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https://www.readbyqxmd.com/read/28434178/massilia-chloroacetimidivorans-sp-nov-a-chloroacetamide-herbicide-degrading-bacterium-isolated-from-soil
#1
Hyosun Lee, Dong-Uk Kim, Sooyeon Park, Jung-Hoon Yoon, Jong-Ok Ka
A Gram-stain negative, rod-shaped, aerobic bacterial strain, designated TA-C7e(T), was isolated from an agricultural soil obtained from Taean region, Korea. Phylogenetically, the strain was grouped with the genus Massilia and shared 95.33-97.97% 16S rRNA sequence similarity with the type strains of other species of the genus Massilia. The DNA-DNA hybridisation between TA-C7e(T) and Massilia haematophila KACC 13771(T), Massilia suwonesis KACC 12635(T), and Massilia yuzhufengensis KACC 16569(T) revealed a low level of relatedness (<40%)...
April 22, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28429167/corynebacterium-defluvii-sp-nov-isolated-from-sewage
#2
Qiu-Li Yu, Zheng-Fei Yan, Xin He, Feng-Hua Tian, Chuan-Wen Jia, Chang-Tian Li
A Gram-positive, aerobic, non-motile, rod-shapeds, cata-lase-positive, and oxidase-negative strain, designated Y49(T), was isolated from sewage collected from Jilin Agricultural University, China. It grew at 20-40°C (optimum at 30°C), at pH 6.0-8.0 (optimum at 7.0) and at 0-1.0% sodium chloride (optimum at 0%). The major isoprenoid quinone was menaquinone-8 (MK-8) and the polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, four unidentified lipids, and two unidentified aminolipids...
April 20, 2017: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/28427044/on-the-reverse-micelle-effect-in-liquid-scintillation-counting
#3
Youcef Nedjadi, Jean-Pascal Laedermann, François Bochud, Claude Bailat
This work looks into the tracks of electrons in nanoemulsive scintillating media using the Monte Carlo Geant4-DNA code which simulates event-by-event interactions of electrons in liquid water down to the eV, without resorting to the condensed history method. It demonstrates that the average number of micelles in which electrons deposit energy is quite large, increasing with their emission energy, decreasing with micelle size, and rising with micelle concentration. The probability of an electron ending its track in a micelle is found to be rather large and micelle size-dependent below 1keV, and approximating the aqueous fraction at higher energies...
April 12, 2017: Applied Radiation and Isotopes
https://www.readbyqxmd.com/read/28425549/nicotinamide-adenine-dinucleotide-detection-based-on-silver-nanoclusters-stabilized-by-a-dumbbell-shaped-probe
#4
Hong-Ya Wang, Jin-Liang Ma, Bin-Cheng Yin, Bang-Ce Ye
We have developed a novel method for detecting nicotinamide adenine dinucleotide (NAD(+)) based on fluorescent silver nanoclusters (AgNCs) stabilized by a dumbbell-shaped DNA template containing two cytosine-loops joined in a dsDNA stem. The design involves two types of components: a dumbbell-shaped DNA template and three enzymes. In the presence of NAD(+) as a cofactor, Escherichia coli DNA ligase (E.coli DNA ligase) catalyzes template ligation to generate a sealed (no terminal nucleotides) dumbbell-shaped structure, preventing digestion by exonuclease III (Exo III) and exonuclease I (Exo I)...
April 20, 2017: Analyst
https://www.readbyqxmd.com/read/28424942/serratia-bozhouensis-sp-nov-isolated-from-sewage-samples-of-a-dairy-farm
#5
Fei Shang, Ting Xue, Man Wang, Xiaolin Chen, Li Yu, Ming Zhang
A Gram-negative, rod-shaped, salt-tolerant, non-pigmented, and non-spore-forming bacterium, designated strain W1(T) (type strain CICC 23797 = CGMCC1.14949), was isolated from sewage samples of a dairy farm in Bozhou, Anhui, China. Strain W1 was resistant to lincomycin, troleandomycin, rifamycin, and vancomycin. Sequence analysis of the 16S rDNA gene revealed that the strain showed sequence similarity of 98.2% with the closest related species Serratia quinivorans CP6a(T). The genomic DNA G+C content of the isolate was 52...
April 20, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28424339/discovery-of-double-stranded-genomic-dna-in-circulating-exosomes
#6
Raghu Kalluri, Valerie S LeBleu
It is becoming increasingly clear that small vesicles released from cells (extracellular vesicles [EVs]) represent a heterogeneous population implicated in cell-to-cell communication. The classifications and nomenclature of EVs are evolving as enrichment strategies and specific characteristics are being unraveled. At present, physical properties of EVs-namely, size, shape, and density-are often used to identify subpopulations of EVs. A distinct group of EVs, termed exosomes, largely defined by their small size (∼40-150 nm) and proposed subcellular origin, has been extensively studied in several aspects of cancer biology...
April 19, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28424282/formation-of-a-viral-replication-focus-in-sulfolobus-cells-infected-by-the-rudivirus-sirv2
#7
Laura Martínez-Alvarez, Ling Deng, Xu Peng
Viral factories are compartmentalized centres for viral replication and assembly in infected eukaryotic cells. Here, we report the formation of a replication focus by the prototypical archaeal virus SIRV2 in the model archaeon Sulfolobus. This rod-shaped virus belongs to the viral family rudiviridae, carrying linear dsDNA genomes, which are very common in geothermal environments. We demonstrate that SIRV2 DNA synthesis is confined to a focus near the periphery of infected cells. Moreover, viral and cellular replication proteins are recruited to, and concentrated in, the viral replication focus...
April 19, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28421811/characterization-of-ornithobacterium-rhinotracheale-field-isolates-from-hungary
#8
Réka Szabó, Enikő Wehmann, László Makrai, Csaba Nemes, Éva Gyuris, Ákos Thuma, Tibor Magyar
Ornithobacterium rhinotracheale is a widely distributed rod-shaped gram-negative bacterium that infects several avian species including chickens and turkeys. It is associated with respiratory signs, growth retardation, mortality, and reduced egg production thus causing severe economic losses to the poultry industries. In this study, 37 field isolates of O. rhinotracheale, collected from various locations in Hungary between 1997 and 2015, were identified and molecularly characterized by the analysis of partial 16S rRNA gene sequences, enterobacterial repetitive intergenic consensus (ERIC)-PCR and random amplified polymorphic DNA (RAPD) PCR assays with the OPG11, OPH19, and M13 primers...
April 19, 2017: Avian Pathology: Journal of the W.V.P.A
https://www.readbyqxmd.com/read/28419835/the-architecture-and-function-of-the-chromatin-replication-machinery
#9
REVIEW
Thomas Cr Miller, Alessandro Costa
Genomic DNA in eukaryotic cells is packaged into nucleosome arrays. During replication, nucleosomes need to be dismantled ahead of the advancing replication fork and reassembled on duplicated DNA. The architecture and function of the core replisome machinery is now beginning to be elucidated, with recent insights shaping our view on DNA replication processes. Simultaneously, breakthroughs in our mechanistic understanding of epigenetic inheritance allow us to build new models of how histone chaperones integrate with the replisome to reshuffle nucleosomes...
April 15, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28418026/the-cac2-subunit-is-essential-for-productive-histone-binding-and-nucleosome-assembly-in-caf-1
#10
Francesca Mattiroli, Yajie Gu, Jeremy L Balsbaugh, Natalie G Ahn, Karolin Luger
Nucleosome assembly following DNA replication controls epigenome maintenance and genome integrity. Chromatin assembly factor 1 (CAF-1) is the histone chaperone responsible for histone (H3-H4)2 deposition following DNA synthesis. Structural and functional details for this chaperone complex and its interaction with histones are slowly emerging. Using hydrogen-deuterium exchange coupled to mass spectrometry, combined with in vitro and in vivo mutagenesis studies, we identified the regions involved in the direct interaction between the yeast CAF-1 subunits, and mapped the CAF-1 domains responsible for H3-H4 binding...
April 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28417635/crystallization-of-amphiphilic-dna-c-stars
#11
Ryan A Brady, Nicholas J Brooks, Pietro Cicuta, Lorenzo Di Michele
Many emerging technologies require materials with well-defined three-dimensional nanoscale architectures. Production of these structures is currently underpinned by self-assembling amphiphilic macromolecules or engineered all-DNA building blocks. Both of these approaches produce restricted ranges of crystal geometries due to synthetic amphiphiles' simple shape and limited specificity, or the technical difficulties in designing space-filling DNA motifs with targeted shapes. We have overcome these limitations with amphiphilic DNA nanostructures, or "C-Stars", that combine the design freedom and facile functionalization of DNA-based materials with robust hydrophobic interactions...
April 20, 2017: Nano Letters
https://www.readbyqxmd.com/read/28417190/larkinella-harenae-sp-nov-isolated-from-korean-beach-soil
#12
Su-Jin Park, Jae-Jin Lee, Seung-Yeol Lee, Dae Sung Lee, Myung Kyum Kim, Leonid N Ten, Hee-Young Jung
A Gram-negative, short rod-shaped, gliding motile, and pale pink-pigmented bacterial strain, designated 15J9-9(T), was isolated from the soil of Iho Tewoo Beach, Jeju Island, Korea, and characterized taxonomically using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain 15J9-9(T) belonged to the family Cytophagaceae and was related to Larkinella bovis M2T2B15(T) (96.5% similarity), Larkinella arboricola Z0532(T) (95.3% similarity), and Larkinella insperata LMG 22510(T) (95...
April 17, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28416702/massive-horizontal-transfer-of-transposable-elements-in-insects
#13
Jean Peccoud, Vincent Loiseau, Richard Cordaux, Clément Gilbert
Horizontal transfer (HT) of genetic material is central to the architecture and evolution of prokaryote genomes. Within eukaryotes, the majority of HTs reported so far are transfers of transposable elements (TEs). These reports essentially come from studies focusing on specific lineages or types of TEs. Because of the lack of large-scale survey, the amount and impact of HT of TEs (HTT) in eukaryote evolution, as well as the trends and factors shaping these transfers, are poorly known. Here, we report a comprehensive analysis of HTT in 195 insect genomes, representing 123 genera and 13 of the 28 insect orders...
April 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28415454/development-of-a-dna-liposome-complex-for-gene-delivery-applications
#14
M Rasoulianboroujeni, G Kupgan, F Moghadam, M Tahriri, A Boughdachi, P Khoshkenar, J J Ambrose, N Kiaie, D Vashaee, J D Ramsey, L Tayebi
The association structures formed by cationic liposomes and DNA (Deoxyribonucleic acid)-liposome have been effectively utilized as gene carriers in transfection assays. In this research study, cationic liposomes were prepared using a modified lipid film hydration method consisting of a lyophilization step for gene delivery applications. The obtained results demonstrated that the mean particle size had no significant change while the polydispersity (PDI) increased after lyophilization. The mean particle size slightly reduced after lyophilization (520±12nm to 464±25nm) while the PDI increased after lyophilization (0...
June 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28415169/understanding-the-origin-of-liquid-crystal-ordering-of-ultrashort-double-stranded-dna
#15
Suman Saurabh, Yves Lansac, Yun Hee Jang, Matthew A Glaser, Noel A Clark, Prabal K Maiti
Recent experiments have shown that short double-stranded DNA (dsDNA) fragments having six- to 20-base pairs exhibit various liquid crystalline phases. This violates the condition of minimum molecular shape anisotropy that analytical theories demand for liquid crystalline ordering. It has been hypothesized that the liquid crystalline ordering is the result of end-to-end stacking of dsDNA to form long supramolecular columns which satisfy the shape anisotropy criterion necessary for ordering. To probe the thermodynamic feasibility of this process, we perform molecular dynamics simulations on ultrashort (four base pair long) dsDNA fragments, quantify the strong end-to-end attraction between them, and demonstrate that the nematic ordering of the self-assembled stacked columns is retained for a large range of temperature and salt concentration...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28412903/phage-life-cycles-behind-bacterial-biodiversity
#16
Tomasz Olszak, Agnieszka Latka, Bartosz Roszniowski, Miguel Angel Valvano, Zuzanna Drulis-Kawa
Bacteriophages (phages or bacterial viruses) are the most abundant biological entities in our planet; their influence reaches far beyond the microorganisms they parasitize. Phages are present in every environment and shape up every bacterial population in both active and passive ways. They participate in the circulation of organic matter and drive the evolution of microorganisms by horizontal gene transfer at unprecedented scales. The mass flow of genetic information in the microbial world influences the biosphere and poses challenges for science and medicine...
April 13, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28410407/bacterial-amyloid-curli-acts-as-a-carrier-for-dna-to-elicit-an-autoimmune-response-via-tlr2-and-tlr9
#17
Sarah A Tursi, Ernest Y Lee, Nicole J Medeiros, Michael H Lee, Lauren K Nicastro, Bettina Buttaro, Stefania Gallucci, Ronald Paul Wilson, Gerard C L Wong, Çagla Tükel
Bacterial biofilms are associated with numerous human infections. The predominant protein expressed in enteric biofilms is the amyloid curli, which forms highly immunogenic complexes with DNA. Infection with curli-expressing bacteria or systemic exposure to purified curli-DNA complexes triggers autoimmunity via the generation of type I interferons (IFNs) and anti-double-stranded DNA antibodies. Here, we show that DNA complexed with amyloid curli powerfully stimulates Toll-like receptor 9 (TLR9) through a two-step mechanism...
April 14, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28409640/polymer-pen-chemical-lift-off-lithography
#18
Xiaobin Xu, Qing Yang, Kevin M Cheung, Chuanzhen Zhao, Natcha Wattanatorn, Jason Nathaniel Belling, John M Abendroth, Liane S Slaughter, Chad A Mirkin, Anne M Andrews, Paul S Weiss
We designed and fabricated large arrays of polymer pens having sub-20-nm tips to perform chemical lift-off lithography (CLL). As such, we developed a hybrid patterning strategy called polymer-pen chemical lift-off lithography (PPCLL). We demonstrated PPCLL patterning using pyramidal and v shaped polymer-pen arrays. Associated simulations revealed a nanometer-scale quadratic relationship between contact linewidths of the polymer pens and two other variables: polymer-pen base linewidths and vertical compression distances...
April 14, 2017: Nano Letters
https://www.readbyqxmd.com/read/28406032/deposition-of-dna-nanostructures-on-highly-oriented-pyrolytic-graphite
#19
Karen B Ricardo, Anqin Xu, Muhammad Salim, Feng Zhou, Haitao Liu
We report the deposition of DNA origami nanostructures on highly oriented pyrolytic graphite (HOPG). The DNA origami goes through a structural rearrangement and the DNA base is exposed to interact with the graphite surface. Exposure to ambient air, which is known to result in a hydrophilic-to-hydrophobic wetting transition of HOPG, does not significantly impact the deposition yield or the shape deformation of DNA nanostructures. The deposited DNA nanostructures maintain their morphology for at least a week and promote site-selective chemical vapor deposition of SiO2...
April 13, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28402891/brownian-ratchet-mechanism-for-faithful-segregation-of-low-copy-number-plasmids
#20
Longhua Hu, Anthony G Vecchiarelli, Kiyoshi Mizuuchi, Keir C Neuman, Jian Liu
Bacterial plasmids are extrachromosomal DNA that provides selective advantages for bacterial survival. Plasmid partitioning can be remarkably robust. For high-copy-number plasmids, diffusion ensures that both daughter cells inherit plasmids after cell division. In contrast, most low-copy-number plasmids need to be actively partitioned by a conserved tripartite ParA-type system. ParA is an ATPase that binds to chromosomal DNA; ParB is the stimulator of the ParA ATPase and specifically binds to the plasmid at a centromere-like site, parS...
April 11, 2017: Biophysical Journal
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