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https://www.readbyqxmd.com/read/29048858/-simultaneous-determination-of-diminazene-aceturate-and-isometamidium-chloride-residues-in-cattle-tissues-by-high-performance-liquid-chromatography-with-solid-phase-extraction
#1
Yuhui Zhou, Zhenling Zeng, Jingxian Yu, Rong Liu, Lihua Pan, Qiuyu Zhong, Hong Chen
A method for the simultaneous determination of trypanocidal diminazene aceturate (DIM) and isometamidium chloride (ISM) that containing benzamidine groups in cattle tissues was developed by high performance liquid chromatography (HPLC) with solid-phase extraction (SPE). The tissue samples were extracted with different proportions of water-acetonitrile, then were cleaned up by Oasis WCX cartridges. DIM and ISM were separated by HPLC with a Spherisorb CN column (250 mm×4.6 mm, 5 μm). Acetonitrile-0.05 mol/L ammonium formate solution (pH 2...
September 8, 2017: Se Pu, Chinese Journal of Chromatography
https://www.readbyqxmd.com/read/29039844/soil-microbial-diversity-drives-the-priming-effect-along-climate-gradients-a-case-study-in-madagascar
#2
Kanto Razanamalala, Tantely Razafimbelo, Pierre-Alain Maron, Lionel Ranjard, Nicolas Chemidlin, Mélanie Lelièvre, Samuel Dequiedt, Volaniaina H Ramaroson, Claire Marsden, Thierry Becquer, Jean Trap, Eric Blanchart, Laetitia Bernard
The priming effect in soil is proposed to be generated by two distinct mechanisms: 'stoichiometric decomposition' and/or 'nutrient mining' theories. Each mechanism has its own dynamics, involves its own microbial actors, and targets different soil organic matter (SOM) pools. The present study aims to evaluate how climatic parameters drive the intensity of each priming effect generation mechanism via the modification of soil microbial and physicochemical properties. Soils were sampled in the center of Madagascar, along climatic gradients designed to distinguish temperature from rainfall effects...
October 17, 2017: ISME Journal
https://www.readbyqxmd.com/read/29039843/acetoclastic-methanosaeta-are-dominant-methanogens-in-organic-rich-antarctic-marine-sediments
#3
Stephanie A Carr, Florence Schubotz, Robert B Dunbar, Christopher T Mills, Robert Dias, Roger E Summons, Kevin W Mandernack
Despite accounting for the majority of sedimentary methane, the physiology and relative abundance of subsurface methanogens remain poorly understood. We combined intact polar lipid and metagenome techniques to better constrain the presence and functions of methanogens within the highly reducing, organic-rich sediments of Antarctica's Adélie Basin. The assembly of metagenomic sequence data identified phylogenic and functional marker genes of methanogens and generated the first Methanosaeta sp. genome from a deep subsurface sedimentary environment...
October 17, 2017: ISME Journal
https://www.readbyqxmd.com/read/29039418/rapid-nonlinear-image-scanning-microscopy
#4
Ingo Gregor, Martin Spiecker, Roman Petrovsky, Jörg Großhans, Robert Ros, Jörg Enderlein
Image scanning microscopy (ISM) doubles the resolution of a conventional confocal microscope for super-resolution imaging. Here, we describe an all-optical ISM design based on rescanning microscopy for two-photon-excited fluorescence and second-harmonic generation that allows straightforward implementation into existing microscopes. The design offers improved sensitivity and high frame rates relative to those of existing systems. We demonstrate its utility using fixed and living specimens as well as collagen hydrogels...
October 16, 2017: Nature Methods
https://www.readbyqxmd.com/read/29036099/image-formation-in-image-scanning-microscopy-including-the-case-of-two-photon-excitation
#5
Colin J R Sheppard, Marco Castello, Giorgio Tortarolo, Giuseppe Vicidomini, Alberto Diaspro
The effect of combining the image scanning microscopy (ISM) technique with two-photon fluorescence microscopy is analyzed. The effective spatial frequency cutoff can be doubled, as compared with conventional two-photon fluorescence microscopy, and the magnitude of the optical transfer function near the cutoff of conventional two-photon microscopy is increased by orders of magnitude. For the two-photon case, it is found that the optimum pixel reassignment factor in ISM is not equal to one half, as is often assumed in single-photon fluoresence image scanning microscopy, because the excitation and detection point spread functions are different...
August 1, 2017: Journal of the Optical Society of America. A, Optics, Image Science, and Vision
https://www.readbyqxmd.com/read/29032180/genomic-analysis-of-isometamidium-chloride-resistance-in-trypanosoma-congolense
#6
Eliane Tihon, Hideo Imamura, Frederik Van den Broeck, Lieve Vermeiren, Jean-Claude Dujardin, Jan Van Den Abbeele
Isometamidium Chloride (ISM) is one of the principal drugs used to counteract Trypanosoma congolense infection in livestock, both as a prophylactic as well as a curative treatment. However, numerous cases of ISM resistance have been reported in different African regions, representing a significant constraint in the battle against Animal African Trypanosomiasis. In order to identify genetic signatures associated with ISM resistance in T. congolense, the sensitive strain MSOROM7 was selected for induction of ISM resistance in a murine host...
October 6, 2017: International Journal for Parasitology, Drugs and Drug Resistance
https://www.readbyqxmd.com/read/29028869/mg-rast-version-4-lessons-learned-from-a-decade-of-low-budget-ultra-high-throughput-metagenome-analysis
#7
Folker Meyer, Saurabh Bagchi, Somali Chaterji, Wolfgang Gerlach, Ananth Grama, Travis Harrison, Tobias Paczian, William L Trimble, Andreas Wilke
As technologies change, MG-RAST is adapting. Newly available software is being included to improve accuracy and performance. As a computational service constantly running large volume scientific workflows, MG-RAST is the right location to perform benchmarking and implement algorithmic or platform improvements, in many cases involving trade-offs between specificity, sensitivity and run-time cost. The work in [Glass EM, Dribinsky Y, Yilmaz P, et al. ISME J 2014;8:1-3] is an example; we use existing well-studied data sets as gold standards representing different environments and different technologies to evaluate any changes to the pipeline...
September 26, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29028006/polymorphism-of-antibiotic-inactivating-enzyme-driven-by-ecology-expands-the-environmental-resistome
#8
Dae-Wi Kim, Cung Nawl Thawng, Jung-Hye Choi, Kihyun Lee, Chang-Jun Cha
The environmental resistome has been recognized as the origin and reservoir of antibiotic resistance genes and considered to be dynamic and ever expanding. In this study, a targeted gene sequencing approach revealed that the polymorphic diversity of the aminoglycoside-inactivating enzyme AAC(6')-Ib was ecological niche-specific. AAC(6')-Ib-cr, previously known as a clinical variant, was prevalent in various soils and the intestines of chickens and humans, suggesting that this variant might not have arisen from adaptive mutations in the clinic but instead originated from the environment...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29028005/microbiome-and-infectivity-studies-reveal-complex-polyspecies-tree-disease-in-acute-oak-decline
#9
Sandra Denman, James Doonan, Emma Ransom-Jones, Martin Broberg, Sarah Plummer, Susan Kirk, Kelly Scarlett, Andrew R Griffiths, Maciej Kaczmarek, Jack Forster, Andrew Peace, Peter N Golyshin, Francis Hassard, Nathan Brown, John G Kenny, James E McDonald
Decline-diseases are complex and becoming increasingly problematic to tree health globally. Acute Oak Decline (AOD) is characterized by necrotic stem lesions and galleries of the bark-boring beetle, Agrilus biguttatus, and represents a serious threat to oak. Although multiple novel bacterial species and Agrilus galleries are associated with AOD lesions, the causative agent(s) are unknown. The AOD pathosystem therefore provides an ideal model for a systems-based research approach to address our hypothesis that AOD lesions are caused by a polymicrobial complex...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29028004/geobiological-feedbacks-and-the-evolution-of-thermoacidophiles
#10
Daniel R Colman, Saroj Poudel, Trinity L Hamilton, Jeff R Havig, Matthew J Selensky, Everett L Shock, Eric S Boyd
Oxygen-dependent microbial oxidation of sulfur compounds leads to the acidification of natural waters. How acidophiles and their acidic habitats evolved, however, is largely unknown. Using 16S rRNA gene abundance and composition data from 72 hot springs in Yellowstone National Park, Wyoming, we show that hyperacidic (pH<3.0) hydrothermal ecosystems are dominated by a limited number of archaeal lineages with an inferred ability to respire O2. Phylogenomic analyses of 584 existing archaeal genomes revealed that hyperacidophiles evolved independently multiple times within the Archaea, each coincident with the emergence of the ability to respire O2, and that these events likely occurred in the recent evolutionary past...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29028003/bacterial-secretion-of-d-arginine-controls-environmental-microbial-biodiversity
#11
Laura Alvarez, Alena Aliashkevich, Miguel A de Pedro, Felipe Cava
Bacteria face tough competition in polymicrobial communities. To persist in a specific niche, many species produce toxic extracellular effectors to interfere with the growth of nearby microbes. These effectors include the recently reported non-canonical D-amino acids (NCDAAs). In Vibrio cholerae, the causative agent of cholera, NCDAAs control cell wall integrity in stationary phase. Here, an analysis of the composition of the extracellular medium of V. cholerae revealed the unprecedented presence of D-Arg. Compared with other D-amino acids, D-Arg displayed higher potency and broader toxicity in terms of the number of bacterial species affected...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29028002/cyanophage-encoded-lipid-desaturases-oceanic-distribution-diversity-and-function
#12
Sheila Roitman, Ellen Hornung, José Flores-Uribe, Itai Sharon, Ivo Feussner, Oded Béjà
Cyanobacteria are among the most abundant photosynthetic organisms in the oceans; viruses infecting cyanobacteria (cyanophages) can alter cyanobacterial populations, and therefore affect the local food web and global biochemical cycles. These phages carry auxiliary metabolic genes (AMGs), which rewire various metabolic pathways in the infected host cell, resulting in increased phage fitness. Coping with stress resulting from photodamage appears to be a central necessity of cyanophages, yet the overall mechanism is poorly understood...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29028001/soil-protist-communities-form-a-dynamic-hub-in-the-soil-microbiome
#13
Wu Xiong, Alexandre Jousset, Sai Guo, Ida Karlsson, Qingyun Zhao, Huasong Wu, George A Kowalchuk, Qirong Shen, Rong Li, Stefan Geisen
Soil microbes are essential for soil fertility. However, most studies focus on bacterial and/or fungal communities, while the top-down drivers of this microbiome composition, protists, remain poorly understood. Here, we investigated how soil amendments affect protist communities and inferred potential interactions with bacteria and fungi. Specific fertilization treatments impacted both the structure and function of protist communities. Organic fertilizer amendment strongly reduced the relative abundance of plant pathogenic protists and increased bacterivorous and omnivorous protists...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29028000/influence-of-resistance-breeding-in-common-bean-on-rhizosphere-microbiome-composition-and-function
#14
Lucas William Mendes, Jos M Raaijmakers, Mattias de Hollander, Rodrigo Mendes, Siu Mui Tsai
The rhizosphere microbiome has a key role in plant growth and health, providing a first line of defense against root infections by soil-borne pathogens. Here, we investigated the composition and metabolic potential of the rhizobacterial community of different common bean (Phaseolus vulgaris) cultivars with variable levels of resistance to the fungal root pathogen Fusarium oxysporum (Fox). For the different bean cultivars grown in two soils with contrasting physicochemical properties and microbial diversity, rhizobacterial abundance was positively correlated with Fox resistance...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29027999/a-population-genomics-approach-shows-widespread-geographical-distribution-of-cryptic-genomic-forms-of-the-symbiotic-fungus-rhizophagus-irregularis
#15
Romain Savary, Frédéric G Masclaux, Tania Wyss, Germain Droh, Joaquim Cruz Corella, Ana Paula Machado, Joseph B Morton, Ian R Sanders
Arbuscular mycorrhizal fungi (AMF; phylum Gomeromycota) associate with plants forming one of the most successful microbe-plant associations. The fungi promote plant diversity and have a potentially important role in global agriculture. Plant growth depends on both inter- and intra-specific variation in AMF. It was recently reported that an unusually large number of AMF taxa have an intercontinental distribution, suggesting long-distance gene flow for many AMF species, facilitated by either long-distance natural dispersal mechanisms or human-assisted dispersal...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29027998/temporal-dynamics-of-uncultured-viruses-a-new-dimension-in-viral-diversity
#16
Ksenia Arkhipova, Timofey Skvortsov, John P Quinn, John W McGrath, Christopher Cr Allen, Bas E Dutilh, Yvonne McElarney, Leonid A Kulakov
Recent work has vastly expanded the known viral genomic sequence space, but the seasonal dynamics of viral populations at the genome level remain unexplored. Here we followed the viral community in a freshwater lake for 1 year using genome-resolved viral metagenomics, combined with detailed analyses of the viral community structure, associated bacterial populations and environmental variables. We reconstructed 8950 complete and partial viral genomes, the majority of which were not persistent in the lake throughout the year, but instead continuously succeeded each other...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29027997/microdiversification-in-genome-streamlined-ubiquitous-freshwater-actinobacteria
#17
Stefan M Neuenschwander, Rohit Ghai, Jakob Pernthaler, Michaela M Salcher
Actinobacteria of the acI lineage are the most abundant microbes in freshwater systems, but there are so far no pure living cultures of these organisms, possibly because of metabolic dependencies on other microbes. This, in turn, has hampered an in-depth assessment of the genomic basis for their success in the environment. Here we present genomes from 16 axenic cultures of acI Actinobacteria. The isolates were not only of minute cell size, but also among the most streamlined free-living microbes, with extremely small genome sizes (1...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29027996/aquatic-urban-ecology-at-the-scale-of-a-capital-community-structure-and-interactions-in-street-gutters
#18
Vincent Hervé, Boris Leroy, Albert Da Silva Pires, Pascal Jean Lopez
In most cities, streets are designed for collecting and transporting dirt, litter, debris, storm water and other wastes as a municipal sanitation system. Microbial mats can develop on street surfaces and form microbial communities that have never been described. Here, we performed the first molecular inventory of the street gutter-associated eukaryotes across the entire French capital of Paris and the non-potable waters sources. We found that the 5782 OTUs (operational taxonomic units) present in the street gutters which are dominated by diatoms (photoautotrophs), fungi (heterotrophs), Alveolata and Rhizaria, includes parasites, consumers of phototrophs and epibionts that may regulate the dynamics of gutter mat microbial communities...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/28994824/single-cell-genomics-of-uncultured-marine-alveolates-shows-paraphyly-of-basal-dinoflagellates
#19
Jürgen F H Strassert, Anna Karnkowska, Elisabeth Hehenberger, Javier Del Campo, Martin Kolisko, Noriko Okamoto, Fabien Burki, Jan Janouškovec, Camille Poirier, Guy Leonard, Steven J Hallam, Thomas A Richards, Alexandra Z Worden, Alyson E Santoro, Patrick J Keeling
Marine alveolates (MALVs) are diverse and widespread early-branching dinoflagellates, but most knowledge of the group comes from a few cultured species that are generally not abundant in natural samples, or from diversity analyses of PCR-based environmental SSU rRNA gene sequences. To more broadly examine MALV genomes, we generated single cell genome sequences from seven individually isolated cells. Genes expected of heterotrophic eukaryotes were found, with interesting exceptions like presence of proteorhodopsin and vacuolar H(+)-pyrophosphatase...
October 10, 2017: ISME Journal
https://www.readbyqxmd.com/read/28984847/mycorrhizal-fungi-show-regular-community-compositions-in-natural-ecosystems
#20
Erik Verbruggen, Merlin Sheldrake, Luke D Bainard, Baodong Chen, Tobias Ceulemans, Johan De Gruyter, Maarten Van Geel
Dissimilarity overlap curve analysis has shown that 'universality' is a common feature in many complex microbial communities, suggesting that the same taxa interact in a similar manner when shared between communities. We present evidence that arbuscular mycorrhizal fungi, common plant root symbionts, show universal community compositions in natural ecosystems and that this pattern is conserved even at larger spatial scales. However, universality was not detected in agricultural ecosystems potentially implying that agricultural symbiont communities are formed in a different manner...
October 6, 2017: ISME Journal
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