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Community assembly

Inimary T Toby, Mikhail K Levin, Edward A Salinas, Scott Christley, Sanchita Bhattacharya, Felix Breden, Adam Buntzman, Brian Corrie, John Fonner, Namita T Gupta, Uri Hershberg, Nishanth Marthandan, Aaron Rosenfeld, William Rounds, Florian Rubelt, Walter Scarborough, Jamie K Scott, Mohamed Uduman, Jason A Vander Heiden, Richard H Scheuermann, Nancy Monson, Steven H Kleinstein, Lindsay G Cowell
BACKGROUND: The genes that produce antibodies and the immune receptors expressed on lymphocytes are not germline encoded; rather, they are somatically generated in each developing lymphocyte by a process called V(D)J recombination, which assembles specific, independent gene segments into mature composite genes. The full set of composite genes in an individual at a single point in time is referred to as the immune repertoire. V(D)J recombination is the distinguishing feature of adaptive immunity and enables effective immune responses against an essentially infinite array of antigens...
October 6, 2016: BMC Bioinformatics
Stephen J Jacquemin, Mark Pyron
BACKGROUND: Aquatic habitats have been altered over the past century due to a variety of anthropogenic influences. Ecomorphology is an area of aquatic ecology that can both directly and indirectly assess the effects of habitat alterations on organisms. However, few studies have explored long term trends in morphological variation. Long term changes in morphology can potentially impact niche and ultimately contribute to organismal success and the ecosystem. Therefore, in this study we assessed long term morphological variation with body size, sex, time, and hydrology using museum collections of five species of Cyprinidae (Minnows) from lentic and lotic systems over the past 100 years to gain insight into long term patterns in morphology...
October 20, 2016: BMC Ecology
Siavash Isazadeh, Shameem Jauffur, Dominic Frigon
Effect of ecological variables on community assembly of heterotrophic bacteria at eight full-scale and two pilot-scale activated sludge wastewater treatment plants (AS-WWTPs) were explored by pyrosequencing of 16S rRNA gene amplicons. In total, 39 samples covering a range of abiotic factors spread over space and time were analyzed. A core bacterial community of 24 families detected in at least six of the eight AS-WWTPs was defined. In addition to the core families, plant-specific families (observed at <50% AS-WWTPs) were found to be also important in the community structure...
October 19, 2016: MicrobiologyOpen
Laura M Cisneros, Matthew E Fagan, Michael R Willig
BACKGROUND: Assembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms...
2016: PeerJ
Scott Ferrenberg, Alexander S Martinez, Akasha M Faist
BACKGROUND: Understanding patterns of biodiversity is a longstanding challenge in ecology. Similar to other biotic groups, arthropod community structure can be shaped by deterministic and stochastic processes, with limited understanding of what moderates the relative influence of these processes. Disturbances have been noted to alter the relative influence of deterministic and stochastic processes on community assembly in various study systems, implicating ecological disturbances as a potential moderator of these forces...
2016: PeerJ
Chhaya M Werner, Kurt J Vaughn, Katharine L Stuble, Kristina Wolf, Truman P Young
The order of species arrival can dramatically alter the trajectory of community development. While there is experimental evidence that priority effects can be important drivers of community structure early on, the persistence and duration of these effects is unclear. Here we report on a community assembly experiment in which a mix of four native grasses and a mix of four native forbs were planted on their own, together, or with one-year priority over the other guild. We found positive effects of priority for both grasses and forbs in the initial years of the experiment...
September 2016: Ecological Applications: a Publication of the Ecological Society of America
Julian C Shillcock, Michael Hawrylycz, Sean Hill, Hanchuan Peng
Large-scale brain initiatives such as the US BRAIN initiative and the European Human Brain Project aim to marshall a vast amount of data and tools for the purpose of furthering our understanding of brains. Fundamental to this goal is that neuronal morphologies must be seamlessly reconstructed and aggregated on scales up to the whole rodent brain. The experimental labor needed to manually produce this number of digital morphologies is prohibitively large. The BigNeuron initiative is assembling community-generated, open-source, automated reconstruction algorithms into an open platform, and is beginning to generate an increasing flow of high-quality reconstructed neurons...
February 24, 2016: Brain Informatics
Marek S Skrzypek, Jonathan Binkley, Gail Binkley, Stuart R Miyasato, Matt Simison, Gavin Sherlock
The Candida Genome Database (CGD, is a freely available online resource that provides gene, protein and sequence information for multiple Candida species, along with web-based tools for accessing, analyzing and exploring these data. The mission of CGD is to facilitate and accelerate research into Candida pathogenesis and biology, by curating the scientific literature in real time, and connecting literature-derived annotations to the latest version of the genomic sequence and its annotations...
October 13, 2016: Nucleic Acids Research
Mikael Pontarp, Owen L Petchey
The expected link between competitive exclusion and community trait overdispersion has been used to infer competition in local communities, and trait clustering has been interpreted as habitat filtering. Such community assembly process inference has received criticism for ignoring trophic interactions, as competition and trophic interactions might create similar trait patterns. While other theoretical studies have generally demonstrated the importance of predation for coexistence, ours provides the first quantitative demonstration of such effects on assembly process inference, using a trait-based ecological model to simulate the assembly of a competitive primary consumer community with and without the influence of trophic interactions...
October 12, 2016: Proceedings. Biological Sciences
Johan Asplund, David A Wardle
Lichens occur in most terrestrial ecosystems; they are often present as minor contributors, but in some forests, drylands and tundras they can make up most of the ground layer biomass. As such, lichens dominate approximately 8% of the Earth's land surface. Despite their potential importance in driving ecosystem biogeochemistry, the influence of lichens on community processes and ecosystem functioning have attracted relatively little attention. Here, we review the role of lichens in terrestrial ecosystems and draw attention to the important, but often overlooked role of lichens as determinants of ecological processes...
October 11, 2016: Biological Reviews of the Cambridge Philosophical Society
Francisca Mutapi
Schistosomiasis, commonly known as bilharzia, is a parasitic disease prevalent in Africa, Asia and South America. The majority of the cases occur in Sub-Saharan Africa where schistosomiasis is a major public health problem impacting on child health and development as well as adult health when infections become chronic. Control of schistosomiasis is by treatment of infected people with the antihelminthic drug praziquantel. Current schistosome control programmes advocated by the World Health Assembly in 2001 are aimed at regular school-based integrated deworming strategies in order to reduce development of severe morbidity, promote school health and to improve cognitive potential of children...
October 12, 2016: Parasitology
Stefano Levi Mortera, Federica Del Chierico, Pamela Vernocchi, Maria M Rosado, Agnese Cavola, Marco Chierici, Luisa Pieroni, Andrea Urbani, Rita Carsetti, Isabella Lante, Bruno Dallapiccola, Lorenza Putignani
At birth, contact with external stimuli, such as nutrients derived from food, is necessary to modulate the symbiotic balance between commensal and pathogenic bacteria, protect against bacterial dysbiosis, and initiate the development of the mucosal immune response. Among a variety of different feeding patterns, breastfeeding represents the best modality. In fact, the capacity of breast milk to modulate the composition of infants' gut microbiota leads to beneficial effects on their health. In this study, we used newborn mice as a model to evaluate the effect of parental genetic background (i...
2016: Frontiers in Microbiology
Kevin C Lee, Stephen D J Archer, Rachel H Boyle, Donnabella C Lacap-Bugler, Jayne Belnap, Stephen B Pointing
A common feature of microbial colonization in deserts is biological soil crusts (BSCs), and these comprise a complex community dominated by Cyanobacteria. Rock substrates, particularly sandstone, are also colonized by microbial communities. These are separated by bare sandy soil that also supports microbial colonization. Here we report a high-throughput sequencing study of BSC and cryptoendolith plus adjacent bare soil communities in the Colorado Plateau Desert, Utah, USA. Bare soils supported a community with low levels of recoverable DNA and high evenness, whilst BSC yielded relatively high recoverable DNA, and reduced evenness compared to bare soil due to specialized crust taxa...
2016: Frontiers in Microbiology
Qing Mao, Serban Ciotlos, Rebecca Yu Zhang, Madeleine P Ball, Robert Chin, Paolo Carnevali, Nina Barua, Staci Nguyen, Misha R Agarwal, Tom Clegg, Abram Connelly, Ward Vandewege, Alexander Wait Zaranek, Preston W Estep, George M Church, Radoje Drmanac, Brock A Peters
BACKGROUND: Since the completion of the Human Genome Project in 2003, it is estimated that more than 200,000 individual whole human genomes have been sequenced. A stunning accomplishment in such a short period of time. However, most of these were sequenced without experimental haplotype data and are therefore missing an important aspect of genome biology. In addition, much of the genomic data is not available to the public and lacks phenotypic information. FINDINGS: As part of the Personal Genome Project, blood samples from 184 participants were collected and processed using Complete Genomics' Long Fragment Read technology...
October 11, 2016: GigaScience
Celine A Mandon, Loïc Jacques Blum, Christophe Andre Marquette
3D printing technologies will impact in a near future the biosensor community, both at the sensor prototyping level and the sensing layer or-ganization level. The present study aimed at demonstrating the capacity of one 3D printing technique, the Digital Light Processing (DLP), to produce hydrogel sensing layers with 3D shapes unreachable using conventional molding procedures. The first model of sensing layer was com-posed of a sequential enzymatic reaction (glucose oxidase and peroxidase) which generated chemiluminescent signal in the presence of glucose and luminol...
October 11, 2016: Analytical Chemistry
Yuma Takahashi, Koh-Ichi Takakura, Masakado Kawata
Understanding the mechanisms shaping the spatiotemporal distribution of species has long been a central concern of ecology and evolutionary biology. Contemporary patterns of plant assemblies suggest that sexual interactions among species, i.e., reproductive interference, lead to the exclusive distributions of closely related species that share pollinators. However, the fitness consequences and the initial ecological/evolutionary responses to reproductive interference remain unclear in nature, since reproductive isolation or allopatric distribution has already been achieved in the natural community...
2016: PloS One
Joseph A LaManna, Thomas E Martin
Understanding the causes underlying changes in species diversity is a fundamental pursuit of ecology. Animal species richness and composition often change with decreased forest structural complexity associated with logging. Yet differences in latitude and forest type may strongly influence how species diversity responds to logging. We performed a meta-analysis of logging effects on local species richness and composition of birds across the world and assessed responses by different guilds (nesting strata, foraging strata, diet, and body size)...
October 10, 2016: Biological Reviews of the Cambridge Philosophical Society
Stuart P McElroy, Philip S Jones, Denise V Barrault
With industry increasingly sourcing preclinical drug discovery projects from academia it is important that new academic discoveries are enabled through translation with HTS-ready assays. However, many scientifically interesting, novel molecular targets lack associated high-quality, robust assays suitable for hit finding and development. To bridge this gap, the Scottish Universities Life Sciences Alliance (SULSA) established a fund to develop assays to meet quality criteria such as those of the European Lead Factory...
October 5, 2016: Drug Discovery Today
Ronald D Bassar, Troy Simon, William Roberts, Joseph Travis, David N Reznick
Species coexistence may result by chance when co-occurring species do not strongly interact or it may be an evolutionary outcome of strongly interacting species adapting to each other. While patterns like character displacement indicate that coexistence has often been an evolutionary outcome, it is unclear how often the evolution of coexistence represents adaptation in only one species or reciprocal adaptation among all interacting species. Here we demonstrate a strong role for evolution in the coexistence of guppies and killifish in Trinidadian streams...
October 8, 2016: Evolution; International Journal of Organic Evolution
Xubin Pan
BACKGROUND: Species-area relationship (SAR), endemics-area relationship (EAR) and overlap-area relationship (OAR) are three important concepts in biodiversity study. The application of fundamental equations linking the SAR, EAR and OAR, can enrich the axiomatic framework of the species-area theory and deepen our understanding of the mechanisms of community assembly. RESULTS: Two fundamental equations are derived and extended to power law model and random replacement model of species-area distribution...
October 7, 2016: BMC Ecology
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