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https://www.readbyqxmd.com/read/28644617/dynamic-covalent-chemistry-of-carbon-dioxide-opportunities-to-address-environmental-issues
#1
Jean Septavaux, Geoffroy Germain, Julien Leclaire
Extraction and purification of basic chemicals from complex mixtures has been a persistent issue throughout the development of the chemical sciences. The chemical industry and academic research have grown over the centuries by following a deconstruction-reconstruction approach, reminiscent of the metabolism process. Chemists have designed and optimized extraction, purification, and transformation processes of molecules from natural deposits (fossil fuels, biomass, ores), in order to reassemble them into complex adducts...
June 23, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28644126/extensive-horizontal-gene-transfer-in-cheese-associated-bacteria
#2
Kevin S Bonham, Benjamin E Wolfe, Rachel J Dutton
Acquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly-sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4,844 protein coding genes...
June 23, 2017: ELife
https://www.readbyqxmd.com/read/28643787/single-virus-genomics-reveals-hidden-cosmopolitan-and-abundant-viruses
#3
Francisco Martinez-Hernandez, Oscar Fornas, Monica Lluesma Gomez, Benjamin Bolduc, Maria Jose de la Cruz Peña, Joaquín Martínez Martínez, Josefa Anton, Josep M Gasol, Riccardo Rosselli, Francisco Rodriguez-Valera, Matthew B Sullivan, Silvia G Acinas, Manuel Martinez-Garcia
Microbes drive ecosystems under constraints imposed by viruses. However, a lack of virus genome information hinders our ability to answer fundamental, biological questions concerning microbial communities. Here we apply single-virus genomics (SVGs) to assess whether portions of marine viral communities are missed by current techniques. The majority of the here-identified 44 viral single-amplified genomes (vSAGs) are more abundant in global ocean virome data sets than published metagenome-assembled viral genomes or isolates...
June 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28642991/extensive-overlap-of-tropical-rainforest-bacterial-endophytes-between-soil-plant-parts-and-plant-species
#4
Emmanuel Haruna, Noraziah M Zin, Dorsaf Kerfahi, Jonathan M Adams
The extent to which distinct bacterial endophyte communities occur between different plant organs and species is poorly known and has implications for bioprospecting efforts. Using the V3 region of the bacterial 16S ribosomal RNA (rRNA) gene, we investigated the diversity patterns of bacterial endophyte communities of three rainforest plant species, comparing leaf, stem, and root endophytes plus rhizosphere soil community. There was extensive overlap in bacterial communities between plant organs, between replicate plants of the same species, between plant species, and between plant organ and rhizosphere soil, with no consistent clustering by compartment or host plant species...
June 22, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28642740/multigenerational-influences-of-the-fut2-gene-on-the-dynamics-of-the-gut-microbiota-in-mice
#5
Philipp Rausch, Sven Künzel, Abdulhadi Suwandi, Guntram A Grassl, Philip Rosenstiel, John F Baines
The FUT2 gene encodes an α-1,2-fucosyltransferase responsible for the expression of ABO histo-blood-group antigens on mucosal surfaces and bodily secretions. Individuals who carry at least one functional allele are known as "secretors," whereas those homozygous for loss-of-function mutations are known as "non-secretors." Non-secretor individuals are more susceptible to chronic inflammatory disorders such as Crohn's Disease, which may be mediated by alterations in the microbiota. Here, we investigated the dynamics of microbial community assembly with respect to genotype using a Fut2-deficient mouse model, taking the genotype of the maternal lineage over two generations into account...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28642735/functional-and-compositional-stability-of-bacterial-metacommunities-in-response-to-salinity-changes
#6
Mercè Berga, Yinghua Zha, Anna J Székely, Silke Langenheder
Disturbances and environmental change are important factors determining the diversity, composition, and functioning of communities. However, knowledge about how natural bacterial communities are affected by such perturbations is still sparse. We performed a whole ecosystem manipulation experiment with freshwater rock pools where we applied salinity disturbances of different intensities. The aim was to test how the compositional and functional resistance and resilience of bacterial communities, alpha- and beta-diversity and the relative importance of stochastic and deterministic community assembly processes changed along a disturbance intensity gradient...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28640897/impact-of-selected-non-steroidal-anti-inflammatory-pharmaceuticals-on-microbial-community-assembly-and-activity-in-sequencing-batch-reactors
#7
Cong Jiang, Jinju Geng, Haidong Hu, Haijun Ma, Xingsheng Gao, Hongqiang Ren
This study covers three widely detected non-steroidal anti-inflammatory pharmaceuticals (NSAIDs), diclofenac (DCF), ibuprofen (IBP) and naproxen (NPX), as NSAIDs pollutants. The objective is to evaluate the impact of NSAIDs at their environmental concentrations on microbial community assembly and activity. The exposure experiments were conducted under three conditions (5 μg L-1 DCF, 5 μg L-1 DCF+5 μg L-1 IBP and 5 μg L-1 DCF+5 μg L-1 IBP+ 5 μg L-1 NPX) in sequencing batch reactors (SBRs) for 130 days...
2017: PloS One
https://www.readbyqxmd.com/read/28637243/nanopore-sequencing-data-analysis-state-of-the-art-applications-and-challenges
#8
Alberto Magi, Roberto Semeraro, Alessandra Mingrino, Betti Giusti, Romina D'Aurizio
The nanopore sequencing process is based on the transit of a DNA molecule through a nanoscopic pore, and since the 90s is considered as one of the most promising approaches to detect polymeric molecules. In 2014, Oxford Nanopore Technologies (ONT) launched a beta-testing program that supplied the scientific community with the first prototype of a nanopore sequencer: the MinION. Thanks to this program, several research groups had the opportunity to evaluate the performance of this novel instrument and develop novel computational approaches for analyzing this new generation of data...
June 16, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28631400/effects-of-uranium-concentration-on-microbial-community-structure-and-functional-potential
#9
Brodie Sutcliffe, Anthony A Chariton, Andrew J Harford, Grant C Hose, Greenfield Paul, Liam D H Elbourne, Yalchin Oytam, Sarah Stephenson, David J Midgley, Ian T Paulsen
Located in the Northern Territory of Australia, Ranger uranium mine is directly adjacent to the UNESCO World Heritage listed Kakadu National Park, with rehabilitation targets needed to ensure the site can be incorporated into the park following the mine's closure in 2026. This study aimed to understand the impact of uranium concentration on microbial communities, in order to identify and describe potential breakpoints in microbial ecosystem services. This is the first study to report in situ deployment of uranium-spiked sediments along a concentration gradient (0 - 4,000 mg U/kg), with the study design maximising the advantages of both field surveys and laboratory manipulative studies...
June 19, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28627464/analysis-of-protein-complexes-in-arabidopsis-leaves-using-size-exclusion-chromatography-and-label-free-protein-correlation-profiling
#10
Uma K Aryal, Zachary McBride, Donglai Chen, Jun Xie, Daniel B Szymanski
Protein complexes are fundamentally important for diverse cellular functions, and create functionalities that could never be achieved by a single polypeptide. Knowledge of the protein complex assemblies that exist in plant cells are limited. To close this gap, we applied an integrative proteomic approach that combines cell fractionation, protein chromatography and quantitative mass spectrometry (MS) to analyze the oligomerization state of thousands of proteins in a single experiment. Soluble extracts from intact Arabidopsis leaves were fractionated using size exclusion chromatography (SEC), and abundance profiles across the column fractions were quantified using label-free precursor ion (MS1) intensity...
June 13, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28617645/the-implications-of-eco-evolutionary-processes-for-the-emergence-of-marine-plankton-community-biogeography
#11
Boris Sauterey, Ben Ward, Jonathan Rault, Chris Bowler, David Claessen
Models of community assembly have been used to illustrate how the many functionally diverse species that compose plankton food webs can coexist. However, the evolutionary processes leading to the emergence of plankton food webs and their interplay with migratory processes and spatial heterogeneity are yet to be explored. We study the eco-evolutionary dynamics of a modeled plankton community structured in both size and space and physiologically constrained by empirical data. We demonstrate that a complex yet ecologically and evolutionarily stable size-structured food web can emerge from an initial set of two monomorphic phytoplankton and zooplankton populations...
July 2017: American Naturalist
https://www.readbyqxmd.com/read/28616183/dissecting-spatiotemporal-patterns-of-functional-diversity-through-the-lens-of-darwin-s-naturalization-conundrum
#12
Sara E Campbell, Nicholas E Mandrak
Darwin's naturalization conundrum describes the paradigm that community assembly is regulated by two opposing processes, environmental filtering and competitive interactions, which predict both similarity and distinctiveness of species to be important for establishment. Our goal is to use long-term, large-scale, and high-resolution temporal data to examine diversity patterns over time and assess whether environmental filtering or competition plays a larger role in regulating community assembly processes. We evaluated Darwin's naturalization conundrum and how functional diversity has changed in the Laurentian Great Lakes fish community from 1870 to 2010, which has experienced frequent introductions of non-native species and extirpations of native species...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28616180/sustained-functional-composition-of-pollinators-in-restored-pastures-despite-slow-functional-restoration-of-plants
#13
Marie Winsa, Erik Öckinger, Riccardo Bommarco, Regina Lindborg, Stuart P M Roberts, Johanna Wärnsberg, Ignasi Bartomeus
Habitat restoration is a key measure to counteract negative impacts on biodiversity from habitat loss and fragmentation. To assess success in restoring not only biodiversity, but also functionality of communities, we should take into account the re-assembly of species trait composition across taxa. Attaining such functional restoration would depend on the landscape context, vegetation structure, and time since restoration. We assessed how trait composition of plant and pollinator (bee and hoverfly) communities differ between abandoned, restored (formerly abandoned) or continuously grazed (intact) semi-natural pastures...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28615110/an-accident-at-work-traumatic-lesions-in-the-skeleton-of-a-4th-millennium-bce-wagon-driver-from-sharakhalsun-russia
#14
K Tucker, N Berezina, S Reinhold, A Kalmykov, A Belinskiy, J Gresky
The study of ante-mortem trauma is a popular and important aspect of palaeopathological analysis. The majority of publications focus on a particular assemblage, skeletal element or type of fracture, with case studies of single individuals with multiple/unusual traumata being much rarer in the literature. This paper presents the case of an adult male from the Bronze Age site of Sharakhalsun, Russia, buried, uniquely, in a sitting position on a fully assembled wagon, who displayed evidence for multiple healed ante-mortem fractures of the cranium, axial and appendicular skeleton...
June 1, 2017: Homo: Internationale Zeitschrift Für die Vergleichende Forschung Am Menschen
https://www.readbyqxmd.com/read/28613433/a-weight-of-evidence-framework-for-environmental-assessments-inferring-qualities
#15
Glenn Suter, Susan Cormier, Mace Barron
The weighing of heterogeneous evidence such as conventional laboratory toxicity tests, field tests, biomarkers, and community surveys is essential to environmental assessments. Evidence synthesis and weighing is needed to determine causes of observed effects, hazards posed by chemicals or other agents, the completeness of remediation, and other environmental qualities. As part of its guidelines for WoE in ecological assessments, the U.S. Environmental Protection Agency has developed a generally applicable framework...
June 14, 2017: Integrated Environmental Assessment and Management
https://www.readbyqxmd.com/read/28611807/size-and-reproductive-traits-rather-than-leaf-economic-traits-explain-plant-community-composition-in-species-rich-annual-vegetation-along-a-gradient-of-land-use-intensity
#16
Inga Dirks, Rita Dumbur, Patrick Lienin, Michael Kleyer, José M Grünzweig
Agricultural land use imposes a major disturbance on ecosystems worldwide, thus greatly modifying the taxonomic and functional composition of plant communities. However, mechanisms of community assembly, as assessed by plant functional traits, are not well known for dryland ecosystems under agricultural disturbance. Here we investigated trait responses to disturbance intensity and availability of resources to identify the main drivers of changes in composition of semiarid communities under diverging land use intensities...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28608022/manipulation-of-local-environment-produces-different-diversity-outcomes-depending-on-location-within-a-river-network
#17
Brett M Tornwall, Christopher M Swan, Bryan L Brown
Ecologists have long been interested in mechanisms governing community composition and assembly. Spatial connectivity is one potential mechanism that can have a large influence on community processes. In accordance with network metrics such as closeness and betweenness, headwater streams are more isolated than mainstem streams. Theory and observational studies predict that community structure in isolated locations of dispersal networks should respond more strongly to manipulations of local conditions, whereas well-connected communities subject to high levels of dispersal should not respond strongly to local manipulations...
June 13, 2017: Oecologia
https://www.readbyqxmd.com/read/28607843/ecophylogeny-of-the-endospheric-root-fungal-microbiome-of-co-occurring-agrostis-stolonifera
#18
Amandine Lê Van, Achim Quaiser, Marie Duhamel, Sophie Michon-Coudouel, Alexis Dufresne, Philippe Vandenkoornhuyse
BACKGROUND: Within the root endosphere, fungi are known to be important for plant nutrition and resistance to stresses. However, description and understanding of the rules governing community assembly in the fungal fraction of the plant microbiome remains scarce. METHODS: We used an innovative DNA- and RNA-based analysis of co-extracted nucleic acids to reveal the complexity of the fungal community colonizing the roots of an Agrostis stolonifera population. The normalized RNA/DNA ratio, designated the 'mean expression ratio', was used as a functional trait proxy...
2017: PeerJ
https://www.readbyqxmd.com/read/28607222/indium-doped-sno2-nanobelts-for-high-performance-transparent-and-flexible-photosensors-by-a-facile-assembly
#19
Shahid Muhammad, Yuting Wang, Jun Yang, Tianjun Li, Yang Xing, Jing Cheng, Mengfei Zhang, Chunlei Wan, Wei Pan
Flexible and transparent electronics is the emerging future technology for the optoelectronics devices. Recently, it has attracted a considerable attention from the research community due to its prodigious commercial applications. Herein, we report highly flexible and transparent ultraviolet photosensors based on indium doped tin oxide nanobelts with enhanced photosensitivity and recovery speed at the same time, as compared to the pure SnO2 nanobelts. The opto-electronics properties of the nanobelts photosensors have been found in strong relation with indium doping concentration and the grain size of the nanobelts...
June 13, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28604713/phagocytosis-inspired-behaviour-in-synthetic-protocell-communities-of-compartmentalized-colloidal-objects
#20
Laura Rodríguez-Arco, Mei Li, Stephen Mann
The spontaneous assembly of micro-compartmentalized colloidal objects capable of controlled interactions offers a step towards rudimentary forms of collective behaviour in communities of artificial cell-like entities (synthetic protocells). Here we report a primitive form of artificial phagocytosis in a binary community of synthetic protocells in which multiple silica colloidosomes are selectively ingested by self-propelled magnetic Pickering emulsion (MPE) droplets comprising particle-free fatty acid-stabilized apertures...
June 12, 2017: Nature Materials
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