Search

Background: WOX genes are a class of plant-specific transcription factors. The WUSCHEL-related homeobox (WOX) family is a member of the homeobox transcription factor superfamily. Previous studies have shown that WOX members play important roles in plant growth and development. However, studies of the WOX gene family in blueberry plants have not been reported. Results: In order to understand the biological function of the WOX gene family in blueberries, bioinformatics were used methods to identify WOX gene family members in the blueberry genome, and analyzed the basic physical and chemical properties, gene structure, gene motifs, promoter cis-acting elements, chromosome location, evolutionary relationships, expression pattern of these family members and predicted their functions. Finally, 12 genes containing the WOX domain were identified and found to be distributed on eight chromosomes. Phylogenetic tree analysis showed that the blueberry WOX gene family had three major branches: ancient branch, middle branch, and WUS branch. Blueberry WOX gene family protein sequences differ in amino acid number, molecular weight, isoelectric point and hydrophobicity. Predictive analysis of promoter cis-acting elements showed that the promoters of the VdWOX genes contained abundant light response, hormone, and stress response elements. The VdWOX genes were induced to express in both stems and leaves in response to salt and drought stress. Conclusions: Our results provided comprehensive characteristics of the WOX gene family and important clues for further exploration of its role in the growth, development and resistance to various stress in blueberry plants. [ABSTRACT FROM AUTHOR]

Both parasitoids and entomopathogenic fungi are becoming increasingly crucial for managing pest populations. Therefore, it is essential to carefully consider the potential impact of entomopathogenic fungi on parasitoids due to their widespread pathogenicity and the possible overlap between these biological control tools during field applications. However, despite their importance, little research has been conducted on the pathogenicity of entomopathogenic fungi on parasitoids. In our study, we aimed to address this knowledge gap by investigating the interaction between the well-known entomopathogenic fungus Beauveria bassiana, and the pupal endoparasitoid Pteromalus puparum. Our results demonstrated that the presence of B. bassiana significantly affected the survival rates of P. puparum under laboratory conditions. The pathogenicity of B. bassiana on P. puparum was dose- and time-dependent, as determined via through surface spraying or oral ingestion. RNA-Seq analysis revealed that the immune system plays a primary and crucial role in defending against B. bassiana. Notably, several upregulated differentially expressed genes (DEGs) involved in the Toll and IMD pathways, which are key components of the insect immune system, and antimicrobial peptides were rapidly induced during both the early and late stages of infection. In contrast, a majority of genes involved in the activation of prophenoloxidase and antioxidant mechanisms were downregulated. Additionally, we identified downregulated DEGs related to cuticle formation, olfactory mechanisms, and detoxification processes. In summary, our study provides valuable insights into the interactions between P. puparum and B. bassiana, shedding light on the changes in gene expression during fungal infection. These findings have significant implications for the development of more effective and sustainable strategies for pest management in agriculture. [ABSTRACT FROM AUTHOR]

Objective: To explore the mechanism of psoralen synergized with exosomes (exos)-loaded SPC25 on nucleus pulposus (NP) cell senescence in intervertebral disc degeneration (IVDD). Methods: IVDD cellular models were established on NP cells by tert-butyl hydroperoxide (TBHP) induction, followed by the treatment of psoralen or/and exos from adipose-derived stem cells (ADSCs) transfected with SPC25 overexpression vector (ADSCs-oe-SPC25-Exos). The viability, cell cycle, apoptosis, and senescence of NP cells were examined, accompanied by the expression measurement of aggrecan, COL2A1, Bcl-2, Bax, CDK2, p16, and p21. Results: After TBHP-induced NP cells were treated with psoralen or ADSCs-oe-SPC25-Exos, cell proliferation and the expression of aggrecan, COL2A1, Bcl-2, and CDK2 were promoted; however, the expression of Bax, p16, p21, and inflammatory factors was decreased, and cell senescence, cycle arrest, and apoptosis were inhibited. Of note, psoralen combined with ADSCs-oe-SPC25-Exos further decelerated NP cell senescence and cycle arrest compared to psoralen or ADSCs-oe-SPC25-Exos alone. Conclusion: Combined treatment of psoralen and ADSCs-oe-SPC25-Exos exerted an alleviating effect on NP cell senescence, which may provide an insightful idea for IVDD treatment. [ABSTRACT FROM AUTHOR]

Serine proteases (SPs) and their homologs (SPHs) are among the best-characterized gene families. They are involved in several physiological processes, including digestion, embryonic development and immunity. In the current study, a total of 177 SPs-related genes were characterized in the genome of Ostrinia furnacalis. The activation site of SPs/SPHs and enzyme specificity of SPs were identified, and the findings showed that most of the SPs analyzed possessed trypsin substrate specificity. Several SPs/SPHs with similar simple gene structures had tandem repeat-like distributions on the scaffold, indicated that gene expansion has occurred in this large family. Furthermore, we constructed 30 RNA sequencing libraries including four with developmental stage and four middle larval stage tissues to study the transcript levels of these genes. Differentially upregulated and downregulated genes were obtained via data analysis. More than one-quarter of the genes were specifically identified as highly expressed in the midgut in compared to the other three tissues evaluated. In the current study, the domain structure, gene location and phylogenetic relationship of genes in O. furnacalis were explored. Orthologous comparisons of SPs/SPHs between model insects and O. furnacalis indicated their possible functions. This information provides a basis for understanding the functional roles of this large family. [ABSTRACT FROM AUTHOR]

Background: Circular RNAs (circRNAs) can act as microRNA (miRNA) sponges, thus regulating gene expression. The role of circRNAs in the process of oxygen-glucose deprivation/reoxygenation (OGD/R) is unclear. Here, we explored the mechanism underlying Circ VRK1 in human brain microvascular endothelial cells (HBMVECs) injury induced by OGD/R. Methods: The OGD/R cell model was established in HBMVECs. The microarray was applied to detect differentially expressed circRNAs, followed by subcellular fractionation assay. Colony formation assay, flow cytometry, ELISA, tube formation, Transwell and western blot assays were performed for loss-of-function assay. HE staining, TTC staining, immunohistochemistry and western blot were performed in an established mouse model. The relationships between Circ VRK1 and miR-17, and between miR-17 and PTEN were detected by bioinformatics and dual-luciferase assays. Rescue experiments were conducted in vitro and in vivo, and PI3K/AKT activity was detected by Western Blot. Results: Circ VRK1, predominantly present in the cytoplasm of cells, was upregulated in the HBMVECs exposed to OGD/R. Circ VRK1 downregulation decreased proliferation, migration, tube formation, inflammatory factors and oxidative stress, while increased apoptosis in HBMVECs. Moreover, Circ VRK1 silencing reduced neurological damage, cerebral infarct size, CD34-positive cell counts and VEGF expression in mice. Circ VRK1 mediated PTEN expression and the PI3K/AKT pathway by targeting miR-17. Deletion of miR-17 inhibited the effects of Circ VRK1 siRNA, and silencing of PTEN suppressed the effects of miR-17 inhibitor. Conclusion: Circ VRK1 was upregulated during OGD/R. Circ VRK1 downregulation regulates PTEN expression by targeting miR-17, thereby promoting PI3K/AKT pathway activity to alleviate OGD/R injury. [ABSTRACT FROM AUTHOR]

Oxidative stress and impaired autophagy are the hallmarks of cardiac aging. However, there are no specific drugs available to prevent cardiac aging. Curcumin is a natural polyphenolic drug with antioxidant, antiaging, and autophagy-promoting effects. Here, we describe the preventive role of Curcumin in cardiac aging through the induction of autophagy and the restoration of autophagy via the SIRT1/AMPK/mTOR pathway. The number of cells positive for senescence-associated β-galactosidase, P53, P16, and intracellular ROS increased significantly in senescent cardiomyocytes, stimulated using D-galactose. Curcumin reversed this effect in a dose-dependent manner. Curcumin-induced autophagy increased the expression of SIRT1and phosphorylated AMPK and decreased phosphorylated mTOR in a dose-dependent manner. SIRT1-siRNA-mediated knockdown inhibited the antioxidation, antiaging, the promotion of autophagy, and the SIRT1/AMPK/mTOR pathway activation effect of curcumin. Therefore, curcumin could be an effective anticardiac aging drug. [ABSTRACT FROM AUTHOR]

Gene expression programming (GEP) uses simple linear coding to solve complex modeling problems. However, the performance is limited by the effectiveness of the selected method of evaluating population individuals, the breadth and depth of the search domain for the solution, and the ability of accuracy of correcting the solution based on historical data. Therefore, a new dual-mode GEP prediction algorithm based on irregularity and similar period is proposed. It takes measures to specialize origin data to reserve the elite individuals, reevaluate the target individuals, and process data and solutions via the similar period mode, which avoids the tendency to get stuck in local optimum and the complexity of the precisions of correcting complex modeling problems due to insufficiency scope of the search domain, and subsequently, better convergence results are obtained. If we take the leek price and the sunspot observation data as the sample to compare the new algorithm with the GEP simulation test, the results indicate that the new algorithm possesses more powerful exploration ability and higher precision. Under the same accuracy requirements, the new algorithm can find the individual faster. Additionally, the conclusion can be drawn that the performance of new algorithm is better on the condition that we take another set of sunspot observations as samples, combining the ARIMA algorithm and BP neural network prediction algorithm for simulation and comparison with the new algorithm. [ABSTRACT FROM AUTHOR]

Long non-coding RNA (lncRNA) of plant species undergoes dynamic regulation and acts in developmental and stress regulation. Presently, there is little information regarding the identification of lncRNAs in jujube (Ziziphus jujuba Mill.), and it is uncertain whether the lncRNAs could respond to heat stress (HS) or not. In our previous study, a cultivar (Hqing1-HR) of Z. jujuba were treated by HS (45°C) for 0, 1, 3, 5 and 7 days, and it was found that HS globally changed the gene expression by RNA sequencing (RNA-seq) experiments and informatics analyses. In the current study, 8260 lncRNAs were identified successfully from the previous RNA-seq data, and it indicated that lncRNAs expression was also altered globally, suggesting that the lncRNAs might play vital roles in response to HS. Furthermore, bioinformatics analyses of potential target mRNAs of lncRNAs with cis-acting mechanism were performed, and it showed that multiple differentially expressed (DE) mRNAs co-located with DElncRNAs were highly enriched in pathways associated with response to stress and regulation of metabolic process. Taken together, these findings not only provide a comprehensive identification of lncRNAs but also useful clues for molecular mechanism response to HS in jujube. [ABSTRACT FROM AUTHOR]

Objective. This study is aimed at investigating the predictive value of CENPA in hepatocellular carcinoma (HCC) development. Methods. Using integrated bioinformatic analysis, we evaluated the CENPA mRNA expression in tumor and adjacent tissues and correlated it with HCC survival and clinicopathological features. A Cox regression hazard model was also performed. Results. CENPA mRNA was significantly upregulated in tumor tissues compared with that in adjacent tissues, which were validated in The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) series (all P < 0.01). In the Kaplan-Meier plotter platform, the high level of CENPA mRNA was significantly correlated with overall survival (OS), disease-free survival (DFS), recurrence-free survival (RFS), and progression-free survival (PFS) in HCC patients (all log rank P < 0.01). For validation in GSE14520 and pan-TCGA dataset, HCC patients with CNEPA mRNA overexpression had poor OS compared with those with low CENPA mRNA (log rank P = 0.025 and P < 0.0001 , respectively), and those with high CENPA had poor DFS in TCGA (log rank P = 0.0001). Additionally, CENPA mRNA were upregulated in HCC patients with alpha-fetoprotein (AFP) elevation, advanced TNM stage, larger tumor size, advanced AJCC stage, advanced pathology grade, and vascular invasion (all P < 0.05). A Cox regression model including CENPA, OIP5, and AURKB could predict OS in HCC patients effectively (AUC = 0.683). Conclusion. Overexpressed in tumors, CENPA might be an oncogenic factor in the development of HCC patients. [ABSTRACT FROM AUTHOR]

• Microarray and bioinformatics analysis in human chondrocytes treated with T-2 toxin and deoxynivalenol was performed. • The toxic effects of T-2 toxin and deoxynivalenol may involve in multiple biological processes and signal pathways by some specific pathway. • T-2 toxin and deoxynivalenol had different toxic characteristics although they showed some similar toxic mechanism in human chondrocytes. T-2 toxin and deoxynivalenol (DON) are two representative mycotoxins that are commonly found in cereals and agricultural products. As T-2 toxin and DON are considered the cause of Kashin-Beck disease, a special osteoarticular disease, chondrocytes would be a vital target site for these toxins. To fully understand the toxicity effects of T-2 toxin and DON on chondrocytes, the present study investigated and compared the gene expression profiles and underlying mechanisms of T-2 toxin and DON on cultured human chondrocytes by microarray and bioinformatics analysis. Normal human chondrocytes were treated with T-2 toxin at 0.01 μg/ml and DON at 1.0 μg/ml for 72 h and analyzed by microarray using Affymetrix Human Gene Chip. Comprehensive analysis, including gene ontology, pathways and gene-gene networks was performed to identify the crucial gene functions, related signal pathways and key genes. A total of 175 and 237 differentially expressed genes were identified in human chondrocytes for T-2 toxin and DON treatment, respectively. Of these, 47 had the same expression tendencies in the two groups. The protein–protein interaction network analysis showed that the 10 hub genes were different between the two groups. Our results provide a comprehensive understanding of the toxic mechanism of T-2 toxin and DON on human chondrocytes and suggest that although T-2 toxin and DON showed some similar toxic mechanisms in human chondrocytes, they also had different toxic characteristics. [ABSTRACT FROM AUTHOR]

Lipid metabolism is considered one of the important factors affecting residual feed intake (RFI). However, the relationship between RFI and expression of lipid metabolism-related genes is unknown in meat-type ducks. To address this issue, a total of 1,000 male meat-type ducks with similar body weight were randomly selected to measure body weight gain and feed intake from 21 to 42 d of age to estimate RFI. The 8 greatest- (high RFI [ HRFI ]) and lowest- (low RFI [LRFI]) ranking birds were then selected for the present study. Relative expressions of key genes, namely sirtuin 1 (Sirt1), forkhead box O1 (Foxo1), peroxisome proliferator-activated receptor gamma (PPARγ), sterol regulatory element-binding transcription factor 1c (SREBP - 1c), fas cell surface death receptor (FAS), acetyl-CoA carboxylase alpha (ACC), carnitine palmitoyltransferase 1A (CPT1A), and acyl-CoA oxidase 1 (ACOX1), were then determined in the HRFI and LRFI ducks by quantitative PCR. The results showed that RFI, feed conversion ratio (FCR), and average daily feed intake (ADFI) were significantly lower (P < 0.05) in LRFI ducks than in HRFI ducks. In addition, expression of Sirt1 , Foxo1 , CPT1A , and ACOX1 were significantly higher in LRFI ducks than in HRFI ducks (P < 0.05), whereas PPARγ and FAS expression levels were significantly lower in LRFI ducks than in HRFI ducks (P < 0.01). Correlation analysis showed that Sirt1 , CPT1A , and ACOX1 expressions were significantly negatively correlated with FCR (r = −0.81 to −0.93; P < 0.01), whereas PPARγ and FAS expressions were significantly positively correlated with FCR (r = 0.74 to 0.87; P < 0.01). PPARγ expression was significantly positively correlated with RFI (r = 0.83; P < 0.01), whereas CPT1A and ACOX1 expressions were significantly negatively correlated with RFI (r = −0.84 to −0.89; P < 0.01). Sirt1 mRNA expression was positively correlated with Foxo1 , CPT1A , and ACOX1 mRNA expression (r = 0.78 to 0.92; P < 0.01). Association of Foxo1 with CPT1A and ACOX1 was positive (r = 0.88 to 0.96; P < 0.01). These results suggest that genes related to fatty acid oxidation are upregulated in the liver of ducks with high feed efficiency, while genes associated with lipid synthesis are downregulated. Furthermore, the inclusion of lipid metabolism-related genes in future breeding programs might be beneficial for selecting ducks with greater feed efficiency phenotype. [ABSTRACT FROM AUTHOR]

Background/Aims: To explore the potential role of miR-544a in spinal cord injury and the possible mechanism involved. Methods: We established a mouse model with spinal cord injury to examine the changes in grip force recovery of the forelimb or the posterior limb of the mouse. Microarray was performed to achieve differentiated miRNAs in the mice. The expressions of miR-544a, MCP-1, IL36B and IL17B after spinal cord injury were detected by qRT-PCR. Subsequently, miR-544a was overexpressed to observe changes in inflammation and grip strength after spinal cord injury. Target gene of miR-544a was then predicted using bioinformatics technology. Finally, dual luciferase reporter gene assay was used to verify the binding of miR-544a to its target gene. Results: Using mice models with spinal cord injury, we found that the strength of their four limbs began to recover 7 days after injury. The results of microarray and qRT-PCR confirmed that mir-544a level in mice with spinal cord injury decreased with increase of injury time, while the levels of inflammatory genes MCP-1 (monocyte chemoattractant protein-1), IL1 (interleukin-1) and TNF-α (tumor necrosis factor alpha) IL36B (interleukin-36 beta) and IL17B (interleukin-17 beta) were significantly increased. However, overexpression of miR-544a in the mice significantly reduced the level of inflammation and restored their grip strength in their four limbs. Finally, we found that miR-544a can bind to the NEUROD4 (Neurogenic differentiation 4) 3'UTR (Untranslated Region) region through bioinformatics website prediction, which was further confirmed by dual luciferase reporter assay. NEUROD4 level was significantly reduced following the overexpression of miR-544a. Conclusion: The expression of miR-544a was significantly decreased after spinal cord injury. High expression of miR-544a could alleviate the inflammation caused by spinal cord injury and promote the recovery of spinal cord via the inhibition of NEUROD4. [ABSTRACT FROM AUTHOR]

Highlights • Feeding regimens effected gene expression of FADS1 and FADS2 in adipose tissue. • The content of n-3 PUFA, especially EPA and DHA is higher in pastured sheep. • Different tissues have variable sensibilities to feeding regimens. Abstract The present study investigated the effects of two feeding regimens on meat quality, fatty acid profile and metabolism as it relates to gene expression in Sunit sheep. Two feeding regimens were used (pasture feeding and barn feeding, PF and BF) each containing 10 Sunit sheep. Results of this study indicated that PF sheep had significantly (P < 0.05) higher L* and b* values in their muscle compared to BF sheep. Also, the fatty acid composition of longissimus dorsi muscle and subcutaneous adipose tissues differed between feeding regimens. In this respect, concentrations of palmitic acid (C16:0) in the subcutaneous adipose tissue were significantly (P < 0.05) higher in BF sheep. Pastured sheep exhibited greater concentrations of polyunsaturated fatty acids (PUFA) including: linolenic acid (C18:3) (P < 0.001), DHA (P < 0.05), EPA (P < 0.001) and CLA cis-9, trans-11(P < 0.05) in their muscle compared to BF sheep. The expression of nine candidate genes related to fatty acid metabolism were analyzed by qPCR. In longissimus dorsi muscle, expression of acetyl CoA carboxylase (ACACA; P < 0.05) was up-regulated in BF sheep. Expression of the peroxisome proliferator activated receptor (PPARγ) (P < 0.05), stearoyl CoA desaturase (SCD) (P < 0.01), fatty acid desaturase1 (FADS1) (P < 0.05) and fatty acid desaturase 2 (FADS2) (P < 0.05) were up-regulated in PF sheep. Pasture feeding also increased (P < 0.05) expression of lipoprotein lipase (LPL), PPARγ, SCD, FADS1and fatty acid elongase 5 (Elove5) in the subcutaneous adipose tissue, however, the feeding regimens did not change expression of fatty acid synthase (FASN) and carnitine palmitoyl transferase I (CPT1). The results of this study indicated that the feeding regimen could be an important tool in manipulating the fatty acid profile of animal adipose tissue by altering the gene expression of enzymes involved in fat metabolism. [ABSTRACT FROM AUTHOR]

Aquaporin 5 (AQP‑5) is a water channel protein that is closely associated with non‑small cell lung cancer tissues. The present study aimed to investigate the mechanism of tanshinol treatment on AQP‑5 in the lung tissue of rats with sepsis. Animals in a rat sepsis model were randomly divided into six groups including blank control (ctrl), sham operation (SO), model (sepsis), low dose tanshinol (5 mg/kg/day; Tan‑L), moderate dose tanshinol (10 mg/kg/day; Tan‑M) and high dose tanshinol (20 mg/kg/day; Tan‑H) groups. After 7 days of administration, the expression level of AQP‑5 mRNA was detected by reverse transcription‑quantitative polymerase chain reaction. The levels of interleukin‑6 (IL‑6) and tumor necrosis factor α (TNF‑α) were measured by ELISA. Hematoxylin and eosin staining was used for histopathological observation. The expression levels of AQP‑5, P38 and phosphorylated (P)‑P38 protein in lung tissues were detected by western blot analysis. The expression levels of AQP‑5 in the sepsis group were significantly decreased compared with those in ctrl and SO groups (P<0.01), while the levels of TNF‑α, IL‑6 and p‑P38 were significantly increased in sepsis group compared with those in ctrl and SO groups (P<0.01). Following tanshinol intervention, the expression levels of AQP‑5 were significantly increased, while the levels of TNF‑α, IL‑6 and p‑P38 were decreased compared with those in sepsis group. Tanshinol may upregulate the expression of AQP‑5 by inhibiting the inflammatory cytokines and phosphorylation of P38, therefore protecting the lung tissue of rats with sepsis. [ABSTRACT FROM AUTHOR]

As a pioneer plant, Sesbania cannabina is cultivated on a large scale for saline-alkali land improvement in China. Here, a native galactomannan (GalM) and a series of its hydrolysates (GalM40, GalM50 and GalM65) were obtained from S. cannabina seed by water extraction, β-mannanase hydrolysate and ethanol precipitation. As elucidated by HPAEC, NMR, FT-IR and HPGPC, GalM was characterized as a β-1,4-linked d -mannose polymer with single α-1,6-linked d -galactose side chain in a 2.4:1 M ratio, and had a molecular weight of 1.42 × 10 6 Da. MTT assay showed that these four fractions had significant inhibitory effect on A549, Hela, HepG2 and MCF-7 in a dose-dependent manner, and that GalM40 with second-highest M W (1.47 × 10 4 Da) possessed higher activity amongst those fractions. Such strong inhibition effect on the growth of human cancer cells might derive from its ability to increase caspase-12 expression, as revealed from immunohistochemical analysis. In sum, this paper characterizes the molecular structure of S. cannabina galactomannan with anticancer activity, and this new knowledge will provide a basis for its further structure-properties research and ultimately, develop new possibilities for its use in high-value applications, such as functional food. [ABSTRACT FROM AUTHOR]

T-2 toxin and deoxynivalenol (DON) are secondary metabolites produced by Fusarium fungi and are commonly found on food and feed. Although T-2 toxin and DON have been suggested as the etiology of Kashin-Beck disease (KBD), an endemic osteochondropathy, little is known about the mechanism when human chondrocytes are exposed to T-2 toxin and DON. The purpose of this study is to identify the gene expression differences and underlying molecular changes modulated by T-2 toxin and DON in vitro in human chondrocytes. After the experiments of cell viability, the gene expression profiles were analyzed in cells that were treated with 0.01 μg/ml T-2 toxin and 1.0 μg/ml DON for 72 h by Affymetrix Human Gene Chip. The array results showed that 882 and 2118 genes were differentially expressed for T-2 toxin and DON exposure, respectively. Enrichment analysis revealed that diverse cellular processes including DNA damage, cell cycle regulation and metabolism of extracellular matrix were affected when human chondrocytes were exposed to T-2 toxin and DON. These results demonstrate the gene expression differences and molecular mechanism of cultured human chondrocytes exposure to T-2 toxin and DON, and provide a new insight into future research in the etiology of KBD. [ABSTRACT FROM AUTHOR]

In insects, serine proteases (SPs) and serine protease homologs (SPHs) constitute a large family of proteins involved in multiple physiological processes such as digestion, development, and immunity. Here we identified 145 SPs and 38 SPHs in the genome of an endoparasitoid, Pteromalus puparum . Gene duplication and tandem repeats were observed in this large SPs/SPHs family. We then analyzed the expression profiles of SP/SPH genes in response to different microbial infections (Gram-positive bacterium Micrococcus luteus , Gram-negative bacterium Escherichia coli , and entomopathogenic fungus Beauveria bassiana ), as well as in different developmental stages and tissues. Some SPs/SPHs also displayed distinct expression patterns in venom gland, suggesting their specific physiological functions as venom proteins. Our finding lays groundwork for further research of SPs and SPHs expressed in the venom glands. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) play important roles in the tumorigenesis of glioma. Recent studies showed that miR-155 expression was increased in types of cancer, including glioma. However, the underlying mechanism of miR-155 on glioma is still unclear. In the present study, expression of miR-155 and caudal-type homeobox 1 (CDX1) was determined in glioma tissues by qRT-PCR, and the regulatory axis was further studied in glioma cells. We showed that miR-155 expression was significantly increased in glioma tissues while CDX1 expression was decreased. Correlation analysis revealed that miR-155 was negatively correlated with CDX1 expression in glioma tissues. Moreover, Kaplan–Meier analysis indicated that patients with high miR-155 expression had a poor overall survival. In addition, our results showed that the translation of CDX1 expression could be suppressed by miR-155 mimics. And miR-155 mimics promoted glioma cell proliferation could be reversed by CDX1 overexpression. In vivo assay, we showed that miR-155 overexpression promoted the progress of tumor formation. Therefore, we suggested that miR-155 might promote glioma cell growth partially by targeting CDX1, which provided a novel therapeutic strategy for glioma patients. [ABSTRACT FROM AUTHOR]

Background: NONO-TFE3 rearranged renal cell carcinoma (NONO-TFE3 rRCC) is one of a subtype of TFE3 rRCCs with high malignancy and poor prognosis. Compared with clear cell RCC, NONO-TFE3 rRCC shows a preference for mitochondrial respiration. We recently identified that the upregulation of nicotinamide ribokinase 2 (NMRK2) was associated with enhanced mitochondrial respiration and tumor progression in TFE3 rRCC. Methods: A tumor-bearing mouse model was established to verify the pro-oncogenic effect of NMRK2 on NONO-TFE3 rRCC. Then the expression of NMRK2 RNA and protein was detected in cell lines and patient specimens. The NMRK2 transcripts were Sanger-sequenced and blasted at NCBI website. We constructed dCas13b-HA system to investigate the factors binding with NMRK2 RNA. We also used molecular experiments like RIP-seq, IP-MS, FISH and fluorescence techniques to explore the mechanisms that long non-coding RNA (lncRNA) like NMRK2 mRNA promoted the mitochondrial respiration of NONO-TFE3 rRCC. The efficacy of the combination of shRNA (NMRK2)-lentivirus and metformin on NONO-TFE3 rRCC was assessed by CCK-8 assay. Results: In this study, we confirmed that NMRK2 showed transcriptional-translational conflict and functioned as lncRNA like mRNA in the NONO-TFE3 rRCC. Furthermore, we revealed the molecular mechanism that NONO-TFE3 fusion suppressed the translation of NMRK2 mRNA. Most importantly, three major pathways were shown to explain the facilitation effects of lncRNA like NMRK2 mRNA on the mitochondrial respiration of NONO-TFE3 rRCC in an NAD+ kinase-independent manner. Finally, the efficacy of combination of shRNA (NMRK2)-lentivirus and metformin on NONO-TFE3 rRCC was demonstrated to be superior than either agent alone. Conclusions: Overall, our data comprehensively demonstrated the mechanisms for the enhanced mitochondrial respiration in NONO-TFE3 rRCC and proposed lncRNA like NMRK2 mRNA as a therapy target for NONO-TFE3 rRCC. [ABSTRACT FROM AUTHOR]

Existing works show that the rotation forest algorithm has competitive performance in terms of classification accuracy for gene expression data. However, most existing works only focus on the classification accuracy and neglect the classification costs. In this study, we propose a cost-sensitive rotation forest algorithm for gene expression data classification. Three classification costs, namely misclassification cost, test cost and rejection cost, are embedded into the rotation forest algorithm. This extension of the rotation forest algorithm is named as cost-sensitive rotation forest algorithm. Experimental results show that the cost-sensitive rotation forest algorithms effectively reduce the classification cost and make the classification result more reliable. [ABSTRACT FROM AUTHOR]

The objective was to examine the protective effect of resveratrol (RSV) on myocardial ischemia/reperfusion (IR) injury and whether the mechanism was related to vascular endothelial growth factor B (VEGF-B) signaling pathway. Rat hearts were isolated for Langendorff perfusion test and H9c2 cells were used for in vitro assessments. RSV treatment significantly improved left ventricular function, inhibited CK-MB release, and reduced infarct size in comparison with IR group ex vivo . RSV treatment markedly decreased cell death and apoptosis of H9c2 cells during IR. We found that RSV was responsible for the up-regulation of VEGF-B mRNA and protein level, which caused the activation of Akt and the inhibition of GSK3β. Additionally, RSV prevented the generation of reactive oxygen species (ROS) by up-regulating the expression of MnSOD either in vitro or ex vivo . We also found that the inhibition of VEGF-B abolished the cardioprotective effect of RSV, increased apoptosis, and led to the down-regulation of phosphorylated Akt, GSK3β, and MnSOD in H9c2 cells. These results demonstrated that RSV was able to attenuate myocardial IR injury via promotion of VEGF-B/antioxidant signaling pathway. Therefore, the up-regulation of VEGF-B can be a promising modality for clinical myocardial IR injury therapy. [ABSTRACT FROM AUTHOR]

Accumulated evidence indicates that rare variants exert a vital role on predisposition and progression of human diseases, which provides neoteric insights into disease etiology. In the current study, based on three independently retrospective studies of 5,016 lung cancer patients and 5,181 controls, we analyzed the associations between five rare polymorphisms (i.e., p.Glu116Lys, p.Asn118Ser, p.Arg138Cys, p.Ala195Thr and p.Leu259Phe) in MKK7 and lung cancer risk and prognosis. To decipher the precise mechanisms of MKK7 rare variants on lung cancer, a series of biological experiments was further performed. We found that the MKK7 p.Glu116Lys rare polymorphism was significantly associated with lung cancer risk, progression and prognosis. Compared with Glu/Glu common genotype, the 116Lys rare variants (Lys/Glu/+ Lys/Lys) presented an adverse effect on lung cancer susceptibility (odds ratio [OR] = 3.29, 95% confidence interval [CI] = 2.70–4.01). These rare variants strengthened patients’ clinical progression that patients with 116Lys variants had a significantly higher metastasis rate and advanced N, M stages at diagnosis. In addition, the patients with 116Lys variants also contributed to worse cancer prognosis than those carriers with Glu/Glu genotype (hazard ratio [HR] = 1.53, 95% CI = 1.32–1.78). Functional experiments further verified that the MKK7 p.116Lys variants altered the expression of several cancer-related genes and thus affected lung cancer cells proliferation, tumor growth and metastasis in vivo and in vitro. Taken together, our findings proposed that the MKK7 p.Glu116Lys rare polymorphism incurred a pernicious impact on lung cancer risk and prognosis through modulating expressions of a serial of cancer-related genes. [ABSTRACT FROM AUTHOR]

Background: Pulmonary arterial hypertension is characterized by increased pressure overload that leads to right ventricular hypertrophy (RVH). GPR91 is a formerly orphan G-protein-coupled receptor (GPCR) that has been characterized as a receptor for succinate; however, its role in RVH remains unknown. Methods and Results: We investigated the role of succinate-GPR91 signaling in a pulmonary arterial banding (PAB) model of RVH induced by pressure overload in SD rats. GPR91 was shown to be located in cardiomyocytes. In the sham and PAB rats, succinate treatment further aggravated RVH, up-regulated RVH-associated genes and increased p-Akt/t-Akt levels in vivo. In vitro, succinate treatment up-regulated the levels of the hypertrophic gene marker anp and p-Akt/t-Akt in cardiomyocytes. All these effects were inhibited by the PI3K antagonist wortmannin both in vivo and in vitro. Finally, we noted that the GPR91-PI3K/Akt axis was also up-regulated compared to that in human RVH. Conclusions: Our findings indicate that succinate-GPR91 signaling may be involved in RVH via PI3K/Akt signaling in vivo and in vitro. Therefore, GPR91 may be a novel therapeutic target for treating pressure overload-induced RVH. [ABSTRACT FROM AUTHOR]

More and more miRNAs have been shown to regulate gene expression in the heart and dysregulation of their expression has been linked to cardiovascular diseases including the miR-199a/214 cluster. However, the signature of circulating miR-214 expression and its possible roles during the development of heart failure has been less well studied. In this study, we elucidated the biological and clinical significance of miR-214 dysregulation in heart failure. Firstly, circulating miR-214 was measured by quantitative PCR, and we found that miR-214 was upregulated in the serum of chronic heart failure patients, as well as in hypertrophic and failing hearts of humans and mice. Adeno-associated virus serotype 9 (AAV9)-mediated miR-214 silencing attenuates isoproterenol (ISO) infusion-induced cardiac dysfunction and impairment of cardiac angiogenesis in mice. Mechanistically, miR-214 overexpression reduces angiogenesis of HUVECs by targeting XBP1, an important transcription factor of unfolded protein response, and XBP1 silencing decreases HUVECs proliferation and angiogenesis similar to miR-214 overexpression. Furthermore, ectopic expression of XBP1 enhances endothelial cells proliferation and tube formation, and reverses anti-angiogenic effect of miR-214 over expression. All these findings suggest that miR-214 is an important regulator of angiogenesis in heart in vitro and in vivo, likely via regulating the expression of XBP1, and demonstrate that miR-214 plays an essential role in the control/inhibition of cardiac angiogenesis. J. Cell. Physiol. 230: 1964-1973, 2015. © 2015 The Authors. Journal of Cellular Physiology published by Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Simple Summary: The interactions between parasitoids and their host have always attracted much attention, and parasitoids manipulate the host physiology to benefit the survival and development of their offspring. It is critical to analyze these physiological regulatory mechanisms. In this study, using RNA-sequencing analysis, we clarified the effects of parasitization on host gene expression of Microplitis manilae, a dominant larval parasitoid of Spodoptera frugiperda. Several differentially expressed genes were identified in S. frugiperda larvae at 2 h, 24 h, and 48 h post-parasitization. Among these, many genes were implicated in host metabolism and immunity. Further qPCR results involving 20 differentially expressed metabolism, and immune-related genes were consistent with the expression profiles of the RNA-seq data, which confirmed the physiological manipulation of M. manilae on host S. frugiperda. These results contribute to defining the molecular basis of wasps' successful parasitization and facilitate their application. It has been extensively found that parasitoids manipulate host physiology to benefit the survival and development of their offspring. However, the underlying regulatory mechanisms have not received much attention. To reveal the effects of parasitization of the larval solitary endoparasitoid Microplitis manilae (Hymenoptera: Braconidae) on host Spodoptera frugiperda (Lepidoptera: Noctuidae), one of the most destructive agricultural pests in China, deep-sequencing-based transcriptome analysis was conducted to compare the host gene expression levels after 2 h, 24 h, and 48 h parasitization. A total of 1861, 962, and 108 differentially expressed genes (DEGs) were obtained from the S. frugiperda larvae at 2 h, 24 h, and 48 h post-parasitization, respectively, compared with unparasitized controls. The changes in host gene expressions were most likely caused by the injection of wasp parasitic factors, including PDVs, that were injected along with the eggs during oviposition. Based on the functional annotations in GO and KEGG databases, we revealed that most DEGs were implicated in host metabolism and immunity. Further analysis of the common DEGs in three comparisons between the unparasitized and parasitized groups identified four genes, including one unknown and three prophenoloxidase (PPO) genes. Moreover, 46 and 7 common DEGs involved in host metabolism and immunity were identified at two or three time points after parasitization, respectively. Among these, most DEGs showed increased expressions at 2 h post-wasp parasitization while exhibiting significantly decreased expression levels at 24 h post-parasitization, demonstrating the expression regulations of M. manilae parasitization on host metabolism and immune-related genes. Further qPCR verification in 20 randomly selected DEGs confirmed the accuracy and reproducibility of the gene expression profiles generated from RNA-seq. This study reveals the molecular regulatory network about how host insects respond to wasp parasitism, laying a solid foundation for revealing the physiological manipulation of wasp parasitization on host insects, which facilitates the development of biological control practices for parasitoids. [ABSTRACT FROM AUTHOR]

WRKY, named for its special heptapeptide conserved sequence WRKYGOK, is one of the largest transcription factor families in plants and is widely involved in plant responses to biotic, abiotic, and hormonal stresses, especially the important regulatory function in response to drought stress. However, there is no complete comprehensive analysis of this family in H. perforatum, which is one of the most extensively studied plants and is probably the best-known herbal medicine on the market today, serving as an antidepressant, neuroprotective, an antineuralgic, and an antiviral. Here, we identified 86 HpWRKY genes according to the whole genome database of H. perforatum, and classified them into three groups through phylogenetic analysis. Gene structure, conserved domain, motif, cis-elements, gene ontology, and expression profiling were performed. Furthermore, it was found that HpWRKY85, a homologous gene of AtWRKY75, showed obvious responses to drought treatment. Subcellular localization analysis indicated that this protein was localized in the nucleus by the Arabidopsis protoplasts transient transfection. Meanwhile, HpWRKY85-overexpressing Arabidopsis plants showed a stronger ability of root growth and scavenging endogenous reactive oxygen species. The results provide a reference for further understanding the role of HpWRKY85 in the molecular mechanism of drought resistance of H. perforatum. [ABSTRACT FROM AUTHOR]

Cyprininae is the largest subfamily (>1300 species) of the family Cyprinidae and contains more polyploid species (∼400) than any other group of fishes. We examined the phylogenetic relationships of the Cyprininae based on extensive taxon, geographical, and genomic sampling of the taxa, using both mitochondrial and nuclear genes to address the phylogenetic challenges posed by polyploidy. Four datasets were analyzed in this study: two mitochondrial gene datasets (465 and 791 taxa, 5604 bp), a mitogenome dataset (85 taxa, 14,771 bp), and a cloned nuclear RAG1 dataset (97 taxa, 1497 bp). Based on resulting trees, the subfamily Cyprininae was subdivided into 11 tribes: Probarbini (new; Probarbus + Catlocarpio ), Labeonini Bleeker, 1859 ( Labeo & allies), Torini Karaman, 1971 ( Tor , Labeobarbus & allies), Smiliogastrini Bleeker, 1863 ( Puntius , Enteromius & allies), Poropuntiini ( Poropuntius & allies), Cyprinini Rafinesque, 1815 ( Cyprinus & allies), Acrossocheilini (new; Acrossocheilus & allies), Spinibarbini (new; Spinibarbus ), Schizothoracini McClelland, 1842 ( Schizothorax & allies), Schizopygopsini Mirza, 1991 ( Schizopygopsis & allies), and Barbini Bleeker, 1859 ( Barbus & allies). Phylogenetic relationships within each tribe were discussed. Two or three distinct RAG1 lineages were identified for each of the following tribes Torini, Cyprinini, Spinibarbini, and Barbini, indicating their hybrid origin. The hexaploid African Labeobarbus & allies and Western Asian Capoeta are likely derived from two independent hybridization events between their respective maternal tetraploid ancestors and Cyprinion . [ABSTRACT FROM AUTHOR]

Objective: Exercise training (ET) provides a cardioprotective effect against pathological cardiac hypertrophy. Nitric oxide (NO) plays an important role in modulating cardiac hypertrophy. However, few studies explore the relationship between NO signaling and the inhibitory effect of ET on pathological cardiac remodeling. Methods: In this study, we evaluated ET effects on isoproterenol (ISO)-induced cardiac hypertrophy in female mice. Moreover, L-NAME (Nω-nitro-L-arginine methyl ester), a nonselective NO synthase (NOS) inhibitor, was used to assess the involvement of NO signaling in cardiac hypertrophy. Morphological and echocardiographic variables were assessed. Cardiac hypertrophy-related gene expression was detected by real-time PCR and the protein levels of NOS signaling molecules were determined by Western blot. Results:L-NAME treatment prevented the beneficial effects of ET against the increase in heart weight (HW)/body weight (BW), HW/tibia length and lung weight/BW and echocardiographic variables following ISO injection. Also, L-NAME co-administration reversed ET-induced inhibition of myocardial fibrosis and fetal gene reactivation in ISO-treated mice. Furthermore, L-NAME treatment prevented ET-mediated up-regulation of phosphorylated endothelial NOS and plasma NO in ISO-treated mice. Conclusions: Our findings demonstrate that L-NAME treatment could abolish ET-induced cardioprotection against pathological cardiac hypertrophy and that NOS modulation may be involved in the antihypertrophic effects induced by ET. © 2015 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

The TATA box is the core sequence of the promoter and the binding site of many transcription factors. Based on the presence or absence of TATA box, genes can be defined as TATA-containing or TATA-less genes. Many important stress-response functions and highly variable expression patterns are found to be correlated with the TATA box. However, until now, the relationships and differences between TATA-containing and TATA-less genes remain unclear. In this study, based on the transcriptional profiling of the Saccharomyces cerevisiae genome, the perturbation sensitivity (PS) network is constructed. The topological and biological properties are used to investigate differences between TATA-containing and TATA-less genes. Significant differences are found in all topological properties and most of the biological properties. Notably, the TF number, determined mathematically by the number of transcription factors regulating a gene, demonstrates the highest discrimination between TATA-containing and TATA-less genes when all properties are estimated by the F-score. [ABSTRACT FROM AUTHOR]

Growth hormone (GH) is a key regulatory factor in animal growth, development and metabolism. Based on the expression level of the GH receptor, the chicken liver is a major target organ of GH, but the biological effects of GH on the chicken liver are not fully understood. In this work we identified mRNAs and miRNAs that are regulated by GH in primary hepatocytes from female chickens through RNA-seq, and analyzed the functional relevance of these mRNAs and miRNAs through GO enrichment analysis and miRNA target prediction. A total of 164 mRNAs were found to be differentially expressed between GH-treated and control chicken hepatocytes, of which 112 were up-regulated and 52 were down-regulated by GH. A total of 225 chicken miRNAs were identified by the RNA-Seq analysis. Among these miRNAs 16 were up-regulated and 1 miRNA was down-regulated by GH. The GH-regulated mRNAs were mainly involved in growth and metabolism. Most of the GH-upregulated or GH-downregulated miRNAs were predicted to target the GH-downregulated or GH-upregulated mRNAs, respectively, involved in lipid metabolism. This study reveals that GH regulates the expression of many mRNAs involved in metabolism in female chicken hepatocytes, which suggests that GH plays an important role in regulating liver metabolism in female chickens. The results of this study also support the hypothesis that GH regulates lipid metabolism in chicken liver in part by regulating the expression of miRNAs that target the mRNAs involved in lipid metabolism. [ABSTRACT FROM AUTHOR]

Proteins are responsible for performing the vast majority of cellular functions which are critical to a cell's survival. The knowledge of the subcellular localization of proteins can provide valuable information about their molecular functions. Therefore, one of the fundamental goals in cell biology and proteomics is to analyze the subcellular localizations and functions of these proteins. Recent large-scale human genomics and proteomics studies have made it possible to characterize human proteins at a subcellular localization level. In this study, according to the annotation in Swiss-Prot, 8842 human proteins were classified into seven subcellular localizations. Human proteins in the seven subcellular localizations were compared by using topological properties, biological properties, codon usage indices, mRNA expression levels, protein complexity and physicochemical properties. All these properties were found to be significantly different in the seven categories. In addition, based on these properties and pseudo-amino acid compositions, a machine learning classifier was built for the prediction of protein subcellular localization. The study presented here was an attempt to address the aforementioned properties for comparing human proteins of different subcellular localizations. We hope our findings presented in this study may provide important help for the prediction of protein subcellular localization and for understanding the general function of human proteins in cells. [ABSTRACT FROM AUTHOR]

Background: Clear cell renal cell carcinoma (ccRCC), the most common urological malignancy, has an unfavorable prognosis and an unknown mechanism of progression. Through survival analyses screening of The Cancer Genome Atlas (TCGA) dataset, we identified Visual system homeobox1 (VSX1) as a novel potential prognostic biomarker in ccRCC and subsequently investigated the oncogenic role of VSX1 in ccRCC.Methods: The differential expression of VSX1 in human tumors and the clinical prognoses were analyzed in the TCGA dataset and Gene Expression Omnibus. Spearman's correlation coefficient was determined for the correlation analysis of VSX1 expression and other genes of interest. The roles of VSX1 in cell proliferation, invasion, and migration of ccRCC cells were evaluated via the CCK-8 assay, colony formation assay, and Transwell assay, respectively. Further results were demonstrated by western blotting, immunohistochemistry, qRT-PCR, tumor sphere formation, flow cytometry, and the dual‑luciferase reporter assay.Results: VSX1 mRNA upregulation was generally observed in multiple human malignancies from the TCGA database and was confirmed in ccRCC clinical specimens from our department. High VSX1 expression usually indicated that overall and disease-free survival were unfavorable for patients with ccRCC. In terms of mechanism, knockdown or overexpression of VSX1 affected ccRCC aggressiveness in vitro. The dual-luciferase reporter gene assay implied that VSX1 overexpression significantly increased the luciferase activity of TMEM44, FKBP10, and TRIB3, which indicated that VSX1 promoted ccRCC invasiveness via transcriptional regulation of these genes. The significantly enhanced growth in vitro that was induced by stable VSX1 overexpression was almost restored to normal by the knockdown of FKBP10.Conclusions: This study demonstrated that VSX1 was a novel prognostic biomarker in ccRCC and that high VSX1 expression promoted cell proliferation, invasion, and migration in ccRCC via transcriptional activation of downstream target genes. [ABSTRACT FROM AUTHOR]

Abstract: Cancer cells adapt to chronic stress in the tumor microenvironment by inducing the expression of glucose-regulated protein 78 (GRP78), a major endoplasmic reticulum chaperone with Ca2+-binding and antiapoptotic properties. The effect in and potential role of its expression in progression of and prognosis for gastric cancer (GC) are unclear. In the present study, we investigated the clinical value of GRP78 expression in judgment of the severity of and prognosis for GC in a retrospective cohort study of 160 patients who underwent D2 radical gastrectomy and adjuvant chemotherapy. GRP78 expression was detected using immunohistochemistry. The relationships of GRP78 expression with age, sex, differentiation, invasion depth, disease stage, lymph node metastasis, and time to recurrence (TTR) were analyzed. The GRP78 expression was higher in tumors from patients with deep tumor infiltration, with poor differentiation, at late disease stages, and with lymph node metastasis than that in tumors from patients without. Also, GRP78 positivity was associated with short TTR (hazard ratio [HR], 1.75; 95% confidence interval [CI], 1.07–4.85; P =0.041). Subgroup analysis revealed that the HR in the GRP78-high group increased significantly in patients who did not receive taxane-containing regimens (HR, 2.21; 95% CI, 1.23–7.36; P =0.038). In contrast, in the patients who received taxane-based chemotherapy, the association between GRP78 positivity and increased risk of recurrence was not statistically significant (HR, 1.16; 95% CI, 0.81–2.98; P =0.111). In the patients with GRP78 expression, those who underwent taxane-containing chemotherapy had longer median TTRs than did those who did not undergo this treatment (P =0.017). Downregulation of GRP78 expression markedly inhibited proliferation of the GC cells at the G1 phase, whereas GRP78 overexpression promoted cell-cycle progression. These findings suggest that GRP78 overexpression promotes GC cells proliferation and is an independent indicator of poor prognosis for GC. [Copyright &y& Elsevier]

Highlights: [•] miR-181b promotes cell proliferation and suppresses apoptosis in cervical cancer cell lines. [•] Adenylyl cyclase 9 (AC9) transcript is a direct target of miR-181b. [•] Knockdown of AC9 increases cell proliferation and decreases apoptosis in cervical cancer cell lines. [•] miR-181b is upregulated in cervical cancer tissues. [Copyright &y& Elsevier]

Mitogen-activated protein kinase-activated protein kinase 2 (MAPKAPK2) is recognized as oncogenic and simulative role on tumorigenesis by virtue of abnormal expression in cancer including nasopharyngeal carcinoma (NPC). We hypothesized that the copy number variation (CNV)-30450, which duplicates the MAPKAPK2 promoter, may affect MAPKAPK2 expression and be associated with NPC risk. In two independent case–control panels of southern and eastern Chinese with a total of 1590 NPC patients and 1979 cancer-free controls, we investigated the association between CNV-30450 and NPC risk by genotyping the CNV-30450 with the TaqMan assay, and tested its biological effect. Consistent findings were observed in the two populations, that the increased copy number of CNV-30450 was associated with increased risk of NPC (3/4-copy versus 2-copy: odds ratio = 1.28, 95% confidence interval = 1.10–1.49), in which lies a biological mechanism that the adverse genotypes enhanced the promoter activity of MAPKAPK2 and elevated MAPKAPK2 expression. Moreover, the CNV-30450 adverse genotypes significantly interacted with Epstein–Barr virus (EBV) infection on increasing NPC risk (P = 0.035), and the genotype–phenotype correlation was only significant in EBV-positive cases (P = 0.037) but not in EBV-negative ones (P = 0.366). These data suggest that the functional CNV-30450 in the MAPKAPK2 promoter elevates the NPC risk with a modulation by EBV infection, which may be an indicator of susceptibility to NPC.Summary: This case–control study suggests that the functional CNV-30450 in the MAPKAPK2 promoter elevates the NPC risk with a modulation by EBV infection, which may be an indicator of susceptibility to NPC. [ABSTRACT FROM AUTHOR]

Background: The inhibitor of growth (ING) family is involved in multiple cellular functions, but the role of ING2 in gastric cancer progression is unclear. Aim: To investigate the effects of ING2 gene knockdown on chemosensitivity to 5-fluorouracil (5-FU) in human gastric cancer cells and its possible mechanisms. Methods: Short hairpin RNA (shRNA) targeting ING2 (shING2) was transfected into MGC-803 cells using Lipofectamine 2000, and stable transfection cell lines were established using G418. Cell viability, cell cycle distribution, cell apoptosis, and invasive ability were measured to determine the influence of ING2 knockdown on cell biologic characteristics. Messenger RNA (mRNA) and protein levels of ING2, cyclin D1, NF-kappaB/p65, and several matrix metalloproteinases (MMPs) were determined by use of real-time polymerase chain reaction (PCR) or Western blotting, respectively. Results: Our results showed that ING2 knockdown induced cell apoptosis and inhibited cell viability significantly ( P < 0.05). Additionally, ING2 knockdown induced a specific G0/G1 arrest. Furthermore, the suppression of ING2 could enhance the chemosensitivity of gastric cancer cells to 5-FU significantly. Moreover, knockdown of ING2 expression significantly reduced cellular metastatic ability and expression of MMPs in MGC-803 cells. The expression of cyclin D1 and NF-kappaB/p65 was also markedly inhibited in MGC-803/shING2 cells compared with control cells. Conclusions: ING2 not only plays an essential role in the growth and invasion of MGC-803 cells but also represents a potential approach to chemosensitization therapy in human gastric cancer. [ABSTRACT FROM AUTHOR]

This study is designed to examine the radiosensitizing effects of coexpression of doublecortin (DCX) and secreted protein and rich in cysteine (SPARC). Previously, we showed that downregulation of SPARC by small interfering RNA increased radioresistance of U-87MG glioma cells. Therefore, overexpression of SPARC might increase radiosensitivity of glioma cells. But SPARC has been shown to promote glioma cell invasion both in vitro and vivo. In order to radiosensitize glioma cells without stimulating invasion, we chose DCX, which is a well-characterized anti-tumor gene, to coexpress with SPARC. An adenovirus-mediated double gene expression system was constructed and applied to U251 and A172 glioma cell lines. Our data showed that coexpression of DCX and SPARC collaboratively diminished radioresistance of glioma cells, interfered with cell cycle turnover and increased irradiation-induced apoptosis. In addition, transwell assay revealed that coexpression was able to counteract the invasion-promoting effects of SPARC, and even inhibited intrinsic invasion, evidenced by less invading cells in double gene overexpressed group than that of control adenovirus-treated group. In conclusion, genetic engineering combining two or more genes might be a more effective method to overcome radioresistance of glioma cells. [ABSTRACT FROM AUTHOR]

CD133 is a pivotal marker of cancer stem cells (CSCs), which is involved in tumorigenesis and cancer progression. Recent studies have identified CD133 to be a prognostic factor for cancer rested with its expression and genetic variants. Here, we hypothesized that the single nuclear polymorphisms (SNPs) in CD133 may be associated with lung cancer risk and prognosis. Based on three independent case–control analyses with a total of 2332 lung cancer cases and 2457 controls, the gene-based association analysis with 13 polymorphisms of CD133 suggested that CD133 is a susceptible gene for lung cancer (P = 0.043) and that the SNP rs2240688A>C in the 3′-untranslated region of CD133 is the most significant associated SNP with the risk of lung cancer (P = 0.020); further analysis showed that the rs2240688C variant genotypes (CA+CC) harbored a decreased risk of lung cancer (odds ratio = 0.80; 95% confidence interval (CI) = 0.72–0.90) and conferred a favorable survival for lung cancer patients (median survival time: 15 months) compared with AA genotype (median survival time: 11 months, log-rank test: P = 3.31 × 10–6; Cox model: hazards ratio = 0.81, 95% CI = 0.70–0.94). Functional assays revealed that the rs2240688A to rs2240688C transition gained a new binding of the microRNA hsa-miR-135a/b and decreased the CD133 expression. Our data suggest that the functional polymorphism rs2240688A>C in CD133 is associated with lung cancer risk and survival. This SNP may be a functional biomarker to predict risk and prognosis of lung cancer. [ABSTRACT FROM PUBLISHER]

Abstract: Aims: Recent studies suggested that nuclear factor kappa B (NF-κB) plays a key role in the pathogenesis of renal injury. This study investigated whether NF-κB inhibition attenuates progressive renal damage in aldosterone/salt-induced renal injury and its mechanisms. Main methods: Adult male rats were uninephrectomized and treated with one of the following for 4weeks: vehicle (0.5% ethanol, subcutaneously); vehicle/1% NaCl (1% NaCl in drinking solution); aldosterone/1% NaCl (1% NaCl in drinking solution and aldosterone, 0.75μg/h, subcutaneously); or aldosterone/1%NaCl+pyrrolidine dithiocarbamate (PDTC), an inhibitor of NF-κB (100mg/kg/day, by gavage). The activity of NF-κB was measured by EMSA and immunohistochemistry, CTGF and ICAM-1 were measured by Western blot and real-time PCR, and TGF-β and CTGF were measured by immunohistochemistry. Key findings: Rats that received aldosterone/1% NaCl exhibited hypertension and severe renal injury. Renal cortical mRNA levels of CTGF, TGF-β, ICAM-1 and collagen IV, protein expression of CTGF and ICAM-1, and NF-κB–DNA binding activity were significantly upregulated in rats that received aldosterone/1% NaCl. Treatment with PDTC significantly decreased the percentage of cells positive for CTGF and TGF-β; mRNA levels of CTGF, TGF-β, ICAM-1 and collagen IV, and protein levels of CTGF and ICAM-1 were also inhibited by PDTC. Significance: These data suggest that the NF-κB signal pathway plays a role in the progression of aldosterone/salt-induced renal injury. [Copyright &y& Elsevier]

Abstract: Vibrio parahaemolyticus is the leading cause of seafood-associated bacterial gastroenteritis and is a moderately halophilic, salt-requiring bacterium. Global gene expression profiles of V. parahaemolyticus grown under 2% and 0.66% NaCl were compared to define the low-salt stimulon. The ectABC-lysC operon for synthesis of the compatible solute ectoine, as well as three compatible solute transport systems, namely ProU (glycine betaine), OpuD1 (glycine betaine) and Pot2 (spermidine), was up-regulated under 2% NaCl relative to 0.66% NaCl. The 2% NaCl condition favored the inducible expression of OmpW, OmpN and OmpA2, while repressed the expression of OmpA1, OmpU and VP1008. These results indicated that, to master the hyperosmotic stress of saline environments, V. parahaemolyticus might not only accumulate osmoprotectants through uptake or endogenous synthesis of compatible solutes, but also remodel its profiles of outer membrane protein to restore its cell membrane. The above differentially regulated genes will provide novel candidates for the further investigation of the molecular mechanisms of osmoadaptation in V. parahaemolyticus. [Copyright &y& Elsevier]

A whole-genome DNA microarray was constructed to dissect expression profiles of Vibrio parahaemolyticus in response to a sudden temperature downshift from 37 to 10 °C. The mRNA level of each gene at each of three time points (20, 40 and 60 min after temperature downshift) was compared with that just before cold treatment. Clustering analysis of time-course data revealed nine gene clusters with different time-dependent expression patterns. Downregulation of metabolism-related genes was obviously dominant over upregulation at all time points. The distinct negative regulation of metabolism-related genes would account for a generally reduced cellular protein pool resulting from the sudden temperature downshift. In contrast, cold shock had a ‘neutral and balanced’ regulatory action on nonmetabolic cellular pathways, which likely brought about the remodelling of cell envelope structures and transport/binding functions. We identified a 171-bp 5′-untranslated region in the cspA transcript. The cspA gene encoded cold shock protein A (CspA), and CspA was shown to be the major cold shock protein in V. parahaemolyticus. Evident regulatory motifs were conserved within the cspA promoter regions of Escherichia coli and V. parahaemolyticus. These two bacteria likely use the same mechanism to regulate the cold-inducible expression of cspA. [ABSTRACT FROM AUTHOR]

Background: The consumption of omega 3 polyunsaturated fatty acids (PUFAs) is important for human health and is closely associated with cell proliferation and differentiation. This study aimed to investigate the influence of omega 3 PUFAs on embryonic stem cell (ESC) proliferation and explore potential mechanisms that mediate these effects. Methods: In this study, we isolated ESCs from fad3b-expressing transgenic mice. We detected the fatty-acid composition of ESCs using gas chromatography-mass spectroscopy, analyzed cell-cycle phases using flow cytometry, and detected gene expression using real-time polymerase chain reaction (PCR) and western blots. Results: The amount of omega 3 PUFAs significantly increased in fad3b versus control ESCs. However, the growth of fad3b ESCs was slower than that of control cells, and most fad3b ESCs were in a prolonged G0/G1 phase after being passaged for 18 h. Therefore, we hypothesized that fad3b expression inhibited the cell cycle in ESCs by increasing the expression of P21, which then decreased the expression of cyclin-dependent kinase 4 (Cdk4). We found that pretreatment of fad3b ESCs with PD0325901, a P21 inhibitor, clearly attenuated the inhibitory effects of P21 on Cdk4, and resumed the cell cycle. Conclusions: Expression of the fad3b gene in ESCs increased the omega 3 PUFA content, which inhibited cell proliferation by prolonging the G1 phase but did not arrest the G0-to-G1 or G1-to-S transitions. The prolonged G1 phase in fad3b ESCs was probably induced by downregulation of Cdk4 expression via p21 upregulation. These results suggest that accumulation of omega 3 PUFAs in vivo may beneficially affect ESC differentiation and that fad3b ESCs may be a useful tool for investigating related mechanisms. [ABSTRACT FROM AUTHOR]

Background: The epithelial-mesenchymal transition (EMT) plays an indispensable role in the development and progression of Endometrial cancer (EC). Nevertheless, little evidence is reported to uncover the functionality and application of EMT-related molecules in the prognosis of EC. This study aims to develop novel molecular markers for prognosis prediction in patients with EC. Methods: RNA sequencing profiles of EC patients obtained from The Cancer Genome Atlas (TCGA) database were used to screen differential expression genes (DEGs) between tumors and normal tissues. The Cox regression model with the LASSO method was utilized to identify survival-related DEGs and to establish a prognostic signature whose performance was evaluated by Kaplan–Meier curve, receiver operating characteristic (ROC) and calibration curve. Eventually, functional enrichment analysis and cellular experiments were performed to reveal the roles of prognosis-related genes in EC progression. Results: A total of 540 EMT-related DEGs in EC were screened, and subsequently a four-gene risk signature comprising SIRT2, SIX1, CDKN2A and PGR was established to predict overall survival of EC. This risk signature could serve as a meaningfully independent indicator for EC prognosis via multivariate Cox regression (HR = 2.002, 95%CI = 1.433–2.798; P < 0.001). The nomogram integrating the risk signature and clinical characteristics exhibited robust validity and performance at predicting EC overall survival indicated by ROC and calibration curve. Functional enrichment analysis revealed that the EMT-related genes risk signature was associated with extracellular matrix organization, mesenchymal development and cellular component morphogenesis, suggesting its possible relevance to epithelial-mesenchymal transition and cancer progression. Functionally, we demonstrated that the silencing of SIX1, SIRT2 and CDKN2A expression could accelerate the migratory and invasive capacities of tumor cells, whereas the downregulation of PGR dramatically inhibited cancer cells migration and invasion. Conclusions: Altogether, a novel four-EMT-related genes signature was a potential biomarker for EC prognosis. These findings might help to ameliorate the individualized prognostication and therapeutic treatment of EC patients. [ABSTRACT FROM AUTHOR]

The aberrant differentiation of osteoclasts is a key feature of the pathogenesis of osteoporosis, which has a devastating impact on human health. While the effects of Orientin (Ori) on osteoporosis, particularly on RANKL‐stimulated osteoclast production and activation, remain still unclear, Ori has been found to display several biological activities, including antioxidant and anti‐inflammatory. In this work, we investigated the possible pathways through which Ori suppressed RANKL‐induced osteoclast development and showed for the first time that it does so. The macrophages from the bone marrow (BMMs) were cultivated and then treated with Ori after being stimulated with RANKL. Then, TRAP‐positive multinucleated cells were counted, and F‐actin ring analysis was used to assess Ori's impact on mature osteoclast development. In addition, dihydroethidium (DHE) staining was used to evaluate the impact of Ori on RANKL‐induced reactive oxygen species (ROS). In addition, we performed western blotting and quantitative RT‐PCR analysis to investigate probable causes of these downregulation effects. We discovered that Ori inhibits the creation of osteoclasts, the gene and protein expressions unique to osteoclasts, and the ROS production. By activating Nrf2 and other ROS‐scavenging enzymes, Ori reduces intracellular ROS levels. The expression of the main transcription factor of osteoclast development, c‐Fos, was downregulated together with NFATc1, CTSK, and NFATc2, thanks to Ori's inhibition of RANKL‐induced NF‐κB. Consistent with its in vitro antiosteoclastogenic action, Ori therapy in the ovariectomized (OVX) rat model was also able to restore bone mass and improve microarchitecture in the distal femurs. Together, our results demonstrate that Ori is a flavonoid molecule with therapeutic promise for bone illnesses associated with osteoclasts, such as osteoporosis. [ABSTRACT FROM AUTHOR]

The conventional method for construction of stable expression cell lines is mainly based on random integration. However, one drawback of random integration is that the target gene might be integrated into a heterochromatin region or an unstable region of chromatin, thus requiring multiple rounds of selection to obtain desirable expressing cell lines. Rational cell line construction can overcome this shortcoming by integrating transgenes specifically into a stable hot spot within the genome. As such, the discovery of novel effective hot spots becomes critical for this new method of cell line construction. Here we report a practical method for discovery of new stable hot spots through random integration of lentivirus. We describe the thorough study of a hot spot located at NW_006880285.1. The expression stability of this hot spot was verified by detecting Zsgreen1 reporter gene expression for over 50 passages. When cells were adapted to suspension culture, they continuously expressed the Zsgreen1 reporter gene. In addition, this cell suspension was able to stably express the reporter gene for an additional 50 passages. Another finding was that cells with the NGGH gene inserted into the same hot spot were also able to stably express respective protein over 50 passages. In summary, this research offers an easy and new method for researchers to identify stable hot spots within the Chinese Hamster Ovary (CHO) genome on their own, thus contributing to the development of site-specific integration studies in the future. [ABSTRACT FROM AUTHOR]

Recently, epigenetics involved in the regulation of gene expression has become a research hotspot. This study evaluated N4-acetylcytidine (ac4c) RNA acetylation in the spinal dorsal horn (SDH) of rats with cancer-induced bone pain (CIBP). The ac4C-specific RIP sequencing and NAT10-specific RIP sequencing were performed to identify the differences in ac4C acetylation and gene expression in the SDH between CIBP and sham groups, the relationship with the acetylation-modifying enzyme NAT10, and association analysis was performed. By interfering with the NAT10 expression, the relationship between some up-regulated genes and ac4C acetylation in CIBP was verified. In this study, we demonstrated that bone cancer increases the levels of NAT10 and the overall acetylation, inducing differential ac4C patterns in the SDH of rats. Through verification experiments, it was found that ac4C acetylation of some genes is regulated by NAT10, and differential ac4C patterns in RNA determine the expression of this RNA. We exposed that some CIBP-related gene expression was altered in the SDH of rats, which was regulated by differentially expressed ac4C acetylation. [ABSTRACT FROM AUTHOR]

Simple Summary: High-concentrate diets can damage the barrier function of the rumen epithelium and lead to inflammation, which may result in digestive and metabolic disorders and growth retardation in lambs. The phenolic phytonutrients, such as cinnamaldehyde, eugenol, and capsicum oleoresin, have been suggested to act as rumen modifiers. Our results show that a blend of cinnamaldehyde, eugenol, and capsicum oleoresin (CEC) supplementation improved the growth performance and rumen health of lambs fed a high-concentrate diet, which could be due to reducing inflammation and apoptosis, protecting barrier function, and modulating the bacterial community. We investigated the effects of CEC on the fermentation characteristics, epithelial gene expression, and bacterial community in the rumen of lambs fed a high-concentrate diet. Twenty-four 3-month-old female crossbred lambs with an initial body weight of 30.37 ± 0.57 kg were randomly allocated to consume a diet supplemented with 80 mg/kg CEC (CEC) or not (CON). The experiment consisted of a 14 d adaptation period and a 60 d data collection period. Compared with the CON group, the CEC group had higher ADG, epithelial cell thickness, ruminal butyrate proportion, and lower ammonia nitrogen concentration. Increases in the mRNA expression of Occludin and Claudin-4, as well as decreases in the mRNA expression of apoptotic protease activating factor-1 (Apaf-1), cytochrome c (Cyt-C), Caspase-8, Caspase-9, Caspase-3, Caspase-7, and toll-like receptor 4 (TLR4), were observed in the CEC group. Moreover, CEC treatment also decreased the concentration of IL-1β, IL-12, and TNF-α. Supplementation with CEC altered the structure and composition of the rumen bacterial community, which was indicated by the increased relative abundances of Firmicutes, Synergistota, Rikenellaceae_RC9_gut_group, Olsenella, Schwartzia, Erysipelotrichaceae_UCG-002, Lachnospiraceae_NK3A20_group, Acetitomaculum, [Eubacterium]_ruminantium_group, Prevotellaceae_UCG-004, Christensenellaceae_R-7_group, Sphaerochaeta, Pyramidobacter, and [Eubacterium]_eligens_group, and the decreased relative abundances of Acidobacteriota, Chloroflexi, Gemmatimonadota, and MND1. Furthermore, Spearman correlation analysis revealed that the altered rumen bacteria were closely correlated with rumen health-related indices. Dietary CEC supplementation improved growth performance, reduced inflammation and apoptosis, protected barrier function, and modulated the bacterial community of lambs fed a high-concentrate diet. [ABSTRACT FROM AUTHOR]

Breast cancer is a highly harmful malignant tumor, which poses a great threat to women's body and mind, and the mortality rate ranks second among all women's diseases. The incidence rate accounts for 7-10% of various malignant tumors in the whole body, second only to uterine cancer in women, and has become the main cause of threatening women's health. Advanced breast cancer is often considered an incurable disease. The family of heterogeneous nuclear ribonucleoprotein complexes is composed of about 20 hnRNP proteins with molecular weights ranging from 32 to 120 kDa, and they are named according to their molecular weights. Among them, hnRNPA2 and hnRNPB1 are the two most important members of the hnRNP family, both derived from the same gene on chromosome 7p15. Therefore, research to understand the molecular mechanism and process of breast cancer progression has an important role in promoting the current medical research on breast cancer treatment methods. Therefore, studying the mechanism of tumorigenesis is the key to tumor prevention and treatment. Therefore, this paper proposes that A2/B1 promotes the stability of NRF2 mRNA and inhibits ferroptosis and cell proliferation in breast cancer cells. The article mainly introduces the disease diagnosis method based on artificial neural network and its neural network algorithm. In the experimental part, the activity of hnRNP A2/B1 on cancer cells is deeply studied. The results show that the absorbance of the MTT method increases continuously with the extension of the culture time, and the maximum reaches 1.2. This fully shows that its absorption capacity is very strong, especially after 24 hours, the absorption rate rises from 0.6 to 0.9, which shows that 24 hours is the best absorption time. And it can also be found that hnRNPA2/B1 has a significant inhibitory effect on breast cancer cells; it can reduce the effect on breast cancer cell cycle and apoptosis. [ABSTRACT FROM AUTHOR]

We present a selection design that couples S-adenosylmethionine–dependent methylation to growth. We demonstrate its use in improving the enzyme activities of not only N-type and O-type methyltransferases by 2-fold but also an acetyltransferase of another enzyme category when linked to a methylation pathway in Escherichia coli using adaptive laboratory evolution. We also demonstrate its application for drug discovery using a catechol O-methyltransferase and its inhibitors entacapone and tolcapone. Implementation of this design in Saccharomyces cerevisiae is also demonstrated. [ABSTRACT FROM AUTHOR]

Studies in E. sinensis have shown that ubiquitination mediated by Cullin-RING E3 ligases (CRLs) plays important roles in spermatogenesis. In other species, CRLs are also essential in cell cycle progression, DNA replication, signal transduction, gene transcription, and development. The catalytic RING component, the RING box protein, is an important part of CRLs. However, there have been few studies on CRLs in crustaceans. In this study, we cloned two RING box protein genes from the Chinese mitten crab, Eriocheir sinensis , termed Es -RBX1 and Es -RBX2 The full length Es -RBX1 cDNA comprises 741 nucleotides, and encodes a protein of 124 amino acid residues, whereas the Es -RBX2 cDNA comprises 1325 nucleotides, and encodes a protein of 110 amino acid residues. Bioinformatics analysis showed that the domains and structure of the RBX proteins have been highly conserved during evolution. Quantitative real-time polymerase chain reaction and western blotting showed that Es -RBX1 is highly expressed in the testis, particularly during the spermatocyte stage, whereas Es -RBX2 did not show specific expression in the male reproductive system. Furthermore, Es -RBX1 is mainly distributed in the nucleus, and changed its location with the development of the nucleus. Co-immunoprecipitation showed that Es -RBX1 could bind Cullin4. These results suggested that Es -RBX1 plays a key role in spermatogenesis of E. sinensis though forming a complex with Cullin4. [ABSTRACT FROM AUTHOR]