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https://www.readbyqxmd.com/read/28318367/combinatorial-control-of-messenger-rnas-by-pumilio-nanos-and-brain-tumor-proteins
#1
René M Arvola, Chase A Weidmann, Traci M Tanaka Hall, Aaron C Goldstrohm
Eukaryotes possess a vast array of RNA-binding proteins (RBPs) that affect mRNAs in diverse ways to control protein expression. Combinatorial regulation of mRNAs by RBPs is emerging as the rule. No example illustrates this as vividly as the partnership of three Drosophila RBPs, Pumilio, Nanos and Brain Tumor, which have overlapping functions in development, stem cell maintenance and differentiation, fertility and neurological processes. Here we synthesize thirty years of research with new insights into their molecular functions and mechanisms of action...
March 20, 2017: RNA Biology
https://www.readbyqxmd.com/read/28302208/-diagnostic-values-of-prealbumin-and-retinol-binding-protein-for-liver-damage-caused-by-different-degrees-of-neonatal-asphyxia
#2
Yun-Su Zou, Yan Guo, Rui Cheng, Xiao-Guang Zhou, Zhao-Lan Cao
OBJECTIVE: To investigate the diagnostic values of prealbumin (PAB) and retinol-binding protein (RBP) for liver damage caused by mild or severe asphyxia. METHODS: A retrospective analysis was performed on 185 neonates (including 84 premature infants and 101 full-term infants) with asphyxia. Based on the Apgar score, they were divided into two groups: mild asphyxia group (n=150) and severe asphyxia group (n=35). The levels of PAB, RBP, alanine aminotransferase (ALT), and aspartate aminotransferase (AST) were measured and compared...
March 2017: Zhongguo Dang Dai Er Ke za Zhi, Chinese Journal of Contemporary Pediatrics
https://www.readbyqxmd.com/read/28302205/-value-of-nutritional-risk-screening-in-evaluating-adverse-clinical-outcomes-in-children-with-severe-pneumonia
#3
Xiao-Hui Guo, Yan-Feng Sun, Jiang-Bo Wang, Shu-Zhen Han, Jing Miao, Min Cui
OBJECTIVE: To investigate the nutritional risk in children with severe pneumonia using the Screening Tool for the Assessment of Malnutrition in Paediatrics (STAMP) and the association between nutritional risk and adverse clinical outcomes. METHODS: According to the STAMP score, 216 children with severe pneumonia were classified into high nutritional risk group (HR group; n=98), moderate nutritional risk group (MR group; n=65), and low nutritional risk group (LR group; n=53)...
March 2017: Zhongguo Dang Dai Er Ke za Zhi, Chinese Journal of Contemporary Pediatrics
https://www.readbyqxmd.com/read/28299664/roles-of-runx-in-b-cell-immortalisation
#4
Michelle J West, Paul J Farrell
RUNX1 and RUNX3 are the main RUNX genes expressed in B lymphocytes. Both are expressed throughout B-cell development and play key roles at certain key developmental transitions. The tumour-associated Epstein-Barr virus (EBV) has potent B-cell transforming ability and manipulates RUNX3 and RUNX1 transcription through novel mechanisms to control B cell growth. In contrast to resting mature B cells where RUNX1 expression is high, in EBV-infected cells RUNX1 levels are low and RUNX3 levels are high. Downregulation of RUNX1 in these cells results from cross-regulation by RUNX3 and serves to relieve RUNX1-mediated growth repression...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28298391/vitamin-a-supplementation-redirects-the-flow-of-retinyl-esters-from-peripheral-to-central-organs-of-neonatal-rats-raised-under-vitamin-a-marginal-conditions
#5
Joanna K Hodges, Libo Tan, Michael H Green, A Catharine Ross
Background: Vitamin A (VA; retinol) supplementation is used to reduce child mortality in countries with high rates of malnutrition. Existing research suggests that neonates (<1 mo old) may have a limited capacity to store VA in organs other than the liver; however, knowledge about VA distribution and kinetics in individual, nonhepatic organs is limited.Objective: We examined retinol uptake and turnover in nonhepatic organs, including skin, brain, and adipose tissue, in neonatal rats without and after VA supplementation...
March 15, 2017: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28288585/hypertonic-saline-attenuates-expression-of-notch-signaling-and-proinflammatory-mediators-in-activated-microglia-in-experimentally-induced-cerebral-ischemia-and-hypoxic-bv-2-microglia
#6
Wen-Xin Zeng, Yong-Li Han, Gao-Feng Zhu, Lin-Qiang Huang, Yi-Yu Deng, Qiao-Sheng Wang, Wen-Qiang Jiang, Miao-Yun Wen, Qian-Peng Han, Di Xie, Hong-Ke Zeng
BACKGROUND: Ischemic stroke is a major disease that threatens human health in ageing population. Increasing evidence has shown that neuroinflammatory mediators play crucial roles in the pathophysiology of cerebral ischemia injury. Notch signaling is recognized as the cell fate signaling but recent evidence indicates that it may be involved in the inflammatory response in activated microglia in cerebral ischemia. Previous report in our group demonstrated hypertonic saline (HS) could reduce the release of interleukin-1 beta and tumor necrosis factor-alpha in activated microglia, but the underlying molecular and cellular mechanisms have remained uncertain...
March 14, 2017: BMC Neuroscience
https://www.readbyqxmd.com/read/28286323/switchsense-a-new-technology-to-study-protein-rna-interactions
#7
Antoine Cléry, Thibault J M Sohier, Thomas Welte, Andreas Langer, Frédéric H T Allain
Characterization of RNA-binding protein interactions with RNA became inevitable to properly understand the cellular mechanisms involved in gene expression regulation. Structural investigations bring information at the atomic level on these interactions and complementary methods such as Isothermal Titration Calorimetry (ITC) and Surface Plasmon Resonance (SPR) are commonly used to quantify the affinity of these RNA-protein complexes and evaluate the effect of mutations affecting these interactions. The switchSENSE technology has recently been developed and already successfully used to investigate protein interactions with different types of binding partners (DNA, protein/peptide or even small molecules)...
March 9, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28279688/role-of-human-lipocalin-proteins-in-abdominal-obesity-after-acute-pancreatitis
#8
Ruma G Singh, Sayali A Pendharkar, Lindsay D Plank, Maxim S Petrov
Lipocalin proteins are small regulatory peptides implicated in metabolism, inflammation, and immunity. Although lipocalin proteins have been linked to various clinical conditions, their role in the acute inflammatory setting, such as acute pancreatitis (AP), has only been sparsely investigated. Two members of the lipocalin family, lipocalin-2 (LCN-2) and retinol binding protein -4 (RBP-4), play an important role in obesity and insulin resistance. In this study, we analysed circulating levels of LCN-2 and RBP-4 in 92 individuals after AP, of whom 41 individuals had abdominal obesity and 51 did not...
March 7, 2017: Peptides
https://www.readbyqxmd.com/read/28274760/a-combined-sequence-and-structure-based-method-for-discovering-enriched-motifs-in-rna-from-in-vivo-binding-data
#9
Maya Polishchuk, Inbal Paz, Refael Kohen, Rona Mesika, Zohar Yakhini, Yael Mandel-Gutfreund
RNA binding proteins (RBPs) play an important role in regulating many processes in the cell. RBPs often recognize their RNA targets in a specific manner. In addition to the RNA primary sequence, the structure of the RNA has been shown to play a central role in RNA recognition by RBPs. In recent years, many experimental approaches, both in-vitro and in-vivo, were developed and employed to identify and characterize RBP targets and extract their binding specificities. In-vivo binding techniques, such as CrossLinking and ImmunoPrecipitation (CLIP)-based methods, enable the characterization of protein binding sites on RNA targets...
March 5, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28267151/regulation-of-striatal-dopamine-responsiveness-by-notch-rbp-j-signaling
#10
M Toritsuka, S Kimoto, K Muraki, M Kitagawa, T Kishimoto, A Sawa, K Tanigaki
Dopamine signaling is essential for reward learning and fear-related learning, and thought to be involved in neuropsychiatric diseases. However, the molecular mechanisms underlying the regulation of dopamine responsiveness is unclear. Here we show the critical roles of Notch/RBP-J signaling in the regulation of dopamine responsiveness in the striatum. Notch/RBP-J signaling regulates various neural cell fate specification, and neuronal functions in the adult central nervous system. Conditional deletion of RBP-J specifically in neuronal cells causes enhanced response to apomorphine, a non-selective dopamine agonist, and SKF38393, a D1 agonist, and impaired dopamine-dependent instrumental avoidance learning, which is corrected by SCH23390, a D1 antagonist...
March 7, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28263887/mapping-specificity-landscapes-of-rna-protein-interactions-by-high-throughput-sequencing
#11
Eckhard Jankowsky, Michael E Harris
To function in a biological setting, RNA binding proteins (RBPs) have to discriminate between alternative binding sites in RNAs. This discrimination can occur in the ground state of an RNA-protein binding reaction, in its transition state, or in both. The extent by which RBPs discriminate at these reaction states defines RBP specificity landscapes. Here, we describe the HiTS-Kin and HiTS-EQ techniques, which combine kinetic and equilibrium binding experiments with high throughput sequencing to quantitatively assess substrate discrimination for large numbers of substrate variants at ground and transition states of RNA-protein binding reactions...
March 2, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28245811/rna-protein-binding-motifs-mining-with-a-new-hybrid-deep-learning-based-cross-domain-knowledge-integration-approach
#12
Xiaoyong Pan, Hong-Bin Shen
BACKGROUND: RNAs play key roles in cells through the interactions with proteins known as the RNA-binding proteins (RBP) and their binding motifs enable crucial understanding of the post-transcriptional regulation of RNAs. How the RBPs correctly recognize the target RNAs and why they bind specific positions is still far from clear. Machine learning-based algorithms are widely acknowledged to be capable of speeding up this process. Although many automatic tools have been developed to predict the RNA-protein binding sites from the rapidly growing multi-resource data, e...
February 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28244490/the-rna-binding-protein-qki5-regulates-primary-mir-124-1-processing-via-a-distal-rna-motif-during-erythropoiesis
#13
Fang Wang, Wei Song, Hongmei Zhao, Yanni Ma, Yuxia Li, Di Zhai, Jingnan Pi, Yanmin Si, Jiayue Xu, Lei Dong, Rui Su, Mengmeng Zhang, Yong Zhu, Xiaoxia Ren, Fei Miao, Wenjie Liu, Feng Li, Junwu Zhang, Aibin He, Ge Shan, Jingyi Hui, Linfang Wang, Jia Yu
MicroRNA (miRNA) biogenesis is finely controlled by complex layers of post-transcriptional regulators, including RNA-binding proteins (RBPs). Here, we show that an RBP, QKI5, activates the processing of primary miR-124-1 (pri-124-1) during erythropoiesis. QKI5 recognizes a distal QKI response element and recruits Microprocessor through interaction with DGCR8. Furthermore, the recruited Microprocessor is brought to pri-124-1 stem loops by a spatial RNA-RNA interaction between two complementary sequences. Thus, mutations disrupting their base-pairing affect the strength of QKI5 activation...
March 2017: Cell Research
https://www.readbyqxmd.com/read/28239422/differential-regulation-of-riboflavin-supply-genes-in-vibrio-cholerae
#14
Ignacio Sepúlveda Cisternas, Alexia Torres, Andrés Fuentes Flores, Víctor Antonio García Angulo
BACKGROUND: Riboflavin is the precursor of important redox cofactors such as flavin mononucleotide (FMN) and flavin adenine dinucleotide, required for several biological processes. Vibrio cholerae, a pathogenic bacterium responsible for the cholera disease, possesses the ability to biosynthesize de novo as well as to uptake riboflavin through the riboflavin biosynthetic pathway (RBP) and the RibN importer, respectively. The intra-organism relationship between riboflavin biosynthesis and uptake functions has not been studied...
2017: Gut Pathogens
https://www.readbyqxmd.com/read/28231410/transcriptomic-analyses-of-rna-binding-proteins-reveal-eif3c-promotes-cell-proliferation-in-hepatocellular-carcinoma
#15
Tangjian Li, Shengli Li, Di Chen, Bing Chen, Tao Yu, Fangyu Zhao, Qifeng Wang, Ming Yao, Shenglin Huang, Zhiao Chen, Xianghuo He
RNA-binding proteins (RBPs) play fundamental roles in the RNA life cycle. The aberrant expression of RBPs is often observed in human disease, including cancer. In this study, we screened for the expression levels of 1,542 human RBPs in The Cancer Genome Atlas liver hepatocellular carcinoma (TCGA LIHC) samples and found 92 consistently up-regulated RBP genes in HCC compared with normal samples. Additionally, we performed a Kaplan-Meier analysis and found that high expression of 15 RBP genes was associated with poor prognosis in patients with HCC...
February 23, 2017: Cancer Science
https://www.readbyqxmd.com/read/28230851/using-hiclip-to-identify-rna-duplexes-that-interact-with-a-specific-rna-binding-protein
#16
Yoichiro Sugimoto, Anob M Chakrabarti, Nicholas M Luscombe, Jernej Ule
The structure of RNA molecules has a critical role in regulating gene expression, largely through influencing their interactions with RNA-binding proteins (RBPs). RNA hybrid and individual-nucleotide resolution UV cross-linking and immunoprecipitation (hiCLIP) is a transcriptome-wide method of monitoring these interactions by identifying RNA duplexes bound by a specific RBP. The hiCLIP protocol consists of the following steps: in vivo cross-linking of RBPs to their bound RNAs; partial RNA digestion and purification of RNA duplexes interacting with the specific RBP using immunoprecipitation; ligation of the two arms of RNA duplexes via a linker; reverse transcription; cDNA library amplification; and finally high-throughput DNA sequencing...
March 2017: Nature Protocols
https://www.readbyqxmd.com/read/28213841/sitagliptin-down-regulates-retinol-binding-protein-4-and-reduces-insulin-resistance-in-gestational-diabetes-mellitus-a-randomized-and-double-blind-trial
#17
Xia Sun, Zhendong Zhang, Hui Ning, Hong Sun, Xianghong Ji
Gestational diabetes mellitus (GDM) is a condition that affects increasing number of pregnant women worldwide. Sitagliptin was reported to alleviate symptoms of type 2 diabetes mellitus by reducing serum levels of retinol-binding protein 4 (RBP-4). We investigated the effectiveness of sitagliptin on insulin sensitivity parameters in GDM patients. Pregnant GDM women in the 2nd trimester were recruited for this study. Participants were then assigned randomly to sitagliptin treatment group or placebo treatment group, and administered sitagliptin or placebo daily for 16 weeks...
February 17, 2017: Metabolic Brain Disease
https://www.readbyqxmd.com/read/28196397/evolved-distal-tail-carbohydrate-binding-modules-of-lactobacillus-phage-j-1-a-novel-type-of-anti-receptor-widespread-among-lactic-acid-bacteria-phages
#18
Maria-Eugenia Dieterle, Silvia Spinelli, Irina Sadovskaya, Mariana Piuri, Christian Cambillau
Bacteriophage replication requires specific host-recognition. Some siphophages harbour a large complex, the baseplate, at the tip of their non-contractile tail. This baseplate holds receptor binding proteins (RBPs) that can recognize the host cell-wall polysaccharide (CWPS) and specifically attach the phage to its host. While most phages possess a dedicated RBP, the phage J-1 that infects Lactobacillus casei seemed to lack one. We have shown that the phage J-1 distal tail protein (Dit) plays a role in host recognition and that its sequence comprises two inserted modules compared to "classical" Dits...
February 14, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28195151/in-patients-with-chronic-aplastic-anemia-bone-marrow-derived-mscs-regulate-the-treg-th17-balance-by-influencing-the-notch-rbp-j-foxp3-ror%C3%AE-t-pathway
#19
Hongbo Li, Lin Wang, Yan Pang, Zujun Jiang, Zenghui Liu, Haowen Xiao, Haijia Chen, Xiaohu Ge, Hai Lan, Yang Xiao
The standard treatment for aplastic anemia (AA) in young patients is a matched sibling hematopoietic stem cell transplant. Transfusion of a chronic AA patient with allogeneic bone marrow-derived mesenchymal stromal cells (BMMSCs) is currently being developed as a cell-based therapy, and the safety and efficacy of such transfusions are being continuously improved. Nevertheless, the mechanisms by which BMMSCs exert their therapeutic effects remain to be elucidated. In this study, mesenchymal stromal cells (MSCs) obtained from bone marrow donors were concentrated and intravenously injected into 15 chronic AA patients who had been refractory to prior immunosuppressive therapy...
February 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28194024/regnase-1-a-rapid-response-ribonuclease-regulating-inflammation-and-stress-responses
#20
REVIEW
Renfang Mao, Riyun Yang, Xia Chen, Edward W Harhaj, Xiaoying Wang, Yihui Fan
RNA-binding proteins (RBPs) are central players in post-transcriptional regulation and immune homeostasis. The ribonuclease and RBP Regnase-1 exerts critical roles in both immune cells and non-immune cells. Its expression is rapidly induced under diverse conditions including microbial infections, treatment with inflammatory cytokines and chemical or mechanical stimulation. Regnase-1 activation is transient and is subject to negative feedback mechanisms including proteasome-mediated degradation or mucosa-associated lymphoid tissue 1 (MALT1) mediated cleavage...
February 13, 2017: Cellular & Molecular Immunology
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