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Miwa Isshiki, Satoshi Hirayama, Tsuyoshi Ueno, Masayuki Ito, Ayaka Furuta, Kouji Yano, Kotoko Yamatani, Masami Sugihara, Mayumi Idei, Takashi Miida
BACKGROUND: Rapid turnover proteins (RTPs), such as transthyretin (TTR), retinol binding protein (RBP), and transferrin (Tf), provide an accurate assessment of nutritional status but are susceptible to inflammation. Lipid-related markers, which have short half-lives in serum, may be better suited for nutritional assessment. We sought to identify sensitive nutritional markers unaffected by inflammation. METHODS: Fasting serum samples were collected from 30 malnourished inpatients and 25 healthy volunteers...
March 11, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
Shu Yang, Junwen Wang, Raymond T Ng
BACKGROUND: Characterizing the binding preference of RNA-binding proteins (RBP) is essential for us to understand the interaction between an RBP and its RNA targets, and to decipher the mechanism of post-transcriptional regulation. Experimental methods have been used to generate protein-RNA binding data for a number of RBPs in vivo and in vitro. Utilizing the binding data, a couple of computational methods have been developed to detect the RNA sequence or structure preferences of the RBPs...
March 12, 2018: BMC Bioinformatics
Lei Li, Konrad U Förstner, Yanjie Chao
RNA-binding proteins (RBPs) function in all aspects of RNA processes including stability, structure, export, localization and translation, and control gene expression at the posttranscriptional level. To investigate the roles of RBPs and their direct RNA ligands in vivo, recent global approaches combining RNA immunoprecipitation and deep sequencing (RIP-seq) as well as UV-cross-linking (CLIP-seq) have become instrumental in dissecting RNA-protein interactions. However, the computational analysis of these high-throughput sequencing data is still challenging...
2018: Methods in Molecular Biology
Xin Yu, Heyi Zheng, Matthew T V Chan, William K K Wu
Increasing studies have suggested that dysregulation of RNA-binding proteins (RBPs) contributes to cancer progression. Neuro-oncological ventral antigen 1 (NOVA1) is a novel RBP and plays an important role in tumour development. However, the expression and role of NOVA1 in melanoma remain unknown. In this study, we indicated that NOVA1 expression was up-regulated in melanoma samples and cell lines. Moreover, we demonstrated that knockdown of NOVA1 suppressed melanoma cell proliferation, migration and invasion in both A375 and A875 cell lines...
March 2, 2018: Journal of Cellular and Molecular Medicine
Edyta Kisielnicka, Ryuji Minasaki, Christian R Eckmann
RNA-binding proteins (RBPs) are important regulators of gene expression programs, especially during gametogenesis. How the abundance of particular RBPs is restricted to defined stages of meiosis remains largely elusive. Here, we report a molecular pathway that subjects two nonrelated but broadly evolutionarily conserved translational regulators (CPB-3/CPEB and GLD-1/STAR) to proteosomal degradation in Caenorhabditis elegans germ cells at the transition from pachytene to diplotene of meiotic prophase. Both RBPs are recognized by the same ubiquitin ligase complex, containing the molecular scaffold Cullin-1 and the tumor suppressor SEL-10/FBXW7 as its substrate recognition subunit...
March 1, 2018: Proceedings of the National Academy of Sciences of the United States of America
Bastian Popper, Antonia Demleitner, Valerie J Bolivar, Gretchen Kusek, Abigail Snyder-Keller, Rico Schieweck, Sally Temple, Michael A Kiebler
Staufen2 (Stau2) is a double-stranded RNA-binding protein (RBP) involved in posttranscriptional gene expression control in neurons. In flies, staufen contributes to learning and long-term memory formation. To study the impact of mammalian Stau2 on behavior, we generated a novel gene-trap mouse model that yields significant constitutive downregulation of Stau2 (Stau2GT ). In order to investigate the effect of Stau2 downregulation on hippocampus-dependent behavior, we performed a battery of behavioral assays, i...
February 26, 2018: Neurobiology of Learning and Memory
Yaron Orenstein, Uwe Ohler, Bonnie Berger
BACKGROUND: RNA-binding proteins (RBPs) play vital roles in many processes in the cell. Different RBPs bind RNA with different sequence and structure specificities. While sequence specificities for a large set of 205 RBPs have been reported through the RNAcompete compendium, structure specificities are known for only a small fraction. The main limitation lies in the design of the RNAcompete technology, which tests RBP binding against unstructured RNA probes, making it difficult to infer structural preferences from these data...
February 20, 2018: BMC Genomics
Ignacio Sepúlveda-Cisternas, Luis Lozano Aguirre, Andrés Fuentes Flores, Ignacio Vásquez Solis de Ovando, Víctor Antonio García-Angulo
Vibrio cholerae, a pandemic diarrheagenic bacterium, is able to synthesize the essential vitamin riboflavin through the riboflavin biosynthetic pathway (RBP) and also to internalize it through the RibN importer. In bacteria, the way riboflavin biosynthesis and uptake functions correlate is unclear. To gain insights into the role of the riboflavin provision pathways in the physiology of V. cholerae, we analyzed the transcriptomics response to extracellular riboflavin and to deletions of ribD (RBP-deficient strain) or ribN...
February 16, 2018: Scientific Reports
Jack C-C Hsu, David W Reid, Alyson M Hoffman, Devanand Sarkar, Christopher V Nicchitta
Astrocyte elevated gene-1 (AEG-1), an oncogene whose overexpression promotes tumor cell proliferation, angiogenesis, invasion, and enhanced chemoresistance, is thought to function primarily as a scaffolding protein, regulating PI3K/Akt and Wnt/β-catenin signaling pathways. Here we report that AEG-1 is an endoplasmic reticulum (ER) resident integral membrane RNA-binding protein (RBP). Examination of the AEG-1 RNA interactome by HITS-CLIP and PAR-CLIP methodologies revealed a high enrichment for endomembrane organelle-encoding transcripts, most prominently those encoding ER resident proteins, and within this cohort, for integral membrane protein-encoding RNAs...
February 7, 2018: RNA
Tino Köster, Katja Meyer
Research into the regulation of gene expression underwent a shift from focusing on DNA-binding proteins as key transcriptional regulators to RNA-binding proteins (RBPs) that come into play once transcription has been initiated. RBPs orchestrate all RNA-processing steps in the cell. To obtain a global view of in vivo targets, the RNA complement associated with particular RBPs is determined via immunoprecipitation of the RBP and subsequent identification of bound RNAs via RNA-seq. Here, we describe technical advances in identifying RBP in vivo targets and their binding motifs...
February 8, 2018: Trends in Plant Science
F E Marmisolle, M L García, C A Reyes
Background: Due to the nature of viral RNA genomes, RNA viruses depend on many RNA-binding proteins (RBP) of viral and host origin for replication, dissemination and evasion of host RNA degradation pathways. Some viruses interfere with the microRNA (miRNA) pathway to generate better fitness. The development of an adjusted, reliable and sensitive ribonucleoprotein immunoprecipitation (RIP) assay is needed to study the interaction between RBP of different origin (including viral origin) and miRNA precursors...
2018: Plant Methods
Kinga Musiał, Danuta Zwolińska
OBJECTIVES: Vitamin D-binding protein (VDBP), retinol-binding protein (RBP)4, and heat shock proteins (hsp) are markers of tubular function and apoptosis, accompanying chronic kidney disease (CKD) from its earliest stages. Fractional excretion of proteins with urine is a marker of tubular damage. The aim of study was to assess the usefulness of fractional excretion (FE) of VDBP, RBP4, HSF1 and Hsp27 as markers of tubular damage in the course of CKD. METHODS: The study group consisted of 70 children with CKD stages 1-5, treated conservatively, and 12 age-matched controls with normal kidney function...
February 6, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
Nam Seok Lee, Han Soo Kim, Se Eun Park, Matthias Blüher, Cheol-Young Park, Byung-Soo Youn
Elevated circulating Retinol-binding protein 4 (RBP4) has been associated with insulin resistance, dyslipidemia, and hypertension. However, many commonly used RBP4 ELISAs have limited dynamic range. We therefore developed an enzyme-linked immunosorbent sandwich assay (ELISA) employing a novel immunoglobulin A (IgA)-type capture mAb called AG102 instead of IgG subtypes, which was selected for its stability, capture efficiency, and specificity for human RBP 4. These features of RBP4 have hampered the development of quantitative immunological assays...
February 7, 2018: Scientific Reports
Davide Barbagallo, Angela Caponnetto, Matilde Cirnigliaro, Duilia Brex, Cristina Barbagallo, Floriana D'Angeli, Antonio Morrone, Rosario Caltabiano, Giuseppe Maria Barbagallo, Marco Ragusa, Cinzia Di Pietro, Thomas Birkballe Hansen, Michele Purrello
Circular RNAs (circRNAs) have recently emerged as a new class of RNAs, highly enriched in the brain and very stable within cells, exosomes and body fluids. To analyze their involvement in glioblastoma multiforme (GBM) pathogenesis, we assayed the expression of twelve circRNAs, physiologically enriched in several regions of the brain, through real-time PCR in a cohort of fifty-six GBM patient biopsies and seven normal brain parenchymas. We focused on hsa_circ_0001445 (circSMARCA5): it was significantly downregulated in GBM biopsies as compared to normal brain tissues ( p -value < 0...
February 6, 2018: International Journal of Molecular Sciences
Crystal D Karakochuk, Amanda M Henderson, Kaitlyn L I Samson, Abeer M Aljaadi, Angela M Devlin, Elodie Becquey, James P Wirth, Fabian Rohner
Recently, a multiplex ELISA (Quansys Biosciences) was developed that measures ferritin, soluble transferrin receptor (sTfR), retinol-binding protein (RBP), C-reactive protein (CRP), α¹-acid glycoprotein (AGP), thyroglobulin, and histidine-rich protein 2. Our primary aim was to conduct a method-comparison study to compare five biomarkers (ferritin, sTfR, RBP, CRP, and AGP) measured with the Quansys assay and a widely-used s-ELISA (VitMin Lab, Willstaett, Germany) with use of serum samples from 180 women and children from Burkina Faso, Cambodia, and Malaysia...
February 2, 2018: Diagnostics
Shuo Chen, Yang Zhao
Circular RNAs (circRNAs) are universal and diverse endogenous noncoding RNAs (ncRNAs) that are widely found in eukaryotic cells. They form a covalently closed, continuous stable loop structure without 3' or 5' tails, which are different from linear RNAs. As new members of the ncRNAs, circRNAs' formation, function, and mechanism are attracting increased research attention. CircRNAs play important roles in all kinds of cancer and may be potential novel biomarkers and therapeutic targets for cancer treatment through their function as microRNA (miRNA) molecular "sponges", RNA-binding protein (RBP) sponges, protein translators, and gene transcription regulators...
February 2, 2018: Histology and Histopathology
Taro Iwamoto, Jessica Dorschner, Meenakshi Jolly, Xiangyang Huang, Timothy B Niewold
Objective: The type I interferon pathway is activated in many patients with systemic lupus erythematosus (SLE), and anti-double-stranded DNA (dsDNA) and anti-RNA binding protein autoantibodies are correlated with high interferon-α (IFNα) activity. We studied whether antiphospholipid (APL) antibodies, which should not stimulate Toll-like receptors, are also associated with high levels of IFNα activity. Methods: Serum IFNα activity was measured in patients with SLE using the WISH cell bioassay...
2018: Lupus Science & Medicine
Sajad Sofi, Julia C Fitzgerald, Désirée Jähn, Bernhard Dumoulin, Sabine Stehling, Hartmut Kuhn, Christoph Ufer
The guanine-rich RNA sequence binding factor 1 (GRSF1) constitutes an ubiquitously occurring RNA-binding protein (RBP), which belongs to the family of heterogeneous nuclear ribonucleoprotein F/H (hnRNP F/H). It has been implicated in nuclear, cytosolic and mitochondrial RNA metabolism. Although the crystal structures of GRSF1 orthologs have not been solved, amino acid alignments with similar RNA-binding proteins suggested the existence of three RNA-binding domains designated quasi-RNA recognition motifs (qRRMs)...
January 20, 2018: Biochimica et Biophysica Acta
Ishwarlal Jialal, Sridevi Devaraj
Metabolic syndrome (MetS) is a common global problem that comprises the cardio-metabolic cluster and predisposes to both diabetes and cardiovascular diseases. Although the pathogenic mechanisms have not been elucidated, both increased inflammation and insulin resistance play a pivotal role. It appears that both monocyte/macrophages and adipose tissue (AT) conspire to accentuate both the pro-inflammatory state and increased insulin resistance. Whilst there are scant data on visceral adipose tissue (VAT) and epicardial adipose tissue (EAT) biology, there are data on subcutaneous adipose tissue (SAT) dysregulation...
January 20, 2018: Hormone Molecular Biology and Clinical Investigation
Markus Jabs, Adam J Rose, Lorenz H Lehmann, Jacqueline Taylor, Iris Moll, Tjeerd P Sijmonsma, Stefanie E Herberich, Sven W Sauer, Gernot Poschet, Giuseppina Federico, Carolin Mogler, Eva-Maria Weis, Hellmut G Augustin, Minhong Yan, Norbert Gretz, Roland M Schmid, Ralf H Adams, Hermann-Joseph Gröne, Rüdiger Hell, Jürgen G Okun, Johannes Backs, Peter P Nawroth, Stephan Herzig, Andreas Fischer
Background -Nutrients are transported through endothelial cells before being metabolized in muscle cells. However, little is known about the regulation of endothelial transport processes. Notch signaling is a critical regulator of metabolism and angiogenesis during development. Here, we studied how genetic and pharmacological manipulation of endothelial Notch signaling in adult mice affects endothelial fatty acid transport, cardiac angiogenesis, and heart function. Methods -Endothelial-specific Notch inhibition was achieved by conditional genetic inactivation of Rbp-jκ in adult mice to analyze fatty acid metabolism and heart function...
January 20, 2018: Circulation
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