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https://www.readbyqxmd.com/read/28630803/putative-archaeal-viruses-from-the-mesopelagic-ocean
#1
Dean R Vik, Simon Roux, Jennifer R Brum, Ben Bolduc, Joanne B Emerson, Cory C Padilla, Frank J Stewart, Matthew B Sullivan
Oceanic viruses that infect bacteria, or phages, are known to modulate host diversity, metabolisms, and biogeochemical cycling, while the viruses that infect marine Archaea remain understudied despite the critical ecosystem roles played by their hosts. Here we introduce "MArVD", for Metagenomic Archaeal Virus Detector, an annotation tool designed to identify putative archaeal virus contigs in metagenomic datasets. MArVD is made publicly available through the online iVirus analytical platform. Benchmarking analysis of MArVD showed it to be >99% accurate and 100% sensitive in identifying the 127 known archaeal viruses among the 12,499 viruses in the VirSorter curated dataset...
2017: PeerJ
https://www.readbyqxmd.com/read/28611032/genome-wide-dynamics-of-nascent-noncoding-rna-transcription-in-porcine-heart-after-myocardial-infarction
#2
Minna U Kaikkonen, Paavo Halonen, Oscar Hsin-Fu Liu, Tiia A Turunen, Juho Pajula, Pierre Moreau, Ilakya Selvarajan, Tomi Tuomainen, Einari Aavik, Pasi Tavi, Seppo Ylä-Herttuala
BACKGROUND: Microarrays and RNA sequencing are widely used to profile transcriptome remodeling during myocardial ischemia. However, the steady-state RNA analysis lacks in sensitivity to detect all noncoding RNA species and does not provide separation between transcriptional and post-transcriptional regulations. Here, we provide the first comprehensive analysis of nascent RNA profiles of mRNAs, primary micro-RNAs, long noncoding RNAs, and enhancer RNAs in a large animal model of acute infarction...
June 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/28587357/differential-proteomic-screening-and-identification-for-non-traumatic-necrotic-femoral-osseous-tissue
#3
Peng Yan, Yeping Zhu, Hui Zhao, Yanyan Lu, Yuzhong Gao
Currently, there is a lack of effective early screening and detection methods for femoral head necrosis. Current research on most orthopedic diseases focuses on proteomics in the preliminary stage. The recent fluorescence differential in gel electrophoresis (DIGE) has advantages such as a high reproducibility, high sensitivity, high throughput, and high dynamic range. It is currently one of the most widely used quantitative proteomic research means. We conducted this study to investigate the pathogenesis of non-traumatic femoral head necrosis using the fluorescence DIGE to screen non-traumatic femoral head necrosis based on proteomics and provide a theoretical basis for screening possible biomarkers and molecular targeted treatment...
June 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28555145/rna-seq-analysis-of-diverse-rice-genotypes-to-identify-the-genes-controlling-coleoptile-growth-during-submerged-germination
#4
Sheng-Kai Hsu, Chih-Wei Tung
The rate of coleoptile elongation varies between different rice varieties that are grown under water during the germination stage. Compared to sensitive varieties, submergence-tolerant rice exhibits substantial coleoptile elongation in order to uptake oxygen (O2) from the surface and thus have a better chance to survive water stress. We conducted RNA-seq analysis in order to investigate 7-day-old shoot transcriptome dynamics in six rice genotypes that exhibit different coleoptile elongation rates under water...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28549739/characterization-of-a-major-facilitator-superfamily-transporter-in-shiraia-bambusicola
#5
Huaxiang Deng, Ruijie Gao, Xiangru Liao, Yujie Cai
Reactive oxygen species (ROS) generated by photo-activated hypocrellin from Shiraia bambusicola are detrimental to cellular macromolecules. However, S. bambusicola can still maintain excellent morphology during continuous hypocrellin production, indicating an extraordinary autoresistance system that protects against the harmful ROS. In this study, a major facilitator superfamily transporter (MFS) was isolated from S. bambusicola and deleted using the clustered regularly interspaced short palindromic repeat sequences (CRISPR)/Cas9 system...
May 24, 2017: Research in Microbiology
https://www.readbyqxmd.com/read/28547846/multiline-balanced-ssfp-for-rapid-functional-imaging-at-ultrahigh-field
#6
Philipp Ehses, Klaus Scheffler
PURPOSE: The goal of this study is to develop and evaluate a multiline balanced steady-state free-precession (bSSFP) sequence for passband functional MRI at ultrahigh field. METHODS: Passband bSSFP functional MRI experiments using a visual task were performed on a 9.4 T system with echo trains ranging from one up to seven echoes. We analyze the acquisition efficiency, temporal and thermal signal-to-noise ratio, as well as the observed blood oxygen-level-dependent (BOLD) signal changes...
May 25, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28542499/lipidomic-and-metabolic-changes-in-the-p4-type-atpase-atp10d-deficient-c57bl-6j-wild-type-mice-upon-rescue-of-atp10d-function
#7
Alexander Sigruener, Christian Wolfrum, Alfred Boettcher, Thomas Kopf, Gerhard Liebisch, Evelyn Orsó, Gerd Schmitz
BACKGROUND: Sequence variants near the human gene for P4-type ATPase, class V, type 10D (ATP10D) were shown to significantly associate with circulating hexosylceramide d18:1/16:0 and d18:1/24:1 levels, obesity, insulin resistance, plasma high density lipoprotein (HDL), coronary stenotic index and intracranial atherosclerotic index. In mice Atp10d is associated with HDL modulation and C57BL/6 mice expressing a truncated, non-functional form of ATP10D easily develop obesity and insulin resistance on high-fat diet...
2017: PloS One
https://www.readbyqxmd.com/read/28503732/imaging-short-lived-reactive-oxygen-species-ros-with-endogenous-contrast-mri
#8
Rong-Wen Tain, Alessandro M Scotti, Weiguo Li, Xiaohong Joe Zhou, Kejia Cai
PURPOSE: To characterize the relaxation properties of reactive oxygen species (ROS) for the development of endogenous ROS contrast magnetic resonance imaging (MRI). MATERIALS AND METHODS: ROS-producing phantoms and animal models were imaged at 9.4T MRI to obtain T1 and T2 maps. Egg white samples treated with varied concentrations of hydrogen peroxide (H2 O2 ) were used to evaluate the effect of produced ROS in T1 and T2 for up to 4 hours. pH and temperature changes due to H2 O2 treatment in egg white were also monitored...
May 15, 2017: Journal of Magnetic Resonance Imaging: JMRI
https://www.readbyqxmd.com/read/28503178/transcriptomic-response-of-chinese-yew-taxus-chinensis-to-cold-stress
#9
Delong Meng, Xianghua Yu, Liyuan Ma, Jin Hu, Yili Liang, Xueduan Liu, Huaqun Yin, Hongwei Liu, Xiaojia He, Diqiang Li
Taxus chinensis is a rare and endangered shrub, highly sensitive to temperature changes and widely known for its potential in cancer treatment. How gene expression of T. chinensis responds to low temperature is still unknown. To investigate cold response of the genus Taxus, we obtained the transcriptome profiles of T. chinensis grown under normal and low temperature (cold stress, 0°C) conditions using Illumina Miseq sequencing. A transcriptome including 83,963 transcripts and 62,654 genes were assembled from 4...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28447993/synthesis-of-1-2-azaborines-and-the-preparation-of-their-protein-complexes-with-t4-lysozyme-mutants
#10
Hyelee Lee, Shih-Yuan Liu
We describe a general synthesis of 1,2-azaborines using standard air-free techniques and protein complex preparation with T4 lysozyme mutants by vapor diffusion. Oxygen- and moisture-sensitive compounds are prepared and isolated under an inert atmosphere (N2) using either a vacuum gas manifold or a glove box. As an example of azaborine synthesis, we demonstrate the synthesis and purification of the volatile N-H-B-ethyl-1,2-azaborine by a five-step sequence involving distillation and column chromatography for the isolation of products...
March 25, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28439033/genome-wide-identification-of-resd-nsrr-and-fur-binding-in-bacillus-subtilis-during-anaerobic-fermentative-growth-by-in-vivo-footprinting
#11
Onuma Chumsakul, Divya P Anantsri, Tai Quirke, Taku Oshima, Kensuke Nakamura, Shu Ishikawa, Michiko M Nakano
Upon oxygen limitation, the Bacillus subtilis ResE sensor kinase and its cognate ResD response regulator play primary roles in transcriptional activation of genes functioning in anaerobic respiration. The nitric oxide (NO)-sensitive NsrR repressor controls transcription to support nitrate respiration. In addition, the ferric uptake repressor (Fur) can modulate transcription under anaerobic conditions. However, whether these controls are direct or indirect has been investigated only in a gene-specific manner...
April 24, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28424572/functional-sensitivity-of-2d-simultaneous-multi-slice-echo-planar-imaging-effects-of-acceleration-on-g-factor-and-physiological-noise
#12
Nick Todd, Oliver Josephs, Peter Zeidman, Guillaume Flandin, Steen Moeller, Nikolaus Weiskopf
Accelerated data acquisition with simultaneous multi-slice (SMS) imaging for functional MRI studies leads to interacting and opposing effects that influence the sensitivity to blood oxygen level-dependent (BOLD) signal changes. Image signal to noise ratio (SNR) is decreased with higher SMS acceleration factors and shorter repetition times (TR) due to g-factor noise penalties and saturation of longitudinal magnetization. However, the lower image SNR is counteracted by greater statistical power from more samples per unit time and a higher temporal Nyquist frequency that allows for better removal of spurious non-BOLD high frequency signal content...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28400512/convergence-of-dna-methylation-and-phosphorothioation-epigenetics-in-bacterial-genomes
#13
Chao Chen, Lianrong Wang, Si Chen, Xiaolin Wu, Meijia Gu, Xi Chen, Susu Jiang, Yunfu Wang, Zixin Deng, Peter C Dedon, Shi Chen
Explosive growth in the study of microbial epigenetics has revealed a diversity of chemical structures and biological functions of DNA modifications in restriction-modification (R-M) and basic genetic processes. Here, we describe the discovery of shared consensus sequences for two seemingly unrelated DNA modification systems, (6m)A methylation and phosphorothioation (PT), in which sulfur replaces a nonbridging oxygen in the DNA backbone. Mass spectrometric analysis of DNA from Escherichia coli B7A and Salmonella enterica serovar Cerro 87, strains possessing PT-based R-M genes, revealed d(GPS(6m)A) dinucleotides in the GPS(6m)AAC consensus representing ∼5% of the 1,100 to 1,300 PT-modified d(GPSA) motifs per genome, with (6m)A arising from a yet-to-be-identified methyltransferase...
April 25, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28391398/arabidopsis-abi5-plays-a-role-in-regulating-ros-homeostasis-by-activating-catalase-1-transcription-in-seed-germination
#14
Chao Bi, Yu Ma, Zhen Wu, Yong-Tao Yu, Shan Liang, Kai Lu, Xiao-Fang Wang
It has been known that ABA INSENSITIVE 5 (ABI5) plays a vital role in regulating seed germination. In the present study, we showed that inhibition of the catalase activity with 3-amino-1,2,4-triazole (3-AT) inhibits seed germination of Col-0, abi5 mutants and ABI5-overexpression transgenic lines. Compared with Col-0, the seeds of abi5 mutants showed more sensitive to 3-AT during seed germination, while the seeds of ABI5-overexpression transgenic lines showed more insensitive. H2O2 showed the same effect on seed germination of Col-0, abi5 mutants and ABI5-overexpression transgenic lines as 3-AT...
May 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28373123/sensitivity-and-specificity-considerations-for-fmri-encoding-decoding-and-mapping-of-auditory-cortex-at-ultra-high-field
#15
Michelle Moerel, Federico De Martino, Valentin G Kemper, Sebastian Schmitter, An T Vu, Kâmil Uğurbil, Elia Formisano, Essa Yacoub
Following rapid technological advances, ultra-high field functional MRI (fMRI) enables exploring correlates of neuronal population activity at an increasing spatial resolution. However, as the fMRI blood-oxygenation-level-dependent (BOLD) contrast is a vascular signal, the spatial specificity of fMRI data is ultimately determined by the characteristics of the underlying vasculature. At 7T, fMRI measurement parameters determine the relative contribution of the macro- and microvasculature to the acquired signal...
March 31, 2017: NeuroImage
https://www.readbyqxmd.com/read/28367140/transcriptomics-indicates-active-and-passive-metronidazole-resistance-mechanisms-in-three-seminal-giardia-lines
#16
Brendan R E Ansell, Louise Baker, Samantha J Emery, Malcolm J McConville, Staffan G Svärd, Robin B Gasser, Aaron R Jex
Giardia duodenalis is an intestinal parasite that causes 200-300 million episodes of diarrhoea annually. Metronidazole (Mtz) is a front-line anti-giardial, but treatment failure is common and clinical resistance has been demonstrated. Mtz is thought to be activated within the parasite by oxidoreductase enzymes, and to kill by causing oxidative damage. In G. duodenalis, Mtz resistance involves active and passive mechanisms. Relatively low activity of iron-sulfur binding proteins, namely pyruvate:ferredoxin oxidoreductase (PFOR), ferredoxins, and nitroreductase-1, enable resistant cells to passively avoid Mtz activation...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28361707/investigation-and-identification-of-protein-carbonylation-sites-based-on-position-specific-amino-acid-composition-and-physicochemical-features
#17
Shun-Long Weng, Kai-Yao Huang, Fergie Joanda Kaunang, Chien-Hsun Huang, Hui-Ju Kao, Tzu-Hao Chang, Hsin-Yao Wang, Jang-Jih Lu, Tzong-Yi Lee
BACKGROUND: Protein carbonylation, an irreversible and non-enzymatic post-translational modification (PTM), is often used as a marker of oxidative stress. When reactive oxygen species (ROS) oxidized the amino acid side chains, carbonyl (CO) groups are produced especially on Lysine (K), Arginine (R), Threonine (T), and Proline (P). Nevertheless, due to the lack of information about the carbonylated substrate specificity, we were encouraged to develop a systematic method for a comprehensive investigation of protein carbonylation sites...
March 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28295824/wavelet-entropy-of-bold-time-series-an-application-to-rolandic-epilepsy
#18
Lalit Gupta, Jacobus F A Jansen, Paul A M Hofman, René M H Besseling, Anton J A de Louw, Albert P Aldenkamp, Walter H Backes
PURPOSE: To assess the wavelet entropy for the characterization of intrinsic aberrant temporal irregularities in the time series of resting-state blood-oxygen-level-dependent (BOLD) signal fluctuations. Further, to evaluate the temporal irregularities (disorder/order) on a voxel-by-voxel basis in the brains of children with Rolandic epilepsy. MATERIALS AND METHODS: The BOLD time series was decomposed using the discrete wavelet transform and the wavelet entropy was calculated...
March 11, 2017: Journal of Magnetic Resonance Imaging: JMRI
https://www.readbyqxmd.com/read/28274623/oxygen-exposure-effects-on-the-dechlorinating-activities-of-a-trichloroethene-dechlorination-microbial-consortium
#19
Na Liu, Haijun Li, Mengyan Li, Longzhen Ding, Chih-Huang Weng, Cheng-Di Dong
The aim of this work was to study the effects of the presence of oxygen on the dechlorination of trichloroethene by a microbial consortium containing D. mccartyi. The 16S rRNA and reductive dechlorination genes of the functional bacteria and the non-dechlorinators were monitored. Exposing the consortium to oxygen altered the overall biotransformation rate of the dechlorination process, biotransformation processes prolonged with oxygen concentrations changing from 0 to 7.2mg/L, however, trichloroethylene was eventually dechlorinated to ethene...
February 28, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28273720/recurrence-of-glioblastoma-is-associated-with-elevated-microvascular-transit-time-heterogeneity-and-increased-hypoxia
#20
Andreas Stadlbauer, Kim Mouridsen, Arnd Doerfler, Mikkel Bo Hansen, Stefan Oberndorfer, Max Zimmermann, Michael Buchfelder, Gertraud Heinz, Karl Roessler
Dynamic susceptibility contrast (DSC) perfusion MRI provide information about differences in macro- and microvasculature when executed with gradient-echo (GE; sensitive to macrovasculature) and spin-echo (SE; sensitive to microvasculature) contrast. This study investigated whether there are differences between macro- and microvascular transit time heterogeneity (MVTH and µVTH) and tissue oxygen tension (PO2mit) in newly-diagnosed and recurrent glioblastoma. Fifty-seven patients with glioblastoma (25 newly-diagnosed/32 recurrent) were examined with GE- and SE-DSC perfusion sequences, and a quantitative blood-oxygen-level-dependent (qBOLD) approach...
January 1, 2017: Journal of Cerebral Blood Flow and Metabolism
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