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Ingrid Guilvout, Sébastien Brier, Mohamed Chami, Véronique Hourdel, Olivera Francetic, Anthony P Pugsley, Julia Chamot-Rooke, Gerard H M Huysmans
Members of a group of multimeric secretion pores that assemble independently of any known membrane-embedded insertase in Gram-negative bacteria fold into a prepore before membrane-insertion occurs. The mechanisms and the energetics that drive the folding of these proteins are poorly understood. Here, equilibrium unfolding and hydrogen/deuterium exchange monitored by mass spectrometry indicated that a loss of 4-5 kJ/mol/protomer in the N3-domain that is peripheral to the membrane-spanning C-domain in the dodecameric secretin PulD, the founding member of this class, prevents pore formation by destabilizing the prepore into a poorly structured dodecamer as visualized by electron microscopy...
November 30, 2016: Journal of Biological Chemistry
Syed Ali Rizvi, Fred Usoh, Anil Hingorani, Eleanor Iadgarova, Pamela Boniscavage, Justin Eisenberg, Enrico Ascher, Natalie Marks
OBJECTIVE: Delayed maturation of arteriovenous fistulae (AVF) among patients who require hemodialysis (HD) can lead to catheter sepsis with its resultant morbidity and mortality. Some have proposed that sequential balloon-assisted maturation (BAM) may accelerate the maturation times of these accesses. On the other hand, serial balloon angioplasty of normal vein may result in stenosis and delay maturation. Although the safety of BAM has been shown, direct comparison to non-matured AVF has not been explored...
November 26, 2016: Annals of Vascular Surgery
Locedie Mansueto, Roven Rommel Fuentes, Frances Nikki Borja, Jeffery Detras, Juan Miguel Abriol-Santos, Dmytro Chebotarov, Millicent Sanciangco, Kevin Palis, Dario Copetti, Alexandre Poliakov, Inna Dubchak, Victor Solovyev, Rod A Wing, Ruaraidh Sackville Hamilton, Ramil Mauleon, Kenneth L McNally, Nickolai Alexandrov
We describe updates to the Rice SNP-Seek Database since its first release. We ran a new SNP-calling pipeline followed by filtering that resulted in complete, base, filtered and core SNP datasets. Besides the Nipponbare reference genome, the pipeline was run on genome assemblies of IR 64, 93-11, DJ 123 and Kasalath. New genotype query and display features are added for reference assemblies, SNP datasets and indels. JBrowse now displays BAM, VCF and other annotation tracks, the additional genome assemblies and an embedded VISTA genome comparison viewer...
November 29, 2016: Nucleic Acids Research
Sumit Bam Shrestha, Qing Song
Training a Spiking Neural Network using SpikeProp and its derivatives faces stability issues. Surges, marked by a sudden rise in learning cost, are a common occurrence during the learning process. They disrupt the learning process and often destabilize the process resulting in failure. A proper learning rate, which is neither too small nor too big, is important to minimize surges. Furthermore, external disturbances due to imperfection in sample data as well as internal disturbances are additional destabilizing source during the learning process...
November 8, 2016: Neural Networks: the Official Journal of the International Neural Network Society
Daniela Ciumac, Richard A Campbell, Hai Xu, Luke A Clifton, Arwel V Hughes, John R P Webster, Jian R Lu
Many antimicrobial peptides (AMPs) target bacterial membranes and they kill bacteria by causing structural disruptions. One of the fundamental issues however lies in the selective responses of AMPs to different cell membranes as a lack of selectivity can elicit toxic side effects to mammalian host cells. A key difference between the outer surfaces of bacterial and mammalian cells is the charge characteristics. We report a careful study of the binding of one of the representative AMPs, with the general sequence G(IIKK)4I-NH2 (G4), to the spread lipid monolayers of DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) and DPPG (1,2-dipalmitoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (sodium salt)) mimicking the charge difference between them, using the combined measurements from Langmuir trough, Brewster angle microscopy (BAM) and neutron reflection (NR)...
November 3, 2016: Colloids and Surfaces. B, Biointerfaces
Raffaele Spanò, Anita Muraglia, Maria R Todeschi, Marta Nardini, Paolo Strada, Ranieri Cancedda, Maddalena Mastrogiacomo
Chronic skin ulcers, consequence of diabetes and other pathological conditions, heavily compromise the patients' life quality and represent a high and constantly growing cost for National Health Services. Autologous Platelet Rich Plasma (PRP), has been proposed to treat these lesions. The absence of guidelines for the PRP production and the need of a fresh preparation for each treatment lead us to develop a protocol for the production of an allogenic PRP based bioactive membrane (BAM), standardized for platelet concentration and growth factor release...
November 13, 2016: Journal of Tissue Engineering and Regenerative Medicine
Jeremy Bakelar, Susan K Buchanan, Nicholas Noinaj
The β-barrel assembly machinery (BAM) is a multicomponent complex responsible for the biogenesis of β-barrel outer membrane proteins (OMPs) in Gram-negative bacteria, with conserved systems in both mitochondria and chloroplasts. Given its importance in the integrity of the outer membrane and in the assembly of surface exposed virulence factors, BAM is an attractive therapeutic target against pathogenic bacteria, particularly multidrug-resistant strains. While the mechanism for how BAM functions remains elusive, previous structural studies have described each of the individual components of BAM, offering only a few clues to how the complex functions...
November 14, 2016: FEBS Journal
Takeshi Ogasawara, Yinhe Cheng, Tzy-Hwa Kathy Tzeng
This paper introduces a high-throughput software tool framework called sam2bam that enables users to significantly speed up pre-processing for next-generation sequencing data. The sam2bam is especially efficient on single-node multi-core large-memory systems. It can reduce the runtime of data pre-processing in marking duplicate reads on a single node system by 156-186x compared with de facto standard tools. The sam2bam consists of parallel software components that can fully utilize multiple processors, available memory, high-bandwidth storage, and hardware compression accelerators, if available...
2016: PloS One
Cédric Peleman, Michael Camilleri, Irene Busciglio, Duane Burton, Leslie Donato, Alan R Zinsmeister
: bile acid malabsorption (BAM). BAs are passively absorbed to a different extent along the mammalian colon, so that levels are lower in the feces than in proximal colon. Our aim was to explore associations among total, primary, and secretory BA in stool and colonic transit in patients with irritable bowel syndrome-diarrhea (IBS-D) without overt BAM. METHODS: In a cross-sectional observational study of 116 patients with IBS-D recruited from local communities in Minnesota, we measured total and individual main fecal BA excretion, fecal fat and fecal weight over 48 hrs, fasting serum levels of C4 (surrogate for BA synthesis), and overall colonic transit by scintigraphy (geometric center at 24 hrs and 48 hrs)...
November 14, 2016: Clinical Gastroenterology and Hepatology
Ellen M Adams, Dominique Verreault, Thilina Jayarathne, Richard E Cochran, Elizabeth A Stone, Heather C Allen
Transition metals are known to be enriched in organic-coated marine aerosols, but the impact these cations have on their surface properties is not well understood. Here the effect of Zn(2+) enrichment on the surface properties of a dipalmitoylphosphatidylcholine (DPPC) monolayer was investigated and compared to that of the alkaline earth metal Sr(2+), an ion not enriched in aerosols. Phase behavior of the DPPC film on concentrated aqueous solutions was probed with surface pressure-area isotherms while domain morphology was monitored with Brewster angle microscopy (BAM)...
November 30, 2016: Physical Chemistry Chemical Physics: PCCP
Jia Li, Wenguang Wang, Jiuzhi Li, Mulati Rexiati, Henqing An, Feng Wang, Yujie Wang
BACKGROUND: Hair follicle stem cells (HFSCs) were reported to have multidirectional differentiation ability and could be differentiated into melanocytes, keratin cells, smooth muscle cells, and neurons. However, the functionality of HFSCs in bladder tissue regeneration is unknown. METHODS: This study was conducted to build HFSCs vs bladder acellular matrix (BAM) complexes (HFSCs-BAM complexes) in vitro and evaluated whether HFSCs have well biocompatibility with BAM...
November 2016: Medicine (Baltimore)
Falko O Rottke, Burkhard Schulz, Klaus Richau, Karl Kratz, Andreas Lendlein
The applicability of nulling-based ellipsometric mapping as a complementary method next to Brewster angle microscopy (BAM) and imaging ellipsometry (IE) is presented for the characterization of ultrathin films at the air-water interface. First, the methodology is demonstrated for a vertically nonmoving Langmuir layer of star-shaped, 4-arm poly(ω-pentadecalactone) (PPDL-D4). Using nulling-based ellipsometric mapping, PPDL-D4-based inhomogeneously structured morphologies with a vertical dimension in the lower nm range could be mapped...
2016: Beilstein Journal of Nanotechnology
L Hu, L M Ma, S Zheng, X He, H Wang, E W Brown, T S Hammack, G Zhang
Isothermal amplification assay is a novel simple detection technology that amplifies DNA with high speed, efficiency, and specificity under isothermal conditions. The objective of this study was to evaluate the effectiveness of the 3M Molecular Detection System (MDS) and ANSR Pathogen Detection System (PDS) for the detection of Salmonella in egg products as compared to the Food and Drug Administration's Bacteriological Analytical Manual (BAM) culture method and a modified culture method (3M MDS and ANSR PDS preferred method)...
November 2, 2016: Poultry Science
Mansour Nazari, Mohsen Hajizadeh
BACKGROUND: Scorpions are arthropods of medical importance which are classified in Arachnida and commonly found in hot and dry environments. Notably, no extensive study has been conducted in Bam County in relation to research involving scorpions. METHODS: The study was piloted from May to November 2013 in the identification of scorpion fauna and epidemiological survey of scorpions sting cases were completed from April 2008 to March 2012. Scorpion specimens were collected at night using UV light...
June 30, 2016: Global Journal of Health Science
Takfarinas Kentache, Ahmed Ben Abdelkrim, Thierry Jouenne, Emmanuelle De, Julie Hardouin
Since several decades, many bacteria, among which A. baumannii, have shown their ability to colonize the upper surface of static liquids, forming a biofilm at the air-liquid interface named pellicle. Despite the ubiquity of these pellicles in both natural and artificial environments, few studies have investigated this biofilm type. The present data set provides the first description of the whole proteome of A. baumannii cells grown as pellicle, using a label-free mass spectrometry approach. Results accord with the general findings reporting that sessile bacteria are far more resistant to detrimental conditions than their planktonic counterparts, by the accumulation of stress proteins...
October 31, 2016: Molecular & Cellular Proteomics: MCP
Rujuta A Bam, Derek Hansen, Alivelu Irrinki, Andrew Mulato, Gregg S Jones, Joseph Hesselgesser, Christian R Frey, Tomas Cihlar, Stephen R Yant
GS-9620 is a potent and selective oral Toll-like receptor 7 (TLR7) agonist that directly activates plasmacytoid dendritic cells (pDCs). GS-9620 suppressed hepatitis B virus (HBV) in animal models of chronic infection and transiently activated HIV expression ex vivo in latently-infected peripheral blood mononuclear cells (PBMCs) from virally suppressed patients. Currently, GS-9620 is under clinical evaluation for treating chronic HBV infection and for reducing latent reservoirs in virally-suppressed HIV-infected patients...
October 31, 2016: Antimicrobial Agents and Chemotherapy
Zhicong Huang, Erman Ayday, Huang Lin, Raeka S Aiyar, Adam Molyneaux, Zhenyu Xu, Jacques Fellay, Lars M Steinmetz, Jean-Pierre Hubaux
In clinical genomics, the continuous evolution of bioinformatic algorithms and sequencing platforms makes it beneficial to store patients' complete aligned genomic data in addition to variant calls relative to a reference sequence. Due to the large size of human genome sequence data files (varying from 30GB to 200GB depending on coverage), two major challenges facing genomics laboratories are the costs of storage and the efficiency of the initial data processing. In addition, privacy of genomic data is becoming an increasingly serious concern; yet no standard data storage solutions exist that enable compression, encryption, and selective retrieval...
October 27, 2016: Genome Research
Uma R Chandran, Olga P Medvedeva, M Michael Barmada, Philip D Blood, Anish Chakka, Soumya Luthra, Antonio Ferreira, Kim F Wong, Adrian V Lee, Zhihui Zhang, Robert Budden, J Ray Scott, Annerose Berndt, Jeremy M Berg, Rebecca S Jacobson
BACKGROUND: The Cancer Genome Atlas Project (TCGA) is a National Cancer Institute effort to profile at least 500 cases of 20 different tumor types using genomic platforms and to make these data, both raw and processed, available to all researchers. TCGA data are currently over 1.2 Petabyte in size and include whole genome sequence (WGS), whole exome sequence, methylation, RNA expression, proteomic, and clinical datasets. Publicly accessible TCGA data are released through public portals, but many challenges exist in navigating and using data obtained from these sites...
2016: PloS One
Bam Paneru, Rafet Al-Tobasei, Yniv Palti, Gregory D Wiens, Mohamed Salem
Bacterial cold-water disease caused by Flavobacterium psychrophilum is one of the major causes of mortality of salmonids. Three genetic lines of rainbow trout designated as ARS-Fp-R (resistant), ARS-Fp-C (control) and ARS-Fp-S (susceptible) have significant differences in survival rate following F. psychrophilum infection. Previous study identified transcriptome differences of immune-relevant protein-coding genes at basal and post infection levels among these genetic lines. Using RNA-Seq approach, we quantified differentially expressed (DE) long non-coding RNAs (lncRNAs) in response to F...
October 27, 2016: Scientific Reports
Jonathan Yde, Stephen Keely, Qi Wu, Johan F Borg, Natalia Lajczak, Aoife O'Dwyer, Peter Dalsgaard, Robert A Fenton, Hanne B Moeller
In normal individuals, the epithelium of the colon absorbs 1.5-2 l of water a day to generate dehydrated feces. However, in the condition of bile acid malabsorption (BAM), an excess of bile acids in the colon results in diarrhea. Several studies have attempted to address the mechanisms contributing to BAM induced by various bile acids. However, none have addressed a potential dysregulation of aquaporin (AQP) water channels, which are responsible for the majority of transcellular water transport in epithelial cells, as a contributing factor to the onset of diarrhea and the pathogenesis of BAM...
2016: Frontiers in Nutrition
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