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https://www.readbyqxmd.com/read/28239422/differential-regulation-of-riboflavin-supply-genes-in-vibrio-cholerae
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
https://www.readbyqxmd.com/read/28193894/rules-of-rna-specificity-of-hnrnp-a1-revealed-by-global-and-quantitative-analysis-of-its-affinity-distribution
#8
Niyati Jain, Hsuan-Chun Lin, Christopher E Morgan, Michael E Harris, Blanton S Tolbert
Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a multipurpose RNA-binding protein (RBP) involved in normal and pathological RNA metabolism. Transcriptome-wide mapping and in vitro evolution identify consensus hnRNP A1 binding motifs; however, such data do not reveal how surrounding RNA sequence and structural context modulate affinity. We determined the affinity of hnRNP A1 for all possible sequence variants (n = 16,384) of the HIV exon splicing silencer 3 (ESS3) 7-nt apical loop. Analysis of the affinity distribution identifies the optimal motif 5'-YAG-3' and shows how its copy number, position in the loop, and loop structure modulate affinity...
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28191469/rna-binding-protein-dnd1-promotes-breast-cancer-apoptosis-by-stabilizing-the-bim-mrna-in-a-mir-221-binding-site
#9
Feng Cheng, Ying Pan, Yi-Min Lu, Lei Zhu, Shuzheng Chen
RNA-binding proteins (RBPs) and miRNAs are capable of controlling processes in normal development and cancer. Both of them could determine RNA transcripts fate from synthesis to decay. One such RBP, Dead end (Dnd1), is essential for regulating germ-cell viability and suppresses the germ-cell tumors development, yet how it exerts its functions in breast cancer has remained unresolved. The level of Dnd1 was detected in 21 cancerous tissues paired with neighboring normal tissues by qRT-PCR. We further annotated TCGA (The Cancer Genome Atlas) mRNA expression profiles and found that the expression of Dnd1 and Bim is positively correlated (p = 0...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28190776/regulators-of-alternative-polyadenylation-operate-at-the-transition-from-mitosis-to-meiosis
#10
Lingjuan Shan, Chan Wu, Di Chen, Lei Hou, Xin Li, Lixia Wang, Xiao Chu, Yifeng Hou, Zhaohui Wang
In the sexually reproductive organisms, gametes are produced by meiosis following a limited mitotic amplification. However, the intrinsic program switching cells from mitotic to meiotic cycle is unclear. Alternative polyadenylation (APA) is a highly conserved means of gene regulation and is achieved by the RNA 3'-processing machinery to generate diverse 3'UTR profiles. In Drosophila spermatogenesis, we observed distinct profiles of transcriptome-wide 3'UTR between mitotic and meiotic cells. In mutant germ cells stuck in mitosis, 3'UTRs of hundreds of genes were consistently shifted...
January 27, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28183268/genetic-and-functional-characterisation-of-the-lactococcal-p335-phage-host-interactions
#11
Jennifer Mahony, Joana Oliveira, Barry Collins, Laurens Hanemaaijer, Gabriele Andrea Lugli, Horst Neve, Marco Ventura, Thijs R Kouwen, Christian Cambillau, Douwe van Sinderen
BACKGROUND: Despite continuous research efforts, bacterio(phages) infecting Lactococcus lactis starter strains persist as a major threat to dairy fermentations. The lactococcal P335 phages, which are currently classified into four sub-groups (I-IV), are the second most frequently isolated phage group in an industrial dairy context. RESULTS: The current work describes the isolation and comparative genomic analysis of 17 novel P335 group phages. Detailed analysis of the genomic region of P335 phages encoding the so-called "baseplate", which includes the receptor binding protein (RBP) was combined with a functional characterization of the RBP of sub-group III and IV phages...
February 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28177944/metformin-depresses-overactivated-notch1-hes1-signaling-in-colorectal-cancer-patients-with-type-2-diabetes-mellitus
#12
Bin Yang, Can-Ze Huang, Tao Yu, Sheng-Ning Zhou, Qi Liu, Gao-Jie Liu, Shuang Chen, Fang-Hai Han
The function of metformin in colorectal cancer (CRC) patients with diabetes mellitus (DM) remains a controversial topic because studies are increasingly focusing on epidemiologic features. We examined Notch1/Hes1 signaling in CRC with DM (DM-CRC) and investigated alterations in signaling caused by metformin treatment. For this purpose, information on pathological characteristics was collected from each patient. The proliferation of epithelium labeled with proliferating cell nuclear antigen and the differentiation of goblet cells were investigated using immunohistochemistry and periodic acid-Schiff staining, respectively...
February 7, 2017: Anti-cancer Drugs
https://www.readbyqxmd.com/read/28166727/whole-genome-sequencing-of-a-plasmodium-vivax-clinical-isolate-exhibits-geographical-characteristics-and-high-genetic-variation-in-china-myanmar-border-area
#13
Shen-Bo Chen, Yue Wang, Kokouvi Kassegne, Bin Xu, Hai-Mo Shen, Jun-Hu Chen
BACKGROUND: Currently in China, the trend of Plasmodium vivax cases imported from Southeast Asia was increased especially in the China-Myanmar border area. Driven by the increase in P. vivax cases and stronger need for vaccine and drug development, several P. vivax isolates genome sequencing projects are underway. However, little is known about the genetic variability in this area until now. RESULTS: The sequencing of the first P. vivax isolate from China-Myanmar border area (CMB-1) generated 120 million paired-end reads...
February 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28155674/numerical-prediction-of-thrombus-risk-in-an-anatomically-dilated-left-ventricle-the-effect-of-inflow-cannula-designs
#14
Sam Liao, Benjamin Simpson, Michael Neidlin, Tim A S Kaufmann, Zhiyong Li, Maria A Woodruff, Shaun D Gregory
BACKGROUND: Implantation of a rotary blood pump (RBP) can cause non-physiological flow fields in the left ventricle (LV) which may trigger thrombosis. Different inflow cannula geometry can affect LV flow fields. The aim of this study was to determine the effect of inflow cannula geometry on intraventricular flow under full LV support in a patient specific model. METHODS: Computed tomography angiography imaging of the LV was performed on a RBP candidate to develop a patient-specific model...
December 28, 2016: Biomedical Engineering Online
https://www.readbyqxmd.com/read/28152989/small-quantity-lipid-based-nutrient-supplements-containing-different-amounts-of-zinc-along-with-diarrhea-and-malaria-treatment-increase-iron-and-vitamin-a-status-and-reduce-anemia-prevalence-but-do-not-affect-zinc-status-in-young-burkinabe-children-a-cluster
#15
Souheila Abbeddou, Elizabeth Yakes Jimenez, Jérome W Somé, Jean Bosco Ouédraogo, Kenneth H Brown, Sonja Y Hess
BACKGROUND: We assessed the effects of providing a package of interventions including small-quantity lipid-based nutrient supplements (SQ-LNS) containing 0, 5 or 10 mg zinc and illness treatment to Burkinabe children from 9 to 18 months of age, on biomarkers of zinc, iron and vitamin A status at 18 months and compared with a non-intervention cohort (NIC). METHODS: Using a two-stage cluster randomized trial design, communities were randomly assigned to the intervention cohort (IC) or NIC, and extended family compounds within the IC were randomly assigned to different treatment groups...
February 2, 2017: BMC Pediatrics
https://www.readbyqxmd.com/read/28152069/subclinical-inflammation-influences-the-association-between-vitamin-a-and-iron-status-among-schoolchildren-in-ghana
#16
Abdul-Razak Abizari, Fusta Azupogo, Inge D Brouwer
BACKGROUND AND OBJECTIVE: In resource-poor settings, micronutrient deficiencies such as vitamin A deficiency may co-exist with iron-deficiency. In this study we assessed the iron and vitamin A status of schoolchildren and the association between vitamin A and iron status. METHODS: A cross-sectional design using the baseline data of a dietary intervention trial conducted among randomly selected 5-12 years old schoolchildren (n = 224) from 2 rural schools in northern Ghana...
2017: PloS One
https://www.readbyqxmd.com/read/28143578/circular-rnas-in-human-cancer
#17
REVIEW
Yumin Wang, Yongzhen Mo, Zhaojian Gong, Xiang Yang, Mo Yang, Shanshan Zhang, Fang Xiong, Bo Xiang, Ming Zhou, Qianjin Liao, Wenling Zhang, Xiayu Li, Xiaoling Li, Yong Li, Guiyuan Li, Zhaoyang Zeng, Wei Xiong
CircRNAs are a novel type of RNAs. With the newly developed technology of next-generation sequencing (NGS), especially RNA-seq technology, over 30,000 circRNAs have already been found. Owing to their unique structure, they are more stable than linear RNAs. CircRNAs play important roles in the carcinogenesis of cancer. The expression of circRNAs is correlated with patients' clinical characteristics, and circRNAs play a vital role in many aspects of malignant phenotypes, including cell cycle, apoptosis, vascularization, and invasion; metastasis as a RNA sponge, binding to RBP; or translation...
January 31, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28142333/identification-of-the-active-protein-in-rice-bran-protein-having-an-inhibitory-activity-of-cholesterol-micellar-solubility
#18
Jilite Wang, Masaya Shimada, Satoshi Nagaoka
In our previous study, rice bran protein (RBP) inhibited cholesterol micellar solubility in vitro and decreased serum cholesterol level in rats. In the present study, RBP was separated and purified by size-exclusion chromatography and reversed-phase chromatography. The active protein of RBP related to cholesterol micellar solubility was identified as lectin and non-specific lipid-transfer protein 1 using MALDI-TOF mass spectrometry analysis.
February 1, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/28142187/spatial-regulation-of-the-kh-domain-rna-binding-protein-rnc1-mediated-by-a-crm1-independent-nuclear-export-system-in-schizosaccharomyces-pombe
#19
Ryosuke Satoh, Yasuhiro Matsumura, Akitomo Tanaka, Makoto Takada, Yuna Ito, Kanako Hagihara, Masahiro Inari, Ayako Kita, Akira Fukao, Toshinobu Fujiwara, Shinya Hirai, Tokio Tani, Reiko Sugiura
RNA-binding proteins (RBPs) play important roles in the posttranscriptional regulation of gene expression, including mRNA stability, transport and translation. Fission yeast rnc1(+) encodes a K Homology (KH)-type RBP, which binds and stabilizes the Pmp1 MAPK phosphatase mRNA thereby suppressing the Cl(-) hypersensitivity of calcineurin deletion and MAPK signaling mutants. Here, we analyzed the spatial regulation of Rnc1 and discovered a putative nuclear export signal (NES)Rnc1 , which dictates the cytoplasmic localization of Rnc1 in a Crm1-independent manner...
January 31, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28138077/both-maintenance-and-avoidance-of-rna-binding-protein-interactions-constrain-coding-sequence-evolution
#20
Savisaar Rosina, Laurence D Hurst
While the principal force directing coding sequence (CDS) evolution is selection on protein function, to ensure correct gene expression CDSs must also maintain interactions with RNA-binding proteins (RBPs). Understanding how our genes are shaped by these RNA-level pressures is necessary for diagnostics and for improving transgenes. However, the evolutionary impact of the need to maintain RBP interactions remains unresolved. Are coding sequences constrained by the need to specify RBP binding motifs? If so, what proportion of mutations are affected? Might sequence evolution also be constrained by the need not to specify motifs that might attract unwanted binding, for instance because it would interfere with exon definition? Here, we have scanned human CDSs for motifs that have been experimentally determined to be recognized by RBPs...
January 30, 2017: Molecular Biology and Evolution
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