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https://www.readbyqxmd.com/read/27871973/par-clip-and-streamlined-small-rna-cdna-library-preparation-protocol-for-the-identification-of-rna-binding-protein-target-sites
#1
Daniel Benhalevy, Hannah L McFarland, Aishe A Sarshad, Markus Hafner
The study of protein-RNA interactions is critical for our understanding of cellular processes and regulatory circuits controlled by RNA binding proteins (RBPs). Recent next generation sequencing-based approaches significantly promoted our understanding of RNA biology and its importance for cell function. We present a streamlined protocol for Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP), a technique that allows for the characterization of RBP binding sites on target RNAs at nucleotide resolution and transcriptome-wide scale...
November 18, 2016: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/27860518/molecular-dynamics-of-fmrp-and-other-rna-binding-proteins-in-meg-01-differentiation-the-role-of-mrnp-complexes-in-non-neuronal-development
#2
M McCoy, D Poliquin-Duchesneau, F Corbin
Asymmetrically differentiating cells are formed with the aid of RNA-binding proteins (RBPs), which can bind, stabilize, regulate, and transport target mRNAs. The loss of RBPs in neurons may lead to severe neurodevelopmental diseases such as the Fragile X Syndrome with the absence of the Fragile X Mental Retardation Protein (FMRP). Because the latter is ubiquitous and shares many similarities with other RBPs involved in the development of peripheral cells, we suggest that FMRP would have a role in the differentiation of all tissues where it is expressed...
December 2016: Biochemistry and Cell Biology, Biochimie et Biologie Cellulaire
https://www.readbyqxmd.com/read/27855659/mtor-and-mapk-from-localized-translation-control-to-epilepsy
#3
REVIEW
Helena F Pernice, Rico Schieweck, Michael A Kiebler, Bastian Popper
BACKGROUND: Epilepsy is one of the most common neurological diseases characterized by excessive hyperexcitability of neurons. Molecular mechanisms of epilepsy are diverse and not really understood. All in common is the misregulation of proteins that determine excitability such as potassium and sodium channels as well as GABA receptors; which are all known as biomarkers for epilepsy. Two recently identified key pathways involve the kinases mechanistic target of rapamycin (mTOR) and mitogen-activated protein kinases (MAPK)...
November 17, 2016: BMC Neuroscience
https://www.readbyqxmd.com/read/27852147/rna-binding-protein-hur-is-translocated-in-astrocytes-following-spinal-cord-injury-and-promotes-the-inflammatory-response
#4
Thaddaeus Kwan, Candace L Floyd, Soojin Kim, Peter H King
Inflammation plays a prominent role in the events following traumatic injury to the central nervous system (CNS). The initial inflammatory response is driven by mediators such as TNF-α and IL-1β which are produced by activated astrocytes and microglia at the site of injury. These factors are regulated post-transcriptionally by RNA binding proteins (RBP) that interact with adenylate and uridylate rich elements (ARE) in the 3'-untranslated region of the mRNA. HuR is one of these RBPs and generally functions as a positive regulator of ARE-containing mRNAs...
November 16, 2016: Journal of Neurotrauma
https://www.readbyqxmd.com/read/27847111/the-epstein-barr-virus-ebna2-protein-induces-a-subset-of-notch-target-genes-in-thyroid-cancer-cell-lines-but-fails-to-suppress-proliferation
#5
Sean Golden, Xiao-Min Yu, Scott Odorico, Vansh Jain, Ana Marin, Shidong Ma, Shannon Kenney, Herbert Chen
BACKGROUND: Epstein-Barr virus is associated with lymphoid and epithelial malignancies and has been reported to infect thyroid cells. The Epstein-Barr virus protein, EBNA2, regulates viral and cellular promoters by binding to RBP-jκ. Similarly, NOTCH1, a tumor suppressor protein in thyroid epithelial cells, competes with EBNA2 for binding to overlapping sites on RBP-jκ. EBNA2 activates a subset of NOTCH-responsive genes in lymphocytes and myocytes; however, the effect of EBNA2 expression on NOTCH targets in epithelial cells is unknown...
November 12, 2016: Surgery
https://www.readbyqxmd.com/read/27830501/vitamin-a-transport-and-cell-signaling-by-the-retinol-binding-protein-receptor-stra6
#6
Noa Noy
Vitamin A, retinol, circulates in blood bound to retinol binding protein (RBP). In some tissues, the retinol-RBP complex (holo-RBP) is recognized by a membrane receptor, termed STRA6, which mediates uptake of retinol into cells. Recent studies have revealed that, in addition to serving as a retinol transporter, STRA6 is a ligand-activated cell surface signaling receptor that, upon binding of holo-RBP activates JAK/STAT signaling, culminating in the induction of STAT target genes. It has further been shown that retinol transport and cell signaling by STRA6 are critically interdependent and that both are coupled to intracellular vitamin A metabolism...
2016: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/27822970/overlapping-riboflavin-supply-pathways-in-bacteria
#7
Víctor Antonio García-Angulo
Riboflavin derivatives are essential cofactors for a myriad of flavoproteins. In bacteria, flavins importance extends beyond their role as intracellular protein cofactors, as secreted flavins are a key metabolite in a variety of physiological processes. Bacteria obtain riboflavin through the endogenous riboflavin biosynthetic pathway (RBP) or by the use of importer proteins. Bacteria frequently encode multiple paralogs of the RBP enzymes and as for other micronutrient supply pathways, biosynthesis and uptake functions largely coexist...
November 8, 2016: Critical Reviews in Microbiology
https://www.readbyqxmd.com/read/27822292/uv-crosslinked-mrna-binding-proteins-captured-from-leaf-mesophyll-protoplasts
#8
Zhicheng Zhang, Kurt Boonen, Piero Ferrari, Liliane Schoofs, Ewald Janssens, Vera van Noort, Filip Rolland, Koen Geuten
BACKGROUND: The complexity of RNA regulation is one of the current frontiers in animal and plant molecular biology research. RNA-binding proteins (RBPs) are characteristically involved in post-transcriptional gene regulation through interaction with RNA. Recently, the mRNA-bound proteome of mammalian cell lines has been successfully cataloged using a new method called interactome capture. This method relies on UV crosslinking of proteins to RNA, purifying the mRNA using complementary oligo-dT beads and identifying the crosslinked proteins using mass spectrometry...
2016: Plant Methods
https://www.readbyqxmd.com/read/27806063/biomarker-profiles-in-women-with-pcos-and-pcos-offspring-a-pilot-study
#9
Nadine M P Daan, Maria P H Koster, Marlieke A de Wilde, Gerdien W Dalmeijer, Annemieke M V Evelein, Bart C J M Fauser, Wilco de Jager
OBJECTIVE: To study metabolic/inflammatory biomarker risk profiles in women with PCOS and PCOS offspring. DESIGN: Cross-sectional comparison of serum biomarkers. SETTING: University Medical Center Utrecht. PATIENTS: Hyperandrogenic PCOS women (HA-PCOS, n = 34), normoandrogenic PCOS women (NA-PCOS, n = 34), non-PCOS reference population (n = 32), PCOS offspring (n = 14, age 6-8 years), and a paedriatic reference population (n = 30)...
2016: PloS One
https://www.readbyqxmd.com/read/27802174/neural-specificity-of-the-rna-binding-protein-elav-is-achieved-by-post-transcriptional-repression-in-non-neural-tissues
#10
Piero Sanfilippo, Peter Smibert, Hong Duan, Eric C Lai
Drosophila Elav is the founding member of the conserved family of Hu RNA-binding proteins (RBPs), which play crucial and diverse roles in post-transcriptional regulation. Elav has long served as the canonical neuronal marker. Surprisingly, although Elav has a well-characterized neural cis-regulatory module, we find endogenous Elav is also ubiquitously transcribed and post-transcriptionally repressed in non-neural settings. Mutant clones of multiple miRNA pathway components derepress ubiquitous Elav protein...
December 1, 2016: Development
https://www.readbyqxmd.com/read/27801831/antioxidant-enzyme-activities-and-lipid-oxidation-in-rape-brassica-campestris-l-bee-pollen-added-to-salami-during-processing
#11
Yawei Zhang, Fengtian Yang, Muneer Ahmed Jamali, Zengqi Peng
The present research investigated the antioxidant effect of rape (Brassica campestris L.) bee pollen (RBP) on salami during processing. Eight flavonoids in RBP ethanol extract were quantified by high-performance liquid chromatography-mass spectrometry (HPLC-MS) analysis, and quercetin, rutin, and kaempferol were the major bioactive compounds. The RBP ethanol extract exhibited higher total antioxidant capacity than 6-hydroxy-2,5,7,8-tertramethylchromancarboxylic acid (trolox) at the same concentration. The salami with 0...
October 28, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/27794430/down-regulation-of-rbp-j-mediated-by-microrna-133a-suppresses-dendritic-cells-and-functions-as-a-potential-tumor-suppressor-in-osteosarcoma
#12
Xuren Gao, Dong Han, Weimin Fan
BACKGROUND AND OBJECTIVE: In recent years, immunotherapy for the treatment of tumors have been established. Dendritic cells (DCs) are extremely efficient and professional antigen presenting cells (APCs), which are an important target for immune therapeutic interventions in cancer. In present study, we investigated whether RBP-J signaling regulated by miR-133a was involved in the DCs mediated tumor suppressor in osteosarcoma. METHODS: DCs were isolated from 30 osteosarcoma patients and 30 healthy subjects...
October 26, 2016: Experimental Cell Research
https://www.readbyqxmd.com/read/27775788/local-bone-marrow-renin-angiotensin-system-in-the-genesis-of-leukemia-and-other-malignancies
#13
I C Haznedaroglu, U Y Malkan
The existence of a local renin-angiotensin system (RAS) specific to the hematopoietic bone marrow (BM) microenvironment had been proposed two decades ago. Most of the RAS molecules including ACE, ACE2, AGT, AGTR1, AGTR2, AKR1C4, AKR1D1, ANPEP, ATP6AP2, CMA1, CPA3, CTSA, CTSD, CTSG, CYP11A1, CYP11B1, CYP11B2, CYP17A1, CYP21A2, DPP3, EGFR, ENPEP, GPER, HSD11B1, HSD11B2, IGF2R, KLK1, LNPEP, MAS1, MME, NR3C1, NR3C2, PREP, REN, RNPEP, and THOP1 are locally present in the BM microenvironment. Local BM RAS peptides control the hematopoietic niche, myelopoiesis, erythropoiesis, thrombopoiesis and the development of other cellular lineages...
October 2016: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/27773703/n-glycoform-dependent-interactions-of-megalin-with-its-ligands
#14
Makoto Hirano, Kiichiro Totani, Tomohiko Fukuda, Jianguo Gu, Akemi Suzuki
BACKGROUND: Megalin is a 600-kDa single-spanning transmembrane glycoprotein and functions as an endocytic receptor, distributed not only in the kidney but also in other tissues. Structurally and functionally distinct ligands for megalin have been identified. Megalin has 30 potential N-glycosylation sites in its extracellular domain. We found that megalin interacts with its ligands in a glycoform-dependent manner. METHODS: Distribution of megalin and glycans was histochemically analyzed in mouse kidneys...
October 20, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27771580/an-rrm-containing-mei2-like-mct1-plays-a-negative-role-in-the-seed-germination-and-seedling-growth-of-arabidopsis-thaliana-in-the-presence-of-aba
#15
Lili Gu, Hyun Ju Jung, Kyung Jin Kwak, Sy Nguyen Dinh, Yeon-Ok Kim, Hunseung Kang
Despite an increasing understanding of the essential role of the Mei2 gene encoding an RNA-binding protein (RBP) in premeiotic DNA synthesis and meiosis in yeasts and animals, the functional roles of the mei2-like genes in plant growth and development are largely unknown. Contrary to other mei2-like RBPs that contain three RNA-recognition motifs (RRMs), the mei2 C-terminal RRM only (MCT) is unique in that it harbors only the last C-terminal RRM. Although MCTs have been implicated to play important roles in plants, their functional roles in stress responses as well as plant growth and development are still unknown...
October 13, 2016: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/27768870/rna-structure-switches-rbp-binding
#16
Zheng Luo, Qin Yang, Li Yang
RNA sequence motifs are not sufficient for association with RBPs. In this issue of Molecular Cell, Taliaferro et al. (2016) demonstrate that, other than sequence motif, RNA secondary structure plays a repressive role on RBP binding, both in vitro and in vivo.
October 20, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27765618/optimization-of-par-clip-for-transcriptome-wide-identification-of-binding-sites-of-rna-binding-proteins
#17
Aitor Garzia, Cindy Meyer, Pavel Morozov, Marcin Sajek, Thomas Tuschl
Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) in combination with next-generation sequencing is a powerful method for identifying endogenous targets of RNA-binding proteins (RBPs). Depending on the characteristics of each RBP, key steps in the PAR-CLIP procedure must be optimized. Here we present a comprehensive step-by-step PAR-CLIP protocol with detailed explanations of the critical steps. Furthermore, we report the application of a new PAR-CLIP data analysis pipeline to three distinct RBPs targeting different annotation categories of cellular RNAs...
October 17, 2016: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/27749333/validation-of-the-raycome-rbp-1200-upper-arm-pulse-wave-device-in-children-aged-3-12-years-according-to-the-association-for-the-advancement-of-medical-instrumentation-protocol
#18
Jie Dong, Hongbo Dong, Peiyu Ye, Yinkun Yan, Bo Xi, Jie Mi
OBJECTIVE: To validate the accuracy of Raycome RBP-1200 used for blood pressure (BP) measurements in Chinese children aged 3-12 years according to the Association for the Advancement of Medical Instrumentation (AAMI)/International Organization for Standardization 81060-2:2013(E) protocol. METHODS: A prospective observational study was carried out using 'the same arm sequential method' as described in the AAMI protocol. Eighty-seven children participated in this examination and 255 paired-determinations were analyzed...
October 4, 2016: Blood Pressure Monitoring
https://www.readbyqxmd.com/read/27742911/quantifying-rna-binding-sites-transcriptome-wide-using-do-rip-seq
#19
Cindo O Nicholson, Matthew B Friedersdorf, Jack D Keene
RNA-binding proteins (RBPs) and non-coding RNAs orchestrate post-transcriptional processes through the recognition of specific sites on targeted transcripts. Thus, understanding the connection between binding to specific sites and active regulation of the whole transcript is essential. Many immunoprecipitation techniques have been developed that identify either whole transcripts or binding sites of RBPs on each transcript using cell lysates. However, none of these methods simultaneously measures the strength of each binding site, and quantifies binding to whole transcripts...
October 14, 2016: RNA
https://www.readbyqxmd.com/read/27741146/the-efficacy-and-safety-of-tenofovir-alafenamide-versus-tenofovir-disoproxil-fumarate-in-antiretroviral-regimens-for-hiv-1-therapy-meta-analysis
#20
Huilian Wang, Xi Lu, Xudong Yang, Nan Xu
BACKGROUND: To date, a definite conclusion about efficiency and safety of tenofovir alafenamide for patients with HIV-1 is not available. The aim of the study was to investigate the efficacy and safety of TAF versus TDF in antiretroviral regimens for patients with HIV-1. METHODS: PUBMED, MEDLINE, and EMBASE database were searched in March 2016, with no language restriction, for randomized controlled trials (RCTs). RESULTS: Six RCTs (n = 5888) met entry criteria...
October 2016: Medicine (Baltimore)
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