfort of operation. Devices are categorized as control rod devices, knob-type devices, and steering wheels according to the various modes of operation of the tractor cab. Steering wheels are also included. The ease of handling of a number of different components was ranked according to how well they performed on the fast evaluation approach for the upper limbs. After that, in accordance with the concept that underpins this evaluation approach, the comfortable range of motion of human upper limb joints is evaluated while undergoing a variety of manipulation modalities. In conjunction with the structure of the human body and the characteristics of its movement, a streamlined point-line structure model of the human upper limb is constructed, with the H-point serving as the reference point. The problem of figuring out how to distribute the control components in the best possible way has been solved, and the optimal distribution range diagram of the steering wheel has been obtained. The ideal height for the distribution of control rod devices is around 300-400 millimeters, whereas the ideal height for the distribution of knob-type devices is approximately 200-500 millimeters. In conclusion, the cab design of the KAT2204 tractor is improved upon thanks to the analysis done in this study, which can be found above. The legitimacy of the research conclusion is confirmed by the fact that the RULA value is lower than 2, which is proved by the fact that the design findings are validated by the Creo Manikin module. The ergonomics of the tractor cab were taken into consideration when using this research approach as a reference.
Ergonomics , Public Health , Agriculture , Equipment Design , Humans , Upper Extremity
Gastric cancer is a gastrointestinal tumor with high morbidity and mortality rates. Several factors influence its progression, cell death being an important element. In this review, we summarized the effects of necrosis, apoptosis, necroptosis, pyroptosis, ferroptosis, and eight less common cell death modalities on gastric cancer cells and the tumor microenvironment, detailed the molecular mechanisms of various cell death and their major regulatory pathways in gastric cancer, explored the prevalence and complexity of cell death in gastric cancer progression and highlighted the potentials of cell death-related therapies in gastric cancer.
NFE2L3, also known as NFE2L3, is a nuclear transcription factor associated with the pathogenesis and progression of human tumors. To systematically and comprehensively investigate the role of NFE2L3 in tumors, a pan-cancer analysis was performed using multi-omics data, including gene expression analysis, diagnostic and prognostic analysis, epigenetic methylation analysis, gene alteration analysis, immune feature analysis, functional enrichment analysis, and tumor cell functional status analysis. Furthermore, the molecular mechanism of NFE2L3 in liver hepatocellular carcinoma (LIHC) was explored. The relationship between NFE2L3 expression and survival prognosis of patients with LIHC was analyzed and a nomogram prediction model was constructed. Our study showed that NFE2L3 expression was upregulated in most cancers, suggesting that NFE2L3 may play an important role in promoting cancer progression. NFE2L3 expression is closely related to DNA methylation, genetic alteration, immune signature, and tumor cell functional status in pan-cancers. Furthermore, NFE2L3 was demonstrated to be an independent risk factor for LIHC, and the nomogram model based on NFE2L3 expression had good prediction efficiency for the overall survival of patients with LIHC. In summary, our study indicated that NFE2L3 may be an important molecular biomarker for the diagnosis and prognosis of pan-cancer. NFE2L3 is expected to be a potential molecular target for the treatment of tumors.
Background: Gastric cancer is one of the common malignant tumors of the digestive system worldwide, posing a serious threat to human health. A growing number of studies have demonstrated the important role that lipid droplets play in promoting cancer progression. However, few studies have systematically evaluated the role of lipid droplet metabolism-related genes (LDMRGs) in patients with gastric cancer. Methods: We identified two distinct molecular subtypes in the TCGA-STAD cohort based on LDMRGs expression. We then constructed risk prediction scoring models in the TCGA-STAD cohort by lasso regression analysis and validated the model with the GSE15459 and GSE66229 cohorts. Moreover, we constructed a nomogram prediction model by cox regression analysis and evaluated the predictive efficacy of the model by various methods in STAD. Finally, we identified the key gene in LDMRGs, ABCA1, and performed a systematic multi-omics analysis in gastric cancer. Results: Two molecular subtypes were identified based on LDMRGs expression with different survival prognosis and immune infiltration levels. lasso regression models were effective in predicting overall survival (OS) of gastric cancer patients at 1, 3 and 5 years and were validated in the GEO database with consistent results. The nomogram prediction model incorporated additional clinical factors and prognostic molecules to improve the prognostic predictive value of the current TNM staging system. ABCA1 was identified as a key gene in LDMRGs and multi-omics analysis showed a strong correlation between ABCA1 and the prognosis and immune status of patients with gastric cancer. Conclusion: This study reveals the characteristics and possible underlying mechanisms of LDMRGs in gastric cancer, contributing to the identification of new prognostic biomarkers and providing a basis for future research.
Heterosis contributes a big proportion to hybrid performance in maize, especially for grain yield. It is attractive to explore the underlying genetic architecture of hybrid performance and heterosis. Considering its complexity, different from former mapping method, we developed a series of linear mixed models incorporating multiple polygenic covariance structures to quantify the contribution of each genetic component (additive, dominance, additive-by-additive, additive-by-dominance, and dominance-by-dominance) to hybrid performance and midparent heterosis variation and to identify significant additive and non-additive (dominance and epistatic) quantitative trait loci (QTL). Here, we developed a North Carolina II population by crossing 339 recombinant inbred lines with two elite lines (Chang7-2 and Mo17), resulting in two populations of hybrids signed as Chang7-2 × recombinant inbred lines and Mo17 × recombinant inbred lines, respectively. The results of a path analysis showed that kernel number per row and hundred grain weight contributed the most to the variation of grain yield. The heritability of midparent heterosis for 10 investigated traits ranged from 0.27 to 0.81. For the 10 traits, 21 main (additive and dominance) QTL for hybrid performance and 17 dominance QTL for midparent heterosis were identified in the pooled hybrid populations with two overlapping QTL. Several of the identified QTL showed pleiotropic effects. Significant epistatic QTL were also identified and were shown to play an important role in ear height variation. Genomic selection was used to assess the influence of QTL on prediction accuracy and to explore the strategy of heterosis utilization in maize breeding. Results showed that treating significant single nucleotide polymorphisms as fixed effects in the linear mixed model could improve the prediction accuracy under prediction schemes 2 and 3. In conclusion, the different analyses all substantiated the different genetic architecture of hybrid performance and midparent heterosis in maize. Dominance contributes the highest proportion to heterosis, especially for grain yield, however, epistasis contributes the highest proportion to hybrid performance of grain yield.
The NF-ĸB transcription factor is a critical regulator of immune homeostasis and inflammatory responses and is a critical factor in the pathogenesis of inflammatory disease. The pathways to NF-ĸB activation are paradigms for signal-induced ubiquitination and proteasomal degradation, control of transcription factor function by subcellular localisation, and the control of gene transcription and physiological processes by signal transduction mechanisms. Despite the importance of NF-ĸB in disease, the NF-ĸB pathway remains unexploited for the treatment of inflammatory disease. Our understanding of NF-ĸB comes mostly from studies of transgenic mice and cell lines where components of the pathway have been deleted or over expressed. Recent advances in quantitative proteomics offer new opportunities to understand the NF-ĸB pathway using the absolute abundance of individual pathway components. We have analysed available quantitative proteomic datasets to establish the structure of the NF-ĸB pathway in human immune cells under both steady state and activated conditions. This reveals a conserved NF-κB pathway structure across different immune cell lineages and identifies important differences to the current model of the NF-ĸB pathway. These include the findings that the IKK complex in most cells is likely to consist predominantly of IKKß homodimers, that the relative abundancies of IκB proteins show strong cell type variation, and that the components of the non-canonical NF-ĸB pathway are significantly increased in activated immune cells. These findings challenge aspects of our current view of the NF-κB pathway and identify outstanding questions important for defining the role of key components in regulating inflammation and immunity.
NF-kappa B , Proteomics , Animals , Humans , I-kappa B Kinase/metabolism , Mice , NF-kappa B/metabolism , Protein Serine-Threonine Kinases , Signal Transduction
Phosphorus (P) deficiency is an important challenge the world faces while having to increase crop yields. It is therefore necessary to select maize (Zea may L.) genotypes with high phosphorus use efficiency (PUE). Here, we extensively analyzed the biomass, grain yield, and PUE-related traits of 359 maize inbred lines grown under both low-P and normal-P conditions. A significant decrease in grain yield per plant and biomass, an increase in PUE under low-P condition, as well as significant correlations between the two treatments were observed. In a genome-wide association study, 49, 53, and 48 candidate genes were identified for eleven traits under low-P, normal-P conditions, and in low-P tolerance index (phenotype under low-P divided by phenotype under normal-P condition) datasets, respectively. Several gene ontology pathways were enriched for the genes identified under low-P condition. In addition, seven key genes related to phosphate transporter or stress response were molecularly characterized. Further analyses uncovered the favorable haplotype for several core genes, which is less prevalent in modern lines but often enriched in a specific subpopulation. Collectively, our research provides progress in the genetic dissection and molecular characterization of PUE in maize.
Gene Expression Regulation, Plant , Phosphorus/metabolism , Plant Proteins/metabolism , Polymorphism, Single Nucleotide , Quantitative Trait Loci , Stress, Physiological , Zea mays/genetics , Chromosome Mapping , Chromosomes, Plant , Genome-Wide Association Study , Phenotype , Plant Proteins/genetics , Zea mays/growth & development , Zea mays/metabolism
Exosomes are a type of extracellular microvesicles with a diameter of 40-160 nm. Circular RNA (circRNA) is a type of closed circular RNA molecule that is highly conserved in evolution. Exosomal circRNA plays a vital role in the proliferation, invasion, migration, and drug resistance of digestive system tumors. In this study, we used The Cancer Genome Atlas (TCGA) database, UALCAN, Python crawler, miRTargetLink Human, Database for Annotation, Visualization, and Integrated Discovery (DAVID), micBioinformatic online tool, and Cytoscape software (3.7.1). The results showed that circ-RanGAP1 in gastric cancer, circUHRF1 in hepatocellular carcinoma, and circFMN2 in colorectal cancer regulate the malignant behavior of tumors and affect the expression of their host gene through sponging miR-877-3p, miR-449c-5p, and miR-1182, respectively. Twenty exosomal circRNAs regulate 6,570 target genes through sponging 23 miRNAs. Firstly, 270 of those target genes are regulated by two or more miRNAs, which are highly correlated with 83 tumor-related pathways and six Kyoto Encyclopedia of Genes and Genomes pathways. Secondly, 1,146 target genes were significantly differentially expressed in corresponding digestive system tumors, and functional enrichment analysis revealed that 78 of those were involved in 20 cancer-related pathways. In short, the bioinformatics analysis showed that these exosomal circRNAs are stably expressed in body fluids, and regulate the occurrence and development of gastric cancer, hepatocellular carcinoma, colorectal cancer, and other digestive system tumors through sponging miRNAs. Exosomal circRNAs may be used as biomarkers for the diagnosis of disease and identification of effective therapeutic targets in the future, as well as improve the prognosis of patients with digestive system tumors.
As oil production in the Permian Basin surges, the impact of shale production on groundwater resources has become a growing concern. Most existing studies focus on the impact of shale production on shallow freshwater aquifers. There is little understanding of the shale development's impact on other groundwater resources (e.g., deep carbonate aquifers and deep basin meteoric aquifers). The possible natural hydraulic connections between shallow aquifers and formation water suggest such an impact can be consequential. This study explores the relationship between shale production and groundwater using produced water (PW) samples from active unconventional oil wells. Focusing on the most productive portion of the Permian Basin-the four-county region in Southeast New Mexico between 2007 and 2016, a large produced water dataset allows us to analyze the conditional correlations between shale oil production and PW constituents. The results suggest that (1) expanding from primarily conventional wells to unconventional wells during the recent shale boom has led to dramatic increases of the TDS, chloride, sodium, and calcium levels in groundwater (i.e., producing formation). (2) Nearby oil well density positively correlates with the TDS, chloride, and sodium levels in the PW samples.
Groundwater/chemistry , Hydraulic Fracking/methods , Minerals/analysis , Natural Gas/analysis , Oil and Gas Fields/chemistry , Water Pollutants, Chemical/analysis , New Mexico
Spinach (Spinacia oleracea L.) is commonly considered a dioecious plant with heterogametic (XY) and homogametic (XX) sex chromosomes. The characteristic is also utilized for the production of spinach hybrid seeds. However, the molecular mechanisms of sex determination in spinach are still unclear because of a lack of genomic and transcriptomic information. In this study, RNA sequencing (RNA-seq) was performed in male and female inflorescences to provide insight into the molecular basis of sex determination in spinach. Comparative transcriptome analyses showed that 2278 differentially expressed genes (DEGs) were identified between male and female inflorescences. A high correlation between the RNA-Seq and qRT-PCR validation for DEGs was observed. Among these, 182 DEGs were annotated to transcription factors including the MYB family protein, bHLH family, and MADS family, suggesting these factors might play a vital role in sex determination. Moreover, 26 DEGs related to flower development, including nine ABCE class genes, were detected. Expression analyses of hormone pathways showed that brassinosteroids may be key hormones related to sex determination in spinach. Overall, this study provides a large amount of DEGs related to sexual expression and lays a foundation for unraveling the regulatory mechanism of sex determination in spinach.
Inflorescence , Spinacia oleracea , Transcriptome , Gene Expression Profiling , Gene Expression Regulation, Plant , Inflorescence/genetics , Spinacia oleracea/genetics
A major consequence of climate change is the growing precipitation variability around many parts of the world leading to increased occurrences of floods. While there has been a rich literature on flood risk in the urban context, flood risk in the agricultural sector has been understudied. The goal of this study is to estimate the impact of flood risk on farmland values in a watershed with active agricultural activities. The novelty of the study is to use the spatial boundary discontinuities along floodplains as a way to control unobserved spatial heterogeneities in a regression analysis framework. Using parcel-level data from Lancaster County (Pennsylvania, USA), we show that cropland is more vulnerable to potential flood risk compared to noncrop farmland. Specifically, cropland parcels on average experience a 13% (or $3,895/acre in 2015 USD, with the 95% confidence interval being [$510, $7352]) value reduction if exposed to a 1% or higher annual chance of flooding. The flood risk impact on noncrop farmland is statistically insignificant. The difference between cropland and noncrop farmland in valuing the potential flood risk implies different flood preparedness and risk management strategies. Based on the empirical findings, policy implications for flood insurance, agricultural water management, land-use practice, and other flood mitigation strategies are explored.
