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Gene module

Christelle Langevin, Jean-Pierre Levraud, Pierre Boudinot
Tripartite motif (TRIM) family or RBCC proteins comprises characteristic zinc-binding domains (a RING (R), a B-box type 1 (B1) and a B-box type 2 (B2)) and coiled-coil (CC) domain followed by a C-terminus variable domain. There are about 80 different TRIM proteins in human, but more than 200 in zebrafish with several large gene expansions (ftr >70 genes; btr >30 genes; trim35 > 30 genes). Repertoires of trim genes in fish are variable across fishes, but they have been remarkably diversified independently in a number of species...
December 11, 2018: Fish & Shellfish Immunology
Xingliang Wang, Andrias O O Reilly, Martin S Williamson, Alin M Puinean, Yihua Yang, Shuwen Wu, Yidong Wu
Glutamate-gated chloride channels (GluCls) are found only in invertebrates and mediate fast inhibitory neurotransmission. The structural and functional diversity of GluCls are produced through assembly of multiple subunits and via posttranscriptional alternations. Alternative splicing is the most common way to achieve this in insect GluCls and splicing occurs primarily at exons 3 and 9. As expression pattern and pharmacological properties of exon 9 alternative splices in invertebrate GluCls remain poorly understood, the cDNAs encoding three alternative splice variants (9a, 9b and 9c) of the PxGluCl gene from the diamondback moth Plutella xylostella were constructed and their pharmacological characterizations were examined using electrophysiological studies...
December 11, 2018: Insect Biochemistry and Molecular Biology
Esther Arnaiz, Carla Sole, Lorea Manterola, Leire Iparraguirre, David Otaegui, Charles H Lawrie
Circular RNAs (circRNAs) are a novel class of regulatory RNAs that despite being relatively abundant have only recently begun to be explored. There are many thousands of genes that appear capable of producing circRNAs, however the function of all but a handful remain to be determined. What is emerging about these highly conserved molecules is that they play important roles in biology and cancer biology in particular. The most explored function of circRNAs is as master regulators of gene expression that act to sequester or ´sponge´ other gene expression regulators, in particular miRNAs...
December 11, 2018: Seminars in Cancer Biology
Xiaoling Wu, Jiamei Zhang, Chenjie Ma, Wu Li, Jin Zeng, Yujiong Wang, Guangcun Deng
Mycobacterium tuberculosis (Mtb)-induced autophagy of alveolar macrophages has been confirmed to play a central role in the pathogenesis of tuberculosis. Growing evidence indicates that excessive or uncontrolled autophagic activity, which results in type II programmed cell death, can be regulated by many factors, including Wnt/β-catenin signalling. Wnt/β-catenin signalling has been demonstrated to be involved in multiple diseases through the regulation of autophagy; however, its exact role in regulating autophagy induced by Mtb remains unclear...
December 11, 2018: Microbial Pathogenesis
Theeraphol Jatuponwiphat, Pramote Chumnanpuen, Sarah Othman, Teerasak E-Kobon, Wanwipa Vongsangnak
Pasteurella multocida causes respiratory infectious diseases in a multitude of birds and mammals. A number of virulence-associated genes were reported across different strains of P. multocida, including those involved in the iron transport and metabolism. Comparative iron-associated genes of P. multocida among different animal hosts towards their interaction networks have not been fully revealed. Therefore, this study aimed to identify the iron-associated genes from core- and pan-genomes of fourteen P. multocida strains and to construct iron-associated protein interaction networks using genome-scale network analysis which might be associated with the virulence...
December 11, 2018: Microbial Pathogenesis
Priya S Shah, Nichole Link, Gwendolyn M Jang, Phillip P Sharp, Tongtong Zhu, Danielle L Swaney, Jeffrey R Johnson, John Von Dollen, Holly R Ramage, Laura Satkamp, Billy Newton, Ruth Hüttenhain, Marine J Petit, Tierney Baum, Amanda Everitt, Orly Laufman, Michel Tassetto, Michael Shales, Erica Stevenson, Gabriel N Iglesias, Leila Shokat, Shashank Tripathi, Vinod Balasubramaniam, Laurence G Webb, Sebastian Aguirre, A Jeremy Willsey, Adolfo Garcia-Sastre, Katherine S Pollard, Sara Cherry, Andrea V Gamarnik, Ivan Marazzi, Jack Taunton, Ana Fernandez-Sesma, Hugo J Bellen, Raul Andino, Nevan J Krogan
Mosquito-borne flaviviruses, including dengue virus (DENV) and Zika virus (ZIKV), are a growing public health concern. Systems-level analysis of how flaviviruses hijack cellular processes through virus-host protein-protein interactions (PPIs) provides information about their replication and pathogenic mechanisms. We used affinity purification-mass spectrometry (AP-MS) to compare flavivirus-host interactions for two viruses (DENV and ZIKV) in two hosts (human and mosquito). Conserved virus-host PPIs revealed that the flavivirus NS5 protein suppresses interferon stimulated genes by inhibiting recruitment of the transcription complex PAF1C and that chemical modulation of SEC61 inhibits DENV and ZIKV replication in human and mosquito cells...
December 13, 2018: Cell
Veijo Nurminen, Antonio Neme, Sabine Seuter, Carsten Carlberg
The myeloid master regulator CCAAT enhancer-binding protein alpha (CEBPA) is known as a pioneer factor. In this study, we report the CEBPA cistrome of THP-1 human monocytes after stimulation with the vitamin D receptor (VDR) ligand 1α,25-dihydroxyvitamin D3 (1,25(OH)2 D3 ) for 2, 8 and 24 h. About a third of the genomic VDR binding sites co-located with those of CEBPA. In parallel, the binding strength of 5% of the CEBPA cistrome, i.e. some 1500 sites, is significantly (p < 0.001) affected by 1,25(OH)2 D3 ...
December 11, 2018: Biochimica et biophysica acta. Gene regulatory mechanisms
Kinga Kochan-Jamrozy, Jarosław Króliczewski, Adrianna Moszyńska, James F Collawn, Rafal Bartoszewski
Solid tumor microenvironments are often subjected to various levels of hypoxia. Although regulation of gene expression has been examined extensively, most studies have focused on prolonged hypoxia. The tumor microenvironment, however, experiences waves of hypoxia and reoxygenation that stimulate the expression of pro-angiogenic factors that promote blood vessel formation. In this study, we examined human umbilical vascular endothelial cells (HUVECs) under waves of intermittent (cyclic) hypoxia to determine how this process compares to prolonged hypoxia, and more importantly, how this influences the microRNA profiles that potentially affect the posttranscriptional regulation of angiogenic genes...
December 11, 2018: Cellular Signalling
Thomas S O'Leary, Julia Snyder, Sakthivel Sadayappan, Sharlene M Day, Michael J Previs
RATIONALE: Truncation mutations in the MYBPC3 gene, encoding for cardiac myosin-binding protein C (MyBP-C), are the leading cause of hypertrophic cardiomyopathy (HCM). Whole heart, fiber and molecular studies demonstrate that MyBP-C is a potent modulator of cardiac contractility, but how these mutations contribute to HCM is unresolved. OBJECTIVES: To readdress whether MYBPC3 truncation mutations result in loss of MyBP-C content and/or the expression of truncated MyBP-C from the mutant allele and determine how these mutations effect myofilament sliding in human myocardium...
December 11, 2018: Journal of Molecular and Cellular Cardiology
Fatemeh Khadangi, Angelo Azzi
α-Tocopherol is the only tocopherol that has been shown to prevent the human deficiency disease Ataxia with Isolated Vitamin E Deficiency (AVED), and thus it is the only one that, for humans, can be called vitamin E. Vitamin E in addition to preventing AVED has documented immune boosting properties and an activity against nonalcoholic hepatosteatosis and low-grade inflammation. Epidemiological studies indicating that vitamin E could prevent cardiovascular events, neurodegenerative disease, macular degeneration, and cancer were in general not confirmed by clinical intervention studies...
December 14, 2018: IUBMB Life
Paula Renata Alves da Silva, Márcia Soares Vidal, Cleiton de Paula Soares, Valéria Polese, Michelle Zibetti Tadra-Sfeir, Emanuel Maltempi de Souza, Jean Luiz Simões-Araújo, José Ivo Baldani
The stalk apoplast fluid of sugarcane contains different sugars, organic acids and amino acids that may supply the demand for carbohydrates by endophytic bacteria including diazotrophs P. tropica (syn. B. tropica) strain Ppe8, isolated from sugarcane, is part of the bacterial consortium recommended as inoculant to sugarcane. However, little information has been accumulated regarding this plant-bacterium interaction considering that it colonizes internal sugarcane tissues. Here, we made use of the RNA-Seq transcriptomic analysis to study the influence of sugarcane stalk apoplast fluid on Ppe8 gene expression...
2018: PloS One
Jianhan Zhang, Xu Han, Yihan Lin
Regulation of cellular ATP level is critical for diverse biological processes and may be defective in diseases such as cancer and mitochondrial disorders. While mitochondria play critical roles in ATP level regulation, we still lack a systematic and quantitative picture of how individual mitochondrial-related genes contribute to cellular ATP level and how dysregulated ATP levels may affect downstream cellular processes. Advances in genetically encoded ATP biosensors have provided new opportunities for addressing these issues...
December 14, 2018: PLoS Biology
Teresa Fazia, Roberta Pastorino, Serena Notartomaso, Carla Busceti, Tiziana Imbriglio, Milena Cannella, Davide Gentilini, Gabriele Morani, Anna Ticca, Pierpaolo Bitti, Carlo Berzuini, Tamas Dalmay, Giuseppe Battaglia, Luisa Bernardinelli
Acid Sensing Ion Channel (ASICs) are proton-gated channels involved in multiple biological functions such as: pain modulation, mechanosensation, neurotransmission and neurodegeneration. Earlier, we described the genetic association, within the Nuoro population, between multiple sclerosis (MS) and rs28936, located in ASIC2 3'UTR. Here we investigated the potential involvement of ASIC2 in MS inflammatory process. We induced experimental autoimmune encephalomyelitis (EAE) in wild-type (WT), knockout Asic1-/- and Asic2-/- mice and observed a significant reduction of clinical score in Asic1-/- mice and a significant reduction of the clinical score in Asic2-/- mice in a limited time window (i...
December 14, 2018: European Journal of Neuroscience
Emilie Le Rhun, Caroline von Achenbach, Birthe Lohmann, Manuela Silginer, Hannah Schneider, Kristan Meetze, Emese Szabo, Michael Weller
TG02 is a novel cyclin-dependent kinase (CDK) inhibitor and thought to act mainly via CDK-9 inhibition-dependent depletion of short-lived oncoproteins such as MCL-1 or c-MYC. We studied the activity of TG02 in 9 human long-term glioma cell lines (LTC) and 5 glioma-initiating cell lines (GIC) using various cell death assays in vitro and in the LN-229 LTC and ZH-161 GIC models in vivo. TG02 exhibits strong anti-tumor cell activity with EC50 concentrations in the nanomolar range. Median survival in the LN-229 and ZH-161 models was moderately prolonged by TG02...
December 14, 2018: International Journal of Cancer. Journal International du Cancer
Alejandra Velásquez, Edwin Mellisho, Fidel O Castro, Lleretny Rodríguez-Álvarez
The high metabolic activity to which the dairy cattle are exposed for maintain milk production altered steroid metabolism that affect reproductive physiology and reducing oocyte competence. Our aims were 1) to characterize the competence of immature oocytes collected from dairy cattle based on the expression of genes in cumulus cells and 2) to improve oocyte competence to support pre-implantation embryo development by the supplementation of maturation medium with BMP15 and/or AMH. Oocyte donors were identified at the moment of ovary collection and grouped by involuntarily culled dairy cows (Holstein breed) or beef cattle...
December 13, 2018: Molecular Reproduction and Development
Xuan Shu, Shenyou Shu, Hongqiu Cheng
BACKGROUND: Increasing evidence indicates that long non-coding RNAs (lncRNAs) play crucial regulatory roles in epithelial-mesenchymal transition (EMT). However, the regulatory mechanisms during EMT of the medial edge epithelium (MEE) remain elusive. The aim of this work is to reveal a novel lncRNA-regulated dysfunction of EMT involved in the development of cleft palate (CP). METHODS: C57BL/6 J mice at embryonic gestation day 14.5 (n = 6, 3 case samples vs. 3 control samples) were used to establish the CP model for lncRNA-mRNA co-expression profile analysis after high-throughput sequencing...
December 12, 2018: Molecular Genetics & Genomic Medicine
Lena-Sophie Martis, Ove Wiborg, Megan C Holmes, Anjanette P Harris
Major depressive disorder (MDD) is a leading contributor to the global burden of disease. However, the causal relationship of risk factors, such as genetic predisposition or experience of augmented stress, remain unknown. Numerous studies in humans and rodents have implicated brain-derived neurotrophic factor (BDNF) in MDD pathology, as a genetic risk factor and a factor regulated by stress. Until now, the majority of preclinical studies have employed genetically modified mice as their model of choice. However, mice display a limited behavioural repertoire and lack expression of circulating BDNF, which is present in rats and humans...
December 13, 2018: Genes, Brain, and Behavior
Hyunhee Joo, Chae Woo Lim, Sung Chul Lee
Plants have evolved complex defense mechanisms to adapt and survive under adverse growth conditions. Abscisic acid (ABA) is a phytohormone that plays a pivotal role in the stress response, especially regulation of the stomatal aperture in response to drought. Here, we identified the pepper CaASRF1 (Capsicum annuum ABA Sensitive RING Finger E3 ligase 1) gene, which modulates drought stress tolerance via ABA-mediated signalling. CaASRF1 contains a C3H2C3 type RING finger domain, which functions as an E3 ligase by attaching ubiquitins to the target proteins...
December 12, 2018: Plant Journal: for Cell and Molecular Biology
Ehsan Saburi, Hadi Atabati, Ladan Kabiri, Asma Behdari, Mina Azizi, Abdolreza Ardeshirylajimi, Seyed Ehsan Enderami, Sayyed Mohammad-Hossein Ghaderian, Mohsen Nafar, Mahmoud Parvin, Mir Davood Omrani
Renal failures treatment has been faced with several problems during the last decades. Kidney tissue engineering has been created many hopes to improve treatment procedures with scaffold fabrication that can modulate kidney cells/stem cells migration to the lesion site and increase the survival of these cells at that site with imitating the role of the kidney extracellular matrix. In this study, bone morphogenetic protein-7 (BMP7) as a vital factor for kidney development and regeneration was incorporated in the polycaprolactone (PCL) nanofibers and after morphological, mechanical, and biocompatible characterization, proliferation, and survival of the human embryonic kidney cells (HEK) were investigated using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), flow cytometry, and gene expression while cultured on scaffolds...
December 12, 2018: Journal of Cellular Biochemistry
Cuijiang Wang, Fei Wang, Fen Lin, Xiaohong Duan, Binna Bi
OBJECTIVE: This study aims to test the effect of naproxen treatment and the biological target of naproxen for treating osteoarthritis (OA). METHODS: Differentially expressed genes (DEGs) in OA synovial tissues and normal counterparts were analyzed by messenger RNA microarray analysis. R package (weighted gene coexpression network analysis) was used to divide DEGs into several modules and determine the hub genes in each module. The expression level of prostaglandin-endoperoxide synthase 1 ( PTGS1) in OA synovial cells and tissues was verified by a quantitative real-time polymerase chain reaction and western blot...
December 12, 2018: Journal of Cellular Physiology
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