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https://www.readbyqxmd.com/read/28228471/novel-layers-of-rna-polymerase-iii-control-affecting-trna-gene-transcription-in-eukaryotes
#1
REVIEW
Ewa Leśniewska, Magdalena Boguta
RNA polymerase III (Pol III) transcribes a limited set of short genes in eukaryotes producing abundant small RNAs, mostly tRNA. The originally defined yeast Pol III transcriptome appears to be expanding owing to the application of new methods. Also, several factors required for assembly and nuclear import of Pol III complex have been identified recently. Models of Pol III based on cryo-electron microscopy reconstructions of distinct Pol III conformations reveal unique features distinguishing Pol III from other polymerases...
February 2017: Open Biology
https://www.readbyqxmd.com/read/28227982/analysis-of-the-sleep-eeg-in-the-complexity-domain
#2
Sara Mariani, Ana F T Borges, Teresa Henriques, Robert J Thomas, Samuel J Leistedt, Paul Linkowski, Jean-Pol Lanquart, Ary L Goldberger, Madalena D Costa, Sara Mariani, Ana F T Borges, Teresa Henriques, Robert J Thomas, Samuel J Leistedt, Paul Linkowski, Jean-Pol Lanquart, Ary L Goldberger, Madalena D Costa, Teresa Henriques, Robert J Thomas, Madalena D Costa, Samuel J Leistedt, Paul Linkowski, Ary L Goldberger, Jean-Pol Lanquart, Sara Mariani, Ana F T Borges
Conventional sleep analysis relies primarily on electroencephalogram (EEG) waveform features assessed in concert with eye movements, respiration and muscle tone. We explore a complementary "complexity domain" approach based on multiscale entropy (MSE) analysis of EEG signals and discuss its relationships to standard sleep analysis and to that based on electrocardiogram (ECG)-derived cardiopulmonary coupling (CPC). We observe a progressive decrease in complexity associated with decreased arousability, as measured by both conventional sleep scoring and CPC analysis...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226937/design-of-a-bio-inspired-pneumatic-artificial-muscle-with-self-contained-sensing
#3
Onder Erin, Nishant Pol, Luis Valle, Yong-Lae Park, Onder Erin, Nishant Pol, Luis Valle, Yong-Lae Park, Nishant Pol, Luis Valle, Onder Erin, Yong-Lae Park
Pneumatic artificial muscles (PAMs) are one of the most famous linear actuators in bio-inspired robotics. They can generate relatively high linear force considering their form factors and weights. Furthermore, PAMs are inexpensive compared with traditional electromagnetic actuators (e.g. DC motors) and also inherently light and compliant. In robotics applications, however, they typically require external sensing mechanisms due to their nonlinear behaviors, which may make the entire mechanical system bulky and complicated, limiting their use in simple systems...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28224978/methylated-antibody-affinity-purification-to-improve-proteomic-identification-of-plant-rna-polymerase-pol-v-complex-and-the-interacting-proteins
#4
Guochen Qin, Jun Ma, Xiaomei Chen, Zhaoqing Chu, Yi-Min She
Affinity purification followed by enzymatic digestion and mass spectrometry has been widely utilized for the sensitive detection of interacting proteins and protein complexes in various organisms. In plants, the method is technically challenging due to the low abundance proteins, non-specific binding and difficulties of eluting interacting proteins from antibody beads. In this report, we describe a strategy to modify antibodies by reductive methylation of lysines without affecting their binding properties, followed by on-bead digestion of bound proteins with endoproteinase Lys-C...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28223953/predicting-future-reading-problems-based-on-pre-reading-auditory-measures-a-longitudinal-study-of-children-with-a-familial-risk-of-dyslexia
#5
Jeremy M Law, Maaike Vandermosten, Pol Ghesquière, Jan Wouters
Purpose: This longitudinal study examines measures of temporal auditory processing in pre-reading children with a family risk of dyslexia. Specifically, it attempts to ascertain whether pre-reading auditory processing, speech perception, and phonological awareness (PA) reliably predict later literacy achievement. Additionally, this study retrospectively examines the presence of pre-reading auditory processing, speech perception, and PA impairments in children later found to be literacy impaired. Method: Forty-four pre-reading children with and without a family risk of dyslexia were assessed at three time points (kindergarten, first, and second grade)...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28223413/transcriptional-activation-of-lipogenesis-by-insulin-requires-phosphorylation-of-med17-by-ck2
#6
Jose A Viscarra, Yuhui Wang, Il-Hwa Hong, Hei Sook Sul
De novo lipogenesis is precisely regulated by nutritional and hormonal conditions. The genes encoding various enzymes involved in this process, such as fatty acid synthase (FASN), are transcriptionally activated in response to insulin. We showed that USF1, a key transcription factor for FASN activation, directly interacted with the Mediator subunit MED17 at the FASN promoter. This interaction recruited Mediator, which can bring POL II and other general transcription machinery to the complex. Moreover, we showed that MED17 was phosphorylated at Ser(53) by casein kinase 2 (CK2) in the livers of fed mice or insulin-stimulated hepatocytes, but not in the livers of fasted mice or untreated hepatocytes...
February 21, 2017: Science Signaling
https://www.readbyqxmd.com/read/28222757/spatiotemporal-dynamics-of-hiv-1-transmission-in-france-1999-2014-and-impact-of-targeted-prevention-strategies
#7
Antoine Chaillon, Asma Essat, Pierre Frange, Davey M Smith, Constance Delaugerre, Francis Barin, Jade Ghosn, Gilles Pialoux, Olivier Robineau, Christine Rouzioux, Cécile Goujard, Laurence Meyer, Marie-Laure Chaix
BACKGROUND: Characterizing HIV-1 transmission networks can be important in understanding the evolutionary patterns and geospatial spread of the epidemic. We reconstructed the broad molecular epidemiology of HIV from individuals with primary HIV-1 infection (PHI) enrolled in France in the ANRS PRIMO C06 cohort over 15 years. RESULTS: Sociodemographic, geographic, clinical, biological and pol sequence data from 1356 patients were collected between 1999 and 2014. Network analysis was performed to infer genetic relationships, i...
February 21, 2017: Retrovirology
https://www.readbyqxmd.com/read/28218421/frameshift-mutational-target-gene-analysis-identifies-similarities-and-differences-in-constitutional-mismatch-repair-deficiency-and-lynch-syndrome
#8
Claudia Maletzki, Maja Huehns, Ingrid Bauer, Tim Ripperger, Maureen M Mork, Eduardo Vilar, Sabine Klöcking, Heike Zettl, Friedrich Prall, Michael Linnebacher
Mismatch-repair deficient (MMR-D) malignancies include Lynch Syndrome (LS), which is secondary to germline mutations in one of the MMR genes, and the rare childhood-form of constitutional mismatch repair-deficiency (CMMR-D); caused by bi-allelic MMR gene mutations. A hallmark of LS-associated cancers is microsatellite instability (MSI), characterized by coding frameshift mutations (cFSM) in target genes. By contrast, tumors arising in CMMR-D patients are thought to display a somatic mutation pattern differing from LS...
February 20, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28217959/anti-rnpc3-antibodies-as-a-marker-of-cancer-associated-scleroderma
#9
Ami A Shah, George Xu, Antony Rosen, Laura K Hummers, Fredrick M Wigley, Stephen J Elledge, Livia Casciola-Rosen
INTRODUCTION: Prior studies have demonstrated an increased risk of cancer-associated scleroderma in patients with RNA polymerase III (POL) autoantibodies and in patients negative for anti-centromere (CENP), anti-topoisomerase-1 (TOPO), and anti-POL antibodies (referred to as CENP/TOPO/POL (CTP)-Negative). In a recent study of 16 CTP-negative scleroderma patients with coincident cancer, we found that 25% had autoantibodies to RNPC3, a member of the minor spliceosome complex. In this investigation, we validated the relationship between anti-RNPC3 antibodies and cancer and examined the associated clinical phenotype in a large sample of scleroderma patients...
February 19, 2017: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/28215569/cardiac-phenotype-and-long-term-prognosis-of-arrhythmogenic-right-ventricular-cardiomyopathy-dysplasia-patients-with-late-presentation
#10
Aditya Bhonsale, Anneline S J M Te Riele, Abhishek C Sawant, Judith A Groeneweg, Cynthia A James, Brittney Murray, Crystal Tichnell, Thomas P Mast, Michelle J van der Pols, Maarten J M Cramer, Dennis Dooijes, Jeroen F van der Heijden, Harikrishna Tandri, J Peter van Tintelen, Daniel P Judge, Richard N W Hauer, Hugh Calkins
BACKGROUND: The clinical profile of Arrhythmogenic Right Ventricular Cardiomyopathy/ Dysplasia patients with late presentation (ARVC/D) is unknown. OBJECTIVE: To characterize the genotype, cardiac phenotype and long term outcomes of ARVC/D patients with late presentation (age≥ 50 years at diagnosis) METHODS: 502 patients with ARVC/D diagnosis from Johns Hopkins and Utrecht registries were studied and long term clinical outcomes ascertained. RESULTS: Late presentation was seen in 104 (21%) patients (38% PKP2 carriers) with 3% ≥ 65 years at diagnosis...
February 12, 2017: Heart Rhythm: the Official Journal of the Heart Rhythm Society
https://www.readbyqxmd.com/read/28213782/prognosis-of-residual-axillary-disease-after-neoadjuvant-chemotherapy-in-clinically-node-positive-breast-cancer-patients-isolated-tumor-cells-and-micrometastases-carry-a-better-prognosis-than-macrometastases
#11
T J A van Nijnatten, J M Simons, M Moossdorff, L de Munck, M B I Lobbes, C C van der Pol, L B Koppert, E J T Luiten, M L Smidt
PURPOSE: The aim of this study was to compare disease-free survival (DFS) and overall survival (OS) between clinically node-positive breast cancer patients, treated with neoadjuvant chemotherapy (NAC), with axillary pathologic complete response (ypN0), residual axillary isolated tumor cells or micrometastases (ypNitc/mi), and residual axillary macrometastases (ypN1-3). METHODS: All patients diagnosed with clinically node-positive primary invasive breast cancer treated with NAC and subsequent axillary lymph node dissection between 2005 and 2008 were retrospectively analyzed...
February 17, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28213523/identification-of-regions-in-the-spt5-subunit-of-dsif-that-are-involved-in-promoter-proximal-pausing
#12
Yijun Qiu, David S Gilmour
DRB-sensitivity inducing factor (DSIF(2), or Spt4/5) is a conserved transcription elongation factor that both inhibits and stimulates transcription elongation in metazoans. In Drosophila and vertebrates, DSIF together with negative elongation factor (NELF) associates with RNA polymerase II (Pol II) during early elongation and causes Pol II to pause in the promoter proximal region of genes. The mechanism of how DSIF establishes pausing is not known. We constructed Spt5 mutant forms of DSIF and tested their capacity to restore promoter proximal pausing to DSIF-depleted Drosophila nuclear extracts...
February 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28212793/mir-634-is-a-pol-iii-dependent-intronic-microrna-regulating-alternative-polyadenylated-isoforms-of-its-host-gene-prkca
#13
Elvezia Maria Paraboschi, Giulia Cardamone, Valeria Rimoldi, Stefano Duga, Giulia Soldà, Rosanna Asselta
BACKGROUND: The protein kinase C alpha (PRKCA) gene, coding for a Th17-cell-selective kinase, shows a complex splicing pattern, with at least 2 stable alternative transcripts characterized by an alternative upstream polyadenylation site. Polymorphisms in this gene were associated with several conditions, including multiple sclerosis, asthma, schizophrenia, and cancer. The presence of a microRNA (miRNA), i.e. miR-634, within intron 15 of the PRKCA gene, suggests the intriguing possibility that this miRNA might play a role in the susceptibility to these pathologies...
February 14, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28209295/aluternative-regulation-for-gene-expression
#14
REVIEW
Ling-Ling Chen, Li Yang
Alu elements belong to the primate-specific SINE family of retrotransposons and constitute almost 11% of the human genome. Alus are transcribed by RNA polymerase (Pol) III and are inserted back into the genome with the help of autonomous LINE retroelements. Since Alu elements are preferentially located near to or within gene-rich regions, they can affect gene expression by distinct mechanisms of action at both DNA and RNA levels. In this review we focus on recent advances of how Alu elements are pervasively involved in gene regulation...
February 10, 2017: Trends in Cell Biology
https://www.readbyqxmd.com/read/28208684/a-real-time-high-performance-computation-architecture-for-multiple-moving-target-tracking-based-on-wide-area-motion-imagery-via-cloud-and-graphic-processing-units
#15
Kui Liu, Sixiao Wei, Zhijiang Chen, Bin Jia, Genshe Chen, Haibin Ling, Carolyn Sheaff, Erik Blasch
This paper presents the first attempt at combining Cloud with Graphic Processing Units (GPUs) in a complementary manner within the framework of a real-time high performance computation architecture for the application of detecting and tracking multiple moving targets based on Wide Area Motion Imagery (WAMI). More specifically, the GPU and Cloud Moving Target Tracking (GC-MTT) system applied a front-end web based server to perform the interaction with Hadoop and highly parallelized computation functions based on the Compute Unified Device Architecture (CUDA©)...
February 12, 2017: Sensors
https://www.readbyqxmd.com/read/28208357/oscillatory-pulses-and-wave-trains-in-a-bistable-reaction-diffusion-system-with-cross-diffusion
#16
Evgeny P Zemskov, Mikhail A Tsyganov, Werner Horsthemke
We study waves with exponentially decaying oscillatory tails in a reaction-diffusion system with linear cross diffusion. To be specific, we consider a piecewise linear approximation of the FitzHugh-Nagumo model, also known as the Bonhoeffer-van der Pol model. We focus on two types of traveling waves, namely solitary pulses that correspond to a homoclinic solution, and sequences of pulses or wave trains, i.e., a periodic solution. The effect of cross diffusion on wave profiles and speed of propagation is analyzed...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28206745/atomistic-molecular-dynamics-simulations-of-mitochondrial-dna-polymerase-%C3%AE-novel-mechanisms-of-function-and-pathogenesis
#17
Liliya Euro, Outi Haapanen, Tomasz Róg, Ilpo Vattulainen, Anu Suomalainen, Vivek Sharma
DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex...
February 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28198498/early-selection-of-sugarcane-using-path-analysis
#18
R P Barbosa, F Alcântara Neto, L M Gravina, G A Gravina, M G T Portela, A A C Bezerra
The aim of this study was to analyze sugarcane (Saccharum officinarum) biometric and technological data, obtained at different timepoints, using path analysis. The experiment was conducted in União, PI, Brazil, and evaluated 12 sugarcane genotypes (RB036066, RB9438, RB935744, RB021764, RB021754, RB021534, RB966229, RB977540, RB863129, and RB987935, and the varieties RB92579 and RB867515 as controls) in a randomized block design with four replications. Data were collected at six timepoints that were spaced 30 days apart (90, 120, 150, 180, 210, and 240 days)...
February 8, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28195873/niace-score-for-hepatocellular-carcinoma-patients-treated-by-surgery-or-transarterial-chemoembolization
#19
Xavier Adhoute, Guillaume Pénaranda, Jean Luc Raoul, Emilie Bollon, Bernard Pol, Yves P Letreut, Hervé Perrier, Olivier Bayle, Olivier Monnet, Patrick Beaurain, Cyril Muller, Jean Hardwigsen, Gaëlle Lefolgoc, Paul Castellani, Jean P Bronowicki, Marc Bourlière
BACKGROUND AND AIMS: Hepatocellular carcinoma (HCC) prognostic scores could be useful in addition to the Barcelona Clinic Liver Cancer (BCLC) system to clarify patient prognosis and guide treatment decision. The NIACE (tumor Nodularity, Infiltrative nature of the tumor, serum Alpha-fetoprotein level, Child-Pugh stage, ECOG performance status) score distinguishes different prognosis groups among BCLC A, B, and C HCC patients. Our aims are to evaluate the NIACE score and its additive value in two HCC cohorts treated either by surgery or by chemoembolization, and then according to the BCLC recommendations...
February 13, 2017: European Journal of Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28192614/cone-beam-ct-based-adaptive-planning-improves-permanent-prostate-brachytherapy-dosimetry-an-analysis-of-1266-patients
#20
Hendrik Westendorp, Carel J Hoekstra, Jos J Immerzeel, Sandrine M G van de Pol, Charles G H J Niël, Robert A J Kattevilder, Tonnis T Nuver, André W Minken, Marinus A Moerland
PURPOSE: To evaluate adaptive planning for permanent prostate brachytherapy and to identify the prostate regions that needed adaptation. METHODS AND MATERIALS: After the implantation of stranded seeds, using real-time intraoperative planning, a transrectal ultrasound (TRUS)-scan was obtained and contoured. The positions of seeds were determined on a C-arm cone-beam Computed Tomography (CBCT)-scan. The CBCT-scan was registered to the TRUS-scan using fiducial gold markers...
February 13, 2017: Medical Physics
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