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Gutschner Tony T Department of Genomic Medicine, The University of Texas M.D. Anderson Cancer Center, 1901 East Road, Houston, TX, 77054, USA, - - 2015
Long noncoding RNAs (lncRNAs) are a functional and structural diverse class of cellular transcripts that comprise the largest fraction of the human transcriptome. However, detailed functional analysis lags behind their rapid discovery. This might be partially due to the lack of loss-of-function approaches that efficiently reduce the expression of these ...
Izuta Yusuke Y Department of Bioscience, School of Science and Technology, Kwansei Gakuin University. 2-1 Gakuen, Sanda-shi, Hyogo-ken 669-1337, - - 2014
Biological roles of most protocadherins are a largely unsolved problem. Therefore, we cloned cDNA for Xenopus laevis protocadherin-9 and characterized its properties to elucidate the role. The deduced amino acid sequence was highly homologous to those of mammalian protocadherin-9s. Xenopus laevis protocadherin-9 expressed from the cDNA in L cells showed ...
Stefanovic Snezana S Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, - - 2014
Fragile X syndrome (FXS) is the most common inherited form of intellectual disability caused by the CGG trinucleotide expansion in the 3'-untranslated region of the FMR1 gene on the X chromosome, that silences the expression of the Fragile X mental retardation protein (FMRP). FMRP has been shown to bind to ...
Peng Yi Y Cell, Molecular and Developmental Biology and Biophysics Program, Johns Hopkins University, Baltimore, MD - - 2014
The Sm-like protein Hfq (host factor Q-beta phage) facilitates regulation by bacterial small noncoding RNAs (sRNAs) in response to stress and other environmental signals. Here, we present a low-resolution model of Escherichia coli Hfq bound to the rpoS mRNA, a bacterial stress response gene that is targeted by three different ...
Zeglinski Matthew R MR University of - - 2014
Remodeling of the extracellular matrix (ECM) is beneficial during the acute wound healing stage following tissue injury. In the short term, resident fibroblasts and myofibroblasts regulate the matrix remodeling process through production of matricellular protein components which provide structural support to the damaged tissue. This process is largely governed by ...
Bernkopf Dominic B - - 2014
Axin and conductin/axin2 are structurally related inhibitors of Wnt/β-catenin signalling that promote degradation of β-catenin. Whereas axin is constitutively expressed, conductin is a Wnt target gene implicated in negative feedback regulation. Here we show that axin and conductin differ in their functional interaction with the upstream Wnt pathway component Dvl. ...
Rog-Zielinska E A EA Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, - - 2014
Glucocorticoid levels rise dramatically in late gestation to mature foetal organs in readiness for postnatal life. Immature heart function may compromise survival. Cardiomyocyte glucocorticoid receptor (GR) is required for the structural and functional maturation of the foetal heart in vivo, yet the molecular mechanisms are largely unknown. Here we asked ...
Mazin Pavel V PV Research Institute of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119992, Russian Federation Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny 19, Moscow 127994, Russian - - 2014
The avian bacterial pathogen Mycoplasma gallisepticum is a good model for systems studies due to small genome and simplicity of regulatory pathways. In this study, we used RNA-Seq and MS-based proteomics to accurately map coding sequences, transcription start sites (TSSs) and transcript 3'-ends (T3Es). We used obtained data to investigate ...
Vaidya Hitesh H Department of Biochemistry, Memorial University, St. John's, NL A1B3X9, Canada. - - 2014
Omega (n)-3 polyunsaturated fatty acids (PUFA), namely docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), are known to reduce the risk of insulin resistance and ameliorate obesity-associated disorders. DHA and EPA structured in the phospholipid form possess superior biological effects compared to the triglyceride form available in fish oil. In this ...
Ishihara Takaya T Department of Protein Biochemistry, Institute of Life Science, Kurume University, Kurume, - - 2014
Mitochondria are dynamic organelles, and their fusion and fission regulate cellular signaling, development, and mitochondrial homeostasis including mtDNA distribution. Cardiac myocytes have a specialized cytoplasmic structure where large mitochondria are aligned into tightly packed myofibril bundles; however, recent studies have revealed that mitochondrial dynamics also play important roles in the ...
Choe Junho J Division of Life Sciences, Korea University, Seoul 136-701, Republic of - - 2014
It has long been considered that intron-containing (spliced) mRNAs are translationally more active than intronless mRNAs (identical mRNA not produced by splicing). The splicing-dependent translational enhancement is mediated, in part, by the exon junction complex (EJC). Nonetheless, the molecular mechanism by which each EJC component contributes to the translational enhancement ...
Engelhorn Julia J Université Grenoble Alpes, UMR5168, F-38041 Grenoble, France CNRS, UMR5168, F-38054 Grenoble, France CEA, iRTSV, Laboratoire Physiologie Cellulaire et Végétale, F-38054 Grenoble, France INRA, F-38054 Grenoble, - - 2014
The morphological variability of the flower in angiosperms, combined with its relatively simple structure, makes it an excellent model to study cell specification and the establishment of morphogenetic patterns. Flowers are the products of floral meristems, which are determinate structures that generate four different types of floral organs before terminating. ...
Ausländer Simon S Department of Biosystems Science and Engineering, ETH Zurich, Basel, - - 2014
RNAs are ideal for the design of gene switches that can monitor and program cellular behavior because of their high modularity and predictable structure-function relationship. We have assembled an expression platform with an embedded modular ribozyme scaffold that correlates self-cleavage activity of designer ribozymes with transgene translation in bacteria and ...
Wang Xiao X Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, - - 2014
Cellular RNAs can be chemically modified over a hundred different ways. These modifications were once thought to be static, discrete, and utilized to fine-tune RNA structure and function. However, recent studies have revealed that some modifications, like mRNA methylation, can be reversed, and these reversible modifications may play active roles ...
Wang Ting T Arizona Respiratory Center and Department of Medicine, University of Arizona, Tucson, AZ, - - 2014
Myosin light-chain kinase (MYLK) is a gene known to be significantly associated with severe asthma in African Americans. Here we further examine the molecular function of a single-nucleotide polymorphism (SNP), located in the non-muscle myosin light-chain kinase isoform (nmMLCK), in asthma susceptibility and pathobiology. We identified nmMLCK variant (reference SNP: ...
Hui Monica P MP Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Microbiology, New York University School of Medicine, New York, NY - - 2014
mRNA degradation is an important mechanism for controlling gene expression in bacterial cells. This process involves the orderly action of a battery of cellular endonucleases and exonucleases, some universal and others present only in certain species. These ribonucleases function with the assistance of ancillary enzymes that covalently modify the 5' ...
Di Chao C MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, - - 2014
Recently, in addition to poly(A)+ long noncoding RNAs (lncRNAs), many lncRNAs without poly(A) tails, have been characterized in mammals. However, the non-polyA lncRNAs and their conserved motifs, especially those associated with environmental stresses, have not been fully investigated in plant genomes. We performed poly(A)- RNA-seq for seedlings of Arabidopsis thaliana ...
Doi Ayano A Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan. Electronic address: - - 2014
The early steps of mammary tumorigenesis include loss of epithelial cell polarity, escape from anoikis, and acquisition of proliferative capacity. The genes responsible for these processes are predicted to be early diagnostic markers or new therapeutic targets. Here we tested 51 genes coamplified with ERBB2 in the 17q12-21 amplicon for ...
Agarwala Prachi P Proteomics and Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, - - 2014
Secondary structures in 5' UTR of mRNAs play a critical role in regulating protein synthesis. Though studies have indicated the role of secondary structure G-quadruplex in translational regulation, position-specific effect of G-quadruplex in naturally occurring mRNAs is still not understood. As a pre-initiation complex recognises 5' cap of the mRNA ...
Fischer-Kešo Regina R Division of Vascular Oncology and Metastasis, German Cancer Research Center, DKFZ-ZMBH Alliance, Heidelberg, Germany Department of Vascular Biology and Tumor Angiogenesis (CBTM), Medical Faculty Mannheim, Heidelberg University, Mannheim, - - 2014
Plakophilins 1 and 3 (PKP1/3) are members of the arm-repeat family of catenin proteins and serve as structural components of desmosomes important for cell-cell-adhesion. In addition, PKP1/3 occur as soluble proteins outside of desmosomes, yet their role in the cytoplasm is not known so far. We found that cytoplasmic PKP1/3 ...
Pilkington Guy R GR Human Retrovirus Pathogenesis Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, - - 2014
Post-transcriptional regulatory mechanisms of several complex and simple retroviruses and retroelements have been elucidated, with the exception of the gammaretrovirus family. We found that, similar to the other retroviruses, gag gene expression of MuLV and XMRV depends on post-transcriptional regulation mediated via an RNA sequence overlapping the pro-pol open reading ...
Vigetti Davide D University of Insubria, - - 2014
Changes in the microenvironment organization within vascular walls are critical events in the pathogenesis of vascular pathologies, including atherosclerosis and restenosis. Hyaluronan (HA) accumulation into artery walls supports vessel thickening and is involved in many cardiocirculatory diseases. Excessive cytosolic glucose can enter the hexosamine biosynthetic pathway, increase UDP-N-acetylglucosamine (UDP-GlcNAc) availability, ...
Nomura Tsuyoshi T Protein Development Center, Sysmex Corporation, 1548 Simo-okudomi, Sayama, Saitama 350-1332, Japan; The International Center for Biotechnology, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-8071, Japan. Electronic address: - - 2014
The baculovirus-silkworm recombinant protein expression system is an excellent method for achieving high-level expression and post-translational modifications, especially glycosylation. However, the presence of paucimannosidic-type N-glycan in glycoproteins restricts their clinical use. Paucimannosidic-type N-glycan is produced by insect-specific membrane-binding-type β-N-acetylglucosaminidase (GlcNAcase). In the silkworm, BmGlcNAcase1, BmGlcNAcase2, and BmFDL are membrane-binding-type GlcNAcases. ...
Bu Zhongyuan Z State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, - - 2014
Day-length is important for regulating the transition to reproductive development (flowering) in plants. In the model plant Arabidopsis thaliana, the transcription factor CONSTANS (CO) promotes expression of the florigen FLOWERING LOCUS T (FT), constituting a key flowering pathway under long-day photoperiods. Recent studies have revealed that FT expression is regulated ...
Wang Bin B Department of Genetics, Geisel School of Medicine, Dartmouth, Hanover, New Hampshire, United States of - - 2014
In the negative feedback loop comprising the Neurospora circadian oscillator, the White Collar Complex (WCC) formed from White Collar-1 (WC-1) and White Collar-2 (WC-2) drives transcription of the circadian pacemaker gene frequency (frq). Although FRQ-dependent repression of WCC has been extensively studied, the mechanism by which the WCC initiates a ...
Tschowri Natalia N Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, - - 2014
The cyclic dinucleotide c-di-GMP is a signaling molecule with diverse functions in cellular physiology. Here, we report that c-di-GMP can assemble into a tetramer that mediates the effective dimerization of a transcription factor, BldD, which controls the progression of multicellular differentiation in sporulating actinomycete bacteria. BldD represses expression of sporulation genes ...
Piecyk Karolina K Faculty of Chemistry, University of Warsaw, 02-093, Warsaw, - - 2014
Synthetic analogs of the 5' end of mRNA (cap structure) are widely used in molecular studies on mechanisms of cellular processes such as translation, intracellular transport, splicing, and turnover. The best-characterized cap binding protein is translation initiation factor 4E (eIF4E). Recognition of the mRNA cap by eIF4E is a critical, ...
Turner Jonathan D JD Institute of Immunology, Centre de Recherche Public de la Santé/Laboratoire National de Santé, 20A rue Auguste Lumière, L-1950 Luxembourg, - - 2014
GR transcripts display a remarkable heterogeneity in their 5' untranslated regions (5'UTRs). These variable 5'UTRs are encoded by a series of alternative 1st exons, and together with their associated promoters they maintain tissue-specific GR expression levels. In this study we over-expressed GR transcripts containing individual 1st exons, and assessed their ...
Tocchini Cristina C Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; University of Basel, Basel, - - 2014
The mechanisms controlling cell fate determination and reprogramming are fundamental for development. A profound reprogramming, allowing the production of pluripotent cells in early embryos, takes place during the oocyte-to-embryo transition. To understand how the oocyte reprogramming potential is controlled, we sought Caenorhabditis elegans mutants in which embryonic transcription is initiated ...
Huang Qiang Q Trauma Center of Daping Hospital, Third Military Medical University, Chongqing 404100, P.R. - - 2014
An understanding of the regulatory mechanisms that drive Staphylococcus aureus biofilm formation may lead to the development of an effective strategy to control the increasing number of refractory clinical infections it causes. The present study examined the effects of the antimicrobial agent human β‑defensin 3 (hBD‑3) and the antibiotics vancomycin and ...
Zach Lolita L Technion school of Medicine, - - 2014
Initial steps in protein synthesis are highly regulated processes as they define the reading frame of the translation machinery. Eukaryotic translation initiation is a process facilitated by numerous factors (eIFs), aimed to form a scanning mechanism towards the initiation codon. Translation initiation of the main open reading frame (ORF) in ...
Moqtaderi Zarmik Z Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA - - 2014
In Saccharomyces cerevisiae, previous measurements of mRNA stabilities have been determined on a per-gene basis. We and others have recently shown that yeast genes give rise to a highly heterogeneous population of mRNAs thanks to extensive alternative 3' end formation. Typical genes can have fifty or more distinct mRNA isoforms ...
Kronstad Lisa M LM Department of Plant and Microbial Biology, University of California, Berkeley, California, - - 2014
The Kaposi's sarcoma-associated herpesvirus (KSHV) ORF36 protein kinase is translated as a downstream gene from the ORF35-37 polycistronic mRNA via a unique mechanism involving short upstream open reading frames (uORFs) located in the 5' untranslated region. Here, we confirm that ORF35-37 is functionally dicistronic during infection and demonstrate that mutation ...
Poliakova Kseniia K Department of Clinical Research, University of Bern, Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland; Department of Dermatology, Inselspital, Bern University Hospital, Bern, - - 2014
BPAG1a and BPAG1b (BPAG1a/b) constitute two major isoforms encoded by the dystonin (Dst) gene and show homology with MACF1a and MACF1b. These proteins are members of the plakin family, giant multi-modular proteins able to connect the intermediate filament, microtubule and microfilament cytoskeletal networks with each other and to distinct cell ...
Zhang Chunni C 1] Key Laboratory of Plant Protection Resources and Pest Integrated Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China [2] Department of Entomology and BIO5 Institute, University of Arizona, Tucson, AZ 85721, - - 2014
How polyphagous herbivores up-regulate their counterdefense genes in response to a broad range of structurally different allelochemicals remains largely unknown. To test whether this is accomplished by having more allelochemical-response elements or the similar number of functionally more diverse elements, we mapped out the cis-acting elements mediating the induction of ...
Bai Baoling B Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, - - 2014
The methylation status of DNA methylation regions (DMRs) of the imprinted gene IGF2/Igf2 is associated with neural tube defects (NTDs), which are caused by a failure of the neural tube to fold and close and are the second-most common birth defect; however, the characterization of the expression level of IGF2/Igf2 ...
Bandara H M H N - - 2013
AIM: To investigate the time- and concentration-dependent effects of Escherichia coli biofilm supernatant on Candida biofilm development, and to assess the effect of E. coli supernatant on Candida albicans hypha-specific genes (HSGs) expression. METHODS: The effect of E. coli biofilm supernatant on six Candida spp. was assessed by tetrazolium salt (XTT) reduction ...
Banerjee Mohua - - 2013
Biofilm formation is associated with the ability of Candida albicans, the major human fungal pathogen, to resist antifungal therapies and grow on tissues, catheters, and medical devices. In order to better understand the relationship between C. albicans morphology and biofilm formation, we examined biofilms generated in response to expression of ...
Andreev Dmitri E - - 2012
We have previously shown that translation driven by the 5' UTR of Apaf-1 mRNA is relatively efficient in the absence of m7G-cap, but no IRES is involved. Nevertheless, it may be speculated that a "silent" IRES is activated under apoptosis conditions. Here, we show that translation of the mRNA with ...
Bandara H M H N HM Oral Biosciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong City, Hong - - 2013
Elucidation of bacterial and fungal interactions in multispecies biofilms will have major impacts on understanding the pathophysiology of infections. The objectives of this study were to (i) evaluate the effect of Pseudomonas aeruginosa lipopolysaccharide (LPS) on Candida albicans hyphal development and transcriptional regulation, (ii) investigate protein expression during biofilm formation, ...
Christner Martin - - 2012
Biofilm formation is essential for Staphylococcus epidermidis pathogenicity in implant-associated infections. Nonetheless, large proportions of invasive Staphylococcus epidermidis isolates fail to form a biofilm in vitro. We here tested the hypothesis that this apparent paradox is related to the existence of superimposed regulatory systems suppressing a multicellular biofilm life style ...
Kim Sangmin - - 2012
Overexpression of HER2 correlates with more aggressive tumors and increased resistance to cancer chemotherapy. However, a functional comparison between the HER2(high)/HER3 and the HER2(low)/HER3 dimers on tumor metastasis has not been conducted. Herein we examined the regulation mechanism of heregulin- β1 (HRG)-induced MMP-1 and -9 expression in breast cancer cell ...
Sun Siyuan - - 2012
Tetrahydropalmatine (THP), with one chiral centre, is one of the major constituents of Rhizoma corydalis. THP is considered to possess analgesic, sedative, hypnotic actions and cardiac protection. The aim of this study was to elucidate the stereoselective interaction between THP and ABC transporters. The present study investigated three most important ...
Fukunaga Masakazu - - 2012
Indoleamine 2,3-dioxygenase 1 (IDO1) catabolizes tryptophan to kynurenine at the first step of tryptophan metabolism. Recently, in addition to IDO1, a new isoform called IDO2 was identified. In this study, we examined the tissue expression pattern of IDO2 mRNA and the cellular localization of expressed IDO2 protein in mice. IDO1 ...
Shrestha Smeeta - - 2012
Tetratricopeptide repeat domain 9A (TTC9A) belongs to a family of TTC9 proteins. Its induction by progesterone in breast cancer cells was associated with marked growth inhibition and induction of focal adhesion. TTC9A interacts specifically with actin-binding protein tropomyosin Tm5NM-1 which stabilizes actin filament and focal adhesion. However, the function of ...
Spanheimer Philip M - - 2012
BACKGROUND: The RET proto-oncogene is expressed as part of the estrogen receptor (ER) cluster in breast cancer. We sought to determine if TFAP2C regulates Ret expression directly or indirectly through ER. METHODS: Chromatin immunoprecipitation sequencing (ChIP-Seq) and gel-shift assay were used to identify TFAP2C binding sites in the RET promoter ...
Fatunmbi Matilda - - 2012
HER2/neu overexpression leads to poorer prognosis and higher risk of disease reoccurrence in breast cancer patients. The causative factors responsible for increasing HER2/neu expression levels on mammary cells are not known. We investigated whether factors associated with inflammation or metastasis could induce HER2/neu expression on human mammary epithelial cells (HMECs). ...
Zcharia Eyal - - 2012
Halofuginone, a low-molecular-weight quinazolinone alkaloid that inhibits collagen α1(I), has been shown to suppress cancer growth, metastasis, and angiogenesis. These activities were attributed in part to the inhibition of matrix metalloproteinase-2 (MMP-2). The present study was carried out to explore the molecular mechanism underlying this effect. We found a marked ...
Wang Chen - - 2012
BACKGROUND AND AIMS: MicroRNAs (miRNAs) are short noncoding RNAs that regulate gene expression by targeting mRNAs. Our previous study found that miR-29b strongly regulates the migration and invasion of breast cancer cells. Here, we aimed to identify the mRNAs targeted by miR-29b. METHODS: We used microarray experiments in conjunction with ...
Baek Seung Ho - - 2012
Context: Nobiletin is one of the citrus bioflavonoids and can be found in citrus fruits such as lemons, oranges, tangerines, and grapefruits. The most studied properties of nobiletin are its anti-inflammatory and anticancer activities. Objective: The exact mechanisms of how nobiletin inhibits tumor metastasis and invasion are still not fully ...
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