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Modeling gene regulation

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https://www.readbyqxmd.com/read/28088729/new-insights-into-aox2-transcriptional-regulation-in-chlamydomonas-reinhardtii
#1
Mariya Ostroukhova, Zhanneta Zalutskaya, Elena Ermilova
A feature of the mitochondrial electron transport chain in plants, some protists and many fungi is the presence of two terminal oxidases, the energy-conserving cytochrome oxidase and another termed alternative oxidase (AOX). AOX branches from the main respiratory chain, directly coupling the oxidation of ubiquinol with reduction of oxygen to water. The AOX genes can be divided into two discrete subfamilies, AOX1 and AOX2. Although AOX has been proposed to play essential roles in stress tolerance of organisms, the role of subfamily AOX2 is largely unknown...
December 13, 2016: European Journal of Protistology
https://www.readbyqxmd.com/read/28088658/exposure-to-chronic-early-life-stress-lastingly-alters-the-adipose-tissue-the-leptin-system-and-changes-the-vulnerability-to-western-style-diet-later-in-life-in-mice
#2
K Y Yam, E F G Naninck, M R Abbink, S E la Fleur, L Schipper, J C van den Beukel, A Grefhorst, A Oosting, E M van der Beek, P J Lucassen, A Korosi
Early-life stress (ES) increases the vulnerability to develop psychopathologies and cognitive decline in adulthood. Interestingly, this is often comorbid with metabolic disorders, such as obesity. However, it is unclear whether ES leads to lasting metabolic changes and to what extent this is associated with the ES-induced cognitive impairments. Here, we used an established chronic ES mouse model (from postnatal day (P) 2 to P9) to investigate the short- and long-term effects of ES exposure on parameters of the adipose tissue and the leptin system (i...
December 23, 2016: Psychoneuroendocrinology
https://www.readbyqxmd.com/read/28088579/the-microrna-449-family-inhibits-tgf-%C3%AE-mediated-liver-cancer-cell-migration-by-targeting-sox4
#3
Maria Sandbothe, Reena Buurman, Nicole Reich, Luisa Greiwe, Beate Vajen, Engin Gürlevik, Vera Schäffer, Marlies Eilers, Florian Kühnel, Alejandro Vaquero, Thomas Longerich, Stephanie Roessler, Peter Schirmacher, Michael P Manns, Thomas Illig, Brigitte Schlegelberger, Britta Skawran
BACKGROUND & AIMS: Modulation of microRNA expression is considered for treatment of hepatocellular carcinoma (HCC). Therefore, we characterized the epigenetically regulated microRNA-449 family (miR-449a, miR-449b, miR-449c) with regards to its functional effects and target genes in HCC. METHODS: After transfection of miR-449a, miR-449b, and/or miR-449c, tumor-relevant functional effects were analyzed using in vitro assays and a xenograft mouse model. Binding specificities, target genes, and regulated pathways of each microRNA were identified by microarray analyses...
January 11, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28088409/genome-wide-association-analysis-and-pathways-enrichment-for-lactation-persistency-in-canadian-holstein-cattle
#4
D N Do, N Bissonnette, P Lacasse, F Miglior, M Sargolzaei, X Zhao, E M Ibeagha-Awemu
Lactation persistency (LP), defined as the rate of declining milk yield after milk peak, is an economically important trait for dairy cattle. Improving LP is considered a good alternative method for increasing overall milk production because it does not cause the negative energy balance and other health issues that cows experience during peak milk production. However, little is known about the biology of LP. A genome-wide association study (GWAS) and pathway enrichment were used to explore the genetic mechanisms underlying LP...
January 11, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28088388/activation-of-gr-but-not-pxr-by-dexamethasone-attenuated-acetaminophen-hepatotoxicities-via-fgf21-induction
#5
Saurabh G Vispute, Pengli Bu, Yuan Le, Xingguo Cheng
Glucocorticoid receptor (GR) signaling is indispensable for cell growth and development, and plays important roles in drug metabolism. Fibroblast growth factor (Fgf) 21, an important regulator of glucose, lipid, and energy metabolism, plays a cytoprotective role by attenuating toxicities induced by chemicals such as dioxins, acetaminophen (APAP), and alcohols. The present study investigates the impact of dexamethasone (DEX)-activated GR on Fgf21 expression and how it affects the progression of APAP-induced hepatotoxicity...
January 11, 2017: Toxicology
https://www.readbyqxmd.com/read/28087888/simulated-microgravity-decreases-circulating-iron-in-rats-role-of-inflammation-induced-hepcidin-upregulation
#6
Thibault Cavey, Nicolas Pierre, Kévin Nay, Coralie Allain, Martine Ropert, Olivier Loréal, Frédéric Derbré
During spaceflight, humans exposed to microgravity exhibit an increase of iron storage and a reduction of circulating iron. Such perturbations could promote oxidative stress and anemia in astronauts. The mechanism by which microgravity modulates iron metabolism is still unknown. Herein, we hypothesized that microgravity up-regulates hepcidin, a hormone produced by the liver that is the main controller of iron homeostasis. To test this hypothesis, rats were submitted to hindlimb unloading (HU), the reference model to mimic the effects of microgravity in rodents...
January 13, 2017: Experimental Physiology
https://www.readbyqxmd.com/read/28087782/mutation-supply-and-relative-fitness-shape-the-genotypes-of-ciprofloxacin-resistant-escherichia-coli
#7
Douglas L Huseby, Franziska Pietsch, Gerrit Brandis, Linnéa Garoff, Angelica Tegehall, Diarmaid Hughes
Ciprofloxacin is an important antibacterial drug targeting Type II topoisomerases, highly active against Gram-negatives including Escherichia coli The evolution of resistance to ciprofloxacin in E. coli always requires multiple genetic changes, usually including mutations affecting two different drug target genes, gyrA and parC Resistant mutants selected in vitro or in vivo can have many different mutations in target genes and efflux regulator genes that contribute to resistance. Among resistant clinical isolates the genotype, gyrA S83L D87N, parC S80I is significantly overrepresented suggesting that it has a selective advantage...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087775/rapid-expansion-of-immune-related-gene-families-in-the-house-fly-musca-domestica
#8
Timothy B Sackton, Brian P Lazzaro, Clark G Andrew
The house fly, Musca domestica, occupies an unusual diversity of potentially septic niches compared to other sequenced Dipteran insects and is a vector of numerous diseases of humans and livestock. In the present study, we apply whole-transcriptome sequencing to identify genes whose expression is regulated in adult flies upon bacterial infection. We then combine the transcriptomic data with analysis of rates of gene duplication and loss to provide insight into the evolutionary dynamics of immune-related genes...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087763/circadian-kinetics-of-cell-cycle-progression-in-adult-neurogenic-niches-of-a-diurnal-vertebrate
#9
Veronica Akle, Alexander J Stankiewicz, Vasili Kharchenko, Lili Yu, Peter V Kharchenko, Irina V Zhdanova
: The circadian system may regulate adult neurogenesis via intracellular molecular clock mechanisms or by modifying the environment of neurogenic niches, with daily variation in growth factors or nutrients depending on the animal's diurnal or nocturnal life-style. In a diurnal vertebrate, zebrafish, we studied circadian distribution of immunohistochemical markers of the cell division cycle (CDC) in five of the sixteen neurogenic niches of adult brain, the dorsal telencephalon, habenula, preoptic area, hypothalamus and cerebellum...
January 13, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28087598/bayesian-network-inference-modeling-identifies-trib1-as-a-novel-regulator-of-cell-cycle-progression-and-survival-in-cancer-cells
#10
Rina Gendelman, Heming Xing, Olga K Mirzoeva, Preeti Sarde, Christina Curtis, Heidi Feiler, Paul McDonagh, Joe W Gray, Iya Khalil, W Michael Korn
Molecular networks governing cellular responses to targeted therapies are complex dynamic systems with non-intuitive behaviors. Here we applied a novel computational strategy to infer probabilistic causal relationships between network components based on gene expression. We constructed a model comprised of an ensemble of networks using multidimensional data from cell line models of cell cycle arrest caused by inhibition of MEK1/2. Through simulation of reverse-engineered Bayesian network modeling, we generated predictions of G1-S transition...
January 13, 2017: Cancer Research
https://www.readbyqxmd.com/read/28087428/polycomb-complexes-prc1-and-their-function-in-hematopoiesis
#11
REVIEW
Miguel Vidal, Katharzina Starowicz
Hematopoiesis, the process by which blood cells are continuously produced, is one of the best studied differentiation pathways. Hematological diseases are associated to reiterated mutations in genes encoding important gene expression regulators, including chromatin regulators. Among them, the Polycomb group (PcG) of proteins is an essential system of gene silencing involved in the maintenance of cell identities during differentiation. PcG proteins assemble into two major types of Polycomb repressive complexes (PRC) endowed with distinct histone tail modifying activities...
January 10, 2017: Experimental Hematology
https://www.readbyqxmd.com/read/28086803/compendium-of-tcdd-mediated-transcriptomic-response-datasets-in-mammalian-model-systems
#12
Stephenie D Prokopec, Kathleen E Houlahan, Ren X Sun, John D Watson, Cindy Q Yao, Jamie Lee, Christine P'ng, Renee Pang, Alexander H Wu, Lauren C Chong, Ashley B Smith, Nicholas J Harding, Ivy D Moffat, Jere Lindén, Sanna Lensu, Allan B Okey, Raimo Pohjanvirta, Paul C Boutros
BACKGROUND: 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is the most potent congener of the dioxin class of environmental contaminants. Exposure to TCDD causes a wide range of toxic outcomes, ranging from chloracne to acute lethality. The severity of toxicity is highly dependent on the aryl hydrocarbon receptor (AHR). Binding of TCDD to the AHR leads to changes in transcription of numerous genes. Studies evaluating the transcriptional changes brought on by TCDD may provide valuable insight into the role of the AHR in human health and disease...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28086769/effect-of-ginseng-extract-on-the-tgf-%C3%AE-1-signaling-pathway-in-ccl4-induced-liver-fibrosis-in-rats
#13
Mohamed M Hafez, Sherifa S Hamed, Manal F El-Khadragy, Zeinab K Hassan, Salim S Al Rejaie, Mohamed M Sayed-Ahmed, Naif O Al-Harbi, Khalid A Al-Hosaini, Mohamed M Al-Harbi, Ali R Alhoshani, Othman A Al-Shabanah, Shakir Dekhal Alsharari
BACKGROUND: Liver diseases are major global health problems. Ginseng extract has antioxidant, immune-modulatory and anti-inflammatory activities. This study investigated the effect of ginseng extract on carbon tetrachloride (CCl4)-induced liver fibrosis in rats. METHODS: Male Wistar rats were divided into four groups: control group, ginseng group, CCl4 group and CCl4 + ginseng group. Liver injury was induced by the intraperitoneal (I.P) injection of 3 ml/kg CCl4 (30% in olive oil) weekly for 8 weeks...
January 13, 2017: BMC Complementary and Alternative Medicine
https://www.readbyqxmd.com/read/28086749/evolution-of-the-angiopoietin-like-gene-family-in-teleosts-and-their-role-in-skin-regeneration
#14
Rita A Costa, João C R Cardoso, Deborah M Power
BACKGROUND: The skin in vertebrates is a protective barrier and damage is rapidly repaired to re-establish barrier function and maintain internal homeostasis. The angiopoietin-like (ANGPTL) proteins are a family of eight secreted glycoproteins with an important role in skin repair and angiogenesis in humans. In other vertebrates their existence and role in skin remains largely unstudied. The present study characterizes for the first time the homologues of human ANGPTLs in fish and identifies the candidates that share a conserved role in skin repair using a regenerating teleost skin model over a 4-day healing period...
January 13, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28080960/myogenic-regulatory-transcription-factors-regulate-growth-in-rhabdomyosarcoma
#15
Inês M Tenente, Madeline N Hayes, Myron S Ignatius, Karin McCarthy, Marielle Yohe, Sivasish Sindiri, Berkley Gryder, Mariana L Oliveira, Ashwin Ramakrishnan, Qin Tang, Eleanor Y Chen, G Petur Nielsen, Javed Khan, David M Langenau
Rhabdomyosarcoma (RMS) is a pediatric malignacy of muscle with myogenic regulatory transcription factors MYOD and MYF5 being expressed in this disease. Consensus in the field has been that expression of these factors likely reflects the target cell of transformation rather than being required for continued tumor growth. Here, we used a transgenic zebrafish model to show that Myf5 is sufficient to confer tumor-propagating potential to RMS cells and caused tumors to initiate earlier and have higher penetrance...
January 12, 2017: ELife
https://www.readbyqxmd.com/read/28079752/changes-in-dorsal-root-ganglion-gene-expression-in-response-to-spinal-cord-stimulation
#16
Dana M Tilley, David L Cedeño, Courtney A Kelley, Margaret DeMaegd, Ramsin Benyamin, Ricardo Vallejo
BACKGROUND AND OBJECTIVES: Spinal cord stimulation (SCS) has been shown to influence pain-related genes in the spinal cord directly under the stimulating electrodes. There is limited information regarding changes occurring at the dorsal root ganglion (DRG). This study evaluates gene expression in the DRG in response to SCS therapy. METHODS: Rats were randomized into experimental or control groups (n = 6 per group). Experimental animals underwent spared-nerve injury, implantation of lead, and continuous SCS (72 hours)...
January 11, 2017: Regional Anesthesia and Pain Medicine
https://www.readbyqxmd.com/read/28079159/socs1-favors-the-epithelial-mesenchymal-transition-in-melanoma-promotes-tumor-progression-and-prevents-antitumor-immunity-by-pd-l1-expression
#17
R Berzaghi, V S C Maia, F V Pereira, F M Melo, M S Guedes, C S T Origassa, J B Scutti, A L Matsuo, N O S Câmara, E G Rodrigues, L R Travassos
Silencing of SOCS1 protein with shRNAi lentivirus (shR-SOCS1) led to partial reversion of the tumorigenic phenotype of B16F10-Nex2 melanoma cells. SOCS1 silencing inhibited cell migration and invasion as well as in vitro growth by cell cycle arrest at S phase with increased cell size and nuclei. Down-regulation of SOCS1 decreased the expression of epidermal growth factor receptor, Ins-Rα, and fibroblast growth factor receptors. The present work aimed at analyzing the SOCS1 cell signaling and expression of proteins relevant to tumor development...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28078611/hyperbaric-oxygen-prevents-cognitive-impairments-in-mice-induced-by-d-galactose-by-improving-cholinergic-and-anti-apoptotic-functions
#18
Chunxia Chen, Luying Huang, Zhihuan Nong, Yaoxuan Li, Wan Chen, Jianping Huang, Xiaorong Pan, Guangwei Wu, Yingzhong Lin
Our previous study demonstrated that hyperbaric oxygen (HBO) improved cognitive impairments mainly by regulating oxidative stress, inflammatory responses and aging-related gene expression. However, a method for preventing cognitive dysfunction has yet to be developed. In the present study, we explored the protective effects of HBO on the cholinergic system and apoptosis in D-galactose (D-gal)-treated mice. A model of aging was established via systemic intraperitoneal injection of D-gal daily for 8 weeks. HBO was administered during the last 2 weeks of D-gal injection...
January 11, 2017: Neurochemical Research
https://www.readbyqxmd.com/read/28078514/the-molecular-basis-of-the-organization-of-repetitive-dna-containing-constitutive-heterochromatin-in-mammals
#19
REVIEW
Gohei Nishibuchi, Jérôme Déjardin
Constitutive heterochromatin is composed mainly of repetitive elements and represents the typical inert chromatin structure in eukaryotic cells. Approximately half of the mammalian genome is made of repeat sequences, such as satellite DNA, telomeric DNA, and transposable elements. As essential genes are not present in these regions, most of these repeat sequences were considered as junk DNA in the past. However, it is now clear that these regions are essential for chromosome stability and the silencing of neighboring genes...
January 11, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28078083/over-expression-of-toll-like-receptor-2-up-regulates-heme-oxygenase-1-expression-and-decreases-oxidative-injury-in-dairy-goats
#20
Shoulong Deng, Kun Yu, Wuqi Jiang, Yan Li, Shuotian Wang, Zhuo Deng, Yuchang Yao, Baolu Zhang, Guoshi Liu, Yixun Liu, Zhengxing Lian
BACKGROUND: Mastitis, an infection caused by Gram-positive bacteria, produces udder inflammation and oxidative injury in milk-producing mammals. Toll-like receptor 2 (TLR2) is important for host recognition of invading Gram-positive microbes. Over-expression of TLR2 in transgenic dairy goats is a useful model for studying various aspects of infection with Gram-positive bacteria, in vivo. METHODS: We over-expressed TLR2 in transgenic dairy goats. Pam3CSK4, a component of Gram-positive bacteria, triggered the TLR2 signal pathway by stimulating the monocytes-macrophages from the TLR2-positive transgenic goats, and induced over-expression of activator protein-1 (AP-1), phosphatidylinositol 3-kinase (PI3K) and transcription factor nuclear factor kappa B (NF-κB) and inflammation factors downstream of the signal pathway...
2017: Journal of Animal Science and Biotechnology
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