RNA-Seq Analysis Revealed circRNAs and Genes Associated with Abdominal Fat Deposition in Ducks.

Fat deposition is an important factor affecting meat quality and feed conversion efficiency in meat ducks. This study aims to identify key circRNAs and genes affecting abdominal fat deposition. The correlations between abdominal fat and other growth performances were analyzed in 304 F2 generation of Cherry Valley duck Runzhou Crested White ducks, and an RNA-seq analysis of abdominal fat tissues from ducks with high and low rates of abdominal fat was performed. Growth performance results showed that Abdominal fat ratio and Intramuscular fat were significantly higher in the high rates of abdominal fat (HF)group than in the low rates of abdominal fat (LF) group for ducks. RNA-seq analysis of abdominal fat tissue unveiled 85 upregulated and 72 downregulated circRNAs among the differentially expressed ones. Notably, 74 circRNAs displayed more than four-fold differential expression, constituting 47.13% of the differentially expressed genes. Functional enrichment analysis of the differentially expressed circRNA source and target genes indicated that 17 circRNAs might partake in regulating duck abdominal fat production by influencing pathways like PPAR signaling, lipid droplets, and triglyceride metabolism. Lastly, multiple circRNA-microRNA-messenger RNA interaction networks were constructed. The results of this study establish the groundwork for understanding the molecular mechanisms that regulate abdominal fat deposition in ducks, offering a theoretical reference for the selective breeding of high-quality meat-producing ducks.

Heavy Metals in Agricultural Soils: Sources, Influencing Factors, and Remediation Strategies.

Soil heavy metal pollution is a global environmental challenge, posing significant threats to eco-environment, agricultural development, and human health. In recent years, advanced and effective remediation strategies for heavy metal-contaminated soils have developed rapidly, and a systematical summarization of this progress is important. In this review paper, first, the anthropogenic sources of heavy metals in agricultural soils, including atmospheric deposition, animal manure, mineral fertilizers, and pesticides, are summarized. Second, the accumulation of heavy metals in crops as influenced by the plant characteristics and soil factors is analyzed. Then, the reducing strategies, including low-metal cultivar selection/breeding, physiological blocking, water management, and soil amendment are evaluated. Finally, the phytoremediation in terms of remediation efficiency and applicability is discussed. Therefore, this review provides helpful guidance for better selection and development of the control/remediation technologies for heavy metal-contaminated agricultural soils.

DeLIVR: a deep learning approach to IV regression for testing nonlinear causal effects in transcriptome-wide association studies.

Transcriptome-wide association studies (TWAS) have been increasingly applied to identify (putative) causal genes for complex traits and diseases. TWAS can be regarded as a two-sample two-stage least squares method for instrumental variable (IV) regression for causal inference. The standard TWAS (called TWAS-L) only considers a linear relationship between a gene's expression and a trait in stage 2, which may lose statistical power when not true. Recently, an extension of TWAS (called TWAS-LQ) considers both the linear and quadratic effects of a gene on a trait, which however is not flexible enough due to its parametric nature and may be low powered for nonquadratic nonlinear effects. On the other hand, a deep learning (DL) approach, called DeepIV, has been proposed to nonparametrically model a nonlinear effect in IV regression. However, it is both slow and unstable due to the ill-posed inverse problem of solving an integral equation with Monte Carlo approximations. Furthermore, in the original DeepIV approach, statistical inference, that is, hypothesis testing, was not studied. Here, we propose a novel DL approach, called DeLIVR, to overcome the major drawbacks of DeepIV, by estimating a related but different target function and including a hypothesis testing framework. We show through simulations that DeLIVR was both faster and more stable than DeepIV. We applied both parametric and DL approaches to the GTEx and UK Biobank data, showcasing that DeLIVR detected additional 8 and 7 genes nonlinearly associated with high-density lipoprotein (HDL) cholesterol and low-density lipoprotein (LDL) cholesterol, respectively, all of which would be missed by TWAS-L, TWAS-LQ, and DeepIV; these genes include BUD13 associated with HDL, SLC44A2 and GMIP with LDL, all supported by previous studies.

LncRNA MIR210HG promotes the proliferation, migration, and invasion of lung cancer cells by inhibiting the transcription of SH3GL3.

Lung cancer (LCa), the most frequent malignancy worldwide, causes millions of mortalities each year. Overexpression of the long noncoding RNA MIR210HG in LCa has been established; however, a more comprehensive investigation into its biological role within LCa is imperative. This study aimed to validate the MIR210H levels in LCa tissues and cells. The expression of indicated genes was evaluated using quantitative real-time polymerase chain reaction (qRT-PCR) and/or Western blotting. The viability, proliferation, migration, and invasion of LCa cells were measured using the 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT), colony formation, wound healing, and transwell assays, respectively. The methylation levels of LCa cells were determined via methylation-specific PCR; additionally, chromatin immunoprecipitation or RNA immunoprecipitation assays were performed to determine the targeting relationship between DNA methyltransferase 1 (DNMT1) and the SH3-domain containing CRB2 like 3 (SH3GL3) promoters and the interaction between DNMT1 and MIR210HG, respectively. Our findings revealed the upregulation of MIR210HG, coupled with a diminished expression of SH3GL3 in LCa tissues and cells. Knockdown of MIR210HG or overexpression of SH3GL3 suppressed the proliferative, migratory, and invasive capacities of the cells. DNMT1 bound to the SH3GL3 promoter region, and MIR210HG inhibited the transcription of SH3GL3 by recruiting DNMT1. These findings indicate that MIR210HG facilitates LCa cell growth and metastasis by repressing SH3GL3 transcription via the recruitment of DNMT1 to the SH3GL3 promoter region.

Research Note: Transcriptome analysis reveals differentially expressed genes regulated muscle development in Pekin ducks during dietary threonine deficiency.

To investigate the underlying molecular mechanism of threonine (Thr) regulation on the development of breast muscle in Pekin ducks, 240 male Pekin ducks at 1 d of age were fed a Thr deficiency diet (Thr-D), Thr sufficiency diet (Thr-S), or Thr excess diet (Thr-E) for 21 d. The results showed that Thr-D reduced body weight (BW), average weight gain (ADG), and average feed intake (ADFI), and increased the feed/gain (F/G) in Pekin ducks (P < 0.05), and Thr-E did not affect BW, ADG, ADFI, or F/G (P > 0.05), compared with Thr-S. The diameter and cross-sectional area of the breast muscle fibers in the Thr-S group were larger than those in the Thr-D group (P < 0.05). RNA sequencing revealed 1,300 differential expressed genes (DEGs) between the Thr-D and Thr-S groups, of which 625 were upregulated and 675 were downregulated by Thr-D. KEGG analysis showed that the upregulated genes were enriched in mTOR, FoxO, Wnt, fat digestion and absorption, and other signaling pathways. The downregulated genes were enriched in the MAPK signaling, glycolysis/gluconeogenesis, adipocytokine signaling, and biosynthesis of unsaturated fatty acids signaling pathways. The genes of Wnt family member 3a (Wnt3a), myogenin, myozenin 2, and insulin like growth factor 2 mRNA binding protein were upregulated, and platelet derived growth factor subunit B, PDGF receptor beta and Wnt4 were downregulated by Thr deficiency, which involving in muscle development. Our findings indicated that Thr increased breast fiber size, perhaps because Thr affected the proliferation and differentiation of satellite cells in breast muscle of ducks after hatch. Our results provide novel insights into new understanding of the molecular mechanisms underlying breast muscle development in ducks subjected to dietary Thr.

Phytoremediation strategies for heavy metal-contaminated soil by selecting native plants near mining areas in Inner Mongolia.

Phytoremediation technology, as an eco-friendly and cost-effective approach, is widely used to restore soil contaminated by heavy metal(loid)s. However, the adaptability and absorption capacity of plants to multiple elements are the crucial factors affecting the application of phytoremediation in mining areas. In this study, dominant native plant species and their paired soils were collected near a lead-zinc mine in Inner Mongolia, to assess the ecological risk of heavy metal(loid)s and phytoremediation potential. The results showed that Cd and As were the dominant soil pollutants, with levels of 90.91% and 100%, respectively, exceeding the risk intervention values for soil contamination of agricultural land. The rates of Pb, Cu, and Zn exceeding the risk screening values were 69.70%, 60.61%, and 96.97%, respectively. Extremely high ecological risk of heavy metal(loid)s was observed in this area. The ability of native plants accumulating heavy metals varied among species. The bioconcentration factor (BCF) varied from 0.14 to 2.59 for Cd, 0.02 to 0.45 for As, 0.06 to 0.76 for Pb, 0.05 to 2.69 for Cr, 0.15 to 1.00 for Cu, and 0.22 to 4.10 for Zn. Chinese Cinquefoil Herb (Potentilla chinensis Ser.) showed the potential to accumulate multiple toxic elements based on the biomass, shoot content, translocation factor (TF), BCF, and metal extraction rate (MER), while, other species showed the potential to accumulate single toxic element: goosefoot (Chenopodium album L.), Lespedeza daurica (Laxm.) Schindl. and peashrubs (Caragana korshinskii Kom.), Herba Artemisiae Scopariae (Artemisia capillaris Thunb.), alfalfa (Medicago sativa L.), and Moldavian Dragonhead (Dracocephalum moldavica L.) for Cd, As, Cr, Cu, and Zn, respectively. Furthermore, wild leek (Allium ramosum L.), cogongrass (Imperata cylindrica (L.) Beauv.), fringed sagebrush (Artemisia frigida Willd.), and field bindweed (Convolvulus arvensis L.) were selected for phytostabilization of specific elements, considering the heavy metal contents in the roots and low TF values. This study provides a reference for selecting appropriate species for the remediation of heavy metal-contaminated soils in certain mining areas.

Genetic diversity and breed identification of Chinese and Vietnamese local chicken breeds based on microsatellite analysis.

South Asia and Southeast Asia are the origins of domestic chickens and are rich in poultry genetic resources, resulting in many unique local chicken breeds. However, with the rapid intensification of poultry farming worldwide, many local chicken breeds are threatened with extinction. In response to China's "One Belt, One Road" policy, it is imperative to strengthen the conservation and breeding of local chicken breeds in China and Vietnam. This study characterized 18 microsatellite molecular genetic markers to analyze the genetic diversity of 21 local chicken populations in southern China (Yunnan and Guangxi Provinces) and Vietnam, breed identification tags for microsatellite loci were constructed. The results showed that a total of 377 alleles were detected in all breeds, and the most alleles (44) and the highest polymorphic information content (0.7820) were detected at the LEI0094 locus. The average polymorphic information content (PIC) content of the whole population was 0.65, indicating moderate polymorphism. The genetic diversity of the whole population was rich, except for two loci MCW0111 and MCW0016, that showed heterozygote excess at microsatellite loci, and the population had high genetic differentiation. The Vietnamese breeds showed low pairwise fixation coefficient (FST) and Nei's standard genetic distance (DS) between them. According to the neighbor-joining dendrogram constructed by DS and the analysis of population genetic structure using the structure program, Longshengfeng chicken, Yunlong dwarf chicken, Tengchong white chicken, Xiayan chicken, and Daweishan mini chicken are similar, and Xishuangbanna game fowl, Wuding chicken, and Lanping silky chicken are similar to Yanjin black-bone chicken. In addition, excluding Dongtao chicken, other Vietnamese breeds are clustered together, indicating that the southern chicken breeds are closely related and have experienced better breeding. Overall, the whole population is rich in genetic resources, and the chicken breeds in the three regions are genetically close because of geographical factors and human activities. Dongtao chicken in Vietnamese, Chinese Yunnan local chicken breeds (Gallus gallus spadiceus), and red jungle fowl chickens (Gallus gallus) may have the same origin. We also constructed unique microsatellite molecular markers for 20 cultivars using 15 microsatellite loci. This study provides valuable insights to facilitate breed identification, improve cultivar protection, and new germplasm construction.

China's Yunnan, Guangxi, and Vietnam are rich in biodiversity, and a wide variety of local chicken breeds exist. Due to the rapid development of intensive farming, the biodiversity of chicken breeds in these two regions has gradually decreased. To protect the diversity of local breeds, and to promote the exchange of germplasm resources and the creation of new germplasm between China and Vietnam, this study analyzed the genetic diversity of some chicken breeds in Yunnan, Guangxi, and Vietnam by using microsatellite molecular markers. Studies have shown that the entire population has rich genetic resources, and Vietnamese chickens have a strong kinship with some local chicken breeds in Yunnan Province, China, and there is also a high degree of hybridization between Vietnamese local chickens. In addition, since some chicken breeds have more similarities in appearance, this study constructed unique molecular tags for different breed-specific alleles as one of the methods to accurately distinguish different breeds for breed protection and subsequent breeding.

[Enrichment Characteristics of Heavy Metals and Health Risk in Different Vegetables].

The health risk caused by heavy metal accumulation in vegetables is of great concern. In this study, a database of heavy metal content in a vegetable-soil system in China was constructed through literature review and field sample collection. A systematic analysis of seven heavy metal contents in edible parts of vegetables and their bioaccumulation capacity among different vegetables was also performed. Additionally, the non-carcinogenic health risks of four types vegetables were assessed by using Monte Carlo simulation (MCS). The mean values of Cd, As, Pb, Cr, Hg, Cu, and Zn in the edible parts of the vegetables were 0.093, 0.024, 0.137, 0.118, 0.007, 0.622, and 3.272 mg·kg-1, and the exceedance rates of the five toxic elements were:Pb (18.5%)>Cd (12.9%)>Hg (11.5%)>Cr (4.03%)>As (0.21%). Leafy vegetables showed high Cd enrichment, and root vegetables showed high Pb enrichment, with mean bioconcentration factors of 0.264 and 0.262, respectively. Generally, legumes vegetables and solanaceous vegetables showed lower bioaccumulation for heavy metals. The health risk results indicated that the non-carcinogenic risk for single elements of vegetable intake was within the acceptable range, with the health risk for children being higher than that for adults. The mean non-carcinogenic risk for single elements were:Pb>Hg>Cd>As>Cr. The multi-element combined non-carcinogenic risks of four types vegetables were:leafy vegetables>root vegetables>legume vegetables>solanaceous vegetables. Planting lower-heavy metal bioaccumulation vegetables in heavy metal-contaminated farmland is an effective method to minimize the health risk.

Proteomic and phosphoproteomic analysis reveal threonine deficiency increases hepatic lipid deposition in Pekin ducks via reducing STAT phosphorylation.

Dietary threonine (Thr) deficiency enhances triglyceride (TG) deposition in the liver of Pekin ducks, which injures hepatic function and impairs growth performance. However, the underlying molecular mechanisms remain unclear. In the present study, we investigated the effects of dietary Thr deficiency on the expressions of proteins and phosphoproteins in liver of Pekin ducks, to identify the underlying molecular changes. A total of 300 one-day-old ducklings were divided into 3 groups with 10 replicates of 10 birds. All ducks were fed corn-wheat-peanut meal diets containing 0.46%, 0.71%, and 0.96% Thr, respectively, from 1 to 21 days of age. Growth performance, serum parameters, hepatic TG content, and expression of genes involved in lipid metabolism of Pekin ducks were determined. A Thr deficiency group (Thr-D, 0.46% Thr) and a Thr sufficiency group (Thr-S, 0.71% Thr) were selected for subsequent proteomic and phosphoproteomic analysis. The results showed that Thr-D reduced the growth performance (P < 0.001), and increased the plasma concentrations of cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and hepatic TG (P < 0.05). Thr-D increased gene expression related to fatty acid and TG synthesis (P < 0.05). A total of 176 proteins and 259 phosphosites (containing 198 phosphoproteins) were observed to be differentially expressed as a result of Thr-D. The upregulated proteins were enriched in the pathway related to amino acid metabolism, peroxisome. The downregulated proteins were enriched in linolenic and arachidonic acid metabolism, and the Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling pathway. The upregulated phosphoproteins were enriched in the pathways related to fatty acid biosynthesis, fructose and mannose metabolism, and glycolysis/gluconeogenesis. Thr-D reduced the phosphorylation of STAT1 at S729 and STAT3 at S728, and expression of STAT5B. In contrast, Thr-D increased non-receptor tyrosine-protein kinase (TYK2) expression and STAT1 phosphorylation at S649. Taken together, dietary Thr-D increased hepatic TG accumulation by upregulating the expression of genes and proteins, and phosphoproteins related to fatty acid and triglyceride synthesis. Furthermore, these processes might be regulated by the JAK-STAT signaling pathway, especially the phosphorylation of STAT1 and STAT3.

Deep Learning-Based Feature Extraction with MRI Data in Neuroimaging Genetics for Alzheimer's Disease.

The prognosis and treatment of patients suffering from Alzheimer's disease (AD) have been among the most important and challenging problems over the last few decades. To better understand the mechanism of AD, it is of great interest to identify genetic variants associated with brain atrophy. Commonly, in these analyses, neuroimaging features are extracted based on one of many possible brain atlases with FreeSurf and other popular software; this, however, may cause the loss of important information due to our incomplete knowledge about brain function embedded in these suboptimal atlases. To address the issue, we propose convolutional neural network (CNN) models applied to three-dimensional MRI data for the whole brain or multiple, divided brain regions to perform completely data-driven and automatic feature extraction. These image-derived features are then used as endophenotypes in genome-wide association studies (GWASs) to identify associated genetic variants. When we applied this method to ADNI data, we identified several associated SNPs that have been previously shown to be related to several neurodegenerative/mental disorders, such as AD, depression, and schizophrenia.

Source-specific risk assessment for cadmium in wheat and maize: Towards an enrichment model for China.

Cadmium (Cd) pollution of agricultural soil is of public concern due to its high potential toxicity and mobility. This study aimed to reveal the risk of Cd accumulation in soil and wheat/maize systems, with a specific focus on the source-specific ecological risk, human health risk and Cd enrichment model. For this we investigated more than 6100 paired soil and grain samples with 216 datasets including soil Cd contents, soil pH and grain Cd contents of 85 sites from China. The results showed that mining activities, sewage irrigation, industrial activities and agricultural practices were the critical factors causing Cd accumulation in wheat and maize cultivated sites. Thereinto, mining activities contributed to a higher Cd accumulation risk in the southwest China and Middle Yellow River regions; sewage irrigation influenced the Cd accumulation in the North China Plain. In addition, the investigated sites were classified into different categories by comparing their soil and grain Cd contents with the Chinese soil screening values and food safety values, respectively. Cd enrichment models were developed to predict the Cd levels in wheat and maize grains. The results showed that the models exhibited a good performance for predicting the grain Cd contents among safe and warning sites of wheat (R2 = 0.61 and 0.72, respectively); while the well-fitted model for maize was prone to the overestimated sites (R2 = 0.77). This study will provide national viewpoints for the risk assessments and prediction of Cd accumulation in soil and wheat/maize systems.

Effects of Fatty-Type and Lean-Type on Growth Performance and Lipid Droplet Metabolism in Pekin Ducks.

The reasons for differences in lipid depositions between fatty-type (F-T) and lean-type (L-T) ducks remain unknown. The present study aimed to compare the growth performance, lipid deposition, and gene expression related to lipid droplet formation in F-T and L-T Pekin ducks. One-day-old, 140 each L-T and F-T male ducks were selected and distributed separately into 20 replicate cages. All ducks were fed commercial diets up to 35 d of age. F-T ducks had a higher average daily gain from 21 to 28 d of age. On 35-day-old, F-T ducks had higher serum levels of high- and low-density lipoprotein cholesterol, cholesterol, albumin, and hydroxybutyrate dehydrogenase activity than L-T ducks. F-T ducks had higher abdominal fat and subcutaneous fat percentages than those in L-T ducks. Liver histological examination showed that L-T ducks contained more lipid droplets in the liver, which gradually decreased with increasing age. The average adipocyte area and diameter of abdominal fat and subcutaneous fat in the F-T and L-T ducks increased with age and were higher in F-T ducks than those in L-T ducks. Furthermore, the gene expression of perilipin 1, perilipin 2, angiopoietin-like protein 4, adipose triglyceride lipase, alpha/beta-hydrolase domain-containing protein 5 (ABHD5), and serine/threonine kinase 17a in the liver, abdominal fat, and subcutaneous fat of F-T ducks was higher than that in L-T ducks, and it increased with age. Compared to L-T ducks, F-T ducks had higher expression of ABHD5 in the abdominal fat and subcutaneous fat and lower expression in the liver. Thus, F-T ducks displayed lower hepatic lipid deposition and a higher percentage of abdominal fat and subcutaneous fat, suggesting that F-T ducks had higher lipid storage capacity due to increased gene expression related to lipid droplets.

Induction of the ER stress response in NRVMs is linked to cardiotoxicity caused by celastrol.

Celastrol is a quinone methide triterpenoid extracted from the root bark of Tripterygium wilfordii Hook F, and it exhibits extensive biological activities such as anti-cancer effects. However, narrow therapeutic window together with undesired side effects limit its clinical application. In this study, we explore celastrol's cardiotoxicity using the methods of histology and cell biology. The results show that celastrol administration dose-dependently induces cardiac dysfunction in mice as manifested by left ventricular dilation, myocardial interstitial fibrosis, and cardiomyocyte hypertrophy. Exposure to celastrol greatly decreases neonatal rat ventricular myocyte (NRVM) viability and promotes its apoptosis. More importantly, we demonstrate that celastrol exerts its pro-apoptotic effects through endoplasmic reticulum (ER) stress and unfolded protein response. Furthermore, siRNA targeting C/EBP homologous protein, a pivotal component of ER stress-mediated apoptosis, effectively prevents the pro-apoptotic effect of celastrol. Taken together, our results demonstrate the potential cardiotoxicity of celastrol and a direct involvement of ER stress in the celastrol-induced apoptosis of NRVMs. Thus, we recommend careful evaluation of celastrol's cardiovascular effects when using it in the clinic.

Accumulation of potentially toxic elements in Chinese tea (Camellia sinensis): Towards source apportionment and health risk assessment.

Tea (Camellia sinensis) is a popular beverage that is consumed globally. However, a better understanding of potentially toxic elements (PTEs) content in tea leaves and infusion is necessary to minimize risk on human health. Therefore, 249 tea samples (grown in different areas) covering six types of tea were collected in China to investigate the PTEs contents, identify their potential source and assess the health risk associated with drinking tea. PTE contents in tea leaves across six tea types were ND-0.900 (Cd), 0.005-2.133 (As), ND-5.679 (Pb), ND-13.86 (Cr), 1.601-22.93 (Ni), ND-2.048 (Se), 0.109-622.4 (F), 13.02-269.9 (Rb), 1.845-50.88 (Sr), and 2.796-53.23 (Ba) mg/kg. The result of tea infusion showed that 14.3 %-44.1 % (green tea), 14.5 %-46.7 % (black tea), 10.5 %-25.3 % (dark tea), 13.6 %-34.2 % (oolong tea), 16.9 %-40.7 % (yellow tea), and 19.9 %-35.1 % (white tea) of F were released. All tea types, except green tea, exhibited comparatively low leachability of Cd, As, Pb and Cr in tea infusion. The source apportionment revealed that PTEs in tea leaves mainly originated from soil parental materials, while industrial activities, fertilizer application, and manufacturing processes may contribute to exogenous Se, Cd, As, and Cr accumulation. Health risk assessment indicated that F in tea infusion dominated the health risk. Humans may be exposed to a higher health risk by drinking green tea compared to that of other tea types. Nevertheless, the long-term tea consumption is less likely to contribute to pronounced non-carcinogenic and carcinogenic risks. This study confirmed that tea consumption is an important and direct pathway of PTEs uptake in humans. The health risk associated with drinking tea should be of concern.

BML-111 alleviates inflammatory response of alveolar epithelial cells via miR-494/Slit2/Robo4 signalling axis to improve acute lung injury.

Acute lung injury (ALI) is a common, variously induced lung cell injury with high mortality. It is also an early stage of acute respiratory distress syndrome. BML-111 is a lipoxin A4 receptor agonist that plays an important role in inflammation. However, its function on ALI remains unclear. To explore whether BML-111 is involved in ALI and its regulatory molecular mechanism, we constructed an in vitro ALI model by stimulating primary mouse alveolar epithelial cells (AECs) with lipopolysaccharide (LPS). The downstream target of microRNA (miR)-494 was predicted by Targetscan. The apoptosis and expression of inflammatory cytokines were analysed by RT-qPCR, Western blot, and ELISA. BML-111 treatment alleviated LPS-induced apoptosis and the production of inflammatory cytokines, such as tumour necrosis factor α, interleukin (IL)-6, IL-1ß, in primary mouse AECs via downregulating miR-494. MiR-494 targeted and downregulated slit guidance ligand 2 (Slit2) in primary mouse AECs. BML-111 activated the Slit2/roundabout guidance receptor 4 (Robo4) axis via downregulating miR-494 to reduce LPS-induced damage in AECs. This study elucidated that miR-494 on BML-111 alleviated LPS-induced ALI in primary mouse AECs via downregulating miR-494 and subsequently activating the Slit2/Robo4 axis. These findings provided a new idea for the prevention and treatment of ALI and respiratory distress syndrome.

The risks of sulfur addition on cadmium accumulation in paddy rice under different water-management conditions.

Recently, the application of sulfur (S) has been recommended to control the accumulation of cadmium (Cd) in rice in contaminated paddy soil. However, the effects of exogenous S on Cd transfer in paddy rice systems under different water-management practices have not been systematically investigated. Pot experiments were performed to monitor the composition of soil pore water and the Cd accumulation in iron plaque and rice tissue were compared under different S (0 and 200 mg/kg Na2SO4) and water (continuous and discontinuous flooding) treatments. Sulfur application significantly increased Cd concentrations in soil pore water under discontinuous flooding conditions, but slightly reduced them under continuous flooding. Moreover, the oxidation/reduction potential (Eh) was the most critical factor that affected the Cd levels. When the Eh exceeded -42.5 mV, S became the second critical factor, and excessive S application promoted Cd dissolution. In addition, S addition elevated the Cd levels in iron plaque and reduced the Cd transfer from the iron plaque to rice roots. In rice, S addition inhibited Cd transfer from the rice roots to the straw; thus, more Cd was stored in the rice roots. Nevertheless, additional S application increased the Cd content in the rice grains by 72% under discontinuous flooding, although this effect was mitigated by continued flooding. Under simulated practical water management conditions, S addition increased the risk of Cd contamination in rice, suggesting that S application should be reconsidered as a paddy fertilization strategy.

Histone acetylome-wide associations in immune cells from individuals with active Mycobacterium tuberculosis infection.

Host cell chromatin changes are thought to play an important role in the pathogenesis of infectious diseases. Here we describe a histone acetylome-wide association study (HAWAS) of an infectious disease, on the basis of genome-wide H3K27 acetylation profiling of peripheral blood granulocytes and monocytes from persons with active Mycobacterium tuberculosis (Mtb) infection and healthy controls. We detected >2,000 differentially acetylated loci in either cell type in a Singapore Chinese discovery cohort (n = 46), which were validated in a subsequent multi-ethnic Singapore cohort (n = 29), as well as a longitudinal cohort from South Africa (n = 26), thus demonstrating that HAWAS can be independently corroborated. Acetylation changes were correlated with differential gene expression. Differential acetylation was enriched near potassium channel genes, including KCNJ15, which modulates apoptosis and promotes Mtb clearance in vitro. We performed histone acetylation quantitative trait locus (haQTL) analysis on the dataset and identified 69 candidate causal variants for immune phenotypes among granulocyte haQTLs and 83 among monocyte haQTLs. Our study provides proof-of-principle for HAWAS to infer mechanisms of host response to pathogens.

Study on the Automatic Identification of ABX3 Perovskite Crystal Structure Based on the Bond-Valence Vector Sum.

Perovskite materials have a variety of crystal structures, and the properties of crystalline materials are greatly influenced by geometric information such as the space group, crystal system, and lattice constant. It used to be mostly obtained using calculations based on density functional theory (DFT) and experimental data from X-ray diffraction (XRD) curve fitting. These two techniques cannot be utilized to identify materials on a wide scale in businesses since they require expensive equipment and take a lot of time. Machine learning (ML), which is based on big data statistics and nonlinear modeling, has advanced significantly in recent years and is now capable of swiftly and reliably predicting the structures of materials with known chemical ratios based on a few key material-specific factors. A dataset encompassing 1647 perovskite compounds in seven crystal systems was obtained from the Materials Project database for this study, which used the ABX3 perovskite system as its research object. A descriptor called the bond-valence vector sum (BVVS) is presented to describe the intricate geometry of perovskites in addition to information on the usual chemical composition of the elements. Additionally, a model for the automatic identification of perovskite structures was built through a comparison of various ML techniques. It is possible to identify the space group and crystal system using just a small dataset of 10 feature descriptors. The highest accuracy is 0.955 and 0.974, and the highest correlation coefficient (R2) value of the lattice constant can reach 0.887, making this a quick and efficient method for determining the crystal structure.