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https://www.readbyqxmd.com/read/28097669/mathematical-modeling-of-rotary-blood-pumps-in-a-pulsatile-in-vitro-flow-environment
#1
Tohid Pirbodaghi
Nowadays, sacrificing animals to develop medical devices and receive regulatory approval has become more common, which increases ethical concerns. Although in vivo tests are necessary for development and evaluation of new devices, nonetheless, with appropriate in vitro setups and mathematical models, a part of the validation process can be performed using these models to reduce the number of sacrificed animals. The main aim of this study is to present a mathematical model simulating the hydrodynamic function of a rotary blood pump (RBP) in a pulsatile in vitro flow environment...
January 18, 2017: Artificial Organs
https://www.readbyqxmd.com/read/28081581/differences-in-gene-expression-and-gene-associations-in-epicardial-fat-compared-to-subcutaneous-fat
#2
J Yim, S W Rabkin
Epicardial adipose tissue (EAT) plays a role in cardiac physiology and may contribute to the development of coronary artery disease. Our objective was to determine whether there was a significant difference in gene expression in EAT compared to subcutaneous adipose tissue (SAT) and to identify potential relationships. MEDLINE and EMBASE were searched using the key terms "Epicardial Adipose Tissue" or "Epicardial Fat" in combination with "RNA", "mRNA", or "gene". The entry criteria were studies that presented primary data including expression levels of mRNA in human EAT compared with SAT and an expression of variance (SD)...
January 12, 2017: Hormone and Metabolic Research, Hormon- und Stoffwechselforschung, Hormones et Métabolisme
https://www.readbyqxmd.com/read/28080204/identification-of-hur-target-circular-rnas-uncovers-suppression-of-pabpn1-translation-by-circpabpn1
#3
Kotb Abdelmohsen, Amaresh C Panda, Rachel Munk, Ioannis Grammatikakis, Dawood B Dudekula, Supriyo De, Jiyoung Kim, Ji Heon Noh, Kyoung Mi Kim, Jennifer L Martindale, Myriam Gorospe
HuR influences gene expression programs and hence cellular phenotypes by binding to hundreds of coding and noncoding linear RNAs. However, whether HuR binds to circular RNAs (circRNAs) and impacts on their function is unknown. Here, we have identified en masse circRNAs binding HuR in human cervical carcinoma HeLa cells. One of the most prominent HuR target circRNAs was hsa_circ_0031288, renamed CircPABPN1 as it arises from the PABPN1 pre-mRNA. Further analyses revealed that HuR did not influence CircPABPN1 abundance; interestingly, however, high levels of CircPABPN1 suppressed HuR binding to PABPN1 mRNA...
January 12, 2017: RNA Biology
https://www.readbyqxmd.com/read/28076789/reduced-insulin-igf-1-signaling-restores-the-dynamic-properties-of-key-stress-granule-proteins-during-aging
#4
Marie C Lechler, Emily D Crawford, Nicole Groh, Katja Widmaier, Raimund Jung, Janine Kirstein, Jonathan C Trinidad, Alma L Burlingame, Della C David
Low-complexity "prion-like" domains in key RNA-binding proteins (RBPs) mediate the reversible assembly of RNA granules. Individual RBPs harboring these domains have been linked to specific neurodegenerative diseases. Although their aggregation in neurodegeneration has been extensively characterized, it remains unknown how the process of aging disturbs RBP dynamics. We show that a wide variety of RNA granule components, including stress granule proteins, become highly insoluble with age in C. elegans and that reduced insulin/insulin-like growth factor 1 (IGF-1) daf-2 receptor signaling efficiently prevents their aggregation...
January 10, 2017: Cell Reports
https://www.readbyqxmd.com/read/28069467/validity-and-reliability-of-a-french-version-of-reflux-symptom-index
#5
Jérôme R Lechien, Kathy Huet, Camille Finck, Mohamad Khalife, Anne-Françoise Fourneau, Véronique Delvaux, Myriam Piccaluga, Bernard Harmegnies, Sven Saussez
OBJECTIVE: To develop a French version of the Reflux Symptom Index (Fr-RSI) and to assess its internal consistency, reliability, and clinical validity. STUDY DESIGN: Controlled, prospective trial. MATERIALS AND METHODS: Forty-four patients with a reflux finding score > 7 and an Fr-RSI > 13 were enrolled and treated with 20 mg of pantoprazole twice daily and diet changes for 3 months. Ninety asymptomatic subjects were also included in the study...
January 6, 2017: Journal of Voice: Official Journal of the Voice Foundation
https://www.readbyqxmd.com/read/28062840/the-properties-of-the-rna-binding-protein-nf90-are-considerably-modulated-by-complex-formation-with-nf45
#6
Tobias Schmidt, Paul Knick, Hauke Lilie, Susann Friedrich, Ralph Peter Golbik, Sven-Erik Behrens
Nuclear factor 90 (NF90) is an RNA-binding protein (RBP) that regulates post-transcriptionally the expression of various mRNAs. NF90 was recently shown to be capable of discriminating between different RNA substrates. This is mediated by an adaptive and co-operative interplay between three RNA-binding motifs (RBMs) in the protein's C-terminus. In many cell types, NF90 exists predominantly in a complex with NF45. Here, we compared the RNA-binding properties of the purified NF90 monomer and the NF90-NF45 heterodimer by biophysical and biochemical means, and demonstrate that the interaction with NF45 considerably affects the characteristics of NF90...
January 15, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28053162/postar-a-platform-for-exploring-post-transcriptional-regulation-coordinated-by-rna-binding-proteins
#7
Boqin Hu, Yu-Cheng T Yang, Yiming Huang, Yumin Zhu, Zhi John Lu
We present POSTAR (http://POSTAR.ncrnalab.org), a resource of POST-trAnscriptional Regulation coordinated by RNA-binding proteins (RBPs). Precise characterization of post-transcriptional regulatory maps has accelerated dramatically in the past few years. Based on new studies and resources, POSTAR supplies the largest collection of experimentally probed (∼23 million) and computationally predicted (approximately 117 million) RBP binding sites in the human and mouse transcriptomes. POSTAR annotates every transcript and its RBP binding sites using extensive information regarding various molecular regulatory events (e...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28039930/interacting-protein-partners-of-arabidopsis-rna-binding-protein-atrbp45b
#8
Meenakumari Muthuramalingam, Yixing Wang, Yongfang Li, Ramamurthy Mahalingam
• RNA binding proteins (RBPs), important players in post-transcriptional gene regulation usually exist in ribonuclear complexes. However, even in model systems like Arabidopsis characterization of RBP associated proteins are limited. In this study, we investigated the interacting proteins of the Arabidopsis AtRBP45b, which is involved in stress signaling. • In vivo localization of AtRBP45b was conducted using 35S-GFP. FLAG-tagged AtRBP45b under the control of 35S promoter in the Atrbp45b-1 mutant background was used to pull down AtRBP45b interacting proteins...
December 31, 2016: Plant Biology
https://www.readbyqxmd.com/read/28035070/elucidation-of-the-genetic-and-epigenetic-landscape-alterations-in-rna-binding-proteins-in-glioblastoma
#9
Shruti Bhargava, Vikas Patil, Kulandaivelu Mahalingam, Kumaravel Somasundaram
RNA binding proteins (RBPs) have been implicated in cancer development. An integrated bioinformatics analysis of RBPs (n = 1756) in various datasets (n = 11) revealed several genetic and epigenetically altered events among RBPs in glioblastoma (GBM). We identified 13 mutated and 472 differentially regulated RBPs in GBM samples. Mutations in AHNAK predicted poor prognosis. Copy number variation (CNV), DNA methylation and miRNA targeting contributed to RBP differential regulation. Two sets of differentially regulated RBPs that may be implicated in initial astrocytic transformation and glioma progression were identified...
December 27, 2016: Oncotarget
https://www.readbyqxmd.com/read/28018921/low-serum-levels-of-prealbumin-retinol-binding-protein-and-retinol-are-frequent-in-adult-type-1-diabetic-patients
#10
Luis Forga, Federico Bolado, María José Goñi, Ibai Tamayo, Berta Ibáñez, Carlos Prieto
Aim. To determine the serum prealbumin (PA), retinol binding protein (RBP), and retinol levels in adult patients with type 1 diabetes (T1D) and to analyze some factors related to those levels. Methods. A total of 93 patients (47 women) were studied. Age, gender, BMI, duration of diabetes, chronic complications, HbA1c, lipid profile, creatinine, albumin, PA, RBP, and retinol were recorded. High and low parameter groups were compared by Mann-Whitney U and χ(2) tests. Correlation between parameters was analyzed by Spearman's test...
2016: Journal of Diabetes Research
https://www.readbyqxmd.com/read/28013300/notch4-signaling-pathway-of-endothelial-progenitor-cells-in-a-kawasaki-disease-model-induced-by-lactobacillus-casei-cell-wall-extract
#11
Huafeng Wang, Yuanyuan Xia, Songling Fu, Wei Wang, Chunhong Xie, Yiying Zhang, Fangqi Gong
The Notch4 signaling pathway of endothelial progenitor cells (EPCs) may play a crucial role in Kawasaki disease (KD). We investigated the proliferation, adhesion, migration, angiogenesis, and expression levels of Notch4, recombination signal-binding protein-Jκ (RBP-Jκ), P-selectin, and vascular cell adhesion molecule-1 (VCAM-1) of bone marrow (BM) EPCs in a KD model induced by Lactobacillus casei cell wall extract. The numbers of BM EPCs decreased significantly in the KD models. The Notch4 expression level on the EPC surface was higher in the KD models than in the controls...
December 24, 2016: Journal of Vascular Research
https://www.readbyqxmd.com/read/28011057/the-ischemic-nephrotoxic-acute-kidney-injury-and-the-use-of-renal-biomarkers-in-clinical-practice
#12
REVIEW
Michele Andreucci, Teresa Faga, Antonio Pisani, Maria Perticone, Ashour Michael
The term Acute Renal Failure (ARF) has been replaced by the term Acute Kidney Injury (AKI). AKI indicates an abrupt (within 24-48h) decrease in Glomerular Filtraton Rate, due to renal damage, that causes fluid and metabolic waste retention and alteration of electrolyte and acid-base balance. The renal biomarkers of AKI are substances or processes that are indicators of normal or impaired function of the kidney. The most used renal biomarker is still serum creatinine that is inadequate for several reasons, one of which is its inability to differentiate between hemodynamic changes of renal function ("prerenal azotemia") from intrinsic renal failure or obstructive nephropathy...
December 21, 2016: European Journal of Internal Medicine
https://www.readbyqxmd.com/read/28008714/bioinformatic-tools-for-analysis-of-clip-ribonucleoprotein-data
#13
REVIEW
Supriyo De, Myriam Gorospe
Investigating the interactions of RNA-binding proteins (RBPs) with RNAs is a complex task for molecular and computational biologists. The molecular biology techniques and the computational approaches to understand RBP-RNA (or ribonucleoprotein, RNP) interactions have advanced considerably over the past few years and numerous and diverse software tools have been developed to analyze these data. Accordingly, laboratories interested in RNP biology face the challenge of choosing adequately among the available software tools those that best address the biological problem they are studying...
December 23, 2016: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/28007900/extensive-cryptic-splicing-upon-loss-of-rbm17-and-tdp43-in-neurodegeneration-models
#14
Qiumin Tan, Hari Krishna Yalamanchili, Jeehye Park, Antonia De Maio, Hsiang-Chih Lu, Ying-Wooi Wan, Joshua J White, Vitaliy V Bondar, Layal S Sayegh, Xiuyun Liu, Yan Gao, Roy V Sillitoe, Harry T Orr, Zhandong Liu, Huda Y Zoghbi
Splicing regulation is an important step of post-transcriptional gene regulation. It is a highly dynamic process orchestrated by RNA-binding proteins (RBPs). RBP dysfunction and global splicing dysregulation have been implicated in many human diseases, but the in vivo functions of most RBPs and the splicing outcome upon their loss remain largely unexplored. Here we report that constitutive deletion of Rbm17, which encodes an RBP with a putative role in splicing, causes early embryonic lethality in mice and that its loss in Purkinje neurons leads to rapid degeneration...
October 7, 2016: Human Molecular Genetics
https://www.readbyqxmd.com/read/28004272/rice-bran-protein-hydrolysates-attenuate-diabetic-nephropathy-in-diabetic-animal-model
#15
Kampeebhorn Boonloh, Eun Soo Lee, Hong Min Kim, Mi Hye Kwon, You Mi Kim, Patchareewan Pannangpetch, Bunkerd Kongyingyoes, Upa Kukongviriyapan, Supawan Thawornchinsombut, Eun Young Lee, Veerapol Kukongviriyapan, Choon Hee Chung
INTRODUCTION: Diabetic nephropathy (DN) is an important microvascular complication of uncontrolled diabetes. The features of DN include albuminuria, extracellular matrix alterations, and progressive renal insufficiency. Rice bran protein hydrolysates (RBPs) have been reported to have antihyperglycemic, lipid-lowering, and anti-inflammatory effects in diabetic rats. Our study was to investigate the renoprotective effects of RBP in diabetic animals and mesangial cultured cells. METHODS: Eight-week-old male db/m and db/db mice were orally treated with tap water or RBP (100 or 500 mg/kg/day) for 8 weeks...
December 21, 2016: European Journal of Nutrition
https://www.readbyqxmd.com/read/28003131/crispr-cas9-mediated-integration-enables-tag-eclip-of-endogenously-tagged-rna-binding-proteins
#16
Eric L Van Nostrand, Chelsea Gelboin-Burkhart, Ruth Wang, Gabriel A Pratt, Steven M Blue, Gene W Yeo
Identification of in vivo direct RNA targets for RNA binding proteins (RBPs) provides critical insight into their regulatory activities and mechanisms. Recently, we described a methodology for enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP) using antibodies against endogenous RNA binding proteins. However, in many cases it is desirable to profile targets of an RNA binding protein for which an immunoprecipitation-grade antibody is lacking. Here we describe a scalable method for using CRISPR/Cas9-mediated homologous recombination to insert a peptide tag into the endogenous RNA binding protein locus...
December 18, 2016: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28000798/identification-and-evaluation-of-novel-drug-targets-against-the-human-fungal-pathogen-aspergillus-fumigatus-with-elaboration-on-the-possible-role-of-rna-binding-protein
#17
Saeid Malekzadeh, Soroush Sardari, Parisa Azerang, Dorsa Khorasanizadeh, Solmaz Agha Amiri, Mohammad Azizi, Nazanin Mohajerani, Vahid Khalaj
BACKGROUND: Aspergillus fumigatus is an airborne opportunistic fungal pathogen that can cause fatal infections in immunocompromised patients. Although the current anti-fungal therapies are relatively efficient, some issues such as drug toxicity, drug interactions, and the emergence of drug-resistant fungi have promoted the intense research toward finding the novel drug targets. METHODS: In search of new antifungal drug targets, we have used a bioinformatics approach to identify novel drug targets...
2017: Iranian Biomedical Journal
https://www.readbyqxmd.com/read/27990575/dynamic-landscape-of-alternative-polyadenylation-during-retinal-development
#18
Wenyan Hu, Shengguo Li, Ji Yeon Park, Sridhar Boppana, Ting Ni, Miaoxin Li, Jun Zhu, Bin Tian, Zhi Xie, Mengqing Xiang
The development of the central nervous system (CNS) is a complex process that must be exquisitely controlled at multiple levels to ensure the production of appropriate types and quantity of neurons. RNA alternative polyadenylation (APA) contributes to transcriptome diversity and gene regulation, and has recently been shown to be widespread in the CNS. However, the previous studies have been primarily focused on the tissue specificity of APA and developmental APA change of whole model organisms; a systematic survey of APA usage is lacking during CNS development...
December 18, 2016: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/27990086/are-adipokines-associated-with-gestational-diabetes-mellitus
#19
Ümit Görkem, Ferit Kerim Küçükler, Cihan Toğrul, Tayfun Güngör
OBJECTIVE: To investigate the association of maternal serum levels of chemerin, retinol binding protein-4 (RBP-4), and visfatin with gestational diabetes mellitus (GDM). MATERIAL AND METHODS: 158 pregnant women were screened between 24 and 28 weeks of gestation. They were divided into two groups: GDM group (n=76) and control group (n=82). Maternal serum concentrations of chemerin, RBP-4, visfatin, insulin, and homeostasis model assessment-insulin resistance (HOMA-IR) were assessed...
2016: Journal of the Turkish German Gynecological Association
https://www.readbyqxmd.com/read/27930710/urb-rip-an-adaptable-and-efficient-approach-for-immunoprecipitation-of-rnas-and-associated-rnas-proteins
#20
Kyle A Cottrell, Sergej Djuranovic
Post-transcriptional regulation of gene expression is an important process that is mediated by interactions between mRNAs and RNA binding proteins (RBP), non-coding RNAs (ncRNA) or ribonucleoproteins (RNP). Key to the study of post-transcriptional regulation of mRNAs and the function of ncRNAs such as long non-coding RNAs (lncRNAs) is an understanding of what factors are interacting with these transcripts. While several techniques exist for the enrichment of a transcript whether it is an mRNA or an ncRNA, many of these techniques are cumbersome or limited in their application...
2016: PloS One
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