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https://www.readbyqxmd.com/read/28644444/energy-and-carbon-metabolisms-in-a-deep-terrestrial-subsurface-fluid-microbial-community
#1
Lily Momper, Sean P Jungbluth, Michael D Lee, Jan P Amend
The terrestrial deep subsurface is a huge repository of microbial biomass, but in relation to its size and physical heterogeneity, few sites have been investigated in detail. Here, we applied a culture-independent metagenomic approach to characterize the microbial community composition in deep (1500 meters below surface) terrestrial fluids. Samples were collected from a former gold mine in Lead, South Dakota, USA, now Sanford Underground Research Facility (SURF). We reconstructed 74 genomes from metagenomes (MAGs), enabling the identification of common metabolic pathways...
June 23, 2017: ISME Journal
https://www.readbyqxmd.com/read/28644443/unexpected-genomic-features-in-widespread-intracellular-bacteria-evidence-for-motility-of-marine-chlamydiae
#2
Astrid Collingro, Stephan Köstlbacher, Marc Mussmann, Ramunas Stepanauskas, Steven J Hallam, Matthias Horn
Chlamydiae are obligate intracellular bacteria comprising important human pathogens and symbionts of protists. Molecular evidence indicates a tremendous diversity of chlamydiae particularly in marine environments, yet our current knowledge is based mainly on terrestrial representatives. Here we provide first insights into the biology of marine chlamydiae representing three divergent clades. Our analysis of single-cell amplified genomes revealed hallmarks of the chlamydial lifestyle, supporting the ancient origin of their characteristic developmental cycle and major virulence mechanisms...
June 23, 2017: ISME Journal
https://www.readbyqxmd.com/read/28644442/linking-the-development-and-functioning-of-a-carnivorous-pitcher-plant-s-microbial-digestive-community
#3
David W Armitage
Ecosystem development theory predicts that successional turnover in community composition can influence ecosystem functioning. However, tests of this theory in natural systems are made difficult by a lack of replicable and tractable model systems. Using the microbial digestive associates of a carnivorous pitcher plant, I tested hypotheses linking host age-driven microbial community development to host functioning. Monitoring the yearlong development of independent microbial digestive communities in two pitcher plant populations revealed a number of trends in community succession matching theoretical predictions...
June 23, 2017: ISME Journal
https://www.readbyqxmd.com/read/28632811/management-of-poorly-controlled-indolent-systemic-mastocytosis-using-narrowband-uvb-phototherapy
#4
Zain Husain, Dylan Waterman, Kathleen Ellison, Jennifer A DeSimone
The mastocytoses comprise a group of proliferative stem cell disorders defined by the abnormal accumulation of mast cells (MCs) in the skin or other body tissues including the bone marrow, gastrointestinal tract, and liver. Systemic mastocytosis is defined by the presence of one major and one minor criterion or 3 minor criteria delineated by the World Health Organization (WHO). We present the case of a 57-year-old woman with a 10-year history of red-brown pruritic maculopapular lesions on the upper and lower extremities and trunk who was originally diagnosed with cutaneous mastocytosis...
May 2017: Cutis; Cutaneous Medicine for the Practitioner
https://www.readbyqxmd.com/read/28627727/development-of-hgf-binding-aptamers-with-the-combination-of-g4-promoter-derived-aptamer-selection-and-in-silico-maturation
#5
Tomomi Yokoyama, Kaori Tsukakoshi, Wataru Yoshida, Taiki Saito, Kentaro Teramoto, Nasa Savory, Koichi Abe, Kazunori Ikebukuro
We describe the selection of aptamers based on bioinformatics-based approaches without Systematic Evolution of Ligands by EXponential enrichment (SELEX). SELEX is a potent method; however, it is time intensive and the PCR-amplification step, which is essential step for SELEX, leads to the loss of good aptamers. We have developed an aptamer-screening method, G4 promoter-derived aptamer selection (G4PAS), and an aptamer-improving method, in silico maturation (ISM). They are based on in silico sequence selection and computer assisted directed evolution, respectively...
June 19, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28622287/a-niche-for-cyanobacteria-producing-chlorophyll-f-within-a-microbial-mat
#6
Satoshi Ohkubo, Hideaki Miyashita
Acquisition of additional photosynthetic pigments enables photosynthetic organisms to survive in particular niches. To reveal the ecological significance of chlorophyll (Chl) f, we investigated the distribution of Chl and cyanobacteria within two microbial mats. In a 7-mm-thick microbial mat beneath the running water of the Nakabusa hot spring, Japan, Chl f was only distributed 4.0-6.5 mm below the surface, where the intensity of far-red light (FR) was higher than that of photosynthetically active radiation (PAR)...
June 16, 2017: ISME Journal
https://www.readbyqxmd.com/read/28589305/discriminating-ability-of-abbreviated-impactor-measurement-approach-aim-to-detect-changes-in-mass-median-aerodynamic-diameter-mmad-of-an-albuterol-salbutamol-pmdi-aerosol
#7
J David Christopher, Rajni B Patel, Jolyon P Mitchell, Terrence P Tougas, Adrian P Goodey, Jorge Quiroz, Patrik U Andersson, Svetlana Lyapustina
This article reports on results from a two-lab, multiple impactor experiment evaluating the abbreviated impactor measurement (AIM) concept, conducted by the Cascade Impaction Working Group of the International Pharmaceutical Aerosol Consortium on Regulation and Science (IPAC-RS). The goal of this experiment was to expand understanding of the performance of an AIM-type apparatus based on the Andersen eight-stage non-viable cascade impactor (ACI) for the assessment of inhalation aerosols and sprays, compared with the full-resolution version of that impactor described in the pharmacopeial compendia...
June 6, 2017: AAPS PharmSciTech
https://www.readbyqxmd.com/read/28589122/the-future-of-bronchopulmonary-dysplasia-emerging-pathophysiological-concepts-and-potential-new-avenues-of-treatment
#8
REVIEW
Jennifer J P Collins, Dick Tibboel, Ismé M de Kleer, Irwin K M Reiss, Robbert J Rottier
Yearly more than 15 million babies are born premature (<37 weeks gestational age), accounting for more than 1 in 10 births worldwide. Lung injury caused by maternal chorioamnionitis or preeclampsia, postnatal ventilation, hyperoxia, or inflammation can lead to the development of bronchopulmonary dysplasia (BPD), one of the most common adverse outcomes in these preterm neonates. BPD patients have an arrest in alveolar and microvascular development and more frequently develop asthma and early-onset emphysema as they age...
2017: Frontiers in Medicine
https://www.readbyqxmd.com/read/28585941/ubiquity-and-quantitative-significance-of-bacterioplankton-lineages-inhabiting-the-oxygenated-hypolimnion-of-deep-freshwater-lakes
#9
Yusuke Okazaki, Shohei Fujinaga, Atsushi Tanaka, Ayato Kohzu, Hideo Oyagi, Shin-Ichi Nakano
The oxygenated hypolimnion accounts for a volumetrically significant part of the global freshwater systems. Previous studies have proposed the presence of hypolimnion-specific bacterioplankton lineages that are distinct from those inhabiting the epilimnion. To date, however, no consensus exists regarding their ubiquity and abundance, which is necessary to evaluate their ecological importance. The present study investigated the bacterioplankton community in the oxygenated hypolimnia of 10 deep freshwater lakes...
June 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28585940/identifying-the-core-seed-bank-of-a-complex-boreal-bacterial-metacommunity
#10
Clara Ruiz-González, Juan Pablo Niño-García, Steven W Kembel, Paul A Del Giorgio
Seed banks are believed to contribute to compositional changes within and across microbial assemblages, but the application of this concept to natural communities remains challenging. Here we describe the core seed bank of a bacterial metacommunity from a boreal watershed, using the spatial distribution of bacterial operational taxonomic units (OTUs) across 223 heterogeneous terrestrial, aquatic and phyllosphere bacterial assemblages. Taxa were considered potential seeds if they transitioned from rare to abundant somewhere within the metacommunity and if they were ubiquitous and able to persist under unfavorable conditions, the latter assessed by checking their presence in three deeply sequenced samples (one soil, one river and one lake, 2...
June 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28585939/linking-rhizosphere-microbiome-composition-of-wild-and-domesticated-phaseolus-vulgaris-to-genotypic-and-root-phenotypic-traits
#11
Juan E Pérez-Jaramillo, Víctor J Carrión, Mirte Bosse, Luiz F V Ferrão, Mattias de Hollander, Antonio A F Garcia, Camilo A Ramírez, Rodrigo Mendes, Jos M Raaijmakers
Plant domestication was a pivotal accomplishment in human history, but also led to a reduction in genetic diversity of crop species compared to their wild ancestors. How this reduced genetic diversity affected plant-microbe interactions belowground is largely unknown. Here, we investigated the genetic relatedness, root phenotypic traits and rhizobacterial community composition of modern and wild accessions of common bean (Phaseolus vulgaris) grown in agricultural soil from the highlands of Colombia, one of the centers of common bean diversification...
June 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28585938/genomics-and-metagenomics-of-trimethylamine-utilizing-archaea-in-the-human-gut-microbiome
#12
Guillaume Borrel, Angela McCann, Jennifer Deane, Marta C Neto, Denise B Lynch, Jean-François Brugère, Paul W O'Toole
The biological significance of Archaea in the human gut microbiota is largely unclear. We recently reported genomic and biochemical analyses of the Methanomassiliicoccales, a novel order of methanogenic Archaea dwelling in soil and the animal digestive tract. We now show that these Methanomassiliicoccales are present in published microbiome data sets from eight countries. They are represented by five Operational Taxonomic Units present in at least four cohorts and phylogenetically distributed into two clades...
June 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28585937/nitrogen-cost-minimization-is-promoted-by-structural-changes-in-the-transcriptome-of-n-deprived-prochlorococcus-cells
#13
Robert W Read, Paul M Berube, Steven J Biller, Iva Neveux, Andres Cubillos-Ruiz, Sallie W Chisholm, Joseph J Grzymski
Prochlorococcus is a globally abundant marine cyanobacterium with many adaptations that reduce cellular nutrient requirements, facilitating growth in its nutrient-poor environment. One such genomic adaptation is the preferential utilization of amino acids containing fewer N-atoms, which minimizes cellular nitrogen requirements. We predicted that transcriptional regulation might further reduce cellular N budgets during transient N limitation. To explore this, we compared transcription start sites (TSSs) in Prochlorococcus MED4 under N-deprived and N-replete conditions...
June 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28585936/letting-go-bacterial-genome-reduction-solves-the-dilemma-of-adapting-to-predation-mortality-in-a-substrate-restricted-environment
#14
Michael Baumgartner, Stefan Roffler, Thomas Wicker, Jakob Pernthaler
Resource limitation and predation mortality are major determinants of microbial population dynamics, and optimization for either aspect is considered to imply a trade-off with respect to the other. Adaptation to these selective factors may, moreover, lead to disadvantages at rich growth conditions. We present an example of a concomitant evolutionary optimization to both, substrate limitation and predation in an aggregate-forming freshwater bacterial isolate, and we elucidate an underlying genomic mechanism...
June 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28585935/shifts-in-rhizosphere-fungal-community-during-secondary-succession-following-abandonment-from-agriculture
#15
S Emilia Hannula, Elly Morriën, Mattias de Hollander, Wim H van der Putten, Johannes A van Veen, Wietse de Boer
Activities of rhizosphere microbes are key to the functioning of terrestrial ecosystems. It is commonly believed that bacteria are the major consumers of root exudates and that the role of fungi in the rhizosphere is mostly limited to plant-associated taxa, such as mycorrhizal fungi, pathogens and endophytes, whereas less is known about the role of saprotrophs. In order to test the hypothesis that the role of saprotrophic fungi in rhizosphere processes increases with increased time after abandonment from agriculture, we determined the composition of fungi that are active in the rhizosphere along a chronosequence of ex-arable fields in the Netherlands...
June 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28585934/crenothrix-are-major-methane-consumers-in-stratified-lakes
#16
Kirsten Oswald, Jon S Graf, Sten Littmann, Daniela Tienken, Andreas Brand, Bernhard Wehrli, Mads Albertsen, Holger Daims, Michael Wagner, Marcel Mm Kuypers, Carsten J Schubert, Jana Milucka
Methane-oxidizing bacteria represent a major biological sink for methane and are thus Earth's natural protection against this potent greenhouse gas. Here we show that in two stratified freshwater lakes a substantial part of upward-diffusing methane was oxidized by filamentous gamma-proteobacteria related to Crenothrix polyspora. These filamentous bacteria have been known as contaminants of drinking water supplies since 1870, but their role in the environmental methane removal has remained unclear. While oxidizing methane, these organisms were assigned an 'unusual' methane monooxygenase (MMO), which was only distantly related to 'classical' MMO of gamma-proteobacterial methanotrophs...
June 6, 2017: ISME Journal
https://www.readbyqxmd.com/read/28574490/capturing-the-genetic-makeup-of-the-active-microbiome-in-situ
#17
Esther Singer, Michael Wagner, Tanja Woyke
More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates...
June 2, 2017: ISME Journal
https://www.readbyqxmd.com/read/28571627/directed-evolution-of-thermomyces-lanuginosus-lipase-to-enhance-methanol-tolerance-for-efficient-production-of-biodiesel-from-waste-grease
#18
Kaiyuan Tian, Kee Tai, Bryan Jian Wei Chua, Zhi Li
Engineering a methanol tolerant lipase is of great importance in biodiesel production. Here, the first semi-rational method for directed enzyme evolution to enhance methanol tolerance by targeting high B-factor residues for iterative saturation mutagenesis (ISM) is reported. The best double mutant, TLL-S105C/D27R, retained 71% of its original activity after incubation in methanol, showing 30% greater methanol tolerance than TLL. TLL-S105C/D27R also displayed 27% higher activity over TLL. Structure modelling suggested that the increased stability of TLL-S105C/D27R was caused by the formation of a new hydrogen bond which stabilized the protein structure...
May 19, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28567680/determination-of-a-new-index-of-sexual-maturity-ism-in-zebra-mussel-using-flow-cytometry-interest-in-ecotoxicology
#19
Gabrielle Magniez, Alban Franco, Alain Geffard, Damien Rioult, Isabelle Bonnard, Laurence Delahaut, Sandrine Joachim, Gaëlle Daniele, Emmanuelle Vulliet, Jean-Marc Porcher, Marc Bonnard
The global dynamic spread of chemical contamination through the aquatic environment calls for the development of biomarkers of interest. Reproduction is a key element to be considered because it is related to the sustainability of species. Spermatogenesis is a complex process that leads to the formation of mature germ cells, whose steps and impairments need to be finely described in ecotoxicological analyses. The physiological process has been commonly described by histological analyses of gonads in different taxa...
May 31, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28556091/incremental-sampling-methodology-applications-for-background-screening-assessments
#20
Penelope S Pooler, Philip E Goodrum, Deana Crumbling, Leah D Stuchal, Stephen M Roberts
This article presents the findings from a numerical simulation study that was conducted to evaluate the performance of alternative statistical analysis methods for background screening assessments when data sets are generated with incremental sampling methods (ISMs). A wide range of background and site conditions are represented in order to test different ISM sampling designs. Both hypothesis tests and upper tolerance limit (UTL) screening methods were implemented following U.S. Environmental Protection Agency (USEPA) guidance for specifying error rates...
May 29, 2017: Risk Analysis: An Official Publication of the Society for Risk Analysis
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