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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
Maria John Newton, Jatinder Kumar
BACKGROUND: Inflammatory Bowel Disease ( IBD) can't be controlled easily and the recurrence is most challenging issue for the physicians. There are various controlled and colon targeted drug delivery sytems are 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 smaler 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...
December 30, 2016: 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
Peter Walentek
Cilia play a plethora of roles in normal development and homeostasis as well as in disease. Their involvement in cell signalling processes and ability to inhibit cell cycle progression make them especially interesting subjects of investigation in the context of tumour formation and malignancy. Several key transcription factors regulate the transcriptional programme in cilia formation and some of these, eg RFX factors and FOXJ1, are implicated in cancer formation. Furthermore, RFX factors and FOXJ1 are increasingly being explored for their potential as markers to diagnose, classify and predict the outcome of cancers in patients, including recent work published in this journal on aggressive ependymoma and choroid plexus tumours...
May 2016: Journal of Pathology
Yves B Beaulieu, Jorge A Leon Machado, Sylvain Ethier, Luc Gaudreau, Viktor Steimle
Multiple relationships between ubiquitin-proteasome mediated protein turnover and transcriptional activation have been well documented, but the underlying mechanisms are still poorly understood. One way to induce degradation is via ubiquitination of the N-terminal α-amino group of proteins. The major histocompatibility complex (MHC) class II transactivator CIITA is the master regulator of MHC class II gene expression and we found earlier that CIITA is a short-lived protein. Using stable and transient transfections of different CIITA constructs into HEK-293 and HeLa cell lines, we show here that the extreme N-terminal end of CIITA isoform III induces both rapid degradation and transactivation...
2016: PloS One
Yujian Wu, Xiangjing Hu, Zhen Li, Min Wang, Sisi Li, Xiuxia Wang, Xiwen Lin, Shangying Liao, Zhuqiang Zhang, Xue Feng, Si Wang, Xiuhong Cui, Yanling Wang, Fei Gao, Rex A Hess, Chunsheng Han
The regulatory factor X (RFX) family of transcription factors is crucial for ciliogenesis throughout evolution. In mice, Rfx1-4 are highly expressed in the testis where flagellated sperm are produced, but the functions of these factors in spermatogenesis remain unknown. Here, we report the production and characterization of the Rfx2 knockout mice. The male knockout mice were sterile due to the arrest of spermatogenesis at an early round spermatid step. The Rfx2-null round spermatids detached from the seminiferous tubules, forming large multinucleated giant cells that underwent apoptosis...
February 8, 2016: Scientific Reports
Ivona Pandrea, Cuiling Xu, Jennifer L Stock, Daniel N Frank, Dongzhu Ma, Benjamin B Policicchio, Tianyu He, Jan Kristoff, Elaine Cornell, George S Haret-Richter, Anita Trichel, Ruy M Ribeiro, Russell Tracy, Cara Wilson, Alan L Landay, Cristian Apetrei
Increased chronic immune activation and inflammation are hallmarks of HIV/SIV infection and are highly correlated with progression to AIDS and development of non-AIDS comorbidities, such as hypercoagulability and cardiovascular disease. Intestinal dysfunction resulting in microbial translocation has been proposed as a lead cause of systemic immune activation and hypercoagulability in HIV/SIV infection. Our goal was to assess the biological and clinical impact of a therapeutic strategy designed to reduce microbial translocation through reduction of the microbial content of the intestine (Rifaximin-RFX) and of gut inflammation (Sulfasalazine-SFZ)...
January 2016: PLoS Pathogens
Ran Elkon, Beatrice Milon, Laura Morrison, Manan Shah, Sarath Vijayakumar, Manoj Racherla, Carmen C Leitch, Lorna Silipino, Shadan Hadi, Michèle Weiss-Gayet, Emmanuèle Barras, Christoph D Schmid, Aouatef Ait-Lounis, Ashley Barnes, Yang Song, David J Eisenman, Efrat Eliyahu, Gregory I Frolenkov, Scott E Strome, Bénédicte Durand, Norann A Zaghloul, Sherri M Jones, Walter Reith, Ronna Hertzano
Sensorineural hearing loss is a common and currently irreversible disorder, because mammalian hair cells (HCs) do not regenerate and current stem cell and gene delivery protocols result only in immature HC-like cells. Importantly, although the transcriptional regulators of embryonic HC development have been described, little is known about the postnatal regulators of maturating HCs. Here we apply a cell type-specific functional genomic analysis to the transcriptomes of auditory and vestibular sensory epithelia from early postnatal mice...
October 15, 2015: Nature Communications
A Branchini, M Baroni, F Burini, F Puzzo, F Nicolosi, R Mari, D Gemmati, F Bernardi, M Pinotti
BACKGROUND: The homologous coagulation factor X (FX), VII (FVII), IX (FIX) and protein C (PC) display striking differences in the carboxyl-terminus, with that of FX being the most extended. This region is essential for FVII, FIX and PC secretion. OBJECTIVES: To provide experimental evidence for the role of the FX carboxyl-terminus. METHODS: Recombinant FX (rFX) variants were expressed in multiple eukaryotic cell systems. Protein and activity levels were evaluated by ELISA, coagulant and amidolytic assays...
August 2015: Journal of Thrombosis and Haemostasis: JTH
Radha Senthilkumar, Gomathi Nandagopal, Daphne Ronald
The verbose nature of XML has been mulled over again and again and many compression techniques for XML data have been excogitated over the years. Some of the techniques incorporate support for querying the XML database in its compressed format while others have to be decompressed before they can be queried. XML compression in which querying is directly supported instantaneously with no compromise over time is forced to compromise over space. In this paper, we propose the compressor, QRFXFreeze, which not only reduces the space of storage but also supports efficient querying...
2015: TheScientificWorldJournal
Y Wu, J-F Zhang, T Xu, L Xu, J Qiao, F Liu, H Shan, X Jiang
BACKGROUND: In this study, we aimed to discover potential gene targets for treating childhood asthmatics. METHODS: With the microarray data downloaded from Gene Expression Omnibus (GEO) database, we explored the common differentially expressed genes (DEGs) in children with severe asthma and mild asthma (SA vs. MA) or healthy controls (SA vs. HC). Then we performed hierarchical clustering, function and pathway enrichment analysis for the common DEGs. RESULTS: A total of 81 genes were identified to be differentially expressed in SA vs...
January 2016: Allergologia et Immunopathologia
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