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Gene module

Bo Wang, Jing Xu, Jianjie Gao, Xiaoyan Fu, Hongjuan Han, Zhenjun Li, Lijuan Wang, Yongsheng Tian, Rihe Peng, Quanhong Yao
Phenol is a common water pollutant because of its broad industrial applications. Biological method is a promising alternative to conventional physical and chemical methods for removing this toxic pollutant from the environment. In this study, two metabolic modules were introduced into Escherichia coli, the widely used host for various genetic manipulations, to elucidate the metabolic capacity of E. coli for phenol degradation. The first module catalysed the conversion of phenol to catechol, whereas the second module cleaved catechol into the three carboxylic acid circulating intermediates by the ortho-cleavage pathway...
March 16, 2019: Journal of Hazardous Materials
Anna Lewinska, Jolanta Klukowska-Rötzler, Anna Deregowska, Jagoda Adamczyk-Grochala, Maciej Wnuk
Medulloblastoma (MB) is a common and highly aggressive pediatric brain tumor of a heterogeneous nature. According to transcriptome-based profiling, four molecular subgroups of MB have been revealed, namely WNT, SHH, Group 3 and Group 4. High MYC mRNA expression and MYC gene amplification in MB have been considered as indicators of poor prognosis. However, the role of c-Myc in MB biology is still not well established. In the present study, the effects of c-Myc activation in UW228-MycER MB cell line were investigated using 4-hydroxytamoxifen (4-OHT) induction system...
March 13, 2019: Redox Biology
In Young Lee, Jane Melissa Lim, Hyunchu Cho, Eunju Kim, Yeonsil Kim, Hye-Kyung Oh, Woo Seok Yang, Kyung-Hye Roh, Hyun Woo Park, Jung-Soon Mo, Je-Hyun Yoon, Hyun Kyu Song, Eui-Ju Choi
The nuclear factor (NF)-κB pathway plays a central role in inflammatory and immune responses, with aberrant activation of NF-κB signaling being implicated in various human disorders. Here, we show that mammalian ste20-like kinase 1 (MST1) is a previously unrecognized component of the tumor necrosis factor α (TNFα) receptor 1 signaling complex (TNF-RSC) and attenuates TNFα-induced NF-κB signaling. Genetic ablation of MST1 in mouse embryonic fibroblasts and bone marrow-derived macrophages potentiated the TNFα-induced increase in IκB kinase (IKK) activity, as well as the expression of NF-κB target genes...
March 21, 2019: Molecular Cell
Pengfei Guo, Chang-Hyun Lee, Huiyan Lei, Yonggang Zheng, Katiuska Daniela Pulgar Prieto, Duojia Pan
The Hippo tumor suppressor pathway regulates tissue growth in Drosophila by restricting the activity of the transcriptional coactivator Yorkie (Yki), which normally complexes with the TEF/TEAD family DNA-binding transcription factor Scalloped (Sd) to drive the expression of growth-promoting genes. Given its pivotal role as a central hub in mediating the transcriptional output of Hippo signaling, there is great interest in understanding the molecular regulation of the Sd-Yki complex. In this study, we identify Nerfin-1 as a transcriptional repressor that antagonizes the activity of the Sd-Yki complex by binding to the TEA DNA-binding domain of Sd...
March 22, 2019: ELife
Mercedes Del Río-Moreno, Emilia Alors-Pérez, Sandra González-Rubio, Gustavo Ferrín, Oscar Reyes, Manuel Rodríguez-Perálvarez, Marina E Sánchez-Frías, Rafael Sánchez-Sánchez, Sebastián Ventura, José López-Miranda, Rhonda D Kineman, Manuel de la Mata, Justo P Castaño, Manuel D Gahete, Raúl M Luque
CONTEXT: Non-alcoholic fatty liver disease (NAFLD) is a common obesity-associated pathology characterized by hepatic fat accumulation, which can progress to fibrosis, cirrhosis and hepatocellular carcinoma. Obesity is associated with profound changes in gene expression patterns of the liver, which could contribute to the onset of comorbidities. OBJECTIVE: Since these alterations might be linked to a dysregulation of the splicing process, we aimed to determine whether the dysregulation in the expression of splicing machinery components could be associated with NAFLD...
March 22, 2019: Journal of Clinical Endocrinology and Metabolism
Tamires A Bitencourt, Felipe B Oliveira, Pablo R Sanches, Antonio Rossi, Nilce M Martinez-Rossi
PURPOSE: Trichophyton rubrum is a dermatophyte that causes most human superficial mycoses worldwide. The spliceosome, a large ribonucleoprotein complex responsible for pre-mRNA processing, may confer adaptive advantages to deal with different stresses. Here, we assessed the structural aspects of the Prp4 kinase protein and other pre-mRNA-splicing factors (Prps) in T. rubrum grown in different protein sources and exposed to antifungal drugs. METHODOLOGY: Quantitative Reverse Transcription PCR (RT-PCR) assessed the modulation of prp1, prp31, prp8 and prp4 kinase genes after exposure of T...
March 22, 2019: Journal of Medical Microbiology
Qiuli Li, Weichao Chen, Ming Song, Wenkuan Chen, Zhongyuan Yang, Ankui Yang
Head and neck squamous cell carcinoma (HNSCC) is a lethal disease with suboptimal survival outcomes. In this study, we aimed to find an independent prognostic factor of head and neck squamous cell carcinoma and investigate its effect on tumor cell proliferation, apoptosis, migration progress and cell cycle phase. Weighted gene co-expression network analysis (WGCNA) is an analysis method for mining module information in chip data through soft threshold. In this article, it was used to divide differential genes into different modules and determined the ten hub genes...
March 22, 2019: Cancer Biology & Therapy
Carrie Q Sun, Rebecca S Arnold, Chia-Ling Hsieh, Julia R Dorin, Fei Lian, Zhenghong Li, John A Petros
Human beta-defensin-1 (hBD-1) is one of a number of small cationic host-defense peptides. Besides its well-known broad-spectrum antimicrobial function, hBD-1 has recently been identified as a chromosome 8p tumor-suppressor gene. The role of hBD-1 in modulating the host immune response to oncogenesis, associated with cell signaling and potential therapeutic applications, has become increasingly appreciated over time. In this study, multiple approaches were used to illustrate hBD-1 anti-tumor activities. Results demonstrate that hBD-1 peptide alters human epidermal growth factor receptor 2 (HER2) signal transduction and represses retroviral-mediated transgene expression in cancer cells...
March 22, 2019: Cancer Biology & Therapy
Jiawei Wang, Xue Gao, Jing Liu, Jing Wang, Yue Zhang, Tonghe Zhang, Han Zhang
PURPOSE: To evaluate the effect of conbercept on the expression of long noncoding RNAs (lncRNAs) and mRNAs in the fibrovascular membranes of proliferative diabetic retinopathy (PDR) patients. METHODS: Twenty patients, diagnosed with PDR, who underwent pars plana vitrectomy (PPV), were recruited for this study. Ten patients were treated for PPV alone (Control Group), and the others received conbercept injections before PPV (Treated Group). The fibrovascular membranes were harvested during surgery...
March 22, 2019: Acta Ophthalmologica
Guodong Sun, Wenjing Zhang, Jing Wang
Objective: The complete molecular mechanism that cyclophosphamide (CPA) induces the cell death is still unknown. To further reveal the mechanism of CPA contributing to prostate cancer, we conducted analysis on gene expression profile of E-GEOD-42913 to identify attractor modules by integrating systemic module inference with attract method. Methods: First, case and control protein-protein interaction (PPI) networks were inferred based on Spearman correlation coefficient; then clique merging algorithm was performed to explore modules in the reweighted PPI network, and these modules were compared with each other so as to select similar modules; in the following, attractor modules were identified via attract method; finally, pathway enrichment analysis of genes in attractor modules was carried out...
March 2019: Journal of Cancer Research and Therapeutics
Dong Sun Oh, Heung Kyu Lee
Macroautophagy/autophagy has been implicated in cytoplasmic and viral antigen presentation on major histocompatibility complex (MHC) class II molecules. However, the role of autophagy in the presentation of phagocytized tumor-associated antigens in vivo remains unclear. Following the administration of apoptotic tumor cells and in vivo chemotherapy, mice with a dendritic cell-specific deletion of Atg5, a key autophagy gene, exhibit reduced CD4+ T-cell priming but not CD8+ cytotoxic T-cell priming. Interestingly, Atg5-deficient dendritic cells have an elevated expression of scavenger receptor CD36 and show excessive lipid accumulation...
March 22, 2019: Autophagy
Inga Dry, Katie Nightingale, Jack Ferguson, John Hopkins, Robert Dalziel
Ovine herpesvirus-2 (OvHV-2) is the causative agent of the sheep-associated form of malignant catarrhal fever, a usually fatal lymphoproliferative disease of bison, deer and cattle. Malignant catarrhal fever is a major cause of cattle loss in Africa with approximately 7% affected annually; and in North America has significant impact on bison farming. Research into the mechanisms by which OvHV-2 induces disease in susceptible species has been hampered by a lack of a cell culture system for the virus. Ov2 is a bZIP protein encoded by OvHV-2...
March 21, 2019: Veterinary Research Communications
Shun Sawatsubashi, Koichi Nishimura, Jinichi Mori, Alexander Kouzmenko, Shigeaki Kato
Vitamin D (VD) is essential for bone health, and VD or its analogues are widely used in clinics to ameliorate bone loss. The targets and mode of VD anti-osteoporotic actions appear to be different from those of other classes of drugs modulating bone remodeling. VD exerts its biological activities through the nuclear VD receptor (VDR)-mediated transcriptional regulation of target mRNA and non-coding RNA genes. VD-induced gene regulation involves epigenetic modifications of chromatin conformation at the target loci as well as reconfiguration of higher-order chromosomal organization through VDR-mediated recruitment of various regulatory factors...
February 2019: Journal of Bone Metabolism
Dan Gong, Zhiwen Zeng, Fengming Yi, Jianbing Wu
The apoptosis machinery is compromised in liver cancer (LC). The underlying mechanism needs to be further investigated. Histone deacetylases (HDAC) have multiple and strong biochemical activities. This study tests a hypothesis that HDAC11 prevents LC cell (LCC) apoptosis via modulating the p53 gene transcription. In this study, the LC tissues were collected from patients with LC. The LCCs were purified by magnetic cell sorting. The gene transcription activities of the LCCs were analyzed by immunoprecipitation (IP) and chromatin IP...
2019: American Journal of Translational Research
Zhiqing Chen, Zhi Liu, Lin Shen, Han Jiang
Fracture is the most common disease in the orthopedics. Long non-coding small nucleolar RNA host gene 7 (SNHG7) has been confirmed to enhance cell proliferation and decrease cell apoptosis in many cancers. However, the role of SNHG7 in skeletal fracture remains largely to be elucidated. In the current study, we observed SNHG7 was down-regulated in femoral neck fracture tissues. In addition, SNHG7 knockdown inhibited proliferation and migration, induced apoptosis, reduced activity in osteoblast cells in vitro...
2019: American Journal of Translational Research
Ana Moya-Beltrán, Camila Rojas-Villalobos, Mauricio Díaz, Nicolás Guiliani, Raquel Quatrini, Matías Castro
Cyclic and linear nucleotides are key elements of the signal transduction networks linking perception of the environment to specific cellular behavior of prokaryotes. These molecular mechanisms are particularly important in bacteria exposed to different, and frequently simultaneous, types of extreme conditions. This is the case in acidithiobacilli, a group of extremophilic bacteria thriving in highly acidic biotopes, that must also cope with significant variations in temperature, osmotic potentials and concentrations of various transition metals and metalloids...
2019: Frontiers in Microbiology
Ting Chen, Matthew K H Wong, Ben C B Chan, Anderson O L Wong
In fish models, seasonal change in feeding is under the influence of water temperature. However, the effects of temperature on appetite control can vary among fish species and the mechanisms involved have not been fully characterized. Using goldfish ( Carassius auratus ) as a model, seasonal changes in feeding behavior and food intake were examined in cyprinid species. In our study, foraging activity and food consumption in goldfish were found to be reduced with positive correlation to the gradual drop in water temperature occurring during the transition from summer (28...
2019: Frontiers in Endocrinology
Nicolai Franzmeier, Jinyi Ren, Alexander Damm, Gemma Monté-Rubio, Mercè Boada, Agustín Ruiz, Alfredo Ramirez, Frank Jessen, Emrah Düzel, Octavio Rodríguez Gómez, Tammie Benzinger, Alison Goate, Celeste M Karch, Anne M Fagan, Eric McDade, Katharina Buerger, Johannes Levin, Marco Duering, Martin Dichgans, Marc Suárez-Calvet, Christian Haass, Brian A Gordon, Yen Ying Lim, Colin L Masters, Daniel Janowitz, Cihan Catak, Steffen Wolfsgruber, Michael Wagner, Esther Milz, Sonia Moreno-Grau, Stefan Teipel, Michel J Grothe, Ingo Kilimann, Martin Rossor, Nick Fox, Christoph Laske, Jasmeer Chhatwal, Peter Falkai, Robert Perneczky, Jae-Hong Lee, Annika Spottke, Henning Boecker, Frederic Brosseron, Klaus Fliessbach, Michael T Heneka, Peter Nestor, Oliver Peters, Manuel Fuentes, Felix Menne, Josef Priller, Eike J Spruth, Christiana Franke, Anja Schneider, Christine Westerteicher, Oliver Speck, Jens Wiltfang, Claudia Bartels, Miguel Ángel Araque Caballero, Coraline Metzger, Daniel Bittner, Stephen Salloway, Adrian Danek, Jason Hassenstab, Igor Yakushev, Peter R Schofield, John C Morris, Randall J Bateman, Michael Ewers
In Alzheimer's disease (AD), a single-nucleotide polymorphism in the gene encoding brain-derived neurotrophic factor (BDNFVal66Met ) is associated with worse impact of primary AD pathology (beta-amyloid, Aβ) on neurodegeneration and cognitive decline, rendering BDNFVal66Met an important modulating factor of cognitive impairment in AD. However, the effect of BDNFVal66Met on functional networks that may underlie cognitive impairment in AD is poorly understood. Using a cross-validation approach, we first explored in subjects with autosomal dominant AD (ADAD) from the Dominantly Inherited Alzheimer Network (DIAN) the effect of BDNFVal66Met on resting-state fMRI assessed functional networks...
March 21, 2019: Molecular Psychiatry
A Sánchez-Melgar, J L Albasanz, R Guixà-González, N Saleh, J Selent, M Martín
Resveratrol (RSV) is a natural polyphenolic antioxidant with a proven protective role in several human diseases involving oxidative stress, although the molecular mechanism underlying this effect remains unclear. The present work tried to elucidate the molecular mechanism of RSV's role on signal transduction modulation. Our biochemical analysis, including radioligand binding, real time PCR, western blotting and adenylyl cyclase activity, and computational studies provide insights into the RSV binding pathway, kinetics and the most favored binding pose involving adenosine receptors, mainly A2A subtype...
March 18, 2019: Free Radical Biology & Medicine
Lea Duempelmann, Fabio Mohn, Yukiko Shimada, Daniele Oberti, Aude Andriollo, Silke Lochs, Marc Bühler
Small RNAs trigger the formation of epialleles that are silenced across generations. Consequently, RNA-directed epimutagenesis is associated with persistent gene repression. Here, we demonstrate that small interfering RNA-induced epimutations in fission yeast are still inherited even when the silenced gene is reactivated, and descendants can reinstate the silencing phenotype that only occurred in their ancestors. This process is mediated by the deposition of a phenotypically neutral molecular mark composed of tri-methylated histone H3 lysine 9 (H3K9me3)...
March 5, 2019: Molecular Cell
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