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Debora Sugiaman-Trapman, Morana Vitezic, Eeva-Mari Jouhilahti, Anthony Mathelier, Gilbert Lauter, Sougat Misra, Carsten O Daub, Juha Kere, Peter Swoboda
BACKGROUND: Evolutionarily conserved RFX transcription factors (TFs) regulate their target genes through a DNA sequence motif called the X-box. Thereby they regulate cellular specialization and terminal differentiation. Here, we provide a comprehensive analysis of all the eight human RFX genes (RFX1-8), their spatial and temporal expression profiles, potential upstream regulators and target genes. RESULTS: We extracted all known human RFX1-8 gene expression profiles from the FANTOM5 database derived from transcription start site (TSS) activity as captured by Cap Analysis of Gene Expression (CAGE) technology...
March 6, 2018: BMC Genomics
Mi-Ran Seo, Jieun Kim, Yangsoon Lee, Dong-Gyun Lim, Hyunjoo Pai
Clostridium difficile infection (CDI) is a major healthcare-associated infection. Aim of this study was to investigate the genetic relatedness of the endemic C. difficile PCR ribotype 018 strains in an institution and changes to their characteristics during five-year period. A total of 207 isolates obtained from inpatients at Hanyang University Hospital from 2009 to 2013 were analyzed using multilocus variable-number tandem-repeat analysis (MLVA). Minimum inhibitory concentrations (MICs) of several antibiotics were determined...
February 2, 2018: International Journal of Antimicrobial Agents
Laura Julien, Julie Chassagne, Cécile Peccate, Stéphanie Lorain, France Piétri-Rouxel, Olivier Danos, Sofia Benkhelifa-Ziyyat
Adeno-associated virus (AAV) transduction efficiency depends on the way in which cellular proteins process viral genomes in the nucleus. In this study, we have investigated the binding of nuclear proteins to the double stranded D (dsD) sequence of the AAV inverted terminal repeat (ITRs) by electromobility shift assay. We present here several lines of evidence that transcription factors belonging to the RFX protein family bind specifically and selectively to AAV2 and AAV1 dsD sequences. Using supershift experiments, we characterize complexes containing RFX1 homodimers and RFX1/RFX3 heterodimers...
January 9, 2018: Scientific Reports
Elizabeth A De Stasio, Katherine P Mueller, Rosemary J Bauer, Alexander J Hurlburt, Sophie A Bice, Sophie L Scholtz, Prasad Phirke, Debora Sugiaman-Trapman, Loraina A Stinson, Haili B Olson, Savannah L Vogel, Zabdiel Ek-Vazquez, Yagmur Esemen, Jessica Korzynski, Kelsey Wolfe, Bonnie N Arbuckle, He Zhang, Gaelen Lombard-Knapp, Brian P Piasecki, Peter Swoboda
Regulatory Factor X (RFX) transcription factors (TFs) are best known for activating genes required for ciliogenesis in both vertebrates and invertebrates. In humans, eight RFX TFs have a variety of tissue-specific functions, while in the worm Caenorhabditis elegans , the sole RFX gene, daf-19 , encodes a set of nested isoforms. Null alleles of daf-19 confer pleiotropic effects including altered development with a dauer constitutive phenotype, complete absence of cilia and ciliary proteins, and defects in synaptic protein maintenance...
March 2018: Genetics
Irina Sedykh, Abigail N Keller, Baul Yoon, Laura Roberson, Oleg V Moskvin, Yevgenya Grinblat
BACKGROUND: Rfx winged-helix transcription factors, best known as key regulators of core ciliogenesis, also play ciliogenesis-independent roles during neural development. Mammalian Rfx4 controls neural tube morphogenesis via both mechanisms. RESULTS: We set out to identify conserved aspects of rfx4 gene function during vertebrate development and to establish a new genetic model in which to analyze these mechanisms further. To this end, we have generated frame-shift alleles in the zebrafish rfx4 locus using CRISPR/Cas9 mutagenesis...
April 2018: Developmental Dynamics: An Official Publication of the American Association of Anatomists
Noah Dukler, Gregory T Booth, Yi-Fei Huang, Nathaniel Tippens, Colin T Waters, Charles G Danko, John T Lis, Adam Siepel
Most studies of responses to transcriptional stimuli measure changes in cellular mRNA concentrations. By sequencing nascent RNA instead, it is possible to detect changes in transcription in minutes rather than hours and thereby distinguish primary from secondary responses to regulatory signals. Here, we describe the use of PRO-seq to characterize the immediate transcriptional response in human cells to celastrol, a compound derived from traditional Chinese medicine that has potent anti-inflammatory, tumor-inhibitory, and obesity-controlling effects...
November 2017: Genome Research
Brian P Piasecki, Thomas A Sasani, Alexander T Lessenger, Nicholas Huth, Shane Farrell
Cilia are conserved cellular structures that facilitate sensory-based processes, including those required for neuronal and kidney functions. Here, we show that the human mitogen activated kinase-15 (MAPK-15) ortholog in Caenorhabditis elegans encodes a ciliary protein. A strain harboring a mutation in the catalytic site of the kinase domain results in ciliary-specific defects in tail neurons of both hermaphrodite and male worms, manifesting in dye uptake, dendrite extension, and male mating behavior defects...
July 26, 2017: Cytoskeleton
Liping Ma, Laijin Su, Hui Liu, Feng Zhao, Deqing Zhou, Delin Duan
Noroviruses are the primary pathogens associated with shellfish-borne gastroenteritis outbreaks. These viruses remain stable in oysters, suggesting an active mechanism for virus concentration. In this study, a deep RNA sequencing technique was used to analyze the transcriptome profiles of Pacific oysters at different time points after inoculation with norovirus (GII.4). We obtained a maximum of 65, 294, 698 clean sample reads. When aligned to the reference genome, the average mapping ratio of clean data was approximately 65%...
July 2017: Fish & Shellfish Immunology
Jennifer M Baker, Carli J Riester, Blair M Skinner, Austin W Newell, Wesley D Swingley, Michael T Madigan, Deborah O Jung, Marie Asao, Min Chen, Patrick C Loughlin, Hao Pan, Yuankui Lin, Yaqiong Li, Jacob Shaw, Mindy Prado, Chris Sherman, Joseph Kuo-Hsiang Tang, Robert E Blankenship, Tingting Zhao, Jeffrey W Touchman, W Matthew Sattley
Rhodoferax antarcticus is an Antarctic purple nonsulfur bacterium and the only characterized anoxygenic phototroph that grows best below 20 °C. We present here a high-quality draft genome of Rfx. antarcticus strain ANT.BR(T), isolated from an Antarctic microbial mat. The circular chromosome (3.8 Mbp) of Rfx. antarcticus has a 59.1% guanine + cytosine (GC) content and contains 4036 open reading frames. In addition, the bacterium contains a sizable plasmid (198.6 kbp, 48.4% GC with 226 open reading frames) that comprises about 5% of the total genetic content...
February 21, 2017: Microorganisms
Arushi Varshney, Laura J Scott, Ryan P Welch, Michael R Erdos, Peter S Chines, Narisu Narisu, Ricardo D'O Albanus, Peter Orchard, Brooke N Wolford, Romy Kursawe, Swarooparani Vadlamudi, Maren E Cannon, John P Didion, John Hensley, Anthony Kirilusha, Lori L Bonnycastle, D Leland Taylor, Richard Watanabe, Karen L Mohlke, Michael Boehnke, Francis S Collins, Stephen C J Parker, Michael L Stitzel
Genome-wide association studies (GWAS) have identified >100 independent SNPs that modulate the risk of type 2 diabetes (T2D) and related traits. However, the pathogenic mechanisms of most of these SNPs remain elusive. Here, we examined genomic, epigenomic, and transcriptomic profiles in human pancreatic islets to understand the links between genetic variation, chromatin landscape, and gene expression in the context of T2D. We first integrated genome and transcriptome variation across 112 islet samples to produce dense cis-expression quantitative trait loci (cis-eQTL) maps...
February 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
Ian K Quigley, Chris Kintner
Cooperative transcription factor binding at cis-regulatory sites in the genome drives robust eukaryotic gene expression, and many such sites must be coordinated to produce coherent transcriptional programs. The transcriptional program leading to motile cilia formation requires members of the DNA-binding forkhead (Fox) and Rfx transcription factor families and these factors co-localize to cilia gene promoters, but it is not clear how many cilia genes are regulated by these two factors, whether these factors act directly or indirectly, or how these factors act with specificity in the context of a 3-dimensional genome...
January 2017: PLoS Genetics
Jatinder Kumar, Amaldoss M J Newton
BACKGROUND: Inflammatory Bowel Disease (IBD) cannot be controlled easily and the recurrence is the most challenging issue for the physicians. There are various controlled and colon targeted drug delivery systems available for the treatment with limited success rate. Nanoparticles prepared by using the colon targeted polymers such as chitosan may improve the IBD due to their smaller size, unique physico chemical properties and targeting potential. OBJECTIVE: The aim of this investigation was designed to formulate and develop a colon targeted polysaccharide nanoparticles of rifaximin (RFX) by using linear polysaccharide chitosan, for the improvement of rifaximin solubility, overall therapeutic efficacy and colon targeting...
2017: Recent Patents on Inflammation & Allergy Drug Discovery
G Donders, G Bellen, F Donders, J Pinget, I Vandevelde, T Michiels, J Byamughisa
The vaginal composition of African women is more often lactobacillus-deficient compared to that of women from other areas around the world. Lactobacillus-deficient microflora is a known risk factor for serious health problems, such as preterm birth, cervix cancer, and entrapment of human immunodeficiency virus (HIV) and other sexually transmitted infections (STIs). The aim of this study was to assess the effect of local vaginal antibiotic or antiseptic treatment on abnormal vaginal flora (AVF), aerobic vaginitis (AV), and bacterial vaginosis (BV) among women in rural, semi-urban, and urban areas in Uganda, as compared to placebo...
April 2017: European Journal of Clinical Microbiology & Infectious Diseases
Kristiina Tammimies, Andrea Bieder, Gilbert Lauter, Debora Sugiaman-Trapman, Rachel Torchet, Marie-Estelle Hokkanen, Jan Burghoorn, Eero Castrén, Juha Kere, Isabel Tapia-Páez, Peter Swoboda
DYX1C1, DCDC2, and KIAA0319 are three of the most replicated dyslexia candidate genes (DCGs). Recently, these DCGs were implicated in functions at the cilium. Here, we investigate the regulation of these DCGs by Regulatory Factor X transcription factors (RFX TFs), a gene family known for transcriptionally regulating ciliary genes. We identify conserved X-box motifs in the promoter regions of DYX1C1, DCDC2, and KIAA0319 and demonstrate their functionality, as well as the ability to recruit RFX TFs using reporter gene and electrophoretic mobility shift assays...
October 2016: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
Ahmed S Saad, Abdallah M Hamdy, Fathy M Salama, Mohamed Abdelkawy
Two sensitive and accurate stability-indicating chromatographic methods were developed and validated for the determination of rafoxanide (RFX). Degradation products were identified by mass spectrometry and IR spectroscopy. The first is ultra-performance liquid chromatography method where separation was performed using acetonitrile:0.005 M potassium dihydrogen orthophosphate (pH 3.5) in a ratio of 80:20 by volume as a mobile phase using a Hypersil GOLD™ C8 column 1.9 mm (50 × 2.1 mm), UV detection was adjusted at 220 nm and the flow rate was 0...
July 1, 2016: Journal of Chromatographic Science
R Lorenzini, F Auriemma, A Fassina, E Martines, D Terranova, F Sattin
The reversed field pinch (RFP) device RFX-mod features strong internal transport barriers when the plasma accesses states with a single dominant helicity. Such transport barriers enclose a hot helical region with high confinement whose amplitude may vary from a tiny one to an amplitude encompassing an appreciable fraction of the available volume. The transition from narrow to wide thermal structures has been ascribed so far to the transport reduction that occurs when the dominant mode separatrix, which is a preferred location for the onset of stochastic field lines, disappears...
May 6, 2016: Physical Review Letters
M Zaupa, E Sartori, M Dalla Palma, F Fellin, D Marcuzzi, M Pavei, A Rizzolo
Megavolt ITER Injector Concept Advancement is the full scale prototype of the heating and current drive neutral beam injectors for ITER, to be built at Consorzio RFX (Padova). The engineering design of its components is challenging: the total heat loads they will be subjected to (expected between 2 and 19 MW), the high heat fluxes (up to 20 MW/m(2)), and the beam pulse duration up to 1 h, set demanding requirements for reliable active cooling circuits. In support of the design, the thermo-hydraulic behavior of each cooling circuit under steady state condition has been investigated by using one-dimensional models...
February 2016: Review of Scientific Instruments
M Cavenago, G Serianni, M De Muri, P Agostinetti, V Antoni, C Baltador, M Barbisan, L Baseggio, M Bigi, V Cervaro, F Degli Agostini, E Fagotti, T Kulevoy, N Ippolito, B Laterza, A Minarello, M Maniero, R Pasqualotto, S Petrenko, M Poggi, D Ravarotto, M Recchia, E Sartori, M Sattin, P Sonato, F Taccogna, V Variale, P Veltri, B Zaniol, L Zanotto, S Zucchetti
Neutral Beam Injectors (NBIs), which need to be strongly optimized in the perspective of DEMO reactor, request a thorough understanding of the negative ion source used and of the multi-beamlet optics. A relatively compact radio frequency (rf) ion source, named NIO1 (Negative Ion Optimization 1), with 9 beam apertures for a total H(-) current of 130 mA, 60 kV acceleration voltage, was installed at Consorzio RFX, including a high voltage deck and an X-ray shield, to provide a test bench for source optimizations for activities in support to the ITER NBI test facility...
February 2016: Review of Scientific Instruments
M Barbisan, C Baltador, B Zaniol, M Cavenago, U Fantz, R Pasqualotto, G Serianni, L Vialetto, D Wünderlich
NIO1 (Negative Ion Optimization 1) is a compact and flexible radio frequency H(-) ion source, developed by Consorzio RFX and INFN-LNL. The aim of the experimentation on NIO1 is the optimization of both the production of negative ions and their extraction and beam optics. In the initial phase of its commissioning, NIO1 was operated with nitrogen, but now the source is regularly operated also with hydrogen. To evaluate the source performances, an optical emission spectroscopy diagnostic was installed. The system includes a low resolution spectrometer in the spectral range of 300-850 nm and a high resolution (50 pm) one, to study, respectively, the atomic and the molecular emissions in the visible range...
February 2016: Review of Scientific Instruments
V Variale, M Cavenago, P Agostinetti, P Sonato, L Zanotto
Commercial viability of thermonuclear fusion power plants depends also on minimizing the recirculation power used to operate the reactor. The neutral beam injector (NBI) remains one of the most important method for plasma heating and control. For the future fusion power plant project DEMO, a NBI wall plug efficiency at least of 0.45 is required, while efficiency of present NBI project is about 0.25. The D(-) beam from a negative ion source is partially neutralized by a gas cell, which leaves more than 40% of energy in residual beams (D(-) and D(+)), so that an ion beam energy recovery system can significantly contribute to optimize efficiency...
February 2016: Review of Scientific Instruments
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