keyword
MENU ▼
Read by QxMD icon Read
search

RBP

keyword
https://www.readbyqxmd.com/read/28636238/segmental-domain-selective-perdeuteration-and-small-angle-neutron-scattering-for-structural-analysis-of-multi-domain-proteins
#1
Miriam Sonntag, Pravin Jagtap, Bernd Simon, Marie-Sousai Appavou, Arie Geerlof, Ralf Stehle, Frank Gabel, Janosch Hennig, Michael Sattler
Multi-domain proteins play critical roles in fine-tuning essential processes in cellular signaling and gene regulation. Typically, multiple globular domains that are connected by flexible linkers undergo dynamic re-arrangements upon binding to protein, DNA or RNA ligands. RNA binding proteins (RBPs) represent an important class of multi-domain proteins, which regulate gene expression by recognizing linear or structured RNA sequence motifs. Here, we employ segmental perdeuteration of the three RNA recognition motif (RRM) domains in the RBP TIA-1 using Sortase A-mediated protein ligation...
June 21, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28634384/alternative-splicing-regulates-distinct-subcellular-localization-of-epithelial-splicing-regulatory-protein-1-esrp1-isoforms
#2
Yueqin Yang, Russ P Carstens
Epithelial-Splicing-Regulatory-Protein 1 (Esrp1) is a cell-type specific RNA-binding protein (RBP) that is essential for mammalian development through maintenance of epithelial cell properties including barrier function. Esrp1 also regulates splicing during the epithelial to mesenchymal transition (EMT). It contains three highly conserved RNA recognition motifs (RRMs) in the absence of other clearly defined protein domains. Esrp1 itself is also alternatively spliced to produce multiple protein isoforms. Here we determined that two competing alternative 5' splice sites in exon 12 yield Esrp1 isoforms with differential nucleocytoplasmic localization...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28622300/the-als-linked-e102q-mutation-in-sigma-receptor-1-leads-to-er-stress-mediated-defects-in-protein-homeostasis-and-dysregulation-of-rna-binding-proteins
#3
Alice Dreser, Jan Tilmann Vollrath, Antonio Sechi, Sonja Johann, Andreas Roos, Alfred Yamoah, Istvan Katona, Saeed Bohlega, Dominik Wiemuth, Yuemin Tian, Axel Schmidt, Jörg Vervoorts, Marc Dohmen, Cordian Beyer, Jasper Anink, Eleonora Aronica, Dirk Troost, Joachim Weis, Anand Goswami
Amyotrophic lateral sclerosis (ALS) is characterized by the selective degeneration of motor neurons (MNs) and their target muscles. Misfolded proteins which often form intracellular aggregates are a pathological hallmark of ALS. Disruption of the functional interplay between protein degradation (ubiquitin proteasome system and autophagy) and RNA-binding protein homeostasis has recently been suggested as an integrated model that merges several ALS-associated proteins into a common pathophysiological pathway...
June 16, 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28621838/the-effect-of-compliant-inflow-cannulae-on-the-hemocompatibility-of-rotary-blood-pump-circuits-in-an-in-vitro-model
#4
Jo P Pauls, Deepika Nandakumar, Jarod Horobin, Justin D Prendeville, Michael J Simmonds, John F Fraser, Geoff Tansley, Shaun D Gregory
Rotary blood pumps (RBPs) are used for mechanical circulatory support in heart failure patients but exhibit a reduced response to preload changes, which can lead to ventricular suction events. A passive control system, in the form of a compliant inflow cannula (IC), has been developed to mitigate suction, although this device may cause significant hemolysis. This study compared the incidence of mechanically induced hemolysis of two compliant IC designs (strutted and nonstrutted) with a rigid IC (control) in a blood circulation loop over 90 min...
June 16, 2017: Artificial Organs
https://www.readbyqxmd.com/read/28621679/circular-rnas-a-novel-type-of-biomarker-and-genetic-tools-in-cancer
#5
REVIEW
Yi-Neng Han, Sheng-Qiang Xia, Yuan-Yuan Zhang, Jun-Hua Zheng, Wei Li
Circular RNAs (circRNAs) are a novel type of universal and diverse endogenous noncoding RNAs (ncRNAs) and they form a covalently closed continuous loop without 5' or 3' tails unlike linear RNAs. Most circRNAs are presented with characteristics of abundance, stability, conservatism, and often exhibiting tissue/developmental-stage-specific expression. CircRNAs are generated either from exons or introns by back splicing or lariat introns. CircRNAs play important roles as miRNA sponges, gene transcription and expression regulators, RNA-binding protein (RBP) sponges and protein/peptide translators...
June 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28620751/impact-of-a-rectal-and-bladder-preparation-protocol-on-prostate-cancer-outcome-in-patients-treated-with-external-beam-radiotherapy
#6
A Maggio, D Gabriele, E Garibaldi, S Bresciani, E Delmastro, A Di Dia, A Miranti, M Poli, T Varetto, M Stasi, P Gabriele
PURPOSE AND OBJECTIVE: To test the hypothesis that a rectal and bladder preparation protocol is associated with an increase in prostate cancer specific survival (PCSS), clinical disease free survival (CDFS) and biochemical disease free survival (BDFS). PATIENTS AND METHODS: From 1999 to 2012, 1080 prostate cancer (PCa) patients were treated with three-dimensional conformal radiotherapy (3DCRT). Of these patients, 761 were treated with an empty rectum and comfortably full bladder (RBP) preparation protocol, while for 319 patients no rectal/bladder preparation (NRBP) protocol was adopted...
June 15, 2017: Strahlentherapie und Onkologie: Organ der Deutschen Röntgengesellschaft ... [et Al]
https://www.readbyqxmd.com/read/28615251/adjusting-retinol-binding-protein-concentrations-for-inflammation-biomarkers-reflecting-inflammation-and-nutritional-determinants-of-anemia-brinda-project
#7
REVIEW
Leila M Larson, Sorrel Ml Namaste, Anne M Williams, Reina Engle-Stone, O Yaw Addo, Parminder S Suchdev, James P Wirth, Victor Temple, Mary Serdula, Christine A Northrop-Clewes
Background: The accurate estimation of the prevalence of vitamin A deficiency (VAD) is important in planning and implementing interventions. Retinol-binding protein (RBP) is often used in population surveys to measure vitamin A status, but its interpretation is challenging in settings where inflammation is common because RBP concentrations decrease during the acute-phase response.Objectives: We aimed to assess the relation between RBP concentrations and inflammation and malaria in preschool children (PSC) (age range: 6-59 mo) and women of reproductive age (WRA) (age range: 15-49 y) and to investigate adjustment algorithms to account for these effects...
June 14, 2017: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28611215/genome-wide-crispr-screen-identifies-hnrnpl-as-a-prostate-cancer-dependency-regulating-rna-splicing
#8
Teng Fei, Yiwen Chen, Tengfei Xiao, Wei Li, Laura Cato, Peng Zhang, Maura B Cotter, Michaela Bowden, Rosina T Lis, Shuang G Zhao, Qiu Wu, Felix Y Feng, Massimo Loda, Housheng Hansen He, X Shirley Liu, Myles Brown
Alternative RNA splicing plays an important role in cancer. To determine which factors involved in RNA processing are essential in prostate cancer, we performed a genome-wide CRISPR/Cas9 knockout screen to identify the genes that are required for prostate cancer growth. Functional annotation defined a set of essential spliceosome and RNA binding protein (RBP) genes, including most notably heterogeneous nuclear ribonucleoprotein L (HNRNPL). We defined the HNRNPL-bound RNA landscape by RNA immunoprecipitation coupled with next-generation sequencing and linked these RBP-RNA interactions to changes in RNA processing...
June 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28611064/cytoplasmic-poly-a-binding-protein-1-pabpc1-interacts-with-the-rna-binding-protein-hnrnpll-and-thereby-regulates-immunoglobulin-secretion-in-plasma-cells
#9
Yuanzheng Peng, Juanjuan Yuan, Zhenchao Zhang, Xing Chang
Increasing evidence indicates that alternative processing of mRNA, including alternative splicing, 3' alternative polyadenylation, and regulation of mRNA stability/translation, represents a major mechanism contributing to protein diversification. For example, in alternative polyadenylation, the 3' end of the immunoglobulin heavy chain mRNA is processed during B cell differentiation, and this processing involves RNA binding proteins (RBPs). Heterogeneous nuclear RNA nucleoside protein L-like (hnRNPLL) is an RBP expressed in terminally differentiated lymphocytes, such as memory T cells and plasma cells...
June 13, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28592461/rbm24-promotes-u1-snrnp-recognition-of-the-mutated-5-splice-site-in-the-ikbkap-gene-of-familial-dysautonomia
#10
Kenji Ohe, Mayumi Yoshida, Akiko Nakano-Kobayashi, Motoyasu Hosokawa, Yukiya Sako, Maki Sakuma, Yukiko Okuno, Tomomi Usui, Kensuke Ninomiya, Takayuki Nojima, Naoyuki Kataoka, Masatoshi Hagiwara
The 5' splice site mutation (IVS20+6T>C) of the inhibitor of kappa light polypeptide gene enhancer in B cells, kinase complex-associated protein (IKBKAP) gene in familial dysautonomia (FD) is at the sixth intronic nucleotide of the 5' splice site. It is known to weaken U1 snRNP recognition and result in aberrantly spliced mRNA product in neuronal tissue, but normally spliced mRNA in other tissues. Aberrantly spliced IKBKAP mRNA abrogates IKK complex-associated protein (IKAP)/elongator protein 1 (ELP1) expression and results in a defect of neuronal cell development in FD...
June 7, 2017: RNA
https://www.readbyqxmd.com/read/28589356/characterization-of-the-b-cell-transcriptome-bound-by-rna-binding-proteins-with-iclip
#11
Manuel D Díaz-Muñoz, Elisa Monzón-Casanova, Martin Turner
Posttranscriptional regulation of gene expression shapes the B cell transcriptome and controls messenger RNA (mRNA) translation into protein. Recent reports have highlighted the importance of RNA binding proteins (RBPs) for mRNA splicing, subcellular location, stability, and translation during B lymphocyte development, activation, and differentiation. Here we describe individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) in primary lymphocytes, a method that maps RNA-protein interactions in a genome-wide scale allowing mechanistic analysis of RBP function...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28577020/assessment-of-the-diagnostic-value-of-different-biomarkers-in-relation-to-various-stages-of-diabetic-nephropathy-in-type-2-diabetic-patients
#12
Khalid Al-Rubeaan, Khalid Siddiqui, Mohammed A Al-Ghonaim, Amira M Youssef, Ahmed H Al-Sharqawi, Dhekra AlNaqeb
Albuminuria is widely used to indicate early phases of diabetic nephropathy although it is limited by the fact that structural damage might precede albumin excretion. This necessitates identifying better biomarkers that diagnose or predict diabetic nephropathy. This is a cross-sectional hospital based study recruiting type 2 diabetic patients cohort aged 35-75 years with diabetes duration of ≥10 years. Out of total eligible 467 patients, 200 patients were with normal albumin excretion, 184 patients with microalbuminuria and 83 patients with macroalbuminuria...
June 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28576851/urinary-tamm-horsfall-protein-albumin-vitamin-d-binding-protein-and-retinol-binding-protein-as-early-biomarkers-of-chronic-kidney-disease-in-dogs
#13
Fernanda Chacar, Márcia Kogika, Talita R Sanches, Douglas Caragelasco, Cínthia Martorelli, Camila Rodrigues, Jose Manuel C Capcha, Dennis Chew, Lúcia Andrade
Proteinuria is a marker and mediator of chronic kidney disease (CKD). In clinical practice, the urinary protein-to-creatinine ratio (UP/C) is of limited usefulness, because it indicates only the magnitude of proteinuria and not the origin of the loss (glomerular or tubular). The complete assessment of proteinuria includes quantitative and qualitative evaluations, both of which are required in order to optimize the therapy. In addition to measuring the UP/C, we performed SDS-PAGE and western blotting to determine the expression of albumin, vitamin D-binding protein (VDBP), retinol-binding protein (RBP), and Tamm-Horsfall protein (THP) in urine samples of 49 dogs: healthy (control) dogs (n = 9); and dogs with CKD (n = 40), stratified by stage...
June 2017: Physiological Reports
https://www.readbyqxmd.com/read/28575488/a-deep-boosting-based-approach-for-capturing-the-sequence-binding-preferences-of-rna-binding-proteins-from-high-throughput-clip-seq-data
#14
Shuya Li, Fanghong Dong, Yuexin Wu, Sai Zhang, Chen Zhang, Xiao Liu, Tao Jiang, Jianyang Zeng
Characterizing the binding behaviors of RNA-binding proteins (RBPs) is important for understanding their functional roles in gene expression regulation. However, current high-throughput experimental methods for identifying RBP targets, such as CLIP-seq and RNAcompete, usually suffer from the false negative issue. Here, we develop a deep boosting based machine learning approach, called DeBooster, to accurately model the binding sequence preferences and identify the corresponding binding targets of RBPs from CLIP-seq data...
May 30, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28573168/analysis-of-in-vivo-interaction-between-rna-binding-proteins-and-their-rna-targets-by-uv-cross-linking-and-immunoprecipitation-clip-method
#15
Pamela Bielli, Claudio Sette
RNA metabolism is tightly controlled across different tissues and developmental stages, and its dysregulation is one of the molecular hallmarks of cancer. Through direct binding to specific sequence element(s), RNA binding proteins (RBPs) play a pivotal role in co- and post-transcriptional RNA regulatory events. We have recently demonstrated that, in pancreatic cancer cells, acquisition of a drug resistant (DR)-phenotype relied on upregulation of the polypyrimidine tract binding protein (PTBP1), which in turn is recruited to the pyruvate kinase pre-mRNA and favors splicing of the oncogenic PKM2 variant...
May 20, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28551428/delivery-of-riboflavin-5-monophosphate-into-the-cornea-can-liposomes-provide-any-enhancement-effects
#16
Neva Kandzija, Vitaliy V Khutoryanskiy
Keratoconus is a progressive condition caused by the thinning of the cornea, which eventually deforms the front surface of the eye into a cone shape leading to ghosting, multiple images, glare and several other vision problems. Currently keratoconus is treated with UV-induced ribofiavin-mediated collagen cross-linking, which requires a physical removal of the corneal epithelium under topical anesthesia. This study reports the penetration of riboflavin (Rb) and its more water-soluble form, riboflavin-5'- monophosphate (RbP), into the bovine cornea ex vivo...
May 24, 2017: Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28534775/learning-rotation-invariant-local-binary-descriptor
#17
Yueqi Duan, Jiwen Lu, Jianjiang Feng, Jie Zhou
In this paper, we propose a rotation-invariant local binary descriptor (RI-LBD) learning method for visual recognition. Compared with hand-crafted local binary descriptors such as LBP and its variants which require strong prior knowledge, local binary feature learning methods are more efficient and dataadaptive. Unlike existing learning-based local binary descriptors such as compact binary face descriptor (CBFD) and simultaneous local binary feature learning and encoding (SLBFLE) which are susceptible to rotations, our RI-LBD first categorizes each local patch into a rotational binary pattern (RBP), and then jointly learns the orientation for each pattern and the projection matrix to obtain rotation-invariant local binary descriptors...
May 16, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28531099/vitamin-a-status-of-women-and-children-in-yaound%C3%A3-and-douala-cameroon-is-unchanged-one-year-after-initiation-of-a-national-vitamin-a-oil-fortification-program
#18
Reina Engle-Stone, Martin Nankap, Alex Ndjebayi, Marie-Madeleine Gimou, Avital Friedman, Marjorie J Haskell, Ann Tarini, Kenneth H Brown
Vitamin A (VA) fortification of cooking oil is considered a cost-effective strategy for increasing VA status, but few large-scale programs have been evaluated. We conducted representative surveys in Yaoundé and Douala, Cameroon, 2 years before and 1 year after the introduction of a mandatory national program to fortify cooking oil with VA. In each survey, 10 different households were selected within each of the same 30 clusters (n = ~300). Malaria infection and plasma indicators of inflammation and VA (retinol-binding protein, pRBP) status were assessed among women aged 15-49 years and children aged 12-59 months, and casual breast milk samples were collected for VA and fat measurements...
May 20, 2017: Nutrients
https://www.readbyqxmd.com/read/28529064/analysis-of-post-transcriptional-regulation-during-cancer-progression-using-a-donor-derived-isogenic-model-of-tumorigenesis
#19
Laura S Bisogno, Jack D Keene
Post-transcriptional regulation of gene expression by RNA binding proteins (RBPs) and non-coding RNAs plays an important role in global gene expression. Many post-transcriptional regulators are misexpressed and misregulated in cancers, resulting in altered programs of protein biosynthesis that can drive tumor progression. While comparative studies of several RBPs and microRNAs expressed in various cancer types have been reported, a model system that can be used to quantify RBP regulation and functional outcomes during the initiation and early stages of tumorigenesis is lacking...
May 18, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28516119/affinity-pulldown-of-biotinylated-rna-for-detection-of-protein-rna-complexes
#20
Amaresh C Panda, Jennifer L Martindale, Myriam Gorospe
RNA-binding proteins (RBPs) have recently emerged as crucial players in the regulation of gene expression. The interactions of RBPs with target mRNAs control the levels of gene products by altering different regulatory steps, including pre-mRNA splicing and maturation, nuclear mRNA export, and mRNA stability and translation (Glisovic et al., 2008). There are several methodologies available today to identify RNAs bound to specific RBPs; some detect only recombinant molecules in vitro, others detect recombinant and endogenous molecules, while others detect only endogenous molecules...
December 20, 2016: Bio-protocol
keyword
keyword
95884
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"