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Ichimura Kazuo K NARO Institute of Floricultural Science, Fujimoto, Tsukuba, Ibaraki 305-8519, Japan. Electronic address: - - 2014
To clarify whether climacteric-like increases in ethylene production of senescing petals are also induced in the absence of the gynoecium in cut carnation (Dianthus caryophyllus cv. Barbara) flowers, we compared ethylene production and expression of ethylene-biosynthesis genes in detached petals and in petals, which remained on flowers (attached petals). No ...
Long Zi-Wen ZW Department of Gastric cancer and soft tissue sarcoma surgery, Fudan University, Shanghai Cancer Center, No. 270, Dongan Road, Shanghai, 200032, - - 2014
Messenger RNA (mRNA) acts as template for protein synthesis. The matrix metalloproteinase-7 (MMP-7) protein and its mRNA expression have been suggested to be involved in the development of various diseases and cancers. We aimed to study associations between the MMP-7 protein and mRNA expression in gastric carcinoma (GC) patients. We ...
Guiliano David B DB David Guiliano, Izabela Lenart, Edward Tsao, Nasim Yousaf, Paul Kellam, Greg Towers and Antony N. Antoniou, Division of Infection and Immunity/Centre of Rheumatology, Rayne Building, 5 University Street, University College London, London, WC1E 6JF; School of Health, Sport and Bioscience, University of East London, London, E15 - - 2014
Objective. HLA-B27 forms misfolded heavy chain dimers, which may predispose individuals to inflammatory arthritis by inducing endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). We wanted to define the role of the UPR induced ER associated degradation (ERAD) pathway in the disposal of HLA-B27 dimeric conformers. Methods. HeLa ...
Mark Glover J N JN Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada. Electronic address: - - 2014
Antisense RNAs have long been known to regulate diverse aspects of plasmid biology. Here we review the FinOP system that modulates F plasmid gene expression through regulation of the F plasmid transcription factor, TraJ. FinOP is a two component system composed of an antisense RNA, FinP, which represses TraJ translation, ...
García-Fuster M J MJ Laboratorio de Neurofarmacología, IUNICS-IdISPa, Universitat de les Illes Balears (UIB), and Redes Temáticas de Investigación Cooperativa en Salud-Red de Trastornos Adictivos (RETICS-RTA), Cra. Valldemossa km 7.5, E-07122 Palma de Mallorca, - - 2014
Enhanced brain apoptosis (neurons and glia) may be involved in major depression (MD) and schizophrenia (SZ), mainly through the activation of the intrinsic (mitochondrial) apoptotic pathway. In the extrinsic death pathway, pro-apoptotic Fas-associated death domain (FADD) adaptor and its non-apoptotic p-Ser194 FADD form have critical roles interacting with other death ...
Yu Chun-Ying CY Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, - - 2014
Global transcriptome investigations often result in the detection of an enormous number of transcripts composed of non-co-linear sequence fragments. Such 'aberrant' transcript products may arise from post-transcriptional events or genetic rearrangements, or may otherwise be false positives (sequencing/alignment errors or in vitro artifacts). Moreover, post-transcriptionally non-co-linear ('PtNcl') transcripts can arise ...
Mungamuri S K SK Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, - - 2014
Chromatin conformation has a major role in all cellular decisions. We showed previously that P53 pro-apoptotic target promoters are enriched with H3K9me3 mark and induction of P53 abrogates this repressive chromatin conformation by downregulating SUV39H1, the writer of this mark present on these promoters. In the present study, we demonstrate ...
Hansen Allison K AK 1] Department of Entomology, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA [2] Department of Ecology and Evolutionary Biology, Microbial Diversity Institute, Yale University, New Haven, CT, - - 2014
Genome architecture of a microbe markedly changes when it transitions from a free-living lifestyle to an obligate symbiotic association within eukaryotic cells. These symbiont genomes experience numerous rearrangements and massive gene loss, which is expected to radically alter gene regulatory networks compared with those of free-living relatives. As such, it ...
Wagner Mathias M Department of Pathology, University of Saarland Medical School, Homburg Saar, - - 2014
The present study is one of the few that includes tissue samples in the evaluation of target prediction algorithms designed to detect microRNA (miRNA) sequences that might interact with particular messenger RNA (mRNA) sequences. Twelve different target prediction tools were used to find miRNA sequences that might interact with CCL20 ...
Yokoshi Moe M Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, - - 2014
It has been proposed that Ataxin-2, a member of the like-Sm (LSm) protein family, participates in the regulation of RNA metabolism through interaction with PABPC1. However, the exact biological mechanism and in vivo targets remain unknown. Here, we report that Ataxin-2 binds directly to RNAs in a PABPC1-independent manner. High-throughput sequencing ...
Erben Esteban D ED Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, - - 2014
In trypanosomatids, gene expression is regulated mainly by post-transcriptional mechanisms, which affect mRNA processing, translation and degradation. Currently, our understanding of factors that regulate either mRNA stability or translation is rather limited. We know that often, the regulators are proteins that bind to the 3'-untranslated region; they presumably interact with ...
Hogg Rebecca R Faculty of Life Sciences, The University of Manchester, Oxford Road, Manchester, M13 - - 2014
Removal of intron regions from pre-messenger RNA (pre-mRNA) requires spliceosome assembly with pre-mRNA, then subsequent spliceosome remodeling to allow activation for the two steps of intron removal. Spliceosome remodeling is carried out through the action of DExD/H-box ATPases that modulate RNA-RNA and protein-RNA interactions. The ATPase Prp16 remodels the spliceosome ...
Gupta Sachin Kumar SK The Mina and Everard Goodman Faculty of Life Sciences, and Advanced Materials and Nanotechnology Institute; Bar-Ilan University; Ramat-Gan, - - 2014
In trypanosomes, mRNAs are processed by trans-splicing; in this process, a common exon, the spliced leader, is added to all mRNAs from a small RNA donor, the spliced leader RNA (SL RNA). However, little is known regarding how this process is regulated. In this study we investigated the function of ...
Barrios Alvaro P AP Nucleus Millennium in Stress and Addiction, Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, - - 2014
Mammalian genomes harbor three CoREST genes. rcor1 encodes CoREST (CoREST1) and the paralogues rcor2 and rcor3 encode CoREST2 and CoREST3, respectively. Here, we describe specific properties of transcriptional complexes formed by CoREST proteins with the histone demethylase LSD1/KDM1A and histone deacetylases HDAC1/2 and the finding that all three CoRESTs express ...
Malbert-Colas Laurence L Cibles Thérapeutiques, Equipe Labellisée Ligue Contre le Cancer, INSERM Unité 940, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, 27 rue Juliette Dodu, 75010 Paris, - - 2014
Regulated protein synthesis via changes in mRNA structures forms an important part of how prokaryotic cells adapt protein expression in response to changes in the environment. Little is known regarding how this concept has adapted to regulate mRNA translation via signaling pathways in mammalian cells. Here, we show that following ...
Thackray Alana M AM University of Cambridge, Department of Veterinary Medicine, Madingley Road, Cambridge, CB3 OES, - - 2014
Prion diseases are characterized by a conformational change in the normal host protein PrPC. While the majority of mature PrPC is tethered to the plasma membrane by a glycosylphosphatidyl-inositol anchor, topological variants of this protein can arise during its biosynthesis. Here we have generated Drosophila transgenic for cytosolic ovine PrP ...
Paul Benjamin C BC NYU Voice Center, Department of Otolaryngology, New York University School of Medicine, New York, - - 2014
Objective. To determine the efficacy of small interfering RNA (siRNA) targeting Smad3 to mediate fibroplasia in vitro, to investigate the temporal regulation of Smad3 following vocal fold (VF) injury, and to determine the local and distal effects of Smad3 siRNA vocal fold injection. Study Design. In vitro and in vivo ...
King Isabelle I Gladstone Institutes, United - - 2014
microRNA (miRNA) maturation is regulated by interaction of particular miRNA precursors with specific RNA-binding proteins. Following their biogenesis, mature miRNAs are incorporated into the RNA-Induced Silencing Complex (RISC) where they interact with mRNAs to negatively regulate protein production. However, little is known about how mature miRNAs are regulated at the ...
Holcman D D Applied Mathematics and Computational Biology, IBENS, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 , Paris, France, - - 2014
Messenger RNAs (mRNAs) can be repressed and degraded by small non-coding RNA molecules. In this paper, we formulate a coarsegrained Markov-chain description of the post-transcriptional regulation of mRNAs by either small interfering RNAs (siRNAs) or microRNAs (miRNAs). We calculate the probability of an mRNA escaping from its domain before it ...
Saramago Margarida M Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, - - 2014
Ribonucleases (RNases) are key factors in the control of biological processes, since they modulate the processing, degradation and quality control of RNAs. This review gives many illustrative examples of the role of RNases in the regulation of small RNAs (sRNAs). RNase E and PNPase have been shown to degrade the ...
Griseri Paola P 1 U.O.C Medical Genetics, Institute Giannina Gaslini , Genoa, Italy - - 2014
Control of mRNA half-life plays a central role in normal development and disease. Several pathological conditions, such as inflammation and cancer, tightly correlate with deregulation in mRNA stability of pro-inflammatory genes. Among these, pro-angiogenesis cytokines, which play a crucial role in the formation of new blood vessels, normally show rapid ...
Vreeland Amanda C AC Departments of - - 2014
The RNA-binding protein HuR binds at 3' UTR regions of target transcripts thereby protecting them against degradation. We show that HuR directly interacts with cellular retinoic acid-binding protein 2 (CRABP2), a protein known to transport RA from the cytosol to the nuclear receptor RAR. Association with CRABP2 dramatically increases the ...
Jha Bhaskar Anand BA Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D69120 Heidelberg. - - 2014
Pumilio domain RNA-binding proteins are known mainly as post-transcriptional repressors of gene expression which reduce mRNA translation and stability. Trypanosoma brucei has 11 PUF proteins. We show here that PUF2 is in the cytosol, with roughly the same number of molecules per cell as there are mRNAs. Although PUF2 exhibits ...
Baghban Roghayyeh R Department of Biology, Faculty of Basic Sciences, Shahed University, Tehran-Qom Express Way Tehran, - - 2014
Botulinum neurotoxins (BoNTs) result in severe and often fatal disease, botulism. Common remedial measures such as equine antitoxin and human botulism immunoglobulin in turn are problematic and time-consuming. Therefore diagnosis and therapy of BoNTs are vital. The Variable domain of heavy-chain antibodies(VHH) has unique features such as ability to identify, ...
Takahashi Melissa K - - 2014
RNA regulators are emerging as powerful tools to engineer synthetic genetic networks or rewire existing ones. A potential strength of RNA networks is that they may be able to propagate signals on timescales that are set by the fast degradation rates of RNAs. However, a current bottleneck to verifying this ...
Kumar Santosh - - 2014
MiRNAs are one of the key epigenetic regulators of the gene expression. They act through hybridization with their target mRNA and modulate the level of respective proteins via different mechanisms. Various cancer conditions are known to be associated with up or down regulation of the oncogenic and tumor suppressor miRNAs ...
Shi Lihua L Division of Allergy Immunology, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA - - 2014
Noncoding RNAs have been implicated in the regulation of expression of numerous genes; however, the mechanism is not fully understood. We identified bidirectional, long noncoding RNAs upstream of the TNF gene using five different methods. They arose in a region where the repressors LRRFIP1, EZH2, and SUZ12 were demonstrated to ...
Mao Yuanhui Y College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China, Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi 712100, China and College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, - - 2014
Messenger RNA (mRNA) secondary structure decreases the elongation rate, as ribosomes must unwind every structure they encounter during translation. Therefore, the strength of mRNA secondary structure is assumed to be reduced in highly translated mRNAs. However, previous studies in vitro reported a positive correlation between mRNA folding strength and protein ...
Chawla Geetanjali G Department of Biology, Indiana University, Bloomington, IN 47405, - - 2014
Adenosine deaminases acting on RNAs (ADARs) convert adenosine residues to inosines in primary microRNA (pri-miRNA) transcripts to alter the structural conformation of these precursors and the subsequent functions of the encoded microRNAs (miRNAs). Here we show that RNA editing by Drosophila ADAR modulates the expression of three co-transcribed miRNAs encoded ...
Xie Ping P Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China. Electronic address: - - 2014
Translocation is an essential step in the elongation cycle of protein synthesis in which mRNA that is coupled with tRNAs by codon-anticodon interaction is moved through the ribosome. It has been well documented that the kinetics of mRNA translocation generally shows biphasic character. However, the physical basis of the phenomenon ...
Chabelskaya Svetlana S Université de Rennes 1, Inserm U835-UPRES EA 2311, Biochimie Pharmaceutique, 2 avenue du Prof. Léon Bernard, 35043 Rennes, - - 2014
In pathogens, the accurate programming of virulence gene expression is essential for infection. It is achieved by sophisticated arrays of regulatory proteins and ribonucleic acids (sRNAs), but in many cases their contributions and connections are not yet known. Based on genetic, biochemical and structural evidence, we report that the expression ...
Singh Aditi A Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D69120 Heidelberg, - - 2014
The trypanosome zinc finger protein ZC3H11 binds to AU-rich elements in mRNAs. It is essential for survival of the mammalian-infective bloodstream form, where it stabilizes several mRNAs including some encoding chaperones, and is also required for stabilization of chaperone mRNAs during the heat-shock response in the vector-infective procyclic form. When ...
Schueler Markus - - 2014
RNA-binding proteins (RBPs) mediate mRNA biogenesis, translation and decay. We recently developed an approach to profile transcriptome-wide RBP contacts on polyadenylated transcripts by next-generation sequencing. A comparison of such profiles from different biological conditions has the power to unravel dynamic changes in protein-contacted cis-regulatory mRNAs regions without a priori knowledge ...
Srinivasan Sumana S Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India. - - 2014
A Gene Regulatory Network (GRN) represents complex connections between genes in a cell which interact with each other through their RNA and protein expression products, thereby determining the expression levels of mRNA and proteins required for functioning of the cell. Microarray experiments yield the log fold change in mRNA abundance ...
de Messieres Michel M Department of Physics, Institute for Physical Science and Technology Biophysics Program, University of Maryland, College Park, - - 2014
Secondary or tertiary structure in an mRNA, such as a pseudoknot, can create a physical barrier that requires the ribosome to generate additional force to translocate. The presence of such a barrier can dramatically increase the probability that the ribosome will shift into an alternate reading frame, in which a ...
Webb Shaun - - 2014
Nrd1 and Nab3 are essential sequence-specific yeast RNA binding proteins that function as a heterodimer in the processing and degradation of diverse classes of RNAs. These proteins also regulate several mRNA coding genes; however, it remains unclear exactly what percentage of the mRNA component of the transcriptome these proteins control. ...
Sharawat Surender Kumar - - 2014
Objective Quantitative assessment of BAX transcripts and protein in acute myeloid leukemia (AML). Methods We quantitatively evaluated BAX gene transcripts by real-time polymerase chain reaction (TaqMan probe chemistry) and protein expression by flow cytometry. Results Consecutive 112 AML patients with a median age of 16 (1-59) years were recruited in ...
Zhang Yan Y Department of Neurology, McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of - - 2014
Prion diseases are rare and aggressive neurodegenerative disorders caused by the accumulation of misfolded, toxic conformations of the prion protein (PrP). Therapeutic strategies directed at reducing the levels of PrP offer the best chance of delaying or halting disease progression. The challenge, though, is to define pharmacologic targets that result ...
Durruthy-Durruthy Jens J Institute for Stem Cell Biology and Regenerative Medicine, Department of Obstetrics and Gynecology and Department of Genetics, Stanford University, Stanford, California, United States of - - 2014
Data suggest that clinical applications of human induced pluripotent stem cells (hiPSCs) will be realized. Nonetheless, clinical applications will require hiPSCs that are free of exogenous DNA and that can be manufactured through Good Manufacturing Practice (GMP). Optimally, derivation of hiPSCs should be rapid and efficient in order to minimize ...
Meyer Swanhild U SU Physiology Weihenstephan, ZIEL Research Center for Nutrition and Food Sciences, Technische Universität München, Weihenstephaner Berg 3, D-85354, Freising, - - 2014
Protein coding RNAs are posttranscriptionally regulated by microRNAs, a class of small noncoding RNAs. Insights in messenger RNA (mRNA) and microRNA (miRNA) regulatory interactions facilitate the understanding of fine-tuning of gene expression and might allow better estimation of protein synthesis. However, in silico predictions of mRNA-microRNA interactions do not take ...
Li Jingyi Jessica JJ Department of Statistics, University of California , Berkeley, CA , USA ; Departments of Statistics and Human Genetics, University of California , Los Angeles, CA , - - 2014
Large scale surveys in mammalian tissue culture cells suggest that the protein expressed at the median abundance is present at 8,000-16,000 molecules per cell and that differences in mRNA expression between genes explain only 10-40% of the differences in protein levels. We find, however, that these surveys have significantly underestimated ...
Chang Kenneth - - 2014
In Drosophila, long-term effects of RNA interference (RNAi) must be achieved by integrating into the genome a template from which an RNAi trigger is transcribed by cellular RNA polymerases, generally RNA polymerase II or III. With encoded triggers, not only can essentially permanent silencing be achieved, but control can also ...
Reznik Boris B Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of - - 2014
The tristetraprolin (TTP) family of zinc-finger proteins, TTP, BRF1 and BRF2, regulate the stability of a subset of mRNAs containing 3'UTR AU-rich elements (AREs), including mRNAs coding for cytokines, transcription factors, and proto-oncogenes. To better understand the mechanism by which TTP-family proteins control mRNA stability in mammalian cells, we aimed ...
Yang Hong H Cell Biology Group; Department of Surgery; University of Maryland School of Medicine; Baltimore, MD USA ; Baltimore Veterans Affairs Medical Center; Baltimore, MD - - 2014
Intestinal epithelial tight junctions (TJs) are a specialized structure that determines the cell polarity and prevents the diffusion of toxins, allergens, and pathogens from the lumen into the tissue. TJs are highly dynamic and its constituent protein complexes undergo continuously remodeling and turnover under tight regulation by numerous extracellular and ...
Xu Enshun E University of California at - - 2013
P63, a p53 family member, plays pivotal roles in epidermal development, aging, and tumorigenesis. Thus, understanding how p63 expression is controlled has biological and clinical importance. RBM24 is an RNA-binding protein and shares a high sequence similarity with RBM38, a critical regulator of p63. In the current study, we investigated ...
Tian Rui R Rui Tian, Rui-Lan Wang, Hui Xie, Wei Jin, Kang-Long Yu, Intensive Care Unit, First People's Hospital, Shanghai Jiaotong University, Shanghai 201620, - - 2013
To investigate whether miRNA-155 (miR-155) dysregulates apical junctional complex (AJC) protein expression in experimental severe acute pancreatitis (SAP). Twenty-four male BALB/c mice were randomly assigned to two groups: the SAP group (n = 12) receiving sequential intraperitoneal injection of 50 µg/kg caerulein and 10 mg/kg lipopolysaccharide over 6 h, and ...
Hassan Tidi - - 2013
Retention of abnormal alpha-1 antitrypsin activates the unfolded protein response in alpha-1 antitrypsin deficient monocytes. The regulatory role of microRNAs in unfolded protein responses and chronic obstructive pulmonary disease pathogenesis has not been investigated. To investigate microRNA expression and function in MM and ZZ monocytes and identify microRNA(s) regulating the ...
Duval Mélodie M Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire-CNRS, Strasbourg, - - 2013
Regulation of translation initiation is well appropriate to adapt cell growth in response to stress and environmental changes. Many bacterial mRNAs adopt structures in their 5' untranslated regions that modulate the accessibility of the 30S ribosomal subunit. Structured mRNAs interact with the 30S in a two-step process where the docking ...
Liu Hui-Hui - - 2013
The C1q-domain-containing (C1qDC) proteins, which are involved in various processes of vertebrates, are important pattern recognition receptors in innate immunity of invertebrates. In present study, a novel C1qDC was identified from Mytilus coruscus (designated as McC1qDC), which was 917 bp in length encoding 236 amino acids with a typical signal ...
Lutz Benjamin - - 2013
Riboswitches are part of noncoding regions of messenger RNA (mRNA) that act as RNA sensors regulating gene expression of the downstream gene. Typically, one out of two distinct conformations is formed depending on ligand binding when the transcript leaves RNA polymerase (RNAP). Elongation of the RNA chain by RNAP, folding ...
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