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Background: A growing number of studies have shown that Yin Yang 1 (YY1) promotes the development of multiple tumours. The purpose of the current study was to determine the mechanism by which YY1 mediates neuroendocrine differentiation of prostate cancer (NEPC) cells undergoing cellular plasticity. Methods: Using the Cancer Genome Atlas and Gene Expression Omnibus (GEO) databases, we bioinformatically analyzed YY1 expression in prostate cancer (PCa). Aberrant YY1 expression was validated in different PCa tissues and cell lines via quantitative reverse transcription polymerase chain reaction, western blotting, and immunohistochemistry. In vivo and in vitro functional assays verified the oncogenicity of YY1 in PCa. Further functional assays showed that ectopic expression of YY1 promoted cellular plasticity in PCa cells via epithelial‐mesenchymal transition induction and neuroendocrine differentiation. Results: Androgen deprivation therapy induced a decrease in YY1 protein ubiquitination, enhanced its stability, and thus enhanced the transcriptional activity of FZD8. Castration enhanced FZD8 binding to Wnt9A and mediated cellular plasticity by activating the non‐canonical Wnt (FZD8/FYN/STAT3) pathway. Conclusions: We identified YY1 as a novel dysregulated transcription factor that plays an important role in NEPC progression in this study. We believe that an in‐depth investigation of the mechanism underlying YY1‐mediated disease may lead to improved NEPC therapies. [ABSTRACT FROM AUTHOR]

Background: Multiple myeloma (MM) is a fatal malignant tumor in hematology. Mitophagy plays vital roles in the pathogenesis and drug sensitivity of MM. Methods: We acquired transcriptomic expression data and clinical index of MM patients from NCI public database, and 36 genes involved in mitophagy from the gene set enrichment analysis (GSEA) database. Least absolute shrinkage and selection operator (LASSO) Cox regression analysis was conducted to construct a risk score prognostic model. Kaplan–Meier survival analysis and receiver operation characteristic curves (ROC) were conducted to identify the efficiency of prognosis and diagnosis. ESTIMATE algorithm and immune-related single-sample gene set enrichment analysis (ssGSEA) was performed to uncover the level of immune infiltration. QRT-PCR was performed to verify gene expression in clinical samples of MM patients. The sensitivity to chemotherapy drugs was evaluated upon the database of the genomics of drug sensitivity in cancer (GDSC). Results: Fifty mitophagy-related genes were differently expressed in two independent cohorts. Ten out of these genes were identified to be related to MM overall survival (OS) rate. A prognostic risk signature model was built upon on these genes: VDAC1, PINK1, VPS13C, ATG13, and HUWE1, which predicted the survival of MM accurately and stably both in training and validation cohorts. MM patients suffered more adverse prognosis showed more higher risk core. In addition, the risk score was considered as an independent prognostic element for OS of MM patients by multivariate cox regression analysis. Functional pathway enrichment analysis of differentially expressed genes (DEGs) based on risk score showed terms of cell cycle, immune response, mTOR pathway, and MYC targets were obviously enriched. Furthermore, MM patients with higher risk score were observed lower immune scores and lower immune infiltration levels. The results of qRT-PCR verified VDAC1, PINK1, and HUWE1 were dysregulated in new diagnosed MM patients. Finally, further analysis indicated MM patients showed more susceptive to bortezomib, lenalidomide and rapamycin in high-risk group. Conclusion: Our research provided a neoteric prognostic model of MM based on mitophagy genes. The immune infiltration level based on risk score paved a better understanding of the participation of mitophagy in MM. Highlights: The study reported a mitophagy-related genes signature in multiple myeloma. The mitophagy-related genes signature had ideal prognostic independence in multiple myeloma. A nomogram to predict the overall survival of multiple myeloma was built by combining the five-gene signature, LDH and ISS stage. Immune infiltration was related to the mitophagy-related risk signature. [ABSTRACT FROM AUTHOR]

Background: Chronic alcohol consumption in adults can induce various cardiac toxicities such as arrhythmias, cardiomyopathy, and heart failure. Prenatal alcohol exposure can increase the risk of developing congenital heart defects among offspring. Understanding the molecular mechanisms underlying long‐term alcohol exposure‐induced cardiotoxicity can help guide the development of therapeutic strategies. Methods: Cardiomyocytes derived from human‐induced pluripotent stem cells (hiPSC‐CMs) were engineered into cardiac spheroids and treated with clinically relevant concentrations of ethanol (17 and 50 mM) for 5 weeks. The cells were then analyzed for changes in mitochondrial features, transcriptomic and metabolomic profiles, and integrated omics outcomes. Results: Following chronic ethanol treatment of hiPSC‐CMs, a decrease in mitochondrial membrane potential and respiration and changes in expression of mitochondrial function‐related genes were observed. RNA‐sequencing analysis revealed changes in various metabolic processes, heart development, response to hypoxia, and extracellular matrix‐related activities. Metabolomic analysis revealed dysregulation of energy metabolism and increased metabolites associated with the upregulation of inflammation. Integrated omics analysis further identified functional subclusters and revealed potentially affected pathways associated with cardiac toxicities. Conclusion: Chronic ethanol treatment of hiPSC‐CMs resulted in overall decreased mitochondrial function, increased glycolysis, disrupted fatty acid oxidation, and impaired cardiac structural development. [ABSTRACT FROM AUTHOR]

Adventitious root (AR) development is an extremely complex biological process that is affected by many intrinsic factors and extrinsic stimuli. Some WUSCHEL-related homeobox (WOX) transcription factors have been reported to play important roles in AR development, but their functional relationships with auxin signaling are poorly understood, especially the developmental plasticity of roots in response to adversity stress. Here, we identified that the WOX11/12a– SMALL AUXIN UP RNA36 (SAUR36) module mediates AR development through the auxin pathway in poplar, as well as under salt stress. PagWOX11/12a displayed inducible expression during AR development, and overexpression of PagWOX11/12a significantly promoted AR development and increased salt tolerance in poplar, whereas dominant repression of PagWOX11/12a produced the opposite phenotype. PagWOX11/12a proteins directly bind to the SAUR36 promoter to regulate SAUR36 transcription, and this binding was enhanced during salt stress. Genetic modification of PagWOX11/12a–PagSAUR36 expression revealed that the PagWOX11/12a –PagSAUR36 module is crucial for controlling AR development via the auxin pathway. Overall, our results indicate that a novel WOX11 –SAUR –auxin signaling regulatory module is required for AR development in poplar. These findings provide key insights and a better understanding of the involvement of WOX11 in root developmental plasticity in saline environments. [ABSTRACT FROM AUTHOR]

Plant roots can be colonized by many symbiotic fungi, whereas it is unclear whether and how symbiotic fungi including arbuscular mycorrhizal fungi and endophytic fungi promote phosphorus (P) uptake in Camellia oleifera plants. The objective of the present study was to analyze the effect of inoculation with a culturable endophytic fungus (Piriformospora indica), three arbuscular mycorrhizal fungi (Funneliformis mosseae, Diversispora versiformis, and Rhizophagus intraradices), and mixture of F. mosseae, D. versiformis and R. intraradices on plant growth, root architecture, soil Olsen-P, soil phosphatase activities, leaf and root P concentrations, and phosphate transporter gene expressions, in order to explore the potential and mechanism of these symbiotic fungi on P acquisition. All the symbiotic fungi colonized roots of C. oleifera after 16 weeks, with P. indica showing the best effect on fungal colonization. All the symbiotic fungi significantly increased acid, neutral, and total phosphatase activities in the soil, accompanied with an elevation of soil Olsen-P, of which P. indica presented the best effect. All symbiotic fungal treatments, except D. versiformis, significantly promoted plant growth, coupled with an increase in root total length, area, and volume. Symbiotic fungi almost up-regulated root CoPHO1-3 expressions as well as leaf CoPHO1-1, CoPHO1-3, and CoPHT1;4 expressions. Correlation analysis showed that P concentrations in leaves and roots were significantly positively correlated with root morphological variables (length, volume, and surface area) and soil acid, neutral and total phosphatase activities. It is concluded that symbiotic fungi, especially P. indica, played an important role in P uptake of C. oleifera plants through regulating root architecture, part plant phosphate transporter gene expressions and soil phosphatase activities. [ABSTRACT FROM AUTHOR]

Objective. The therapeutic effect of drugs for functional dyspepsia (FD) is still limited. Ganoderic acid A (GAA) has anti-inflammatory and cellular protective activities. The aim of this study is to explore the therapeutic effect of GAA on FD. Methods. The FD rat model was established via tail damping and forced exercise fatigue. The gastric emptying rate and intestinal propulsion rate of the rats in each group were then detected, and the pathological damage of gastric antrum and duodenum tissues was observed by hematoxylin-eosin (HE) staining. An enzyme-linked immunosorbent assay (ELISA) was conducted to determine the levels of motilin (MTL), vasoactive intestinal peptide (VIP), leptin, gastrin (GAS), calcitonin gene-related peptide (CGRP), and somatostatin (SS) in plasma, and Western blot was used to detect the protein expression levels of occludin, zonula occluden-1 (ZO-1), and junctional adhesion molecule-1 (JAM-1) in the duodenal tissue. Results. Treatment with GAA significantly raised the gastric emptying rate and intestinal propulsion rate of FD rats and histologically alleviated the gastric and duodenal damage. Meanwhile, GAA positively regulated the secretion of brain-gut proteins, such as upregulation of MTL, GAS, and SS and downregulation of VIP, leptin, and CGRP. In addition, GAA treatment increased the protein expression levels of occludin, ZO-1, and JAM-1 in the duodenal tissue of the FD rats. Conclusion. GAA may exhibit protective effects on FD by regulating the secretion of brain-gut peptide, protecting the intestinal barrier and improving gastrointestinal motility. [ABSTRACT FROM AUTHOR]

Nitrogen (N 2)-fixing legumes can be used for phytoremediation of toxic heavy metal Mercury (Hg) contaminated soil, but N 2 -fixation highly relies on phosphorus (P) availability for nodule formation and functioning. Here, we characterized the significance of P deficiency for Hg accumulation and toxicity in woody legume plants. Consequences for foliar and root traits of rhizobia inoculation, Hg exposure (+Hg) and low P (-P) supply, individually and in combination were characterized at both the metabolite and transcriptome levels in seedlings of two Robinia pseudoacacia L. provenances originating from contrasting climate and soil backgrounds, i.e., GS in northwest and the DB in northeast China. Our results reveal that depleted P mitigates the toxicity of Hg at the transcriptional level. In leaves of Robinia depleted P reduced oxidative stress and improved the utilization strategy of C, N and P nutrition; in roots depleted P regulated the expression of genes scavenging oxidative stress and promoting cell membrane synthesis. Rhizobia inoculation significantly improved the performance of both Robinia provenances under individual and combined +Hg and -P by promoting photosynthesis, increasing foliar N and P content and reducing H 2 O 2 and MDA accumulation despite enhanced Hg uptake. DB plants developed more nodules, had higher biomass and accumulated higher Hg amounts than GS plants and thus are suggested as the high potential Robinia provenance for future phytoremediation of Hg contaminated soils with P deficiency. Soil pollution and nutrient depletion constitute serious threats for human and environmental health. However, information on the responses of plants to combined Hg pollution and P depletion has so far not been reported, at both, the metabolite and transcriptome levels. In the present study, we characterized the interaction of Hg exposure with P depletion in Robinia -rhizobia associations of two Robinia provenances originating from different environments at the metabolic and transcriptional levels. Provenance-specific differences in Robinia performance upon rhizobia inoculation at Hg and low P exposure were identified. From these results we recommend one of the two Robinia provenances for future remediation of Hg contaminated soils with low P content. [Display omitted] • P depletion showed antagonistic effects when combined with Hg exposure on Robinia-rhizobia symbiosis. • Rhizobia inoculation improved plant performance under combined Hg and depleted P. • Provenance-specific responses of Robinia plants. • Mechanisms in physiological and transcriptional levels were reported. • The DB provenance is feasible than GS for phytoremediation of Hg exposure in P-depleted soil. [ABSTRACT FROM AUTHOR]

This study aimed to analyze the role of the FcepsilonRI (FcεRI) signaling pathway in the pathogenesis of benign lymphoepithelial lesion of lacrimal gland (LGBLEL). Transcriptomic analysis was performed on LGBLEL and orbital cavernous hemangioma (CH) patients diagnosed via histopathology in Beijing Tongren Hospital, Capital Medical University, between July 2010 and October 2013. Four LGBLEL and three orbital CH patients, diagnosed between October 2018 and August 2019, were randomly selected as experimental and control groups, respectively. RT-PCR, immunohistochemical staining, and western blotting were used to verify genes and proteins related to the FcεRI signaling pathway. Transcriptomic analysis showed that the FcεRI signaling pathway was upregulated in the LGBLEL compared with the CH group. The mRNA expression levels of important genes including SYK, p38, JNK, PI3K, and ERK were significantly increased in the LGBLEL group (P = 0.0066, P = 0.0002, P = 0.0003, P < 0.0001, P < 0.0001, respectively). Immunohistochemical staining results showed that SYK, p38, and ERK were positively expressed in LGBLEL, while JNK and PI3K were not. The protein contents of P-SYK, P-p38, P-JNK, P-PI3K, and P-ERK were significantly higher in the LGBLEL than in the CH group (P = 0.0169, P = 0.0074, P = 0.0046, P = 0.0157, P = 0.0156, respectively). The FcεRI signaling pathway participates in the pathogenesis of LGBLEL. [ABSTRACT FROM AUTHOR]

The rupture of atherosclerotic plaques is essential for cardiovascular and cerebrovascular events. Identification of the key genes related to plaque rupture is an important approach to predict the status of plaque and to prevent the clinical events. In the present study, we downloaded two expression profiles related to the rupture of atherosclerotic plaques (GSE41571 and GSE120521) from GEO database. 11 samples in GSE41571 were used to identify the differentially expressed genes (DEGs) and to construct the weighted gene correlation network analysis (WGCNA) by R software. The gene oncology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment tool in DAVID website, and the Protein-protein interactions in STRING website were used to predict the functions and mechanisms of genes. Furthermore, we mapped the hub genes extracted from WGCNA to DEGs, and constructed a sub-network using Cytoscape 3.7.2. The key genes were identified by the molecular complex detection (MCODE) in Cytoscape. Further validation was conducted using dataset GSE120521 and human carotid endarterectomy (CEA) plaques. Results: In our study, 868 DEGs were identified in GSE41571. Six modules with 236 hub genes were identified through WGCNA analysis. Among these six modules, blue and brown modules were of the highest correlations with ruptured plaques (with a correlation of 0.82 and −0.9 respectively). 72 hub genes were identified from blue and brown modules. These 72 genes were the most likely ones being related to cell adhesion, extracellular matrix organization, cell growth, cell migration, leukocyte migration, PI3K-Akt signaling, focal adhesion, and ECM-receptor interaction. Among the 72 hub genes, 45 were mapped to the DEGs (logFC > 1.0, p-value < 0.05). The sub-network of these 45 hub genes and MCODE analysis indicated 3 clusters (13 genes) as key genes. They were LOXL1, FBLN5, FMOD, ELN, EFEMP1 in cluster 1, RILP, HLA-DRA, HLA-DMB, HLA-DMA in cluster 2, and SFRP4, FZD6, DKK3 in cluster 3. Further expression detection indicated EFEMP1, BGN, ELN, FMOD, DKK3, FBLN5, FZD6, HLA-DRA, HLA-DMB, HLA-DMA, and RILP might have potential diagnostic value. [ABSTRACT FROM AUTHOR]

Based on central dogma of genetics, protein is the embodiment and executor of genetic function, post‐translational modifications (PTMs) of protein are particularly important and involved in almost all aspects of cell biology and pathogenesis. Studies have shown that ionizing radiation (IR) alters gene expression much more profoundly and a broad variety of cell‐process pathways, lots of proteins are modified and activated. Our understanding of the protein in response to ionizing radiation is steadily increasing. Among the various biological processes known to induce radioresistance, PTMs have attracted marked attention in recent years. The present review summarizes the latest knowledge about how PTMs response to ionizing radiation and pathway analysis were conducted. The data provided insights into biological effects of IR and contributing to the development of novel IR‐based strategies. [ABSTRACT FROM AUTHOR]

Background: Synthetic biology requires toolbox of promoters to finely tune gene expression levels for building up efficient cell factories. Yeast promoters owned variable core promoter regions between the TATA-box and transcriptional starting site (TSS) at the length mostly around 20–80 bases. This region allowed flexible design of artificial promoter but potentially demand special base motifs to maintain or enhance the promoter's strength. Results: Here, we designed and screened the base motifs and tested the activities of yeast artificial core promoters. Different 30 bases of artificial sequences led to variable expression levels of CrtY enzyme which determined the lycopene–carotene compositions, represented in the colony-color spectrum of red–orange–yellow. The upstream sequences of two strong promoter PEXP1 and PGPD and two starting strains with distinguishable lycopene production levels were utilized to characterize the promoter sequences. Different partition designs of T-rich or G/C-rich base motifs led to distinguishable colony-color distributions. Finally, we screened a champion promoter with a highest 5.5-fold enhancement of lycopene–carotene transformation. Another selected promoter generated a highest beta-carotene production as 7.4 mg/g DCW. Conclusions: This work offered an approach to redesign promoter with artificial sequences. We concluded that the core promoter region could be designated as 30 bases and different base motifs would enhance or weaken the promoter's strength. Generally, more T-rich elements, higher %T and lower G/C percentage were beneficial to enhance the strength of artificial core promoter. [ABSTRACT FROM AUTHOR]

Simple Summary: Despite recent improvement in chemotherapy regimens for pancreatic adenocarcinoma (PDAC), the clinical outcomes are still unsatisfactory compared to other solid tumors. Radiotherapy was demonstrated to improve locoregional control of PDAC; however, the survival benefit of radiotherapy in localized PDAC is undefined due to early distant progression in the majority of patients. Upfront chemotherapy for localized PDAC was suggested recently to avoid radical local therapy for patients of localized PDAC high risk of distant metastasis. Potential tissue biomarkers were developed to select PDAC patients who will benefit from local radiotherapy. This review summarizes potential tissue biomarkers reported to predict the efficacy and survival benefits of radiotherapy for localized PDAC including SMAD4, a biomarker validated in a prospective clinical trial to correlate with failure pattern of localized PDAC after radiotherapy. In particular, we describe Krüppel-like factor 10 (KLF10), lost in two thirds of PDAC patients, in association with distant metastasis and radio-resistance of PDAC. From tumor tissues of patients with resectable PDAC enrolled to a clinical trial, we demonstrated that the combination of KLF10 and SMAD4 expression in tumor tissues may help select those who may benefit the most from additional radiotherapy. Though promising, these potential biomarkers should be validated in prospective clinical trials. The prognosis of pancreatic adenocarcinoma (PDAC) remains poor, with a 5-year survival rate of 12%. Although radiotherapy is effective for the locoregional control of PDAC, it does not have survival benefits compared with systemic chemotherapy. Most patients with localized PDAC develop distant metastasis shortly after diagnosis. Upfront chemotherapy has been suggested so that patients with localized PDAC with early distant metastasis do not have to undergo radical local therapy. Several potential tissue markers have been identified for selecting patients who may benefit from local radiotherapy, thereby prolonging their survival. This review summarizes these biomarkers including SMAD4, which is significantly associated with PDAC failure patterns and survival. In particular, Krüppel-like factor 10 (KLF10) is an early response transcription factor of transforming growth factor (TGF)-β. Unlike TGF-β in advanced cancers, KLF10 loss in two-thirds of patients with PDAC was associated with rapid distant metastasis and radioresistance; thus, KLF10 can serve as a predictive and therapeutic marker for PDAC. For patients with resectable PDAC, a combination of KLF10 and SMAD4 expression in tumor tissues may help select those who may benefit the most from additional radiotherapy. Future trials should consider upfront systemic therapy or include molecular biomarker-enriched patients without early distant metastasis. [ABSTRACT FROM AUTHOR]

Aim: The aim of this study is to establish a method for determination of eupatilin in Folium artemisiae Argyi and observe the inhibitory effect of Folium artemisiae Argyi extract on human hepatoma SMMC-7721 cells. Methods: High-performance liquid chromatograph system with 2910 pump, 2930 UV detector, and N2000 workstation was used for determination of eupatilin in Folium artemisiae Argyi. Human hepatoma SMMC-7721 cells were cultured and cell proliferation was measured using the MTT assay. The expression protein levels of p53, Topo II, and bcl-2 were detected using Western blotting. Results: Eupatilin exhibited a linearity range of 0.5--3.0 µg/mL and a recovery of 100.72%, relevant standard derivation = 2.28%. Folium artemisiae Argyi extract had marked cytostatic and cytotoxic effects on SMMC-7721 cells, inhibited the SMMC-7721 colony formation in a dose-dependent manner. Folium artemisiae Argyi extract already possessed delayed effect after treating SMMC-7721 cells for 8 h, which became obvious at 12 h from treatment. After drug withdrawal, cells still tended to apoptosis. Folium artemisiae Argyi extract could inhibit p53, Topo II, and bcl-2 expressions in tumor cells. The present method for determination of eupatilin is simple, fast, accurate, sensitive, and reproducible. Conclusion: Hepatoma SMMC-7721 cells are quite sensitive to Folium artemisiae Argyi extract, which may be associated with its suppression of p53, Topo II, and bcl-2 expressions. [ABSTRACT FROM AUTHOR]

Glucagon-like peptide-1 (GLP-1) plays a role in the regulation of adipogenesis; however, the precise underlying molecular mechanism has not been fully defined. Wnt was recently identified as an important regulator of adipogenesis. This study aimed to investigate the involvement of the Wnt signaling pathway in the effects of GLP-1 on adipocyte differentiation. 3T3-L1 cells were induced to differentiate. The changes in the expression levels of adipogenic transcription factors and Wnts and the phosphorylation level and subcellular localization of β-catenin were quantified after GLP-1 treatment. GLP-1 stimulated adipocyte differentiation and lipid accumulation, which were accompanied by the expression of adipocyte marker genes. The expression of Wnt4 was upregulated in the process of adipocyte differentiation, which was further enhanced by treatment with GLP-1. β-catenin, an important mediator of the Wnt pathway, was immediately dephosphorylated and translocated from cytoplasm to nucleus when differentiation was induced. In the presence of GLP-1, however, β-catenin was redirected to the cell plasma membrane leading to its decreased accumulation in the nucleus. Knockdown of Wnt4 blocked the effect of GLP-1 on the cellular localization of β-catenin and expression level of adipogenic transcription factors. Our findings showed that GLP-1 promoted adipogenesis through the modulation of the Wnt4/β-catenin signaling pathway, suggesting that the GLP-1-Wntβ-catenin system might be a new target for the treatment of metabolic disease. [ABSTRACT FROM AUTHOR]

Purpose: To confirm whether flotillin 2 (FLOT2) is a direct target of miR-34a and miR-34a/FLOT2 pathway plays a key role in melanoma proliferation and metastasis. Methods: First, miR-34a and FLOT2 expressions were both detected in human tissues and cell lines by qRT-PCR. Then, after transfection of mimics/inhibitor of miR-34a into melanoma cell lines, MTT, colony formation, scratch migration assays and transwell invasion assays were performed to evaluate the impact of miR-34a on cell proliferation and metastasis. Western blot, qRT-RCR and dual luciferase reporter gene assays were carried out to confirm whether FLOT2 is a direct target gene of miR-34a. In functional recovery experiments, proliferation and metastasis ability of WM35 and WM451 was tested after being co-transfected with miR-34a inhibitor/si-FLOT2 or miR-34a mimics/FLOT2 cDNA to confirm that FLOT2 is downregulated by miR-34a. Results: The miR-34a significantly lower-expressed in metastasis melanoma tissues compared to in situ melanoma, nevi and normal skin whereas FLOT2 has an opposite trend. The level of miR-34a and FLOT2 in different melanoma cell lines was also texted and found that metastatic melanoma cell lines has lower miR-34a expression and higher FLOT2 expression compare to in situ melanoma cell line. MiR-34a overexpression profoundly inhibits WM451 cell proliferation and metastasis, whereas miR-34a reduction had a promoting effect to proliferation and metastasis of WM35. Results of Western blot, qRT-RCR and dual luciferase reporter gene assays revealed that FLOT2 is a direct target gene of miR-34a. Furthermore, overexpression/blockage of FLOT2 could attenuate effect of miR-34a overexpression/inhibition which indicated miR-34a suppresses melanoma biological behavior partially through FLOT2 inhibition. Conclusions: Our study confirmed that miR-34a is involved in the tumor inhibition of melanoma by directly targeting FLOT2 gene. This finding provides potential novel strategies for therapeutic interventions of melanoma. [ABSTRACT FROM AUTHOR]

Though nanomaterials are considered as drug carriers or imaging reagents targeting the central nervous system their cytotoxicity effect on neuronal cells has not been well studied. In this study, we treated PC12 cells, a model neuronal cell line, with a nanomaterial that is widely accepted for medical use, superparamagnetic iron oxide nanoparticles (SPIONs). Our results suggest that, after treated with SPIONs, the expression pattern of the cellular miRNAs changed widely in PC12 cells. As potential miRNA targets, NMDAR, one of the candidate mRNAs that were selected using GO and KEGG pathway enrichment, was significantly down regulated by SPIONs treatment. We further illustrated that SPIONs may induce cell death through NMDAR suppression. This study revealed a NMDAR neurotoxic effect of SPIONs and provides a reliable approach for assessing the neurocytotoxic effects of nanomaterials based on the comprehensive annotation of miRNA profiling. [ABSTRACT FROM AUTHOR]

Methyl jasmonate (MeJA) plays important roles on growth, gene expression and metabolite accumulation in plants. In this study, the physiological and biochemical characteristics, transcriptome and metabolome profiles of Isatis indigotica Fort., responded to MeJA were explored. Under the treatment, the contents of dry matter, chlorophyll and carotenoids increased significantly, while the water content did not. And the contents of soluble protein, flavonoid and lignin were also raised significantly, but the soluble sugar decreased. Besides, the enzyme activities of phenylalanine ammonia lyase (PAL), lipoxygenase (LOX), polyphenol oxidase (PPO), peroxidase (POD), catalase (CAT) and superoxide dismutase (SOD) increased, showing certain resistance characteristics of this plant. Based on RNA-seq, 31,769 unigenes were functionally annotated, and 2725 differential expressed genes (DEGs) identified. Among them, 57 DEGs covered most of the catalytic steps in general biosynthesis pathways of jasmonic acid, glucosinolates and phenylpropanoid. Referring to the metabolomics analysis, 175 significant differential metabolites were detected by GC-MS, combined with LC-MS method. Moreover, 53 differential metabolites were identified by the multivariate statistical analysis, mainly enriched in 37 different metabolic pathways, with most differential metabolites found in phenylalanine metabolism pathway. The results provided the comprehensive analysis on growth, transcriptome and metabolite profiles responded to MeJA, and gave new insights into revealing and enriching the functions of MeJA, contributing to explore the key genes and their functions on growth and metabolite accumulation and regulation process in I. indigotica. • MeJA could improve the seedling growth and enhance the resistance of I. indigotica. • A total of 2725 genes differentially expressed in response to MeJA. • 175 metabolites differentially changed in response to MeJA. [ABSTRACT FROM AUTHOR]

Motivation: Unlike traditional diagnosis of an existing disease state, detecting the pre-disease state just before the serious deterioration of a disease is a challenging task, because the state of the system may show little apparent change or symptoms before this critical transition during disease progression. By exploring the rich interaction information provided by high-throughput data, the dynamical network biomarker (DNB) can identify the pre-disease state, but this requires multiple samples to reach a correct diagnosis for one individual, thereby restricting its clinical application.Results: In this article, we have developed a novel computational approach based on the DNB theory and differential distributions between the expressions of DNB and non-DNB molecules, which can detect the pre-disease state reliably even from a single sample taken from one individual, by compensating insufficient samples with existing datasets from population studies. Our approach has been validated by the successful identification of pre-disease samples from subjects or individuals before the emergence of disease symptoms for acute lung injury, influenza and breast cancer.Contact: lnchen@sibs.ac.cn.Supplementary information: Supplementary data are available at Bioinformatics online. [ABSTRACT FROM PUBLISHER]

Highlights: [•] Inactivation of crr and tyrA increased the yield of L-phenylalanine (Phe). [•] Uninhibited manner aroG15 showed thermostability and the highest Phe concentration among all the aroG mutants. [•] The genetic switch of gene expression was used to precisely control biomass accumulation and Phe synthesis. [•] Jointly expressing yddG and tyrB shifted equilibrium towards Phe synthesis and remited the feedback regulation. [•] Engineering of Phe producer was done to illustrate the effectiveness of systematic level engineering. [ABSTRACT FROM AUTHOR]

Background and Aims: Increasing studies show that messenger RNA (mRNA) levels of local IGF-system are overexpressed in cancer tissue of patients with colorectal cancer (CRC). However, the influence of type 2 diabetes (T2DM) on the expression of insulin-like growth factor-1 (IGF-1) and IGF-1 receptor (IGF-1R) mRNA in colorectal cancer tissue and adjacent non-cancerous tissue (ANCT) is unknown. The aim of this study was to assess mRNA expression of IGF-1 and IGF-1R in paired samples of cancer tissue and ANCT between colorectal adenocarcinoma (CA) patients with and without T2DM. Methods: To quantify the levels of IGF-1 and IGF-1R mRNA in CA, we analyzed the expression of IGF-1 and IGF-1R mRNA levels in paired samples of cancer tissue and ANCT in CA patients with and without T2DM using real-time reverse transcription-polymerase chain reaction (RT-PCR). Results: mRNA levels of IGF-1 and IGF-1R were significantly higher in cancer tissue compared with its ANCT in CA patients with and without T2DM. Compared with the CA group, significantly higher levels of IGF-1 and IGF-1R mRNA were observed in cancer tissue in CA with T2DM group. No significant differences were observed in the role of cancer locations, Dukes stages and diabetes duration on mRNA expression of IGF-1. After adjusting for age, gender and Dukes stages, multivariate analysis indicated IGF-1 mRNA level was a risk factor for prognosis (p <0.05). Conclusions: Our results support the hypothesis that IGF system plays an important role in CRC. Further larger studies are needed. [Copyright &y& Elsevier]

Highlights: [•] ER stress-induced cell apoptosis is significant after 6h reperfusion in MCAO rats. [•] Pinocembrin can decrease ER stress-induced neuronal apoptosis. [•] Pinocembrin can attenuate the expression of ER stress apoptotic proteins. [•] Pinocembrin reduces expression of CHOP/GADD153 by regulating PERK-elF2α-ATF4 pathway. [ABSTRACT FROM AUTHOR]

Abstract: The concentration of glutathione (GSH), the most abundant intracellular free thiol and an important antioxidant, is decreased in the lung in both fibrotic diseases and experimental fibrosis models. The underlying mechanisms and biological significance of GSH depletion, however, remain unclear. Transforming growth factor β (TGF-β) is the most potent and ubiquitous profibrogenic cytokine and its expression is increased in almost all fibrotic diseases. In this study, we show that increasing TGF-β1 expression in mouse lung to a level comparable to those found in lung fibrotic diseases by intranasal instillation of AdTGF-β1223/225, an adenovirus expressing constitutively active TGF-β1, suppressed the expression of both catalytic and modifier subunits of glutamate–cysteine ligase (GCL), the rate-limiting enzyme in de novo GSH synthesis, decreased GSH concentration, and increased protein and lipid peroxidation in mouse lung. Furthermore, we show that increasing TGF-β1 expression activated JNK and induced activating transcription factor 3, a transcriptional repressor involved in the regulation of the catalytic subunit of GCL, in mouse lung. Control virus (AdDL70-3) had no significant effect on any of these parameters, compared to saline-treated control. Concurrent with GSH depletion, TGF-β1 induced lung epithelial apoptosis and robust pulmonary fibrosis. Importantly, lung GSH levels returned to normal, whereas fibrosis persisted at least 21 days after TGF-β1 instillation. Together, the data suggest that increased TGF-β1 expression may contribute to the GSH depletion observed in pulmonary fibrosis diseases and that GSH depletion may be an early event in, rather than a consequence of, fibrosis development. [Copyright &y& Elsevier]

Abstract: The present paper is to examine whether liquiritigenin is able to attenuate the Alzheimer''s-like learning and memory deficits in a transgenic (Tg) mouse model that over-expresses amyloid protein precursor (APP), and explores the underlying mechanisms. Consistent with our previous observations, we found that treatment with liquiritigenin improved the behavioral performance of Tg mice and it attenuated the protein expression of oligomeric form of amyloid β-peptide (Aβ). Furthermore, treatment with liquiritigenin inhibited astrocytosis in the hippocampus, and it may through its inhibitory activities on Notch-2, an important molecular regulating neural proliferation and differentiation. These findings provide evidence for beneficial activity of liquiritigenin in a mouse model of Alzheimer''s disease and support the continued investigation of Notch signaling pathway as a target for treatment of Alzheimer''s disease. [Copyright &y& Elsevier]

Abstract: A putative serine protease gene was cloned from the genomic DNA of Vibrio parahaemolyticus FYZ8621.4. The gene consisted of 1779 base pairs and encoded a 592 amino acid protein. The gene was expressed in Escherichia coli. The expressed protease was purified by Ni-NTA His-Bind Resin column and showed a 63 kDa band on SDS–PAGE. The protease exhibited proteolytic activity on gelatin agar plate and showed maximal proteolytic activity at pH 8.0 and 37 °C. It hydrolyzed N-α-benzoyl-l-tyrosine p-nitroanilide (BAPNA), but did not N-benzoyl-l-arginine ethylester (BAEE), N-benzoyl-l-tyrosine ethylester (BTEE) and N-acetyl-l-tyrosine ethylester (ATEE). Mutants at conserved residues Asp51 (Asp51–Asn), His89 (His89–Asp) and Ser318 (Ser318–Leu, Ser318–Pro) lost proteolytic activities completely. The protein was confirmed to belong to serine protease. The purified serine protease was toxic to zebrafish with a LD50 of 15.4 μg/fish. A DNA vaccine was constructed by inserting the mutated serine protease (Ser318–Pro) gene into pEGFP-N1 plasmid. The pEGFP-N1/m-vps was transfected in HeLa cells. The serine protease was confirmed to be expressed by fluorescence microscopy observation and Western blotting analysis. The pEGFP-N1/m-vps was further observed to express in muscle of the injected turbot (Scophthalmus maximus) by Western blotting seven days after immunization. Efficient protection against lethal V. parahaemolyticus challenge was observed on the vaccinated turbot with pEGFP-N1/m-vps, with the highest relative percent survival (RPS) of 96.11%. Significant specific antibody responses were also observed in the turbot vaccinated with the DNA vaccine. The results indicated that the serine protease might be a potential virulence factor and could be used as an efficient vaccine candidate for the disease control caused by V. parahaemolyticus. [Copyright &y& Elsevier]

Abstract: Neural cell adhesion molecule (NCAM) has been implicated in tumor metastasis yet its function in melanoma progression remains unclear. Here, we demonstrate that stably silencing NCAM expression in mouse melanoma B16F0 cells perturbs their cellular invasion and metastatic dissemination in vivo. The pro-invasive function of NCAM is exerted via dual mechanisms involving both cAMP-dependent protein kinase (PKA) and phosphatidylinositol 3-kinase (PI3K) pathways. Pharmacologic inhibition of PKA and PI3K leads to impaired cellular invasion. In contrast, forced expression of constitutively activated Akt, the major downstream target of PI3K, restores the defective cellular invasiveness of NCAM knock-down (KD) B16F0 cells. Furthermore, attenuation of either PKA or Akt activity in NCAM KD cells is shown to affect their common downstream target, transcription factor cAMP response element binding protein (CREB), which in turn down-regulates mRNA expression of matrix metalloproteinase-2 (MMP-2), thus contributes to impaired cellular invasion and metastasis of melanoma cells. Together, these findings indicate that NCAM potentiates cellular invasion and metastasis of melanoma cells through stimulation of PKA and PI3K signaling pathways thus suggesting the potential implication of anti-NCAM strategy in melanoma treatment. [Copyright &y& Elsevier]

Abstract: Background: Prognosis of patients with gastric cancer (GC) is generally poor due to the lack of non-invasive tools for GC detection. The purpose of present study was to identify a serum microRNA (miRNA) expression profile that can serve as a novel diagnostic biomarker for GC detection and to assess its clinical applications in monitoring disease progression. Methods: Serum samples were taken from 164 GC patients and 127 age- and gender-matched tumour-free controls. An initial screening of miRNA expression by Solexa sequencing was performed using serum samples pooled from 20 patients and 20 controls, respectively. Differential expression was validated using hydrolysis probe-based stem-loop quantitative reverse transcription polymerase chain reaction (qRT-PCR) in individuals samples, the samples were arranged in two phases. Results: The Solexa sequencing results demonstrated that 19 serum miRNAs were markedly upregulated in the GC patients compared to the controls. The qRT-PCR analysis further identified a profile of five serum miRNAs (miR-1, miR-20a, miR-27a, miR-34 and miR-423-5p) as a biomarker for GC detection. The analysis results showed that the expression level of five serum miRNAs was correlated to tumour stage. The areas under the receiver operating characteristic (ROC) curve of this five-serum miRNA signature were 0.879 (95% confidence interval (CI) 0.822–0.936) and 0.831 (95% CI 0.767–0.898) for the two sets of serum samples, respectively, markedly higher than those of the biomarkers carcinoembryonic antigen (CEA) (0.503) and carbohydrate antigen 19-9 (CA19-9) (0.600). Conclusions: We identified five-miRNA signature for GC diagnosis by genome-wide serum miRNA expression profiling. Expression levels of this serum miRNA-based biomarker also indicate tumour progression stages. [Copyright &y& Elsevier]

• miR-25802 upregulation is involved in the pathological progression of AD. • miR-25802 regulates microglia-mediated neuroinflammation in AD. • miR-25802 targets KLF4 to regulate NF-κB signaling. • The miR-25802/KLF4/NF-κB axis has a regulatory role in cognitive deficits in AD. Microglia-mediated neuroinflammation plays a critical role in the occurrence and progression of Alzheimer's disease (AD). In recent years, studies have increasingly explored microRNAs as biomarkers and treatment interventions for AD. This study identified a novel microRNA termed miR-25802 from our high-throughput sequencing dataset of an AD model and explored its role and the underlying mechanism. The results confirmed the miRNA properties of miR-25802 based on bioinformatics and experimental verification. Expression of miR-25802 was increased in the plasma of AD patients and in the hippocampus of APP/PS1 and 5 × FAD mice carrying two and five familial AD gene mutations. Functional studies suggested that overexpression or inhibition of miR-25802 respectively aggravated or ameliorated AD-related pathology, including cognitive disability, Aβ deposition, microglial pro-inflammatory phenotype activation, and neuroinflammation, in 5 × FAD mice and homeostatic or LPS/IFN-γ-stimulated EOC20 microglia. Mechanistically, miR-25802 negatively regulates KLF4 by directly binding to KLF4 mRNA, thus stimulating microglia polarization toward the pro-inflammatory M1 phenotype by promoting the NF-κB-mediated inflammatory response. The results also showed that inhibition of miR-25802 increased microglial anti-inflammatory M2 phenotype activity and suppressed NF-κB-mediated inflammatory reactions in the brains of 5 × FAD mice, while overexpression of miR-25802 exacerbated microglial pro-inflammatory M1 activity by enhancing NF-κB pathways. Of note, AD-associated manifestations induced by inhibition or overexpression of miR-25802 via the NF-κB signaling pathway were reversed by KLF4 silencing or upregulation. Collectively, these results provide the first evidence that miR-25802 is a regulator of microglial activity and establish the role of miR-25802/KLF4/NF-κB signaling in microglia-mediated neuroinflammation, suggesting potential therapeutic targets for AD. [ABSTRACT FROM AUTHOR]

Aim: To investigate the long non‐coding RNA DLG1 Antisense RNA 1 (lncRNA DLG1‐AS1) mechanism in cervical cancer cells with gemcitabine (GEM) resistance. Methods: Quantitative real‐time polymerase chain reaction (qRT‐PCR) was used to detect DLG1‐AS1, miR‐16‐5p, and hepatoma‐derived growth factor (HDGF) expression in cervical cancer cells. The effects of DLG1‐AS1 knockdown on cell viability, proliferation, and apoptosis were investigated in GEM‐resistant cervical cancer cells. The binding of DLG1‐AS1 with miR‐16‐5p and of miR‐16‐5p with HDGF was confirmed through dual‐luciferase reporter assays. HDGF expression was detected through Western blotting. A xenograft model was established using stably transfected GEM‐resistant cervical cancer cells to detect the role of DLG1‐AS1 in tumorigenesis in vivo. Results: DLG1‐AS1 expression was significantly elevated in HeLa/GEM and SiHa/GEM cells. DLG1‐AS1 silencing significantly reduced the viability and proliferation of GEM‐resistant cervical cancer cells. DLG1‐AS1 also promoted GEM sensitivity in cervical cancer cells by inhibiting miR‐16‐5p. Moreover, the tumor volume in nude mice in the DLG1‐AS1 knockdown group decreased after GEM treatment. In addition, DLG1‐AS1 targeted miR‐16‐5p, and miR‐16‐5p targeted HDGF. The miR‐16‐5p inhibitor reversed the DLG1‐AS1 knockdown effect in GEM‐resistant cervical cancer cells. Conclusion: Knockdown of DLG1‐AS1 promoted GEM sensitivity in cervical cancer cells by regulating miR‐16‐5p/HDGF. [ABSTRACT FROM AUTHOR]

Background: Disease progression in biosystems is not always a steady process but is occasionally abrupt. It is important but challenging to signal critical transitions in complex biosystems. Methods: In this study, based on the theoretical framework of dynamic network biomarkers (DNBs), we propose a model-free method, edge-based relative entropy (ERE), to identify temporal key biomolecular associations/networks that may serve as DNBs and detect early-warning signals of the drastic state transition during disease progression in complex biological systems. Specifically, by combining gene‒gene interaction (edge) information with the relative entropy, the ERE method converts gene expression values into network entropy values, quantifying the dynamic change in a biomolecular network and indicating the qualitative shift in the system state. Results: The proposed method was validated using simulated data and real biological datasets of complex diseases. The applications show that for certain diseases, the ERE method helps to reveal so-called "dark genes" that are non-differentially expressed but with high ERE values and of essential importance in both gene regulation and prognosis. Conclusions: The proposed method effectively identified the critical transition states of complex diseases at the network level. Our study not only identified the critical transition states of various cancers but also provided two types of new prognostic biomarkers, positive and negative edge biomarkers, for further practical application. The method in this study therefore has great potential in personalized disease diagnosis. [ABSTRACT FROM AUTHOR]

Renal cell cancers typically exhibit high metastasis and recurrence, and this is thought to be due to renal cancer stem cells (CSCs). Meanwhile, aberrant activation of Sonic hedgehog (Shh) signaling is linked with CSCs. Resveratrol has direct or indirect impacts on the pathological activities of CSCs. However, the effects of resveratrol on renal CSCs remain to be elucidated. We cultured renal CSCs in serum-free medium. Western blotting was used to analyze the expression levels of related proteins. The mRNA changes were detected by qRT-PCR after resveratrol treatment. The CD133+ cells were quantified by flow cytometry analysis. Immunofluorescence staining images showed the changes in CD44 and Smoothened expression in the cell spheres. Renal CSCs were enriched by tumorsphere formation assays of ACHN and 786-O cells. Resveratrol treatments markedly decreased the size and number of cell spheres and downregulated the expression of the Shh pathway-related proteins and CSCs markers. Moreover, we observed that resveratrol inhibited cell proliferation and induced cell apoptosis, while purmorphamine upregulated the Shh pathway and weakened the effects of resveratrol on renal CSCs. These results suggested that resveratrol is a potential novel therapeutic agent that targets inactivation of renal CSCs by affecting the function of the Shh pathway. [ABSTRACT FROM AUTHOR]

TssJ-3 is an outer-membrane lipoprotein and is one of the key components of the type VI secretion system in Burkholderia pseudomallei. TssJ translocates effector proteins to target cells to induce innate immune response in the host. However, the tssJ gene has not been identified in B. pseudomallei and its function in this bacterium has not yet been characterized. tssJ-3 knockout and tssJ-3- complemented B. pseudomallei strains were constructed to determine the effects of tssJ-3 on bacterial growth, biofilm formation, flagellum synthesis, motility, host cell infection, and gene expression in B. pseudomallei. We found that the ΔtssJ-3 mutant strain of B. pseudomallei showed significantly suppressed biofilm formation, flagellum synthesis, bacterial growth, motility, and bacterial invasion into host cells (A549 cells). Furthermore, the ΔtssJ-3 mutation downregulated multiple key genes, including biofilm and flagellum-related genes in B. pseudomallei and induced interleukin-8 gene expression in host cells. These results suggest that tssJ-3 , an important gene controlling TssJ-3 protein expression, has regulatory effects on biofilm formation and flagellum synthesis in B. pseudomallei. In addition, B. pseudomallei- derived tssJ-3 contributes to cell infiltration and intracellular replication. This study provides a molecular basis of tssJ-3 for developing therapeutic strategies against B. pseudomallei infections. • We report functional studies of tssJ-3 gene from Burkholderia pseudomallei. • The tssJ-3 gene may influence bacterial quorum sensing and is crucial for biofilm formation. • The tssJ-3 gene has regulatory effects on biofilm formation and flagellum synthesis in Burkholderia pseudomallei. • Burkholderia pseudomallei -derived tssJ-3 contributes to cell infiltration and intracellular replication. • The gene expression of the biofilm-related genes, flagellar genes, and virulence genes were affected in the tssJ-3. [ABSTRACT FROM AUTHOR]

The critical point or pivotal threshold of cell transition occurs in early embryonic development when cell differentiation culminates in its transition to specific cell fates, at which the cell population undergoes an abrupt and qualitative shift. Revealing such critical points of cell transitions can track cellular heterogeneity and shed light on the molecular mechanisms of cell differentiation. However, precise detection of critical state transitions proves challenging when relying on single-cell RNA sequencing data due to their inherent sparsity, noise, and heterogeneity. In this study, diverging from conventional methods like differential gene analysis or static techniques that emphasize classification of cell types, an innovative computational approach, single-cell gene association entropy (SGAE), is designed for the analysis of single-cell RNA-seq data and utilizes gene association information to reveal critical states of cell transitions. More specifically, through the translation of gene expression data into local SGAE scores, the proposed SGAE can serve as an index to quantitatively assess the resilience and critical properties of genetic regulatory networks, consequently detecting the signal of cell transitions. Analyses of five single-cell datasets for embryonic development demonstrate that the SGAE method achieves better performance in facilitating the characterization of a critical phase transition compared with other existing methods. Moreover, the SGAE value can effectively discriminate cellular heterogeneity over time and performs well in the temporal clustering of cells. Besides, biological functional analysis also indicates the effectiveness of the proposed approach. [ABSTRACT FROM AUTHOR]

Background: Immunotherapy is a vital component in cancer treatment. However, due to the complex genetic bases of cancer, a clear prediction index for efficacy has not been established. Tumor mutation burden (TMB) is one of the essential factors that affect immunotherapeutic efficacies, but it has not been determined whether the mutation is associated with the survival of Skin Cutaneous Melanoma (SKCM) patients. This study aimed at evaluating the correlation between TMB and immune infiltration.Methods: Somatic mutation profiles (n = 467), transcriptome data (n = 471), and their clinical information (n = 447) of all SKCM samples were downloaded from The Cancer Genome Atlas (TCGA) database. For each sample, TMB was calculated as the number of variants per megabase. Based on K-M survival analysis, they were allocated into the high-TMB and low-TMB groups (the optimal cutoff was determined by the 'surv_cutpoint' algorithm of survival R package). Then, Gene ontology (GO) and Gene Set Enrichment Analyses (GSEA) were performed, with immune-associated biological pathways found to be significantly enriched in the low-TMB group. Therefore, immune genes that were differentially expressed between the two groups were evaluated in Cox regression to determine their prognostic values, and a four-gene TMB immune prognostic model (TMB-IP) was constructed.Results: Elevated TMB levels were associated with better survival outcomes in SKCM patients. Based on the cutoff value in OS analysis, they were divided into high-TMB and low-TMB groups. GSEA revealed that the low-TMB group was associated with immunity while intersection analysis revealed that there were 38 differentially expressed immune-related genes between the two groups. Four TMB-associated immune genes were used to construct a TMB-IP model. The AUC of the ROC curve of this model reached a maximum of 0.75 (95%CI, 0.66-0.85) for OS outcomes. Validation in each clinical subgroup confirmed the efficacy of the model to distinguish between high and low TMB-IP score patients.Conclusions: In SKCM patients, low TMB was associated with worse survival outcomes and enriched immune-associated pathways. The four TMB-associated immune genes model can effectively distinguish between high and low-risk patients. [ABSTRACT FROM AUTHOR]

Epidemiological studies have established that exposure to tungsten increases the risk of developing cardiovascular diseases. However, no studies have investigated how tungsten affects cardiac function or the development of cardiovascular disease. Inhalation of tungsten particulates is relevant in occupational settings, and inhalation of particulate matter has a known causative role in driving cardiovascular disease. This study examined if acute inhalation to tungsten particulates affects cardiac function and leads to heart tissue alterations. Female BALB/c mice were exposed to Filtered Air or 1.5 ± 0.23 mg/m3 tungsten particles, using a whole-body inhalation chamber, 4 times over the course of two weeks. Inhalation exposure resulted in mild pulmonary inflammation characterized by an increased percentage and number of macrophages and metabolomic changes in the lungs. Cardiac output was significantly decreased in the tungsten-exposed group. Additionally, A′, an indicator of the amount of work required by the atria to fill the heart was elevated. Cardiac gene expression analysis revealed, tungsten exposure increased expression of pro-inflammatory cytokines, markers of remodeling and fibrosis, and oxidative stress genes. These data strongly suggest exposure to tungsten results in cardiac injury characterized by early signs of diastolic dysfunction. Functional findings are in parallel, demonstrating cardiac oxidative stress, inflammation, and early fibrotic changes. Tungsten accumulation data would suggest these cardiac changes are driven by systemic consequences of pulmonary damage. • Inhalation of tungsten particulates results in mild inflammation and metabolomic changes in the lungs. • Inhalation of tungsten results in early signs of cardiac injury (decreased cardiac output and increased atrial workload). • Tungsten increases expression of pro-inflammatory, cardiac remodeling, and oxidative stress genes in the heart. • Tungsten accumulation data would suggest these cardiac changes are driven by systemic consequences of pulmonary damage. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • 13 novel potential sRNAs were found firstly in E. tarda ET13 strain, based on RNA sequencing and bioinformatic analyses. • The expression, conservation, direction and structure of EsR240 were found by RT-PCR, Northern blotting, RACE and bioinformatic analyses. • EsR240 may positively regulate its target genes in E. tarda to maintain intracellular survival within host macrophages and virulence. Abstract Bacterial small non-coding RNAs (sRNAs) are gene expression modulators that respond to environmental changes and pathogenic conditions. In this study, 13 novel sRNAs were identified in the intracellular pathogen, Edwardsiella tarda (E. tarda) ET13 strain, based on RNA sequencing and bioinformatic analyses. Eight of the 13 putative sRNAs from the ET13 strain were transcribed (as indicated by RT-PCR) following exposure to different stresses. The transcription levels of three sRNAs (EsR128, EsR139 and EsR240) were all highly induced under these stress conditions. Northern blot hybridization was employed to verify that EsR240 was expressed in the ET13 strain under both logarithmic and stationary growth phases, and that it formed a single copy transcript in the chromosomes of the ET13 strain. The precise start and end points of EsR240 were determined using 5'and 3' RACE. The conservation of EsR240 was in agreement with the characteristics of sRNA, as indicated by a BLAST analysis. Furthermore, the survival rates of EsR240 mutant were lower than the rates of the wild type ET13 under stress conditions. When the infection time was extended 4 or 6 h, the CFUs of the wild type bacteria increased more significantly within macrophages compared to the mutant. When the intra-peritoneal (i.p.) route of infection was used in mice, the bacterial loads of the tissues in the mice infected with the wild type bacteria were significantly higher than in the mice infected with the mutants. The virulence of the EsR240 mutant was 6.79-fold lower than the wild type bacterium based on the LD 50. In addition, the IntaRNA program was used to predict the target genes of EsR240. Out of the top 10 predicted target genes, 9 genes were regulated by EsR240. These target genes may encode FtsH protease modulator YccA, Na+ and H+ antiporters, FtsX-like permease family protein, glycoside hydrolases or various other proteins. Therefore, EsR240 may positively regulate its target genes in E. tarda to maintain intracellular survival within host macrophages and to increase its virulence. [ABSTRACT FROM AUTHOR]

Background/Aims. The underlying mechanisms of differential responsiveness to IFN remain poorly understood. The elongation factor Tu GTP binding domain-containing protein 2 (EFTUD2), involved in RNA splicing and pre-mRNA processing, was recognized as a novel innate immune regulator of the IFN antihepatitis C virus (HCV) effect. The aim of this study is to elucidate the mechanisms underlying EFTUD2's involvement in IFN-mediated anti-HBV responses. Methods. Using a CRISPR/Cas9 gene-editing system, EFTUD2 single allele knockout HepG2.2.15 cells were constructed. Subsequently, the HBV biomarkers in EFTUD2+/– HepG2.2.15 cells and wild-type (WT) cells with or without IFN-α treatment were detected. And the EFTUD2-regulated genes were then identified using mRNA sequence. Selected gene mRNA variants and their proteins were examined by qRT-PCR and Western blotting. To confirm the effects of EFTUD2 on HBV replication and IFN-stimulated gene (ISG) expression, a rescue experiment in EFTUD2+/– HepG2.2.15 cells was performed by EFTUD2 overexpression. Results. IFN-induced anti-HBV activity was found to be restricted in EFTUD2+/– HepG2.2.15 cells. The mRNA sequence showed that EFTUD2 could regulate classical IFN and virus response genes. Mechanistically, EFTUD2 single allele knockout decreased the expression of ISG-encoded proteins, comprising Mx1, OAS1, and PKR (EIF2AK2), through mediated gene splicing. However, EFTUD2 did not affect the expression of Jak-STAT pathway genes. Furthermore, EFTUD2 overexpression could restore the attenuation of IFN anti-HBV activity and the reduction of ISG resulting from EFTUD2 single allele knockout. Conclusion. EFTUD2, the spliceosome factor, is not IFN-inducible but is an IFN effector gene. EFTUD2 mediates IFN anti-HBV effect through regulation of gene splicing for certain ISGs, including Mx1, OAS1, and PKR. EFTUD2 does not affect IFN receptors or canonical signal transduction components. Therefore, it can be concluded that EFTUD2 regulates ISGs using a novel, nonclassical mechanism. [ABSTRACT FROM AUTHOR]

Purpose: The xerophyte Pugionium cornutum is a salt-tolerant species that can accumulate high amounts of Cl− in shoots for osmotic adjustment under saline condition. However, the molecular basis underlying how P. cornutum uses Cl− as a beneficial osmoticum is not clear yet. In this study, we evaluated the function of a chloride channel PcCLCg from P. cornutum in vacuolar Cl− compartmentalization and plant salt tolerance. Methods: PcCLCg was cloned; its subcellular localization and expression patterns were analyzed; its function in vacuolar Cl− compartmentalization, ion homeostasis and plant salt tolerance were investigated by expression in yeast and Arabidopsis. Results: PcCLCg was located on the tonoplast, the encoding gene was mainly expressed in shoots, and the expression level was induced by Cl−-salts. The expression of PcCLCg could improve the growth and increase the Cl− content of the yeast mutant Δgef1, in which a chloride channel gene ScGEF1 is deleted, under Cl−-salt treatments. The overexpression of PcCLCg in wild-type Arabidopsis or atclcg mutant alleviated the detrimental effects of NaCl stress on plant growth and significantly increased shoot Cl− and Na+ content under NaCl treatments. Interestingly, PcCLCg-overexpressing lines showed an increased expression of SLAH1 and NHX1 in roots and shoots, respectively, while a decreased expression of SOS1 in roots than wild-type under salt stress. Conclusions: The upregulated expression of PcCLCg in shoots is conducive to vacuolar Cl− compartmentalization and regulation of Na+ and Cl− accumulation, thus enhancing the osmotic adjustment capacity in the shoot of P. cornutum under saline conditions. [ABSTRACT FROM AUTHOR]

Background: The genus Acidithiobacillus has been widely concerned due to its superior survival and oxidation ability in acid mine drainage (AMD). However, the contribution of insertion sequence (IS) to their biological evolution and environmental adaptation is very limited. ISs are the simplest kinds of mobile genetic elements (MGEs), capable of interrupting genes, operons, or regulating the expression of genes through transposition activity. ISs could be classified into different families with their own members, possessing different copies. Results: In this study, the distribution and evolution of ISs, as well as the functions of the genes around ISs in 36 Acidithiobacillus genomes, were analyzed. The results showed that 248 members belonging to 23 IS families with a total of 10,652 copies were identified within the target genomes. The IS families and copy numbers among each species were significantly different, indicating that the IS distribution of Acidithiobacillus were not even. A. ferrooxidans had 166 IS members, which may develop more gene transposition strategies compared with other Acidithiobacillus spp. What's more, A. thiooxidans harbored the most IS copies, suggesting that their ISs were the most active and more likely to transpose. The ISs clustered in the phylogenetic tree approximately according to the family, which were mostly different from the evolutionary trends of their host genomes. Thus, it was suggested that the recent activity of ISs of Acidithiobacillus was not only determined by their genetic characteristics, but related with the environmental pressure. In addition, many ISs especially Tn3 and IS110 families were inserted around the regions whose functions were As/Hg/Cu/Co/Zn/Cd translocation and sulfur oxidation, implying that ISs could improve the adaptive capacities of Acidithiobacillus to the extremely acidic environment by enhancing their resistance to heavy metals and utilization of sulfur. Conclusions: This study provided the genomic evidence for the contribution of IS to evolution and adaptation of Acidithiobacillus, opening novel sights into the genome plasticity of those acidophiles. [ABSTRACT FROM AUTHOR]

Purpose. To analyze the changes of refraction and metabolism of the retinal cones under monochromatic lights in guinea pigs. Methods. Sixty guinea pigs were randomly divided into a short-wavelength light (SL) group, a middle-wavelength light (ML) group, and a white light (WL) group. Refraction and axial length were measured before and after 10-week illumination. The densities of S-cones and M-cones were determined by retinal cone immunocytochemistry, and the expressions of S-opsins and M-opsins were determined by real-time PCR and Western blot. Results. After 10-week illumination, the guinea pigs developed relative hyperopia in the SL group and relative myopia in the ML group. Compared with the WL group, the density of S-cones and S-opsins increased while M-cones and M-opsins decreased in the SL group (all, p<0.05); conversely, the density of S-cones and S-opsins decreased while M-cones and M-opsins increased in the ML group (all, p<0.05). Increased S-cones/opsins and decreased M-cones/opsins were induced by short-wavelength lights. Decreased S-cones/opsins and increased M-cones/opsins were induced by middle-wavelength lights. Conclusions. Altered retinal cones/opsins induced by monochromatic lights might be involved in the refractive development in guinea pigs. [ABSTRACT FROM AUTHOR]

Low temperature is a limiting factor of seed germination and plant growth. Although there is a lot information on the response of maize to low temperatures, there is still poorly description of how histone methylation affects maize germination and growth development at low temperatures. In this study, the germination rate and physiological indexes of wild-type maize inbred lines B73 (WT), SDG102 silencing lines (AS), SDG102 overexpressed lines (OE) at germination stage and seedling stage were measured under low temperature stress (4 ℃), and transcriptome sequencing was applied to analyze the differences of gene expression in panicle leaves among different materials. The results showed that the germination rate of WT and OE maize seeds at 4 ℃ was significantly lower than 25 ℃. The content of MDA, SOD and POD of 4 ℃ seeding leaves higher than contrast. Transcriptome sequencing results showed that there were 409 different expression genes (DEGs) between WT and AS, and the DEGs were mainly up-regulated expression in starch and sucrose metabolism and phenylpropanoid biosynthesis. There were 887 DEGs between WT and OE, which were mainly up-regulated in the pathways of plant hormone signal transduction, porphyrin and chlorophyll metabolism. This result could provide a theoretical basis for analyzing the growth and development of maize from the perspective of histone methylation modification. [ABSTRACT FROM AUTHOR]

Background: Deterioration of normal intestinal epithelial cells is crucial for colorectal tumorigenesis. However, the process of epithelial cell deterioration and molecular networks that contribute to this process remain unclear. Methods: Single-cell data and clinical information were downloaded from the Gene Expression Omnibus (GEO) database. We used the recently proposed dynamic network biomarker (DNB) method to identify the critical stage of epithelial cell deterioration. Data analysis and visualization were performed using R and Cytoscape software. In addition, Single-Cell rEgulatory Network Inference and Clustering (SCENIC) analysis was used to identify potential transcription factors, and CellChat analysis was conducted to evaluate possible interactions among cell populations. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set variation analysis (GSVA) analyses were also performed. Results: The trajectory of epithelial cell deterioration in adenoma to carcinoma progression was delineated, and the subpopulation of pre-deteriorated epithelial cells during colorectal cancer (CRC) initialization was identified at the single-cell level. Additionally, FOS/JUN were identified as biomarkers for pre-deteriorated epithelial cell subpopulations in CRC. Notably, FOS/JUN triggered low expression of P53-regulated downstream pro-apoptotic genes and high expression of anti-apoptotic genes through suppression of P53 expression, which in turn inhibited P53-induced apoptosis. Furthermore, malignant epithelial cells contributed to the progression of pre-deteriorated epithelial cells through the GDF signaling pathway. Conclusions: We demonstrated the trajectory of epithelial cell deterioration and used DNB to characterize pre-deteriorated epithelial cells at the single-cell level. The expression of DNB-neighboring genes and cellular communication were triggered by DNB genes, which may be involved in epithelial cell deterioration. The DNB genes FOS/JUN provide new insights into early intervention in CRC. [ABSTRACT FROM AUTHOR]

DNA methylation, a conserved epigenetic mark, is critical for tuning temporal and spatial gene expression. The Arabidopsis thaliana DNA glycosylase/lyase REPRESSOR OF SILENCING 1 (ROS1) initiates active DNA demethylation and is required to prevent DNA hypermethylation at thousands of genomic loci. However, how ROS1 is recruited to specific loci is not well understood. Here, we report the discovery of Arabidopsis AGENET Domain Containing Protein 3 (AGDP3) as a cellular factor that is required to prevent gene silencing and DNA hypermethylation. AGDP3 binds to H3K9me2 marks in its target DNA via its AGD12 cassette. Analysis of the crystal structure of the AGD12 cassette of AGDP3 in complex with an H3K9me2 peptide revealed that dimethylated H3K9 and unmodified H3K4 are specifically anchored into two different surface pockets. A histidine residue located in the methyllysine binding aromatic cage provides AGDP3 with pH‐dependent H3K9me2 binding capacity. Our results uncover a molecular mechanism for the regulation of DNA demethylation by the gene silencing mark H3K9me2. [ABSTRACT FROM AUTHOR]

The protein inhibitor of activated STAT (PIAS) family proteins act as the important negative regulators in janus kinase (JAK)/signal transducer and activator of transcription (STAT) signaling pathway, which can be also involved in regulating the expression of interferon-stimulated genes (ISGs). In the present study, a PIAS homologue (designated as Cg PIAS) was identified from oyster Crassostrea gigas. The open reading frame (ORF) of Cg PIAS cDNA was of 1887 bp encoding a peptide of 628 amino acid residues. The Cg PIAS protein contains a conserved scaffold attachment factor A/B/acinus/PIAS (SAP) domain, a Pro-Ile-Asn-Ile-Thr (PINIT) motif, a RING-finger-like zinc-binding domain (RLD) and two SUMO-interaction Motifs (SIMs). The deduced amino acid sequence of Cg PIAS shared 74.58–81.36% similarity with other PIAS family members in the RLD domain. The mRNA transcripts of Cg PIAS were detected in all the tested tissues with highest level in haemocytes (32.98-fold of mantles, p < 0.001). After poly (I:C) and recombinant Interferon-like protein (r Cg IFNLP) stimulation, the mRNA expression of Cg PIAS in haemocytes significantly up-regulated to the highest level at 48 h (7.38-fold, p < 0.001) and at 24 h (13.08-fold, p < 0.01), respectively. Moreover, the nuclear translocation of Cg PIAS was observed in haemocytes after poly (I:C) stimulation. Biolayer Interferometry (BLI) assay revealed that the recombinant protein Cg PIAS-RLD could interact with the recombinant protein Cg STAT in vitro with the K D value of 3.88 × 10−8 M. In the Cg PIAS-RNAi oysters, the green signals of Cg STAT protein in nucleus of haemocytes increased compared with that in NC-RNAi group, and the mRNA expression of myxovirus resistance (Cg Mx1), oligoadenylate synthase-like proteins (Cg OASL), Cg Viperin and IFN-induced protein 44-like (Cg IFI44L-1) in haemocytes significantly increased at 12 h after poly (I:C) stimulation, which were 2.39-fold (p < 0.05), 2.18-fold (p < 0.001), 1.74-fold (p < 0.05), and 2.89-fold (p < 0.01) of that in control group, respectively. The above results indicated that Cg PIAS negatively regulated the ISG expression by inhibiting STAT activation in oyster C. gigas. • The protein inhibitor of activated STAT (Cg PIAS) was identified from C. gigas. • Cg PIAS showed high expression level in haemocytes, gills and labial palps. • Cg PIAS responded to Poly (I:C) and r Cg IFNLP stimulation. • Cg PIAS negatively regulated the Cg ISGs expression by inhibiting STAT activation. [ABSTRACT FROM AUTHOR]

Dynamic network biomarkers (DNB) can identify the critical state or tipping point of a disease, thereby predicting rather than diagnosing the disease. However, it is difficult to apply the DNB theory to clinical practice because evaluating DNB at the critical state required the data of multiple samples on each individual, which are generally not available, and thus limit the applicability of DNB. In this study, we developed a novel method, i.e., single-sample DNB (sDNB), to detect early-warning signals or critical states of diseases in individual patients with only a single sample for each patient, thus opening a new way to predict diseases in a personalized way. In contrast to the information of differential expressions used in traditional biomarkers to “diagnose disease”, sDNB is based on the information of differential associations, thereby having the ability to “predict disease” or “diagnose near-future disease”. Applying this method to datasets for influenza virus infection and cancer metastasis led to accurate identification of the critical states or correct prediction of the immediate diseases based on individual samples. We successfully identified the critical states or tipping points just before the appearance of disease symptoms for influenza virus infection and the onset of distant metastasis for individual patients with cancer, thereby demonstrating the effectiveness and efficiency of our method for quantifying critical states at the single-sample level. [ABSTRACT FROM AUTHOR]

N6-methyladenosine (m6A) is a ubiquitous reversible epigenetic RNA modification that plays an important role in the regulation of post-transcriptional protein coding gene expression. Liver is a vital organ and plays a major role in metabolism with numerous functions. Information concerning the dynamic patterns of mRNA m6A methylation during postnatal development of liver has been long overdue and elucidation of this information will benefit for further deciphering a multitude of functional outcomes of mRNA m6A methylation. Here, we profile transcriptome-wide m6A in porcine liver at three developmental stages: newborn (0 day), suckling (21 days) and adult (2 years). About 33% of transcribed genes were modified by m6A, with 1.33 to 1.42 m6A peaks per modified gene. m6A was distributed predominantly around stop codons. The consensus motif sequence RRm6ACH was observed in 78.90% of m6A peaks. A negative correlation (average Pearson’s r = -0.45, P < 10−16) was found between levels of m6A methylation and gene expression. Functional enrichment analysis of genes consistently modified by m6A methylation at all three stages showed genes relevant to important functions, including regulation of growth and development, regulation of metabolic processes and protein catabolic processes. Genes with higher m6A methylation and lower expression levels at any particular stage were associated with the biological processes required for or unique to that stage. We suggest that differential m6A methylation may be important for the regulation of nutrient metabolism in porcine liver. [ABSTRACT FROM AUTHOR]

The dynamics of complex diseases are not always smooth; they are occasionally abrupt, i.e. there is a critical state transition or tipping point at which the disease undergoes a sudden qualitative shift. There are generally a few significant differences in the critical state in terms of gene expressions or other static measurements, which may lead to the failure of traditional differential expression-based biomarkers to identify such a tipping point. In this study, we propose a computational method, the direct interaction network-based divergence, to detect the critical state of complex diseases by exploiting the dynamic changes in multivariable distributions inferred from observable samples and local biomolecular direct interaction networks. Such a method is model-free and applicable to both bulk and single-cell expression data. Our approach was validated by successfully identifying the tipping point just before the occurrence of a critical transition for both a simulated data set and seven real data sets, including those from The Cancer Genome Atlas and two single-cell RNA-sequencing data sets of cell differentiation. Functional and pathway enrichment analyses also validated the computational results from the perspectives of both molecules and networks. [ABSTRACT FROM AUTHOR]

Trace amine-associated receptors (TAARs) are a class of G protein-coupled receptors, playing an immunomodulatory function in the neuroinflammatory responses. In the present study, a TAAR homologue with a 7tm_classA_rhodopsin-like domain (designated as Cg TAAR1L) was identified in oyster Crassostrea gigas. The abundant Cg TAAR1L transcripts were detected in visceral ganglia and haemocytes compared to other tissues, which were 55.35-fold and 32.95-fold (p < 0.01) of those in adductor muscle, respectively. The mRNA expression level of Cg TAAR1L in haemocytes significantly increased and reached the peak level at 3 h after LPS or Poly (I:C) stimulation, which was 4.55-fold and 12.35-fold of that in control group, respectively (p < 0.01). After the expression of Cg TAAR1L was inhibited by the injection of its targeted siRNA, the mRNA expression levels of interleukin17s (Cg IL17-1, Cg IL17-5 and Cg IL17-6), and defensin (Cg defh1) significantly decreased at 3 h after LPS stimulation, which was 0.51-fold (p < 0.001), 0.39-fold (p < 0.01), 0.48-fold (p < 0.05) and 0.41-fold (p < 0.05) of that in the control group, respectively. The nuclear translocation of Cg p65 protein was suppressed in the Cg TAAR1L-RNAi oysters. Furthermore, the number of Vibrio splendidus in the haemolymph of Cg TAAR1L-RNAi oysters significantly increased (4.11-fold, p < 0.001) compared with that in the control group. In contrast, there was no significant difference in phagocytic rate of haemocytes to V. splendidus in the Cg TAAR1L-RNAi oysters. These results indicated that Cg TAAR1L played an important role in the immune defense against bacterial infection by inducing the expressions of interleukin and defensin. • The trace amine associated receptor 1 Like (Cg TAAR1L) was identified from C. gigas. • Cg TAAR1L expression was significantly up-regulated after LPS stimulation. • The nucleus translocation of Cg p65 protein was suppressed in the Cg TAAR1L-RNAi oysters. • Cg TAAR1L involved in regulating expression of interleukinss and defensins response against Vibrio splendidus stimulation. [ABSTRACT FROM AUTHOR]

Axin-1, a negative regulator of Wnt signaling, is a versatile scaffold protein involved in centrosome separation and spindle assembly in mitosis, but its function in mammalian oogenesis remains unknown. Here we examined the localization and function of Axin-1 during meiotic maturation in mouse oocytes. Immunofluorescence analysis showed that Axin-1 was localized around the spindle. Knockdown of the Axin1 gene by microinjection of specific short interfering (si)RNA into the oocyte cytoplasm resulted in severely defective spindles, misaligned chromosomes, failure of first polar body (PB1) extrusion, and impaired pronuclear formation. However, supplementing the culture medium with the Wnt pathway activator LiCl improved spindle morphology and pronuclear formation. Downregulation of Axin1 gene expression also impaired the spindle pole localization of γ-tubulin/Nek9 and resulted in retention of the spindle assembly checkpoint protein BubR1 at kinetochores after 8.5 h of culture. Our results suggest that Axin-1 is critical for spindle organization and cell cycle progression during meiotic maturation in mouse oocytes. [ABSTRACT FROM AUTHOR]

The objective of this study was to examine the differences in calpain system, desmin degradation, pH values and water holding capacity ( WHC) between muscles of commercial Meishan and Duroc × Landrace × Yorkshire crossbred pigs. Meishan pork presented better WHC evidenced by lower purge loss at days 1 and 3 and less centrifugation loss at day 1 post mortem ( P < 0.05). pH values at 45 min post mortem in Meishan pork were significantly higher compared to crossbred pork ( P < 0.05). Calpain-1 messenger RNA ( mRNA) expression was lower in Meishan pork compared to that from crossbred pork ( P < 0.05). Additionally, calpain-1 activity, the ratio of calpain-1 to calpastatin activity and desmin degradation were lower in Meishan pork compared to those from crossbred pork samples ( P < 0.05). The results indicate that the calpain system including mRNA expression and activity were different between commercial Meishan and crossbred pork resulting in difference in the degree of desmin degradation during post mortem aging. pH values at 45 min and 24 h post mortem rather than calpain activity and desmin degradation could explain the higher water holding capacity in commercial Meishan pork. [ABSTRACT FROM AUTHOR]

Recently, we have successfully obtained functional IPCs efficiently from umbilical cord blood-derived mesenchymal stem cells by using hypoxia treatment. In this study, we further elaborated that the improved function and viability of IPCs are the result of the interaction β cell development pathway and c-Met/HGF axis induced by hypoxia. We found that hypoxia induced c-MET elevation is efficiently initiated the early stage differentiation IPCs from MSCs, and HGF improved the fully differentiation of IPCs by inducing the expression of NGN3. This finding may contribute to understanding β cell development and the development of stem cell therapy for diabetes. [ABSTRACT FROM AUTHOR]