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Community assembly

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https://www.readbyqxmd.com/read/28818037/association-of-coral-algal-symbionts-with-a-diverse-viral-community-responsive-to-heat-shock
#1
Jan D Brüwer, Shobhit Agrawal, Yi Jin Liew, Manuel Aranda, Christian R Voolstra
BACKGROUND: Stony corals provide the structural foundation of coral reef ecosystems and are termed holobionts given they engage in symbioses, in particular with photosynthetic dinoflagellates of the genus Symbiodinium. Besides Symbiodinium, corals also engage with bacteria affecting metabolism, immunity, and resilience of the coral holobiont, but the role of associated viruses is largely unknown. In this regard, the increase of studies using RNA sequencing (RNA-Seq) to assess gene expression provides an opportunity to elucidate viral signatures encompassed within the data via careful delineation of sequence reads and their source of origin...
August 17, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28815998/architects-of-nature-growing-buildings-with-bacterial-biofilms
#2
Martyn Dade-Robertson, Alona Keren-Paz, Meng Zhang, Ilana Kolodkin-Gal
In his text 'On Architecture', Vitruvius suggested that architecture is an imitation of nature. Here we discuss what happens when we begin using nature in architecture. We describe recent developments in the study of biofilm structure, and propose combining modern architecture and synthetic microbiology to develop sustainable construction approaches. Recently, Kolodkin-Gal laboratory and others revealed a role for precipitation of calcium carbonate in the maturation and assembly of bacterial communities with complex structures...
August 16, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28815132/precision-diagnosis-of-melanoma-and-other-skin-lesions-from-digital-images
#3
Abhishek Bhattacharya, Albert Young, Andrew Wong, Simone Stalling, Maria Wei, Dexter Hadley
Melanoma will affect an estimated 73,000 new cases this year and result in 9,000 deaths, yet precise diagnosis remains a serious problem. Without early detection and preventative care, melanoma can quickly spread to become fatal (Stage IV 5-year survival rate is 20-10%) from a once localized skin lesion (Stage IA 5- year survival rate is 97%). There is no biomarker for melanoma in clinical use, and the current diagnostic criteria for skin lesions remains subjective and imprecise. Accurate diagnosis of melanoma relies on a histopathologic gold standard; thus, aggressive excision of melanocytic skin lesions has been the mainstay of treatment...
2017: AMIA Summits on Translational Science Proceedings
https://www.readbyqxmd.com/read/28814757/top-canopy-nitrogen-allocation-linked-to-increased-grassland-carbon-uptake-in-stands-of-varying-species-richness
#4
Alexandru Milcu, Arthur Gessler, Christiane Roscher, Laura Rose, Zachary Kayler, Dörte Bachmann, Karin Pirhofer-Walzl, Saša Zavadlav, Lucia Galiano, Tina Buchmann, Michael Scherer-Lorenzen, Jacques Roy
Models predict that vertical gradients of foliar nitrogen (N) allocation, increasing from bottom to top of plant canopies, emerge as a plastic response to optimise N utilisation for carbon assimilation. While this mechanism has been well documented in monocultures, its relevance for mixed stands of varying species richness remains poorly understood. We used 21 naturally assembled grassland communities to analyse the gradients of N in the canopy using N allocation coefficients (K N ) estimated from the distribution of N per foliar surface area (KN-F) and ground surface area (KN-G)...
August 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28814645/zygotic-genome-activation-occurs-shortly-after-fertilization-in-maize
#5
Junyi Chen, Nicholas Strieder, Nadia G Krohn, Philippe Cyprys, Stefanie Sprunck, Julia C Engelmann, Thomas Dresselhaus
The formation of a zygote via the fusion of an egg and sperm cell and its subsequent asymmetric division (ACD) herald the start of the plant's life cycle. Zygotic genome activation (ZGA) is thought to occur gradually, with the initial steps of zygote and embryo development being primarily maternally controlled, and subsequent steps being governed by the zygotic genome. Here, using maize (Zea mays) as a model plant system, we determined the timing of zygote development and generated RNA-Seq transcriptome profiles of gametes, zygotes, and apical and basal daughter cells...
August 16, 2017: Plant Cell
https://www.readbyqxmd.com/read/28813450/oral-microbial-community-assembly-under-the-influence-of-periodontitis
#6
Hongju Chen, Shuting Peng, Lin Dai, Quan Zou, Bin Yi, Xianghong Yang, Zhanshan Sam Ma
Several ecological hypotheses (e.g., specific plaque, non-specific plaque and keystone pathogen) regarding the etiology of periodontitis have been proposed since the 1990s, most of which have been centered on the concept of dysbiosis associated with periodontitis. Nevertheless, none of the existing hypotheses have presented mechanistic interpretations on how and why dysbiosis actually occurs. Hubbell's neutral theory of biodiversity offers a powerful null model to test hypothesis regarding the mechanism of community assembly and diversity maintenance from the metagenomic sequencing data, which can help to understand the forces that shape the community dynamics such as dysbiosis...
2017: PloS One
https://www.readbyqxmd.com/read/28812687/community-structure-follows-simple-assembly-rules-in-microbial-microcosms
#7
Jonathan Friedman, Logan M Higgins, Jeff Gore
Microorganisms typically form diverse communities of interacting species, whose activities have tremendous impact on the plants, animals and humans they associate with. The ability to predict the structure of these complex communities is crucial to understanding and managing them. Here, we propose a simple, qualitative assembly rule that predicts community structure from the outcomes of competitions between small sets of species, and experimentally assess its predictive power using synthetic microbial communities composed of up to eight soil bacterial species...
March 27, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812653/adaptation-of-phytoplankton-to-a-decade-of-experimental-warming-linked-to-increased-photosynthesis
#8
C-Elisa Schaum, Samuel Barton, Elvire Bestion, Angus Buckling, Bernardo Garcia-Carreras, Paula Lopez, Chris Lowe, Samraat Pawar, Nicholas Smirnoff, Mark Trimmer, Gabriel Yvon-Durocher
Phytoplankton photosynthesis is a critical flux in the carbon cycle, accounting for approximately 40% of the carbon dioxide fixed globally on an annual basis and fuelling the productivity of aquatic food webs. However, rapid evolutionary responses of phytoplankton to warming remain largely unexplored, particularly outside the laboratory, where multiple selection pressures can modify adaptation to environmental change. Here, we use a decade-long experiment in outdoor mesocosms to investigate mechanisms of adaptation to warming (+4 °C above ambient temperature) in the green alga Chlamydomonas reinhardtii, in naturally assembled communities...
March 20, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28811885/manipulation-of-habitat-isolation-and-area-implicates-deterministic-factors-and-limited-neutrality-in-community-assembly
#9
Terry J Ord, Jack Emblen, Mattias Hagman, Ryan Shofner, Sara Unruh
Theory predicts deterministic and stochastic factors will contribute to community assembly in different ways: Environmental filters should regulate those species that establish in a particular area resulting in the ecological requirements of species being the primary driver of species distributions, while chance and dispersal limitation should dictate the likelihood of species reaching certain areas with the ecology of species being largely neutral. These factors are specifically relevant for understanding how the area and isolation of different habitats or islands interact to affect community composition...
August 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28811648/scale-dependent-changes-in-the-functional-diversity-of-macrophytes-in-subtropical-freshwater-lakes-in-south-china
#10
Hui Fu, Jiayou Zhong, Shaowen Fang, Jianmin Hu, Chunjing Guo, Qian Lou, Guixiang Yuan, Taotao Dai, Zhongqiang Li, Meng Zhang, Wei Li, Jun Xu, Te Cao
Ecological processes are generally scale-dependent and there is little consensus about the relative importance of deterministic versus stochastic processes in driving patterns of biological diversity. We investigated how the relationship between functional dispersion and environmental gradients changes with spatial scale in subtropical freshwater lakes. The functional alpha and beta dispersions of all the tested traits were significantly under-dispersed across spatial scales and along environmental gradients...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28810707/seasonal-and-spatial-variations-of-prokaryoplankton-communities-in-a-salinity-influenced-watershed-china
#11
Anyi Hu, Hongjie Wang, Xiaoyang Yang, Liyuan Hou, Jiangwei Li, Shuang Li, Chang-Ping Yu
Prokaryotes represent the largest biodiversity pool and drive the biogeochemical cycles in fluvial environments. However, the mechanisms underlying the assembly of prokaryotic communities are largely unexplored at taxonomic and functional levels, simultaneously. Here, we investigated the spatio-seasonal distribution of prokaryoplankton communities in a salinity-influenced watershed, China using 16S rRNA gene amplicon sequencing. The OTUs were divided into core and satellite, based on a statistical approach...
August 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28808554/arthropod-communities-on-hybrid-and-parental-cottonwoods-are-phylogenetically-structured-by-tree-type-implications-for-conservation-of-biodiversity-in-plant-hybrid-zones
#12
Karl J Jarvis, Gerard J Allan, Ashley J Craig, Rebecca K Beresic-Perrins, Gina Wimp, Catherine A Gehring, Thomas G Whitham
Although hybridization in plants has been recognized as an important pathway in plant speciation, it may also affect the ecology and evolution of associated communities. Cottonwood species (Populus angustifolia and P. fremontii) and their naturally occurring hybrids are known to support different plant, animal, and microbial communities, but no studies have examined community structure within the context of phylogenetic history. Using a community composed of 199 arthropod species, we tested for differences in arthropod phylogenetic patterns within and among hybrid and parental tree types in a common garden...
August 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28808302/effects-of-one-week-empirical-antibiotic-therapy-on-the-early-development-of-gut-microbiota-and-metabolites-in-preterm-infants
#13
Danping Zhu, Sa Xiao, Jialin Yu, Qing Ai, Yu He, Chen Cheng, Yunhui Zhang, Yun Pan
The early postnatal period is the most dynamic and vulnerable stage in the assembly of intestinal microbiota. Antibiotics are commonly prescribed to newborn preterm babies and are frequently used for a prolonged duration in China. We hypothesized that the prolonged antibiotic therapy would affect the early development of intestinal microbiota and their metabolites. To test this hypothesis, we analyzed the stool microbiota and metabolites in 36 preterm babies with or without antibiotic treatment. These babies were divided into three groups, including two groups treated with the combination of penicillin and moxalactam or piperacillin-tazobactam for 7 days, and the other group was free of antibiotics...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28808103/a-bioarchitectonic-approach-to-the-modular-engineering-of-metabolism
#14
REVIEW
Cheryl A Kerfeld
Dissociating the complexity of metabolic processes into modules is a shift in focus from the single gene/gene product to functional and evolutionary units spanning the scale of biological organization. When viewing the levels of biological organization through this conceptual lens, modules are found across the continuum: domains within proteins, co-regulated groups of functionally associated genes, operons, metabolic pathways and (sub)cellular compartments. Combining modules as components or subsystems of a larger system typically leads to increased complexity and the emergence of new functions...
September 26, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28805396/transport-properties-of-a-two-dimensional-pbse-square-superstructure-in-an-electrolyte-gated-transistor
#15
M Alimoradi Jazi, V A E C Janssen, W H Evers, A Tadjine, C Delerue, L D A Siebbeles, H S J van der Zant, A J Houtepen, D Vanmaekelbergh
Self-assembled nanocrystal solids show promise as a versatile platform for novel optoelectronic materials. Superlattices composed of a single layer of lead-chalcogenide and cadmium-chalcogenide nanocrystals with epitaxial connections between the nanocrystals, present outstanding questions to the community regarding their predicted band structure and electronic transport properties. However, the as-prepared materials are intrinsic semiconductors; to occupy the bands in a controlled way, chemical doping or external gating is required...
August 16, 2017: Nano Letters
https://www.readbyqxmd.com/read/28802076/single-cell-sequencing-unveils-the-lifestyle-and-crispr-based-population-history-of-hydrotalea-sp-in-acid-mine-drainage
#16
J D Medeiros, L R Leite, V S Pylro, F S Oliveira, V M Almeida, G R Fernandes, A C M Salim, F M G Araújo, A C Volpini, G Oliveira, S Cuadros-Orellana
Acid mine drainage (AMD) is characterized by an acid and metal-rich runoff that originates from mining systems. Despite having been studied for many decades, much remains unknown about the microbial community dynamics in AMD sites, especially during their early development, when the acidity is moderate. Here, we describe draft genome assemblies from single cells retrieved from an early-stage AMD sample. These cells belong to the genus Hydrotalea, and is closely related to H. flava. The phylogeny and average nucleotide identity analysis suggest that all single-amplified genomes (SAGs) form two clades that may represent different strains...
August 12, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28800158/using-kbase-to-assemble-and-annotate-prokaryotic-genomes
#17
Benjamin Allen, Meghan Drake, Nomi Harris, Tarah Sullivan
The DOE Systems Biology Knowledgebase (KBase, http://kbase.us/) is an open-access bioinformatics software and data platform for analyzing plants, microbes, and their communities. KBase enables scientists to create, execute, collaborate on, and share reproducible analyses of their biological data in the context of public data and private collaborator data. For microbiologists researching prokaryotes, KBase offers analysis tools for performing quality control and assessment of Next-Generation Sequencing reads, de novo assembly, genome annotation, and tools for analyzing structural and functional features of genomes...
August 11, 2017: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/28796821/legacy-of-historic-ozone-exposure-on-plant-community-and-food-web-structure
#18
M Alejandra Martínez-Ghersa, Analía I Menéndez, Pedro E Gundel, Ana M Folcia, Ana M Romero, Jennifer B Landesmann, Laura Ventura, Claudio M Ghersa
Information on whole community responses is needed to predict direction and magnitude of changes in plant and animal abundance under global changes. This study quantifies the effect of past ozone exposure on a weed community structure and arthropod colonization. We used the soil seed bank resulting from a long-term ozone exposure to reestablish the plant community under a new low-pollution environment. Two separate experiments using the same original soil seed bank were conducted. Plant and arthropod richness and species abundance was assessed during two years...
2017: PloS One
https://www.readbyqxmd.com/read/28783117/the-role-of-functional-amyloids-in-multicellular-growth-and-development-of-gram-positive-bacteria
#19
REVIEW
Anna Dragoš, Ákos T Kovács, Dennis Claessen
Amyloid fibrils play pivotal roles in all domains of life. In bacteria, these fibrillar structures are often part of an extracellular matrix that surrounds the producing organism and thereby provides protection to harsh environmental conditions. Here, we discuss the role of amyloid fibrils in the two distant Gram-positive bacteria, Streptomyces coelicolor and Bacillus subtilis. We describe how amyloid fibrils contribute to a multitude of developmental processes in each of these systems, including multicellular growth and community development...
August 7, 2017: Biomolecules
https://www.readbyqxmd.com/read/28773852/design-of-decorated-self-assembling-peptide-hydrogels-as-architecture-for-mesenchymal-stem-cells
#20
Annj Zamuner, Marta Cavo, Silvia Scaglione, Grazia Maria Lucia Messina, Teresa Russo, Antonio Gloria, Giovanni Marletta, Monica Dettin
Hydrogels from self-assembling ionic complementary peptides have been receiving a lot of interest from the scientific community as mimetic of the extracellular matrix that can offer three-dimensional supports for cell growth or can become vehicles for the delivery of stem cells, drugs or bioactive proteins. In order to develop a 3D "architecture" for mesenchymal stem cells, we propose the introduction in the hydrogel of conjugates obtained by chemoselective ligation between a ionic-complementary self-assembling peptide (called EAK) and three different bioactive molecules: an adhesive sequence with 4 Glycine-Arginine-Glycine-Aspartic Acid-Serine-Proline (GRGDSP) motifs per chain, an adhesive peptide mapped on h-Vitronectin and the growth factor Insulin-like Growth Factor-1 (IGF-1)...
August 26, 2016: Materials
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