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Ginseng, an important medicinal plant, is characterized by its main active component, ginsenosides. Among more than 40 ginsenosides, Rg1 is one of the ginsenosides used for measuring the quality of ginseng. Therefore, the identification and characterization of genes for Rg1 biosynthesis are important to elucidate the molecular basis of Rg1 biosynthesis. In this study, we utilized 39,327 SNPs and the corresponding Rg1 content from 344 core ginseng cultivars from Jilin Province. We conducted a genome-wide association study (GWAS) combining weighted gene co-expression network analysis (WGCNA), SNP-Rg1 content association analysis, and gene co-expression network analysis; three candidate Rg1 genes (PgRg1-1, PgRg1-2, and PgRg1-3) and one crucial candidate gene (PgRg1-3) were identified. Functional validation of PgRg1-3 was performed using methyl jasmonate (MeJA) regulation and RNAi, confirming that this gene regulates Rg1 biosynthesis. The spatial–temporal expression patterns of the PgRg1-3 gene and known key enzyme genes involved in ginsenoside biosynthesis differ. Furthermore, variations in their networks have a significant impact on Rg1 biosynthesis. This study established an accurate and efficient method for identifying candidate genes, cloned a novel gene controlling Rg1 biosynthesis, and identified 73 SNPs significantly associated with Rg1 content. This provides genetic resources and effective tools for further exploring the molecular mechanisms of Rg1 biosynthesis and molecular breeding. [ABSTRACT FROM AUTHOR]

At present, the mechanism of fluorosis-induced damage to the hepatic system is unclear. Studies have shown that excess fluoride causes some degree of damage to the liver, including inflammation. The SDF-1/CXCR4 signaling axis has been reported to have an impact on the regulation of inflammation in human cells. In this study, we investigated the role of the SDF-1/CXCR4 signaling axis and related inflammatory factors in fluorosis through in vitro experiments on human hepatic astrocytes (LX-2) cultured with sodium fluoride. CCK-8 assays showed that the median lethal dose at 24 h was 2 mmol/l NaF, and these conditions were used for subsequent enzyme-linked immunosorbent assays (ELISAs) and quantitative real-time polymerase chain reaction (qPCR) analysis. The protein expression levels of SDF-1/CXCR4 and the related inflammatory factors nuclear factor-κB (NF-κB), interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α) and interleukin 1β (IL-1β) were detected by ELISAs from the experimental and control groups. The mRNA expression levels of these inflammatory indicators were also determined by qPCR in both groups. Moreover, the expression levels of these factors were significantly higher in the experimental group than in the control group at both the protein and mRNA levels (P < 0.05). Excess fluorine may stimulate the SDF-1/CXCR4 signaling axis, activating the inflammatory NF-κB signaling pathway and increasing the expression levels of the related inflammatory factors IL-6, TNF-α and IL-1β. Identification of this mechanism is important for elucidating the pathogenesis of fluorosis-induced liver injury. [ABSTRACT FROM AUTHOR]

Background: Cervical cancer is one of the most common gynecological malignancies. Previous studies have shown that the ethanol extract of Sophora moorcroftiana seeds (EESMS) possesses an antiproliferative effect on several tumors in vitro. Therefore, in this study, we assessed the impact of EESMS on human cervical carcinoma (HeLa) cell proliferation. Methods: The proliferation and apoptotic effects of HeLa cells treated with EESMS were evaluated using 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide assay, dual acridine orange/ethidium bromide double staining, flow cytometry, and western blotting. Single-cell level atomic force microscopy (AFM) was conducted to detect the mechanical properties of HeLa cells, and proteomics and bioinformatics methods were used to elucidate the molecular mechanisms of EESMS. Results: EESMS treatment inhibited HeLa cell proliferation by blocking the G0/G1 phase, increasing the expression of Caspase-3 and affecting its mechanical properties, and the EESMS indicated no significant inhibitory effect on mouse fibroblasts L929 cell line. In total, 218 differentially expressed proteins were identified using two-dimensional electrophoresis, and eight differentially expressed proteins were successfully identified using matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry. The differentially expressed proteins were involved in various cellular and biological processes. Conclusion: This study provides a perspective on how cells change through biomechanics and a further theoretical foundation for the future application of Sophora moorcroftiana as a novel low-toxicity chemotherapy medication for treating human cervical cancer. [ABSTRACT FROM AUTHOR]

Complex human traits are influenced by variation in regulatory DNA through mechanisms that are not fully understood. Because regulatory elements are conserved between humans and mice, a thorough annotation of cis regulatory variants in mice could aid in further characterizing these mechanisms. Here we provide a detailed portrait of mouse gene expression across multiple tissues in a three-way diallel. Greater than 80% of mouse genes have cis regulatory variation. Effects from these variants influence complex traits and usually extend to the human ortholog. Further, we estimate that at least one in every thousand SNPs creates a cis regulatory effect. We also observe two types of parent-of-origin effects, including classical imprinting and a new global allelic imbalance in expression favoring the paternal allele. We conclude that, as with humans, pervasive regulatory variation influences complex genetic traits in mice and provide a new resource toward understanding the genetic control of transcription in mammals.

Panax ginseng as a traditional medicinal plant with a long history of medicinal use. Ginsenoside Ro is the only oleanane-type ginsenoside in ginseng, and has various pharmacological activities, including anti-inflammatory, detoxification, and antithrombotic activities. UDP-dependent glycosyltransferase (UGT) plays a key role in the synthesis of ginsenoside, and the excavation of UGT genes involved in the biosynthesis of ginsenoside Ro has great significance in enriching ginsenoside genetic resources and further revealing the synthesis mechanism of ginsenoside. In this work, ginsenoside-Ro-synthesis-related genes were mined using the P. ginseng reference-free transcriptome database. Fourteen hub transcripts were identified by differential expression analysis and weighted gene co-expression network analysis. Phylogenetic and synteny block analyses of PgUGAT252645, a UGT transcript among the hub transcripts, showed that PgUGAT252645 belonged to the UGT73 subfamily and was relatively conserved in ginseng plants. Functional analysis showed that PgUGAT252645 encodes a glucuronosyltransferase that catalyzes the glucuronide modification of the C3 position of oleanolic acid using uridine diphosphate glucuronide as the substrate. Furthermore, the mutation at 622 bp of its open reading frame resulted in amino acid substitutions that may significantly affect the catalytic activity of the enzyme, and, as a consequence, affect the biosynthesis of ginsenoside Ro. Results of the in vitro enzyme activity assay of the heterologous expression product in E. coli of PgUGAT252645 verified the above analyses. The function of PgUGAT252645 was further verified by the result that its overexpression in ginseng adventitious roots significantly increased the content of ginsenoside Ro. The present work identified a new UGT gene involved in the biosynthesis of ginsenoside Ro, which not only enriches the functional genes in the ginsenoside synthesis pathway, but also provides the technical basis and theoretical basis for the in-depth excavation of ginsenoside-synthesis-related genes. [ABSTRACT FROM AUTHOR]

Simple Summary: Adventitious root formation is a significant limiting factor in the vegetative propagation of economically important plants. Owing to the low germination rates and survival of conventional seed propagation, vegetative propagation remains the best option for large-scale production. Generally, there is a lack of competency for elite plant species cuttings or explants to form adventitious roots. The molecular-level studies of the adventitious root formation have not been explored in many species, such as ramie. As the WUSCEL-related homeobox gene family plays a critical role in promoting vegetative organs and stem cell functioning, we investigated their potential role in adventitious root formation in ramie using genome-wide characterization, gene structure, and expression analysis. The overall result indicated their possible involvement in rooting ramie cuttings. This study thus increases our understanding of the role of these genes and lays a foundation for further studies. A WUSCHEL-related homeobox (WOX) gene family has been implicated in promoting vegetative organs to embryonic transition and maintaining plant embryonic stem cell identity. Using genome-wide analysis, we identified 17 candidates, WOX genes in ramie (Boehmeria nivea). The genes (BnWOX) showed highly conserved homeodomain regions typical of WOX. Based on phylogenetic analysis, they were classified into three distinct groups: modern, intermediate, and ancient clades. The genes displayed 65% and 35% collinearities with their Arabidopsis thaliana and Oryza sativa ortholog, respectively, and exhibited similar motifs, suggesting similar functions. Furthermore, four segmental duplications (BnWOX10/14, BnWOX13A/13B, BnWOX9A/9B, and BnWOX6A/Maker00021031) and a tandem-duplicated pair (BnWOX5/7) among the putative ramie WOX genes were obtained, suggesting that whole-genome duplication (WGD) played a role in WOX gene expansion. Expression profiling analysis of the genes in the bud, leaf, stem, and root of the stem cuttings revealed higher expression levels of BnWOX10 and BnWOX14 in the stem and root and lower in the leaf consistent with the qRT-PCR analysis, suggesting their direct roles in ramie root formation. Analysis of the rooting characteristics and expression in the stem cuttings of sixty-seven different ramie genetic resources showed a possible involvement of BnWOX14 in the adventitious rooting of ramie. Thus, this study provides valuable information on ramie WOX genes and lays the foundation for further research. [ABSTRACT FROM AUTHOR]

The protein phosphatase 2C (PP2C), a key regulator of the ABA signaling pathway, plays important roles in plant growth and development, hormone signaling, and abiotic stress response. Although the PP2C gene family has been identified in many species, systematic analysis was still relatively lacking in ramie (Boehmeria nivea L.). In the present study, we identified 63 BnPP2C genes from the ramie genome, using bioinformatics analysis, and classified them into 12 subfamilies, and this classification was consistently supported by their gene structures and conserved motifs. In addition, we observed that the functional differentiation of the BnPP2C family of genes was restricted and that fragment replication played a major role in the amplification of the BnPP2C gene family. The promoter cis-regulatory elements of BnPP2C genes were mainly involved in light response regulation, phytohormone synthesis, transport and signaling, environmental stress response and plant growth and development regulation. We identified BnPP2C genes with tissue specificity, using ramie transcriptome data from different tissues, in rhizome leaves and bast fibers. The qRT-PCR results showed that the BnPP2C1, BnPP2C26 and BnPP2C27 genes had a strong response to drought, high salt and ABA, and there were a large number of stress-responsive elements in the promoter region of BnPP2C1 and BnPP2C26. The results suggested that BnPP2C1 and BnPP2C26 could be used as the candidate genes for drought and salt tolerance in ramie. These results provide a reference for further studies on the function of the PP2C gene and advance the development of the mechanism of ramie stress response, with a view to providing candidate genes for the molecular breeding of ramie for drought and salt tolerance. [ABSTRACT FROM AUTHOR]

Sodium nitroprusside (SNP), as a nitric oxide donor, is widely used in postharvest fruit physiology and metabolism. Our previous study has indicated that SNP plays a crucial role in postharvest browning control of rambutan, but the molecular mechanism underlying this process is still unclear. In this research, we investigated the gene expression and function of postharvest rambutan in response to SNP during browning. We found 7336 differentially expressed genes (DEGs), among which 2206 were upregulated and 5130 were downregulated. Gene Ontology (GO) enrichment as well as Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed, and the real‐time quantitative PCR (qPCR) data were consistent with transcriptome data. The DEGs relevant to rambutan pericarp browning were mainly involved in anthocyanin biosynthesis, phenolic oxidation, reactive oxygen species (ROS) production, and energy supply. It was shown that SNP regulated the synthesis and degradation of anthocyanins, accumulation of phenols, level of ROS and energy metabolism to suppress the postharvest browning of rambutan. Also, one WRKY transcription factor involved in ROS metabolism was observed to be differentially regulated. These findings add to our insights into the molecular mechanisms of the SNP‐induced browning delays of rambutan, which has implications for subsequent studies on molecular mechanisms of fruit browning. [ABSTRACT FROM AUTHOR]

Tobacco smoking is a major known risk factor for lung cancer. While micronutrients, especially those involved in maintaining DNA integrity and regulating gene expression, may be protective, research on this association is limited. This report aimed to investigate associations of total folate, 5‐methyltetrahydrofolate (5‐mTHF) and vitamin B12 with incident risk of lung cancer, and whether the associations vary by smoking status. A nested case‐control study with 490 incident lung cancer cases and 490 controls matched by age (±1 year), sex, residence, and center, drawn from a community‐based prospective study in China, was conducted from 2016 to 2019. 5‐mTHF accounted for the majority of total folate. Only 4.4% had detectable unmetabolized folic acid. Lung cancer cases had lower levels of 5‐mTHF compared to controls. There was an inverse, nonlinear association between 5‐mTHF and lung cancer, which persisted after adjustment for covariables (P for trend =.001). Compared to the lowest 5‐mTHF quartile, those in higher quartiles had lower risks of lung cancer: second quartile OR = 0.65; 95% CI: 0.45‐0.93; third quartile OR = 0.50; 95% CI: 0.34‐0.74; fourth quartile OR = 0.56; 95% CI: 0.38‐0.83. This inverse association was more pronounced among ever smokers; consistently, the highest risk of lung cancer (OR = 3.21, 95% CI: 1.97‐5.24) was observed among ever smokers with low 5‐mTHF levels compared to participants who never smoked and had higher 5‐mTHF levels. Vitamin B12 was not associated with lung cancer risk. In this sample of Chinese adults without confounding by unmetabolized folic acid, higher levels of 5‐mTHF were associated with lower risk of incident lung cancer. [ABSTRACT FROM AUTHOR]

Purpose. Retinal ischemia–reperfusion injury (RIRI) is the basis of the pathology that leads to many retinal diseases and induces necroptosis and apoptosis. Tumor necrosis factor-α (TNF-α) is critically involved in necroptosis and apoptosis. Delta-opioid receptor (DOR) activation inhibits TNF-α release in our previous studies, it might prevent necroptosis and apoptosis by inhibiting the release of TNF-α. However, the role of TNF-α and DOR in necroptosis and apoptosis of retinal pigment epithelial (RPE) cells remains largely unknown. Here, we explored the mechanisms of TNF-α and DOR in necroptosis and apoptosis using an oxygen-glucose deprivation/reoxygenation (OGD/R) model of adult retinal pigment epithelial cell line-19 (ARPE19) cells. Materials and Methods. ARPE19 cells were exposed to OGD/R conditions to mimic RIRI in vitro. Cell viability was quantified using the Cell Counting Kit-8 (CCK-8) assay. Morphological changes were observed by inverted microscopy. TNF-α protein levels in cell lysates were measured by enzyme-linked immunosorbent assay (ELISA). The DOR agonist TAN-67 and antagonist naltrindole (NTI) were used to pretreat cells for 1 or 2 hours before OGD24/R36 administration. Calcein acetoxymethylester/propidium iodide (Calcein-AM/PI) and Terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) staining were used to detect necroptotic and apoptotic ARPE19 cells, respectively. The protein expression of DOR, p-RIP1 (RIP1), p-RIP3 (RIP3), p-MLKL (MLKL), and cleaved Caspase3 (Caspase3) was measured by western blotting. Results. OGD severely damaged ARPE19 cells. Prolonged reoxygenation significantly increased TNF-α level and decreased DOR expression in ARPE19 cells. Pretreatment with the DOR agonist TAN-67 (10 µM) significantly improved ARPE19 cell viability after OGD24/R36 by reducing the number of necroptotic and apoptotic cells. Furthermore, DOR activation significantly inhibited TNF-α release and suppressed the expression of proteins related to necroptosis and apoptosis, including p-RIP1, p-RIP3, p-MLKL, and cleaved Caspase3, after OGD24/R36. This effect was reversed by the DOR antagonist NTI. Conclusion. These results strongly suggest that DOR activation inhibits necroptosis and apoptosis by decreasing TNF-α release, leading to the prevention of OGD/R-induced injury in ARPE19 cells. This study provides an innovative idea for clinical treatment strategies for retinal damage and vision loss due to RIRI. [ABSTRACT FROM AUTHOR]

Genes are the keys to deciphering the molecular mechanism underlying a biological trait and designing approaches desirable for plant genetic improvement. Ginseng is an important medicinal herb in which ginsenosides have been shown to be the major bioactive component; however, only a few genes involved in ginsenoside biosynthesis have been cloned through orthologue analysis. Here, we report the identification of 21 genes controlling Rb1 biosynthesis by stepwise ginseng transcriptome and Rb1 content integrated analysis. We first identified the candidate genes for Rb1 biosynthesis by integrated analysis of genes with the trait from four aspects, including gene transcript differential expression between highest- and lowest-Rb1 content cultivars, gene transcript expression–Rb1 content correlation, and biological impacts of gene mutations on Rb1 content, followed by the gene transcript co-expression network. Twenty-two candidate genes were identified, of which 21 were functionally validated for Rb1 biosynthesis by gene regulation, genetic transformation, and mutation analysis. These genes were strongly correlated in expression with the previously cloned genes encoding key enzymes for Rb1 biosynthesis. Based on the correlations, a pathway for Rb1 biosynthesis was deduced to indicate the roles of the genes in Rb1 biosynthesis. Moreover, the genes formed a strong co-expression network with the previously cloned Rb1 biosynthesis genes, and the variation in the network was associated with the variation in the Rb1 content. These results indicate that Rb1 biosynthesis is a process of correlative interactions among Rb1 biosynthesis genes. Therefore, this study provides new knowledge, 21 new genes, and 96 biomarkers for Rb1 biosynthesis useful for enhanced research and breeding in ginseng. [ABSTRACT FROM AUTHOR]

Oncogenic RAS mutations are common in multiple myeloma (MM), an incurable malignancy of plasma cells. However, the mechanisms of pathogenic RAS signaling in this disease remain enigmatic and difficult to inhibit therapeutically. We employ an unbiased proteogenomic approach to dissect RAS signaling in MM. We discover that mutant isoforms of RAS organize a signaling complex with the amino acid transporter, SLC3A2, and MTOR on endolysosomes, which directly activates mTORC1 by co-opting amino acid sensing pathways. MM tumors with high expression of mTORC1-dependent genes are more aggressive and enriched in RAS mutations, and we detect interactions between RAS and MTOR in MM patient tumors harboring mutant RAS isoforms. Inhibition of RAS-dependent mTORC1 activity synergizes with MEK and ERK inhibitors to quench pathogenic RAS signaling in MM cells. This study redefines the RAS pathway in MM and provides a mechanistic and rational basis to target this mode of RAS signaling. RAS mutations are commonly found in multiple myeloma (MM). Here, the authors show that oncogenic RAS mutations activate mTORC1 signalling in MM and combining mTORC1 and MEK/ERK inhibitors synergize to improve survival in preclinical models. [ABSTRACT FROM AUTHOR]

Background: Although it has a poor prognosis, patients with lung adenocarcinoma (LUAD) have a relatively higher 5‐year survival period. Thus, it is necessary to identify effective prognostic markers to evaluate the effect of early treatment. RS1 gene encodes retinoschisin, a key protein in congenital retinoschisis, while few studies have been reported on the association between RS1 and cancer prognosis. Methods: We performed bioinformatic analyses based on the data obtained from The Cancer Genome Atlas and Gene Expression Omnibus databases to demonstrate the expression level of RS1 was related to the LUAD prognosis and our findings were verified in‐vitro and clinical samples. Then, we explored the potential mechanism of how RS1 expression influenced the prognosis of LUAD. Results: Compared with normal tissues, the RS1 expression was significantly lower in tumor tissues. The Multivariate Cox regression model showed that RS1 could be used as an independent prognostic indicator. Furthermore, we found significant differences in immune cell infiltration between RS1 high and low expression groups, and the proteasome pathway was found enriched in RS1 low expression samples. Conclusion: In conclusion, our study suggests that RS1 is a novel prognostic biomarker for LUAD. Differences in immune cell infiltration and signaling pathways may contribute to the poor prognosis of LUAD caused by low RS1 expression. [ABSTRACT FROM AUTHOR]

In TCM opinion, most of pneumonia is related to "lung heat". Sophora davidii (Franch.) Skeels flower was first documented in "Guizhou Herbal Medicine", and was recorded as having functions of clearing heat, detoxifying, and cooling blood. It can be used to treat lung heat cough. To investigate main mechanisms of Sophora davidii flower extract (SDFE) in Treating LPS-induced acute Pneumonia. Acute pneumonia models on BEAS-2B cells and rats were established using LPS. The rat model was used to verified the protective effects of SDFE through HE staining, lung tissue W/D ratio assay, white blood cell count analysis, and ammonia-induced coughing test. Network pharmacology was applied to predict the active compounds, core targets and main pathways of SDFE in treating acute pneumonia. Western Blot and ELISA kits were employed to validate representative proteins in selected pathway in vivo and in vitro. HE staining, lung tissue W/D ratio assay, white blood cell count analysis, and ammonia-induced coughing test showed SDFE could improve pathological features (leukocyte infiltration, pulmonary edema, lung injury and cough). Network pharmacology indicated MAPK/NF-κB pathway was the most relevant pathway. SDFE could significantly inhibit the expression of Fos and Jun, and the phosphorylation levels of p38, ERK, JNK, NF-κB and IκB. It also down-regulated the expression of pro-inflammatory factors (TNF-α, IL-6 and IL-1β). SDFE can exert protective effects against acute pneumonia through the MAPK/NF-κB signaling pathway. [Display omitted] • SDFE effectively improves symptoms of LPS-induced acute pneumonia in rats. • SDFE inhibits key pro-inflammatory factors (IL-6, IL-1β, TNF-α) and exhibits significant anti-inflammatory effects. • SDFE suppresses the MAPK/NF-κB pathway by inhibiting the expression of Fos, Jun, and phosphorylation of p38, ERK, JNK, NF-κB, and IκB. • Network pharmacology was applied to predict the core targets and main pathways of SDFE in treating acute pneumonia. [ABSTRACT FROM AUTHOR]

Background. Despite the constant iteration of small-molecule inhibitors and immune checkpoint inhibitors, PRAD (prostate adenocarcinoma) patients with distant metastases and biochemical recurrence maintain a poor survival outcome along with an increasing morbidity in recent years. N7-Methylguanine, a new-found type of RNA modification, has demonstrated an essential role in tumor progression but has hardly been studied for its effect on prostate carcinoma. The current study aimed to seek m7G (N7-methylguanosine) related prognostic biomarkers and potential targets for PRAD treatment. Methods. 42 genes related to m7G were collected from former literatures and GSEA (Gene Set Enrichment Analysis) website. Then, RNA-seq (RNA sequencing) and clinical data from TCGA-PRAD (The Cancer Genome Atlas-Prostate) cohort were retrieved to screen the differentially expressed m7G genes to further construct a multivariate Cox prognostic model for PRAD. Next, GSE116918, a prostate cancer cohort acquired from GEO (Gene Expression Omnibus) database, was analyzed for the external validation group to assess the ability to predict BFFS (biochemical failure-free survival) of our m7G prognostic signature. Kaplan-Meier, ROC (receiver operator characteristic), AUC (areas under ROC curve), and calibration curves were adopted to display the performance of this prognostic signature. In addition, immune infiltration analysis was implemented to evaluate the effect of these m7G genes on immunoinfiltrating cells. Correlation with drug susceptibility of the m7G signature was also analyzed by matching drug information in CellMiner database. Results. The m7G-related prognostic signature, including three genes (EIF3D, EIF4A1, LARP1) illustrated superior prognostic ability for PRAD in both training and validation cohorts. The 5-year AUC were 0.768 for TCGA-PRAD and 0.608 for GSE116918. It can well distinguish patients into different risk groups of biochemical recurrence (p =1e-04 for TCGA-PRAD and p =0.0186 for GSE116918). Immune infiltration analysis suggested potential regulation of m7G genes on neutrophils and dendritic cells in PRAD. Conclusions. A m7G-related prognostic signature was constructed and validated in the current study, giving new sights of m7G methylation in predicting the prognostic and improving the treatment of PRAD. [ABSTRACT FROM AUTHOR]

Objective To study the correlation of the expression of Lipin1 in visceral adipose tissue and Lipin2 in liver tissue with hepatic fat content in rats with intrauterine growth retardation (IUGR). Methods Pregnant rats were given a low-protein (10% protein) diet during pregnancy to establish a model of IUGR in neonatal rats. The pregnant rats in the control group were given a normal-protein (21% protein) diet during pregnancy. The neonatal rats were weighed and liver tissue was collected on day 1 and at weeks 3, 8, and 12 after birth, and visceral adipose tissue was collected at weeks 3, 8, and 12 after birth. The 3.0T 1H-magnetic resonance spectroscopy was used to measure hepatic fat content at weeks 3, 8, and 12 after birth. Real-time PCR was used to measure mRNA expression levels of Lipin2 in liver tissue and Lipin1 in visceral adipose tissue. Western blot was used to measure protein levels of Lipin2 in liver tissue and Lipin1 in visceral adipose tissue. A Pearson correlation analysis was performed to investigate the correlation of mRNA and protein expression of Lipin with hepatic fat content. Results The IUGR group had significantly higher mRNA and protein expression levels of Lipin1 in visceral adipose tissue than the control group at weeks 3, 8, and 12 after birth (P<0.05). Compared with the control group, the IUGR group had significantly lower mRNA and protein expression levels of Lipin2 in liver tissue on day 1 after birth and significantly higher mRNA and protein expression levels of Lipin2 at weeks 1, 3, 8, and 12 after birth (P<0.05). At week 3 after birth, there was no significant difference in hepatic fat content between the IUGR and control groups (P>0.05), while at weeks 8 and 12 after birth, the IUGR group had a significantly higher hepatic fat content than the control group (P<0.05). The protein and mRNA expression levels of Lipin1 were positively correlated with hepatic fat content (r=0.628 and 0.521 respectively; P<0.05), and the protein and mRNA expression levels of Lipin2 were also positively correlated with hepatic fat content (r=0.601 and 0.524 respectively; P<0.05). Conclusions Upregulation of the mRNA and protein expression levels of Lipin1 in visceral adipose tissue and Lipin2 in liver tissue can increase hepatic fat content in rats with IUGR and may be associated with obesity in adulthood. [ABSTRACT FROM AUTHOR]

This document is a retraction notice for an article titled "UPF1 Participates in the Progression of Endometrial Cancer by Inhibiting the Expression of lncRNA PVT1." The retraction is due to concerns about the duplication of images from other unrelated articles in Figures 2 and 3. The authors did not respond to inquiries or provide an explanation for the duplicated images. The retracted article will remain online but will be marked as "Retracted." [Extracted from the article]

Background and Aim: Epigenetic modification is an important part of the pathogenesis of inflammatory bowel disease (IBD). Some studies proved that p62 was involved in inflammatory response and upregulated in IBD patients, and histone modification plays an important role in regulating p62 expression. SETD8, a histone H4K20 methyltransferase, has been reported downregulated in some inflammatory diseases. Here, we investigated the role of SETD8 in the development of IBD and its underlying mechanisms. Methods: An inflammatory cell model was established to elucidate whether SETD8 involved in inflammatory response in macrophages. Three percent dextran sodium sulfate‐induced colitis murine model injection with SETD8 inhibitor was used in our study to investigate whether SETD8 inhibition can affect the progress of IBD. The expression of SETD8 and p62 was measured by qRT‐PCR and western blot. The mRNA level of inflammatory cytokines was analyzed by qRT‐PCR. In addition, chromatin immunoprecipitation‐PCR was performed to identify the mechanism by which SETD8 regulates p62. Results: SETD8 expression obviously decreased in vitro, in vivo models and in IBD patients. In lipopolysaccharide‐activated RAW264.7 cells, knockdown of SETD8 significantly increased the mRNA expression of inducible nitric oxide synthase, cyclooxygenase‐2, TNF‐α, IL‐6, IL‐1β, and MCP‐1. Based on the dataset, we verified that p62 was a target gene of SETD8 and chromatin immunoprecipitation‐PCR assay identified that silence of SETD8 distinctly decreases the H4K20me1 enrichment in the promoter of p62. Moreover, silencing of p62 partly reverses the SETD8 inhibition‐mediated pro‐inflammatory effect in vitro. Finally, SETD8 pharmacological inhibitor (UNC0379) aggravated the disease progression in dextran sodium sulfate‐induced murine colitis. Conclusion: Our findings elucidate an epigenetic mechanism by which SETD8 regulates the p62 expression and restrains the inflammatory response in colitis. Our result suggests that targeting SETD8 may be a promising therapy for IBD. [ABSTRACT FROM AUTHOR]

Laryngeal cancer is a common type of head and neck malignancy. microRNA is implicated in the development and progression of various tumours. The present study aimed to explore the potential roles and mechanisms of miR‐646 in laryngeal carcinoma cells. We detected the expression of miR‐646 and observed that miR‐646 was reduced in laryngeal cell lines. Subsequently, the proliferation, migration and invasion of TU212 and TU686 cells were evaluated using CCK‐8 assays, cell proliferation ELISA BrdU and transwell assays after transfection with miR‐646 mimic. Overexpression of miR‐646 attenuated the proliferative and invasive abilities of TU212 and TU686 cells. Dual luciferase reporter assay confirmed that glutathione peroxidase 1 (GPX1) is a direct target of miR‐646. Interestingly, restoration of GPX1 promoted cell proliferation and migration, and reversed the biological activities of miR‐646 in cell proliferation and migration. It is worth noting that miR‐646 overexpression blocked the activation of PI3K/AKT pathway, and this was partly abrogated by GPX1. 740Y‐P, a PI3K agonist abolished the effects of miR‐646 on cell proliferation and invasion. Taken together, miR‐646 prohibited the proliferation and invasion of laryngeal carcinoma cells through the PI3K/AKT pathway via targeting GPX1. [ABSTRACT FROM AUTHOR]

The immune response within the tumor microenvironment plays a key role in tumorigenesis and determines the clinical outcomes of head and neck squamous cell carcinoma (HNSCC). However, to date, very limited robust and reliable immunological biomarkers have been developed that are capable of estimating prognosis in HNSCC patients. In this study, we aimed to identify the effects of novel immune-related gene signatures (IRGs) that can predict HNSCC prognosis. Based on gene expression profiles and clinical data of HNSCC patient cohorts from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database, a total of 439 highly variable expressed immune-related genes (including 239 upregulated and 200 downregulated genes) were identified by using differential gene expression analysis. Pathway enrichment analysis indicated that these immune-related differentially expressed genes were enriched in inflammatory functions. After process screening in the training TCGA cohort, six immune-related genes (PLAU , STC2 , TNFRSF4 , PDGFA , DKK1 , and CHGB) were significantly associated with overall survival (OS) based on the LASSO Cox regression model. Integrating these genes with clinicopathological features, a multivariable model was built and suggested better performance in determining patients' OS in the testing cohort, and the independent validation cohort. In conclusion, a well-established model encompassing both immune-related gene signatures and clinicopathological factors would serve as a promising tool for the prognostic prediction of HNSCC. [ABSTRACT FROM AUTHOR]

Clear cell renal cell carcinoma (ccRCC) is the most common type of kidney tumor worldwide. Analysis of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases showed that the immune-related gene (IRG) hematopoietic cell signal transducer (HCST) could provide guidance for the diagnosis, prognosis, and treatment of ccRCC. The RNA-seq data of ccRCC tissues were extracted from two databases: TCGA (https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga) and GEO (https://www.ncbi.nlm.nih.gov/geo/). Corresponding clinical information was downloaded from TCGA. Immune-related gene data were extracted from the IMMPORT website (https://www.immport.org/). Differential analysis with R software (https://www.r-project.org/) was used to obtain a prognosis model of ccRCC IRGs. The differences were combined with the clinical data to assess the usefulness of the HCST as a prognostic biomarker. Based on data obtained from the Oncomine (https://www.oncomine.org/), Human Protein Atlas (https://www.proteinatlas.org/), and PubMed (https://pubmed.ncbi.nlm.nih.gov/) databases, the expression levels of the HCST in ccRCC, clinical-pathological indicators of relevance, and influence on prognosis were analyzed. Regulation of the HCST gene in ccRCC was assessed by gene set enrichment analysis (GSEA). In TCGA/GEO databases, the high HCST expression in tumor tissues was significantly correlated to the TMN stage, tumor grade, invasion depth, and lymphatic metastasis (p < 0.05). The overall survival (OS) of patients with high HCST gene expression was significantly lower than that of patients with low HCST gene expression (p < 0.001). Multivariate Cox regression analysis suggested that the HCST expression level [hazard ratio (HR) = 1.630, 95% confidence interval (CI) = 1.042–2.552], tumor cell grade (HR = 1.829, 95% CI = 1.115–3.001), and distant metastasis (HR = 2.634, 95%, CI = 1.562–4.442) were independent risk factors affecting the OS of ccRCC patients (all, p < 0.05). The GSEA study showed that there was significant enrichment in cell adhesion, tumorigenesis, and immune and inflammatory responses in HCST high expression samples. Hematopoietic cell signal transducer expression was closely associated with the levels of infiltrating immune cells around ccRCC tissues, especially dendritic cells (DCs). In conclusion, the present study suggested that the HCST was interrelated to the clinicopathology and poor prognosis of ccRCC. High HCST expression was also closely correlated with the levels of tumor-infiltrating immune cells, especially DCs. [ABSTRACT FROM AUTHOR]

Lineage-specific genes (LSGs) are defined as genes with sequences that are not significantly similar to those in any other lineage. LSGs have been proposed, and sometimes shown, to have significant effects in the evolution of biological function. In this study, two sets of Hanseniaspora spp. LSGs were identified by comparing the sequences of the Kloeckera apiculata genome and of 80 other yeast genomes. This study identified 344 Hanseniaspora -specific genes (HSGs) and 109 genes ('orphan genes') specific to K. apiculata. Three thousand three hundred thirty-one  K. apiculata genes that showed significant similarity to at least one sequence outside the Hanseniaspora were classified into evolutionarily conserved genes. We analyzed their sequence features, functional categories, gene origin, gene structure and gene expression. We also investigated the predicted cellular roles and Gene Ontology categories of the LSGs using functional inference. The patterns of the functions of LSGs do not deviate significantly from genome-wide average. The results showed that a few LSGs were formed by gene duplication, followed by rapid sequence divergence. Many of the HSGs and orphan genes exhibited altered expression in response to abiotic stress. Studying these LSGs might be helpful for understanding the molecular mechanism of yeast adaption. [ABSTRACT FROM AUTHOR]

Ginseng is a valuable herb of traditional Chinese medicine and ginsenosides, the main bioactive components of ginseng, have been proven to have multiple functions in human therapies and health. Methyl jasmonate (MeJA) is an elicitor that has been demonstrated to have a vital influence on ginsenoside biosynthesis. Quantitative real-time polymerase chain reaction (qRT-PCR) has been widely used in quantification of gene expressions. Here, we report the selection and validation of reference genes desirable for normalization of gene expressions quantified by qRT-PCR in ginseng hairy roots treated with MeJA. Twelve reference genes were selected as candidate genes, and their expressions were quantified by qRT-PCR, and analyzed by geNorm, NormFinder and BestKeeper. CYP and EF-1α were shown to be the most stable reference genes in geNorm, CYP was the most stable reference gene in NormFinder, and 18S was the most stable reference gene in BestKeeper. On this basis, we further quantified the relative expression levels of four genes encoding key enzymes that are involved in ginsenoside biosynthesis using CYP and 18S as the reference genes, respectively. Moreover, correlation analysis was performed between the quantified expressions of four genes and the ginsenoside content in MeJA-treated ginseng hairy roots. The results of relative expressions of the four genes quantified using CYP as the reference gene and their significant correlations with the ginsenoside content were better than those using 18S as the reference gene. The CYP gene, hence, was concluded as the most desirable reference gene for quantification of the expressions of genes in MeJA-treated ginseng hairy roots. This finding, therefore, provides information useful for gene research in ginseng, particularly in MeJA-treated ginseng hairy roots, which includes identification and characterization of genes involved in ginsenoside biosynthesis. [ABSTRACT FROM AUTHOR]

Sophora davidii (Franch.) Skeels Flower (SDF) is a characteristic folk medicine in Yunnan and Guizhou, which can be used to prevent the occurrence of tumors. The extract of SDF (SDFE) is confirmed to be antitumor by pre-experiment. However, effective components and anticancer mechanisms of SDFE are still unclear. The purpose of this study was to explore the material basis and action mechanisms of SDFE in the treatment of non-small cell carcinoma (NSCLC). UHPLC-Q-Exactive-Orbitrap-MS/MS was used to identify the chemical components of SDFE. The network pharmacology was applied to screen out the main active components, core genes and related signaling pathways of SDFE in treatment of NSCLC. Molecular docking was used to predict the affinity of major components and core targets. The database was applied to predict the mRNA and protein expression levels of core targets in NSCLC. Finally, the experiments in vitro were performed by CCK-8, flow cytometry and western blot (WB). In this study, 98 chemical components were identified by UHPLC-Q-Exactive- Orbitrap-MS/MS. 5 main active components (namely quercetin, genistein, luteolin, kaempferol, isorhamnetin), 10 core genes (namely TP53, AKT1, STAT3, SRC, MAPK3, EGFR, JUN, EP300, TNF, PIK3R1) and 20 pathways were screened out through network pharmacology. The 5 active ingredients were molecularly docked with the core genes, and most the LibDockScore values were higher than 100. The data collected from the database indicated that TP53, AKT1 and PIK3R1 were closely related to the occurrence of NSCLC. The results of experiment in vitro showed that SDFE promoted NSCLC cells apoptosis by down-regulating the phosphorylation of PI3K, AKT and MDM2, up-regulating the phosphorylation of P53, inhibiting the expression of Bcl-2 and up-regulating the expression of Bax. The combination of network pharmacology, molecular docking, database validation, and in vitro experimental validation effectively demonstrates that SDFE can promote cell apoptosis by regulating PI3K-AKT/MDM2-P53 signaling pathway, so as to treat NSCLC. [Display omitted] • 98 compounds of SDFE were identified by LC-MS/MS, and 77 were validated by reference substances. • SDFE could induce cell apoptosis through PI3K-AKT/MDM2-P53 signaling pathway in vitro. • Network pharmacology, molecular docking and database validation can effectively predict the anti-NSCLC mechanism of SDFE. [ABSTRACT FROM AUTHOR]

Background: Idiopathic pulmonary fibrosis (IPF) is a progressive and lethal fibrotic lung disease with an unknown aetiology. Persistent myofibroblast differentiation is a prominent feature of IPF. Cigarette smoking is a risk factor for IPF and an indicator of poor prognosis. Cigarette smoking induces endoplasmic reticulum (ER) stress, and it has been shown that ER stress promotes fibroblast-to-myofibroblast differentiation in lung fibrosis. In this study, we investigated whether cigarette smoke extract (CSE) promotes lung myofibroblast differentiation via the induction of ER stress. Objectives: Our study concentrates on exploring the relationship between smoking and ER stress in the differentiation of lung fibroblasts to myofibroblasts. Methods: Human embryonic lung fibroblasts (MRC-5 fibroblasts) were stimulated with various doses of CSE. Levels of α-smooth muscle actin (α-SMA) protein were evaluated by immunofluorescence and western blot analyses. ER stress was induced by thapsigargin (TG) and inhibited by 4-phenyl butyric acid (4-PBA). Protein levels of glucose-regulated protein-78 (GRP78), inositol-requiring enzyme 1 (IRE1), X box-binding protein-1 (XBP-1) and activating transcription factor 6 (ATF6) were determined by western blotting. GRP78 siRNA was transfected into MRC-5 cells using Lipofectamine RNAiMAX Reagent. Results: CSE at a concentration of 1.0% significantly increased α-SMA expression in MRC-5 cells. There was no significant cell apoptosis after cells were exposed to CSE. CSE treatment significantly increased the expression of GRP78, IRE1, XBP-1 and ATF6 at the protein level at 48 h. Pretreatment with TG enhanced, whereas pretreatment with 4-PBA inhibited, the CSE-induced expression of α-SMA, GRP78 and XBP-1. Furthermore, knockdown of GRP78 blocked α-SMA expression in MRC-5 cells exposed to CSE. Conclusion: Our data suggested that CSE promotes lung fibroblast-to-myofibroblast differentiation by the induction of ER stress. [ABSTRACT FROM AUTHOR]

Introduction: TET2, a member of the Ten‐Eleven translocation gene family, catalyzes the conversion of 5‐methylcytosine to 5‐hydroxymethylcytosine in DNA. Low expression of TET2 has been reported as a prognostic factor for several types of malignancies in adult patients. However, there have been few data on the effect of TET2 mRNA level on the prognosis of children with ALL so far. Methods: In this study, TET2 expression of samples cryopreserved in the liquid nitrogen from January 1, 2007 through December 31, 2011 was retrospectively analyzed in 136 newly diagnosed ALL patients by real‐time polymerase chain reaction (PCR) assay. The patients' samples were divided into two groups by the median value of patients group and divided into TET2 low and TET2 high groups. Results: A total of 136 childhood ALL patients demonstrated lower TET2 expression than control group (P = .038). TET2 mRNA expression levels were correlated with the disease status. In addition, patients with low TET2 expression had lower platelet counts and lower CR rates. Survival analysis showed that low TET2 expression in children with ALL was associated with lower 5‐year overall survival (OS) (63% vs 88%, P = .011) and event‐free survival (EFS) (60% vs 85%, P = .003). Multivariate analysis revealed that low TET2 expression was an independent poor prognostic factor of OS and EFS. Conclusion: Low expression of TET2 in children with ALL is associated with poor prognosis and can be used as a molecular prognostic marker for risk group stratification. [ABSTRACT FROM AUTHOR]

Background: Adrenocortical carcinoma (ACC) is a rare endocrine malignancy with an unfavorable prognosis and limited treatment options. Nevertheless, no clinically applicable molecular markers have been identified for the progression of ACCs. DNA methylation alterations were found to contribute to the development of ACC in recent decades. Material and Methods: The aims of the current study was to identify the abnormally methylated differentially expressed genes (DEGs) in ACCs, and to elucidate the mechanistic basis for these changes. Analyses were conducted on gene expression and gene methylation profile datasets to identify the aberrantly methylated DEGs. The DAVID software was used to conduct the analyses of functional enrichment on screened genes. Finally, expression was validated, and the relationship between abnormally methylated DEGs and clinical features was determined via the Oncomine database and The Cancer Genome Atlas (TCGA). To further verify the altered expression and methylation status of our identified genes we also validated these changes at the tissue and cellular levels. Results: We screened and identified 92 differentially expressed genes and 802 abnormally methylated genes. Furthermore, seven aberrantly methylated and dysregulated genes were identified and validated, along with a number of functional enriched pathways. Among these seven genes, the expression or methylation status is significantly correlated with different pathological stages and overall rates of survival. In validation, the expression of seven genes were significantly altered and five genes were hypermethylated in ACC. Conclusions: Our study identified abnormally methylated DEGs and potentially affected pathways in ACCs, from which we could begin to understand the basic molecular mechanisms of these alterations. Moreover, these abnormally methylated genes might serve as therapeutic targets and biomarkers to allow ACC patients to be more precisely diagnosed and effectively treated. [ABSTRACT FROM AUTHOR]

We used a modified Walker-Mason scald burn rat model to demonstrate that Pseudomonas aeruginosa, a common opportunistic pathogen in the burn ward and notable biofilm former, establishes biofilms within deep partial-thickness burn wounds in rats.Deep partial-thickness burn wounds, ~10% of the TBSA, were created in anesthetized male Sprague-Dawley rats (350-450 g; n = 84). Immediately post-burn, 100 µl of P. aeruginosa in phosphate-buffered saline at 1 × 103, 1 × 104, or 1 × 105 cells/wound was spread over the burn surface . At 1, 3, 7, and 11 days post-burn, animals were euthanized and blood and tissue were collected for complete blood counts, colony-forming unit (CFU) counts, biofilm gene expression, histology, scanning electron microscopy (SEM), and myeloperoxidase activity in the burn eschar.P. aeruginosa developed robust biofilm wound infections, plateauing at ~1 × 109 CFU/g burn tissue within 7 days regardless of inoculum size. Expression of Pseudomonas alginate genes and other virulence factors in the infected wound indicated formation of mature P. aeruginosa biofilm within the burn eschar. Compared to un-inoculated wounds, P. aeruginosa infection caused both local and systemic immune responses demonstrated by changes in systemic neutrophil counts, histology, and myeloperoxidase activity within the burn wound. Additionally, SEM showed P. aeruginosa enmeshed within an extracellular matrix on the burn surface as well as penetrating 500-600 µm deep into the eschar.P. aeruginosa establishes biofilms within deep partial-thickness burn wounds and invades deep into the burned tissue. This new in vivo biofilm infection model is valuable for testing novel anti-biofilm agents to advance burn care. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Protein levels of Phox2a, mRNA and protein levels of Phox2b were elevated in the locus coeruleus from brain donors of MDD. • CSD significantly increased Phox2a and Phox2b expression in the rat locus coeruleus. • Corticosterone administration increased Phox2b protein levels in the rat locus coeruleus. • Corticosterone increased Phox2a and Phox2b expression in the SK-SY5Y cells. • Corticosterone-induced increase in Phox2 expression may be mediated through corticosteroid receptors. Abstract Phox2a and Phox2b are two homeodomain transcription factors playing a pivotal role in the development of noradrenergic neurons during the embryonic period. However, their expression and function in adulthood remain to be elucidated. Using human postmortem brain tissues, rat stress models and cultured cells, this study aimed to examine the alteration of Phox2a and Phox2b expression. The results show that Phox2a and Phox2b are normally expressed in the human locus coeruleus (LC) in adulthood. Furthermore, the levels of Phox2a protein and mRNA and protein levels of Phox2b were significantly elevated in the LC of brain donors that suffered from the major depressive disorder, as compared to age-matched and psychiatrically normal control donors. Fischer 344 rats subjected to chronic social defeat showed higher mRNA and protein levels of Phox2a and Phox2b in the LC, as compared to non-stressed control rats. In rats chronically administered oral corticosterone, mRNA and protein levels of Phox2b, but not Phox2a, in the LC were significantly increased. In addition, the corticosterone-induced increase in Phox2b protein was reversed by simultaneous treatment with either mifepristone or spironolactone. Exposing SH-SY5Y cells to corticosterone significantly increased expression of Phox2a and Phox2b, which was blocked by corticosteroid receptor antagonists. Taken together, these experiments reveal that Phox2 genes are expressed throughout the lifetime in the LC of humans and Fischer 344 rats. Alterations in their expression may play a role in major depressive disorder and possibly other stress-related disorders through their modulatory effects on the noradrenergic phenotype. [ABSTRACT FROM AUTHOR]

Background: Platelet-derived growth factor alpha (PDGFRA) is a gene encoding tyrosine kinase receptor and both EGFR and PDGFRA activate tyrosine kinases. The implication of PGFRA in many cancers and its prognostic significance irrespective to EGFR status in spinal chordoma, gliomas, and uterine cancers have shown a need for its investigation in oral squamous cell carcinoma (OSCC). We investigated the prognostic value of PDGFRA mRNA expression in OSCC.Patients and Methods: The study was conducted in the department of oral maxillofacial surgery-head and neck oncology, at a tertiary hospital. The data on PDGFRA mRNA expression and immunohistochemical staining status in primary OSCC patients treated for curative surgery from 2010 to 2012 were analyzed. Univariate and multivariate analyses were performed with other cofactors for survival.Results: A total of 114 consecutive patients with primary OSCC who received treatment were studied. Thirty-one patients died of the disease. Strong PDGFRA immunohistochemical staining and high expression of PDGFRA mRNA were associated with positive pN status (P < .001), disease-free survival (P < .001), and overall survival (P < .001) in multivariate cox regression when all other factors such as pN status and histological grading were analyzed. Kaplan-Meier analysis revealed that the 2-year survival and 3-year survival of patients with PDGFRA mRNA low expression were 96.83%. However, 2-year survival for PDGFRA mRNA high expression level was 59.64%, which decreased to 45.57% by 3-years.Conclusion: PDGFRA overexpression in oral SCC, in respect to strong PDGFRA immunohistochemical staining and high PDGFRA mRNA expression, was positively associated with regional metastasis and reduced patient survival. [ABSTRACT FROM AUTHOR]

The accessibility of genomic DNA, as a key determinant of gene-related processes, is dependent on the packing density and structural dynamics of chromatin fiber. However, due to the highly dynamic and heterogeneous properties of chromatin fiber, it is technically challenging to study these properties of chromatin. Here, we report a strategy for dissecting the dynamics of chromatin fibers based on single-molecule magnetic tweezers. Using magnetic tweezers, we can manipulate the chromatin fiber and trace its extension during the folding and unfolding process under tension to investigate the dynamic structural transitions at single-molecule level. The highly accurate and reliable in vitro single-molecule strategy provides a new research platform to dissect the structural dynamics of chromatin fiber and its regulation by different epigenetic factors during gene expression. [ABSTRACT FROM AUTHOR]

Calcium-dependent protein kinases (CPKs) play an essential role in the regulation of pollen tube growth. Although CPK genes have been identified in maize, and some have been functionally characterized, the molecular function of ZmCPKs associated with pollen tube development remains less well studied. Here, we report that a pollen-specific CPK, ZmCPK32, is involved in the regulation of pollen germination and tube extension. ZmCPK32 exhibited CPK activity and was localized on the plasma membrane and punctate internal membrane compartments via N-terminal acylation. In situ hybridization and real-time PCR revealed that ZmCPK32 transcripts accumulated in pollen and expression was dramatically upregulated during shedding. To elucidate the function of this gene, we transiently expressed a ZmCPK32-GFP fusion protein in tobacco pollen using microparticle bombardment. ZmCPK32 accumulation inhibited pollen germination and reduced pollen tube growth, but this effect was abolished when the kinase-inactive variant was expressed, indicating that kinase activity is critical for its regulatory function. In addition, the plasma membrane localization of ZmCPK32 is essential for regulating polar growth, as pollen expressing the cytosol-localized kinase displayed reduced tube length but germinated well. Moreover, the constitutively active form of ZmCPK32 enhanced the reduction in the germination rate, indicating that the specific activation of ZmCPK32 via calcium ions at the cortical growth point is essential for regulating appropriate germination. The results suggest that ZmCPK32 is functionally associated with pollen tube growth, and could represent a potential target for breeding male-sterile maize. [ABSTRACT FROM AUTHOR]

Research advances and analysis in the non‑protein coding part of the human genome have suggested that microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) are associated with tumor initiation, growth and metastasis. Accumulating studies have demonstrated that a class of miRNAs and lncRNAs are dysregulated in hepatocellular carcinoma (HCC) and closely associated with tumorigenesis, diagnosis and prognosis. In the present study, integrative analysis of published data on multi‑level Gene Expression Omnibus (GEO) and a bioinformatics computational approach were used to predict regulatory mechanism networks among differentially expressed mRNAs, miRNAs, and lncRNAs. Firstly, nine microarray expression data sets of mRNAs, miRNAs, and lncRNAs associated with HCC were collected from GEO datasets. Secondly, a total of 628 mRNAs, 15 miRNAs, and 49 lncRNAs were differentially expressed in this integrative analysis. Following this, mRNA, miRNA and lncRNA regulatory or co‑expression networks were constructed. From the construction of the regulatory networks, five miRNAs and ten lncRNAs were identified as key differentially expressed noncoding RNAs associated with HCC progression. Finally, the regulatory effects of ten lncRNAs and miRNAs were validated. The study provides a novel insight into the understanding of the transcriptional regulation of HCC, and differentially expressed lncRNAs targeted and regulated by miRNAs were identified and validated in HCC specimens and cell lines. [ABSTRACT FROM AUTHOR]

Dynamin Guanosine Triphosphate hydrolases (GTPases) are best studied for their role in the terminal membrane fission process of clathrin-mediated endocytosis (CME), but they have also been proposed to regulate earlier stages of CME. Although highly enriched in neurons, dynamin-1 (Dyn1) is, in fact, widely expressed along with Dyn2 but inactivated in non-neuronal cells via phosphorylation by glycogen synthase kinase-3 beta (GSK3β) kinase. Here, we study the differential, isoform-specific functions of Dyn1 and Dyn2 as regulators of CME. Endogenously expressed Dyn1 and Dyn2 were fluorescently tagged either separately or together in two cell lines with contrasting Dyn1 expression levels. By quantitative live cell dual- and triple-channel total internal reflection fluorescence microscopy, we find that Dyn2 is more efficiently recruited to clathrin-coated pits (CCPs) than Dyn1, and that Dyn2 but not Dyn1 exhibits a pronounced burst of assembly, presumably into supramolecular collar-like structures that drive membrane scission and clathrin-coated vesicle (CCV) formation. Activation of Dyn1 by acute inhibition of GSK3β results in more rapid endocytosis of transferrin receptors, increased rates of CCP initiation, and decreased CCP lifetimes but did not significantly affect the extent of Dyn1 recruitment to CCPs. Thus, activated Dyn1 can regulate early stages of CME that occur well upstream of fission, even when present at low, substoichiometric levels relative to Dyn2. Under physiological conditions, Dyn1 is activated downstream of epidermal growth factor receptor (EGFR) signaling to alter CCP dynamics. We identify sorting nexin 9 (SNX9) as a preferred binding partner to activated Dyn1 that is partially required for Dyn1-dependent effects on early stages of CCP maturation. Together, we decouple regulatory and scission functions of dynamins and report a scission-independent, isoform-specific regulatory role for Dyn1 in CME. [ABSTRACT FROM AUTHOR]