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https://www.readbyqxmd.com/read/28630866/cnndel-calling-structural-variations-on-low-coverage-data-based-on-convolutional-neural-networks
#1
Jing Wang, Cheng Ling, Jingyang Gao
Many structural variations (SVs) detection methods have been proposed due to the popularization of next-generation sequencing (NGS). These SV calling methods use different SV-property-dependent features; however, they all suffer from poor accuracy when running on low coverage sequences. The union of results from these tools achieves fairly high sensitivity but still produces low accuracy on low coverage sequence data. That is, these methods contain many false positives. In this paper, we present CNNdel, an approach for calling deletions from paired-end reads...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28630161/insertion-of-proteins-and-lipopolysaccharide-into-the-bacterial-outer-membrane
#2
REVIEW
Istvan Botos, Nicholas Noinaj, Susan K Buchanan
The bacterial outer membrane contains phospholipids in the inner leaflet and lipopolysaccharide (LPS) in the outer leaflet. Both proteins and LPS must be frequently inserted into the outer membrane to preserve its integrity. The protein complex that inserts LPS into the outer membrane is called LptDE, and consists of an integral membrane protein, LptD, with a separate globular lipoprotein, LptE, inserted in the barrel lumen. The protein complex that inserts newly synthesized outer-membrane proteins (OMPs) into the outer membrane is called the BAM complex, and consists of an integral membrane protein, BamA, plus four lipoproteins, BamB, C, D and E...
August 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28628887/determining-concentrations-of-elements-with-different-reaction-channels-in-photon-activation
#3
Z J Sun, K Okafor, S Isa
In photon activation, same element may be activated by the bremsstrahlung beam through different nuclear reaction channels and produce different radioisotopes. These radioisotopes follow their own decay schemes and generate characteristic gamma rays. This phenomenon usually is an interference in spectra analysis, but it also offers a theoretical feasibility to determine the concentration of one element through different reaction channels. To realize this theoretical feasibility, we conducted series of photon activation experiments with sample and reference of known concentrations...
June 13, 2017: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/28616645/groundwater-contamination-with-2-6-dichlorobenzamide-bam-and-perspectives-for-its-microbial-removal
#4
REVIEW
Lea Ellegaard-Jensen, Benjamin Horemans, Bart Raes, Jens Aamand, Lars Hestbjerg Hansen
The pesticide metabolite 2,6-dichlorobenzamide (BAM) is very persistent in both soil and groundwater and has become one of the most frequently detected groundwater micropollutants. BAM is not removed by the physico-chemical treatment techniques currently used in drinking water treatment plants (DWTP); therefore, if concentrations exceed the legal threshold limit, it represents a sizeable problem for the stability and quality of drinking water production, especially in places that depend on groundwater for drinking water...
June 14, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28607033/perception-of-root-active-cle-peptides-requires-coryne-function-in-the-phloem-vasculature
#5
Ora Hazak, Benjamin Brandt, Pietro Cattaneo, Julia Santiago, Antia Rodriguez-Villalon, Michael Hothorn, Christian S Hardtke
Arabidopsis root development is orchestrated by signaling pathways that consist of different CLAVATA3/EMBRYO SURROUNDING REGION (CLE) peptide ligands and their cognate CLAVATA (CLV) and BARELY ANY MERISTEM (BAM) receptors. How and where different CLE peptides trigger specific morphological or physiological changes in the root is poorly understood. Here, we report that the receptor-like protein CLAVATA 2 (CLV2) and the pseudokinase CORYNE (CRN) are necessary to fully sense root-active CLE peptides. We uncover BAM3 as the CLE45 receptor in the root and biochemically map its peptide binding surface...
June 12, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28584130/bam-and-otu-can-regulate-stem-cell-fate-by-stabilizing-cyclin-a
#6
Juliette Mathieu, Jean-René Huynh
No abstract text is available yet for this article.
June 5, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28569500/extreme-dynamics-in-the-bama-%C3%AE-barrel-seam
#7
Pamela Arden Doerner, Marcelo C Sousa
BamA is an essential component of the β-barrel assembly machine (BAM) that is responsible for insertion and folding of β-barrel outer membrane proteins (OMPs) in Gram-negative bacteria. BamA is an OMP itself, and its β-barrel transmembrane domain is thought to catalyze OMP insertion and folding, although the molecular mechanism remains poorly understood. Crystal structures of BamA and complementary molecular dynamics simulations have shown that its β-barrel seam (the interface between the first and last barrel strands) is destabilized...
June 12, 2017: Biochemistry
https://www.readbyqxmd.com/read/28561100/energetic-%C3%AF-conjugated-vinyl-bridged-triazoles-a-thermally-stable-and-insensitive-heterocyclic-cation
#8
Qing Ma, Ya Chen, Longyu Liao, Huanchang Lu, Guijuan Fan, Jinglun Huang
A new family of vinyl bridge 1,1'-(ethane-5-yl)-bis(3,4-diamino-1,2,4-triazolium) salts were explored as novel structural energetic materials. These new salts were further characterized by elemental analysis, infrared and multinuclear NMR spectra. Structural confirmation of nine salts such as 4-11 and 14 was supported by single-crystal X-ray diffraction. Theoretical investigations associated with heats of formation and detonation performance were carried out by employing the Gaussian 09 program and the EXPLO5 V6...
June 13, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28541542/reducing-stock-outs-of-essential-tuberculosis-medicines-a-system-dynamics-modelling-approach-to-supply-chain-management
#9
L Bam, Z M McLaren, E Coetzee, K H von Leipzig
The under-performance of supply chains presents a significant hindrance to disease control in developing countries. Stock-outs of essential medicines lead to treatment interruption which can force changes in patient drug regimens, drive drug resistance and increase mortality. This study is one of few to quantitatively evaluate the effectiveness of supply chain policies in reducing shortages and costs. This study develops a systems dynamics simulation model of the downstream supply chain for amikacin, a second-line tuberculosis drug using 10 years of South African data...
May 24, 2017: Health Policy and Planning
https://www.readbyqxmd.com/read/28540355/analytical-data-of-synthesized-deuterated-isopropyl-myristate-and-data-about-the-influence-of-ipm-ipmdeut-on-the-thermodynamics-and-morphology-of-2d-stratum-corneum-models
#10
J S L Oliveira, S Lange, B Dobner, G Brezesinski
The data in this article shows the effect of isopropyl myristate (IPM) on a 2D Stratum Corneum lipid model. In the first part, the analytical characterization of the synthesized deuterated isopropyl myristate is given. Then a BAM image of the pure Stratum Corneum model used is shown and a dataset of surface-pressure - area isotherms considering various ratios of deuterated and non-deuterated IPM and the Stratum Corneum model mixture is provided. Assuming that after the plateau in the isotherm the area per molecule corresponds only to the Stratum Corneum model (squeezing out of IPM), the value of the area will correspond to the percentage of these lipids in the mixture when considering the pure SC model...
June 2017: Data in Brief
https://www.readbyqxmd.com/read/28532019/characterization-of-bladder-acellular-matrix-hydrogel-with-inherent-bioactive-factors
#11
Dan Jiang, Jianwen Huang, Huili Shao, Xuechao Hu, Lujie Song, Yaopeng Zhang
Bladder acellular matrix (BAM) hydrogel may have great potential in tissue engineering due to outstanding biocompatibility and the presence of inherent bioactive factors in BAM. In this study, we prepared the BAM hydrogel by the method of enzymatic solubilization with pepsin and characterize the microrheological properties of the BAM precursor solution. The structures of the BAM hydrogel were characterized by scanning electron microscope (SEM), Fourier-transform infrared spectroscopy (FTIR) and differential scanning calorimetry (DSC)...
August 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28498947/aminobacter-sp-msh1-invades-sand-filter-community-biofilms-while-retaining-2-6-dichlorobenzamide-degradation-functionality-under-c-and-n-limiting-conditions
#12
Benjamin Horemans, Joke Vandermaesen, Aswini Sekhar, Caroline Rombouts, Johan Hofkens, Lynn Vanhaecke, Dirk Springael
Aminobacter sp. MSH1 is of interest for bioaugmentation of biofiltration units in drinking water treatment plants (DWTPs) due to its ability to degrade the groundwater micropollutant 2,6-dichlorobenzamide (BAM). Using a continuous flow chamber biofilm model, MSH1 was previously shown to colonize surfaces and degrade BAM at trace concentrations as low as 1 μg/L under the oligotrophic conditions found in DWTPs. In DWTP filtration units, MSH1 has to compete with the resident biofilm microbiota for space and nutrients...
June 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28484262/bamclipper-removing-primers-from-alignments-to-minimize-false-negative-mutations-in-amplicon-next-generation-sequencing
#13
Chun Hang Au, Dona N Ho, Ava Kwong, Tsun Leung Chan, Edmond S K Ma
Amplicon-based next-generation sequencing (NGS) has been widely adopted for genetic variation detection in human and other organisms. Conventional data analysis paradigm includes primer trimming before read mapping. Here we introduce BAMClipper that removes primer sequences after mapping original sequencing reads by soft-clipping SAM/BAM alignments. Mutation detection accuracy was affected by the choice of primer handling approach based on real NGS datasets of 7 human peripheral blood or breast cancer tissue samples with known BRCA1/BRCA2 mutations and >130000 simulated NGS datasets with unique mutations...
May 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28484036/bam-dependent-deubiquitinase-complex-can-disrupt-germ-line-stem-cell-maintenance-by-targeting-cyclin-a
#14
Shanming Ji, Chaoyi Li, Lin Hu, Kehui Liu, Jie Mei, Yuewan Luo, Yi Tao, Zongping Xia, Qinmiao Sun, Dahua Chen
Drosophila germ-line stem cells (GSCs) provide an excellent model to study the regulatory mechanisms of stem cells in vivo. Bag of marbles (bam) has been demonstrated to be necessary and sufficient to promote GSC and cystoblast differentiation. Despite extensive investigation of its regulation and genetic functions, the biochemical nature of the Bam protein has been unknown. Here, we report that Bam is an ubiquitin-associated protein and controls the turnover of cyclin A (CycA). Mechanistically, we found that Bam associated with Otu to form a deubiquitinase complex that stabilized CycA by deubiquitination, thus providing a mechanism to explain how ectopic expression of Bam in GSCs promotes differentiation...
May 8, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28451712/studies-of-lipid-monolayers-prepared-from-native-and-model-plant-membranes-in-their-interaction-with-zearalenone-and-its-mixture-with-selenium-ions
#15
Barbara Gzyl-Malcher, Maria Filek, Elżbieta Rudolphi-Skórska, Apolonia Sieprawska
The impact of zearalenone and selenate ions on the monolayers of 1,2-dipalmitoyl-phosphatidylcholine (DPPC), 1,2-dipalmitoyl-3-trimethylammonium-propane (DPTAP), and the lipid mixtures (phospholipids and galactolipids) extracted from wheat plasmalemma has been studied using Langmuir trough technique and Brewster angle microscopy (BAM). The zearalenone is a mycotoxin that exerts toxic effects on the cells of plants and animals. Monolayers' properties were characterized by surface pressure (π)-molecular area (A) isotherms...
April 27, 2017: Journal of Membrane Biology
https://www.readbyqxmd.com/read/28441530/aubergine-controls-germline-stem-cell-self-renewal-and-progeny-differentiation-via-distinct-mechanisms
#16
Xing Ma, Xiujuan Zhu, Yingying Han, Benjamin Story, Trieu Do, Xiaoqing Song, Su Wang, Ying Zhang, Marco Blanchette, Madelaine Gogol, Kate Hall, Allison Peak, Perera Anoja, Ting Xie
Piwi family protein Aubergine (Aub) maintains genome integrity in late germ cells of the Drosophila ovary through Piwi-associated RNA-mediated repression of transposon activities. Although it is highly expressed in germline stem cells (GSCs) and early progeny, it remains unclear whether it plays any roles in early GSC lineage development. Here we report that Aub promotes GSC self-renewal and GSC progeny differentiation. RNA-iCLIP results show that Aub binds the mRNAs encoding self-renewal and differentiation factors in cultured GSCs...
April 24, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28381774/interfacial-properties-of-binary-systems-composed-of-dppc-and-perfluorinated-double-long-chain-salts-with-divalent-counterions-of-separate-electric-charge
#17
Riku Kato, Hiromichi Nakahara, Osamu Shibata
The interfacial behavior of binary monolayers of 1,1'-(1,ω-alkanediyl)-bispyridinium perfluorotetradecanecarboxylate (CnBP(FC14)2, n = 2, 6, or 10) and dipalmitoylphosphatidylcholine (DPPC) was studied using surface pressure (π)-area (A) and surface potential (ΔV)-A isotherm measurements and morphological observations. In a previous study, we showed that the spacer moieties of C2BP(FC14)2 and C6BP(FC14)2 are completely dissociated after spreading on 0.15 M NaCl, whereas the C10BP(FC14)2 spacer moieties do not dissociate in the monolayer state...
April 4, 2017: Journal of Oleo Science
https://www.readbyqxmd.com/read/28369524/ngscheckmate-software-for-validating-sample-identity-in-next-generation-sequencing-studies-within-and-across-data-types
#18
Sejoon Lee, Soohyun Lee, Scott Ouellette, Woong-Yang Park, Eunjung A Lee, Peter J Park
In many next-generation sequencing (NGS) studies, multiple samples or data types are profiled for each individual. An important quality control (QC) step in these studies is to ensure that datasets from the same subject are properly paired. Given the heterogeneity of data types, file types and sequencing depths in a multi-dimensional study, a robust program that provides a standardized metric for genotype comparisons would be useful. Here, we describe NGSCheckMate, a user-friendly software package for verifying sample identities from FASTQ, BAM or VCF files...
March 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28368610/bax-activation-blocks-self-renewal-and-induces-apoptosis-of-human-glioblastoma-stem-cells
#19
Simona Daniele, Deborah Pietrobono, Barbara Costa, Mariateresa Giustiniano, Valeria La Pietra, Chiara Giacomelli, Giuseppe La Regina, Romano Silvestri, Sabrina Taliani, Maria Letizia Trincavelli, Federico Da Settimo, Ettore Novellino, Claudia Martini, Luciana Marinelli
Glioblastoma (GBM) is characterized by a poor response to conventional chemotherapeutic agents, attributed to the insurgence of drug resistance mechanisms and to the presence of a subpopulation of glioma stem cells (GSCs). GBM cells and GSCs present, among others, an overexpression of antiapoptotic proteins and an inhibition of pro-apoptotic ones, which help to escape apoptosis. Among pro-apoptotic inducers, the Bcl-2 family protein Bax has recently emerged as a promising new target in cancer therapy along with first BAX activators (BAM7, Compound 106, and SMBA1)...
April 11, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28363960/genetic-in-stability-of-2-6-dichlorobenzamide-catabolism-in-aminobacter-sp-strain-msh1-biofilms-under-carbon-starvation-conditions
#20
Benjamin Horemans, Bart Raes, Hannelore Brocatus, Jeroen T'Syen, Caroline Rombouts, Lynn Vanhaecke, Johan Hofkens, Dirk Springael
Aminobacter sp. strain MSH1 grows on and mineralizes the groundwater micropollutant 2,6-dichlorobenzamide (BAM) and is of interest for BAM removal in drinking water treatment plants (DWTPs). The BAM-catabolic genes in MSH1 are located on plasmid pBAM1, carrying bbdA, which encodes the conversion of BAM to 2,6-dichlorobenzoic acid (2,6-DCBA) (BbdA(+) phenotype), and plasmid pBAM2, carrying gene clusters encoding the conversion of 2,6-DCBA to tricarboxylic acid (TCA) cycle intermediates (Dcba(+) phenotype). There are indications that MSH1 easily loses its BAM-catabolic phenotype...
June 1, 2017: Applied and Environmental Microbiology
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