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https://www.readbyqxmd.com/read/27930270/halofilum-ochraceum-gen-nov-sp-nov-a-new-gammaproteobacterium-isolated-from-a-marine-solar-saltern
#1
Jun Xia, Jin-Xin Zhao, Jin Sang, Guan-Jun Chen, Zong-Jun Du
A Gram-stain-negative, oxidase-negative, catalase-positive, facultative anaerobe, designated XJ16T, was isolated from a marine solar saltern on the coast of Weihai, China. Cells of the strain XJ16T were long and rod-shaped. The colonies were ochre in color and were able to reduce nitrate to nitrite. Optimal growth occurred at 33-37 °C (range, 20-45 °C) and in the presence of 8-10 % (w/v) NaCl (range, 2-20 %, w/v). The pH range for growth was found to be 6.5-9.5, with optimum growth at pH 7.5-8.0. A phylogenetic analysis based on the 16S rRNA gene sequence demonstrated that strain XJ16T was related to the phylum Proteobacteria...
December 8, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27928571/diffusion-dynamics-of-latex-nanoparticles-coated-with-ssdna-across-a-single-nanopore
#2
Sébastien Balme, Mathilde Lepoitevin, Ludovic F Dumée, Mikhael Bechelany, Jean-Marc Janot
The fundamental understanding of the transport mechanisms of objects across a single nanopore is one key point to develop Coulter counters at the nanoscale for macromolecule or nanoparticle detection. In this area, nanoparticles have been less investigated than biomacromolecules such as DNA or proteins due to their self-aggregation in the presence of salts. In this work, the transport of modified latex nanoparticles across solid-state nanopores was investigated. To prevent their aggregation, their surface was modified with a low molecular weight single strand DNA coating...
December 8, 2016: Soft Matter
https://www.readbyqxmd.com/read/27927716/genome-wide-uniformity-of-human-open-pre-initiation-complexes
#3
William K M Lai, B Franklin Pugh
Transcription of protein-coding and noncoding DNA occurs pervasively throughout the mammalian genome. Their sites of initiation are generally inferred from transcript 5' ends and are thought to be either locally dispersed or focused. How these two modes of initiation relate is unclear. Here, we apply permanganate treatment and chromatin immunoprecipitation (PIP-seq) of initiation factors to identify the precise location of melted DNA separately associated with the preinitiation complex (PIC) and the adjacent paused complex (PC)...
November 10, 2016: Genome Research
https://www.readbyqxmd.com/read/27926820/altererythrobacter-salegens-sp-nov-a-slightly-halophilic-bacterium-isolated-from-surface-sediment
#4
Xiaoyan Liang, Huina Lin, Kailing Wang, Yunjing Liao, Qiliang Lai, Ying Xu, Changyun Wang
A Gram-negative, rod-shaped and slightly halophilic bacterium, strain XY-R17T, was isolated from the surface sediment of Mai Po Inner Deep Bay Ramsar Site birdwatch in Hong Kong. The 16S rRNA gene sequence of strain XY-R17T exhibited a 96.5% similarity to that of the type strain Altererythrobacter atlanticus. Optimal growth occurred at pH 7.0-7.5, 3%-8% (w/v) NaCl, 28-30˚C. The major respiratory quinone was Ubiquinone-10. The principal fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c), summed feature 3 (C16:1ω7c and/or C16:1ω6c) and 11-methyl C18:1ω7c...
December 5, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27926738/corrigendum-mitochondrial-and-nuclear-dna-matching-shapes-metabolism-and-healthy-ageing
#5
Ana Latorre-Pellicer, Raquel Moreno-Loshuertos, Ana Victoria Lechuga-Vieco, Fátima Sánchez-Cabo, Carlos Torroja, Rebeca Acín-Pérez, Enrique Calvo, Esther Aix, Andrés González-Guerra, Angela Logan, María Luisa Bernad-Miana, Eduardo Romanos, Raquel Cruz, Sara Cogliati, Beatriz Sobrino, Ángel Carracedo, Acisclo Pérez-Martos, Patricio Fernández-Silva, Jesús Ruíz-Cabello, Michael P Murphy, Ignacio Flores, Jesús Vázquez, José Antonio Enríquez
No abstract text is available yet for this article.
December 7, 2016: Nature
https://www.readbyqxmd.com/read/27924986/a-nasba-on-microgel-tethered-molecular-beacon-microarray-for-real-time-microbial-molecular-diagnostics
#6
Y Ma, X Dai, T Hong, G B Munk, M Libera
Despite their many advantages and successes, molecular beacon (MB) hybridization probes have not been extensively used in microarray formats because of the complicating probe-substrate interactions that increase the background intensity. We have previously shown that tethering to surface-patterned microgels is an effective means for localizing MB probes to specific surface locations in a microarray format while simultaneously maintaining them in as water-like an environment as possible and minimizing probe-surface interactions...
December 7, 2016: Analyst
https://www.readbyqxmd.com/read/27923845/numerical-and-spatial-patterning-of-yeast-meiotic-dna-breaks-by-tel1
#7
Neeman Mohibullah, Scott Keeney
The Spo11-generated double-strand breaks (DSBs) that initiate meiotic recombination are dangerous lesions that can disrupt genome integrity, so meiotic cells regulate their number, timing, and distribution. Mechanisms of this regulation remain poorly understood. Here, we use Spo11-oligonucleotide complexes, a byproduct of DSB formation, to reveal aspects of the contribution of the Saccharomyces cerevisiae DNA damage-responsive kinase Tel1 (ortholog of mammalian ATM). A tel1Δ mutant has globally increased amounts of Spo11-oligonucleotide complexes and altered Spo11-oligonucleotide lengths, consistent with conserved roles for Tel1 in control of DSB number and processing...
December 6, 2016: Genome Research
https://www.readbyqxmd.com/read/27923682/chitosan-nanoparticles-plus-quercetin-suppress-the-oxidative-stress-modulate-dna-fragmentation-and-gene-expression-in-the-kidney-of-rats-fed-ochratoxin-a-contaminated-diet
#8
Mosaad A Abdel-Wahhab, Abdulhadi Aljawish, Aziza A El-Nekeety, Sekena H Abdel-Aiezm, Nabila S Hassan
This study aimed to evaluate the protective role of chitosan nanoparticles (COS-NPs) singly or plus quercetin (Q) against OTA-induced oxidative stress and renal genotoxicity. Twelve groups of male Sprague-Dawley rats were treated orally for 3 weeks included the control group, animals fed OTA-contaminated diet (3 mg/kg diet); COS-NPs-treated groups at low (140 mg/kg b.w.) or high (280 mg/kg b.w.) dose, Q-treated group (50 mg/kg b.w.), Q plus low or high dose of COS-NPs-treated groups and OTA plus Q and/or COS-NPs at the two tested doses-treated groups...
December 3, 2016: Food and Chemical Toxicology
https://www.readbyqxmd.com/read/27921518/increased-radio-toxicity-in-two-cancerous-cell-lines-irradiated-by-low-and-high-energy-photons-in-the-presence-of-thio-glucose-bound-gold-nanoparticles
#9
Shokouhozaman Soleymanifard, Atefeh Rostami, Seyed Amir Aledavood, Maryam Moghadam Matin, Ameneh Sazgarnia
PURPOSE: Gold nanoparticles modified by thio-glucose have been believed to increase the toxicity of radiotherapy in human malignant cells. We report the effect of thio-glucose-bound gold nanoparticles (Glu-G nanoparticles), 16 nm in size, on two human lung (QU-DB) and breast (MCF7) cancer cell lines combined with kilo and megavoltage X-rays. MATERIALS AND METHODS: The shape and surface characteristics, the size distribution and light absorption spectrum of the prepared nanoparticles were measured by transmission electron microscopy, dynamic light scattering, and Ultraviolet-Visible spectrophotometry, respectively...
December 6, 2016: International Journal of Radiation Biology
https://www.readbyqxmd.com/read/27919246/adjacent-sequences-disclose-potential-for-intra-genomic-dispersal-of-satellite-dna-repeats-and-suggest-a-complex-network-with-transposable-elements
#10
Eva Satović, Tanja Vojvoda Zeljko, Andrea Luchetti, Barbara Mantovani, Miroslav Plohl
BACKGROUND: Satellite DNA (satDNA) sequences are typically arranged as arrays of tandemly repeated monomers. Due to the similarity among monomers, their organizational pattern and abundance, satDNAs are hardly accessible to structural and functional studies and still represent the most obscure genome component. Although many satDNA arrays of diverse length and even single monomers exist in the genome, surprisingly little is known about transition from satDNAs to other sequences. Studying satDNA monomers at junctions and identifying DNA sequences adjacent to them can help to understand the processes that (re)distribute satDNAs and significance that evolution of these sequence elements might have in creating the genomic landscape...
December 6, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27916662/acetylation-of-pcna-sliding-surface-by-eco1-promotes-genome-stability-through-homologous-recombination
#11
Pierre Billon, Jian Li, Jean-Philippe Lambert, Yizhang Chen, Véronique Tremblay, Joseph S Brunzelle, Anne-Claude Gingras, Alain Verreault, Tomohiko Sugiyama, Jean-Francois Couture, Jacques Côté
During DNA replication, proliferating cell nuclear antigen (PCNA) adopts a ring-shaped structure to promote processive DNA synthesis, acting as a sliding clamp for polymerases. Known posttranslational modifications function at the outer surface of the PCNA ring to favor DNA damage bypass. Here, we demonstrate that acetylation of lysine residues at the inner surface of PCNA is induced by DNA lesions. We show that cohesin acetyltransferase Eco1 targets lysine 20 at the sliding surface of the PCNA ring in vitro and in vivo in response to DNA damage...
November 16, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27913728/fission-yeast-stn1-is-crucial-for-semi-conservative-replication-at-telomeres-and-subtelomeres
#12
Masahiro Takikawa, Yusuke Tarumoto, Fuyuki Ishikawa
The CST complex is a phylogenetically conserved protein complex consisting of CTC1/Cdc13, Stn1 and Ten1 that protects telomeres on linear chromosomes. Deletion of the fission yeast homologs stn1 and ten1 results in complete telomere loss; however, the precise function of Stn1 is still largely unknown. Here, we have isolated a high-temperature sensitive stn1 allele (termed stn1-1). stn1-1 cells abruptly lost telomeric sequence almost completely at the restrictive temperature. The loss of chromosomal DNA happened without gradual telomere shortening, and extended to 30 kb from the ends of chromosomes...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27912056/conflict-resolution-in-the-genome-how-transcription-and-replication-make-it-work
#13
REVIEW
Stephan Hamperl, Karlene A Cimprich
The complex machineries involved in replication and transcription translocate along the same DNA template, often in opposing directions and at different rates. These processes routinely interfere with each other in prokaryotes, and mounting evidence now suggests that RNA polymerase complexes also encounter replication forks in higher eukaryotes. Indeed, cells rely on numerous mechanisms to avoid, tolerate, and resolve such transcription-replication conflicts, and the absence of these mechanisms can lead to catastrophic effects on genome stability and cell viability...
December 1, 2016: Cell
https://www.readbyqxmd.com/read/27911258/clostridium-guangxiense-sp-nov-and-clostridium-neuense-sp-nov-two-phylogenetically-closely-related-hydrogen-producing-species-isolated-from-lake-sediment
#14
Xin Zhao, Danyang Li, Shuhong Xu, Zhanghao Guo, Yan Zhang, Lin Man, Binhui Jiang, Xiaomin Hu
Two novel anaerobic, mesophilic, bio-hydrogen producing bacteria, designated strains ZGM211T and G1T, were isolated from lake sediment. 16S rRNA and ATP synthase beta subunit (atpD) gene sequences phylogenetic analysis of strains ZGM211T and G1T revealed an affiliation to the genus Clostridium sensu stricto (cluster I of the clostridia), with Clostridium acetobutylicum as the closest characterized species, showing the same sequence similarity of 96.4% to the type strain (98.9% between the two isolates). Cells of the two strains were rod-shaped...
December 1, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27911253/luteolibacter-flavescens-sp-nov-isolated-from-deep-seawater
#15
Chongya Zhang, Bolin Dong, Ruijun Wang, Yue Su, Shuaibo Han, Xiaoyun Yu, Zhe Zhao, Geyi Fu, Cong Sun, Min Wu
A novel Gram-stain-negative, rod-shaped, non-motile strain, designated GKXT, was isolated from deep seawater. Strain GKXT was able to grow at 20-35 °C (optimum, 25 °C), pH 5.5-9.5 (optimum, 7.5) and 0-4.0 % (w/v) NaCl (optimum, 1.0 %). The major fatty acids were C16:1 ω9c (15.4 %), C16:0 (18.4 %), C14:0 (12.0 %), iso-C14:0 (30.1 %) and anteiso-C15:0 (5.7 %). Strain GKXT contained phosphatidylethanolamine (PE), phosphatidylmethylethanoamine (PME), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG) and one unidentified glycolipid (GL) as the main polar lipids...
December 1, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27910066/traditional-approaches-to-molecular-genetic-analysis
#16
Christopher J Walker, Paul J Goodfellow
Molecular studies of endometrial cancer have evolved with the tools available to researchers: the methods for measuring nucleic acids, protein expression, and combinations thereof. Today "molecular genetic analysis" implies a broad range of indirect and direct tests that yield molecular phenotypes or genotypes, immunotypes, or signatures that were not conceived of when the histologic and biologic heterogeneity was first fully acknowledged.We will provide a historical perspective on molecular genetic studies of endometrial cancers focusing on candidate genes and how early foundational research shaped both our understanding of the disease and current research directions...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27909816/ecological-and-physical-barriers-shape-genetic-structure-of-the-alpine-porcini-boletus-reticuloceps
#17
Bang Feng, Jian Wei Liu, Jianping Xu, Kuan Zhao, Zai Wei Ge, Zhu L Yang
The Alpine porcini, Boletus reticuloceps, is an ectomycorrhizal mushroom distributed in subalpine areas of Southwest China, central China, and Taiwan Island. This distribution pattern makes it an ideal organism to infer how ectomycorrhizal fungi have reacted to historical tectonic and climatic changes, and to illustrate the mechanism for the disjunction of organisms between Southwest China and Taiwan. In this study, we explored the phylogeographic pattern of B. reticuloceps by microsatellite genotyping, DNA sequencing, ecological factor analysis, and species distribution modeling...
December 1, 2016: Mycorrhiza
https://www.readbyqxmd.com/read/27909798/the-loading-of-condensin-in-the-context-of-chromatin
#18
REVIEW
Xavier Robellet, Vincent Vanoosthuyse, Pascal Bernard
The packaging of DNA into chromosomes is a ubiquitous process that enables living organisms to structure and transmit their genome accurately through cell divisions. In the three kingdoms of life, the architecture and dynamics of chromosomes rely upon ring-shaped SMC (Structural Maintenance of Chromosomes) condensin complexes. To understand how condensin rings organize chromosomes, it is essential to decipher how they associate with chromatin filaments. Here, we use recent evidence to discuss the role played by nucleosomes and transcription factors in the loading of condensin at transcribed genes...
December 1, 2016: Current Genetics
https://www.readbyqxmd.com/read/27906128/two-subunits-of-human-orc-are-dispensable-for-dna-replication-and-proliferation
#19
Etsuko Shibata, Manjari Kiran, Yoshiyuki Shibata, Samarendra Singh, Shashi Kiran, Anindya Dutta
The six-subunit Origin Recognition Complex (ORC) is believed to be an essential eukaryotic ATPase that binds to origins of replication as a ring-shaped heterohexamer to load MCM2-7 and initiate DNA replication. We have discovered that human cell lines in culture proliferate with intact chromosomal origins of replication after disruption of both alleles of ORC2 or of the ATPase subunit, ORC1. The ORC1 or ORC2-depleted cells replicate with decreased chromatin loading of MCM2-7 and become critically dependent on another ATPase, CDC6, for survival and DNA replication...
December 1, 2016: ELife
https://www.readbyqxmd.com/read/27905438/epigenetics-gut-microbes-shape-dna
#20
(no author information available yet)
No abstract text is available yet for this article.
November 30, 2016: Nature
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