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The main objective of this paper is to analyze the prognostic and immunological value of CDC45 in kidney renal clear cell carcinoma (KIRC) using single-cell and bulk RNA-sequencing approaches. The expression of CDC45 in KIRC was evaluated by the HPA database, the TCGA-KIRC dataset and verified by PCR analysis and single-cell RNA-sequencing. The ability of CDC45 to independently predict prognosis in KIRC was confirmed by univariate/multivariate regression analysis. Gene set enrichment analysis (GSEA) was employed to explore CDC45-related pathways in KIRC. In addition, Relationships between CDC45 and immunity were also examined. Elevated CDC45 expression in KIRC was demonstrated at mRNA and protein levels. The results of the correlation analysis showed that as CDC45 expression increased, so did the histological grade, clinical stage, and TNM stage of the patients (p < 0.05). Univariate/multivariate regression analysis suggested CDC45 as an independent prognostic factor for KIRC. Seven pathways related to CDC45 were screened through GSEA. Meanwhile, we found that CDC45 was correlated with tumor mutational burden (TMB) and microsatellite instability (MSI) but not tumor neoantigen burden (TNB). Regarding immunity, CDC45 exhibited correlations with the tumor microenvironment, immune cell infiltration, and immune checkpoints. Besides, low CDC45 expression was shown to be associated with a better response to immunotherapy. Single-cell RNA-sequencing revealed that CDC45 was differently expressed in T cells (p < 0.05). CDC45 showed potential as a prognostic biomarker and therapeutic target for KIRC. Meanwhile, the CDC45 low expression group was more sensitive to immunotherapy. [ABSTRACT FROM AUTHOR]

Background: Early prediction of pathological complete response (pCR) is important for deciding appropriate treatment strategies for patients. In this study, we aimed to quantify the dynamic characteristics of dynamic contrast-enhanced magnetic resonance images (DCE-MRI) and investigate its value to improve pCR prediction as well as its association with tumor heterogeneity in breast cancer patients. Methods: The DCE-MRI, clinicopathologic record, and full transcriptomic data of 785 breast cancer patients receiving neoadjuvant chemotherapy were retrospectively included from a public dataset. Dynamic features of DCE-MRI were computed from extracted phase-varying radiomic feature series using 22 CAnonical Time-sereis CHaracteristics. Dynamic model and radiomic model were developed by logistic regression using dynamic features and traditional radiomic features respectively. Various combined models with clinical factors were also developed to find the optimal combination and the significance of each components was evaluated. All the models were evaluated in independent test set in terms of area under receiver operating characteristic curve (AUC). To explore the potential underlying biological mechanisms, radiogenomic analysis was implemented on patient subgroups stratified by dynamic model to identify differentially expressed genes (DEGs) and enriched pathways. Results: A 10-feature dynamic model and a 4-feature radiomic model were developed (AUC = 0.688, 95%CI: 0.635–0.741 and AUC = 0.650, 95%CI: 0.595–0.705) and tested (AUC = 0.686, 95%CI: 0.594–0.778 and AUC = 0.626, 95%CI: 0.529–0.722), with the dynamic model showing slightly higher AUC (train p = 0.181, test p = 0.222). The combined model of clinical, radiomic, and dynamic achieved the highest AUC in pCR prediction (train: 0.769, 95%CI: 0.722–0.816 and test: 0.762, 95%CI: 0.679–0.845). Compared with clinical-radiomic combined model (train AUC = 0.716, 95%CI: 0.665–0.767 and test AUC = 0.695, 95%CI: 0.656–0.714), adding the dynamic component brought significant improvement in model performance (train p < 0.001 and test p = 0.005). Radiogenomic analysis identified 297 DEGs, including CXCL9, CCL18, and HLA-DPB1 which are known to be associated with breast cancer prognosis or angiogenesis. Gene set enrichment analysis further revealed enrichment of gene ontology terms and pathways related to immune system. Conclusion: Dynamic characteristics of DCE-MRI were quantified and used to develop dynamic model for improving pCR prediction in breast cancer patients. The dynamic model was associated with tumor heterogeniety in prognostic-related gene expression and immune-related pathways. [ABSTRACT FROM AUTHOR]

Background: Despite the rapid advances in modern medical technology, kidney renal clear cell carcinoma (KIRC) remains a challenging clinical problem in urology. Researchers urgently search for useful markers to break through the therapeutic conundrum due to its high lethality. Therefore, the study explores the value of ADH5 on overall survival (OS) and the immunology of KIRC. Methods: The gene expression matrix and clinical information on ADH5 in the TCGA database were validated using external databases and qRT-PCR. To confirm the correlation between ADH5 and KIRC prognosis, univariate/multivariate Cox regression analysis was used. We also explored the signaling pathways associated with ADH5 in KIRC and investigated its association with immunity. Results: The mRNA and protein levels showed an apparent downregulation of ADH5 in KIRC. Correlation analysis revealed that ADH5 was directly related to histological grade, clinical stage, and TMN stage (p < 0.05). Univariate and multivariate Cox regression analysis identified ADH5 as an independent factor affecting the prognosis of KIRC. Enrichment analysis looked into five ADH5-related signaling pathways. The results showed no correlation between ADH5 and TMB, TNB, and MSI. From an immunological perspective, ADH5 was found to be associated with the tumor microenvironment, immune cell infiltration, and immune checkpoints. Lower ADH5 expression was associated with greater responsiveness to immunotherapy. Single-cell sequencing revealed that ADH5 is highly expressed in immune cells. Conclusion: ADH5 could be a promising prognostic biomarker and a potential therapeutic target for KIRC. Besides, it was found that KIRC patients with low ADH5 expression were more sensitive to immunotherapy. [ABSTRACT FROM AUTHOR]

Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common congenital facial malformation with a complex, incompletely understood origin. Long noncoding RNAs (lncRNAs) have emerged as pivotal regulators of gene expression, potentially shedding light on NSCL/P's etiology. This study aimed to identify critical lncRNAs and construct regulatory networks to unveil NSCL/P's underlying molecular mechanisms. Integrating gene expression profiles from the Gene Expression Omnibus (GEO) database, we pinpointed 30 dysregulated NSCL/P-associated lncRNAs. Subsequent analyses enabled the creation of competing endogenous RNA (ceRNA) networks, lncRNA-RNA binding protein (RBP) interaction networks, and lncRNA cis and trans regulation networks. RT-qPCR was used to examine the regulatory networks of lncRNA in vivo and in vitro. Furthermore, protein levels of lncRNA target genes were validated in human NSCL/P tissue samples and murine palatal shelves. Consequently, two lncRNAs and three mRNAs: FENDRR (log2FC = − 0.671, P = 0.040), TPT1-AS1 (log2FC = 0.854, P = 0.003), EIF3H (log2FC = − 1.081, P = 0.041), RBBP6 (log2FC = 0.914, P = 0.037), and SRSF1 (log2FC = 0.763, P = 0.026) emerged as potential contributors to NSCL/P pathogenesis. Functional enrichment analyses illuminated the biological functions and pathways associated with these lncRNA-related networks in NSCL/P. In summary, this study comprehensively delineates the dysregulated transcriptional landscape, identifies associated lncRNAs, and reveals pivotal sub-networks relevant to NSCL/P development, aiding our understanding of its molecular progression and setting the stage for further exploration of lncRNA and mRNA regulation in NSCL/P. [ABSTRACT FROM AUTHOR]

[Objective] This study investigated molecular structure, expression characteristics and function of the HTRA gene in Takifugu fasciatus and explored the correlation between HTRA gene and puffer growth. [Method] The 3 UTR, 5 UTR and intermediate fragments of HTRA gene were separately amplified by segmental cloning, the full-length cDNA sequence was obtained after splicing, and bioinformatics analysis was performed. The expression pattern of the HTRA gene in 10 tissues including brain, kidney, liver, spleen, heart, ovary, midgut, gill, skin and muscle and 8 tissues of ovary at 5 different developmental stages (I -V)including brain, kidney, liver, spleen, heart, midgut, gill and muscle was analyzed by quantitative real-time PCR technology. Finally, Sanger sequencing was used to screen the SNP loci related to growth traits in the coding region of HTRA. [Result] The cDNA full-length sequence of HTRA gene in largemouth bass was 2 302 bp in length with a 1 170 bp open reading frame encoding 389 amino acids and 5 exons. The amino acid sequence alignment and phylogenetic tree analysis showed that T. fasciatus had the highest identity (99.53%) with Takifugu rubripes. Spatial structure of HTRi protein showed that it was conserved in fish. The HTRA gene was expressed in 10 different tissues. The highest expression level was in brain, followed by midgut, and the lowest expression was in muscle tissue. The HTRA gene was expressed in 8 different tissues of the ovary at five different developmental periods, with the highest expression in the IV period of ovarian development. A synonymous mutant SNP locus (c.1202 C>G) at 1 202 bp in exon A of the HTRA gene of T. fasciatus was screened and association analysis showed that the SNP loci had significant correlation (P< 0.05) with fatness in T. fasciatus. Individuals with CC genotype had higher fatness than others. [Conclusion] The HTRA gene played important roles in the growth and development of T. fasciatus. It can be used as a candidate gene and molecular maker for selection of new varieties. [ABSTRACT FROM AUTHOR]

Chronic lymphocytic leukemia (CLL) is a subtype of B-cell malignancy with high heterogeneity. XPO1 is highly expressed in many hematological malignancies, which predicts poor prognosis. In the study, we aimed to explore the prognostic role of XPO1 and the therapeutic effect of Selinexor, a selective inhibitor of nuclear export, which targets XPO1. We collected 200 CLL samples in our center to confirm XPO1 mRNA expression and analyzed the correlation between XPO1 expression and prognosis. Then, we decreased XPO1 expression with Selinexor to explore the effect of proliferation inhibition, cell cycle arrest, and apoptosis in CLL cell lines. RNA-Seq was performed to explore potential mechanisms. We analyzed XPO1 expression in a cohort of 150 treatment naive patients and another cohort of 50 relapsed and refractory (R/R) patients and found that XPO1 expression was upregulated in 76% of CLL patients compared with healthy donors. Survival analysis suggested that patients with increased XPO1 expression had inferior treatment-free survival (P = 0.022) and overall survival (P = 0.032). The inhibitor of XPO1, Selinexor, induced apoptosis in primary CLL cells. We showed the effects of Selinexor on proliferation inhibition, cell cycle arrest, and apoptosis in CLL cell lines with JVM3, MEC1, and ibrutinib-resistant (MR) cells via nuclear retention of cargo proteins of IκBα, p65, p50, and FOXO3a. Moreover, downregulation of the NF-κB and FOXO pathways was a common feature of the three CLL cell lines responding to Selinexor, indicating the potential application of XPO1 inhibitor even in the high-risk CLL cells. We identified XPO1 as an unfavorable prognostic factor for CLL patients and provided a rationale for further investigation of the clinically XPO1 targeted therapeutic strategy against CLL. [ABSTRACT FROM AUTHOR]

How cells adapt their gene expression to nutritional changes remains poorly understood. Histone H3T11 is phosphorylated by pyruvate kinase to repress gene transcription. Here, we identify the protein phosphatase 1 (PP1), Glc7 as the enzyme that specifically dephosphorylates H3T11. We also characterize two novel Glc7-containing complexes and reveal their roles in regulating gene expression upon glucose starvation. Specifically, the Glc7–Sen1 complex dephosphorylates H3T11 to activate the transcription of autophagy-related genes. The Glc7–Rif1–Rap1 complex dephosphorylates H3T11 to derepress the transcription of telomere-proximal genes. Upon glucose starvation, Glc7 expression is up-regulated and more Glc7 translocates into the nucleus to dephosphorylate H3T11, leading to induction of autophagy and derepressed transcription of telomere-proximal genes. Furthermore, the functions of PP1/Glc7 and the two Glc7-containing complexes are conserved in mammals to regulate autophagy and telomere structure. Collectively, our results reveal a novel mechanism that regulate gene expression and chromatin structure in response to glucose availability. [ABSTRACT FROM AUTHOR]

Psoriasis is an immune system disorder induced by the interaction of the polygenic background and environmental factors. Tumor necrosis factor-α (TNF-α)-induced protein 8-like 2 (TNFAIP8L2, TIPE2), a regulator of immunity, is differentially expressed in tumors, inflammation, and autoimmune diseases. However, to our knowledge, no study has evaluated TIPE2 expression in patients with psoriasis vulgaris. The present case-control study aimed to determine the expression levels of TIPE2 mRNA in the peripheral blood mononuclear cells (PBMCs) of patients with psoriasis vulgaris and analyze the correlation between TIPE2 and other inflammatory cytokine variations in the pathogenesis of psoriasis vulgaris. Thirty-three patients with psoriasis vulgaris and thirty-one healthy volunteers were enrolled from October 2021 to March 2022. The mRNA expression levels of TIPE2, RELA (NF-κb p65), TNF-α, IL-10, IL-6, and IL-1β in PBMCs were determined using qPCR. The severity of psoriasis vulgaris was determined according to the Psoriasis Area and Severity Index (PASI) scores. TIPE2 mRNA expression significantly decreased, while the expression of RELA, TNF-α, IL-10, IL-6, and IL-1β increased in patients with psoriasis vulgaris compared with that in the healthy control group. In addition, the expression levels of TIPE2, RELA, TNF-α, and IL-1β positively correlated with the PASI score. TIPE2 mRNA expression negatively correlated with IL-6 and positively correlated with TNF-α. Moreover, TIPE2 mRNA expression was higher in the active stage than that in the stationary stage. Notably, TNF-α expression levels were higher in patients with psoriasis vulgaris combined with a history of respiratory infection. TIPE2 may contribute to the pathogenesis of psoriasis and be a potential biomarker of psoriasis vulgaris. [ABSTRACT FROM AUTHOR]

In this paper, we propose a frequentist model averaging method for quantile regression with high‐dimensional covariates. Although research on these subjects has proliferated as separate approaches, no study has considered them in conjunction. Our method entails reducing the covariate dimensions through ranking the covariates based on marginal quantile utilities. The second step of our method implements model averaging on the models containing the covariates that survive the screening of the first step. We use a delete‐one cross‐validation method to select the model weights, and prove that the resultant estimator possesses an optimal asymptotic property uniformly over any compact (0,1) subset of the quantile indices. Our proof, which relies on empirical process theory, is arguably more challenging than proofs of similar results in other contexts owing to the high‐dimensional nature of the problem and our relaxation of the conventional assumption of the weights summing to one. Our investigation of finite‐sample performance demonstrates that the proposed method exhibits very favorable properties compared to the least absolute shrinkage and selection operator (LASSO) and smoothly clipped absolute deviation (SCAD) penalized regression methods. The method is applied to a microarray gene expression data set. [ABSTRACT FROM AUTHOR]

The Acanthopanax senticosus has been shown to have a wide range of pharmacological activities, which are associated with health benefits, such as antioxidant, anti-inflammatory, and antiapoptotic properties. A previous study has shown that the n-butanol fraction of A. senticosus extract had the strongest antioxidant effect in vitro. This study aimed to investigate the effects that the n-butanol fraction of A. senticosus extract could relieve oxidative stress damage through antioxidant and antiapoptotic in the H2O2-stimulated RAW264.7 macrophages and the CCl4-induced liver injury. The result showed that the n-butanol fraction extract could relieve damage by increasing the intracellular antioxidant enzymes (SOD) level, decreasing intracellular ROS and MDA levels, and regulating antioxidant and antiapoptotic-related gene expression levels. The morphological observation of HE, TUNE, and immunohistochemistry staining of liver tissue verified that the n-butanol fraction extract is though anti-oxidative and antiapoptotic to alleviate cellular oxidative damage. The RT-PCR assay showed that the Keap1-Nrf2-ARE and the Bax/Bcl-2 signaling pathway were related to the molecular mechanism of action. The experimental results show that Acanthopanax senticosus extract has a good effect in treating liver injury and enhancing the antioxidant capacity of the body. [ABSTRACT FROM AUTHOR]

Background. Lysine crotonylation (Kcr) is a newly identified posttranslational modification type regulated by various enzymes and coenzymes, including lysine crotonyltransferase, lysine decrotonylase, and binding proteins. However, the role of Kcr regulators in head and neck squamous cell carcinoma (HNSCC) remains unknown. The aim of this study was to establish and validate a Kcr-related prognostic signature of HNSCC and to assess the clinical predictive value of this signature. Methods. The mRNA expression profiles and clinicopathological data from The Cancer Genome Atlas (TCGA) database were downloaded to explore the clinical significance and prognostic value of these regulators in HNSCC. The least absolute shrinkage and selection operator (LASSO) Cox regression model was used to generate the Kcr-related prognostic signature for HNSCC. Subsequently, the GSE65858 dataset from the Gene Expression Omnibus (GEO) database was used to validate the signature. The prognostic value of the signature was evaluated using the Kaplan-Meier survival, receiver operating characteristic (ROC) curve, and univariate and multivariate Cox regression analyses. Results. We established a nine-gene risk signature associated with the prognosis of HNSCC based on Kcr regulators. High-risk patients demonstrated significantly poorer overall survival (OS) than low-risk patients in the training (TCGA) and validation (GEO) datasets. Then, the time-dependent receiver operating characteristic (ROC) curve analysis showed that the nine-gene risk signature was more accurate for predicting the 5-year OS than other clinical parameters, including age, gender, T stage, N stage, and histologic grade in the TCGA and GEO datasets. Moreover, the Cox regression analysis showed that the constructed risk signature was an independent risk factor for HNSCC. Conclusion. Our study identified and validated a nine-gene signature for HNSCC based on Kcr regulators. These results might contribute to prognosis stratification and treatment escalation for HNSCC patients. [ABSTRACT FROM AUTHOR]

Cells need to coordinate gene expression with their metabolic states to maintain cell homeostasis and growth. How cells transduce nutrient availability to appropriate gene expression remains poorly understood. Here we show that glycolysis regulates histone modifications and gene expression by activating protein kinase A (PKA) via the Ras-cyclic AMP pathway. The catalytic subunit of PKA, Tpk2 antagonizes Jhd2-catalyzed H3K4 demethylation by phosphorylating Jhd2 at Ser321 and Ser340 in response to glucose availability. Tpk2-catalyzed Jhd2 phosphorylation impairs its nuclear localization, reduces its binding to chromatin, and promotes its polyubiquitination and degradation by the proteasome. Tpk2-catalyzed Jhd2 phosphorylation also maintains H3K14 acetylation by preventing the binding of histone deacetylase Rpd3 to chromatin. By phosphorylating Jhd2, Tpk2 regulates gene expression, maintains normal chronological life span and promotes autophagy. These results provide a direct connection between metabolism and histone modifications and shed lights on how cells rewire their biological responses to nutrient signals. How cells transduce nutrient availability to appropriate gene expression remains poorly understood. Here the authors show that the nutrient sensor, protein kinase A modulates histone modifications and gene transcription by phosphorylating histone demethylase. [ABSTRACT FROM AUTHOR]

Objective. This study aims to determine the curative effect of Fuyuan Xingshen Decoction combined with butylphthalide sodium chloride injection in acute cerebral infarction (ACI) treatment and its effect on hemodynamics. Methods. In our hospital, a total of 84 ACI patients from May 2020 to February 2022 were randomly divided into two groups: observation and control (n = 42 each). Fuyuan Xingshen Decoction in combination with butylphthalide sodium chloride injection was provided to the observation group, while the control group received butylphthalide sodium chloride injection alone. Both groups' clinical efficacy was observed. Before and after treatment, the neurological function of the two groups was evaluated using the National Institutes of Health Stroke Scale (NIHSS), while the daily living ability of both groups was determined using the Barthel index rating scale. Both groups were investigated for their cognitive function, before and after treatment, by using the Mini-Cog scale and Montreal Cognitive Assessment (MoCA) scale. The pulsatility index (PI), peak velocity (Vp), and mean velocity (Vm) of intracranial arteries were measured by transcranial Doppler ultrasonography before and after treatment. The levels of ubiquitin carboxy-terminal hydrolase-1 (UCH-L1), Fibulin-5, and visinin-like protein-1 (VILIP-1) in serum and the expression levels of miR-34c, miR-25, and miR-182 in peripheral blood of the two groups were compared. Both groups were observed for the incidence of adverse reactions. Results. Compared with the control (71.43%), the observation group exhibited a significantly higher effective rate of around 90.48%. In the observation group, the improvement in NIHSS, Barthel index, Mini-cog, and MoCA scores; hemodynamic indexes including Vp, PI, and Vm; serum UCH-L1, Fibulin-5, and VILIP-1 levels; and the miR-34c, miR-25, and miR-182 expression levels in peripheral blood was better than the control group, with significant difference (all P < 0.05). The incidence of adverse reactions between the groups demonstrated no significant differences (P > 0.05). Conclusions. Fuyuan Xingshen Decoction combined with butylphthalide sodium chloride injection can effectively improve patients' daily living ability, neurological function, cognitive function, and cerebral hemodynamics in the treatment of ACI, with good effect and safety. [ABSTRACT FROM AUTHOR]

Background: Water deficit (WD) has serious effect on the productivity of crops. Formation of cuticular layer with increased content of wax and cutin on leaf surfaces is closely related to drought tolerance. Identification of drought tolerance associated wax components and cutin monomers and the genes responsible for their biosynthesis is essential for understanding the physiological and genetic mechanisms underlying drought tolerance and improving crop drought resistance. Result: In this study, we conducted comparative phenotypic and transcriptomic analyses of two Gossypium hirsutum varieties that are tolerant (XL22) or sensitive (XL17) to drought stress. XL17 consumed more water than XL22, particularly under the WD conditions. WD significantly induced accumulation of most major wax components (C29 and C31 alkanes) and cutin monomers (palmitic acid and stearic acid) in leaves of both XL22 and XL17, although accumulation of the major cutin monomers, i.e., polyunsaturated linolenic acid (C18:3n-3) and linoleic acid (C18:2n-6), were significantly repressed by WD in both XL22 and XL17. According to the results of transcriptome analysis, although many genes and their related pathways were commonly induced or repressed by WD in both XL22 and XL17, WD-induced differentially expressed genes specific to XL22 or XL17 were also evident. Among the genes that were commonly induced by WD were the GhCER1 genes involved in biosynthesis of alkanes, consistent with the observation of enhanced accumulation of alkanes in cotton leaves under the WD conditions. Interestingly, under the WD conditions, several GhCYP86 genes, which encode enzymes catalyzing the omega-hydroxylation of fatty acids and were identified to be the hub genes of one of the co-expression gene modules, showed a different expression pattern between XL22 and XL17 that was in agreement with the WD-induced changes of the content of hydroxyacids or fatty alcohols in these two varieties. Conclusion: The results contribute to our comprehending the physiological and genetic mechanisms underlying drought tolerance and provide possible solutions for the difference of drought resistance of different cotton varieties. [ABSTRACT FROM AUTHOR]

Objective: Systemic lupus erythematosus (SLE) is a prototypical autoimmune disease with differences in prevalence and severity among ancestral groups. This study was undertaken to identify novel genetic components, either shared by or distinct between Asian and European populations. Methods: Both trans‐ancestral and ancestry‐specific meta‐analyses of genome‐wide association studies (GWAS) for SLE were performed, involving 30,604 participants of European, Chinese, or Thai origin. Using public epigenomic data and expression quantitative trait loci, fine‐mapping analyses were conducted to identify putative causal variants and genes for the newly identified loci. Performance of polygenic risk scores for the Thai cohort was evaluated by comparing different training data. Results: A 1‐bp deletion upstream of IFNLR1 was found to be associated with SLE, with the risk allele correlated with increased expression of IFNLR1. This gene encodes interferon‐λ (IFNλ) receptor 1, providing evidence of a role of type III IFN signaling in SLE. An intronic variant in SLC29A3 was found to be associated with SLE in Asians only. The putative risk variant may modulate SLC29A3 expression in a monocyte‐specific manner. SLC29A3 encodes a lysosomal nucleoside transporter, and subsequent analyses suggested that reduced lysosomal function and phagocytosis might be the mechanism underlying this association. Ancestry‐shared loci in or near TAOK3, CHD9, CAMK1D, ATXN1, and TARBP1 and Asian‐specific loci close to PEX2, FCHSD2, and TMEM116 also reached the genome‐wide significant association with SLE. In addition, trans‐ancestral meta‐analysis was shown to be valuable in risk prediction for individuals without ancestry‐matched data. Conclusion: In this study both shared and Asian‐specific loci for SLE were identified, and functional annotation provided evidence of the involvement of increased type III IFN signaling and reduced lysosomal function in SLE. [ABSTRACT FROM AUTHOR]

In elderly people, Alzheimer's disease (AD) is the most common form of dementia. It has been shown that traditional Chinese medicine (TCM) based on phytomedicines enhances the therapeutic effects of modern medicine when taken in conjunction with them. Modern medicine N-methyl-D-aspartate receptor (NMDA) antagonist memantine (Mm) are mainly used in the clinical treatment of AD. TCM Cerebralcare Granule® (CG) has long been an effective treatment for headaches, dizziness, and other symptoms. In this study, we employ a blend of CG and Mm to address Alzheimer's disease-like symptoms and explore their impacts and underlying mechanisms. The objective of our study was to observe the effects of CG combined with Memantine (Mm) on learning and memory impairment of AD mice induced by D-galactose and to explore the mechanism at work. CG and Mm were combined to target multiple pathological processes involved in AD. For a thorough analysis, we performed various experiments such as behavioral detection, pathological detection, proteomic detection, and other experimental methods of detection. It was found that the combination of CG and Mm was significantly effective for improving learning and memory in AD mice as well as brain pathology. The serum and hippocampal tissue of AD mice were significantly enhanced with catalase (CAT), superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px) activities and malondialdehyde (MDA) levels were decreased with this treatment. In AD mice, a combination of Mm and CG (CG + Mm) significantly increased the levels of the anti-inflammatory factors IL-4 and IL-10, decreased the levels of pro-inflammatory factors (IL-6, IL-1β) and tumor necrosis factor-alpha (TNF-α), improved synaptic plasticity by restoring synaptophysin (SYP) and postsynaptic density protein-95 (PSD-95) expression in the hippocampus, enhanced Aβ phagocytosis of microglia in AD mice, and increased mitochondrial respiratory chain enzyme complexes I, II, III, and IV, lead to an increase in the number of functionally active NMDA receptors in the hippocampus. Proteomic analysis GO analysis showed that the positive regulation gene H3BIV5 of G protein coupled receptor signal pathway and synaptic transmission was up-regulated, while the transsynaptic signal of postsynaptic membrane potential and regulation-related gene Q5NCT9 were down-regulated. Most proteins showed significant enriched signal transduction pathway profiles after CG + Mm treatment, based on the KEGG pathway database. The data supported the idea that CG and Mm could be more effective in treating AD mice induced by D-galactose than Mm alone. We provided a basis for the clinical use of CG with Mm. [Display omitted] [ABSTRACT FROM AUTHOR]

Poria cocos (Schw.) Wolf (Polyporaceae, P.cocos), which is born on the pine root, has a history of more than two thousand years of medicine in China. P.cocos was first recorded in the Shennong's Herbal Classic, studies have proved its lipid-lowering effect. The aim of study was to investigate the underlying mechanism of P.cocos extract on hyperlipidemia. Male Sprague-Dawley (SD) rats aged 9–12 weeks were intraperitoneally (IP) injected with Triton-WR 1339 to establish an acute hyperlipidemia model. At 0 h and 20 h after the model was established, low and high doses of P.cocos extract or simvastatin were given twice. After 48 h, the rats were sacrificed, and liver and serum samples were collected for analysis. The cell model was constructed by treating L02 cells with 1% fat emulsion-10% FBS–RPMI 1640 medium for 48 h. At the same time, low and high doses of P.cocos extract and simvastatin were administered. Oil red O staining was used to evaluate the lipid accumulation in the cells, and H&E staining was used to evaluate the liver lesions of rats. Real-time quantitative PCR and western blotting were used to detect the expressions of lipid metabolism-related genes. P.cocos extract relieved lipid accumulation in vitro and alleviated hyperlipidemia in vivo. Both gene and protein expressions of peroxisome proliferator-activated receptor α (PPARα) were shown to be up-regulated by P.cocos extract. Additionally, P.cocos extract down-regulated the expressions of fatty acid synthesis-related genes sterol regulatory element-binding protein-1 (SREBP-1), Acetyl-CoA Carboxylase 1 (ACC1) and fatty acid synthase (FAS), while up-regulated the expressions of cholesterol metabolism-related genes liver X receptor-α (LXRα), ATP-binding cassette transporter A1 (ABCA1), cholesterol 7alpha-hydroxylase (CYP7A1) and low density lipoprotein receptor (LDLR), which were reversed by the treatment with the PPARα inhibitor GW6471. P.cocos extract ameliorates hyperlipidemia and lipid accumulation by regulating cholesterol homeostasis in hepatocytes through PPARα pathway. This study provides evidence that supplementation with P.cocos extract could be a potential strategy for the treatment of hyperlipidemia. [Display omitted] • P.cocos extract alleviated hyperlipidemia in vivo and in vitro. • P.cocos extract regulated lipid metabolism in hepatocytes. • P.cocos extract regulated lipid metabolism in hepatocytes via PPARα pathway. • PPARα inhibitor GW6471 attenuated the lipid-lowering effect of P.cocos extract. • Triterpenes were the main active ingredients in the lipid-lowering P.cocos extract. [ABSTRACT FROM AUTHOR]

This study aimed to identify potential novel drug candidates and targets for Parkinson's disease. First, 970 genes that have been reported to be related to PD were collected from five databases, and functional enrichment analysis of these genes was conducted to investigate their potential mechanisms. Then, we collected drugs and related targets from DrugBank, narrowed the list by proximity scores and Inverted Gene Set Enrichment analysis of drug targets, and identified potential drug candidates for PD treatment. Finally, we compared the expression distribution of the candidate drug-target genes between the PD group and the control group in the public dataset with the largest sample size (GSE99039) in Gene Expression Omnibus. Ten drugs with an FDR < 0.1 and their corresponding targets were identified. Some target genes of the ten drugs significantly overlapped with PD-related genes or already known therapeutic targets for PD. Nine differentially expressed drug-target genes with p < 0.05 were screened. This work will facilitate further research into the possible efficacy of new drugs for PD and will provide valuable clues for drug design. [ABSTRACT FROM AUTHOR]

Studies have shown that tumor microenvironment (TME) might affect drug sensitivity and the classification of colorectal cancer (CRC). Using TME-specific gene signature to identify CRC subtypes with distinctive clinical relevance has not yet been tested. A total of 18 "bulk" RNA-seq datasets (total n = 2269) and four single-cell RNA-seq datasets were included in this study. We constructed a "Signature associated with FOLFIRI resistant and Microenvironment" (SFM) that could discriminate both TME and drug sensitivity. Further, SFM subtypes were identified using K-means clustering and verified in three independent cohorts. Nearest template prediction algorithm was used to predict drug response. TME estimation was performed by CIBERSORT and microenvironment cell populations-counter (MCP-counter) methods. We identified six SFM subtypes based on SFM signature that discriminated both TME and drug sensitivity. The SFM subtypes were associated with distinct clinicopathological, molecular and phenotypic characteristics, specific enrichments of gene signatures, signaling pathways, prognosis, gut microbiome patterns, and tumor lymphocytes infiltration. Among them, SFM-C and -F were immune suppressive. SFM-F had higher stromal fraction with epithelial-to-mesenchymal transition phenotype, while SFM-C was characterized as microsatellite instability phenotype which was responsive to immunotherapy. SFM-D, -E, and -F were sensitive to FOLFIRI and FOLFOX, while SFM-A, -B, and -C were responsive to EGFR inhibitors. Finally, SFM subtypes had strong prognostic value in which SFM-E and -F had worse survival than other subtypes. SFM subtypes enable the stratification of CRC with potential chemotherapy response thereby providing more precise therapeutic options for these patients. [ABSTRACT FROM AUTHOR]

Objective: To study the role of LncRNA CASC15 in oral squamous cell carcinoma. Results: In the present study, we showed that plasma CASC15 was up‐regulated in stage I and II oral squamous cell carcinoma patients than in oral ulcer patients and healthy controls, while no significant correlation was found between oral ulcer patients and healthy controls. Up‐regulation of plasma CASC15 distinguished oral squamous cell carcinoma patients from oral ulcer patients and healthy controls. LncRNA MEG3 was inversely correlated with CASC15 in oral squamous cell carcinoma tissues. In oral squamous cell carcinoma cells, CASC15 over‐expression led to the inhibited expression of MEG3, and MEG3 over‐expression did not alter CASC15 expression. MEG3 over‐expression decreased, while CASC15 over‐expression increased the proliferation rate of oral squamous cell carcinoma cells. In addition, MEG3 over‐expression attenuated the effects of CASC15 over‐expression. Conclusion: Therefore, CASC15 over‐expression may serve as a potential diagnostic biomarker for oral squamous cell carcinoma, and CASC15 may promote oral squamous cell carcinoma cell proliferation by down‐regulating MEG3. [ABSTRACT FROM AUTHOR]

Background. Posterior capsule opacification (PCO), a complication of extracapsular lens extraction surgery that causes visual impairment, is characterized by aberrant proliferation and epithelial-mesenchymal transition (EMT) of lens epithelial cells (LECs). Curcumin, exerting inhibitive effects on cell proliferation and EMT in cancer, serves as a possible antidote towards PCO. Methods. Cellular proliferation of LECs after treatment of curcumin was measured with MTT assay and flow cytometry. The transcriptional and expressional levels of proteins related to proliferation and EMT of LECs were quantified by western blotting and real-time PCR. Results. Curcumin was found to suppress the proliferation of LECs by inducing G2/M arrest via possible inhibition of cell cycle-related proteins including CDK1, cyclin B1, and CDC25C. It had also inactivated proliferation pathways involving ERK1/2 and Akt pathways in LECs. On the other hand, curcumin downregulated the EMT of LECs through blocking the TGF-β/Smad pathway and interfering Notch pathway which play important roles in PCO. Conclusions. This study shows that curcumin could suppress the proliferation and EMT in LECs, and it might be a potential therapeutic protection against visual loss induced by PCO. [ABSTRACT FROM AUTHOR]

Background and Aim. Myeloid-derived suppressor cells (MDSCs) have attracted attention due to their important role in tumor immune escape. Several studies have investigated the involvement of MDSCs into hepatocellular carcinoma (HCC); however, due to the difference of MDSC phenotype, patient types, and sample source among the studies, the results were inconsistent and controversial. The present study aimed to confirm the expression and clinical significance of MDSCs in HBV-related HCC patients. Methods. The percentages of MDSCs, IFN-γ-producing CD4 and CD8 T cells in the peripheral blood of HCC patients, chronic hepatitis B (CHB) patients, and healthy controls (HC) were determined by flow cytometry. The serum concentrations of IL-10 and TNF-α were determined by ELISA. The association of the percentages of MDSCs with tumor burden, liver function parameters, systemic inflammation-related indexes, and IFN-γ-producing T cells was assessed. Results. The percentages of MDSCs and PMN-MDSCs were significantly higher in HCC patients than those in CHB patients and HC. The level of MDSCs was correlated with indirect bilirubin and prealbumin, as well as systemic inflammation response index, monocyte/lymphocyte ratio, and monocyte counts. The frequency of IFN-γ-producing CD8 T cells of HCC patients was lower than that of HC. However, there was no relationship between MDSCs and IFN-γ-producing CD8 T cells. The level of IL-10 in HCC patients was significantly higher than that in CHB patients. Conclusion. MDSCs seem to play an important role in the process leading from chronic HBV infection to HCC. Early inhibiting these cells could affect tumor progression. [ABSTRACT FROM AUTHOR]

Background: Cotton Verticillium wilt is one of the most devastating diseases for cotton production in the world. Although this diseases have been widely studied at the molecular level from pathogens, the molecular basis of V. dahliae interacted with cotton has not been well examined. Results: In this study, RNA-seq analysis was carried out on V. dahliae samples cultured by different root exudates from three cotton cultivars (a susceptible upland cotton cultivar, a tolerant upland cotton cultivar and a resistant island cotton cultivar) and water for 0 h, 6 h, 12 h, 24 h and 48 h. Statistical analysis of differentially expressed genes revealed that V. dahliae responded to all kinds of root exudates but more strongly to susceptible cultivar than to tolerant and resistant cultivars. Go analysis indicated that 'hydrolase activity, hydrolyzing O-glycosyl compounds' related genes were highly enriched in V. dahliae cultured by root exudates from susceptible cotton at early stage of interaction, suggesting genes related to this term were closely related to the pathogenicity of V. dahliae. Additionally, 'transmembrane transport', 'coenzyme binding', 'NADP binding', 'cofactor binding', 'oxidoreductase activity', 'flavin adenine dinucleotide binding', 'extracellular region' were commonly enriched in V. dahliae cultured by all kinds of root exudates at early stage of interaction (6 h and 12 h), suggesting that genes related to these terms were required for the initial steps of the roots infections. Conclusions: Based on the GO analysis results, the early stage of interaction (6 h and 12 h) were considered as the critical stage of V. dahliae-cotton interaction. Comparative transcriptomic analysis detected that 31 candidate genes response to root exudates from cotton cultivars with different level of V. dahliae resistance, 68 response to only susceptible cotton cultivar, and 26 genes required for development of V. dahliae. Collectively, these expression data have advanced our understanding of key molecular events in the V. dahliae interacted with cotton, and provided a framework for further functional studies of candidate genes to develop better control strategies for the cotton wilt disease. [ABSTRACT FROM AUTHOR]

Traumatic brain injury (TBI) is the most common cause of death and permanent disability in people aged <45, and is associated with secondary brain injury and bleed progression, resulting in increased morbidity and mortality. TBI may also induce innate host defense responses characterized by activation of resident microglia and astrocytes, brain microvascular endothelial cells and peripheral blood monocytes. In the present study, 34 patients with moderate-to-severe traumatic brain injury were randomly divided into two groups, including a 7.5% hypertonic saline (HS) treatment group (4 ml/kg) and 3% HS treatment group (4 ml/kg). The results demonstrated that treatment with 7.5% HS decreased the intracranial pressure and improved coagulofibrinolytic homeostasis. Analysis of the monocyte subsets revealed significant reduction in the proportion of cluster of differentiation (CD)14++CD16+ circulating inflammatory monocytes in the 7.5% HS group. In addition, 7.5% HS treatment downregulated the expression of long non-coding (lnc) RNA2448-11 and lncRNA1403 in the peripheral blood mononuclear cells of patients with TBI. Using reverse transcription-quantitative polymerase chain reaction, it was determined that 7.5% HS regulated the expression of tumor necrosis factor-α, interleukin-1β, transforming growth factor-β and thrombomodulin, which are the target genes of lncRNA2448-11 and lncRNA1403. These results indicated that 7.5% HS improved the intracranial pressure and coagulofibrinolytic homeostasis by modulating the phenotype of monocytes through lncRNA2448-11 and lncRNA1403. These findings provided evidence that initial resuscitation with HS imparts functional changes to inflammatory cells following TBI, thereby reducing potential neuroinflammatory events associated with secondary brain injury. [ABSTRACT FROM AUTHOR]

Verticillium wilt (VW), known as the 'cancer' of cotton, is a vascular disease of cotton caused by Verticillium dahliae , which seriously affects the yield and quality of cotton. Upland cotton (Gossypium hirsutum , Gh) has good yield but low resistance to VW, while Sea-island cotton (G. barbadense , Gb) has excellent resistance to VW and good fiber quality but low yield. Creating chromosome segment substitution lines (CSSLs) from progeny of interspecific cross between Gh and Gb is a way to combine the superior traits of Gh and Gb to breed cotton varieties with high yield and fiber quality as well as good disease resistance. In this study, a CSSL population derived from Emian22 (Gh) × 3–79 (Gb) was subject to disease assay in multiple environments to identify VW-resistant CSSLs. The two CSSLs (M20 and M34) showing stable VW-resistance in different assay conditions together with the VW susceptible parent Emian22 were selected for comparative transcriptome analysis to identify genes associated with cotton response to V. dahliae infection. Significant transcriptome changes were found to occur at each time point (24, 48, and 72 h) after V. dahliae infection in all three lines. Gene ontology (GO) analysis of the DEGs identified in each line revealed enriched terms shared by the three lines or unique to each line. Based on gene expression trend analysis, the DEGs identified in M20, M34, and Emian22 were clustered into 8, 8, and 7 cluster, respectively, with one unique to Emian22 and one unique to both M20 and M34. Weighted gene co-expression network analysis (WGCNA) identified 8 modules significantly related to cotton response to V. dahliae infection, especially the cyan module with 22 hub genes, including two genes (Ghi_D02G10111 and Ghi_A03G10581) encoding probable protein phosphatase 2. Suppressing the expression level of Ghi_D02G10111 (GhPP2C52) by virus-induced gene silencing led to the reduction of VW-resistance, implying GhPP2C52 being a positive regulator of VW-resistance. In addition, genes of the ABA and Ca2+ signaling pathways were found to be associated with the response of cotton plants to V. dahliae infection. The findings of the study revealed the molecular difference between the VW-resistant and VW-susceptible cotton lines. Combining the genetic mapping results of the same population, the results of this study will facilitate cloning and molecular characterization of the genes responsible for VW-resistance observed in M20 and M34 and finally accelerate breeding VW-resistant cotton varieties through marker assisted selection and gene editing. [Display omitted] • Verticillium wilt seriously affects the yield and quality of cotton. • Two CSSLs (VW resistant) and Emian22 (VW susceptible) were selected for the materials. • Two genes (Ghi_D02G10111 and Ghi_A03G10581) were considered as good candidates. • The results provide a new theory related to cotton resistance to V. dahliae infection. [ABSTRACT FROM AUTHOR]

Background: This study aimed to explore the relationship between nucleophosmin (NPM1) and patient clinical characteristics. Moreover, we investigated the effect of NPM1 in tumor proliferation and apoptosis of salivary gland adenoid cystic carcinoma (SACC).Materials and Methods: NPM1 expression was examined in 74 specimens of SACC and 31 non-cancerous epithelium adjacent to carcinoma (NCEAC) by immunohistochemistry (IHC). RNA interference technology was used to silence NPM1 expression in SACC cells. We used transwell culture assay, cell counting kit-8 tests, and colony formation assay to test the proliferation, cisplatin resistance, migration, and invasiveness of SACC cells.Results: The nuclear and cytoplasmic expression of NPM1 in SACC tissue was overexpressed and was tightly linked to perineural invasion and lymph node metastasis. The downregulation of NPM1 inhibited proliferation and induced apoptosis in SACC cells. Knockdown of NPM1 expression had no effect on chemoresistance migration, or invasiveness.Conclusions: NPM1 may play an important role in tumor progress in SACC and is a potential biomarker for SACC. [ABSTRACT FROM AUTHOR]

Simple Summary: The study investigated the prostate cancer microenvironment and the correlation between peritumoral collagen and aggressivity of cancer. We used novel and advanced imaging including next-generation sequencing to characterise the expression of collagen in the extracellular matrix. Type and contents of collagen varied according to the Gleason grade in prostate cancer in men with localised prostate cancer undergoing radical surgery. The collagen contents orientation seen on second harmonic generation imaging varied with the grade of cancer and can predict clinically significant prostate cancer. Increased expression of Col1A1 is present in cancer tissues and associated with increased tissue modulus as measured by ultrasound shear wave elastography in prostate cancer. The study adds knowledge to our understanding of prostate cancer and defines the microenvironment of clinically significant prostate cancer, a disease more likely to impact survival and outcome of men who suffer from it. Prostate cancer has a poor prognosis and high mortality rate due to metastases. Extracellular matrix (ECM) re-modelling and stroma composition have been linked to cancer progression, including key components of cell migration, tumour metastasis, and tissue modulus. Moreover, collagens are one of the most significant components of the extracellular matrix and have been ascribed to many aspects of neoplastic transformation. This study characterises collagen re-modelling around localised prostate cancer using the second harmonic generation of collagen (SHG), genotyping and ultrasound shear wave elastography (USWE) measured modulus in men with clinically localised prostate cancer. Tempo-sequence assay for gene expression of COL1A1 and COL3A1 was used to confirm the expression of collagen. Second-harmonic generation imaging and genotyping of ECM around prostate cancer showed changes in content, orientation, and type of collagen according to Gleason grades (cancer aggressivity), and this correlated with the tissue modulus measured by USWE in kilopascals. Furthermore, there were clear differences between collagen orientation and type around normal and cancer tissues. [ABSTRACT FROM AUTHOR]

Liver is one of the major target organs of arsenic toxicity and carcinogenesis. Nuclear factor (erythroid-2 related) factor 2 (Nrf2) is a redox-sensitive transcription factor, regulating critically cellular defense responses against the toxic metallic arsenic in many cell types and tissues. This study was conducted to evaluate the hepato-cellular Nrf2 and Nrf2-regulated antioxidant reactions of sodium arsenite exposure in Chang human hepatocytes. Nrf2 and heme oxygenase-1 (HO-1) protein levels were detected by Western blot, and Nrf2-regulated HO-1 mRNA expressions were determined using semiquantitative RT-PCR by 0∼50 μmol/L of sodium arsenite exposure for 2, 6, 12, and 24 h. We also observed the changes of intracellular reactive oxygen species (ROS) and total cellular glutathione (GSH) by flow cytometry and spectrophotometry, respectively. Our results showed that intracellular ROS were both dose- and time-dependent induced by inorganic arsenic; Cellular Nrf2 protein levels increased rapidly after 2 h of exposure, elevated significantly at 6 h, and reached the maximum at 12 h. The endogenous Nrf2-regulated downstream HO-1 mRNA and protein were also induced dramatically and lasted for as long as 24 h. In addition, intracellular GSH levels elevated in consistent with Nrf2 activation. Our findings here suggest that inorganic arsenic alters cellular redox balance in hepatocytes to trigger Nrf2-regulated antioxidant responses promptly, which may represent an adaptive cell defense mechanism against inorganic arsenic induced liver injuries and hepatoxicity. © 2011 Wiley Periodicals, Inc. Environ Toxicol, 2013. [ABSTRACT FROM AUTHOR]

Backgroud: As a result of changing consumer preferences, cotton (Gossypium Hirsutum L.) from varieties with naturally colored fibers is becoming increasingly sought after in the textile industry. The molecular mechanisms leading to colored fiber development are still largely unknown, although it is expected that the color is derived from flavanoids. Experimental Design: Firstly, four key genes of the flavonoid biosynthetic pathway in cotton (GhC4H, GhCHS, GhF3′H, and GhF3′5′H) were cloned and studied their expression profiles during the development of brown- and white cotton fibers by QRT-PCR. And then, the concentrations of four components of the flavonoid biosynthetic pathway, naringenin, quercetin, kaempferol and myricetin in brown- and white fibers were analyzed at different developmental stages by HPLC. Result: The predicted proteins of the four flavonoid structural genes corresponding to these genes exhibit strong sequence similarity to their counterparts in various plant species. Transcript levels for all four genes were considerably higher in developing brown fibers than in white fibers from a near isogenic line (NIL). The contents of four flavonoids (naringenin, quercetin, kaempferol and myricetin) were significantly higher in brown than in white fibers and corresponding to the biosynthetic gene expression levels. Conclusions: Flavonoid structural gene expression and flavonoid metabolism are important in the development of pigmentation in brown cotton fibers. [ABSTRACT FROM AUTHOR]

Chloroplasts produce singlet oxygen (1O2), which causes changes in nuclear gene expression through plastid-to-nucleus retrograde signaling to increase plant fitness. However, the identity of this 1O2-triggered pathway remains unclear. Here, we identify mutations in GENOMES UNCOUPLED4 (GUN4) and GUN5 as suppressors of phytochrome-interacting factor1 (pif1) pif3 in regulating the photo-oxidative response in Arabidopsis thaliana. GUN4 and GUN5 specifically interact with EXECUTER1 (EX1) and EX2 in plastids, and this interaction is alleviated by treatment with Rose Bengal (RB) or white light. Impaired expression of GUN4, GUN5, EX1, or EX2 leads to insensitivity to excess light and overexpression of EX1 triggers photo-oxidative responses. Strikingly, upon light irradiation or RB treatment, EX1 transiently accumulates in the nucleus and the nuclear fraction of EX1 shows a similar molecular weight as the plastid-located protein. Point mutagenesis analysis indicated that nuclear localization of EX1 is required for its function. EX1 acts as a transcriptional co-activator and interacts with the transcription factors WRKY18 and WRKY40 to promote the expression of 1O2-responsive genes. This study suggests that EX1 may act in plastid-to-nucleus signaling and establishes a 1O2-triggered retrograde signaling pathway that allows plants adapt to changing light environments during chloroplast development. EX1 acts as a plastid-to-nucleus mobile protein that relays 1O2 signals, thus bridging the communication gap between plastids and the nucleus. [ABSTRACT FROM AUTHOR]

Radish (Raphanus sativus L.) is an important worldwide root vegetable crop. Little information of the GRAS gene family was available in radish. Herein, a total of 51 GRAS family members were firstly identified from radish genome, and unevenly located onto nine radish chromosomes. Expression analysis of RsGRAS genes in taproot displayed that RsSCL15a and RsSHRc were highly expressed in the radish cambium, and its expression level was increased with the taproot thickening. Comparative transcriptome analysis revealed that the expression patterns of RsGRAS genes varied upon exposure to different abiotic stresses including heavy metals, salt and heat. The expression level of six RsGRAS genes including RsSHRc was increased under chilling stress in two radish genotypes with different cold tolerance. Further analysis indicated that RsGRAS genes could respond to cold stress rapidly and the expression of RsSHRc was up-regulated at different development stages (cortex splitting and thickening stages) under long-term cold treatment. Transient expression of RsSHRc gene in radish showed that RsSHRc possessed the reliable function of eliminating reactive oxygen species (ROS), inhibiting the formation of malondialdehyde (MDA) and promoting to accumulate proline under cold stress. Together, these findings provided insights into the function of RsGRAS genes in taproot development and chilling stress response in radish. • The GRAS gene family was comprehensively characterized in radish. • Expression analysis indicates RsSHRc might be involved in radish taproot thickening. • Transient expression analysis revealed RsSHRc gene could enhance cold tolerance of radish plants. [ABSTRACT FROM AUTHOR]

• In all, 39 RsNRT genes are systematically identified at genome-wide level in radish. • A range of RsNRTs exhibit significant differential expression under abiotic stresses. • RsNRT1.1a may play a critical role in root NO 3 − uptake under low-nitrogen condition. Radish is an important economical vegetable crop that requires adequate nitrogen supply for taproot formation and enlargement. Nitrate transporter (NRT) family represents a key gatekeeper in modulating nitrogen uptake and utilization in plants. However, the comprehensive characterization of the NRT gene family remains largely unexplored in radish. Herein, a total of 39 RsNRT genes were identified from the radish genome, which were unevenly distributed onto eight chromosomes except Chr3. Phylogenetic analysis indicated that the NRT1 and NRT2 subfamily members from radish, Arabidopsis and Brassica rapa were classified into Cluster I and Cluster II, indicating that the NRT proteins were relatively conserved in the Brassicaceae family. A range of cis -regulatory elements (e.g. AuxRE, ABRE and LTR) in the promoter of RsNRTs were involved in phytohormone and abiotic stress response. Transcriptome-based expression analysis indicated that several RsNRTs showed differential expression under heat, salt or heavy metal stresses. RT-qPCR analysis revealed that six RsNRT genes, including RsNRT1.1a, RsNRT1.2a, RsNRT1.5a, RsNRT2.1b, RsNRT2.2a and RsNRT2.3b , exhibited significantly up-regulated expression under NO 3 − deficiency condition. Notably, the expression of RsNRT1.1a was significantly increased in both the 'NAU-WXQ' (low-N-sensitive) and 'NAU-ZYQ' (low-N-tolerant) genotypes under 5 mM NO 3 − treatment, indicating that it might act as a critical participator in root NO 3 − uptake under low-N supply condition. These results would provide fundamental basis to decipher the molecular mechanisms underlying RsNRT -mediated N absorption and translocation in radish. [ABSTRACT FROM AUTHOR]

Radish (Raphanus sativus L.) is an important cool-season root vegetable crop worldwide. Heat stress (HS) severely restricts radish taproot formation and diminishes its yield and quality. Although WRKY transcription factors (TFs) play pivotal roles in several biotic and/or abiotic stress responses, how WRKY TFs mediate HS regulatory network remains elusive in radish. Herein, a WRKY-Ia TF gene, RsWRKY26 , exhibited dramatically up-regulated expression under heat stress, especially at 8 h and 24 h. RsWRKY26 was localized to the nucleus and displayed transactivation activity in both the yeast and plant cells. Interestingly, the RsWRKY26- overexpressing radish plants exhibited significantly enhanced thermotolerance compared to the control plants, whereas its knock-down plants showed increased thermosensitivity. Both in vitro and in vivo assays showed that RsWRKY26 activated RsHSP70–20 transcription by directly binding to the specific W-box element in its promoter. Moreover, several biochemical assays revealed that a VQ motif-containing protein RsVQ4 interacted with RsWRKY26, which promoted DNA-binding activity of RsWRKY26 to regulate RsHSP70–20 expression. Notably, RsWRKY26 in turn binds to RsVQ4 promoter to activate its transcription, thereby forming a positive feedback loop to cooperatively regulate heat stress response in radish. Together, we revealed a novel RsVQ4-RsWRKY26- RsHSP70–20 module to promote the thermotolerance, which would facilitate dissecting the molecular regulatory network of RsWRKY-mediated thermal morphogenesis in radish. • RsWRKY26 positively regulates thermotolerance by activating RsHSP70-20 transcription. • RsVQ4 physically interacts with RsWRKY26 to promote its DNA-binding activity. • RsWRKY26 binds to RsVQ4 promoter to form a feedback loop enhancing thermotolerance. [ABSTRACT FROM AUTHOR]

Abstract: Nogo receptor 1 (NgR1) mediates the inhibitory effects of several myelin-associated inhibitors (MAIs) on axonal regeneration in the central nervous system. A truncated soluble NgR1 (sNgR) has been reported to act as a decoy receptor to block the actions of MAIs. In this study, we fused the sNgR to nerve growth factor (NGF) and used NGF as a carrier to deliver sNgR to the intercellular space to neutralize MAIs. NGF in NGF–sNgR remained biologically active and induced sprouting of calcitonin gene related peptide containing axons when expressed in the spinal cord using a lentiviral vector (LV). Secreted NGF–sNgR promoted neurite outgrowth of dissociated dorsal root ganglion neurons on myelin protein substrate. In a rat dorsal column transection model, regenerating sensory axons were found to grow into the lesion cavity in animals injected with LV/NGF–sNgR, while in animals injected with LV/GFP or LV/NGF–GFP few sensory axons entered the lesion cavity. The results indicate that NGF–sNgR fusion protein can reduce the inhibition of MAIs and facilitate sensory axon regeneration. The fusion constructs may be modified to target other molecules to promote axonal regeneration and the concept may also be adapted to develop gene therapy strategies to treat other disorders. [Copyright &y& Elsevier]

Abstract: Conidiation is the major mode of reproduction in many filamentous fungi. The Neurospora crassa gene vad-5, which encodes a GAL4-like Zn2Cys6 transcription factor, was suggested to contribute to conidiation in a previous study using a knockout mutant. In this study, we confirmed the positive contribution of vad-5 to conidiation by gene complementation. To understand the role of vad-5 in conidiation, transcriptomic profiles generated by digital gene expression profiling from the vad-5 deletion mutant and the wild-type strain were compared. Among 7559 detected genes, 176 genes were found to be transcriptionally down-regulated and 277 genes transcriptionally upregulated in the vad-5 deletion mutant, using ⩾1-fold change as a cutoff threshold. Among the down-regulated genes, four which were already known to be involved in conidiation –fluffy, ada-6, rca-1, and eas – were examined further in a time course experiment. Transcription of each of the four genes in the vad-5 deletion mutant was lower than in the wild-type strain during conidial development. Phenotypic observation of deletion mutants for 132 genes down-regulated by vad-5 deletion revealed that deletion mutants for 17 genes, including fluffy, ada-6, and eas, produced fewer conidia than the wild type. By phenotypic observation of deletion mutants for 211 genes upregulated in the vad-5 deletion mutant, two types of deletion mutants were found. One type, which produced more conidia than the wild-type strain, includes deletion mutants for previously characterized genes cat-2, cat-3, and sah-1 and for a non-characterized gene NCU07221. Deletion mutants of NCU06302 and NCU11090, representing the second type, produced conidia earlier than the wild-type strain. Based on these conidiation phenotypes, we designated NCU07221 as high conidial production-1 (hcp-1) and named NCU06302 and NCU11090 as early conidial development-1 (ecd-1) and ecd-2, respectively. Given the collective results from this study, we propose that vad-5 exerts an effect on conidiation by activating genes that positively contribute to conidiation as well as by repressing genes that negatively influence conidial development. [Copyright &y& Elsevier]

Abstract: RNA interference (RNAi) is a potent mechanism against a variety of viral infections. Infectious bursal disease virus (IBDV) causes an important disease economically in chickens, which is difficult to control. As part of the development of viral vector-mediated RNAi strategy against the disease, five anti-VP2 small interference RNAs were selected for construction of microRNA (miRNA) expression vectors tailored for avian cells. Transfection of DF-1 cells with the five vectors resulted in significant inhibition of VP2-EGFP reporter gene expression. More effective miVP2A and miVP2E were selected for further study using single or double miRNA expression vectors. After demonstration of specific miRNA expression, the gene silencing effects were determined in the vector-transfected and IBDV-infected cells. Reverse transcriptase PCR and virus titration showed inhibition rates from 76 to 82% on VP2 expression and significant decreases in virus titer by individual and co-expressed miVP2A and miVP2E. The inhibitory effects lasted for at least 120h after infection with IBDV. These data suggest that the miRNAs targeting the VP2 can inhibit efficiently replication of IBDV. [Copyright &y& Elsevier]