Sample records for including functional diversity
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Functional & phylogenetic diversity of copepod communities
NASA Astrophysics Data System (ADS)
Benedetti, F.; Ayata, S. D.; Blanco-Bercial, L.; Cornils, A.; Guilhaumon, F.
2016-02-01
The diversity of natural communities is classically estimated through species identification (taxonomic diversity) but can also be estimated from the ecological functions performed by the species (functional diversity), or from the phylogenetic relationships among them (phylogenetic diversity). Estimating functional diversity requires the definition of specific functional traits, i.e., phenotypic characteristics that impact fitness and are relevant to ecosystem functioning. Estimating phylogenetic diversity requires the description of phylogenetic relationships, for instance by using molecular tools. In the present study, we focused on the functional and phylogenetic diversity of copepod surface communities in the Mediterranean Sea. First, we implemented a specific trait database for the most commonly-sampled and abundant copepod species of the Mediterranean Sea. Our database includes 191 species, described by seven traits encompassing diverse ecological functions: minimal and maximal body length, trophic group, feeding type, spawning strategy, diel vertical migration and vertical habitat. Clustering analysis in the functional trait space revealed that Mediterranean copepods can be gathered into groups that have different ecological roles. Second, we reconstructed a phylogenetic tree using the available sequences of 18S rRNA. Our tree included 154 of the analyzed Mediterranean copepod species. We used these two datasets to describe the functional and phylogenetic diversity of copepod surface communities in the Mediterranean Sea. The replacement component (turn-over) and the species richness difference component (nestedness) of the beta diversity indices were identified. Finally, by comparing various and complementary aspects of plankton diversity (taxonomic, functional, and phylogenetic diversity) we were able to gain a better understanding of the relationships among the zooplankton community, biodiversity, ecosystem function, and environmental forcing.
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NASA Technical Reports Server (NTRS)
Dean, Bruce H. (Inventor)
2009-01-01
A method of recovering unknown aberrations in an optical system includes collecting intensity data produced by the optical system, generating an initial estimate of a phase of the optical system, iteratively performing a phase retrieval on the intensity data to generate a phase estimate using an initial diversity function corresponding to the intensity data, generating a phase map from the phase retrieval phase estimate, decomposing the phase map to generate a decomposition vector, generating an updated diversity function by combining the initial diversity function with the decomposition vector, generating an updated estimate of the phase of the optical system by removing the initial diversity function from the phase map. The method may further include repeating the process beginning with iteratively performing a phase retrieval on the intensity data using the updated estimate of the phase of the optical system in place of the initial estimate of the phase of the optical system, and using the updated diversity function in place of the initial diversity function, until a predetermined convergence is achieved.
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Plant diversity and root traits benefit physical properties key to soil function in grasslands.
Gould, Iain J; Quinton, John N; Weigelt, Alexandra; De Deyn, Gerlinde B; Bardgett, Richard D
2016-09-01
Plant diversity loss impairs ecosystem functioning, including important effects on soil. Most studies that have explored plant diversity effects belowground, however, have largely focused on biological processes. As such, our understanding of how plant diversity impacts the soil physical environment remains limited, despite the fundamental role soil physical structure plays in ensuring soil function and ecosystem service provision. Here, in both a glasshouse and a long-term field study, we show that high plant diversity in grassland systems increases soil aggregate stability, a vital structural property of soil, and that root traits play a major role in determining diversity effects. We also reveal that the presence of particular plant species within mixed communities affects an even wider range of soil physical processes, including hydrology and soil strength regimes. Our results indicate that alongside well-documented effects on ecosystem functioning, plant diversity and root traits also benefit essential soil physical properties. © 2016 The Authors Ecology Letters published by CNRS and John Wiley & Sons Ltd.
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Functional and Taxonomic Diversity of Stinging Wasps in Brazilian Atlantic Rainforest Areas.
Dos Santos, E F; Noll, F B; Brandão, C R F
2014-04-01
Vespoidea are the most functionally diverse superfamily of Hymenoptera. Ecological studies involving this family are primarily based on eusocial groups, including ants and social paper wasps. In the present study, we examine stinging wasp (Vespoidea) faunal diversity in the Atlantic Rain Forest, which is one of the most diverse and threatened ecosystems in the World. Three conservation areas were sampled employing a standardized sample protocol. Families and functional groups of Vespoidea were collected in each area, with the exception ants (Formicidae), and analyzed using diversity analyses, to generate taxonomic diversity and distinctness indices. Results indicated Pompilidae was the most diverse family, and the idiobiont parasitoid type was the most diverse functional group in the three study areas. Núcleo Picinguaba of the Parque Estadual da Serra do Mar was taxonomically and functionally the most diverse and species rich area. Parque Estadual Intervales showed the highest number of dominant species and diversity of koinobiont parasitoids, while the Rebio Sooretama exhibited a decrease in several diversity parameters.
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Faith, Daniel P.
2015-01-01
The phylogenetic diversity measure, (‘PD’), measures the relative feature diversity of different subsets of taxa from a phylogeny. At the level of feature diversity, PD supports the broad goal of biodiversity conservation to maintain living variation and option values. PD calculations at the level of lineages and features include those integrating probabilities of extinction, providing estimates of expected PD. This approach has known advantages over the evolutionarily distinct and globally endangered (EDGE) methods. Expected PD methods also have limitations. An alternative notion of expected diversity, expected functional trait diversity, relies on an alternative non-phylogenetic model and allows inferences of diversity at the level of functional traits. Expected PD also faces challenges in helping to address phylogenetic tipping points and worst-case PD losses. Expected PD may not choose conservation options that best avoid worst-case losses of long branches from the tree of life. We can expand the range of useful calculations based on expected PD, including methods for identifying phylogenetic key biodiversity areas. PMID:25561672
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Matterson, Kenan O.; Freeman, Christopher J.; Archer, Stephanie K.; Thacker, Robert W.
2015-01-01
Recent studies have renewed interest in sponge ecology by emphasizing the functional importance of sponges in a broad array of ecosystem services. Many critically important habitats occupied by sponges face chronic stressors that might lead to alterations in their diversity, relatedness, and functional attributes. We addressed whether proximity to human activity might be a significant factor in structuring sponge community composition, as well as potential functional roles, by monitoring sponge diversity and abundance at two structurally similar sites that vary in distance to areas of high coastal development in Bocas Del Toro, Panama. We surveyed sponge communities at each site using belt transects and differences between two sites were compared using the following variables: (1) sponge species richness, Shannon diversity, and inverse Simpson’s diversity; (2) phylogenetic diversity; (3) taxonomic and phylogenetic beta diversity; (4) trait diversity and dissimilarity; and (5) phylogenetic and trait patterns in community structure. We observed significantly higher sponge diversity at Punta Caracol, the site most distant from human development (∼5 km). Although phylogenetic diversity was lower at Saigon Bay, the site adjacent to a large village including many houses, businesses, and an airport, the sites did not exhibit significantly different patterns of phylogenetic relatedness in species composition. However, each site had a distinct taxonomic and phylogenetic composition (beta diversity). In addition, the sponge community at Saigon included a higher relative abundance of sponges with high microbial abundance and high chlorophyll a concentration, whereas the community at Punta Caracol had a more even distribution of these traits, yielding a significant difference in functional trait diversity between sites. These results suggest that lower diversity and potentially altered community function might be associated with proximity to human populations. This study highlights the importance of evaluating functional traits and phylogenetic diversity in addition to common diversity metrics when assessing potential environmental impacts on benthic communities. PMID:26587347
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Li, Shuai; Dong, Shikui; Zhang, Xiangfeng; Liu, Shiliang; Shi, Jianbin; Gao, Xiaoxia; Swift, David; Xu, Yudan; Shen, Hao; Yang, Mingyue; Margarida, Canhoto Coxixo Ana
2018-04-20
Temperate desert is one of the globally important biomes with unique and valuable biodiversity, which might be threatened by environmental stresses and human disturbance associated with rapid development. However, few studies have documented the spatial distribution of the multifaceted plant diversity of the temperate desert and their relationships with external impacting factors. We sampled multifaceted plant species diversity including taxonomic diversity, functional diversity and phylogenetic diversity in the Alashan Desert along Beijing-Xinjiang Expressway (G6) in Northern China to identify the key factors and process which regulate the multifaceted plant diversity of the temperate desert. We found that the dynamics of species richness, functional richness, and phylogenetic richness along the elevational gradient corresponded to the unimodal model. Species phylogenetic development shifted from aggregation to divergence, while species functional traits were the opposite along the elevational gradient. The sites at an elevation around 1200-1400 m were the key habitats for the occurrence of high plant diversity including species richness, functional richness and phylogenetic richness. There were no significant differences (p > 0.05) in plant diversity at different distances from the road (500 m, 1000 m and 1500 m) and human disturbances (the distance from the nearest human settlements). Temperature, temperature variability, precipitation, precipitation variability, soil physical and chemistry properties showed no significant effects on plant diversity. It was concluded that evolutionary history and functional traits, not environmental or anthropogenic factors were the key determinants of the pattern of multifaceted plant diversity. Copyright © 2018 Elsevier B.V. All rights reserved.
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Faith, Daniel P
2015-02-19
The phylogenetic diversity measure, ('PD'), measures the relative feature diversity of different subsets of taxa from a phylogeny. At the level of feature diversity, PD supports the broad goal of biodiversity conservation to maintain living variation and option values. PD calculations at the level of lineages and features include those integrating probabilities of extinction, providing estimates of expected PD. This approach has known advantages over the evolutionarily distinct and globally endangered (EDGE) methods. Expected PD methods also have limitations. An alternative notion of expected diversity, expected functional trait diversity, relies on an alternative non-phylogenetic model and allows inferences of diversity at the level of functional traits. Expected PD also faces challenges in helping to address phylogenetic tipping points and worst-case PD losses. Expected PD may not choose conservation options that best avoid worst-case losses of long branches from the tree of life. We can expand the range of useful calculations based on expected PD, including methods for identifying phylogenetic key biodiversity areas. © 2015 The Author(s) Published by the Royal Society. All rights reserved.
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USDA-ARS?s Scientific Manuscript database
Natural killer (NK) cells are a diverse population of lymphocytes with a range of biological roles including essential immune functions. NK cell diversity is created by the differential expression of cell surface receptors which modulate activation and function, including multiple subfamilies of C-t...
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Taxonomic and functional trait diversity of wild bees in different urban settings.
Normandin, Étienne; Vereecken, Nicolas J; Buddle, Christopher M; Fournier, Valérie
2017-01-01
Urbanization is one of the major anthropogenic processes contributing to local habitat loss and extirpation of numerous species, including wild bees, the most widespread pollinators. Little is known about the mechanisms through which urbanization impacts wild bee communities, or the types of urban green spaces that best promote their conservation in cities. The main objective of this study was to describe and compare wild bee community diversity, structure, and dynamics in two Canadian cities, Montreal and Quebec City. A second objective was to compare functional trait diversity among three habitat types (cemeteries, community gardens and urban parks) within each city. Bees were collected using pan traps and netting on the same 46 sites, multiple times, over the active season in 2012 and 2013. A total of 32,237 specimens were identified, representing 200 species and 6 families, including two new continental records, Hylaeus communis Nylander (1852) and Anthidium florentinum (Fabricius, 1775). Despite high community evenness, we found significant abundance of diverse species, including exotic ones. Spatio-temporal analysis showed higher stability in the most urbanized city (Montreal) but low nestedness of species assemblages among the three urban habitats in both cities. Our study demonstrates that cities are home to diverse communities of wild bees, but in turn affect bee community structure and dynamics. We also found that community gardens harbour high levels of functional trait diversity. Urban agriculture therefore contributes substantially to the provision of functionally diverse bee communities and possibly to urban pollination services.
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Taxonomic and functional trait diversity of wild bees in different urban settings
Buddle, Christopher M.; Fournier, Valérie
2017-01-01
Urbanization is one of the major anthropogenic processes contributing to local habitat loss and extirpation of numerous species, including wild bees, the most widespread pollinators. Little is known about the mechanisms through which urbanization impacts wild bee communities, or the types of urban green spaces that best promote their conservation in cities. The main objective of this study was to describe and compare wild bee community diversity, structure, and dynamics in two Canadian cities, Montreal and Quebec City. A second objective was to compare functional trait diversity among three habitat types (cemeteries, community gardens and urban parks) within each city. Bees were collected using pan traps and netting on the same 46 sites, multiple times, over the active season in 2012 and 2013. A total of 32,237 specimens were identified, representing 200 species and 6 families, including two new continental records, Hylaeus communis Nylander (1852) and Anthidium florentinum (Fabricius, 1775). Despite high community evenness, we found significant abundance of diverse species, including exotic ones. Spatio-temporal analysis showed higher stability in the most urbanized city (Montreal) but low nestedness of species assemblages among the three urban habitats in both cities. Our study demonstrates that cities are home to diverse communities of wild bees, but in turn affect bee community structure and dynamics. We also found that community gardens harbour high levels of functional trait diversity. Urban agriculture therefore contributes substantially to the provision of functionally diverse bee communities and possibly to urban pollination services. PMID:28286711
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Remote Sensing of a Manipulated Prairie Grassland Experiment to Predict Belowground Processes
NASA Astrophysics Data System (ADS)
Cavender-Bares, J.; Schweiger, A. K.; Hobbie, S. E.; Madritch, M. D.; Wang, Z.; Couture, J. J.; Gamon, J. A.; Townsend, P. A.
2017-12-01
Given the importance of plant biodiversity for providing the ecosystem functions and services on which humans depend, rapid and remote methods of monitoring plant biodiversity across large spatial extents and biological scales are increasingly critical. In North American prairie systems, the ecosystem benefits of diversity are a subject of ongoing investigation and relevance to policy. However, detecting belowground components of ecosystem biodiversity, composition and associated functions are not possible directly through remote sensing. Nevertheless, belowground components of diversity may be linked to aboveground components allowing indirect inferences. Here we test a series of hypotheses about how aboveground functional and chemical diversity and composition of plant communities drive belowground functions, including N mineralization, enzyme activity and microbial biomass, as well as microbial diversity and composition. We hypothesize that the quantity and chemical composition of aboveground inputs to soil drive belowground processes, including decomposition and microbial enzyme activity. We use plant spectra (400 nm to 2500 nm) measured at the leaf and airborne level to determine chemical and functional composition of leaves and canopies in a long-term grassland experiment where diversity is manipulated at the Cedar Creek Ecosystem Science Reserve. We then assess the extent to which belowground chemistry, microbial diversity and composition are predicted from aboveground plant diversity, biomass and chemical composition. We find strong associations between aboveground inputs and belowground enzyme activity and microbial biomass but only weak linkages between aboveground diversity and belowground diversity. We discuss the potential for such approaches and the caveats related to the spatial scale of measurements and spatial resolution of airborne detection.
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Yuan, Zuoqiang; Wang, Shaopeng; Gazol, Antonio; Mellard, Jarad; Lin, Fei; Ye, Ji; Hao, Zhanqing; Wang, Xugao; Loreau, Michel
2016-12-01
Biodiversity can be measured by taxonomic, phylogenetic, and functional diversity. How ecosystem functioning depends on these measures of diversity can vary from site to site and depends on successional stage. Here, we measured taxonomic, phylogenetic, and functional diversity, and examined their relationship with biomass in two successional stages of the broad-leaved Korean pine forest in northeastern China. Functional diversity was calculated from six plant traits, and aboveground biomass (AGB) and coarse woody productivity (CWP) were estimated using data from three forest censuses (10 years) in two large fully mapped forest plots (25 and 5 ha). 11 of the 12 regressions between biomass variables (AGB and CWP) and indices of diversity showed significant positive relationships, especially those with phylogenetic diversity. The mean tree diversity-biomass regressions increased from 0.11 in secondary forest to 0.31 in old-growth forest, implying a stronger biodiversity effect in more mature forest. Multi-model selection results showed that models including species richness, phylogenetic diversity, and single functional traits explained more variation in forest biomass than other candidate models. The models with a single functional trait, i.e., leaf area in secondary forest and wood density in mature forest, provided better explanations for forest biomass than models that combined all six functional traits. This finding may reflect different strategies in growth and resource acquisition in secondary and old-growth forests.
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Chiu, Chun-Huo; Chao, Anne
2014-01-01
Hill numbers (or the “effective number of species”) are increasingly used to characterize species diversity of an assemblage. This work extends Hill numbers to incorporate species pairwise functional distances calculated from species traits. We derive a parametric class of functional Hill numbers, which quantify “the effective number of equally abundant and (functionally) equally distinct species” in an assemblage. We also propose a class of mean functional diversity (per species), which quantifies the effective sum of functional distances between a fixed species to all other species. The product of the functional Hill number and the mean functional diversity thus quantifies the (total) functional diversity, i.e., the effective total distance between species of the assemblage. The three measures (functional Hill numbers, mean functional diversity and total functional diversity) quantify different aspects of species trait space, and all are based on species abundance and species pairwise functional distances. When all species are equally distinct, our functional Hill numbers reduce to ordinary Hill numbers. When species abundances are not considered or species are equally abundant, our total functional diversity reduces to the sum of all pairwise distances between species of an assemblage. The functional Hill numbers and the mean functional diversity both satisfy a replication principle, implying the total functional diversity satisfies a quadratic replication principle. When there are multiple assemblages defined by the investigator, each of the three measures of the pooled assemblage (gamma) can be multiplicatively decomposed into alpha and beta components, and the two components are independent. The resulting beta component measures pure functional differentiation among assemblages and can be further transformed to obtain several classes of normalized functional similarity (or differentiation) measures, including N-assemblage functional generalizations of the classic Jaccard, Sørensen, Horn and Morisita-Horn similarity indices. The proposed measures are applied to artificial and real data for illustration. PMID:25000299
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Chiu, Chun-Huo; Chao, Anne
2014-01-01
Hill numbers (or the "effective number of species") are increasingly used to characterize species diversity of an assemblage. This work extends Hill numbers to incorporate species pairwise functional distances calculated from species traits. We derive a parametric class of functional Hill numbers, which quantify "the effective number of equally abundant and (functionally) equally distinct species" in an assemblage. We also propose a class of mean functional diversity (per species), which quantifies the effective sum of functional distances between a fixed species to all other species. The product of the functional Hill number and the mean functional diversity thus quantifies the (total) functional diversity, i.e., the effective total distance between species of the assemblage. The three measures (functional Hill numbers, mean functional diversity and total functional diversity) quantify different aspects of species trait space, and all are based on species abundance and species pairwise functional distances. When all species are equally distinct, our functional Hill numbers reduce to ordinary Hill numbers. When species abundances are not considered or species are equally abundant, our total functional diversity reduces to the sum of all pairwise distances between species of an assemblage. The functional Hill numbers and the mean functional diversity both satisfy a replication principle, implying the total functional diversity satisfies a quadratic replication principle. When there are multiple assemblages defined by the investigator, each of the three measures of the pooled assemblage (gamma) can be multiplicatively decomposed into alpha and beta components, and the two components are independent. The resulting beta component measures pure functional differentiation among assemblages and can be further transformed to obtain several classes of normalized functional similarity (or differentiation) measures, including N-assemblage functional generalizations of the classic Jaccard, Sørensen, Horn and Morisita-Horn similarity indices. The proposed measures are applied to artificial and real data for illustration.
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M.T. Curzon; A.W. D' Amato; S. Fraver; B.J. Palik; A. Bottero; J.R. Foster; K.E. Gleason
2017-01-01
Concern over global environmental change and associated uncertainty has given rise to greater emphasis on fostering resilience through forest management. We examined the impact of standard silvicultural systems (including clearcutting, shelterwood, and selection) compared with unharvested controls on tree functional identity and functional diversity in three forest...
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Functional, size and taxonomic diversity of fish along a depth gradient in the deep sea.
Mindel, Beth L; Neat, Francis C; Trueman, Clive N; Webb, Thomas J; Blanchard, Julia L
2016-01-01
Biodiversity is well studied in ecology and the concept has been developed to include traits of species, rather than solely taxonomy, to better reflect the functional diversity of a system. The deep sea provides a natural environmental gradient within which to study changes in different diversity metrics, but traits of deep-sea fish are not widely known, hampering the application of functional diversity to this globally important system. We used morphological traits to determine the functional richness and functional divergence of demersal fish assemblages along the continental slope in the Northeast Atlantic, at depths of 300-2,000 m. We compared these metrics to size diversity based on individual body size and species richness. Functional richness and size diversity showed similar patterns, with the highest diversity at intermediate depths; functional divergence showed the opposite pattern, with the highest values at the shallowest and deepest parts of the study site. Species richness increased with depth. The functional implications of these patterns were deduced by examining depth-related changes in morphological traits and the dominance of feeding guilds as illustrated by stable isotope analyses. The patterns in diversity and the variation in certain morphological traits can potentially be explained by changes in the relative dominance of pelagic and benthic feeding guilds. All measures of diversity examined here suggest that the deep areas of the continental slope may be equally or more diverse than assemblages just beyond the continental shelf.
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β-Diversity, Community Assembly, and Ecosystem Functioning.
Mori, Akira S; Isbell, Forest; Seidl, Rupert
2018-05-25
Evidence is increasing for positive effects of α-diversity on ecosystem functioning. We highlight here the crucial role of β-diversity - a hitherto underexplored facet of biodiversity - for a better process-level understanding of biodiversity change and its consequences for ecosystems. A focus on β-diversity has the potential to improve predictions of natural and anthropogenic influences on diversity and ecosystem functioning. However, linking the causes and consequences of biodiversity change is complex because species assemblages in nature are shaped by many factors simultaneously, including disturbance, environmental heterogeneity, deterministic niche factors, and stochasticity. Because variability and change are ubiquitous in ecosystems, acknowledging these inherent properties of nature is an essential step for further advancing scientific knowledge of biodiversity-ecosystem functioning in theory and practice. Copyright © 2018 Elsevier Ltd. All rights reserved.
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Versatile Loading of Diverse Cargo into Functional Polymer Capsules.
Richardson, Joseph J; Maina, James W; Ejima, Hirotaka; Hu, Ming; Guo, Junling; Choy, Mei Y; Gunawan, Sylvia T; Lybaert, Lien; Hagemeyer, Christoph E; De Geest, Bruno G; Caruso, Frank
2015-02-01
Polymer microcapsules are of particular interest for applications including self-healing coatings, catalysis, bioreactions, sensing, and drug delivery. The primary way that polymer capsules can exhibit functionality relevant to these diverse fields is through the incorporation of functional cargo in the capsule cavity or wall. Diverse functional and therapeutic cargo can be loaded into polymer capsules with ease using polymer-stabilized calcium carbonate (CaCO 3 ) particles. A variety of examples are demonstrated, including 15 types of cargo, yielding a toolbox with effectively 500+ variations. This process uses no harsh reagents and can take less than 30 min to prepare, load, coat, and form the hollow capsules. For these reasons, it is expected that the technique will play a crucial role across scientific studies in numerous fields.
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Tobner, Cornelia M; Paquette, Alain; Reich, Peter B; Gravel, Dominique; Messier, Christian
2014-03-01
Increasing concern about loss of biodiversity and its effects on ecosystem functioning has triggered a series of manipulative experiments worldwide, which have demonstrated a general trend for ecosystem functioning to increase with diversity. General mechanisms proposed to explain diversity effects include complementary resource use and invoke a key role for species' functional traits. The actual mechanisms by which complementary resource use occurs remain, however, poorly understood, as well as whether they apply to tree-dominated ecosystems. Here we present an experimental approach offering multiple innovative aspects to the field of biodiversity-ecosystem functioning (BEF) research. The International Diversity Experiment Network with Trees (IDENT) allows research to be conducted at several hierarchical levels within individuals, neighborhoods, and communities. The network investigates questions related to intraspecific trait variation, complementarity, and environmental stress. The goal of IDENT is to identify some of the mechanisms through which individuals and species interact to promote coexistence and the complementary use of resources. IDENT includes several implemented and planned sites in North America and Europe, and uses a replicated design of high-density tree plots of fixed species-richness levels varying in functional diversity (FD). The design reduces the space and time needed for trees to interact allowing a thorough set of mixtures varying over different diversity gradients (specific, functional, phylogenetic) and environmental conditions (e.g., water stress) to be tested in the field. The intention of this paper is to share the experience in designing FD-focused BEF experiments with trees, to favor collaborations and expand the network to different conditions.
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Gill, Aman S; Lee, Angela; McGuire, Krista L
2017-08-15
New York City (NYC) is pioneering green infrastructure with the use of bioswales and other engineered soil-based habitats to provide stormwater infiltration and other ecosystem functions. In addition to avoiding the environmental and financial costs of expanding traditional built infrastructure, green infrastructure is thought to generate cobenefits in the form of diverse ecological processes performed by its plant and microbial communities. Yet, although plant communities in these habitats are closely managed, we lack basic knowledge about how engineered ecosystems impact the distribution and functioning of soil bacteria. We sequenced amplicons of the 16S ribosomal subunit, as well as seven genes associated with functional pathways, generated from both total (DNA-based) and expressed (RNA) soil communities in the Bronx, NYC, NY, in order to test whether bioswale soils host characteristic bacterial communities with evidence for enriched microbial functioning, compared to nonengineered soils in park lawns and tree pits. Bioswales had distinct, phylogenetically diverse bacterial communities, including taxa associated with nutrient cycling and metabolism of hydrocarbons and other pollutants. Bioswale soils also had a significantly greater diversity of genes involved in several functional pathways, including carbon fixation ( cbbL-R [ cbbL gene, red-like subunit] and apsA ), nitrogen cycling ( noxZ and amoA ), and contaminant degradation ( bphA ); conversely, no functional genes were significantly more abundant in nonengineered soils. These results provide preliminary evidence that urban land management can shape the diversity and activity of soil communities, with positive consequences for genetic resources underlying valuable ecological functions, including biogeochemical cycling and degradation of common urban pollutants. IMPORTANCE Management of urban soil biodiversity by favoring taxa associated with decontamination or other microbial metabolic processes is a powerful prospect, but it first requires an understanding of how engineered soil habitats shape patterns of microbial diversity. This research adds to our understanding of urban microbial biogeography by providing data on soil bacteria in bioswales, which had relatively diverse and compositionally distinct communities compared to park and tree pit soils. Bioswales also contained comparatively diverse pools of genes related to carbon sequestration, nitrogen cycling, and contaminant degradation, suggesting that engineered soils may serve as effective reservoirs of functional microbial biodiversity. We also examined both total (DNA-based) and expressed (RNA) communities, revealing that total bacterial communities (the exclusive targets in the vast majority of soil studies) were poor predictors of expressed community diversity, pointing to the value of quantifying RNA, especially when ecological functioning is considered. Copyright © 2017 American Society for Microbiology.
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Lee, Angela; McGuire, Krista L.
2017-01-01
ABSTRACT New York City (NYC) is pioneering green infrastructure with the use of bioswales and other engineered soil-based habitats to provide stormwater infiltration and other ecosystem functions. In addition to avoiding the environmental and financial costs of expanding traditional built infrastructure, green infrastructure is thought to generate cobenefits in the form of diverse ecological processes performed by its plant and microbial communities. Yet, although plant communities in these habitats are closely managed, we lack basic knowledge about how engineered ecosystems impact the distribution and functioning of soil bacteria. We sequenced amplicons of the 16S ribosomal subunit, as well as seven genes associated with functional pathways, generated from both total (DNA-based) and expressed (RNA) soil communities in the Bronx, NYC, NY, in order to test whether bioswale soils host characteristic bacterial communities with evidence for enriched microbial functioning, compared to nonengineered soils in park lawns and tree pits. Bioswales had distinct, phylogenetically diverse bacterial communities, including taxa associated with nutrient cycling and metabolism of hydrocarbons and other pollutants. Bioswale soils also had a significantly greater diversity of genes involved in several functional pathways, including carbon fixation (cbbL-R [cbbL gene, red-like subunit] and apsA), nitrogen cycling (noxZ and amoA), and contaminant degradation (bphA); conversely, no functional genes were significantly more abundant in nonengineered soils. These results provide preliminary evidence that urban land management can shape the diversity and activity of soil communities, with positive consequences for genetic resources underlying valuable ecological functions, including biogeochemical cycling and degradation of common urban pollutants. IMPORTANCE Management of urban soil biodiversity by favoring taxa associated with decontamination or other microbial metabolic processes is a powerful prospect, but it first requires an understanding of how engineered soil habitats shape patterns of microbial diversity. This research adds to our understanding of urban microbial biogeography by providing data on soil bacteria in bioswales, which had relatively diverse and compositionally distinct communities compared to park and tree pit soils. Bioswales also contained comparatively diverse pools of genes related to carbon sequestration, nitrogen cycling, and contaminant degradation, suggesting that engineered soils may serve as effective reservoirs of functional microbial biodiversity. We also examined both total (DNA-based) and expressed (RNA) communities, revealing that total bacterial communities (the exclusive targets in the vast majority of soil studies) were poor predictors of expressed community diversity, pointing to the value of quantifying RNA, especially when ecological functioning is considered. PMID:28576763
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Functional diversification of Argonautes in nematodes: an expanding universe.
Buck, Amy H; Blaxter, Mark
2013-08-01
In the last decade, many diverse RNAi (RNA interference) pathways have been discovered that mediate gene silencing at epigenetic, transcriptional and post-transcriptional levels. The diversity of RNAi pathways is inherently linked to the evolution of Ago (Argonaute) proteins, the central protein component of RISCs (RNA-induced silencing complexes). An increasing number of diverse Agos have been identified in different species. The functions of most of these proteins are not yet known, but they are generally assumed to play roles in development, genome stability and/or protection against viruses. Recent research in the nematode Caenorhabditis elegans has expanded the breadth of RNAi functions to include transgenerational epigenetic memory and, possibly, environmental sensing. These functions are inherently linked to the production of secondary siRNAs (small interfering RNAs) that bind to members of a clade of WAGOs (worm-specific Agos). In the present article, we review briefly what is known about the evolution and function of Ago proteins in eukaryotes, including the expansion of WAGOs in nematodes. We postulate that the rapid evolution of WAGOs enables the exceptional functional plasticity of nematodes, including their capacity for parasitism.
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Xie, Jianping; He, Zhili; Liu, Xinxing; Liu, Xueduan; Van Nostrand, Joy D.; Deng, Ye; Wu, Liyou; Zhou, Jizhong; Qiu, Guanzhou
2011-01-01
Acid mine drainage (AMD) is an extreme environment, usually with low pH and high concentrations of metals. Although the phylogenetic diversity of AMD microbial communities has been examined extensively, little is known about their functional gene diversity and metabolic potential. In this study, a comprehensive functional gene array (GeoChip 2.0) was used to analyze the functional diversity, composition, structure, and metabolic potential of AMD microbial communities from three copper mines in China. GeoChip data indicated that these microbial communities were functionally diverse as measured by the number of genes detected, gene overlapping, unique genes, and various diversity indices. Almost all key functional gene categories targeted by GeoChip 2.0 were detected in the AMD microbial communities, including carbon fixation, carbon degradation, methane generation, nitrogen fixation, nitrification, denitrification, ammonification, nitrogen reduction, sulfur metabolism, metal resistance, and organic contaminant degradation, which suggested that the functional gene diversity was higher than was previously thought. Mantel test results indicated that AMD microbial communities are shaped largely by surrounding environmental factors (e.g., S, Mg, and Cu). Functional genes (e.g., narG and norB) and several key functional processes (e.g., methane generation, ammonification, denitrification, sulfite reduction, and organic contaminant degradation) were significantly (P < 0.10) correlated with environmental variables. This study presents an overview of functional gene diversity and the structure of AMD microbial communities and also provides insights into our understanding of metabolic potential in AMD ecosystems. PMID:21097602
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Deforestation Impacts on Bat Functional Diversity in Tropical Landscapes
García-Morales, Rodrigo; Badano, Ernesto I.; Zuria, Iriana; Galindo-González, Jorge; Rojas-Martínez, Alberto E.; Ávila-Gómez, Eva S.
2016-01-01
Functional diversity is the variability in the functional roles carried out by species within ecosystems. Changes in the environment can affect this component of biodiversity and can, in turn, affect different processes, including some ecosystem services. This study aimed to determine the effect of forest loss on species richness, abundance and functional diversity of Neotropical bats. To this end, we identified six landscapes with increasing loss of forest cover in the Huasteca region of the state of Hidalgo, Mexico. We captured bats in each landscape using mist nets, and calculated functional diversity indices (functional richness and functional evenness) along with species richness and abundance. We analyzed these measures in terms of percent forest cover. We captured 906 bats (Phyllostomidae and Mormoopidae), including 10 genera and 12 species. Species richness, abundance and functional richness per night are positively related with forest cover. Generalized linear models show that species richness, abundance and functional richness per night are significantly related with forest cover, while seasonality had an effect on abundance and functional richness. Neither forest cover nor season had a significant effect on functional evenness. All these findings were consistent across three spatial scales (1, 3 and 5 km radius around sampling sites). The decrease in species, abundance and functional richness of bats with forest loss may have implications for the ecological processes they carry out such as seed dispersal, pollination and insect predation, among others. PMID:27926923
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Plant lectins: the ties that bind in root symbiosis and plant defense.
De Hoff, Peter L; Brill, Laurence M; Hirsch, Ann M
2009-07-01
Lectins are a diverse group of carbohydrate-binding proteins that are found within and associated with organisms from all kingdoms of life. Several different classes of plant lectins serve a diverse array of functions. The most prominent of these include participation in plant defense against predators and pathogens and involvement in symbiotic interactions between host plants and symbiotic microbes, including mycorrhizal fungi and nitrogen-fixing rhizobia. Extensive biological, biochemical, and molecular studies have shed light on the functions of plant lectins, and a plethora of uncharacterized lectin genes are being revealed at the genomic scale, suggesting unexplored and novel diversity in plant lectin structure and function. Integration of the results from these different types of research is beginning to yield a more detailed understanding of the function of lectins in symbiosis, defense, and plant biology in general.
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NASA Astrophysics Data System (ADS)
Joniec, Jolanta; Frąc, Magdalena
2017-10-01
The aim of the study was to evaluate microbial functional diversity based on community level physiological profiling and β-glucosidase activity changes in soil degraded by sulphur mining and subjected to reclamation with various waste. The experiment was set up in the area of the former `Jeziórko' Sulphur Mine (Poland), on a soilless substrate with a particle size distribution of slightly loamy sand. The experimental variants included the application of post-flotation lime, sewage sludge and mineral wool. The analyses of soil samples included the assessment of the following microbiological indices: β-glucosidase activity and functional diversity average well color development and richness). The results indicate that sewage sludge did not exert a significant impact on the functional diversity of microorganisms present in the reclaimed soil. In turn, the application of other types of waste contributed to a significant increase in the parameters of total metabolic activity and functional diversity of the reclaimed soil. However, the temporal analysis of the metabolic profile of soil microorganisms demonstrated that a single application of waste did not yield a durable, stable metabolic profile in the reclaimed soil. Still, there was an increase in β-glucosidase activity, especially in objects treated with sewage sludge.
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Dey, Samrat; Tribedi, Prosun
2018-03-01
Towards bioremediation of recalcitrant materials like synthetic polymer, soil has been recognized as a traditional site for disposal and subsequent degradation as some microorganisms in soil can degrade the polymer in a non-toxic, cost-effective, and environment friendly way. Microbial functional diversity is a constituent of biodiversity that includes wide range of metabolic activities that can influence numerous aspects of ecosystem functioning like ecosystem stability, nutrient availability, ecosystem dynamics, etc. Thus, in the current study, we assumed that microbial functional diversity could play an important role in polymer degradation in soil. To verify this hypothesis, we isolated soil from five different sites of landfill and examined several microbiological parameters wherein we observed a significant variation in heterotrophic microbial count as well as microbial activities among the soil microcosms tested. Multivariate analysis (principle component analysis) based on the carbon sources utilization pattern revealed that soil microcosms showed different metabolic patterns suggesting the variable distribution of microorganisms among the soil microcosms tested. Since microbial functional diversity depends on both microbial richness and evenness, Shannon diversity index was determined to measure microbial richness and Gini coefficient was determined to measure microbial evenness. The tested soil microcosms exhibited variation in both microbial richness and evenness suggesting the considerable difference in microbial functional diversity among the tested microcosms. We then measured polyhydroxybutyrate (PHB) degradation in soil microcosms after desired period of incubation of PHB in soil wherein we found that soil microcosms having higher functional diversity showed enhanced PHB degradation and soil microcosms having lower functional diversity showed reduced PHB degradation. We also noticed that all the tested soil microcosms showed similar pattern in both microbial functional diversity and PHB degradation suggesting a strong positive correlation ( r = 0.95) between microbial functional diversity and PHB degradation. Thus, the results demonstrate that microbial functional diversity plays an important role in PHB degradation in soil by exhibiting versatile microbial metabolic potentials that lead to the enhanced degradation of PHB.
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USDA-ARS?s Scientific Manuscript database
Soil fungi perform a variety of ecosystem functions that are crucial to maintaining agroecosystem sustainability including aggregate stability and soil carbon storage. The purpose of this study was to compare soil fungal communities and functional diversity in integrated crop and livestock (ICL) sy...
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Davies, T Jonathan; Urban, Mark C; Rayfield, Bronwyn; Cadotte, Marc W; Peres-Neto, Pedro R
2016-09-01
Recent studies have supported a link between phylogenetic diversity and various ecological properties including ecosystem function. However, such studies typically assume that phylogenetic branches of equivalent length are more or less interchangeable. Here we suggest that there is a need to consider not only branch lengths but also their placement on the phylogeny. We demonstrate how two common indices of network centrality can be used to describe the evolutionary distinctiveness of network elements (nodes and branches) on a phylogeny. If phylogenetic diversity enhances ecosystem function via complementarity and the representation of functional diversity, we would predict a correlation between evolutionary distinctiveness of network elements and their contribution to ecosystem process. In contrast, if one or a few evolutionary innovations play key roles in ecosystem function, the relationship between evolutionary distinctiveness and functional contribution may be weak or absent. We illustrate how network elements associated with high functional contribution can be identified from regressions between phylogenetic diversity and productivity using a well-known empirical data set on plant productivity from the Cedar Creek Long-Term Ecological Research. We find no association between evolutionary distinctiveness and ecosystem functioning, but we are able to identify phylogenetic elements associated with species of known high functional contribution within the Fabaceae. Our perspective provides a useful guide in the search for ecological traits linking diversity and ecosystem function, and suggests a more nuanced consideration of phylogenetic diversity is required in the conservation and biodiversity-ecosystem-function literature. © 2016 by the Ecological Society of America.
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2015-10-01
that includes physical and neuropsychological evaluations, neuroimaging (MRI, fMRI , DTI), adrenal function tests, and diverse immune, inflammatory...characterized by a profile of concurrent symptoms that typically includes persistent headaches, memory and cognitive difficulties, widespread pain, unexplained...includes physical examinations, neuroimaging (MRI volumetric assessments, fMRI , diffusion tensor imaging), neuropsychological evaluations, assessment
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Díaz-Pérez, Leopoldo; Ortiz, Marco; Cupul-Magaña, Amílcar Leví; Carriquiry, Jose D.; Ríos-Jara, Eduardo; Rodríguez-Troncoso, Alma Paola; García-Rivas, María del Carmen
2016-01-01
This study evaluated the relationship between the indices known as the Reef Health Index (RHI) and two-dimensional Coral Health Index (2D-CHI) and different representative metrics of biological, ecological and functional diversity of fish and corals in 101 reef sites located across seven zones in the western Caribbean Sea. Species richness and average taxonomic distinctness were used to asses biological estimation; while ecological diversity was evaluated with the indices of Shannon diversity and Pielou´s evenness, as well as by taxonomic diversity and distinctness. Functional diversity considered the number of functional groups, the Shannon diversity and the functional Pielou´s evenness. According to the RHI, 57.15% of the zones were classified as presenting a "poor" health grade, while 42.85% were in "critical" grade. Based on the 2D-CHI, 28.5% of the zones were in "degraded" condition and 71.5% were "very degraded". Differences in fish and coral diversity among sites and zones were demonstrated using permutational ANOVAs. Differences between the two health indices (RHI and 2D-CHI) and some indices of biological, ecological and functional diversity of fish and corals were observed; however, only the RHI showed a correlation between the health grades and the species and functional group richness of fish at the scale of sites, and with the species and functional group richness and Shannon diversity of the fish assemblages at the scale of zones. None of the health indices were related to the metrics analyzed for the coral diversity. In general, our study suggests that the estimation of health indices should be complemented with classic community indices, or should at least include diversity indices of fish and corals, in order to improve the accuracy of the estimated health status of coral reefs in the western Caribbean Sea. PMID:27579575
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Díaz-Pérez, Leopoldo; Rodríguez-Zaragoza, Fabián Alejandro; Ortiz, Marco; Cupul-Magaña, Amílcar Leví; Carriquiry, Jose D; Ríos-Jara, Eduardo; Rodríguez-Troncoso, Alma Paola; García-Rivas, María Del Carmen
2016-01-01
This study evaluated the relationship between the indices known as the Reef Health Index (RHI) and two-dimensional Coral Health Index (2D-CHI) and different representative metrics of biological, ecological and functional diversity of fish and corals in 101 reef sites located across seven zones in the western Caribbean Sea. Species richness and average taxonomic distinctness were used to asses biological estimation; while ecological diversity was evaluated with the indices of Shannon diversity and Pielou´s evenness, as well as by taxonomic diversity and distinctness. Functional diversity considered the number of functional groups, the Shannon diversity and the functional Pielou´s evenness. According to the RHI, 57.15% of the zones were classified as presenting a "poor" health grade, while 42.85% were in "critical" grade. Based on the 2D-CHI, 28.5% of the zones were in "degraded" condition and 71.5% were "very degraded". Differences in fish and coral diversity among sites and zones were demonstrated using permutational ANOVAs. Differences between the two health indices (RHI and 2D-CHI) and some indices of biological, ecological and functional diversity of fish and corals were observed; however, only the RHI showed a correlation between the health grades and the species and functional group richness of fish at the scale of sites, and with the species and functional group richness and Shannon diversity of the fish assemblages at the scale of zones. None of the health indices were related to the metrics analyzed for the coral diversity. In general, our study suggests that the estimation of health indices should be complemented with classic community indices, or should at least include diversity indices of fish and corals, in order to improve the accuracy of the estimated health status of coral reefs in the western Caribbean Sea.
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State of the Diversity Practice in Independent Schools
ERIC Educational Resources Information Center
Torres, Amada
2015-01-01
During the spring of 2014, the National Association of Independent Schools (NAIS) commissioned Insightlink Communications, a market research firm, to conduct the second survey on the state of the diversity practice in independent schools. The goals of the study included defining the roles played by diversity practitioners, their functions, and…
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Ding, Long-Jun; Su, Jian-Qiang; Sun, Guo-Xin; Wu, Jin-Shui; Wei, Wen-Xue
2018-02-01
Microbes play key roles in diverse biogeochemical processes including nutrient cycling. However, responses of soil microbial community and functional genes to long-term integrated fertilization (chemical combined with organic fertilization) remain unclear. Here, we used pyrosequencing and a microarray-based GeoChip to explore the shifts of microbial community and functional genes in a paddy soil which received over 21-year fertilization with various regimes, including control (no fertilizer), rice straw (R), rice straw plus chemical fertilizer nitrogen (NR), N and phosphorus (NPR), NP and potassium (NPKR), and reduced rice straw plus reduced NPK (L-NPKR). Significant shifts of the overall soil bacterial composition only occurred in the NPKR and L-NPKR treatments, with enrichment of certain groups including Bradyrhizobiaceae and Rhodospirillaceae families that benefit higher productivity. All fertilization treatments significantly altered the soil microbial functional structure with increased diversity and abundances of genes for carbon and nitrogen cycling, in which NPKR and L-NPKR exhibited the strongest effect, while R exhibited the least. Functional gene structure and abundance were significantly correlated with corresponding soil enzymatic activities and rice yield, respectively, suggesting that the structural shift of the microbial functional community under fertilization might promote soil nutrient turnover and thereby affect yield. Overall, this study indicates that the combined application of rice straw and balanced chemical fertilizers was more pronounced in shifting the bacterial composition and improving the functional diversity toward higher productivity, providing a microbial point of view on applying a cost-effective integrated fertilization regime with rice straw plus reduced chemical fertilizers for sustainable nutrient management.
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FK506-Binding Proteins and Their Diverse Functions.
Tong, Mingming; Jiang, Yu
2015-01-01
FK506 binding proteins (FKBPs) are a family of highly conserved proteins in eukaryotes. The prototype of this protein family, FKBP12, is the binding partner for immunosuppressive drugs FK506 and rapamycin. FKBP12 functions as a cis/trans peptidyl prolyl isomerase (PPIase) that catalyzes interconversion between prolyl cis/trans conformations. Members of the FKBP family contain one or several PPIase domains, which do not always exhibit PPIase activity yet are all essential for their function. FKBPs are involved in diverse cellular functions including protein folding, cellular signaling, apoptosis and transcription. They elicit their function through direct binding and altering conformation of their target proteins, hence acting as molecular switches. In this review, we provide a general summary for the structures and diverse functions of FKBPs found in mammalian cells.
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Musical hallucinations: a brief review of functional neuroimaging findings.
Bernardini, Francesco; Attademo, Luigi; Blackmon, Karen; Devinsky, Orrin
2017-10-01
Musical hallucinations are uncommon phenomena characterized by intrusive and frequently distressful auditory musical percepts without an external source, often associated with hypoacusis, psychiatric illness, focal brain lesion, epilepsy, and intoxication/pharmacology. Their physiological basis is thought to involve diverse mechanisms, including "release" from normal sensory or inhibitory inputs as well as stimulation during seizures, or they can be produced by functional or structural disorders in diverse cortical and subcortical areas. The aim of this review is to further explore their pathophysiology, describing the functional neuroimaging findings regarding musical hallucinations. A literature search of the PubMed electronic database was conducted through to 29 December 2015. Search terms included "musical hallucinations" combined with the names of specific functional neuroimaging techniques. A total of 18 articles, all clinical case reports, providing data on 23 patients, comprised the set we reviewed. Diverse pathological processes and patient populations with musical hallucinations were included in the studies. Converging data from multiple studies suggest that the superior temporal sulcus is the most common site and that activation is the most common mechanism. Further neurobiological research is needed to clarify the pathophysiology of musical hallucinations.
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Grossman, Jake J; Cavender-Bares, Jeannine; Hobbie, Sarah E; Reich, Peter B; Montgomery, Rebecca A
2017-10-01
Over the last two decades, empirical work has established that higher biodiversity can lead to greater primary productivity; however, the importance of different aspects of biodiversity in contributing to such relationships is rarely elucidated. We assessed the relative importance of species richness, phylogenetic diversity, functional diversity, and identity of neighbors for stem growth 3 yr after seedling establishment in a tree diversity experiment in eastern Minnesota. Generally, we found that community-weighted means of key functional traits (including mycorrhizal association, leaf nitrogen and calcium, and waterlogging tolerance) as well as species richness were strong, independent predictors of stem biomass growth. More phylogenetically diverse communities did not consistently produce more biomass than expected, and the trait values or diversity of individual functional traits better predicted biomass production than did a multidimensional functional diversity metric. Furthermore, functional traits and species richness best predicted growth at the whole-plot level (12 m 2 ), whereas neighborhood composition best predicted growth at the focal tree level (0.25 m 2 ). The observed effects of biodiversity on growth appear strongly driven by positive complementary effects rather than by species-specific selection effects, suggesting that synergistic species' interactions rather than the influence of a few important species may drive overyielding. © 2017 by the Ecological Society of America.
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Plant hydraulic diversity buffers forest ecosystem responses to drought
NASA Astrophysics Data System (ADS)
Anderegg, W.; Konings, A. G.; Trugman, A. T.; Pacala, S. W.; Yu, K.; Sulman, B. N.; Sperry, J.; Bowling, D. R.
2017-12-01
Drought impacts carbon, water, and energy cycles in forests and may pose a fundamental threat to forests in future climates. Plant hydraulic transport of water is central to tree drought responses, including curtailing of water loss and the risk of mortality during drought. The effect of biodiversity on ecosystem function has typically been examined in grasslands, yet the diversity of plant hydraulic strategies may influence forests' response to drought. In a combined analysis of eddy covariance measurements, remote-sensing data of plant water content variation, model simulations, and plant hydraulic trait data, we test the degree to which plant water stress schemes influence the carbon cycle and how hydraulic diversity within and across ecosystems affects large-scale drought responses. We find that current plant functional types are not well-suited to capture hydraulic variation and that higher hydraulic diversity buffers ecosystem variation during drought. Our results demonstrate that tree functional diversity, particularly hydraulic diversity, may be critical to simulate in plant functional types in current land surface model projections of future vegetation's response to climate extremes.
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IA channels: diverse regulatory mechanisms.
Carrasquillo, Yarimar; Nerbonne, Jeanne M
2014-04-01
In many peripheral and central neurons, A-type K(+) currents, IA, have been identified and shown to be key determinants in shaping action potential waveforms and repetitive firing properties, as well as in the regulation of synaptic transmission and synaptic plasticity. The functional properties and physiological roles of native neuronal IA, however, have been shown to be quite diverse in different types of neurons. Accumulating evidence suggests that this functional diversity is generated by multiple mechanisms, including the expression and subcellular distributions of IA channels encoded by different voltage-gated K(+) (Kv) channel pore-forming (α) subunits, interactions of Kv α subunits with cytosolic and/or transmembrane accessory subunits and regulatory proteins and post-translational modifications of channel subunits. Several recent reports further suggest that local protein translation in the dendrites of neurons and interactions between IA channels with other types of voltage-gated ion channels further expands the functional diversity of native neuronal IA channels. Here, we review the diverse molecular mechanisms that have been shown or proposed to underlie the functional diversity of native neuronal IA channels.
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Probiotics as an Immune Modulator.
Kang, Hye-Ji; Im, Sin-Hyeog
2015-01-01
Probiotics are nonpathogenic live microorganism that can provide a diverse health benefits on the host when consumed in adequate amounts. Probiotics are consumed in diverse ways including dairy product, food supplements and functional foods with specific health claims. Recently, many reports suggest that certain probiotic strains or multi strain mixture have potent immunomodulatory activity in diverse disorders including allergic asthma, atopic dermatitis and rheumatoid arthritis. However, underlying mechanism of action is still unclear and efficacy of probiotic administration is quite different depending on the type of strains and the amounts of doses. We and others have suggested that live probiotics or their metabolites could interact with diverse immune cells (antigen presenting cells and T cells) and confer them to have immunoregulatory functions. Through this interaction, probiotics could contribute to maintaining immune homeostasis by balancing pro-inflammatory and anti-inflammatory immune responses. However, the effect of probiotics in prevention or modulation of ongoing disease is quite diverse even within a same species. Therefore, identification of functional probiotics with specific immune regulatory property is a certainly important issue. Herein, we briefly review selection methods for immunomodulatory probiotic strains and the mechanism of action of probiotics in immune modulation.
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Negative Impacts of Human Land Use on Dung Beetle Functional Diversity
Barragán, Felipe; Moreno, Claudia E.; Escobar, Federico; Halffter, Gonzalo; Navarrete, Dario
2011-01-01
The loss of biodiversity caused by human activity is assumed to alter ecosystem functioning. However our understanding of the magnitude of the effect of these changes on functional diversity and their impact on the dynamics of ecological processes is still limited. We analyzed the functional diversity of copro-necrophagous beetles under different conditions of land use in three Mexican biosphere reserves. In Montes Azules pastures, forest fragments and continuous rainforest were analyzed, in Los Tuxtlas rainforest fragments of different sizes were analyzed and in Barranca de Metztitlán two types of xerophile scrub with different degrees of disturbance from grazing were analyzed. We assigned dung beetle species to functional groups based on food relocation, beetle size, daily activity period and food preferences, and as measures of functional diversity we used estimates based on multivariate methods. In Montes Azules functional richness was lower in the pastures than in continuous rainforest and rainforest fragments, but fragments and continuous forest include functionally redundant species. In small rainforest fragments (<5 ha) in Los Tuxtlas, dung beetle functional richness was lower than in large rainforest fragments (>20 ha). Functional evenness and functional dispersion did not vary among habitat types or fragment size in these reserves. In contrast, in Metztitlán, functional richness and functional dispersion were different among the vegetation types, but differences were not related to the degree of disturbance by grazing. More redundant species were found in submontane than in crassicaule scrub. For the first time, a decrease in the functional diversity in communities of copro-necrophagous beetles resulting from changes in land use is documented, the potential implications for ecosystem functioning are discussed and a series of variables that could improve the evaluation of functional diversity for this biological group is proposed. PMID:21448292
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Negative impacts of human land use on dung beetle functional diversity.
Barragán, Felipe; Moreno, Claudia E; Escobar, Federico; Halffter, Gonzalo; Navarrete, Dario
2011-03-23
The loss of biodiversity caused by human activity is assumed to alter ecosystem functioning. However our understanding of the magnitude of the effect of these changes on functional diversity and their impact on the dynamics of ecological processes is still limited. We analyzed the functional diversity of copro-necrophagous beetles under different conditions of land use in three Mexican biosphere reserves. In Montes Azules pastures, forest fragments and continuous rainforest were analyzed, in Los Tuxtlas rainforest fragments of different sizes were analyzed and in Barranca de Metztitlán two types of xerophile scrub with different degrees of disturbance from grazing were analyzed. We assigned dung beetle species to functional groups based on food relocation, beetle size, daily activity period and food preferences, and as measures of functional diversity we used estimates based on multivariate methods. In Montes Azules functional richness was lower in the pastures than in continuous rainforest and rainforest fragments, but fragments and continuous forest include functionally redundant species. In small rainforest fragments (<5 ha) in Los Tuxtlas, dung beetle functional richness was lower than in large rainforest fragments (>20 ha). Functional evenness and functional dispersion did not vary among habitat types or fragment size in these reserves. In contrast, in Metztitlán, functional richness and functional dispersion were different among the vegetation types, but differences were not related to the degree of disturbance by grazing. More redundant species were found in submontane than in crassicaule scrub. For the first time, a decrease in the functional diversity in communities of copro-necrophagous beetles resulting from changes in land use is documented, the potential implications for ecosystem functioning are discussed and a series of variables that could improve the evaluation of functional diversity for this biological group is proposed.
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Sircely, Jason; Naeem, Shahid
2012-01-01
Recent studies indicate that species richness can enhance the ability of plant assemblages to support multiple ecosystem functions. To understand how and when ecosystem services depend on biodiversity, it is valuable to expand beyond experimental grasslands. We examined whether plant diversity improves the capacity of agroecosystems to sustain multiple ecosystem services—production of wood and forage, and two elements of soil formation—in two types of smallholder fallows in western Kenya. In 18 grazed and 21 improved fallows, we estimated biomass and quantified soil organic carbon, soil base cations, sand content, and soil infiltration capacity. For four ecosystem functions (wood biomass, forage biomass, soil base cations, steady infiltration rates) linked to the focal ecosystem services, we quantified ecosystem service multi-functionality as (1) the proportion of functions above half-maximum, and (2) mean percentage excess above mean function values, and assessed whether plant diversity or environmental favorability better predicted multi-functionality. In grazed fallows, positive effects of plant diversity best explained the proportion above half-maximum and mean percentage excess, the former also declining with grazing intensity. In improved fallows, the proportion above half-maximum was not associated with soil carbon or plant diversity, while soil carbon predicted mean percentage excess better than diversity. Grazed fallows yielded stronger evidence for diversity effects on multi-functionality, while environmental conditions appeared more influential in improved fallows. The contrast in diversity-multi-functionality relationships among fallow types appears related to differences in management and associated factors including disturbance and species composition. Complementary effects of species with contrasting functional traits on different functions and multi-functional species may have contributed to diversity effects in grazed fallows. Biodiversity and environmental favorability may enhance the capacity of smallholder fallows to simultaneously provide multiple ecosystem services, yet their effects are likely to vary with fallow management. PMID:23209662
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Izzo, Flavia; Schäfer, Martina; Lienau, Philip; Ganzer, Ursula; Stockman, Robert; Lücking, Ulrich
2018-05-04
An unprecedented set of structurally diverse sulfonimidamides (47 compounds) has been prepared by various N-functionalization reactions of tertiary =NH sulfonimidamide 2 aa. These N-functionalization reactions of model compound 2 aa include arylation, alkylation, trifluoromethylation, cyanation, sulfonylation, alkoxycarbonylation (carbamate formation) and aminocarbonylation (urea formation). Small molecule X-ray analyses of selected N-functionalized products are reported. To gain further insight into the properties of sulfonimidamides relevant to medicinal chemistry, a variety of structurally diverse reaction products were tested in selected in vitro assays. The described N-functionalization reactions provide a short and efficient approach to structurally diverse sulfonimidamides which have been the subject of recent, growing interest in the life sciences. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Sattler, T; Pezzatti, G B; Nobis, M P; Obrist, M K; Roth, T; Moretti, M
2014-04-01
Surrogates, such as umbrella species, are commonly used to reduce the complexity of quantifying biodiversity for conservation purposes. The presence of umbrella species is often indicative of high taxonomic diversity; however, functional diversity is now recognized as an important metric for biodiversity and thus should be considered when choosing umbrella species. We identified umbrella species associated with high taxonomic and functional biodiversity in urban areas in Switzerland. We analyzed 39,752 individuals of 574 animal species from 96 study plots and 1397 presences of 262 plant species from 58 plots. Thirty-one biodiversity measures of 7 taxonomic groups (plants, spiders, bees, ground beetles, lady bugs, weevils and birds) were included in within- and across-taxa analyses. Sixteen measures were taxonomical (species richness and species diversity), whereas 15 were functional (species traits including mobility, resource use, and reproduction). We used indicator value analysis to identify umbrella species associated with single or multiple biodiversity measures. Many umbrella species were indicators of high biodiversity within their own taxonomic group (from 33.3% in weevils to 93.8% in birds), to a lesser extent they were indicators across taxa. Principal component analysis revealed that umbrella species for multiple measures of biodiversity represented different aspects of biodiversity, especially with respect to measures of taxonomic and functional diversity. Thus, even umbrella species for multiple measures of biodiversity were complementary in the biodiversity aspects they represented. Thus, the choice of umbrella species based solely on taxonomic diversity is questionable and may not represent biodiversity comprehensively. Our results suggest that, depending on conservation priorities, managers should choose multiple and complementary umbrella species to assess the state of biodiversity. © 2013 Society for Conservation Biology.
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Invited Article: Mask-modulated lensless imaging with multi-angle illuminations
NASA Astrophysics Data System (ADS)
Zhang, Zibang; Zhou, You; Jiang, Shaowei; Guo, Kaikai; Hoshino, Kazunori; Zhong, Jingang; Suo, Jinli; Dai, Qionghai; Zheng, Guoan
2018-06-01
The use of multiple diverse measurements can make lensless phase retrieval more robust. Conventional diversity functions include aperture diversity, wavelength diversity, translational diversity, and defocus diversity. Here we discuss a lensless imaging scheme that employs multiple spherical-wave illuminations from a light-emitting diode array as diversity functions. In this scheme, we place a binary mask between the sample and the detector for imposing support constraints for the phase retrieval process. This support constraint enforces the light field to be zero at certain locations and is similar to the aperture constraint in Fourier ptychographic microscopy. We use a self-calibration algorithm to correct the misalignment of the binary mask. The efficacy of the proposed scheme is first demonstrated by simulations where we evaluate the reconstruction quality using mean square error and structural similarity index. The scheme is then experimentally tested by recovering images of a resolution target and biological samples. The proposed scheme may provide new insights for developing compact and large field-of-view lensless imaging platforms. The use of the binary mask can also be combined with other diversity functions for better constraining the phase retrieval solution space. We provide the open-source implementation code for the broad research community.
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Johnson, Claire; Killinger, Lisa Zaynab; Christensen, Mark G; Hyland, John K; Mrozek, John P; Zuker, R Fred; Kizhakkeveettil, Anupama; Perle, Stephen M; Oyelowo, Tolu
2012-12-01
The purpose of this article is to provide expert viewpoints on the topic of diversity in the chiropractic profession, including cultural competency, diversity in the profession, educational and clinical practice strategies for addressing diversity, and workforce issues. Over the next decades, changing demographics in North America will alter how the chiropractic profession functions on many levels. As the population increases in diversity, we will need to prepare our workforce to meet the needs of future patients and society.
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Response diversity determines the resilience of ecosystems to environmental change.
Mori, Akira S; Furukawa, Takuya; Sasaki, Takehiro
2013-05-01
A growing body of evidence highlights the importance of biodiversity for ecosystem stability and the maintenance of optimal ecosystem functionality. Conservation measures are thus essential to safeguard the ecosystem services that biodiversity provides and human society needs. Current anthropogenic threats may lead to detrimental (and perhaps irreversible) ecosystem degradation, providing strong motivation to evaluate the response of ecological communities to various anthropogenic pressures. In particular, ecosystem functions that sustain key ecosystem services should be identified and prioritized for conservation action. Traditional diversity measures (e.g. 'species richness') may not adequately capture the aspects of biodiversity most relevant to ecosystem stability and functionality, but several new concepts may be more appropriate. These include 'response diversity', describing the variation of responses to environmental change among species of a particular community. Response diversity may also be a key determinant of ecosystem resilience in the face of anthropogenic pressures and environmental uncertainty. However, current understanding of response diversity is poor, and we see an urgent need to disentangle the conceptual strands that pervade studies of the relationship between biodiversity and ecosystem functioning. Our review clarifies the links between response diversity and the maintenance of ecosystem functionality by focusing on the insurance hypothesis of biodiversity and the concept of functional redundancy. We provide a conceptual model to describe how loss of response diversity may cause ecosystem degradation through decreased ecosystem resilience. We explicitly explain how response diversity contributes to functional compensation and to spatio-temporal complementarity among species, leading to long-term maintenance of ecosystem multifunctionality. Recent quantitative studies suggest that traditional diversity measures may often be uncoupled from measures (such as response diversity) that may be more effective proxies for ecosystem stability and resilience. Certain conclusions and recommendations of earlier studies using these traditional measures as indicators of ecosystem resilience thus may be suspect. We believe that functional ecology perspectives incorporating the effects and responses of diversity are essential for development of management strategies to safeguard (and restore) optimal ecosystem functionality (especially multifunctionality). Our review highlights these issues and we envision our work generating debate around the relationship between biodiversity and ecosystem functionality, and leading to improved conservation priorities and biodiversity management practices that maximize ecosystem resilience in the face of uncertain environmental change. © 2012 The Authors. Biological Reviews © 2012 Cambridge Philosophical Society.
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Sullivan, Mary C; Miller, Robin J; Msall, Michael E
2012-10-01
To examine functioning and participation in a diverse U.S. sample of 180 infants at age 17 years. The World Health Organization International Classification of Functioning, Disability and Health model framed functioning and participation domains and contextual factors. Assessment included cognition, executive functioning, academic achievement, personal functioning, community participation, and social involvement. Socioeconomic status, not prematurity, impacted cognitive and academic outcomes. Across neonatal morbidities, male gender and social disadvantage are key determinants of cognitive, academic, and social functioning. Interventions addressing academic and social-behavioral competencies in early school years may potentially optimize long-term preterm outcomes. © 2012, Wiley Periodicals, Inc.
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Code of Federal Regulations, 2010 CFR
2010-07-01
... species diversity or their high social, cultural or economic value. Disturbance regime: Actions, functions... environment that can affect the diversity of plant and animal communities, including species viability, and... be used as surrogates to represent ecological conditions that provide for viability of some other...
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Code of Federal Regulations, 2011 CFR
2011-07-01
... species diversity or their high social, cultural or economic value. Disturbance regime: Actions, functions... environment that can affect the diversity of plant and animal communities, including species viability, and... be used as surrogates to represent ecological conditions that provide for viability of some other...
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The SYK tyrosine kinase: a crucial player in diverse biological functions
Mócsai, Attila; Ruland, Jürgen; Tybulewicz, Victor L. J.
2016-01-01
Spleen tyrosine kinase (SYK) has been known to relay adaptive immune receptor signalling. However, recent reports indicate that SYK also mediates other, unexpectedly diverse biological functions including cellular adhesion, innate immune recognition, osteoclast maturation, platelet activation and vascular development. SYK is activated by C-type lectins and integrins, and activates novel targets including the CARD9/CARMA1–BCL10–MALT1 pathway and the NLRP3 inflammasome. Drosophila studies indicate evolutionary ancient origin of SYK-mediated signalling. Moreover, SYK has a crucial role in autoimmune diseases and haematological malignancies. This Review summarizes our current understanding of SYK functions and the translation of this knowledge for therapeutic purposes. PMID:20467426
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Kembel, Steven W.; O’Connor, Timothy K.; Arnold, Holly K.; Hubbell, Stephen P.; Wright, S. Joseph; Green, Jessica L.
2014-01-01
The phyllosphere—the aerial surfaces of plants, including leaves—is a ubiquitous global habitat that harbors diverse bacterial communities. Phyllosphere bacterial communities have the potential to influence plant biogeography and ecosystem function through their influence on the fitness and function of their hosts, but the host attributes that drive community assembly in the phyllosphere are poorly understood. In this study we used high-throughput sequencing to quantify bacterial community structure on the leaves of 57 tree species in a neotropical forest in Panama. We tested for relationships between bacterial communities on tree leaves and the functional traits, taxonomy, and phylogeny of their plant hosts. Bacterial communities on tropical tree leaves were diverse; leaves from individual trees were host to more than 400 bacterial taxa. Bacterial communities in the phyllosphere were dominated by a core microbiome of taxa including Actinobacteria, Alpha-, Beta-, and Gammaproteobacteria, and Sphingobacteria. Host attributes including plant taxonomic identity, phylogeny, growth and mortality rates, wood density, leaf mass per area, and leaf nitrogen and phosphorous concentrations were correlated with bacterial community structure on leaves. The relative abundances of several bacterial taxa were correlated with suites of host plant traits related to major axes of plant trait variation, including the leaf economics spectrum and the wood density–growth/mortality tradeoff. These correlations between phyllosphere bacterial diversity and host growth, mortality, and function suggest that incorporating information on plant–microbe associations will improve our ability to understand plant functional biogeography and the drivers of variation in plant and ecosystem function. PMID:25225376
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Evaluation of an Integrated Framework for Biodiversity with a New Metric for Functional Dispersion
Presley, Steven J.; Scheiner, Samuel M.; Willig, Michael R.
2014-01-01
Growing interest in understanding ecological patterns from phylogenetic and functional perspectives has driven the development of metrics that capture variation in evolutionary histories or ecological functions of species. Recently, an integrated framework based on Hill numbers was developed that measures three dimensions of biodiversity based on abundance, phylogeny and function of species. This framework is highly flexible, allowing comparison of those diversity dimensions, including different aspects of a single dimension and their integration into a single measure. The behavior of those metrics with regard to variation in data structure has not been explored in detail, yet is critical for ensuring an appropriate match between the concept and its measurement. We evaluated how each metric responds to particular data structures and developed a new metric for functional biodiversity. The phylogenetic metric is sensitive to variation in the topology of phylogenetic trees, including variation in the relative lengths of basal, internal and terminal branches. In contrast, the functional metric exhibited multiple shortcomings: (1) species that are functionally redundant contribute nothing to functional diversity and (2) a single highly distinct species causes functional diversity to approach the minimum possible value. We introduced an alternative, improved metric based on functional dispersion that solves both of these problems. In addition, the new metric exhibited more desirable behavior when based on multiple traits. PMID:25148103
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Barbet-Massin, Morgane; Jetz, Walter
2015-08-01
Animal assemblages fulfill a critical set of ecological functions for ecosystems that may be altered substantially as climate change-induced distribution changes lead to community disaggregation and reassembly. We combine species and community perspectives to assess the consequences of projected geographic range changes for the diverse functional attributes of avian assemblages worldwide. Assemblage functional structure is projected to change highly unevenly across space. These differences arise from both changes in the number of species and changes in species' relative local functional redundancy or distinctness. They sometimes result in substantial losses of functional diversity that could have severe consequences for ecosystem health. Range expansions may counter functional losses in high-latitude regions, but offer little compensation in many tropical and subtropical biomes. Future management of local community function and ecosystem services thus relies on understanding the global dynamics of species distributions and multiscale approaches that include the biogeographic context of species traits. © 2015 John Wiley & Sons Ltd.
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De Palma, Adriana; Kuhlmann, Michael; Bugter, Rob; Ferrier, Simon; Hoskins, Andrew J; Potts, Simon G; Roberts, Stuart P M; Schweiger, Oliver; Purvis, Andy
2017-12-01
Agricultural intensification and urbanization are important drivers of biodiversity change in Europe. Different aspects of bee community diversity vary in their sensitivity to these pressures, as well as independently influencing ecosystem service provision (pollination). To obtain a more comprehensive understanding of human impacts on bee diversity across Europe, we assess multiple, complementary indices of diversity. One Thousand four hundred and forty six sites across Europe. We collated data on bee occurrence and abundance from the published literature and supplemented them with the PREDICTS database. Using Rao's Quadratic Entropy, we assessed how species, functional and phylogenetic diversity of 1,446 bee communities respond to land-use characteristics including land-use class, cropland intensity, human population density and distance to roads. We combined these models with statistically downscaled estimates of land use in 2005 to estimate and map-at a scale of approximately 1 km 2 -the losses in diversity relative to semi-natural/natural baseline (the predicted diversity of an uninhabited grid square, consisting only of semi-natural/natural vegetation). We show that-relative to the predicted local diversity in uninhabited semi-natural/natural habitat-half of all EU27 countries have lost over 10% of their average local species diversity and two-thirds of countries have lost over 5% of their average local functional and phylogenetic diversity. All diversity measures were generally lower in pasture and higher-intensity cropland than in semi-natural/natural vegetation, but facets of diversity showed less consistent responses to human population density. These differences have led to marked spatial mismatches in losses: losses in phylogenetic diversity were in some areas almost 20 percentage points (pp.) more severe than losses in species diversity, but in other areas losses were almost 40 pp. less severe. These results highlight the importance of exploring multiple measures of diversity when prioritizing and evaluating conservation actions, as species-diverse assemblages may be phylogenetically and functionally impoverished, potentially threatening pollination service provision.
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Ciardiello, J J; Stewart, H L; Sore, H F; Galloway, W R J D; Spring, D R
2017-06-01
Recent years have witnessed a global decline in the productivity and advancement of the pharmaceutical industry. A major contributing factor to this is the downturn in drug discovery successes. This can be attributed to the lack of structural (particularly scaffold) diversity and structural complexity exhibited by current small molecule screening collections. Macrocycles have been shown to exhibit a diverse range of biological properties, with over 100 natural product-derived examples currently marketed as FDA-approved drugs. Despite this, synthetic macrocycles are widely considered to be a poorly explored structural class within drug discovery, which can be attributed to their synthetic intractability. Herein we describe a novel complexity-to-diversity strategy for the diversity-oriented synthesis of novel, structurally complex and diverse macrocyclic scaffolds from natural product starting materials. This approach exploits the inherent structural (including functional) and stereochemical complexity of natural products in order to rapidly generate diversity and complexity. Readily-accessible natural product-derived intermediates serve as structural templates which can be divergently functionalized with different building blocks to generate a diverse range of acyclic precursors. Subsequent macrocyclisation then furnishes compounds that are each based around a distinct molecular scaffold. Thus, high levels of library scaffold diversity can be rapidly achieved. In this proof-of-concept study, the natural product quinine was used as the foundation for library synthesis, and six novel structurally diverse, highly complex and functionalized macrocycles were generated. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Melliger, Ramona Laila; Rusterholz, Hans-Peter; Baur, Bruno
2018-01-01
Urbanisation is increasing worldwide and is regarded a major driver of environmental change altering local species assemblages in urban green areas. Forests are one of the most frequent habitat types in urban landscapes harbouring many native species and providing important ecosystem services. By using a multi-taxa approach covering a range of trophic ranks, we examined the influence of degree of urbanisation and forest size on the species richness and functional diversity of plants, and ground surface-active ants and spiders. We conducted field surveys in twenty-six forests in the urban region of Basel, Switzerland. We found that a species’ response to urbanisation varied depending on trophic rank, habitat specificity and the diversity indices used. In plants, species richness decreased with degree of urbanisation, whereas that of both arthropod groups was not affected. However, ants and spiders at higher trophic rank showed greater shifts in species composition with increasing degree of urbanisation, and the percentage of forest specialists in both arthropod groups increased with forest size. Local abiotic site characteristics were also crucial for plant species diversity and species composition, while the structural diversity of both leaf litter and vegetation was important for the diversity of ants and spiders. Our results highlight that even small urban forests can harbour a considerable biodiversity including habitat specialists. Nonetheless, urbanisation directly and indirectly caused major shifts in species composition. Therefore, special consideration needs to be given to vulnerable species, including those with special habitat requirements. Locally adapted management practices could be a step forward to enhance habitat quality in a way to maximize diversity of forest species and thus ensure forest ecosystem functioning; albeit large-scale factors also remain important. PMID:29920553
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Melliger, Ramona Laila; Braschler, Brigitte; Rusterholz, Hans-Peter; Baur, Bruno
2018-01-01
Urbanisation is increasing worldwide and is regarded a major driver of environmental change altering local species assemblages in urban green areas. Forests are one of the most frequent habitat types in urban landscapes harbouring many native species and providing important ecosystem services. By using a multi-taxa approach covering a range of trophic ranks, we examined the influence of degree of urbanisation and forest size on the species richness and functional diversity of plants, and ground surface-active ants and spiders. We conducted field surveys in twenty-six forests in the urban region of Basel, Switzerland. We found that a species' response to urbanisation varied depending on trophic rank, habitat specificity and the diversity indices used. In plants, species richness decreased with degree of urbanisation, whereas that of both arthropod groups was not affected. However, ants and spiders at higher trophic rank showed greater shifts in species composition with increasing degree of urbanisation, and the percentage of forest specialists in both arthropod groups increased with forest size. Local abiotic site characteristics were also crucial for plant species diversity and species composition, while the structural diversity of both leaf litter and vegetation was important for the diversity of ants and spiders. Our results highlight that even small urban forests can harbour a considerable biodiversity including habitat specialists. Nonetheless, urbanisation directly and indirectly caused major shifts in species composition. Therefore, special consideration needs to be given to vulnerable species, including those with special habitat requirements. Locally adapted management practices could be a step forward to enhance habitat quality in a way to maximize diversity of forest species and thus ensure forest ecosystem functioning; albeit large-scale factors also remain important.
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Integrating abundance and functional traits reveals new global hotspots of fish diversity.
Stuart-Smith, Rick D; Bates, Amanda E; Lefcheck, Jonathan S; Duffy, J Emmett; Baker, Susan C; Thomson, Russell J; Stuart-Smith, Jemina F; Hill, Nicole A; Kininmonth, Stuart J; Airoldi, Laura; Becerro, Mikel A; Campbell, Stuart J; Dawson, Terence P; Navarrete, Sergio A; Soler, German A; Strain, Elisabeth M A; Willis, Trevor J; Edgar, Graham J
2013-09-26
Species richness has dominated our view of global biodiversity patterns for centuries. The dominance of this paradigm is reflected in the focus by ecologists and conservation managers on richness and associated occurrence-based measures for understanding drivers of broad-scale diversity patterns and as a biological basis for management. However, this is changing rapidly, as it is now recognized that not only the number of species but the species present, their phenotypes and the number of individuals of each species are critical in determining the nature and strength of the relationships between species diversity and a range of ecological functions (such as biomass production and nutrient cycling). Integrating these measures should provide a more relevant representation of global biodiversity patterns in terms of ecological functions than that provided by simple species counts. Here we provide comparisons of a traditional global biodiversity distribution measure based on richness with metrics that incorporate species abundances and functional traits. We use data from standardized quantitative surveys of 2,473 marine reef fish species at 1,844 sites, spanning 133 degrees of latitude from all ocean basins, to identify new diversity hotspots in some temperate regions and the tropical eastern Pacific Ocean. These relate to high diversity of functional traits amongst individuals in the community (calculated using Rao's Q), and differ from previously reported patterns in functional diversity and richness for terrestrial animals, which emphasize species-rich tropical regions only. There is a global trend for greater evenness in the number of individuals of each species, across the reef fish species observed at sites ('community evenness'), at higher latitudes. This contributes to the distribution of functional diversity hotspots and contrasts with well-known latitudinal gradients in richness. Our findings suggest that the contribution of species diversity to a range of ecosystem functions varies over large scales, and imply that in tropical regions, which have higher numbers of species, each species contributes proportionally less to community-level ecological processes on average than species in temperate regions. Metrics of ecological function usefully complement metrics of species diversity in conservation management, including when identifying planning priorities and when tracking changes to biodiversity values.
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Intraspecific traits change biodiversity effects on ecosystem functioning under metal stress.
Fernandes, Isabel; Pascoal, Cláudia; Cássio, Fernanda
2011-08-01
Studies investigating the impacts of biodiversity loss on ecosystem processes have often reached different conclusions, probably because insufficient attention has been paid to some aspects including (1) which biodiversity measure (e.g., species number, species identity or trait) better explains ecosystem functioning, (2) the mechanisms underpinning biodiversity effects, and (3) how can environmental context modulates biodiversity effects. Here, we investigated how species number (one to three species) and traits of aquatic fungal decomposers (by replacement of a functional type from an unpolluted site by another from a metal-polluted site) affect fungal production (biomass accumulation) and plant litter decomposition in the presence and absence of metal stress. To examine the putative mechanisms that explain biodiversity effects, we determined the contribution of each fungal species to the total biomass produced in multicultures by real-time PCR. In the absence of metal, positive diversity effects were observed for fungal production and leaf decomposition as a result of species complementarity. Metal stress decreased diversity effects on leaf decomposition in assemblages containing the functional type from the unpolluted site, probably due to competitive interactions between fungi. However, dominance effect maintained positive diversity effects under metal stress in assemblages containing the functional type from the metal-polluted site. These findings emphasize the importance of intraspecific diversity in modulating diversity effects under metal stress, providing evidence that trait-based diversity measures should be incorporated when examining biodiversity effects.
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“Click, Click, Cyclize”: A DOS Approach to Sultams Utilizing Vinyl Sulfonamide Linchpins
Zhou, Aihua; Rayabarapu, Dinesh; Hanson, Paul R.
2009-01-01
A diversity-oriented synthesis (DOS) strategy termed “Click, Click, Cyclize” is reported. This approach relies on functional group (FG) pairing between a vinyl sulfonamide and an array of functional groups to synthesize skeletally diverse sultams. Several FG pairing pathways on central tertiary vinyl sulfonamide linchpins have been developed including intramolecular Heck, aza-Michael, ring-closing enyne metathesis, Pauson—Khand, and chemoselective oxidation/Baylis—Hillman reactions. PMID:19115841
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Morris, Katrina M; Wright, Belinda; Grueber, Catherine E; Hogg, Carolyn; Belov, Katherine
2015-08-01
The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction due to the spread of devil facial tumour disease. Polymorphisms in immune genes can provide adaptive potential to resist diseases. Previous studies in diversity at immune loci in wild species have almost exclusively focused on genes of the major histocompatibility complex (MHC); however, these genes only account for a fraction of immune gene diversity. Devils lack diversity at functionally important immunity loci, including MHC and Toll-like receptor genes. Whether there are polymorphisms at devil immune genes outside these two families is unknown. Here, we identify polymorphisms in a wide range of key immune genes, and develop assays to type single nucleotide polymorphisms (SNPs) within a subset of these genes. A total of 167 immune genes were examined, including cytokines, chemokines and natural killer cell receptors. Using genome-level data from ten devils, SNPs within coding regions, introns and 10 kb flanking genes of interest were identified. We found low polymorphism across 167 immune genes examined bioinformatically using whole-genome data. From this data, we developed long amplicon assays to target nine genes. These amplicons were sequenced in 29-220 devils and found to contain 78 SNPs, including eight SNPS within exons. Despite the extreme paucity of genetic diversity within these genes, signatures of balancing selection were exhibited by one chemokine gene, suggesting that remaining diversity may hold adaptive potential. The low functional diversity may leave devils highly vulnerable to infectious disease, and therefore, monitoring and preserving remaining diversity will be critical for the long-term management of this species. Examining genetic variation in diverse immune genes should be a priority for threatened wildlife species. This study can act as a model for broad-scale immunogenetic diversity analysis in threatened species. © 2015 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.
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Microbial biodiversity of the atmosphere
NASA Astrophysics Data System (ADS)
Klein, Ann Maureen
Microorganisms are critical to the functioning of terrestrial and aquatic ecosystems and may also play a role in the functioning of the atmosphere. However, little is known about the diversity and function of microorganisms in the atmosphere. To investigate the forces driving the assembly of bacterial microbial communities in the atmosphere, I measured temporal variation in bacterial diversity and composition over diurnal and inter-day time scales. Results suggest that bacterial communities in the atmosphere markedly vary over diurnal time scales and are likely structured by inputs from both local terrestrial and long-distance sources. To assess the potential functions of bacteria and fungi in the atmosphere, I characterized total and potentially active communities using both RNA- and DNA-based data. Results suggest there are metabolically active microorganisms in the atmosphere that may affect atmospheric functions including precipitation development and carbon cycling. This dissertation includes previously published and unpublished co-authored material.
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Schaller, Jörg; Roscher, Christiane; Hillebrand, Helmut; Weigelt, Alexandra; Oelmann, Yvonne; Wilcke, Wolfgang; Ebeling, Anne; Weisser, Wolfgang W
2016-09-01
Plant diversity is an important driver of nitrogen and phosphorus stocks in aboveground plant biomass of grassland ecosystems, but plant diversity effects on other elements also important for plant growth are less understood. We tested whether plant species richness, functional group richness or the presence/absence of particular plant functional groups influences the Si and Ca concentrations (mmol g(-1)) and stocks (mmol m(-2)) in aboveground plant biomass in a large grassland biodiversity experiment (Jena Experiment). In the experiment including 60 temperate grassland species, plant diversity was manipulated as sown species richness (1, 2, 4, 8, 16) and richness and identity of plant functional groups (1-4; grasses, small herbs, tall herbs, legumes). We found positive species richness effects on Si as well as Ca stocks that were attributable to increased biomass production. The presence of particular functional groups was the most important factor explaining variation in aboveground Si and Ca stocks (mmol m(-2)). Grass presence increased the Si stocks by 140 % and legume presence increased the Ca stock by 230 %. Both the presence of specific plant functional groups and species diversity altered Si and Ca stocks, whereas Si and Ca concentration were affected mostly by the presence of specific plant functional groups. However, we found a negative effect of species diversity on Si and Ca accumulation, by calculating the deviation between mixtures and mixture biomass proportions, but in monoculture concentrations. These changes may in turn affect ecosystem processes such as plant litter decomposition and nutrient cycling in grasslands.
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Chalmandrier, L; Münkemüller, T; Lavergne, S; Thuiller, W
2015-01-01
Different assembly processes drive the spatial structure of meta-communities (beta-diversity). Recently, functional and phylogenetic diversities have been suggested as indicators of these assembly processes. Assuming that diversity is a good proxy for niche overlap, high beta-diversity along environmental gradients should be the result of environmental filtering while low beta-diversity should stem from competitive interactions. So far, studies trying to disentangle the relative importance of these assembly processes have provided mixed results. One reason for this may be that these studies often rely on a single measure of diversity and thus implicitly make a choice on how they account for species relative abundances and how species similarities are captured by functional traits or phylogeny. Here, we tested the effect of gradually scaling the importance of dominance (the weight given to dominant vs. rare species) and species similarity (the weight given to small vs. large similarities) on resulting beta-diversity patterns of an alpine plant meta-community. To this end, we combined recent extensions of the Hill numbers framework with Pagel's phylogenetic tree transformation approach. We included functional (based on the leaf-height-seed spectrum) and phylogenetic facets of beta-diversity in our analysis and explicitly accounted for effects of environmental and spatial covariates. We found that functional beta-diversity, was high when the same weight was given to dominant vs. rare species and to large vs. small species' similarities. In contrast, phylogenetic beta-diversity was low when greater weight was given to dominant species and small species' similarities. Those results suggested that different environments along the gradients filtered different species according to their functional traits, while, the same competitive lineages dominated communities across the gradients. Our results highlight that functional vs. phylogenetic facets, presence-absence vs. abundance structure and different weights of species' dissimilarity provide complementary and important information on the drivers of meta-community structure. By utilizing the full extent of information provided by the flexible frameworks of Hill numbers and Pagel's tree transformation, we propose a new approach to disentangle the patterns resulting from different assembly processes.
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Glowing Worms: Biological, Chemical, and Functional Diversity of Bioluminescent Annelids.
Verdes, Aida; Gruber, David F
2017-07-01
Bioluminescence, the ability to produce light by living organisms, has evolved independently in numerous lineages across the tree of life. Luminous forms are found in a wide range of taxonomic groups from bacteria to vertebrates, although the great majority of bioluminescent organisms are marine taxa. Within the phylum Annelida, bioluminescence is widespread, present in at least 98 terrestrial and marine species that represent 45 genera distributed in thirteen lineages of clitellates and polychaetes. The ecological diversity of luminous annelids is unparalleled, with species occupying a great variety of habitats including both terrestrial and marine ecosystems, from coastal waters to the deep-sea, in benthic and pelagic habitats from polar to tropical regions. This great taxonomic and ecological diversity is matched by the wide array of bioluminescent colors-including yellow light, which is very rare among marine taxa-different emission wavelengths even between species of the same genus, and varying patterns, chemical reactions and kinetics. This diversity of bioluminescence colors and patterns suggests that light production in annelids might be involved in a variety of different functions, including defensive mechanisms like sacrificial lures or aposematic signals, and intraspecific communication systems. In this review, we explore the world of luminous annelids, particularly focusing on the current knowledge regarding their taxonomic and ecological diversity and discussing the putative functions and chemistries of their bioluminescent systems. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology 2017. This work is written by US Government employees and is in the public domain in the US.
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Akiva, Eyal; Copp, Janine N.; Tokuriki, Nobuhiko; Babbitt, Patricia C.
2017-01-01
Insight regarding how diverse enzymatic functions and reactions have evolved from ancestral scaffolds is fundamental to understanding chemical and evolutionary biology, and for the exploitation of enzymes for biotechnology. We undertook an extensive computational analysis using a unique and comprehensive combination of tools that include large-scale phylogenetic reconstruction to determine the sequence, structural, and functional relationships of the functionally diverse flavin mononucleotide-dependent nitroreductase (NTR) superfamily (>24,000 sequences from all domains of life, 54 structures, and >10 enzymatic functions). Our results suggest an evolutionary model in which contemporary subgroups of the superfamily have diverged in a radial manner from a minimal flavin-binding scaffold. We identified the structural design principle for this divergence: Insertions at key positions in the minimal scaffold that, combined with the fixation of key residues, have led to functional specialization. These results will aid future efforts to delineate the emergence of functional diversity in enzyme superfamilies, provide clues for functional inference for superfamily members of unknown function, and facilitate rational redesign of the NTR scaffold. PMID:29078300
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Partitioning of functional and taxonomic diversity in surface-associated microbial communities.
Roth-Schulze, Alexandra J; Zozaya-Valdés, Enrique; Steinberg, Peter D; Thomas, Torsten
2016-12-01
Surfaces, including those submerged in the marine environment, are subjected to constant interactions and colonisation by surrounding microorganisms. The principles that determine the assembly of those epibiotic communities are however poorly understood. In this study, we employed a hierarchical design to assess the functionality and diversity of microbial communities on different types of host surfaces (e.g. macroalgae, seagrasses). We found that taxonomic diversity was unique to each type of host, but that the majority of functions (> 95%) could be found in any given surface community, suggesting a high degree of functional redundancy. However, some community functions were enriched on certain surfaces and were related to host-specific properties (e.g. the degradation of specific polysaccharides). Together these observations support a model, whereby communities on surfaces are assembled from guilds of microorganisms with a functionality that is partitioned into general properties for a surface-associated life-style, but also specific features that mediate host-specificity. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.
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Guernsey, Michael W.; Ritscher, Lars; Miller, Matthew A.; Smith, Daniel A.; Schöneberg, Torsten; Shapiro, Michael D.
2013-01-01
Variation in the melanocortin-1 receptor (Mc1r) is associated with pigmentation diversity in wild and domesticated populations of vertebrates, including several species of birds. Among domestic bird species, pigmentation variation in the rock pigeon ( Columba livia ) is particularly diverse. To determine the potential contribution of Mc1r variants to pigment diversity in pigeons, we sequenced Mc1r in a wide range of pigeon breeds and identified several single nucleotide polymorphisms, including a variant that codes for an amino acid substitution (Val85Met). In contrast to the association between Val85Met and eumelanism in other avian species, this change was associated with pheomelanism in pigeons. In vitro cAMP accumulation and protein expression assays revealed that Val85Met leads to decreased receptor function and reduced cell surface expression of the mutant protein. The reduced in vitro function is consistent with the observed association with reduced eumelanic pigmentation. Comparative genetic and cellular studies provide important insights about the range of mechanisms underlying diversity among vertebrates, including different phenotypic associations with similar mutations in different species. PMID:23977400
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An Integrated Approach to Multicultural Education.
ERIC Educational Resources Information Center
Academic Senate for California Community Colleges, Sacramento.
Multicultural education is an approach to teaching and learning that seeks to empower individuals so that they may function in a diverse, global society. To prepare students for the 21st century, however, community colleges must expand traditional definitions of diversity to include age, religion, culture, sexual orientation, physical or mental…
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Diversity and Function of Microbial Community in Chinese Strong-Flavor Baijiu Ecosystem: A Review
Zou, Wei; Zhao, Changqing; Luo, Huibo
2018-01-01
Strong flavor baijiu (SFB), also called Luzhou-flavor liquor, is the most popular Chinese baijiu. It is manufactured via solid fermentation, with daqu as the starter. Microbial diversity of the SFB ecosystem and the synergistic effects of the enzymes and compounds produced by them are responsible for the special flavor and mouthfeel of SFB. The present review covers research studies focused on microbial community analysis of the SFB ecosystem, including the culturable microorganisms, their metabolic functions, microbial community diversity and their interactions. The review specifically emphasizes on the most recently conducted culture-independent analysis of SFB microbial community diversity. Furthermore, the possible application of systems biology approaches for elucidating the molecular mechanisms of SFB production were also reviewed and prospected. PMID:29686656
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NASA Astrophysics Data System (ADS)
Carvalho, Russell; Wei, Chih-Lin; Rowe, Gilbert; Schulze, Anja
2013-10-01
Patterns of taxonomic and functional diversity in polychaete assemblages were examined in the deep northern Gulf of Mexico, including the first analysis of polychaete feeding guild distribution. An analysis of samples from a total of 51 stations located along 7 transects plus additional nearby sites, indicated that density decreased exponentially with depth, with the central locations having higher densities than the eastern and western regions. Alpha diversity was also highest at the central stations associated with the Mississippi trough. The samples can be grouped into three significant clusters based on thirty percent similarity of species composition. BIO-ENV indicated depth, sediment particle size, and export POC were most important variables explaining distributions. The diversity of polychaete feeding guilds was high in the Mississippi trough, upper and mid-slope regions but declined to a few guilds on the Sigsbee abyssal plain. Combining feeding guild analysis with traditional analysis of species diversity contributes to a clearer understanding of trophic diversity in deep-sea benthic assemblages.
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Functionally diverse reef-fish communities ameliorate coral disease.
Raymundo, Laurie J; Halford, Andrew R; Maypa, Aileen P; Kerr, Alexander M
2009-10-06
Coral reefs, the most diverse of marine ecosystems, currently experience unprecedented levels of degradation. Diseases are now recognized as a major cause of mortality in reef-forming corals and are complicit in phase shifts of reef ecosystems to algal-dominated states worldwide. Even so, factors contributing to disease occurrence, spread, and impact remain poorly understood. Ecosystem resilience has been linked to the conservation of functional diversity, whereas overfishing reduces functional diversity through cascading, top-down effects. Hence, we tested the hypothesis that reefs with trophically diverse reef fish communities have less coral disease than overfished reefs. We surveyed reefs across the central Philippines, including well-managed marine protected areas (MPAs), and found that disease prevalence was significantly negatively correlated with fish taxonomic diversity. Further, MPAs had significantly higher fish diversity and less disease than unprotected areas. We subsequently investigated potential links between coral disease and the trophic components of fish diversity, finding that only the density of coral-feeding chaetodontid butterflyfishes, seldom targeted by fishers, was positively associated with disease prevalence. These previously uncharacterized results are supported by a second large-scale dataset from the Great Barrier Reef. We hypothesize that members of the charismatic reef-fish family Chaetodontidae are major vectors of coral disease by virtue of their trophic specialization on hard corals and their ecological release in overfished areas, particularly outside MPAs.
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Mensah, Sylvanus; Veldtman, Ruan; Assogbadjo, Achille E; Glèlè Kakaï, Romain; Seifert, Thomas
2016-10-01
The relationship between biodiversity and ecosystem function has increasingly been debated as the cornerstone of the processes behind ecosystem services delivery. Experimental and natural field-based studies have come up with nonconsistent patterns of biodiversity-ecosystem function, supporting either niche complementarity or selection effects hypothesis. Here, we used aboveground carbon (AGC) storage as proxy for ecosystem function in a South African mistbelt forest, and analyzed its relationship with species diversity, through functional diversity and functional dominance. We hypothesized that (1) diversity influences AGC through functional diversity and functional dominance effects; and (2) effects of diversity on AGC would be greater for functional dominance than for functional diversity. Community weight mean (CWM) of functional traits (wood density, specific leaf area, and maximum plant height) were calculated to assess functional dominance (selection effects). As for functional diversity (complementarity effects), multitrait functional diversity indices were computed. The first hypothesis was tested using structural equation modeling. For the second hypothesis, effects of environmental variables such as slope and altitude were tested first, and separate linear mixed-effects models were fitted afterward for functional diversity, functional dominance, and both. Results showed that AGC varied significantly along the slope gradient, with lower values at steeper sites. Species diversity (richness) had positive relationship with AGC, even when slope effects were considered. As predicted, diversity effects on AGC were mediated through functional diversity and functional dominance, suggesting that both the niche complementarity and the selection effects are not exclusively affecting carbon storage. However, the effects were greater for functional diversity than for functional dominance. Furthermore, functional dominance effects were strongly transmitted by CWM of maximum plant height, reflecting the importance of forest vertical stratification for diversity-carbon relationship. We therefore argue for stronger complementary effects that would be induced also by complementary light-use efficiency of tree and species growing in the understory layer.
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Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota
Ellegaard, Kirsten M.; Engel, Philipp
2016-01-01
Interactions with microbes affect many aspects of animal biology, including immune system development, nutrition and health. In vertebrates, the gut microbiota is dominated by a small subset of phyla, but the species composition within these phyla is typically not conserved. Moreover, several recent studies have shown that bacterial species in the gut are composed of a multitude of strains, which frequently co-exist in their host, and may be host-specific. However, since the study of intra-species diversity is challenging, particularly in the setting of complex, host-associated microbial communities, our current understanding of the distribution, evolution and functional relevance of intra-species diversity in the gut is scarce. In order to unravel how genomic diversity translates into phenotypic diversity, community analyses going beyond 16S rRNA profiling, in combination with experimental approaches, are needed. Recently, the honeybee has emerged as a promising model for studying gut bacterial communities, particularly in terms of strain-level diversity. Unlike most other invertebrates, the honeybee gut is colonized by a remarkably consistent and specific core microbiota, which is dominated by only eight bacterial species. As for the vertebrate gut microbiota, these species are composed of highly diverse strains suggesting that similar evolutionary forces shape gut community structures in vertebrates and social insects. In this review, we outline current knowledge on the evolution and functional relevance of strain diversity within the gut microbiota, including recent insights gained from mammals and other animals such as the honeybee. We discuss methodological approaches and propose possible future avenues for studying strain diversity in complex bacterial communities. PMID:27708630
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Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota.
Ellegaard, Kirsten M; Engel, Philipp
2016-01-01
Interactions with microbes affect many aspects of animal biology, including immune system development, nutrition and health. In vertebrates, the gut microbiota is dominated by a small subset of phyla, but the species composition within these phyla is typically not conserved. Moreover, several recent studies have shown that bacterial species in the gut are composed of a multitude of strains, which frequently co-exist in their host, and may be host-specific. However, since the study of intra-species diversity is challenging, particularly in the setting of complex, host-associated microbial communities, our current understanding of the distribution, evolution and functional relevance of intra-species diversity in the gut is scarce. In order to unravel how genomic diversity translates into phenotypic diversity, community analyses going beyond 16S rRNA profiling, in combination with experimental approaches, are needed. Recently, the honeybee has emerged as a promising model for studying gut bacterial communities, particularly in terms of strain-level diversity. Unlike most other invertebrates, the honeybee gut is colonized by a remarkably consistent and specific core microbiota, which is dominated by only eight bacterial species. As for the vertebrate gut microbiota, these species are composed of highly diverse strains suggesting that similar evolutionary forces shape gut community structures in vertebrates and social insects. In this review, we outline current knowledge on the evolution and functional relevance of strain diversity within the gut microbiota, including recent insights gained from mammals and other animals such as the honeybee. We discuss methodological approaches and propose possible future avenues for studying strain diversity in complex bacterial communities.
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Cell diversity and network dynamics in photosensitive human brain organoids
Quadrato, Giorgia; Nguyen, Tuan; Macosko, Evan Z.; Sherwood, John L.; Yang, Sung Min; Berger, Daniel; Maria, Natalie; Scholvin, Jorg; Goldman, Melissa; Kinney, Justin; Boyden, Edward S.; Lichtman, Jeff; Williams, Ziv M.; McCarroll, Steven A.; Arlotta, Paola
2017-01-01
In vitro models of the developing brain such as 3D brain organoids offer an unprecedented opportunity to study aspects of human brain development and disease. However, it remains undefined what cells are generated within organoids and to what extent they recapitulate the regional complexity, cellular diversity, and circuit functionality of the brain. Here, we analyzed gene expression in over 80,000 individual cells isolated from 31 human brain organoids. We find that organoids can generate a broad diversity of cells, which are related to endogenous classes, including cells from the cerebral cortex and the retina. Organoids could be developed over extended periods (over 9 months) enabling unprecedented levels of maturity including the formation of dendritic spines and of spontaneously-active neuronal networks. Finally, neuronal activity within organoids could be controlled using light stimulation of photoreceptor-like cells, which may offer ways to probe the functionality of human neuronal circuits using physiological sensory stimuli. PMID:28445462
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Cell diversity and network dynamics in photosensitive human brain organoids.
Quadrato, Giorgia; Nguyen, Tuan; Macosko, Evan Z; Sherwood, John L; Min Yang, Sung; Berger, Daniel R; Maria, Natalie; Scholvin, Jorg; Goldman, Melissa; Kinney, Justin P; Boyden, Edward S; Lichtman, Jeff W; Williams, Ziv M; McCarroll, Steven A; Arlotta, Paola
2017-05-04
In vitro models of the developing brain such as three-dimensional brain organoids offer an unprecedented opportunity to study aspects of human brain development and disease. However, the cells generated within organoids and the extent to which they recapitulate the regional complexity, cellular diversity and circuit functionality of the brain remain undefined. Here we analyse gene expression in over 80,000 individual cells isolated from 31 human brain organoids. We find that organoids can generate a broad diversity of cells, which are related to endogenous classes, including cells from the cerebral cortex and the retina. Organoids could be developed over extended periods (more than 9 months), allowing for the establishment of relatively mature features, including the formation of dendritic spines and spontaneously active neuronal networks. Finally, neuronal activity within organoids could be controlled using light stimulation of photosensitive cells, which may offer a way to probe the functionality of human neuronal circuits using physiological sensory stimuli.
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Biodiversity of arbuscular mycorrhizal fungi and ecosystem function.
Powell, Jeff R; Rillig, Matthias C
2018-03-30
Contents Summary I. pathways of influence and pervasiveness of effects II. AM fungal richness effects on ecosystem functions III. Other dimensions of biodiversity IV. Back to basics - primary axes of niche differentiation by AM fungi V. Functional diversity of AM fungi - a role for biological stoichiometry? VI. Past, novel and future ecosystems VII. Opportunities and the way forward Acknowledgements References SUMMARY: Arbuscular mycorrhizal (AM) fungi play important functional roles in ecosystems, including the uptake and transfer of nutrients, modification of the physical soil environment and alteration of plant interactions with other biota. Several studies have demonstrated the potential for variation in AM fungal diversity to also affect ecosystem functioning, mainly via effects on primary productivity. Diversity in these studies is usually characterized in terms of the number of species, unique evolutionary lineages or complementary mycorrhizal traits, as well as the ability of plants to discriminate among AM fungi in space and time. However, the emergent outcomes of these relationships are usually indirect, and thus context dependent, and difficult to predict with certainty. Here, we advocate a fungal-centric view of AM fungal biodiversity-ecosystem function relationships that focuses on the direct and specific links between AM fungal fitness and consequences for their roles in ecosystems, especially highlighting functional diversity in hyphal resource economics. We conclude by arguing that an understanding of AM fungal functional diversity is fundamental to determine whether AM fungi have a role in the exploitation of marginal/novel environments (whether past, present or future) and highlight avenues for future research. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Gao, B.; Sugiman-Marangos, S; Junop, M
2009-01-01
The Actinobacteria phylum represents one of the largest and most diverse groups of bacteria, encompassing many important and well-characterized organisms including Streptomyces, Bifidobacterium, Corynebacterium and Mycobacterium. Members of this phylum are remarkably diverse in terms of life cycle, morphology, physiology and ecology. Recent comparative genomic analysis of 19 actinobacterial species determined that only 5 genes of unknown function uniquely define this large phylum [1]. The cellular functions of these actinobacteria-specific proteins (ASP) are not known.
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The diverse functions of Src family kinases in macrophages
Abram, Clare L.; Lowell, Clifford A.
2015-01-01
Macrophages are key components of the innate immune response. These cells possess a diverse repertoire of receptors that allow them to respond to a host of external stimuli including cytokines, chemokines, and pathogen-associated molecules. Signals resulting from these stimuli activate a number of macrophage functional responses such as adhesion, migration, phagocytosis, proliferation, survival, cytokine release and production of reactive oxygen and nitrogen species. The cytoplasmic tyrosine kinase Src and its family members (SFKs) have been implicated in many intracellular signaling pathways in macrophages, initiated by a diverse set of receptors ranging from integrins to Toll-like receptors. However, it has been difficult to implicate any given member of the family in any specific pathway. SFKs appear to have overlapping and complementary functions in many pathways. Perhaps the function of these enzymes is to modulate the overall intracellular signaling network in macrophages, rather than operating as exclusive signaling switches for defined pathways. In general, SFKs may function more like rheostats, influencing the amplitude of many pathways. PMID:18508521
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Davies, Wayne I.L.; Tamai, T. Katherine; Zheng, Lei; Fu, Josephine K.; Rihel, Jason; Foster, Russell G.; Whitmore, David; Hankins, Mark W.
2015-01-01
Light affects animal physiology and behavior more than simply through classical visual, image-forming pathways. Nonvisual photoreception regulates numerous biological systems, including circadian entrainment, DNA repair, metabolism, and behavior. However, for the majority of these processes, the photoreceptive molecules involved are unknown. Given the diversity of photophysiological responses, the question arises whether a single photopigment or a greater diversity of proteins within the opsin superfamily detect photic stimuli. Here, a functional genomics approach identified the full complement of photopigments in a highly light-sensitive model vertebrate, the zebrafish (Danio rerio), and characterized their tissue distribution, expression levels, and biochemical properties. The results presented here reveal the presence of 42 distinct genes encoding 10 classical visual photopigments and 32 nonvisual opsins, including 10 novel opsin genes comprising four new pigment classes. Consistent with the presence of light-entrainable circadian oscillators in zebrafish, all adult tissues examined expressed two or more opsins, including several novel opsins. Spectral and electrophysiological analyses of the new opsins demonstrate that they form functional photopigments, each with unique chromophore-binding and wavelength specificities. This study has revealed a remarkable number and diversity of photopigments in zebrafish, the largest number so far discovered for any vertebrate. Found in amphibians, reptiles, birds, and all three mammalian clades, most of these genes are not restricted to teleosts. Therefore, nonvisual light detection is far more complex than initially appreciated, which has significant biological implications in understanding photoreception in vertebrates. PMID:26450929
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NASA Astrophysics Data System (ADS)
Pavlick, R.; Reu, B.; Bohn, K.; Dyke, J.; Kleidon, A.
2010-12-01
The terrestrial biosphere is a complex, self-organizing system which is continually both adapting to and altering its global environment. It also exhibits a vast diversity of vegetation forms and functioning. However, the terrestrial biosphere components within current state-of-the-art Earth System Models abstract this diversity in to a handful of relatively static plant functional types. These coarse and static representations of functional diversity might contribute to overly pessimistic projections regarding terrestrial ecosystem responses to scenarios of global change (e.g. Amazonian and boreal forest diebacks). In the Jena Diversity (JeDi) model, we introduce a new approach to vegetation modelling with a richer representation of functional diversity, based not on plant functional types, but on unavoidable plant ecophysiological trade-offs, which we hypothesize should be more stable in time. The JeDi model tests a large number of plant growth strategies. Each growth strategy is simulated using a set of randomly generated parameter values, which characterize its functioning in terms of carbon allocation, ecophysiology, and phenology, which are then linked to the growing conditions at the land surface. The model is constructed in such a way that these parameters inherently lead to ecophysiological trade-offs, which determine whether a growth strategy is able to survive and reproduce under the prevalent climatic conditions. Kleidon and Mooney (2000) demonstrated that this approach is capable of reproducing the geographic distribution of species richness. More recently, we have shown the JeDi model can explain other biogeographical phenomena including the present-day global pattern of biomes (Reu et al., accepted), ecosystem evenness (Kleidon et al. 2009), and possible mechanisms for biome shifts and biodiversity changes under scenarios of global warming (Reu et al., submitted). We have also evaluated the simulated biogeochemical fluxes from JeDi against a variety of site, field, and satellite observations (Pavlick et al., submitted) following a protocol established by the Carbon-Land Model Intercomparison Project (Randerson et al. 2009). We found that the global patterns of biogeochemical fluxes and land surface properties are reasonably well simulated using this bottom-up trade-off approach and compare favorably with other state of the art terrestrial biosphere models. Here, we present some results from JeDi simulations, wherein we varied the modelled functional diversity to quantify its impact on terrestrial biogeochemical fluxes under both present-day conditions and projected scenarios of global change. We also present results from a set of simulations wherein we vary the ability of the modelled ecosystems to adapt through changes in functional composition, leading to different projection responses of the carbon cycle to global warming. This plant functional tradeoff approach sets the foundation for many applications, including exploring the emergence and climatic impacts of major vegetation transitions throughout the last 400 million years as well as quantifying the significance of preserving functional diversity to hedge against uncertain climates in the future.
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Arnan, Xavier; Cerdá, Xim; Retana, Javier
2015-01-01
We analyze the relative contribution of environmental and spatial variables to the alpha and beta components of taxonomic (TD), phylogenetic (PD), and functional (FD) diversity in ant communities found along different climate and anthropogenic disturbance gradients across western and central Europe, in order to assess the mechanisms structuring ant biodiversity. To this aim we calculated alpha and beta TD, PD, and FD for 349 ant communities, which included a total of 155 ant species; we examined 10 functional traits and phylogenetic relatedness. Variation partitioning was used to examine how much variation in ant diversity was explained by environmental and spatial variables. Autocorrelation in diversity measures and each trait's phylogenetic signal were also analyzed. We found strong autocorrelation in diversity measures. Both environmental and spatial variables significantly contributed to variation in TD, PD, and FD at both alpha and beta scales; spatial structure had the larger influence. The different facets of diversity showed similar patterns along environmental gradients. Environment explained a much larger percentage of variation in FD than in TD or PD. All traits demonstrated strong phylogenetic signals. Our results indicate that environmental filtering and dispersal limitations structure all types of diversity in ant communities. Strong dispersal limitations appear to have led to clustering of TD, PD, and FD in western and central Europe, probably because different historical and evolutionary processes generated different pools of species. Remarkably, these three facets of diversity showed parallel patterns along environmental gradients. Trait-mediated species sorting and niche conservatism appear to structure ant diversity, as evidenced by the fact that more variation was explained for FD and that all traits had strong phylogenetic signals. Since environmental variables explained much more variation in FD than in PD, functional diversity should be a better indicator of community assembly processes than phylogenetic diversity.
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Baker, C S; Vant, M D; Dalebout, M L; Lento, G M; O'Brien, S J; Yuhki, N
2006-05-01
The molecular diversity and phylogenetic relationships of two class II genes of the baleen whale major histocompatibility complex were investigated and compared to toothed whales and out-groups. Amplification of the DQB exon 2 provided sequences showing high within-species and between-species nucleotide diversity and uninterrupted reading frames consistent with functional class II loci found in related mammals (e.g., ruminants). Cloning of amplified products indicated gene duplication in the humpback whale and triplication in the southern right whale, with average nucleotide diversity of 5.9 and 6.3%, respectively, for alleles of each species. Significantly higher nonsynonymous divergence at sites coding for peptide binding (32% for humpback and 40% for southern right) suggested that these loci were subject to positive (overdominant) selection. A population survey of humpback whales detected 23 alleles, differing by up to 21% of their inferred amino acid sequences. Amplification of the DRB exon 2 resulted in two groups of sequences. One was most similar to the DRB3 of the cow and present in all whales screened to date, including toothed whales. The second was most similar to the DRB2 of the cow and was found only in the bowhead and right whales. Both loci showed low diversity among species and apparent loss of function or altered function including interruption of reading frames. Finally, comparison of inferred protein sequence of the DRB3-like locus suggested convergence with the DQB, perhaps resulting from intergenic conversion or recombination.
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New genes as drivers of phenotypic evolution
Chen, Sidi; Krinsky, Benjamin H.; Long, Manyuan
2014-01-01
During the course of evolution, genomes acquire novel genetic elements as sources of functional and phenotypic diversity, including new genes that originated in recent evolution. In the past few years, substantial progress has been made in understanding the evolution and phenotypic effects of new genes. In particular, an emerging picture is that new genes, despite being present in the genomes of only a subset of species, can rapidly evolve indispensable roles in fundamental biological processes, including development, reproduction, brain function and behaviour. The molecular underpinnings of how new genes can develop these roles are starting to be characterized. These recent discoveries yield fresh insights into our broad understanding of biological diversity at refined resolution. PMID:23949544
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New genes as drivers of phenotypic evolution.
Chen, Sidi; Krinsky, Benjamin H; Long, Manyuan
2013-09-01
During the course of evolution, genomes acquire novel genetic elements as sources of functional and phenotypic diversity, including new genes that originated in recent evolution. In the past few years, substantial progress has been made in understanding the evolution and phenotypic effects of new genes. In particular, an emerging picture is that new genes, despite being present in the genomes of only a subset of species, can rapidly evolve indispensable roles in fundamental biological processes, including development, reproduction, brain function and behaviour. The molecular underpinnings of how new genes can develop these roles are starting to be characterized. These recent discoveries yield fresh insights into our broad understanding of biological diversity at refined resolution.
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Genetic diversity of functional food species Spinacia oleracea L. by protein markers.
Rashid, M; Yousaf, Z; Haider, M S; Khalid, S; Rehman, H A; Younas, A; Arif, A
2014-01-01
Exploration of genetic diversity contributes primarily towards crop improvement. Spinaciaoleracea L. is a functional food species but unfortunately the genetic diversity of this vegetable is still unexplored. Therefore, this research was planned to explore the genetic diversity of S. oleracea by using morphological and protein markers. Protein profile of 25 accessions was generated on sodium dodecyl sulphate polyacrylamide gel. Total allelic variation of 27 bands was found. Out of these, 20 were polymorphic and the rest of the bands were monomorphic. Molecular weights of the bands ranged from 12.6 to 91.2 kDa. Major genetic differences were observed in accession 20541 (Peshawar) followed by 20180 (Lahore) and 19902 (AVRDC). Significant differences exist in the protein banding pattern. This variation can further be studied by advanced molecular techniques, including two-dimensional electrophoresis and DNA markers.
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Taylor, Joe D; Cunliffe, Michael
2016-01-01
Mycoplankton have so far been a neglected component of pelagic marine ecosystems, having been poorly studied relative to other plankton groups. Currently, there is a lack of understanding of how mycoplankton diversity changes through time, and the identity of controlling environmental drivers. Using Fungi-specific high-throughput sequencing and quantitative PCR analysis of plankton DNA samples collected over 6 years from the coastal biodiversity time series site Station L4 situated off Plymouth (UK), we have assessed changes in the temporal variability of mycoplankton diversity and abundance in relation to co-occurring environmental variables. Mycoplankton diversity at Station L4 was dominated by Ascomycota, Basidiomycota and Chytridiomycota, with several orders within these phyla frequently abundant and dominant in multiple years. Repeating interannual mycoplankton blooms were linked to potential controlling environmental drivers, including nitrogen availability and temperature. Specific relationships between mycoplankton and other plankton groups were also identified, with seasonal chytrid blooms matching diatom blooms in consecutive years. Mycoplankton α-diversity was greatest during periods of reduced salinity at Station L4, indicative of riverine input to the ecosystem. Mycoplankton abundance also increased during periods of reduced salinity, and when potential substrate availability was increased, including particulate organic matter. This study has identified possible controlling environmental drivers of mycoplankton diversity and abundance in a coastal sea ecosystem, and therefore sheds new light on the biology and ecology of an enigmatic marine plankton group. Mycoplankton have several potential functional roles, including saprotrophs and parasites, that should now be considered within the consensus view of pelagic ecosystem functioning and services. PMID:26943623
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NASA Astrophysics Data System (ADS)
Mason, O. U.; di Meo-Savoie, C. A.; Nakagawa, T.; van Nostrand, J. D.; Rosner, M.; Maruyama, A.; Zhou, J.; Fisk, M. R.; Giovannoni, S. J.
2008-12-01
Oceanic crust covers nearly 70% of the Earth's surface, of which, the upper, sediment layer is estimated to harbor substantial microbial biomass. Marine crust, however, extends several kilometers beyond this surficial layer, and includes the basalt and gabbro layers. The microbial diversity in basalts is well characterized, yet metabolic diversity is unknown. To date, the microflora associated with gabbros, including microbial and metabolic diversity has not been reported. In our analyses basaltic and gabbroic endoliths were analyzed using terminal restriction fragment length polymorphism, cloning and sequencing, and microarray analysis of functional genes. Our results suggest that despite nearly identical chemical compositions of basalt and gabbro the associated microflora did not overlap. Basalt samples harbor a surprising diversity of seemingly cosmopolitan microorganisms, some of which appear to be basalt specialists. Conversely, gabbros have a low diversity of endoliths, none of which appear to be specifically adapted to the gabbroic environment. Microarray analysis (GeoChip) was used to assay for functional gene diversity in basalts and gabbros. In basalt genes coding for previously unreported processes such as carbon fixation, methane-oxidation, methanogenesis, and nitrogen fixation were present, suggesting that basalts harbor previously unrecognized metabolic diversity. Similar processes were observed in gabbroic samples, yet metabolic inference from phylogenetic relationships of gabbroic endoliths with other microorganisms, suggests that hydrocarbon oxidation is the prevailing metabolism in this environment. Our analyses revealed that the basalt and gabbro layers harbor microorganisms with the genetic potential to significantly impact biogeochemical cycling in the lithosphere and overlying hydrosphere.
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Conflicts in maintaining biodiversity at multiple scales.
Lankau, Richard A
2011-05-01
Biodiversity consists of multiple scales, including functional diversity in ecological traits, species diversity and genetic diversity within species, and is declining across the globe, largely in response to human activities. While species extinctions are the most obvious aspect of this, there has also been a more insidious loss of genetic diversity within species. While a vast literature concerns each of these scales of biodiversity, less is known about how different scales affect one another. In particular, genetic and species diversity may influence each other in numerous ways, both positively and negatively. However, we know little about the mechanism behind these patterns. In this issue of Molecular Ecology, Nestmann et al. (2011) experimentally explore the effect of species and functional diversity and composition of grassland plant communities on the genetic structure of one of the component species. Increasing species richness led to greater changes in the genetic composition of the focal populations over 4 years, primarily because of genetic drift in smaller population sizes. However, there were also genetic changes in response to particular plant functional groups, indicating selective differences driven by plant community composition. These results suggest that different levels of biodiversity can trade-off in communities, which may prove a challenge for conservation biologists seeking to preserve all aspects of biodiversity.
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Ecosystem Functions across Trophic Levels Are Linked to Functional and Phylogenetic Diversity
Thompson, Patrick L.; Davies, T. Jonathan; Gonzalez, Andrew
2015-01-01
In experimental systems, it has been shown that biodiversity indices based on traits or phylogeny can outperform species richness as predictors of plant ecosystem function. However, it is unclear whether this pattern extends to the function of food webs in natural ecosystems. Here we tested whether zooplankton functional and phylogenetic diversity explains the functioning of 23 natural pond communities. We used two measures of ecosystem function: (1) zooplankton community biomass and (2) phytoplankton abundance (Chl a). We tested for diversity-ecosystem function relationships within and across trophic levels. We found a strong correlation between zooplankton diversity and ecosystem function, whereas local environmental conditions were less important. Further, the positive diversity-ecosystem function relationships were more pronounced for measures of functional and phylogenetic diversity than for species richness. Zooplankton and phytoplankton biomass were best predicted by different indices, suggesting that the two functions are dependent upon different aspects of diversity. Zooplankton community biomass was best predicted by zooplankton trait-based functional richness, while phytoplankton abundance was best predicted by zooplankton phylogenetic diversity. Our results suggest that the positive relationship between diversity and ecosystem function can extend across trophic levels in natural environments, and that greater insight into variation in ecosystem function can be gained by combining functional and phylogenetic diversity measures. PMID:25693188
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Ecosystem functions across trophic levels are linked to functional and phylogenetic diversity.
Thompson, Patrick L; Davies, T Jonathan; Gonzalez, Andrew
2015-01-01
In experimental systems, it has been shown that biodiversity indices based on traits or phylogeny can outperform species richness as predictors of plant ecosystem function. However, it is unclear whether this pattern extends to the function of food webs in natural ecosystems. Here we tested whether zooplankton functional and phylogenetic diversity explains the functioning of 23 natural pond communities. We used two measures of ecosystem function: (1) zooplankton community biomass and (2) phytoplankton abundance (Chl a). We tested for diversity-ecosystem function relationships within and across trophic levels. We found a strong correlation between zooplankton diversity and ecosystem function, whereas local environmental conditions were less important. Further, the positive diversity-ecosystem function relationships were more pronounced for measures of functional and phylogenetic diversity than for species richness. Zooplankton and phytoplankton biomass were best predicted by different indices, suggesting that the two functions are dependent upon different aspects of diversity. Zooplankton community biomass was best predicted by zooplankton trait-based functional richness, while phytoplankton abundance was best predicted by zooplankton phylogenetic diversity. Our results suggest that the positive relationship between diversity and ecosystem function can extend across trophic levels in natural environments, and that greater insight into variation in ecosystem function can be gained by combining functional and phylogenetic diversity measures.
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Steudel, Bastian; Hallmann, Christine; Lorenz, Maike; Abrahamczyk, Stefan; Prinz, Kathleen; Herrfurth, Cornelia; Feussner, Ivo; Martini, Johannes W R; Kessler, Michael
2016-10-01
It is well known that ecosystem functioning is positively influenced by biodiversity. Most biodiversity-ecosystem functioning experiments have measured biodiversity based on species richness or phylogenetic relationships. However, theoretical and empirical evidence suggests that ecosystem functioning should be more closely related to functional diversity than to species richness. We applied different metrics of biodiversity in an artificial biodiversity-ecosystem functioning experiment using 64 species of green microalgae in combinations of two to 16 species. We found that phylogenetic and functional diversity were positively correlated with biomass overyield, driven by their strong correlation with species richness. At low species richness, no significant correlation between overyield and functional and phylogenetic diversity was found. However, at high species richness (16 species), we found a positive relationship of overyield with functional diversity and a negative relationship with phylogenetic diversity. We show that negative phylogenetic diversity-ecosystem functioning relationships can result from interspecific growth inhibition. The opposing performances of facilitation (functional diversity) and inhibition (phylogenetic diversity) we observed at the 16 species level suggest that phylogenetic diversity is not always a good proxy for functional diversity and that results from experiments with low species numbers may underestimate negative species interactions. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.
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Toussaint, A; Charpin, N; Brosse, S; Villéger, S
2016-03-16
Worldwide biodiversity assessments have mainly focused on species richness but little is known about the diversity of species roles, i.e. functional diversity, while this is a key facet to understanding the consequences of global changes on the ecosystem services to human societies. Here, we report the world pattern of functional diversity of freshwater fish using a database encompassing morphological characteristics of more than 9,000 species. The Neotropical realm hosts more than 75% of global functional diversity while other realms each host less than 25%. This discrepancy is mediated by high functional uniqueness in some diversified Neotropical fish orders. Surprisingly, functional diversity patterns were weakly related to functional vulnerability. In the Neotropics the loss of threatened species will cause a limited loss of functional diversity (<10%) whereas in the Nearctic and Palearctic realms, decline of the functional diversity will reach 43% and 33%, respectively, conferring a high functional vulnerability to these realms. Conservation of the Neotropical fish diversity is a key target to maintain world fish functional diversity, but this should not hide the pressing need to conserve the vulnerable fish faunas of the rest of the world, in which functional diversity is to a large extent supported by threatened species.
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de Bello, Francesco; Carmona, Carlos P; Lepš, Jan; Szava-Kovats, Robert; Pärtel, Meelis
2016-04-01
While an increasing number of indices for estimating the functional trait diversity of biological communities are being proposed, there is a growing demand by ecologists to clarify their actual implications and simplify index selection. Several key indices relate to mean trait dissimilarity between species within biological communities. Among them, the most widely used include (a) the mean species pairwise dissimilarity (MPD) and (b) the Rao quadratic entropy (and related indices). These indices are often regarded as redundant and promote the unsubstantiated yet widely held view that Rao is a form of MPD. Worryingly, existing R functions also do not always simplify the use and differentiation of these indices. In this paper, we show various distinctions between these two indices that warrant mathematical and biological consideration. We start by showing an existing form of MPD that considers species abundances and is different from Rao both mathematically and conceptually. We then show that the mathematical relationship between MPD and Rao can be presented simply as Rao = MPD × Simpson, where the Simpson diversity index is defined as 1 - dominance. We further show that this relationship is maintained for both species abundances and presence/absence. This evidence dismantles the paradigm that the Rao diversity is an abundance-weighted form of MPD and indicates that both indices can differ substantially at low species diversities. We discuss the different interpretations of trait diversity patterns in biological communities provided by Rao and MPD and then provide a simple R function, called "melodic," which avoids the unintended results that arise from existing mainstream functions.
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Biogeographical disparity in the functional diversity and redundancy of corals.
McWilliam, Mike; Hoogenboom, Mia O; Baird, Andrew H; Kuo, Chao-Yang; Madin, Joshua S; Hughes, Terry P
2018-03-20
Corals are major contributors to a range of key ecosystem functions on tropical reefs, including calcification, photosynthesis, nutrient cycling, and the provision of habitat structure. The abundance of corals is declining at multiple scales, and the species composition of assemblages is responding to escalating human pressures, including anthropogenic global warming. An urgent challenge is to understand the functional consequences of these shifts in abundance and composition in different biogeographical contexts. While global patterns of coral species richness are well known, the biogeography of coral functions in provinces and domains with high and low redundancy is poorly understood. Here, we quantify the functional traits of all currently recognized zooxanthellate coral species ( n = 821) in both the Indo-Pacific and Atlantic domains to examine the relationships between species richness and the diversity and redundancy of functional trait space. We find that trait diversity is remarkably conserved (>75% of the global total) along latitudinal and longitudinal gradients in species richness, falling away only in species-poor provinces ( n < 200), such as the Persian Gulf (52% of the global total), Hawaii (37%), the Caribbean (26%), and the East-Pacific (20%), where redundancy is also diminished. In the more species-poor provinces, large and ecologically important areas of trait space are empty, or occupied by just a few, highly distinctive species. These striking biogeographical differences in redundancy could affect the resilience of critical reef functions and highlight the vulnerability of relatively depauperate, peripheral locations, which are often a low priority for targeted conservation efforts.
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Si, Xingfeng; Baselga, Andrés; Leprieur, Fabien; Song, Xiao; Ding, Ping
2016-03-01
Taxonomic diversity considers all species being equally different from each other and thus disregards species' different ecological functions. Exploring taxonomic and functional aspects of biodiversity simultaneously can better understand the processes of community assembly. We analysed taxonomic and functional alpha and beta diversities of breeding bird assemblages on land-bridge islands in the Thousand Island Lake, China. Given the high dispersal ability of most birds at this spatial scale (several kilometres), we predicted (i) selective extinction driving alpha and beta diversities after the creation of land-bridge islands of varying area and (ii) low taxonomic and functional beta diversities that were not correlated to spatial distance. Breeding birds were surveyed on 37 islands annually from 2007 to 2014. We decomposed beta diversity of breeding birds into spatial turnover and nestedness-resultant components, and related taxonomic and functional diversities to island area and isolation using power regression models (for alpha diversity) and multiple regression models on distance matrices (for beta diversity). We then ran simulations to assess the strength of the correlations between taxonomic and functional diversities. Results revealed that both taxonomic and functional alpha diversities increased with island area. The taxonomic nestedness-resultant and turnover components increased and decreased with difference in area, respectively, but functional counterparts did not. Isolation played a minor role in explaining alpha- and beta-diversity patterns. By partitioning beta diversity, we found low levels of overall taxonomic and functional beta diversities. The functional nestedness-resultant component dominated overall functional beta diversity, whereas taxonomic turnover was the dominant component for taxonomic beta diversity. The simulation showed that functional alpha and beta diversities were significantly correlated with taxonomic diversities, and the observed values of correlations were significantly different from null expectations of random extinction. Our assessment of island bird assemblages validated the predictions of no distance effects and low beta diversity due to pervasive dispersal events among islands and also suggested that selective extinction drives taxonomic and functional alpha and beta diversities. The contrasting turnover and nestedness-resultant components of taxonomic and functional beta diversities demonstrate the importance of considering the multifaceted nature of biodiversity when examining community assembly. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.
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Strecker, A.L.; Olden, J.D.; Whittier, Joanna B.; Paukert, C.P.
2011-01-01
To date, the predominant use of systematic conservation planning has been to evaluate and conserve areas of high terrestrial biodiversity. Although studies in freshwater ecosystems have received recent attention, research has rarely considered the potential tradeoffs between protecting different dimensions of biodiversity and the ecological processes that maintain diversity. We provide the first systematic prioritization for freshwaters (focusing on the highly threatened and globally distinct fish fauna of the Lower Colorado River Basin, USA) simultaneously considering scenarios of: taxonomic, functional, and phylogenetic diversity;contemporary threats to biodiversity (including interactions with nonnative species);and future climate change and human population growth. There was 75% congruence between areas of highest conservation priority for different aspects of biodiversity, suggesting that conservation efforts can concurrently achieve strong complementarity among all types of diversity. However, sizable fractions of the landscape were incongruent across conservation priorities for different diversity scenarios, underscoring the importance of considering multiple dimensions of biodiversity and highlighting catchments that contribute disproportionately to taxonomic, functional, and phylogenetic diversity in the region. Regions of projected human population growth were not concordant with conservation priorities;however, higher human population abundance will likely have indirect effects on native biodiversity by increasing demand for water. This will come in direct conflict with projected reductions in precipitation and warmer temperatures, which have substantial overlap with regions of high contemporary diversity. Native and endemic fishes in arid ecosystems are critically endangered by both current and future threats, but our results highlight the use of systematic conservation planning for the optimal allocation of limited resources that incorporates multiple and complementary conservation values describing taxonomic, functional, and phylogenetic diversity. ??2011 by the Ecological Society of America.
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Strecker, Angela L.; Olden, Julian D.; Whittier, Joanna B.; Paukert, Craig P.
2011-01-01
To date, the predominant use of systematic conservation planning has been to evaluate and conserve areas of high terrestrial biodiversity. Although studies in freshwater ecosystems have received recent attention, research has rarely considered the potential trade-offs between protecting different dimensions of biodiversity and the ecological processes that maintain diversity. We provide the first systematic prioritization for freshwaters (focusing on the highly threatened and globally distinct fish fauna of the Lower Colorado River Basin, USA) simultaneously considering scenarios of: taxonomic, functional, and phylogenetic diversity; contemporary threats to biodiversity (including interactions with nonnative species); and future climate change and human population growth. There was 75% congruence between areas of highest conservation priority for different aspects of biodiversity, suggesting that conservation efforts can concurrently achieve strong complementarity among all types of diversity. However, sizable fractions of the landscape were incongruent across conservation priorities for different diversity scenarios, underscoring the importance of considering multiple dimensions of biodiversity and highlighting catchments that contribute disproportionately to taxonomic, functional, and phylogenetic diversity in the region. Regions of projected human population growth were not concordant with conservation priorities; however, higher human population abundance will likely have indirect effects on native biodiversity by increasing demand for water. This will come in direct conflict with projected reductions in precipitation and warmer temperatures, which have substantial overlap with regions of high contemporary diversity. Native and endemic fishes in arid ecosystems are critically endangered by both current and future threats, but our results highlight the use of systematic conservation planning for the optimal allocation of limited resources that incorporates multiple and complementary conservation values describing taxonomic, functional, and phylogenetic diversity.
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Functional Risk Modeling for Lunar Surface Systems
NASA Technical Reports Server (NTRS)
Thomson, Fraser; Mathias, Donovan; Go, Susie; Nejad, Hamed
2010-01-01
We introduce an approach to risk modeling that we call functional modeling , which we have developed to estimate the capabilities of a lunar base. The functional model tracks the availability of functions provided by systems, in addition to the operational state of those systems constituent strings. By tracking functions, we are able to identify cases where identical functions are provided by elements (rovers, habitats, etc.) that are connected together on the lunar surface. We credit functional diversity in those cases, and in doing so compute more realistic estimates of operational mode availabilities. The functional modeling approach yields more realistic estimates of the availability of the various operational modes provided to astronauts by the ensemble of surface elements included in a lunar base architecture. By tracking functional availability the effects of diverse backup, which often exists when two or more independent elements are connected together, is properly accounted for.
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ERIC Educational Resources Information Center
Juang, Linda; Ittel, Angela; Hoferichter, Frances; Gallarin, Miriam
2016-01-01
Adopting a risk and resilience perspective, the current study examined whether family cohesion and peer support functioned as protective factors against the negative effects of racial/ethnic discrimination by peers. The sample included 142 ethnically diverse college students. The results showed that while greater perceived discrimination was…
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Plant Diversity Contributions of Riparian Areas in Watersheds of the Northern Lake States, USA
P. Charles Goebel; Brain J. Palik; Kurt S. Pregitzer
2003-01-01
In most forested watersheds, riparian areas constitute a small proportion of the total land area, yet their contributions to overall plant diversity can be significant. However, little information is available on which portion of riparian areas (defined as functional ecotones comprising all fluvial landforms, including floodplains, terraces, and connecting hillslopes)...
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On the relationship between phylogenetic diversity and trait diversity.
Tucker, Caroline M; Davies, T Jonathan; Cadotte, Marc W; Pearse, William D
2018-05-21
Niche differences are key to understanding the distribution and structure of biodiversity. To examine niche differences, we must first characterize how species occupy niche space, and two approaches are commonly used in the ecological literature. The first uses species traits to estimate multivariate trait space (so-called functional trait diversity, FD); the second quantifies the amount of time or evolutionary history captured by a group of species (phylogenetic diversity, PD). It is often-but controversially-assumed that these putative measures of niche space are at a minimum correlated and perhaps redundant, since more evolutionary time allows for greater accumulation of trait changes. This theoretical expectation remains surprisingly poorly evaluated, particularly in the context of multivariate measures of trait diversity. We evaluated the relationship between phylogenetic diversity and trait diversity using analytical and simulation-based methods across common models of trait evolution. We show that PD correlates with FD increasingly strongly as more traits are included in the FD measure. Our results indicate that phylogenetic diversity can be a useful surrogate for high-dimensional trait diversity, but we also show that the correlation weakens when the underlying process of trait evolution includes variation in rate and optima. © 2018 by the Ecological Society of America.
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Leaf bacterial diversity mediates plant diversity and ecosystem function relationships.
Laforest-Lapointe, Isabelle; Paquette, Alain; Messier, Christian; Kembel, Steven W
2017-06-01
Research on biodiversity and ecosystem functioning has demonstrated links between plant diversity and ecosystem functions such as productivity. At other trophic levels, the plant microbiome has been shown to influence host plant fitness and function, and host-associated microbes have been proposed to influence ecosystem function through their role in defining the extended phenotype of host organisms However, the importance of the plant microbiome for ecosystem function has not been quantified in the context of the known importance of plant diversity and traits. Here, using a tree biodiversity-ecosystem functioning experiment, we provide strong support for the hypothesis that leaf bacterial diversity is positively linked to ecosystem productivity, even after accounting for the role of plant diversity. Our results also show that host species identity, functional identity and functional diversity are the main determinants of leaf bacterial community structure and diversity. Our study provides evidence of a positive correlation between plant-associated microbial diversity and terrestrial ecosystem productivity, and a new mechanism by which models of biodiversity-ecosystem functioning relationships can be improved.
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Jangid, Kamlesh; Kao, Ming-Hung; Lahamge, Aishwarya; Williams, Mark A; Rathbun, Stephen L; Whitman, William B
2016-01-01
K-shuff is a new algorithm for comparing the similarity of gene sequence libraries, providing measures of the structural and compositional diversity as well as the significance of the differences between these measures. Inspired by Ripley's K-function for spatial point pattern analysis, the Intra K-function or IKF measures the structural diversity, including both the richness and overall similarity of the sequences, within a library. The Cross K-function or CKF measures the compositional diversity between gene libraries, reflecting both the number of OTUs shared as well as the overall similarity in OTUs. A Monte Carlo testing procedure then enables statistical evaluation of both the structural and compositional diversity between gene libraries. For 16S rRNA gene libraries from complex bacterial communities such as those found in seawater, salt marsh sediments, and soils, K-shuff yields reproducible estimates of structural and compositional diversity with libraries greater than 50 sequences. Similarly, for pyrosequencing libraries generated from a glacial retreat chronosequence and Illumina® libraries generated from US homes, K-shuff required >300 and 100 sequences per sample, respectively. Power analyses demonstrated that K-shuff is sensitive to small differences in Sanger or Illumina® libraries. This extra sensitivity of K-shuff enabled examination of compositional differences at much deeper taxonomic levels, such as within abundant OTUs. This is especially useful when comparing communities that are compositionally very similar but functionally different. K-shuff will therefore prove beneficial for conventional microbiome analysis as well as specific hypothesis testing.
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Species Pool Functional Diversity Plays a Hidden Role in Generating β-Diversity.
Patrick, Christopher J; Brown, Bryan L
2018-05-01
Functional trait diversity is used as a way to infer mechanistic processes that drive community assembly. While functional diversity within communities is often viewed as a response variable, here we present and test a framework for how functional diversity among taxa in the regional species pool drives the assembly of communities among habitats. We predicted that species pool functional diversity should work with environmental heterogeneity to drive β-diversity. We tested these predictions by modeling empirical patterns in invertebrate communities from 570 streams in 52 watersheds. Our analysis of the field data provided strong support for the inclusion of both functional diversity and environmental heterogeneity in the models, and our predictions were supported when the community was analyzed all together. However, analyses within individual functional feeding guilds revealed strong context dependency in the relative importance of functional diversity, γ-richness, and environmental heterogeneity to β-diversity. We interpret the results to mean that functional diversity can play an important role in driving β-diversity; however, within guilds the nature of interspecific interactions and species pool size complicate the relationship. Future research should test this conceptual model across different ecosystems and in experimental settings using metacommunity mesocosms to enhance our understanding of the role that functional variation plays in generating spatial biodiversity patterns.
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Neave, Matthew J.; Michell, Craig T.; Apprill, Amy; Voolstra, Christian R.
2017-01-01
Endozoicomonas bacteria are globally distributed and often abundantly associated with diverse marine hosts including reef-building corals, yet their function remains unknown. In this study we generated novel Endozoicomonas genomes from single cells and metagenomes obtained directly from the corals Stylophora pistillata, Pocillopora verrucosa, and Acropora humilis. We then compared these culture-independent genomes to existing genomes of bacterial isolates acquired from a sponge, sea slug, and coral to examine the functional landscape of this enigmatic genus. Sequencing and analysis of single cells and metagenomes resulted in four novel genomes with 60–76% and 81–90% genome completeness, respectively. These data also confirmed that Endozoicomonas genomes are large and are not streamlined for an obligate endosymbiotic lifestyle, implying that they have free-living stages. All genomes show an enrichment of genes associated with carbon sugar transport and utilization and protein secretion, potentially indicating that Endozoicomonas contribute to the cycling of carbohydrates and the provision of proteins to their respective hosts. Importantly, besides these commonalities, the genomes showed evidence for differential functional specificity and diversification, including genes for the production of amino acids. Given this metabolic diversity of Endozoicomonas we propose that different genotypes play disparate roles and have diversified in concert with their hosts. PMID:28094347
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Insights into animal and plant lectins with antimicrobial activities.
Dias, Renata de Oliveira; Machado, Leandro Dos Santos; Migliolo, Ludovico; Franco, Octavio Luiz
2015-01-05
Lectins are multivalent proteins with the ability to recognize and bind diverse carbohydrate structures. The glyco -binding and diverse molecular structures observed in these protein classes make them a large and heterogeneous group with a wide range of biological activities in microorganisms, animals and plants. Lectins from plants and animals are commonly used in direct defense against pathogens and in immune regulation. This review focuses on sources of animal and plant lectins, describing their functional classification and tridimensional structures, relating these properties with biotechnological purposes, including antimicrobial activities. In summary, this work focuses on structural-functional elucidation of diverse lectin groups, shedding some light on host-pathogen interactions; it also examines their emergence as biotechnological tools through gene manipulation and development of new drugs.
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Loss of functional diversity of ant assemblages in secondary tropical forests.
Bihn, Jochen H; Gebauer, Gerhard; Brandl, Roland
2010-03-01
Secondary forests and plantations increasingly dominate the tropical wooded landscape in place of primary forests. The expected reduction of biodiversity and its impact on ecological functions provided by these secondary forests are of major concern to society and ecologists. The potential effect of biodiversity loss on ecosystem functioning depends largely on the associated loss in the functional diversity of animal and plant assemblages, i.e., the degree of functional redundancy among species. However, the relationship between species and functional diversity is still poorly documented for most ecosystems. Here, we analyze how changes in the species diversity of ground-foraging ant assemblages translate into changes of functional diversity along a successional gradient of secondary forests in the Atlantic Forest of Brazil. Our analysis uses continuous measures of functional diversity and is based on four functional traits related to resource use of ants: body size, relative eye size, relative leg length, and trophic position. We find a strong relationship between species and functional diversity, independent of the functional traits used, with no evidence for saturation in this relationship. Recovery of species richness and diversity of ant assemblages in tropical secondary forests was accompanied by a proportional increase of functional richness and diversity of assemblages. Moreover, our results indicate that the increase in functional diversity along the successional gradient of secondary forests is primarily driven by rare species, which are functionally unique. The observed loss of both species and functional diversity in secondary forests offers no reason to believe that the ecological functions provided by secondary forests are buffered against species loss through functional redundancy.
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Cachera, Marie; Le Loc'h, François
2017-08-01
The relationships between diversity and ecosystem functioning have become a major focus of science. A crucial issue is to estimate functional diversity, as it is intended to impact ecosystem dynamics and stability. However, depending on the ecosystem, it may be challenging or even impossible to directly measure ecological functions and thus functional diversity. Phylogenetic diversity was recently under consideration as a proxy for functional diversity. Phylogenetic diversity is indeed supposed to match functional diversity if functions are conservative traits along evolution. However, in case of adaptive radiation and/or evolutive convergence, a mismatch may appear between species phylogenetic and functional singularities. Using highly threatened taxa, sharks, this study aimed to explore the relationships between phylogenetic and functional diversities and singularities. Different statistical computations were used in order to test both methodological issue (phylogenetic reconstruction) and overall a theoretical questioning: the predictive power of phylogeny for function diversity. Despite these several methodological approaches, a mismatch between phylogeny and function was highlighted. This mismatch revealed that (i) functions are apparently nonconservative in shark species, and (ii) phylogenetic singularity is not a proxy for functional singularity. Functions appeared to be not conservative along the evolution of sharks, raising the conservational challenge to identify and protect both phylogenetic and functional singular species. Facing the current rate of species loss, it is indeed of major importance to target phylogenetically singular species to protect genetic diversity and also functionally singular species in order to maintain particular functions within ecosystem.
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Li, Wei; Cheng, Ji-Min; Yu, Kai-Liang; Epstein, Howard E.; Guo, Liang; Jing, Guang-Hua; Zhao, Jie; Du, Guo-Zhen
2015-01-01
Past studies have widely documented the decrease in species diversity in response to addition of nutrients, however functional diversity is often independent from species diversity. In this study, we conducted a field experiment to examine the effect of nitrogen and phosphorus fertilization ((NH4)2 HPO4) at 0, 15, 30 and 60 g m-2 yr-1 (F0, F15, F30 and F60) after 4 years of continuous fertilization on functional diversity and species diversity, and its relationship with productivity in an alpine meadow community on the Tibetan Plateau. To this purpose, three community-weighted mean trait values (specific leaf area, SLA; mature plant height, MPH; and seed size, SS) for 30 common species in each fertilization level were determined; three components of functional diversity (functional richness, FRic; functional evenness, FEve; and Rao’s index of quadratic entropy, FRao) were quantified. Our results showed that: (i) species diversity sharply decreased, but functional diversity remained stable with fertilization; (ii) community-weighted mean traits (SLA and MPH) had a significant increase along the fertilization level; (iii) aboveground biomass was not correlated with functional diversity, but it was significantly correlated with species diversity and MPH. Our results suggest that decreases in species diversity due to fertilization do not result in corresponding changes in functional diversity. Functional identity of species may be more important than functional diversity in influencing aboveground productivity in this alpine meadow community, and our results also support the mass ratio hypothesis; that is, the traits of the dominant species influenced the community biomass production. PMID:26295345
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Li, Wei; Cheng, Ji-Min; Yu, Kai-Liang; Epstein, Howard E; Guo, Liang; Jing, Guang-Hua; Zhao, Jie; Du, Guo-Zhen
2015-01-01
Past studies have widely documented the decrease in species diversity in response to addition of nutrients, however functional diversity is often independent from species diversity. In this study, we conducted a field experiment to examine the effect of nitrogen and phosphorus fertilization ((NH4)2 HPO4) at 0, 15, 30 and 60 g m-2 yr-1 (F0, F15, F30 and F60) after 4 years of continuous fertilization on functional diversity and species diversity, and its relationship with productivity in an alpine meadow community on the Tibetan Plateau. To this purpose, three community-weighted mean trait values (specific leaf area, SLA; mature plant height, MPH; and seed size, SS) for 30 common species in each fertilization level were determined; three components of functional diversity (functional richness, FRic; functional evenness, FEve; and Rao's index of quadratic entropy, FRao) were quantified. Our results showed that: (i) species diversity sharply decreased, but functional diversity remained stable with fertilization; (ii) community-weighted mean traits (SLA and MPH) had a significant increase along the fertilization level; (iii) aboveground biomass was not correlated with functional diversity, but it was significantly correlated with species diversity and MPH. Our results suggest that decreases in species diversity due to fertilization do not result in corresponding changes in functional diversity. Functional identity of species may be more important than functional diversity in influencing aboveground productivity in this alpine meadow community, and our results also support the mass ratio hypothesis; that is, the traits of the dominant species influenced the community biomass production.
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Carver, Charles S.; Johnson, Sheri L.; Joormann, Jutta
2010-01-01
Evidence from diverse literatures supports the viewpoint that two modes of self-regulation exist, a lower-order system that responds quickly to associative cues of the moment and a higher-order system that responds more reflectively and planfully; that low serotonergic function is linked to relative dominance of the lower-order system; that how dominance of the lower-order system is manifested depends on additional variables; and that low serotonergic function therefore can promote behavioral patterns as divergent as impulsive aggression and lethargic depression. Literatures reviewed include work on two-mode models; studies of brain function supporting the biological plausibility of the two-mode view and the involvement of serotonergic pathways in functions pertaining to it; and studies relating low serotonergic function to impulsiveness, aggression (including extreme violence), aspects of personality, and depression vulnerability. Substantial differences between depression and other phenomena reviewed are interpreted by proposing that depression reflects both low serotonergic function and low reward sensitivity. The article closes with brief consideration of the idea that low serotonergic function relates to even more diverse phenomena, whose natures depend in part on sensitivities of other systems. PMID:18954161
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Microbial diversity and interactions in subgingival biofilm communities.
Diaz, Patricia I
2012-01-01
The human subgingival environment is a complex environmental niche where microorganisms from the three domains of life meet to form diverse biofilm communities that exist in close proximity to the host. Bacteria constitute the most abundant, diverse and ultimately well-studied component of these communities with about 500 bacterial taxa reported to occur in this niche. Cultivation and molecular approaches are revealing the breadth and depth of subgingival biofilm diversity as part of an effort to understand the subgingival microbiome, the collection of microorganisms that inhabit the gingival crevices. Although these investigations are constructing a pretty detailed taxonomical census of subgingival microbial communities, including inter-subject and temporal variability in community structure, as well as differences according to periodontal health status, we are still at the front steps in terms of understanding community function. Clinical studies that evaluate community structure need to be coupled with biologically relevant models that allow evaluation of the ecological determinants of subgingival biofilm maturation. Functional characteristics of subgingival biofilm communities that still need to be clarified include main metabolic processes that support microbial communities, identification of keystone species, microbial interactions and signaling events that lead to community maturation and the relationship of different communities with the host. This manuscript presents a summary of our current understanding of subgingival microbial diversity and an overview of experimental models used to dissect the functional characteristics of subgingival communities. Future coupling of 'omics'-based approaches with such models will facilitate a better understanding of subgingival ecology opening opportunities for community manipulation. Copyright © 2012 S. Karger AG, Basel.
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Division-Based, Growth Rate Diversity in Bacteria
Gangwe Nana, Ghislain Y.; Ripoll, Camille; Cabin-Flaman, Armelle; Gibouin, David; Delaune, Anthony; Janniere, Laurent; Grancher, Gerard; Chagny, Gaelle; Loutelier-Bourhis, Corinne; Lentzen, Esther; Grysan, Patrick; Audinot, Jean-Nicolas; Norris, Vic
2018-01-01
To investigate the nature and origins of growth rate diversity in bacteria, we grew Escherichia coli and Bacillus subtilis in liquid minimal media and, after different periods of 15N-labeling, analyzed and imaged isotope distributions in individual cells with Secondary Ion Mass Spectrometry. We find a striking inter- and intra-cellular diversity, even in steady state growth. This is consistent with the strand-dependent, hyperstructure-based hypothesis that a major function of the cell cycle is to generate coherent, growth rate diversity via the semi-conservative pattern of inheritance of strands of DNA and associated macromolecular assemblies. We also propose quantitative, general, measures of growth rate diversity for studies of cell physiology that include antibiotic resistance. PMID:29867792
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A meta-analysis of soil biodiversity impacts on the carbon cycle
NASA Astrophysics Data System (ADS)
de Graaff, M.-A.; Adkins, J.; Kardol, P.; Throop, H. L.
2015-03-01
Loss of biodiversity impacts ecosystem functions, such as carbon (C) cycling. Soils are the largest terrestrial C reservoir, containing more C globally than the biotic and atmospheric pools together. As such, soil C cycling, and the processes controlling it, has the potential to affect atmospheric CO2 concentrations and subsequent climate change. Despite the growing evidence of links between plant diversity and soil C cycling, there is a dearth of information on whether similar relationships exist between soil biodiversity and C cycling. This knowledge gap occurs even though there has been increased recognition that soil communities display high levels of both taxonomic and functional diversity and are key drivers of fluxes of C between the atmosphere and terrestrial ecosystems. Here, we used meta-analysis and regression analysis to quantitatively assess how soil biodiversity affects soil C cycling pools and processes (i.e., soil C respiration, litter decomposition, and plant biomass). We compared the response of process variables to changes in diversity both within and across groups of soil organisms that differed in body size, a grouping that typically correlates with ecological function. When studies that manipulated both within- and across-body size group diversity were included in the meta-analysis, loss of diversity significantly reduced soil C respiration (-27.5%) and plant tissue decomposition (-18%) but did not affect above- or belowground plant biomass. The loss of within-group diversity significantly reduced soil C respiration, while loss of across-group diversity did not. Decomposition was negatively affected both by loss of within-group and across-group diversity. Furthermore, loss of microbial diversity strongly reduced soil C respiration (-41%). In contrast, plant tissue decomposition was negatively affected by loss of soil faunal diversity but was unaffected by loss of microbial diversity. Taken together, our findings show that loss of soil biodiversity strongly impacts on soil C cycling processes, and highlight the importance of diversity across groups of organisms (e.g., primary consumers and secondary decomposers) for maintaining full functionality of C cycle processes. However, our understanding of the complex relationships between soil biodiversity and C cycling processes is currently limited by the sheer number of methodological concerns associated with these studies, which can greatly overestimate or underestimate the impact of soil biodiversity on soil C cycling, challenging extrapolation to natural field settings. Future studies should attempt to further elucidate the relative importance of taxonomic diversity (species numbers) versus functional diversity.
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Wu, Nicholas C; Xie, Jia; Zheng, Tianqing; Nycholat, Corwin M; Grande, Geramie; Paulson, James C; Lerner, Richard A; Wilson, Ian A
2017-06-14
Influenza A virus hemagglutinin (HA) initiates viral entry by engaging host receptor sialylated glycans via its receptor-binding site (RBS). The amino acid sequence of the RBS naturally varies across avian and human influenza virus subtypes and is also evolvable. However, functional sequence diversity in the RBS has not been fully explored. Here, we performed a large-scale mutational analysis of the RBS of A/WSN/33 (H1N1) and A/Hong Kong/1/1968 (H3N2) HAs. Many replication-competent mutants not yet observed in nature were identified, including some that could escape from an RBS-targeted broadly neutralizing antibody. This functional sequence diversity is made possible by pervasive epistasis in the RBS 220-loop and can be buffered by avidity in viral receptor binding. Overall, our study reveals that the HA RBS can accommodate a much greater range of sequence diversity than previously thought, which has significant implications for the complex evolutionary interrelationships between receptor specificity and immune escape. Copyright © 2017 Elsevier Inc. All rights reserved.
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Biotic homogenization can decrease landscape-scale forest multifunctionality.
van der Plas, Fons; Manning, Pete; Soliveres, Santiago; Allan, Eric; Scherer-Lorenzen, Michael; Verheyen, Kris; Wirth, Christian; Zavala, Miguel A; Ampoorter, Evy; Baeten, Lander; Barbaro, Luc; Bauhus, Jürgen; Benavides, Raquel; Benneter, Adam; Bonal, Damien; Bouriaud, Olivier; Bruelheide, Helge; Bussotti, Filippo; Carnol, Monique; Castagneyrol, Bastien; Charbonnier, Yohan; Coomes, David Anthony; Coppi, Andrea; Bastias, Cristina C; Dawud, Seid Muhie; De Wandeler, Hans; Domisch, Timo; Finér, Leena; Gessler, Arthur; Granier, André; Grossiord, Charlotte; Guyot, Virginie; Hättenschwiler, Stephan; Jactel, Hervé; Jaroszewicz, Bogdan; Joly, François-Xavier; Jucker, Tommaso; Koricheva, Julia; Milligan, Harriet; Mueller, Sandra; Muys, Bart; Nguyen, Diem; Pollastrini, Martina; Ratcliffe, Sophia; Raulund-Rasmussen, Karsten; Selvi, Federico; Stenlid, Jan; Valladares, Fernando; Vesterdal, Lars; Zielínski, Dawid; Fischer, Markus
2016-03-29
Many experiments have shown that local biodiversity loss impairs the ability of ecosystems to maintain multiple ecosystem functions at high levels (multifunctionality). In contrast, the role of biodiversity in driving ecosystem multifunctionality at landscape scales remains unresolved. We used a comprehensive pan-European dataset, including 16 ecosystem functions measured in 209 forest plots across six European countries, and performed simulations to investigate how local plot-scale richness of tree species (α-diversity) and their turnover between plots (β-diversity) are related to landscape-scale multifunctionality. After accounting for variation in environmental conditions, we found that relationships between α-diversity and landscape-scale multifunctionality varied from positive to negative depending on the multifunctionality metric used. In contrast, when significant, relationships between β-diversity and landscape-scale multifunctionality were always positive, because a high spatial turnover in species composition was closely related to a high spatial turnover in functions that were supported at high levels. Our findings have major implications for forest management and indicate that biotic homogenization can have previously unrecognized and negative consequences for large-scale ecosystem multifunctionality.
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Biotic homogenization can decrease landscape-scale forest multifunctionality
van der Plas, Fons; Manning, Pete; Soliveres, Santiago; Allan, Eric; Scherer-Lorenzen, Michael; Verheyen, Kris; Wirth, Christian; Zavala, Miguel A.; Ampoorter, Evy; Baeten, Lander; Barbaro, Luc; Bauhus, Jürgen; Benavides, Raquel; Benneter, Adam; Bonal, Damien; Bouriaud, Olivier; Bruelheide, Helge; Bussotti, Filippo; Carnol, Monique; Castagneyrol, Bastien; Charbonnier, Yohan; Coppi, Andrea; Bastias, Cristina C.; Dawud, Seid Muhie; De Wandeler, Hans; Domisch, Timo; Finér, Leena; Granier, André; Grossiord, Charlotte; Guyot, Virginie; Hättenschwiler, Stephan; Jactel, Hervé; Jaroszewicz, Bogdan; Joly, François-xavier; Jucker, Tommaso; Koricheva, Julia; Milligan, Harriet; Mueller, Sandra; Muys, Bart; Nguyen, Diem; Pollastrini, Martina; Ratcliffe, Sophia; Raulund-Rasmussen, Karsten; Selvi, Federico; Stenlid, Jan; Valladares, Fernando; Vesterdal, Lars; Zielínski, Dawid; Fischer, Markus
2016-01-01
Many experiments have shown that local biodiversity loss impairs the ability of ecosystems to maintain multiple ecosystem functions at high levels (multifunctionality). In contrast, the role of biodiversity in driving ecosystem multifunctionality at landscape scales remains unresolved. We used a comprehensive pan-European dataset, including 16 ecosystem functions measured in 209 forest plots across six European countries, and performed simulations to investigate how local plot-scale richness of tree species (α-diversity) and their turnover between plots (β-diversity) are related to landscape-scale multifunctionality. After accounting for variation in environmental conditions, we found that relationships between α-diversity and landscape-scale multifunctionality varied from positive to negative depending on the multifunctionality metric used. In contrast, when significant, relationships between β-diversity and landscape-scale multifunctionality were always positive, because a high spatial turnover in species composition was closely related to a high spatial turnover in functions that were supported at high levels. Our findings have major implications for forest management and indicate that biotic homogenization can have previously unrecognized and negative consequences for large-scale ecosystem multifunctionality. PMID:26979952
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NASA Astrophysics Data System (ADS)
Garcia-Comas, C.; Chiba, S.; Sugisaki, H.; Hashioka, T.; Smith, S. L.
2016-02-01
Understanding how species coexist in rich communities and the role of biodiversity on ecosystem-functioning is a long-standing challenge in ecology. Comparing functional diversity to species diversity may shed light on these questions. Here, we analyze copepod species data from the ODATE collection: 3142 samples collected over a period of 40 years, which includes a 10 o x 10o area of the Oyashio-Kuroshio Transition System, east of Japan (western North Pacific). The area hosts species characteristic of subarctic and subtropical communities. 163 copepod species were classified into five categorical functional traits (i.e., size, food, reproduction, thermal affinity and coastal-offshore habitat), following online databases and local taxonomic keys. We observe a general opposite hump-shaped relationship of species evenness (lower at mid-point) and functional diversity (Rao's Q) (higher at mid-point) with species richness. Subtropical Kuroshio communities tend to be richer with higher species evenness, and yet subarctic and transition waters tend to host communities of higher functional diversity. The distribution of trait values within each functional trait was further examined in relation to the Species Abundances Distribution (SAD). In subtropical communities, the distribution of trait values in the species ranking is homogenous, mirroring the frequency of those trait values in the entire community. In contrast, in subarctic communities the distribution of trait values differs along the species rank, with dominant species having favorable trait values more often than expected by chance (i.e., based on the overall frequency of that trait value in the entire community). Our results suggest that subtropical communities may be niche-saturated towards the most adapted trait values, so that merely having the most adapted trait value confers no strong competitive advantage to a species.
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Diversity and Distribution of Freshwater Amphipod Species in Switzerland (Crustacea: Amphipoda)
Altermatt, Florian; Alther, Roman; Fišer, Cene; Jokela, Jukka; Konec, Marjeta; Küry, Daniel; Mächler, Elvira; Stucki, Pascal; Westram, Anja Marie
2014-01-01
Amphipods are key organisms in many freshwater systems and contribute substantially to the diversity and functioning of macroinvertebrate communities. Furthermore, they are commonly used as bioindicators and for ecotoxicological tests. For many areas, however, diversity and distribution of amphipods is inadequately known, which limits their use in ecological and ecotoxicological studies and handicaps conservation initiatives. We studied the diversity and distribution of amphipods in Switzerland (Central Europe), covering four major drainage basins, an altitudinal gradient of>2,500 m, and various habitats (rivers, streams, lakes and groundwater). We provide the first provisional checklist and detailed information on the distribution and diversity of all amphipod species from Switzerland. In total, we found 29 amphipod species. This includes 16 native and 13 non-native species, one of the latter (Orchestia cavimana) reported here for the first time for Switzerland. The diversity is compared to neighboring countries. We specifically discuss species of the genus Niphargus, which are often receiving less attention. We also found evidence of an even higher level of hidden diversity, and the potential occurrence of further cryptic species. This diversity reflects the biogeographic past of Switzerland, and suggests that amphipods are ideally suited to address questions on endemism and adaptive radiations, post-glaciation re-colonization and invasion dynamics as well as biodiversity-ecosystem functioning relationships in aquatic systems. PMID:25354099
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Ethnically Diverse Faculty in Higher Ed: Belonging, Respect, and Role as Cultural Broker
ERIC Educational Resources Information Center
Vázquez-Montilla, Elia; Wilder, Lynn K.; Triscari, Robert
2012-01-01
The authors have completed a pilot study of the state of diverse faculty in higher education in the United States. Inquiries included the areas of belonging (if and how they developed a sense of belonging), professional respect (how colleagues regarded their achievements), and the role of cultural broker (how they functioned as cultural brokers in…
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NASA Astrophysics Data System (ADS)
Boras, Julia A.; Vaqué, Dolors; Maynou, Francesc; Sà, Elisabet L.; Weinbauer, Markus G.; Sala, Maria Montserrat
2015-03-01
To evaluate the main factors shaping bacterioplankton phylogenetic and functional diversity in marine coastal waters, we carried out a two-year study based on a monthly sampling in Blanes Bay (NW Mediterranean). We expected the key factors driving bacterial diversity to be (1) temperature and nutrient concentration, together with chlorophyll a concentration as an indicator of phytoplankton biomass and, hence, a carbon source for bacteria (here called bottom-up factors), and (2) top-down pressure (virus- and protist-mediated mortality of bacteria). Phylogenetic diversity was analyzed by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA. Functional diversity was assessed by using monomeric carbon sources in Biolog EcoPlates and by determining the activity of six extracellular enzymes. Our results indicate that the bacterial phylogenetic and functional diversity in this coastal system is shaped mainly by bottom-up factors. A dendrogram analysis of the DGGE banding patterns revealed three main sample clusters. Two clusters differed significantly in temperature, nitrate and chlorophyll a concentration, and the third was characterized by the highest losses of bacterial production due to viral lysis detected over the whole study period. Protistan grazing had no effect on bacterial functional diversity, since there were no correlations between protist-mediated mortality (PMM) and extracellular enzyme activities, and utilization of only two out of the 31 carbon sources (N-acetyl-D-glucosamine and α-cyclodextrin) was correlated with PMM. In contrast, virus-mediated mortality correlated with changes in the percentage of use of four carbon sources, and also with specific leu-aminopeptidase and β-glucosidase activity. This suggests that viral lysate provides a pool of labile carbon sources, presumably including amino acids and glucose, which may inhibit proteolytic and glucosidic activity. Our results indicate that bottom-up factors play a more important role than top-down factors (i.e. viral lysis and protistan grazing) in shaping bacterial community structure and activity. Furthermore, they suggest that viruses play a more important role than protists in modifying community structure and functional diversity of bacteria in oligotrophic marine coastal waters.
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Biological origins of sexual orientation and gender identity: Impact on health.
O'Hanlan, Katherine A; Gordon, Jennifer C; Sullivan, Mackenzie W
2018-04-01
Gynecologic Oncologists are sometimes consulted to care for patients who present with diverse gender identities or sexual orientations. Clinicians can create more helpful relationships with their patients if they understand the etiologies of these diverse expressions of sexual humanity. Multidisciplinary evidence reveals that a sexually dimorphic spectrum of somatic and neurologic anatomy, traits and abilities, including sexual orientation and gender identity, are conferred together during the first half of pregnancy due to genetics, epigenetics and the diversity of timing and function of sex chromosomes, sex-determining protein secretion, gonadal hormone secretion, receptor levels, adrenal function, maternally ingested dietary hormones, fetal health, and many other factors. Multiple layers of evidence confirm that sexual orientation and gender identity are as biological, innate and immutable as the other traits conferred during that critical time in gestation. Negative social responses to diverse orientations or gender identities have caused marginalization of these individuals with resultant alienation from medical care, reduced self-care and reduced access to medical care. The increased risks for many diseases, including gynecologic cancers are reviewed. Gynecologic Oncologists can potentially create more effective healthcare relationships with their patients if they have this information. Copyright © 2017 Elsevier Inc. All rights reserved.
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Describing functional diversity of brain regions and brain networks
Anderson, Michael L.; Kinnison, Josh; Pessoa, Luiz
2013-01-01
Despite the general acceptance that functional specialization plays an important role in brain function, there is little consensus about its extent in the brain. We sought to advance the understanding of this question by employing a data-driven approach that capitalizes on the existence of large databases of neuroimaging data. We quantified the diversity of activation in brain regions as a way to characterize the degree of functional specialization. To do so, brain activations were classified in terms of task domains, such as vision, attention, and language, which determined a region’s functional fingerprint. We found that the degree of diversity varied considerably across the brain. We also quantified novel properties of regions and of networks that inform our understanding of several task-positive and task-negative networks described in the literature, including defining functional fingerprints for entire networks and measuring their functional assortativity, namely the degree to which they are composed of regions with similar functional fingerprints. Our results demonstrate that some brain networks exhibit strong assortativity, whereas other networks consist of relatively heterogeneous parts. In sum, rather than characterizing the contributions of individual brain regions using task-based functional attributions, we instead quantified their dispositional tendencies, and related those to each region’s affiliative properties in both task-positive and task-negative contexts. PMID:23396162
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Functional variation in a disease resistance gene in populations of Arabidopsis thaliana.
Jorgensen, T H; Emerson, B C
2008-11-01
Analyses of functional genetic diversity in natural populations may provide important new insights into gene function and are necessary to understand the evolutionary processes maintaining diversity itself. The importance of including diversity within and between local populations in such studies is often ignored although many of the processes affecting genetic diversity act on this scale. Here we examine the molecular diversity in RPW8 (Recognition of Powdery Mildew), a gene conferring broad-spectrum resistance to powdery mildews in Arabidopsis thaliana stock-center accessions. Our eight UK study populations of the weedy A. thaliana were from locations judged to be subject to a minimum of anthropogenic disturbance and potentially long established. The majority of populations comprised considerable variation both in disease phenotype and RPW8 genotype. Although resistant individuals shared a major RPW8 genotype, no single allele was uniquely associated with resistance. It is concluded that RPW8 is an essential component of resistance to powdery mildews in A. thaliana, but not the only genetic factor involved in this process. No signature of selection was detected at RPW8 with a microsatellite multilocus test using an empirical null model. Unlike many previous studies of this model plant species, we found high levels of genetic diversity and relatively low differentiation (F(ST) = 0.31) between populations at 14 microsatellite markers. This is judged to be due to our sampling being aimed at potentially long established populations and highlights the importance of population choice for studies of genetic diversity within this species.
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Huang, Liujing; Chen, Hongfeng; Ren, Hai; Wang, Jun; Guo, Qinfeng
2013-06-01
We investigated the effects of major environmental drivers associated with urbanization on species diversity and plant functional traits (PFTs) in the remnant subtropical evergreen broad-leaved forests in Metropolitan Guangzhou (Guangdong, China). Twenty environmental factors including topography, light, and soil properties were used to quantify the effects of urbanization. Vegetation data and soil properties were collected from 30 400-m(2) plots at 6 study sites in urban and rural areas. The difference of plant species diversity and PFTs of remnant forests between urban and rural areas were analyzed. To discern the complex relationships, multivariate statistical analyses (e.g., canonical correspondence analysis and regression analysis) were employed. Pioneer species and stress-tolerant species can survive and vigorously establish their population dominance in the urban environment. The native herb diversity was lower in urban forests than in rural forests. Urban forests tend to prefer the species with Mesophanerophyte life form. In contrast, species in rural forests possessed Chamaephyte and Nanophanerophyte life forms and gravity/clonal growth dispersal mode. Soil pH and soil nutrients (K, Na, and TN) were positively related to herb diversity, while soil heavy metal concentrations (Cu) were negatively correlated with herb diversity. The herb plant species diversity declines and the species in the remnant forests usually have stress-tolerant functional traits in response to urbanization. The factors related to urbanization such as soil acidification, nutrient leaching, and heavy metal pollution were important in controlling the plant diversity in the forests along the urban-rural gradients. Urbanization affects the structure and functional traits of remnant subtropical evergreen broad-leaved forests.
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E.A. Lilleskov; E.A. Hobbie; T.R. Horton
2011-01-01
Anthropogenic nitrogen (N) deposition alters ectomycorrhizal fungal communities, but the effect on functional diversity is not clear. In this review we explore whether fungi that respond differently to N deposition also differ in functional traits, including organic N use, hydrophobicity and exploration type (extent and pattern of extraradical hyphae). ...
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Mediating objects: scientific and public functions of models in nineteenth-century biology.
Ludwig, David
2013-01-01
The aim of this article is to examine the scientific and public functions of two- and three-dimensional models in the context of three episodes from nineteenth-century biology. I argue that these models incorporate both data and theory by presenting theoretical assumptions in the light of concrete data or organizing data through theoretical assumptions. Despite their diverse roles in scientific practice, they all can be characterized as mediators between data and theory. Furthermore, I argue that these different mediating functions often reflect their different audiences that included specialized scientists, students, and the general public. In this sense, models in nineteenth-century biology can be understood as mediators between theory, data, and their diverse audiences.
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Iterative-Transform Phase Retrieval Using Adaptive Diversity
NASA Technical Reports Server (NTRS)
Dean, Bruce H.
2007-01-01
A phase-diverse iterative-transform phase-retrieval algorithm enables high spatial-frequency, high-dynamic-range, image-based wavefront sensing. [The terms phase-diverse, phase retrieval, image-based, and wavefront sensing are defined in the first of the two immediately preceding articles, Broadband Phase Retrieval for Image-Based Wavefront Sensing (GSC-14899-1).] As described below, no prior phase-retrieval algorithm has offered both high dynamic range and the capability to recover high spatial-frequency components. Each of the previously developed image-based phase-retrieval techniques can be classified into one of two categories: iterative transform or parametric. Among the modifications of the original iterative-transform approach has been the introduction of a defocus diversity function (also defined in the cited companion article). Modifications of the original parametric approach have included minimizing alternative objective functions as well as implementing a variety of nonlinear optimization methods. The iterative-transform approach offers the advantage of ability to recover low, middle, and high spatial frequencies, but has disadvantage of having a limited dynamic range to one wavelength or less. In contrast, parametric phase retrieval offers the advantage of high dynamic range, but is poorly suited for recovering higher spatial frequency aberrations. The present phase-diverse iterative transform phase-retrieval algorithm offers both the high-spatial-frequency capability of the iterative-transform approach and the high dynamic range of parametric phase-recovery techniques. In implementation, this is a focus-diverse iterative-transform phaseretrieval algorithm that incorporates an adaptive diversity function, which makes it possible to avoid phase unwrapping while preserving high-spatial-frequency recovery. The algorithm includes an inner and an outer loop (see figure). An initial estimate of phase is used to start the algorithm on the inner loop, wherein multiple intensity images are processed, each using a different defocus value. The processing is done by an iterative-transform method, yielding individual phase estimates corresponding to each image of the defocus-diversity data set. These individual phase estimates are combined in a weighted average to form a new phase estimate, which serves as the initial phase estimate for either the next iteration of the iterative-transform method or, if the maximum number of iterations has been reached, for the next several steps, which constitute the outerloop portion of the algorithm. The details of the next several steps must be omitted here for the sake of brevity. The overall effect of these steps is to adaptively update the diversity defocus values according to recovery of global defocus in the phase estimate. Aberration recovery varies with differing amounts as the amount of diversity defocus is updated in each image; thus, feedback is incorporated into the recovery process. This process is iterated until the global defocus error is driven to zero during the recovery process. The amplitude of aberration may far exceed one wavelength after completion of the inner-loop portion of the algorithm, and the classical iterative transform method does not, by itself, enable recovery of multi-wavelength aberrations. Hence, in the absence of a means of off-loading the multi-wavelength portion of the aberration, the algorithm would produce a wrapped phase map. However, a special aberration-fitting procedure can be applied to the wrapped phase data to transfer at least some portion of the multi-wavelength aberration to the diversity function, wherein the data are treated as known phase values. In this way, a multiwavelength aberration can be recovered incrementally by successively applying the aberration-fitting procedure to intermediate wrapped phase maps. During recovery, as more of the aberration is transferred to the diversity function following successive iterations around the ter loop, the estimated phase ceases to wrap in places where the aberration values become incorporated as part of the diversity function. As a result, as the aberration content is transferred to the diversity function, the phase estimate resembles that of a reference flat.
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Psychosocial Functioning of Young Children with Learning Problems
ERIC Educational Resources Information Center
Gadeyne, Els; Ghesquiere, Pol; Onghena, Patrick
2004-01-01
Background: In this study, psychosocial functioning of different groups of young children with learning problems was investigated using a diverse set of psychosocial variables (including behaviour problems, academic motivation, social preference, and self-concept). Methods: For this purpose, children with low academic achievement, with a specific…
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Analyzing Community College Student Transfer Rates.
ERIC Educational Resources Information Center
Cohen, Arthur M.
The community college mission includes such diverse goals as preparing students for job entry, teaching literacy, and satisfying students' personal interests. Measuring the colleges' transfer rates by no means tacitly elevates the transfer function above these other functions; it merely helps institutions estimate the effects of interventions on…
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Local loss and spatial homogenization of plant diversity reduce ecosystem multifunctionality.
Hautier, Yann; Isbell, Forest; Borer, Elizabeth T; Seabloom, Eric W; Harpole, W Stanley; Lind, Eric M; MacDougall, Andrew S; Stevens, Carly J; Adler, Peter B; Alberti, Juan; Bakker, Jonathan D; Brudvig, Lars A; Buckley, Yvonne M; Cadotte, Marc; Caldeira, Maria C; Chaneton, Enrique J; Chu, Chengjin; Daleo, Pedro; Dickman, Christopher R; Dwyer, John M; Eskelinen, Anu; Fay, Philip A; Firn, Jennifer; Hagenah, Nicole; Hillebrand, Helmut; Iribarne, Oscar; Kirkman, Kevin P; Knops, Johannes M H; La Pierre, Kimberly J; McCulley, Rebecca L; Morgan, John W; Pärtel, Meelis; Pascual, Jesus; Price, Jodi N; Prober, Suzanne M; Risch, Anita C; Sankaran, Mahesh; Schuetz, Martin; Standish, Rachel J; Virtanen, Risto; Wardle, Glenda M; Yahdjian, Laura; Hector, Andy
2018-01-01
Biodiversity is declining in many local communities while also becoming increasingly homogenized across space. Experiments show that local plant species loss reduces ecosystem functioning and services, but the role of spatial homogenization of community composition and the potential interaction between diversity at different scales in maintaining ecosystem functioning remains unclear, especially when many functions are considered (ecosystem multifunctionality). We present an analysis of eight ecosystem functions measured in 65 grasslands worldwide. We find that more diverse grasslands-those with both species-rich local communities (α-diversity) and large compositional differences among localities (β-diversity)-had higher levels of multifunctionality. Moreover, α- and β-diversity synergistically affected multifunctionality, with higher levels of diversity at one scale amplifying the contribution to ecological functions at the other scale. The identity of species influencing ecosystem functioning differed among functions and across local communities, explaining why more diverse grasslands maintained greater functionality when more functions and localities were considered. These results were robust to variation in environmental drivers. Our findings reveal that plant diversity, at both local and landscape scales, contributes to the maintenance of multiple ecosystem services provided by grasslands. Preserving ecosystem functioning therefore requires conservation of biodiversity both within and among ecological communities.
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Zhu, Duo Ju; Wen, Zhong Ming; Zhang, Jing; Tao, Yu; Zeng, Hong Wen; Tang, Yang
2018-02-01
To investigate the effects of the introduction of Robinia pseudoacacia on the functional structure of plant communities, we selected paired-plots of R. pseudoacacia communities and native plant communities across different vegetation zones, i.e., steppe zone, forest-steppe zone, forest zone in hilly-gully region of Loess Plateau, China. We measured several functional characteristics and then compared the functional structures of R. pseudoacacia and native plant communities in different vegetation zones. The results showed that the variation of the functional traits across different vegetation zones were consistent in R. pseudoacacia community and native plant community, including leaf carbon concentration, leaf nitrogen concentration, leaf phosphorus concentration, specific leaf area, and leaf tissue density. The leaf carbon concentration, leaf nitrogen concentration, and specific leaf area of the R. pseudoacacia community were significantly higher than those of the native plant community. The trend of change that the functional diversity indices, i.e., FR ic , FE ve , FD iv , FD is , Rao of the R. pseudoacacia community and the native plant community with vegetation zones were different. The introduction of R. pseudoacacia enhanced the plant community functional diversity in the forest zone but reduced community functional diversity in the steppe zone.
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Jangid, Kamlesh; Kao, Ming-Hung; Lahamge, Aishwarya; Williams, Mark A.; Rathbun, Stephen L.; Whitman, William B.
2016-01-01
K-shuff is a new algorithm for comparing the similarity of gene sequence libraries, providing measures of the structural and compositional diversity as well as the significance of the differences between these measures. Inspired by Ripley’s K-function for spatial point pattern analysis, the Intra K-function or IKF measures the structural diversity, including both the richness and overall similarity of the sequences, within a library. The Cross K-function or CKF measures the compositional diversity between gene libraries, reflecting both the number of OTUs shared as well as the overall similarity in OTUs. A Monte Carlo testing procedure then enables statistical evaluation of both the structural and compositional diversity between gene libraries. For 16S rRNA gene libraries from complex bacterial communities such as those found in seawater, salt marsh sediments, and soils, K-shuff yields reproducible estimates of structural and compositional diversity with libraries greater than 50 sequences. Similarly, for pyrosequencing libraries generated from a glacial retreat chronosequence and Illumina® libraries generated from US homes, K-shuff required >300 and 100 sequences per sample, respectively. Power analyses demonstrated that K-shuff is sensitive to small differences in Sanger or Illumina® libraries. This extra sensitivity of K-shuff enabled examination of compositional differences at much deeper taxonomic levels, such as within abundant OTUs. This is especially useful when comparing communities that are compositionally very similar but functionally different. K-shuff will therefore prove beneficial for conventional microbiome analysis as well as specific hypothesis testing. PMID:27911946
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Sitters, Holly; Di Stefano, Julian; Christie, Fiona; Swan, Matthew; York, Alan
2016-01-01
Animal species diversity is often associated with time since disturbance, but the effects of disturbances such as fire on functional diversity are unknown. Functional diversity measures the range, abundance, and distribution of trait values in a community, and links changes in species composition with the consequences for ecosystem function. Improved understanding of the relationship between time since fire (TSF) and functional diversity is critical given that the frequency of both prescribed fire and wildfire is expected to increase. To address this knowledge gap, we examined responses of avian functional diversity to TSF and two direct measures of environmental heterogeneity, plant diversity, and structural heterogeneity. We surveyed birds across a 70-year chronosequence spanning four vegetation types in southeast Australia. Six bird functional traits were used to derive four functional diversity indices (richness, evenness, divergence, and dispersion) and the effects of TSF, plant diversity and structural heterogeneity on species richness and the functional diversity indices were examined using mixed models. We used a regression tree method to identify traits associated with species more common in young vegetation. Functional richness and dispersion were negatively associated with TSF in all vegetation types, suggesting that recent prescribed fire generates heterogeneous vegetation and provides greater opportunities for resource partitioning. Species richness was not significantly associated with TSF, and is probably an unreliable surrogate for functional diversity in fire-prone systems. A positive, relationship between functional evenness and structural heterogeneity was comnon to all vegetation types, suggesting that fine-scale (tens of meters) structural variation can enhance ecosystem function. Species more common in young vegetation were primarily linked by their specialist diets, indicating that ecosystem services such as seed dispersal and insect control are enhanced in more recently burnt vegetation. We suggest that patchy prescribed fire sustains functional diversity, and that controlled use of patchy fire to break up large expanses of mature vegetation will enhance ecosystem function.
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Human land use promotes the abundance and diversity of exotic species on caribbean islands.
Jesse, Wendy A M; Behm, Jocelyn E; Helmus, Matthew R; Ellers, Jacintha
2018-05-31
Human land use causes major changes in species abundance and composition, yet native and exotic species can exhibit different responses to land use change. Native populations generally decline in human-impacted habitats while exotic species often benefit. In this study, we assessed the effects of human land use on exotic and native reptile diversity, including functional diversity, which relates to the range of habitat use strategies in biotic communities. We surveyed 114 reptile communities from localities that varied in habitat structure and human impact level on two Caribbean islands, and calculated species richness, overall abundance and evenness for every plot. Functional diversity indices were calculated using published trait data, which enabled us to detect signs of trait filtering associated with impacted habitats. Our results show that environmental variation among sampling plots was explained by two PCA ordination axes related to habitat structure (i.e. forest or non-forest) and human impact level (i.e. addition of man-made constructions such as roads and buildings). Several diversity indices were significantly correlated with the two PCA axes, but exotic and native species showed opposing responses. Native species reached the highest abundance in forests, while exotic species were absent in this habitat. Human impact was associated with an increase in exotic abundance and species richness, while native species showed no significant associations. Functional diversity was highest in non-forested environments on both islands, and further increased on St. Martin with the establishment of functionally unique exotic species in non-forested habitat. Habitat structure, rather than human impact, proved to be an important agent for environmental filtering of traits, causing divergent functional trait values across forested and non-forested environments. Our results illustrate the importance of considering various elements of land use when studying its impact on species diversity and the establishment and spread of exotic species. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
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Skin-inspired hydrogel-elastomer hybrids with robust interfaces and functional microstructures
NASA Astrophysics Data System (ADS)
Yuk, Hyunwoo; Zhang, Teng; Parada, German Alberto; Liu, Xinyue; Zhao, Xuanhe
2016-06-01
Inspired by mammalian skins, soft hybrids integrating the merits of elastomers and hydrogels have potential applications in diverse areas including stretchable and bio-integrated electronics, microfluidics, tissue engineering, soft robotics and biomedical devices. However, existing hydrogel-elastomer hybrids have limitations such as weak interfacial bonding, low robustness and difficulties in patterning microstructures. Here, we report a simple yet versatile method to assemble hydrogels and elastomers into hybrids with extremely robust interfaces (interfacial toughness over 1,000 Jm-2) and functional microstructures such as microfluidic channels and electrical circuits. The proposed method is generally applicable to various types of tough hydrogels and diverse commonly used elastomers including polydimethylsiloxane Sylgard 184, polyurethane, latex, VHB and Ecoflex. We further demonstrate applications enabled by the robust and microstructured hydrogel-elastomer hybrids including anti-dehydration hydrogel-elastomer hybrids, stretchable and reactive hydrogel-elastomer microfluidics, and stretchable hydrogel circuit boards patterned on elastomer.
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Chumbler, Neale R.; Quigley, Patricia; Sanford, Jon; Griffiths, Patricia; Rose, Dorian; Morey, Miriam; Ely, E. Wesley; Hoenig, Helen
2010-01-01
Telerehabilitation (TR) is the use of telehealth technologies to provide distant support, rehabilitation services, and information exchange between people with disabilities and their clinical providers. This article discusses the barriers experienced when implementing a TR multi-site randomized controlled trial for stroke patients in their homes, and the lessons learned. The barriers are divided into two sections: those specific to TR and those pertinent to the conduct of tele-research. The TR specific barriers included the rapidly changing telecommunications and health care environment and inconsistent equipment functionality. The barriers applicable to tele-research included the need to meet regulations in diverse departments and rapidly changing research regulations. Lessons learned included the need for: telehealth equipment options to allow for functionality within a diverse telecommunications infrastructure; rigorous pilot testing of all equipment in authentic situations; and on-call and on-site biomedical engineering and/or IT staff. PMID:25945169
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Beyond diversity: how nested predator effects control ecosystem functions.
Schneider, Florian Dirk; Brose, Ulrich
2013-01-01
The global decline in biodiversity is especially evident in higher trophic levels as predators display higher sensitivity to environmental change than organisms from lower trophic levels. This is even more alarming given the paucity of knowledge about the role of individual predator species in sustaining ecosystem functioning. The effect of predator diversity on lower trophic level prey is often driven by the increasing chance of including the most influential species. Furthermore, intraguild predation can cause trophic cascades with net positive effects on basal prey. As a consequence, the effects of losing a predator species appear to be idiosyncratic and it becomes unpredictable how the community's net effect on lower trophic levels changes when species number is declining. We performed a full factorial microcosm experiment with litter layer arthropods to measure the effects of predator diversity and context-dependent identity effects on a detritivore population and microbial biomass. We show that major parts of the observed diversity effect can be assigned to the increasing likelihood of including the most influential predator. Further, the presence of a second predator feeding on the first predator dampens this dominant effect. Including this intraguild predator on top of the first predator is more likely with increasing predator diversity as well. Thus, the overall pattern can be explained by a second identity effect, which is nested into the first. When losing a predator from the community, the response of the lower trophic level is highly dependent on the remaining predator species. We mechanistically explain the net effects of the predator community on lower trophic levels by nested effects of predator identities. These identity effects become predictable when taking the species' body masses into account. This provides a new mechanistic perspective describing ecosystem functioning as a consequence of species composition and yields an understanding beyond simple effects of biodiversity. © 2012 The Authors. Journal of Animal Ecology © 2012 British Ecological Society.
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Lefcheck, Jonathan S; Duffy, J Emmett
2015-11-01
The use of functional traits to explain how biodiversity affects ecosystem functioning has attracted intense interest, yet few studies have a priori altered functional diversity, especially in multitrophic communities. Here, we manipulated multivariate functional diversity of estuarine grazers and predators within multiple levels of species richness to test how species richness and functional diversity predicted ecosystem functioning in a multitrophic food web. Community functional diversity was a better predictor than species richness for the majority of ecosystem properties, based on generalized linear mixed-effects models. Combining inferences from eight traits into a single multivariate index increased prediction accuracy of these models relative to any individual trait. Structural equation modeling revealed that functional diversity of both grazers and predators was important in driving final biomass within trophic levels, with stronger effects observed for predators. We also show that different species drove different ecosystem responses, with evidence for both sampling effects and complementarity. Our study extends experimental investigations of functional trait diversity to a multilevel food web, and demonstrates that functional diversity can be more accurate and effective than species richness in predicting community biomass in a food web context.
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Villéger, Sébastien; Miranda, Julia Ramos; Hernandez, Domingo Flores; Mouillot, David
2012-01-01
The concept of β-diversity, defined as dissimilarity among communities, has been widely used to investigate biodiversity patterns and community assembly rules. However, in ecosystems with high taxonomic β-diversity, due to marked environmental gradients, the level of functional β-diversity among communities is largely overlooked while it may reveal processes shaping community structure. Here, decomposing biodiversity indices into α (local) and γ (regional) components, we estimated taxonomic and functional β-diversity among tropical estuarine fish communities, through space and time. We found extremely low functional β-diversity values among fish communities (<1.5%) despite high dissimilarity in species composition and species dominance. Additionally, in contrast to the high α and γ taxonomic diversities, α and γ functional diversities were very close to the minimal value. These patterns were caused by two dominant functional groups which maintained a similar functional structure over space and time, despite the strong dissimilarity in taxonomic structure along environmental gradients. Our findings suggest that taxonomic and functional β-diversity deserve to be quantified simultaneously since these two facets can show contrasting patterns and the differences can in turn shed light on community assembly rules. PMID:22792395
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Ding, Ning; Yang, Weifang; Zhou, Yunlei; González-Bergonzoni, Ivan; Zhang, Jie; Chen, Kai; Vidal, Nicolas; Jeppesen, Erik; Liu, Zhengwen; Wang, Beixin
2017-01-01
Functional traits and diversity indices have provided new insights into community responses to stressors. Most traits of aquatic organisms have frequently been tested for predictability and geographical stability in response to environmental variables, but such tests of functional diversity indices are rare. We sampled macroinvertebrates at 18 reference sites (RS) and 35 disturbed sites (DS) from headwater streams in the upper Mekong River Basin, Xishuangbanna (XSBN), China. We selected 29 qualitative categories of eight traits and then calculated five functional diversity indices, namely functional richness (FRic), functional evenness (FEve), functional dispersion (FDis), functional divergence (FDiv) and Rao's Quadratic Entropy (RaoQ), and two trait diversity indices, namely trait richness (TR) and trait diversity (TD). We used combination of RLQ and fourth-corner to examine the response of traits and functional diversity to the disturbance and environmental variables. We used variance partitioning to explore the relative role of environmental variables and spatial factors in constraining trait composition and functional diversity. We found that the relative frequency of ten trait categories, and the values of TD, TR, FRic and FDis in RS were significantly different (p<0.05) from DS. In addition, the seven traits (except for "habit") demonstrated a predictable response of trait patterns along the integrative environmental gradients. Environmental variables significantly contributed to most of the traits, functional diversity and trait diversity. However, spatial variables were mainly significant in shaping ecological traits, FRic and FEve. Our results confirm the dominant role of environmental variables in the determination of community trait composition and functional diversity, and substantiate the contribution of spatial vectors in explaining the variance of functional traits and diversity. We conclude that the traits "Refuge", "External protection", "Respiration" and "Body shape", and diversity indices FDis, TD, and TR are promising indicators of stream conditions at XSBN. Copyright © 2016 Elsevier B.V. All rights reserved.
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Novel insights into the microbiology of fermented dairy foods.
Macori, Guerrino; Cotter, Paul D
2018-02-01
Fermentation is a traditional approach to food preservation that, in addition to improving food safety, also confers enhanced organoleptic, nutritional, and health-promoting attributes upon those foods. Dairy products can be fermented by a diverse microbiota. The accompanying microbes can be studied using a variety of different, including 'omics'-based, approaches that can reveal their composition and functionality. These methods have increasingly been recently applied to study fermented dairy foods from the perspective of genetic diversity, functionality and succession. The insights provided by these studies are summarised in this review. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Inorganic pyrophosphatases: structural diversity serving the function
NASA Astrophysics Data System (ADS)
Samygina, V. R.
2016-05-01
The review is devoted to ubiquitous enzymes, inorganic pyrophosphatases, which are essential in all living organisms. Despite the long history of investigations, these enzymes continue to attract interest. The review focuses on the three-dimensional structures of various representatives of this class of proteins. The structural diversity, the relationship between the structure and some properties of pyrophosphatases and various mechanisms of enzyme action related to the structural diversity of these enzymes are discussed. Interactions of pyrophosphatase with other proteins and possible practical applications are considered. The bibliography includes 56 references.
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RanBPM: a potential therapeutic target for modulating diverse physiological disorders.
Das, Soumyadip; Suresh, Bharathi; Kim, Hyongbum Henry; Ramakrishna, Suresh
2017-12-01
The Ran-binding protein microtubule-organizing center (RanBPM) is a highly conserved nucleocytoplasmic protein involved in a variety of intracellular signaling pathways that control diverse cellular functions. RanBPM interacts with proteins that are linked to various diseases, including Alzheimer's disease (AD), schizophrenia (SCZ), and cancer. In this article, we define the characteristics of the scaffolding protein RanBPM and focus on its interaction partners in diverse physiological disorders, such as neurological diseases, fertility disorders, and cancer. Copyright © 2017 Elsevier Ltd. All rights reserved.
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Zheng, Li Ting; Su, Tian; Liu, Xiang Yu; Yin, Fang; Guo, Chao; Tuo, Bin; Yan, En Rong
2018-02-01
Island vegetation plays an important role in biodiversity research across the world. The study of plant diversity in island is helpful for understanding the mechanism of plant diversity maintenance under land-sea interaction. Here, four typical plant communities (Quercus acutissima community, Robinia pseudoacacia community, Pinus thunbergii community and Vitex negundo community) in Miao Archipelago were selected to examine the species, functional and structural diversities and their responses to environmental factors at the community scale by using species diversity indices, functional diversity indices, as well as structural diversity indices. The results showed that the species richness and Rao index of P. thunbergii community was higher than that of Q. acutissima community and R. pseudoacacia community, but the structural diversity was lower. The species diversity and structural diversity of V. Negundo shrub were lower than that of forest community, but the functional diversity was higher than some forest communities. The relationship between the diversity of typical plant communities in island area illustrated a significant positive correlation between species richness with Rao index and tree height diversity, however the correlation with functional evenness was significantly negative. The structural diversity and functional evenness were determined by slope with negative and positive relationships, respectively. Functional heterogeneity, functional divergence and species diversity were affected largely by soil physical and chemical properties, displaying the positive relationship with soil bulk density and soil total carbon content, and a negative relationship with soil water content. In conclusion, diversity pattern of plant community in Miao Archipelago reflected not only the characteristics in mainland vegetation but also the special nature of the sea island.
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Effects of Fishing and Regional Species Pool on the Functional Diversity of Fish Communities
Martins, Gustavo M.; Arenas, Francisco; Neto, Ana I.; Jenkins, Stuart R.
2012-01-01
The potential population and community level impacts of fishing have received considerable attention, but little is known about how fishing influences communities’ functional diversity at regional scales. We examined how estimates of functional diversity differed among 25 regions of variable richness and investigated the functional consequences of removing species targeted by commercial fisheries. Our study shows that fishing leads to substantial losses in functional diversity. The magnitude of such loss was, however, reduced in the more speciose regions. Moreover, the removal of commercially targeted species caused a much larger reduction in functional diversity than expected by random species deletions, which was a consequence of the selective nature of fishing for particular species traits. Results suggest that functional redundancy is spatially variable, that richer biotas provide some degree of insurance against the impact of fishing on communities’ functional diversity and that fishing predominantly selects for particular species traits. Understanding how fishing impacts community functional diversity is key to predict its effects for biodiversity as well as ecosystem functioning. PMID:22952950
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Effects of fishing and regional species pool on the functional diversity of fish communities.
Martins, Gustavo M; Arenas, Francisco; Neto, Ana I; Jenkins, Stuart R
2012-01-01
The potential population and community level impacts of fishing have received considerable attention, but little is known about how fishing influences communities' functional diversity at regional scales. We examined how estimates of functional diversity differed among 25 regions of variable richness and investigated the functional consequences of removing species targeted by commercial fisheries. Our study shows that fishing leads to substantial losses in functional diversity. The magnitude of such loss was, however, reduced in the more speciose regions. Moreover, the removal of commercially targeted species caused a much larger reduction in functional diversity than expected by random species deletions, which was a consequence of the selective nature of fishing for particular species traits. Results suggest that functional redundancy is spatially variable, that richer biotas provide some degree of insurance against the impact of fishing on communities' functional diversity and that fishing predominantly selects for particular species traits. Understanding how fishing impacts community functional diversity is key to predict its effects for biodiversity as well as ecosystem functioning.
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Park, Andrew W; Cleveland, Christopher A; Dallas, Tad A; Corn, Joseph L
2016-06-01
Although many parasites are transmitted between hosts by a suite of arthropod vectors, the impact of vector biodiversity on parasite transmission is poorly understood. Positive relationships between host infection prevalence and vector species richness (SR) may operate through multiple mechanisms, including (i) increased vector abundance, (ii) a sampling effect in which species of high vectorial capacity are more likely to occur in species-rich communities, and (iii) functional diversity whereby communities comprised species with distinct phenologies may extend the duration of seasonal transmission. Teasing such mechanisms apart is impeded by a lack of appropriate data, yet could highlight a neglected role for functional diversity in parasite transmission. We used statistical modelling of extensive host, vector and microparasite data to test the hypothesis that functional diversity leading to longer seasonal transmission explained variable levels of disease in a wildlife population. We additionally developed a simple transmission model to guide our expectation of how an increased transmission season translates to infection prevalence. Our study demonstrates that vector SR is associated with increased levels of disease reporting, but not via increases in vector abundance or via a sampling effect. Rather, the relationship operates by extending the length of seasonal transmission, in line with theoretical predictions.
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A novel system of polymorphic and diverse NK cell receptors in primates.
Averdam, Anne; Petersen, Beatrix; Rosner, Cornelia; Neff, Jennifer; Roos, Christian; Eberle, Manfred; Aujard, Fabienne; Münch, Claudia; Schempp, Werner; Carrington, Mary; Shiina, Takashi; Inoko, Hidetoshi; Knaust, Florian; Coggill, Penny; Sehra, Harminder; Beck, Stephan; Abi-Rached, Laurent; Reinhardt, Richard; Walter, Lutz
2009-10-01
There are two main classes of natural killer (NK) cell receptors in mammals, the killer cell immunoglobulin-like receptors (KIR) and the structurally unrelated killer cell lectin-like receptors (KLR). While KIR represent the most diverse group of NK receptors in all primates studied to date, including humans, apes, and Old and New World monkeys, KLR represent the functional equivalent in rodents. Here, we report a first digression from this rule in lemurs, where the KLR (CD94/NKG2) rather than KIR constitute the most diverse group of NK cell receptors. We demonstrate that natural selection contributed to such diversification in lemurs and particularly targeted KLR residues interacting with the peptide presented by MHC class I ligands. We further show that lemurs lack a strict ortholog or functional equivalent of MHC-E, the ligands of non-polymorphic KLR in "higher" primates. Our data support the existence of a hitherto unknown system of polymorphic and diverse NK cell receptors in primates and of combinatorial diversity as a novel mechanism to increase NK cell receptor repertoire.
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A Novel System of Polymorphic and Diverse NK Cell Receptors in Primates
Rosner, Cornelia; Neff, Jennifer; Roos, Christian; Eberle, Manfred; Aujard, Fabienne; Münch, Claudia; Schempp, Werner; Carrington, Mary; Shiina, Takashi; Inoko, Hidetoshi; Knaust, Florian; Coggill, Penny; Sehra, Harminder; Beck, Stephan; Abi-Rached, Laurent; Reinhardt, Richard; Walter, Lutz
2009-01-01
There are two main classes of natural killer (NK) cell receptors in mammals, the killer cell immunoglobulin-like receptors (KIR) and the structurally unrelated killer cell lectin-like receptors (KLR). While KIR represent the most diverse group of NK receptors in all primates studied to date, including humans, apes, and Old and New World monkeys, KLR represent the functional equivalent in rodents. Here, we report a first digression from this rule in lemurs, where the KLR (CD94/NKG2) rather than KIR constitute the most diverse group of NK cell receptors. We demonstrate that natural selection contributed to such diversification in lemurs and particularly targeted KLR residues interacting with the peptide presented by MHC class I ligands. We further show that lemurs lack a strict ortholog or functional equivalent of MHC-E, the ligands of non-polymorphic KLR in “higher” primates. Our data support the existence of a hitherto unknown system of polymorphic and diverse NK cell receptors in primates and of combinatorial diversity as a novel mechanism to increase NK cell receptor repertoire. PMID:19834558
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Phylogenetic structure of soil bacterial communities predicts ecosystem functioning.
Pérez-Valera, Eduardo; Goberna, Marta; Verdú, Miguel
2015-05-01
Quantifying diversity with phylogeny-informed metrics helps understand the effects of diversity on ecosystem functioning (EF). The sign of these effects remains controversial because phylogenetic diversity and taxonomic identity may interactively influence EF. Positive relationships, traditionally attributed to complementarity effects, seem unimportant in natural soil bacterial communities. Negative relationships could be attributed to fitness differences leading to the overrepresentation of few productive clades, a mechanism recently invoked to assemble soil bacteria communities. We tested in two ecosystems contrasting in terms of environmental heterogeneity whether two metrics of phylogenetic community structure, a simpler measure of phylogenetic diversity (NRI) and a more complex metric incorporating taxonomic identity (PCPS), correctly predict microbially mediated EF. We show that the relationship between phylogenetic diversity and EF depends on the taxonomic identity of the main coexisting lineages. Phylogenetic diversity was negatively related to EF in soils where a marked fertility gradient exists and a single and productive clade (Proteobacteria) outcompete other clades in the most fertile plots. However, phylogenetic diversity was unrelated to EF in soils where the fertility gradient is less marked and Proteobacteria coexist with other abundant lineages. Including the taxonomic identity of bacterial lineages in metrics of phylogenetic community structure allows the prediction of EF in both ecosystems. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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Luck, Gary W.; Carter, Andrew; Smallbone, Lisa
2013-01-01
Examinations of the impact of land-use change on functional diversity link changes in ecological community structure driven by land modification with the consequences for ecosystem function. Yet, most studies have been small-scale, experimental analyses and primarily focussed on plants. There is a lack of research on fauna communities and at large-scales across multiple land uses. We assessed changes in the functional diversity of bird communities across 24 land uses aligned along an intensification gradient. We tested the hypothesis that functional diversity is higher in less intensively used landscapes, documented changes in diversity using four diversity metrics, and examined how functional diversity varied with species richness to identify levels of functional redundancy. Functional diversity, measured using a dendogram-based metric, increased from high to low intensity land uses, but observed values did not differ significantly from randomly-generated expected values. Values for functional evenness and functional divergence did not vary consistently with land-use intensification, although higher than expected values were mostly recorded in high intensity land uses. A total of 16 land uses had lower than expected values for functional dispersion and these were mostly low intensity native vegetation sites. Relations between functional diversity and bird species richness yielded strikingly different patterns for the entire bird community vs. particular functional groups. For all birds and insectivores, functional evenness, divergence and dispersion showed a linear decline with increasing species richness suggesting substantial functional redundancy across communities. However, for nectarivores, frugivores and carnivores, there was a significant hump-shaped or non-significant positive linear relationship between these functional measures and species richness indicating less redundancy. Hump-shaped relationships signify that the most functionally diverse communities occur at intermediate levels of species richness. Interpretations of redundancy thus vary for different functional groups and related ecosystem functions (e.g. pollination), and can be substantially different to relationships involving entire ecological communities. PMID:23696844
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Thompson, Grant L.; Kao-Kniffin, Jenny
2016-01-01
Urban grasslands, landscapes dominated by turfgrasses for aesthetic or recreational groundcovers, are rapidly expanding in the United States and globally. These managed ecosystems are often less diverse than the natural or agricultural lands they replace, leading to potential losses in ecosystem functioning. Research in non-urban systems has provided evidence for increases in multiple ecosystem functions associated with greater plant diversity. To test if biodiversity-ecosystem function findings are applicable to urban grasslands, we examined the effect of plant species and genotypic diversity on three ecosystem functions, using grassland assemblages of increasing diversity that were grown within a controlled environment facility. We found positive effects of plant diversity on reduced nitrate leaching and plant productivity. Soil microbial diversity (Mean Shannon Diversity, H’) of bacteria and fungi were also enhanced in multi-species plantings, suggesting that moderate increments in plant diversity influence the composition of soil biota. The results from this study indicate that plant diversity impacts multiple functions that are important in urban ecosystems; therefore, further tests of urban grassland biodiversity should be examined in situ to determine the feasibility of manipulating plant diversity as an explicit landscape design and function trait. PMID:27243768
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Functional diversity within the Penicillium roqueforti species.
Gillot, Guillaume; Jany, Jean-Luc; Poirier, Elisabeth; Maillard, Marie-Bernadette; Debaets, Stella; Thierry, Anne; Coton, Emmanuel; Coton, Monika
2017-01-16
Penicillium roqueforti is used as a ripening culture for blue cheeses and largely contributes to their organoleptic quality and typical characteristics. Different types of blue cheeses are manufactured and consumed worldwide and have distinct aspects, textures, flavors and colors. These features are well accepted to be due to the different manufacturing methods but also to the specific P. roqueforti strains used. Indeed, inoculated P. roqueforti strains, via their proteolytic and lipolytic activities, have an effect on both blue cheese texture and flavor. In particular, P. roqueforti produces a wide range of flavor compounds and variations in their proportions influence the flavor profiles of this type of cheese. Moreover, P. roqueforti is also characterized by substantial morphological and genetic diversity thus raising the question about the functional diversity of this species. In this context, 55 representative strains were screened for key metabolic properties including proteolytic activity (by determining free NH 2 amino groups) and secondary metabolite production (aroma compounds using HS-Trap GC-MS and mycotoxins via LC-MS/Q-TOF). Mini model cheeses were used for aroma production and proteolysis analyses, whereas Yeast Extract Sucrose (YES) agar medium was used for mycotoxin production. Overall, this study highlighted high functional diversity among isolates. Noteworthy, when only P. roqueforti strains isolated from Protected Designation of Origin (PDO) or Protected Geographical Indication (PGI) blue cheeses were considered, a clear relationship between genetic diversity, population structure and the assessed functional traits was shown. Copyright © 2016 Elsevier B.V. All rights reserved.
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Filling the gap in functional trait databases: use of ecological hypotheses to replace missing data.
Taugourdeau, Simon; Villerd, Jean; Plantureux, Sylvain; Huguenin-Elie, Olivier; Amiaud, Bernard
2014-04-01
Functional trait databases are powerful tools in ecology, though most of them contain large amounts of missing values. The goal of this study was to test the effect of imputation methods on the evaluation of trait values at species level and on the subsequent calculation of functional diversity indices at community level using functional trait databases. Two simple imputation methods (average and median), two methods based on ecological hypotheses, and one multiple imputation method were tested using a large plant trait database, together with the influence of the percentage of missing data and differences between functional traits. At community level, the complete-case approach and three functional diversity indices calculated from grassland plant communities were included. At the species level, one of the methods based on ecological hypothesis was for all traits more accurate than imputation with average or median values, but the multiple imputation method was superior for most of the traits. The method based on functional proximity between species was the best method for traits with an unbalanced distribution, while the method based on the existence of relationships between traits was the best for traits with a balanced distribution. The ranking of the grassland communities for their functional diversity indices was not robust with the complete-case approach, even for low percentages of missing data. With the imputation methods based on ecological hypotheses, functional diversity indices could be computed with a maximum of 30% of missing data, without affecting the ranking between grassland communities. The multiple imputation method performed well, but not better than single imputation based on ecological hypothesis and adapted to the distribution of the trait values for the functional identity and range of the communities. Ecological studies using functional trait databases have to deal with missing data using imputation methods corresponding to their specific needs and making the most out of the information available in the databases. Within this framework, this study indicates the possibilities and limits of single imputation methods based on ecological hypothesis and concludes that they could be useful when studying the ranking of communities for their functional diversity indices.
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Filling the gap in functional trait databases: use of ecological hypotheses to replace missing data
Taugourdeau, Simon; Villerd, Jean; Plantureux, Sylvain; Huguenin-Elie, Olivier; Amiaud, Bernard
2014-01-01
Functional trait databases are powerful tools in ecology, though most of them contain large amounts of missing values. The goal of this study was to test the effect of imputation methods on the evaluation of trait values at species level and on the subsequent calculation of functional diversity indices at community level using functional trait databases. Two simple imputation methods (average and median), two methods based on ecological hypotheses, and one multiple imputation method were tested using a large plant trait database, together with the influence of the percentage of missing data and differences between functional traits. At community level, the complete-case approach and three functional diversity indices calculated from grassland plant communities were included. At the species level, one of the methods based on ecological hypothesis was for all traits more accurate than imputation with average or median values, but the multiple imputation method was superior for most of the traits. The method based on functional proximity between species was the best method for traits with an unbalanced distribution, while the method based on the existence of relationships between traits was the best for traits with a balanced distribution. The ranking of the grassland communities for their functional diversity indices was not robust with the complete-case approach, even for low percentages of missing data. With the imputation methods based on ecological hypotheses, functional diversity indices could be computed with a maximum of 30% of missing data, without affecting the ranking between grassland communities. The multiple imputation method performed well, but not better than single imputation based on ecological hypothesis and adapted to the distribution of the trait values for the functional identity and range of the communities. Ecological studies using functional trait databases have to deal with missing data using imputation methods corresponding to their specific needs and making the most out of the information available in the databases. Within this framework, this study indicates the possibilities and limits of single imputation methods based on ecological hypothesis and concludes that they could be useful when studying the ranking of communities for their functional diversity indices. PMID:24772273
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Forest restoration, biodiversity and ecosystem functioning.
Aerts, Raf; Honnay, Olivier
2011-11-24
Globally, forests cover nearly one third of the land area and they contain over 80% of terrestrial biodiversity. Both the extent and quality of forest habitat continue to decrease and the associated loss of biodiversity jeopardizes forest ecosystem functioning and the ability of forests to provide ecosystem services. In the light of the increasing population pressure, it is of major importance not only to conserve, but also to restore forest ecosystems. Ecological restoration has recently started to adopt insights from the biodiversity-ecosystem functioning (BEF) perspective. Central is the focus on restoring the relation between biodiversity and ecosystem functioning. Here we provide an overview of important considerations related to forest restoration that can be inferred from this BEF-perspective. Restoring multiple forest functions requires multiple species. It is highly unlikely that species-poor plantations, which may be optimal for above-ground biomass production, will outperform species diverse assemblages for a combination of functions, including overall carbon storage and control over water and nutrient flows. Restoring stable forest functions also requires multiple species. In particular in the light of global climatic change scenarios, which predict more frequent extreme disturbances and climatic events, it is important to incorporate insights from the relation between biodiversity and stability of ecosystem functioning into forest restoration projects. Rather than focussing on species per se, focussing on functional diversity of tree species assemblages seems appropriate when selecting tree species for restoration. Finally, also plant genetic diversity and above - below-ground linkages should be considered during the restoration process, as these likely have prominent but until now poorly understood effects at the level of the ecosystem. The BEF-approach provides a useful framework to evaluate forest restoration in an ecosystem functioning context, but it also highlights that much remains to be understood, especially regarding the relation between forest functioning on the one side and genetic diversity and above-ground-below-ground species associations on the other. The strong emphasis of the BEF-approach on functional rather than taxonomic diversity may also be the beginning of a paradigm shift in restoration ecology, increasing the tolerance towards allochthonous species.
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Xu, Yuan; Fan, Xinpeng; Warren, Alan; Zhang, Liquan; Xu, Henglong
2018-02-01
Researches on the functional diversity of benthic ecosystems have mainly focused on macrofauna, and studies on functional structure of ciliate communities have been based only on trophic- or size-groups. Current research was carried out on the changing patterns of classical and functional diversity of benthic ciliates in response to environmental gradients at three sites in a wetland in Yangtze Estuary. The results showed that changes of environmental factors (e.g. salinity, sediment grain size and hydrodynamic conditions) in the Yangtze Estuary induce variability in species composition and functional trait distribution. Furthermore, increased species richness and diversity did not lead to significant changes in functional diversity due to functional redundancy. However, salt water intrusion of Yangtze Estuary during the dry season could cause reduced functional diversity of ciliate communities. Current study provides the first insight into the functional diversity of ciliate communities in response to environmental gradients. Copyright © 2018 Elsevier Ltd. All rights reserved.
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Jang, Sang-Min; Redon, Christophe E.; Aladjem, Mirit I.
2018-01-01
Cullin-RING (Really Interesting New Gene) E3 ubiquitin ligases (CRLs), the largest family of E3 ubiquitin ligases, are functional multi-subunit complexes including substrate receptors, adaptors, cullin scaffolds, and RING-box proteins. CRLs are responsible for ubiquitination of ~20% of cellular proteins and are involved in diverse biological processes including cell cycle progression, genome stability, and oncogenesis. Not surprisingly, cullins are deregulated in many diseases and instances of cancer. Recent studies have highlighted the importance of CRL-mediated ubiquitination in the regulation of DNA replication/repair, including specific roles in chromatin assembly and disassembly of the replication machinery. The development of novel therapeutics targeting the CRLs that regulate the replication machinery and chromatin in cancer is now an attractive therapeutic strategy. In this review, we summarize the structure and assembly of CRLs and outline their cellular functions and their diverse roles in cancer, emphasizing the regulatory functions of nuclear CRLs in modulating the DNA replication machinery. Finally, we discuss the current strategies for targeting CRLs against cancer in the clinic. PMID:29594129
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Self-organization in a diversity induced thermodynamics.
Scirè, Alessandro; Annovazzi-Lodi, Valerio
2017-01-01
In this work we show how global self-organized patterns can come out of a disordered ensemble of point oscillators, as a result of a deterministic, and not of a random, cooperative process. The resulting system dynamics has many characteristics of classical thermodynamics. To this end, a modified Kuramoto model is introduced, by including Euclidean degrees of freedom and particle polarity. The standard deviation of the frequency distribution is the disorder parameter, diversity, acting as temperature, which is both a source of motion and of disorder. For zero and low diversity, robust static phase-synchronized patterns (crystals) appear, and the problem reverts to a generic dissipative many-body problem. From small to moderate diversity crystals display vibrations followed by structure disintegration in a competition of smaller dynamic patterns, internally synchronized, each of which is capable to manage its internal diversity. In this process a huge variety of self-organized dynamic shapes is formed. Such patterns can be seen again as (more complex) oscillators, where the same description can be applied in turn, renormalizing the problem to a bigger scale, opening the possibility of pattern evolution. The interaction functions are kept local because our idea is to build a system able to produce global patterns when its constituents only interact at the bond scale. By further increasing the oscillator diversity, the dynamics becomes erratic, dynamic patterns show short lifetime, and finally disappear for high diversity. Results are neither qualitatively dependent on the specific choice of the interaction functions nor on the shape of the probability function assumed for the frequencies. The system shows a phase transition and a critical behaviour for a specific value of diversity.
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Sakschewski, Boris; von Bloh, Werner; Boit, Alice; Rammig, Anja; Kattge, Jens; Poorter, Lourens; Peñuelas, Josep; Thonicke, Kirsten
2015-01-22
Functional diversity is critical for ecosystem dynamics, stability and productivity. However, dynamic global vegetation models (DGVMs) which are increasingly used to simulate ecosystem functions under global change, condense functional diversity to plant functional types (PFTs) with constant parameters. Here, we develop an individual- and trait-based version of the DGVM LPJmL (Lund-Potsdam-Jena managed Land) called LPJmL- flexible individual traits (LPJmL-FIT) with flexible individual traits) which we apply to generate plant trait maps for the Amazon basin. LPJmL-FIT incorporates empirical ranges of five traits of tropical trees extracted from the TRY global plant trait database, namely specific leaf area (SLA), leaf longevity (LL), leaf nitrogen content (N area ), the maximum carboxylation rate of Rubisco per leaf area (vcmaxarea), and wood density (WD). To scale the individual growth performance of trees, the leaf traits are linked by trade-offs based on the leaf economics spectrum, whereas wood density is linked to tree mortality. No preselection of growth strategies is taking place, because individuals with unique trait combinations are uniformly distributed at tree establishment. We validate the modeled trait distributions by empirical trait data and the modeled biomass by a remote sensing product along a climatic gradient. Including trait variability and trade-offs successfully predicts natural trait distributions and achieves a more realistic representation of functional diversity at the local to regional scale. As sites of high climatic variability, the fringes of the Amazon promote trait divergence and the coexistence of multiple tree growth strategies, while lower plant trait diversity is found in the species-rich center of the region with relatively low climatic variability. LPJmL-FIT enables to test hypotheses on the effects of functional biodiversity on ecosystem functioning and to apply the DGVM to current challenges in ecosystem management from local to global scales, that is, deforestation and climate change effects. © 2015 John Wiley & Sons Ltd.
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Zhang, Ximei; Johnston, Eric R; Barberán, Albert; Ren, Yi; Lü, Xiaotao; Han, Xingguo
2017-10-01
Anthropogenic environmental changes are accelerating the rate of biodiversity loss on Earth. Plant diversity loss is predicted to reduce soil microbial diversity primarily due to the decreased variety of carbon/energy resources. However, this intuitive hypothesis is supported by sparse empirical evidence, and most underlying mechanisms remain underexplored or obscure altogether. We constructed four diversity gradients (0-3) in a five-year plant functional group removal experiment in a steppe ecosystem in Inner Mongolia, China, and quantified microbial taxonomic and functional diversity with shotgun metagenome sequencing. The treatments had little effect on microbial taxonomic diversity, but were found to decrease functional gene diversity. However, the observed decrease in functional gene diversity was more attributable to a loss in plant productivity, rather than to the loss of any individual plant functional group per se. Reduced productivity limited fresh plant resources supplied to microorganisms, and thus, intensified the pressure of ecological filtering, favoring genes responsible for energy production/conversion, material transport/metabolism and amino acid recycling, and accordingly disfavored many genes with other functions. Furthermore, microbial respiration was correlated with the variation in functional composition but not taxonomic composition. Overall, the amount of carbon/energy resources driving microbial gene diversity was identified to be the critical linkage between above- and belowground communities, contrary to the traditional framework of linking plant clade/taxonomic diversity to microbial taxonomic diversity. © 2017 John Wiley & Sons Ltd.
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Thomas, Pious; Sekhar, Aparna C; Shaik, Sadiq Pasha
2017-11-01
Molecular and microscopic analyses reveal enormous non-cultivable endophytic bacteria in grapevine field shoots with functional significance. Diverse bacteria enter tissue cultures through surface-sterilized tissues and survive surreptitiously with varying taxonomic realignments. The study was envisaged to assess the extent of endophytic bacterial association with field shoot tissues of grapevine and the likelihood of introduction of such internally colonizing bacteria in vitro adopting molecular techniques targeting the non-cultivable bacterial community. PowerFood ® -kit derived DNA from surface-sterilized field shoot tips of grapevine Flame Seedless was employed in a preliminary bacterial class-specific PCR screening proving positive for major prokaryotic taxa including Archaea. Taxonomic and functional diversity were analyzed through whole metagenome profiling (WMG) which revealed predominantly phylum Actinobacteria, Proteobacteria, and minor shares of Firmicutes, Bacteroidetes, and Deinococcus-Thermus with varying functional roles ascribable to the whole bacterial community. Field shoot tip tissues and callus derived from stem segments were further employed in 16S rRNA V3-V4 amplicon taxonomic profiling. This revealed elevated taxonomic diversity in field shoots over WMG, predominantly Proteobacteria succeeded by Actinobacteria, Firmicutes, Bacteroidetes, and 15 other phyla including several candidate phyla (135 families, 179 genera). Callus stocks also displayed broad bacterial diversity (16 phyla; 96 families; 141 genera) bearing resemblance to field tissues with Proteobacterial dominance but a reduction in its share, enrichment of Actinobacteria and Firmicutes, disappearance of some field-associated phyla and detection of a few additional taxonomic groups over field community. Similar results were documented during 16S V3-V4 amplicon taxonomic profiling on Thompson Seedless field shoot tip and callus tissues. Video microscopy on tissue homogenates corroborated enormous endophytic bacteria. This study elucidates a vast diversity of cultivation-recalcitrant endophytic bacteria prevailing in grapevine field shoots, their in vitro introduction, and unsuspecting sustenance with possible silent participation in tissue culture processes.
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Xiao, Cuicui; Ran, Shujun; Huang, Zhengwei; Liang, Jingping
2016-01-01
Dental caries has a polymicrobial etiology within the complex oral microbial ecosystem. However, the overall diversity and structure of supragingival plaque microbiota in adult dental health and caries are not well understood. Here, 160 supragingival plaque samples from patients with dental health and different severities of dental caries were collected for bacterial genomic DNA extraction, pyrosequencing by amplification of the 16S rDNA V1–V3 hypervariable regions, and bioinformatic analysis. High-quality sequences (2,261,700) clustered into 10,365 operational taxonomic units (OTUs; 97% identity), representing 453 independent species belonging to 122 genera, 66 families, 34 orders, 21 classes, and 12 phyla. All groups shared 7522 OTUs, indicating the presence of a core plaque microbiome. α diversity analysis showed that the microbial diversity in healthy plaques exceeded that of dental caries, with the diversity decreasing gradually with the severity of caries. The dominant phyla of plaque microbiota included Bacteroidetes, Actinobacteria, Proteobacteria, Firmicutes, Fusobacteria, and TM7. The dominant genera included Capnocytophaga, Prevotella, Actinomyces, Corynebacterium, Neisseria, Streptococcus, Rothia, and Leptotrichia. β diversity analysis showed that the plaque microbial community structure was similar in all groups. Using LEfSe analysis, 25 differentially abundant taxa were identified as potential biomarkers. Key genera (27) that potentially contributed to the differential distributions of plaque microbiota between groups were identified by PLS-DA analysis. Finally, co-occurrence network analysis and function predictions were performed. Treatment strategies directed toward modulating microbial interactions and their functional output should be further developed. PMID:27499752
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Villéger, Sébastien; Mason, Norman W H; Mouillot, David
2008-08-01
Functional diversity is increasingly identified as an important driver of ecosystem functioning. Various indices have been proposed to measure the functional diversity of a community, but there is still no consensus on which are most suitable. Indeed, none of the existing indices meets all the criteria required for general use. The main criteria are that they must be designed to deal with several traits, take into account abundances, and measure all the facets of functional diversity. Here we propose three indices to quantify each facet of functional diversity for a community with species distributed in a multidimensional functional space: functional richness (volume of the functional space occupied by the community), functional evenness (regularity of the distribution of abundance in this volume), and functional divergence (divergence in the distribution of abundance in this volume). Functional richness is estimated using the existing convex hull volume index. The new functional evenness index is based on the minimum spanning tree which links all the species in the multidimensional functional space. Then this new index quantifies the regularity with which species abundances are distributed along the spanning tree. Functional divergence is measured using a novel index which quantifies how species diverge in their distances (weighted by their abundance) from the center of gravity in the functional space. We show that none of the indices meets all the criteria required for a functional diversity index, but instead we show that the set of three complementary indices meets these criteria. Through simulations of artificial data sets, we demonstrate that functional divergence and functional evenness are independent of species richness and that the three functional diversity indices are independent of each other. Overall, our study suggests that decomposition of functional diversity into its three primary components provides a meaningful framework for its quantification and for the classification of existing functional diversity indices. This decomposition has the potential to shed light on the role of biodiversity on ecosystem functioning and on the influence of biotic and abiotic filters on the structure of species communities. Finally, we propose a general framework for applying these three functional diversity indices.
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Whitlock, Raj
2014-01-01
Understanding the effects of intraspecific genetic diversity on the structure and functioning of ecological communities is a fundamentally important part of evolutionary ecology and may also have conservation relevance in identifying the situations in which genetic diversity coincides with species-level diversity.Early studies within this field documented positive relationships between genetic diversity and ecological structure, but recent studies have challenged these findings. Conceptual synthesis has been hampered because studies have used different measures of intraspecific variation (phenotypically adaptive vs. neutral) and have considered different measures of ecological structure in different ecological and spatial contexts. The aim of this study is to strengthen conceptual understanding by providing an empirical synthesis quantifying the relationship between genetic diversity and ecological structure.Here, I present a meta-analysis of the relationship between genetic diversity within plant populations and the structure and functioning of associated ecological communities (including 423 effect sizes from 70 studies). I used Bayesian meta-analyses to examine (i) the strength and direction of this relationship, (ii) the extent to which phenotypically adaptive and neutral (molecular) measures of diversity differ in their association with ecological structure and (iii) variation in outcomes among different measures of ecological structure and in different ecological contexts.Effect sizes measuring the relationship between adaptive diversity (genotypic richness) and both community- and ecosystem-level ecological responses were small, but significantly positive. These associations were supported by genetic effects on species richness and productivity, respectively.There was no overall association between neutral genetic diversity and measures of ecological structure, but a positive correlation was observed under a limited set of demographic conditions. These results suggest that adaptive and neutral genetic diversity should not be treated as ecologically equivalent measures of intraspecific variation.Synthesis. This study advances the debate over whether relationships between genetic diversity and ecological structure are either simply positive or negative, by showing how the strength and direction of these relationships changes with different measures of diversity and in different ecological contexts. The results provide a solid foundation for assessing when and where an expanded synthesis between ecology and genetics will be most fruitful. PMID:25210204
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CA1 pyramidal cell diversity enabling parallel information processing in the hippocampus
Soltesz, Ivan; Losonczy, Attila
2018-01-01
Hippocampal network operations supporting spatial navigation and declarative memory are traditionally interpreted in a framework where each hippocampal area, such as the dentate gyrus, CA3, and CA1, consists of homogeneous populations of functionally equivalent principal neurons. However, heterogeneity within hippocampal principal cell populations, in particular within pyramidal cells at the main CA1 output node, is increasingly recognized and includes developmental, molecular, anatomical, and functional differences. Here we review recent progress in the delineation of hippocampal principal cell subpopulations by focusing on radially defined subpopulations of CA1 pyramidal cells, and we consider how functional segregation of information streams, in parallel channels with nonuniform properties, could represent a general organizational principle of the hippocampus supporting diverse behaviors. PMID:29593317
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Boesch, Austin W; Kappel, James H; Mahan, Alison E; Chu, Thach H; Crowley, Andrew R; Osei-Owusu, Nana Y; Alter, Galit; Ackerman, Margaret E
2018-05-01
As antibodies continue to gain predominance in drug discovery and development pipelines, efforts to control and optimize their activity in vivo have matured to incorporate sophisticated abilities to manipulate engagement of specific Fc binding partners. Such efforts to promote diverse functional outcomes include modulating IgG-Fc affinity for FcγRs to alternatively potentiate or reduce effector functions, such as antibody-dependent cellular cytotoxicity and phagocytosis. While a number of natural and engineered Fc features capable of eliciting variable effector functions have been demonstrated in vitro and in vivo, elucidation of these important functional relationships has taken significant effort through use of diverse genetic, cellular and enzymatic techniques. As an orthogonal approach, we demonstrate use of FcγR as chromatographic affinity ligands to enrich and therefore simultaneously identify favored binding species from a complex mixture of serum-derived pooled polycloncal human IgG, a load material that contains the natural repertoire of Fc variants and post-translational modifications. The FcγR-enriched IgG was characterized for subclass and glycoform composition and the impact of this bioseparation step on antibody activity was measured in cell-based effector function assays including Natural Killer cell activation and monocyte phagocytosis. This work demonstrates a tractable means to rapidly distinguish complex functional relationships between two or more interacting biological agents by leveraging affinity chromatography followed by secondary analysis with high-resolution biophysical and functional assays and emphasizes a platform capable of surveying diverse natural post-translational modifications that may not be easily produced with high purity or easily accessible with recombinant expression techniques. © 2018 Wiley Periodicals, Inc.
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Samanta, Brajogopal; Bhadury, Punyasloke
2016-01-01
Marine chromophytes are taxonomically diverse group of algae and contribute approximately half of the total oceanic primary production. To understand the global patterns of functional diversity of chromophytic phytoplankton, robust bioinformatics and statistical analyses including deep phylogeny based on 2476 form ID rbcL gene sequences representing seven ecologically significant oceanographic ecoregions were undertaken. In addition, 12 form ID rbcL clone libraries were generated and analyzed (148 sequences) from Sundarbans Biosphere Reserve representing the world’s largest mangrove ecosystem as part of this study. Global phylogenetic analyses recovered 11 major clades of chromophytic phytoplankton in varying proportions with several novel rbcL sequences in each of the seven targeted ecoregions. Majority of OTUs was found to be exclusive to each ecoregion, whereas some were shared by two or more ecoregions based on beta-diversity analysis. Present phylogenetic and bioinformatics analyses provide a strong statistical support for the hypothesis that different oceanographic regimes harbor distinct and coherent groups of chromophytic phytoplankton. It has been also shown as part of this study that varying natural selection pressure on form ID rbcL gene under different environmental conditions could lead to functional differences and overall fitness of chromophytic phytoplankton populations. PMID:26861415
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Environmental microbiology as a mosaic of explored ecosystems and issues.
Faure, Denis; Bonin, Patricia; Duran, Robert
2015-09-01
Microbes are phylogenetically (Archaea, Bacteria, Eukarya, and viruses) and functionally diverse. They colonize highly varied environments and rapidly respond to and evolve as a response to local and global environmental changes, including those induced by pollutants resulting from human activities. This review exemplifies the Microbial Ecology EC2CO consortium's efforts to explore the biology, ecology, diversity, and roles of microbes in aquatic and continental ecosystems.
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Wang, Yu; Zhang, Rui; He, Zhili; Van Nostrand, Joy D.; Zheng, Qiang; Zhou, Jizhong; Jiao, Nianzhi
2017-01-01
Microbes play crucial roles in various biogeochemical processes in the ocean, including carbon (C), nitrogen (N), and phosphorus (P) cycling. Functional gene diversity and the structure of the microbial community determines its metabolic potential and therefore its ecological function in the marine ecosystem. However, little is known about the functional gene composition and metabolic potential of bacterioplankton in estuary areas. The East China Sea (ECS) is a dynamic marginal ecosystem in the western Pacific Ocean that is mainly affected by input from the Changjiang River and the Kuroshio Current. Here, using a high-throughput functional gene microarray (GeoChip), we analyzed the functional gene diversity, composition, structure, and metabolic potential of microbial assemblages in different ECS water masses. Four water masses determined by temperature and salinity relationship showed different patterns of functional gene diversity and composition. Generally, functional gene diversity [Shannon–Weaner’s H and reciprocal of Simpson’s 1/(1-D)] in the surface water masses was higher than that in the bottom water masses. The different presence and proportion of functional genes involved in C, N, and P cycling among the bacteria of the different water masses showed different metabolic preferences of the microbial populations in the ECS. Genes involved in starch metabolism (amyA and nplT) showed higher proportion in microbial communities of the surface water masses than of the bottom water masses. In contrast, a higher proportion of genes involved in chitin degradation was observed in microorganisms of the bottom water masses. Moreover, we found a higher proportion of nitrogen fixation (nifH), transformation of hydroxylamine to nitrite (hao) and ammonification (gdh) genes in the microbial communities of the bottom water masses compared with those of the surface water masses. The spatial variation of microbial functional genes was significantly correlated with salinity, temperature, and chlorophyll based on canonical correspondence analysis, suggesting a significant influence of hydrologic conditions on water microbial communities. Our data provide new insights into better understanding of the functional potential of microbial communities in the complex estuarine-coastal environmental gradient of the ECS. PMID:28680420
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The Enzyme Function Initiative†
Gerlt, John A.; Allen, Karen N.; Almo, Steven C.; Armstrong, Richard N.; Babbitt, Patricia C.; Cronan, John E.; Dunaway-Mariano, Debra; Imker, Heidi J.; Jacobson, Matthew P.; Minor, Wladek; Poulter, C. Dale; Raushel, Frank M.; Sali, Andrej; Shoichet, Brian K.; Sweedler, Jonathan V.
2011-01-01
The Enzyme Function Initiative (EFI) was recently established to address the challenge of assigning reliable functions to enzymes discovered in bacterial genome projects; in this Current Topic we review the structure and operations of the EFI. The EFI includes the Superfamily/Genome, Protein, Structure, Computation, and Data/Dissemination Cores that provide the infrastructure for reliably predicting the in vitro functions of unknown enzymes. The initial targets for functional assignment are selected from five functionally diverse superfamilies (amidohydrolase, enolase, glutathione transferase, haloalkanoic acid dehalogenase, and isoprenoid synthase), with five superfamily-specific Bridging Projects experimentally testing the predicted in vitro enzymatic activities. The EFI also includes the Microbiology Core that evaluates the in vivo context of in vitro enzymatic functions and confirms the functional predictions of the EFI. The deliverables of the EFI to the scientific community include: 1) development of a large-scale, multidisciplinary sequence/structure-based strategy for functional assignment of unknown enzymes discovered in genome projects (target selection, protein production, structure determination, computation, experimental enzymology, microbiology, and structure-based annotation); 2) dissemination of the strategy to the community via publications, collaborations, workshops, and symposia; 3) computational and bioinformatic tools for using the strategy; 4) provision of experimental protocols and/or reagents for enzyme production and characterization; and 5) dissemination of data via the EFI’s website, enzymefunction.org. The realization of multidisciplinary strategies for functional assignment will begin to define the full metabolic diversity that exists in nature and will impact basic biochemical and evolutionary understanding, as well as a wide range of applications of central importance to industrial, medicinal and pharmaceutical efforts. PMID:21999478
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The Enzyme Function Initiative.
Gerlt, John A; Allen, Karen N; Almo, Steven C; Armstrong, Richard N; Babbitt, Patricia C; Cronan, John E; Dunaway-Mariano, Debra; Imker, Heidi J; Jacobson, Matthew P; Minor, Wladek; Poulter, C Dale; Raushel, Frank M; Sali, Andrej; Shoichet, Brian K; Sweedler, Jonathan V
2011-11-22
The Enzyme Function Initiative (EFI) was recently established to address the challenge of assigning reliable functions to enzymes discovered in bacterial genome projects; in this Current Topic, we review the structure and operations of the EFI. The EFI includes the Superfamily/Genome, Protein, Structure, Computation, and Data/Dissemination Cores that provide the infrastructure for reliably predicting the in vitro functions of unknown enzymes. The initial targets for functional assignment are selected from five functionally diverse superfamilies (amidohydrolase, enolase, glutathione transferase, haloalkanoic acid dehalogenase, and isoprenoid synthase), with five superfamily specific Bridging Projects experimentally testing the predicted in vitro enzymatic activities. The EFI also includes the Microbiology Core that evaluates the in vivo context of in vitro enzymatic functions and confirms the functional predictions of the EFI. The deliverables of the EFI to the scientific community include (1) development of a large-scale, multidisciplinary sequence/structure-based strategy for functional assignment of unknown enzymes discovered in genome projects (target selection, protein production, structure determination, computation, experimental enzymology, microbiology, and structure-based annotation), (2) dissemination of the strategy to the community via publications, collaborations, workshops, and symposia, (3) computational and bioinformatic tools for using the strategy, (4) provision of experimental protocols and/or reagents for enzyme production and characterization, and (5) dissemination of data via the EFI's Website, http://enzymefunction.org. The realization of multidisciplinary strategies for functional assignment will begin to define the full metabolic diversity that exists in nature and will impact basic biochemical and evolutionary understanding, as well as a wide range of applications of central importance to industrial, medicinal, and pharmaceutical efforts. © 2011 American Chemical Society
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Martiny, Adam C.; Martiny, Jennifer B. H.; Weihe, Claudia; Field, Andrew; Ellis, Julie C.
2011-01-01
Wildlife may facilitate the spread of antibiotic resistance (AR) between human-dominated habitats and the surrounding environment. Here, we use functional metagenomics to survey the diversity and genomic context of AR genes in gulls. Using this approach, we found a variety of AR genes not previously detected in gulls and wildlife, including class A and C β-lactamases as well as six tetracycline resistance gene types. An analysis of the flanking sequences indicates that most of these genes are present in Enterobacteriaceae and various Gram-positive bacteria. In addition to finding known gene types, we detected 31 previously undescribed AR genes. These undescribed genes include one most similar to an uncharacterized gene in Verrucomicrobium and another to a putative DNA repair protein in Lactobacillus. Overall, the study more than doubled the number of clinically relevant AR gene types known to be carried by gulls or by wildlife in general. Together with the propensity of gulls to visit human-dominated habitats, this high diversity of AR gene types suggests that gulls could facilitate the spread of AR. PMID:22347872
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The Genus Cladophora Kützing (Ulvophyceae) as a Globally Distributed Ecological Engineer.
Zulkifly, Shahrizim B; Graham, James M; Young, Erica B; Mayer, Robert J; Piotrowski, Michael J; Smith, Izak; Graham, Linda E
2013-02-01
The green algal genus Cladophora forms conspicuous nearshore populations in marine and freshwaters worldwide, commonly dominating peri-phyton communities. As the result of human activities, including the nutrient pollution of nearshore waters, Cladophora-dominated periphyton can form nuisance blooms. On the other hand, Cladophora has ecological functions that are beneficial, but less well appreciated. For example, Cladophora has previously been characterized as an ecological engineer because its complex structure fosters functional and taxonomic diversity of benthic microfauna. Here, we review classic and recent literature concerning taxonomy, cell biology, morphology, reproductive biology, and ecology of the genus Cladophora, to examine how this alga functions to modify habitats and influence littoral biogeochemistry. We review the evidence that Cladophora supports large, diverse populations of microalgal and bacterial epiphytes that influence the cycling of carbon and other key elements, and that the high production of cellulose and hydrocarbons by Cladophora-dominated periphyton has the potential for diverse technological applications, including wastewater remediation coupled to renewable biofuel production. We postulate that well-known aspects of Cladophora morphology, hydrodynamically stable and perennial holdfasts, distinctively branched architecture, unusually large cell and sporangial size and robust cell wall construction, are major factors contributing to the multiple roles of this organism as an ecological engineer. © 2013 Phycological Society of America.
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Recent advances in plant-herbivore interactions
Burkepile, Deron E.; Parker, John D.
2017-01-01
Plant-herbivore interactions shape community dynamics across marine, freshwater, and terrestrial habitats. From amphipods to elephants and from algae to trees, plant-herbivore relationships are the crucial link generating animal biomass (and human societies) from mere sunlight. These interactions are, thus, pivotal to understanding the ecology and evolution of virtually any ecosystem. Here, we briefly highlight recent advances in four areas of plant-herbivore interactions: (1) plant defense theory, (2) herbivore diversity and ecosystem function, (3) predation risk aversion and herbivory, and (4) how a changing climate impacts plant-herbivore interactions. Recent advances in plant defense theory, for example, highlight how plant life history and defense traits affect and are affected by multiple drivers, including enemy pressure, resource availability, and the local plant neighborhood, resulting in trait-mediated feedback loops linking trophic interactions with ecosystem nutrient dynamics. Similarly, although the positive effect of consumer diversity on ecosystem function has long been recognized, recent advances using DNA barcoding to elucidate diet, and Global Positioning System/remote sensing to determine habitat selection and impact, have shown that herbivore communities are probably even more functionally diverse than currently realized. Moreover, although most diversity-function studies continue to emphasize plant diversity, herbivore diversity may have even stronger impacts on ecosystem multifunctionality. Recent studies also highlight the role of risk in plant-herbivore interactions, and risk-driven trophic cascades have emerged as landscape-scale patterns in a variety of ecosystems. Perhaps not surprisingly, many plant-herbivore interactions are currently being altered by climate change, which affects plant growth rates and resource allocation, expression of chemical defenses, plant phenology, and herbivore metabolism and behavior. Finally, we conclude by noting that although the field is advancing rapidly, the world is changing even more rapidly, challenging our ability to manage these pivotal links in the food chain. PMID:28232868
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Hu, Ning; Li, Hui; Tang, Zheng; Li, Zhongfang; Tian, Jing; Lou, Yilai; Li, Jianwei; Li, Guichun; Hu, Xiaomin
2016-06-17
We examined community diversity, structure and carbon footprint of nematode food web along a chronosequence of T. Sinensis reforestation on degraded Karst. In general, after the reforestation: a serious of diversity parameters and community indices (Shannon-Weinier index (H'), structure index (SI), etc.) were elevated; biomass ratio of fungivores to bacterivores (FFC/BFC), and fungi to bacteria (F/B) were increased, and nematode channel ratio (NCR) were decreased; carbon footprints of all nematode trophic groups, and biomass of bacteria and fungi were increased. Our results indicate that the Karst aboveground vegetation restoration was accompanied with belowground nematode food web development: increasing community complexity, function and fungal dominance in decomposition pathway, and the driving forces included the bottom-up effect (resource control), connectedness of functional groups, as well as soil environments.
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Hu, Ning; Li, Hui; Tang, Zheng; Li, Zhongfang; Tian, Jing; Lou, Yilai; Li, Jianwei; Li, Guichun; Hu, Xiaomin
2016-01-01
We examined community diversity, structure and carbon footprint of nematode food web along a chronosequence of T. Sinensis reforestation on degraded Karst. In general, after the reforestation: a serious of diversity parameters and community indices (Shannon-Weinier index (H′), structure index (SI), etc.) were elevated; biomass ratio of fungivores to bacterivores (FFC/BFC), and fungi to bacteria (F/B) were increased, and nematode channel ratio (NCR) were decreased; carbon footprints of all nematode trophic groups, and biomass of bacteria and fungi were increased. Our results indicate that the Karst aboveground vegetation restoration was accompanied with belowground nematode food web development: increasing community complexity, function and fungal dominance in decomposition pathway, and the driving forces included the bottom-up effect (resource control), connectedness of functional groups, as well as soil environments. PMID:27311984
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Exotic species enhance response diversity to land-use change but modify functional composition.
Stavert, Jamie R; Pattemore, David E; Gaskett, Anne C; Beggs, Jacqueline R; Bartomeus, Ignasi
2017-08-16
Two main mechanisms may buffer ecosystem functions despite biodiversity loss. First, multiple species could share similar ecological roles, thus providing functional redundancy. Second, species may respond differently to environmental change (response diversity). However, ecosystem function would be best protected when functionally redundant species also show response diversity. This linkage has not been studied directly, so we investigated whether native and exotic pollinator species with similar traits (functional redundancy) differed in abundance (response diversity) across an agricultural intensification gradient. Exotic pollinator species contributed most positive responses, which partially stabilized overall abundance of the pollinator community. However, although some functionally redundant species exhibited response diversity, this was not consistent across functional groups and aggregate abundances within each functional group were rarely stabilized. This shows functional redundancy and response diversity do not always operate in concert. Hence, despite exotic species becoming increasingly dominant in human-modified systems, they cannot replace the functional composition of native species. © 2017 The Author(s).
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Special Education at the Crossroad: An Identity Crisis and the Need for a Scientific Reconstruction
ERIC Educational Resources Information Center
Kauffman, James M.; Anastasiou, Dimitris; Maag, John W.
2017-01-01
Special education is losing its identity--its visibility, distinctiveness, budget, and basic functions are all at risk. Special education functions include (a) sorting, categorizing, and labeling students who need it; (b) making the right comparisons; (c) honoring diversity but changing "particular" differences; (d) managing stigma; (e)…
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Bull, R; Scerif, G
2001-01-01
Children's mathematical skills were considered in relation to executive functions. Using multiple measures--including the Wisconsin Card Sorting Task (WCST), dual-task performance, Stroop task, and counting span-it was found that mathematical ability was significantly correlated with all measures of executive functioning, with the exception of dual-task performance. Furthermore, regression analyses revealed that each executive function measure predicted unique variance in mathematics ability. These results are discussed in terms of a central executive with diverse functions (Shallice & Burgess, 1996) and with recent evidence from Miyake, et al. (2000) showing the unity and diversity among executive functions. It is proposed that the particular difficulties for children of lower mathematical ability are lack of inhibition and poor working memory, which result in problems with switching and evaluation of new strategies for dealing with a particular task. The practical and theoretical implications of these results are discussed, along with suggestions for task changes and longitudinal studies that would clarify theoretical and developmental issues related to executive functioning.
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Méndez, Verónica; Wood, Jamie R; Butler, Simon J
2018-05-01
Functional diversity metrics are increasingly used to augment or replace taxonomic diversity metrics to deliver more mechanistic insights into community structure and function. Metrics used to describe landscape structure and characteristics share many of the same limitations as taxonomy-based metrics, particularly their reliance on anthropogenically defined typologies with little consideration of structure, management, or function. However, the development of alternative metrics to describe landscape characteristics has been limited. Here, we extend the functional diversity framework to characterize landscapes based on the diversity of resources available across habitats present. We then examine the influence of resource diversity and provenance on the functional diversities of native and exotic avian communities in New Zealand. Invasive species are increasingly prevalent and considered a global threat to ecosystem function, but the characteristics of and interactions between sympatric native and exotic communities remain unresolved. Understanding their comparative responses to environmental change and the mechanisms underpinning them is of growing importance in predicting community dynamics and changing ecosystem function. We use (i) matrices of resource use (species) and resource availability (habitats) and (ii) occurrence data for 62 native and 25 exotic species and 19 native and 13 exotic habitats in 2015 10 × 10 km quadrats to examine the relationship between native and exotic avian and landscape functional diversity. The numbers of species in, and functional diversities of, native and exotic communities were positively related. Each community displayed evidence of environmental filtering, but it was significantly stronger for exotic species. Less environmental filtering occurred in landscapes providing a more diverse combination of resources, with resource provenance also an influential factor. Landscape functional diversity explained a greater proportion of variance in native and exotic community characteristics than the number of habitat types present. Resource diversity and provenance should be explicitly accounted for when characterizing landscape structure and change as they offer additional mechanistic understanding of the links between environmental filtering and community structure. Manipulating resource diversity through the design and implementation of management actions could prove a powerful tool for the delivery of conservation objectives, be they to protect native species, control exotic species, or maintain ecosystem service provision.
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Ecosystem engineering affects ecosystem functioning in high-Andean landscapes.
Badano, Ernesto I; Marquet, Pablo A
2008-04-01
Ecosystem engineers are organisms that change the distribution of materials and energy in the abiotic environment, usually creating and maintaining new habitat patches in the landscape. Such changes in habitat conditions have been widely documented to affect the distributions and performances of other species but up to now no studies have addressed how such effects can impact the biotically driven physicochemical processes associated with these landscapes, or ecosystem functions. Based on the widely accepted positive relationship between species diversity and ecosystem functions, we propose that the effects of ecosystem engineers on other species could have an impact on ecosystem functions via two mutually inclusive mechanisms: (1) by adding new species into landscapes, hence increasing species diversity; and (2) by improving the performances of species already present in the landscape. To test these hypotheses, we focused on the effects of a high-Andean ecosystem engineer, the cushion plant Azorella monantha, by comparing the accumulation of plant biomass and nitrogen fixed in plant tissues as species richness increases in landscapes with and without the engineer species. Our results show that both ecosystem functions increased with species richness in both landscape types, but landscapes including A. monantha cushions reached higher outcomes of plant biomass and nitrogen fixed in plant tissues than landscapes without cushions. Moreover, our results indicate that such positive effects on ecosystem functions could be mediated by the two mechanisms proposed above. Then, given the conspicuousness of ecosystem engineering in nature and its strong influence on species diversity, and given the well-known relationship between species diversity and ecosystem function, we suggest that the application of the conceptual framework proposed herein to other ecosystems would help to advance our understanding of the forces driving ecosystem functioning.
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NASA Astrophysics Data System (ADS)
Liu, Manqiang; Chen, Xiaoyun; Chen, Chenying; Hu, Zhengkun; Guo, Hui; Li, Junyong; Du, Guozhen; Li, Huixin; Hu, Feng
2017-04-01
Soil biota plays a pivotal role in ecosystem functionality which is of central importance to sustainable services such as food and fiber production. Intensive land use is associated with species loss and subsequent the related functionality loss. Currently, the claim that negligible effects of soil biodiversity loss due to high functional redundancy has been questioned in the face of intense human activities. Recent studies corroborated that soil biodiversity guaranteed functionality following perturbation. Few studies have, however, attempted to explore the intensive land use on the relationship between soil biodiversity and function particularly for the region susceptible to human perturbation and climate change. With increasing demands for livestock on the Qinghai-Tibetan Plateau, extensive fertilization is a common way to fill the gap of grass productivity in the alpine meadow. However, excess chemical fertilizer can lead to the species loss and functionality degradation. Do the fertilizer-induced changes in soil biota lead to a higher risk of functionality? We predicted that fertilization would exacerbate effects of biodiversity-loss on the reduction of functionality. Herein, a dilution-to-extinction approach was used to set up soil biodiversity loss by inoculating serially diluted soil suspension (ranging from 100 to 10-8 levels) from two long-term fertilization treatments to the sterilized soil that has never been fertilized. The two fertilization treatments represented two distinct intensification land use including the unfertilized control (NP0) and a fertilized treatment (NP120) amended with (NH4)2HPO4 annually (120 kg ha-1 yr-1) since 2002 in an alpine meadow on the eastern Qinghai-Tibetan Plateau. Soil microcosms of 2 fertilization levels crossing 8 biodiversity levels were incubated for 8 months. Then, soil community and multi-functionality parameters including carbon (C)and nutrient mineralization, plant growth and functional stability were determined. Dilution resulted in the increasing biodiversity loss indicated by genotypic information (high-throughput sequencing), phenotypic biomarkers (phospholipid fatty acid analysis) and functional profiles enzyme activities and sole C utilization potential). Notably, the decreasing genotypic diversity with dilution was most apparent among the three measured diversity traits, showing high phenotypic and functional redundancy. Fertilization decreased biodiversity, which was associated with the initial community properties. During the 8 months of incubation, the more diversity loss led to the less respired CO2 and correspondingly the more organic C remained in soil, supporting that biodiversity is central for the capability of resource utilization. Fertilization aggravated the decreased extent of C utilization potential particularly at lower biodiversity. Plant biomass and nutrient (nitrogen and phosphorus) uptake depended on the interactions of biodiversity loss and fertilization, showing fertilization-triggered more reductions of functionality with biodiversity loss, which was more related to the diversity and composition of phenotypic and functional profiles than molecular diversity. Out of our expectation, fertilization decreased the functional stability (measured as the decomposition of dead roots following transient heating stress) for high biodiversity treatments but increased it at lower biodiversity. Moreover, enzyme activity pattern indicated low biodiversity treatments were associated labile C transformation, while high biodiversity had high capability in utilizing recalcitrant C. We conclude that changes of community composition and biodiversity by intensive land use can increase the risk of losing diversity insurance on multifunctionality. Future work about the relationship between soil biodiversity and functionality should extrapolate to larger temporal and spatial scales. Exploring the response of fertilization-induced consequence to further biodiversity loss would contribute to understand the mechanisms of ecosystem process and sustainable manage the susceptible alpine meadow ecosystem. Keywords: Biodiversity-ecosystem function; Land-use intensification; Plant productivity; Alpine meadow; Functional diversity
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Mantovani, Alberto; Locati, Massimo
2013-07-01
Macrophages are present in all body compartments, including cancerous tissues, and their functions are profoundly affected by signals from the microenvironment under homeostatic and pathological conditions. Tumor-associated macrophages are a major cellular component of cancer-related inflammation and have served as a paradigm for the plasticity and functional polarization of mononuclear phagocytes. Tumor-associated macrophages can exert dual influence of cancer depending on the activation state, with classically activated (M1) and alternatively activated (M2) cells generally exerting antitumoral and protumoral functions, respectively. These are extremes in a continuum of polarization states in a universe of diversity. Tumor-associated macrophages affect virtually all aspects of tumor tissues, including stem cells, metabolism, angiogenesis, invasion, and metastasis. Progress has been made in defining signaling molecules, transcription factors, epigenetic changes, and repertoire of microRNAs underlying macrophage polarization. Preclinical and early clinical data suggest that macrophages may serve as tools for the development of innovative diagnostic and therapeutic strategies in cancer and chronic nonresolving inflammatory diseases.
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Parasitism and the biodiversity-functioning relationship
Frainer, André; McKie, Brendan G.; Amundsen, Per-Arne; Knudsen, Rune; Lafferty, Kevin D.
2018-01-01
Biodiversity affects ecosystem functioning.Biodiversity may decrease or increase parasitism.Parasites impair individual hosts and affect their role in the ecosystem.Parasitism, in common with competition, facilitation, and predation, could regulate BD-EF relationships.Parasitism affects host phenotypes, including changes to host morphology, behavior, and physiology, which might increase intra- and interspecific functional diversity.The effects of parasitism on host abundance and phenotypes, and on interactions between hosts and the remaining community, all have potential to alter community structure and BD-EF relationships.Global change could facilitate the spread of invasive parasites, and alter the existing dynamics between parasites, communities, and ecosystems.Species interactions can influence ecosystem functioning by enhancing or suppressing the activities of species that drive ecosystem processes, or by causing changes in biodiversity. However, one important class of species interactions – parasitism – has been little considered in biodiversity and ecosystem functioning (BD-EF) research. Parasites might increase or decrease ecosystem processes by reducing host abundance. Parasites could also increase trait diversity by suppressing dominant species or by increasing within-host trait diversity. These different mechanisms by which parasites might affect ecosystem function pose challenges in predicting their net effects. Nonetheless, given the ubiquity of parasites, we propose that parasite–host interactions should be incorporated into the BD-EF framework.
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Advanced nanomaterials–sustainable preparation and their catalytic applications
Sustainable nanomaterials have attracted great attention as highly functionalized nanocatalysts in diverse forms including solid-supported nanocatalysts, graphene materials, and core-shell catalysts among other nanostructures. Technology advancements in last decades have allowed ...
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USDA-ARS?s Scientific Manuscript database
Soil is a diverse natural material characterized by solid, liquid, and gas phases that impart unique chemical, physical, and biological properties. Soil provides many key functions, including supporting plant growth and providing environmental remediation. Monitoring key soil properties and processe...
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A functional genomics screen in planarians reveals regulators of whole-brain regeneration.
Roberts-Galbraith, Rachel H; Brubacher, John L; Newmark, Phillip A
2016-09-09
Planarians regenerate all body parts after injury, including the central nervous system (CNS). We capitalized on this distinctive trait and completed a gene expression-guided functional screen to identify factors that regulate diverse aspects of neural regeneration in Schmidtea mediterranea . Our screen revealed molecules that influence neural cell fates, support the formation of a major connective hub, and promote reestablishment of chemosensory behavior. We also identified genes that encode signaling molecules with roles in head regeneration, including some that are produced in a previously uncharacterized parenchymal population of cells. Finally, we explored genes downregulated during planarian regeneration and characterized, for the first time, glial cells in the planarian CNS that respond to injury by repressing several transcripts. Collectively, our studies revealed diverse molecules and cell types that underlie an animal's ability to regenerate its brain.
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The emerging complexity of ubiquitin architecture.
Ohtake, Fumiaki; Tsuchiya, Hikaru
2017-02-01
Ubiquitylation is an essential post-translational modification (PTM) of proteins with diverse cellular functions. Polyubiquitin chains with different topologies have different cellular roles, and are referred to as a 'ubiquitin code'. Recent studies have begun to reveal that more complex ubiquitin architectures function as important signals in several biological pathways. These include PTMs of ubiquitin itself, such as acetylated ubiquitin and phospho-ubiquitin. Moreover, important roles for heterogeneous polyubiquitin chains, such as mixed or branched chains, have been reported, which significantly increase the diversity of the ubiquitin code. In this review, we describe mass spectrometry-based methods to characterize the ubiquitin signal. We also describe recent advances in our understanding of complex ubiquitin architectures, including our own findings concerning ubiquitin acetylation and branching within polyubiquitin chains. © The Authors 2016. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.
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Zeglin, Lydia H.
2015-01-01
The importance of microbial activity to ecosystem function in aquatic ecosystems is well established, but microbial diversity has been less frequently addressed. This review and synthesis of 100s of published studies on stream microbial diversity shows that factors known to drive ecosystem processes, such as nutrient availability, hydrology, metal contamination, contrasting land-use and temperature, also cause heterogeneity in bacterial diversity. Temporal heterogeneity in stream bacterial diversity was frequently observed, reflecting the dynamic nature of both stream ecosystems and microbial community composition. However, within-stream spatial differences in stream bacterial diversity were more commonly observed, driven specifically by different organic matter (OM) compartments. Bacterial phyla showed similar patterns in relative abundance with regard to compartment type across different streams. For example, surface water contained the highest relative abundance of Actinobacteria, while epilithon contained the highest relative abundance of Cyanobacteria and Bacteroidetes. This suggests that contrasting physical and/or nutritional habitats characterized by different stream OM compartment types may select for certain bacterial lineages. When comparing the prevalence of physicochemical effects on stream bacterial diversity, effects of changing metal concentrations were most, while effects of differences in nutrient concentrations were least frequently observed. This may indicate that although changing nutrient concentrations do tend to affect microbial diversity, other environmental factors are more likely to alter stream microbial diversity and function. The common observation of connections between ecosystem process drivers and microbial diversity suggests that microbial taxonomic turnover could mediate ecosystem-scale responses to changing environmental conditions, including both microbial habitat distribution and physicochemical factors. PMID:26042102
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Gondo, Tatsuo; Ohno, Yoshio; Nakashima, Jun; Hashimoto, Takeshi; Nakagami, Yoshihiro; Tachibana, Masaaki
2017-02-01
To identify preoperative factors correlated with postoperative early renal function in patients who had undergone radical cystectomy (RC) and intestinal urinary diversion. We retrospectively identified 201 consecutive bladder cancer patients without distant metastasis who had undergone RC at our institution between 2003 and 2012. The estimated glomerular filtration rate (eGFR) was calculated using the modified Chronic Kidney Disease Epidemiology equation before RC and 3 months following RC. Univariate and stepwise multiple linear regression analyses were applied to estimate postoperative renal function and to identify significant preoperative predictors of postoperative renal function. Patients who had undergone intestinal urinary diversion and were available for the collection of follow-up data (n = 164) were eligible for the present study. Median preoperative and postoperative eGFRs were 69.7 (interquartile range [IQR] 56.3-78.0) and 70.7 (IQR 57.3-78.1), respectively. In univariate analyses, age, preoperative proteinuria, thickness of abdominal subcutaneous fat tissue (TSF), preoperative serum creatinine level, preoperative eGFR, and urinary diversion type were significantly associated with postoperative eGFR. In a stepwise multiple linear regression analysis, preoperative eGFR, age, and TSF were significant factors for predicting postoperative eGFR (p < 0.001, p = 0.02, and p = 0.046, respectively). The estimated postoperative eGFRs correlated well with the actual postoperative eGFRs (r = 0.65, p < 0.001). Preoperative eGFR, age, and TSF were independent preoperative factors for determining postoperative renal function in patients who had undergone RC and intestinal urinary diversion. These results may be used for patient counseling before surgery, including the planning of perioperative chemotherapy administration.
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Origin and functional diversification of an amphibian defense peptide arsenal.
Roelants, Kim; Fry, Bryan G; Ye, Lumeng; Stijlemans, Benoit; Brys, Lea; Kok, Philippe; Clynen, Elke; Schoofs, Liliane; Cornelis, Pierre; Bossuyt, Franky
2013-01-01
The skin secretion of many amphibians contains an arsenal of bioactive molecules, including hormone-like peptides (HLPs) acting as defense toxins against predators, and antimicrobial peptides (AMPs) providing protection against infectious microorganisms. Several amphibian taxa seem to have independently acquired the genes to produce skin-secreted peptide arsenals, but it remains unknown how these originated from a non-defensive ancestral gene and evolved diverse defense functions against predators and pathogens. We conducted transcriptome, genome, peptidome and phylogenetic analyses to chart the full gene repertoire underlying the defense peptide arsenal of the frog Silurana tropicalis and reconstruct its evolutionary history. Our study uncovers a cluster of 13 transcriptionally active genes, together encoding up to 19 peptides, including diverse HLP homologues and AMPs. This gene cluster arose from a duplicated gastrointestinal hormone gene that attained a HLP-like defense function after major remodeling of its promoter region. Instead, new defense functions, including antimicrobial activity, arose by mutation of the precursor proteins, resulting in the proteolytic processing of secondary peptides alongside the original ones. Although gene duplication did not trigger functional innovation, it may have subsequently facilitated the convergent loss of the original function in multiple gene lineages (subfunctionalization), completing their transformation from HLP gene to AMP gene. The processing of multiple peptides from a single precursor entails a mechanism through which peptide-encoding genes may establish new functions without the need for gene duplication to avoid adaptive conflicts with older ones.
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Origin and Functional Diversification of an Amphibian Defense Peptide Arsenal
Roelants, Kim; Fry, Bryan G.; Ye, Lumeng; Stijlemans, Benoit; Brys, Lea; Kok, Philippe; Clynen, Elke; Schoofs, Liliane; Cornelis, Pierre; Bossuyt, Franky
2013-01-01
The skin secretion of many amphibians contains an arsenal of bioactive molecules, including hormone-like peptides (HLPs) acting as defense toxins against predators, and antimicrobial peptides (AMPs) providing protection against infectious microorganisms. Several amphibian taxa seem to have independently acquired the genes to produce skin-secreted peptide arsenals, but it remains unknown how these originated from a non-defensive ancestral gene and evolved diverse defense functions against predators and pathogens. We conducted transcriptome, genome, peptidome and phylogenetic analyses to chart the full gene repertoire underlying the defense peptide arsenal of the frog Silurana tropicalis and reconstruct its evolutionary history. Our study uncovers a cluster of 13 transcriptionally active genes, together encoding up to 19 peptides, including diverse HLP homologues and AMPs. This gene cluster arose from a duplicated gastrointestinal hormone gene that attained a HLP-like defense function after major remodeling of its promoter region. Instead, new defense functions, including antimicrobial activity, arose by mutation of the precursor proteins, resulting in the proteolytic processing of secondary peptides alongside the original ones. Although gene duplication did not trigger functional innovation, it may have subsequently facilitated the convergent loss of the original function in multiple gene lineages (subfunctionalization), completing their transformation from HLP gene to AMP gene. The processing of multiple peptides from a single precursor entails a mechanism through which peptide-encoding genes may establish new functions without the need for gene duplication to avoid adaptive conflicts with older ones. PMID:23935531
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Global biogeography of Prochlorococcus genome diversity in the surface ocean.
Kent, Alyssa G; Dupont, Chris L; Yooseph, Shibu; Martiny, Adam C
2016-08-01
Prochlorococcus, the smallest known photosynthetic bacterium, is abundant in the ocean's surface layer despite large variation in environmental conditions. There are several genetically divergent lineages within Prochlorococcus and superimposed on this phylogenetic diversity is extensive gene gain and loss. The environmental role in shaping the global ocean distribution of genome diversity in Prochlorococcus is largely unknown, particularly in a framework that considers the vertical and lateral mechanisms of evolution. Here we show that Prochlorococcus field populations from a global circumnavigation harbor extensive genome diversity across the surface ocean, but this diversity is not randomly distributed. We observed a significant correspondence between phylogenetic and gene content diversity, including regional differences in both phylogenetic composition and gene content that were related to environmental factors. Several gene families were strongly associated with specific regions and environmental factors, including the identification of a set of genes related to lower nutrient and temperature regions. Metagenomic assemblies of natural Prochlorococcus genomes reinforced this association by providing linkage of genes across genomic backbones. Overall, our results show that the phylogeography in Prochlorococcus taxonomy is echoed in its genome content. Thus environmental variation shapes the functional capabilities and associated ecosystem role of the globally abundant Prochlorococcus.
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Solis-Gabriel, Lizet; Mendoza-Arroyo, Wendy; Boege, Karina; Del-Val, Ek
2017-01-01
Tropical dry forests (TDFs) have been widely transformed by human activities worldwide and the ecosystem services they provide are diminishing. There has been an urgent call for conservation and restoration of the degraded lands previously occupied by TDFs. Restoration experiences aim to recover species diversity and ecological functions. Different restoration strategies have been used to maximize plant performance including weeding, planting or using artificial mulching. In this investigation, we evaluated whether different restoration practices influence animal arrival and the reestablishment of biotic interactions. We particularly evaluated lepidopteran larvae diversity and caterpillar predation on plants established under different restoration treatments (mulching, weeding and control) in the Pacific West Coast of México. This study corroborated the importance of plant host identity for lepidopteran presence in a particular area. Lepidopteran diversity and herbivory rates were not affected by the restoration treatment but they were related to tree species. In contrast, caterpillar predation marks were affected by restoration treatment, with a greater number of predation marks in control plots, while caterpillar predation marks among plant species were not significantly different. This study highlights the importance of considering the introduction of high plant species diversity when planning TDF restoration to maximize lepidopteran diversity and ecosystem functioning.
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Solis-Gabriel, Lizet; Mendoza-Arroyo, Wendy
2017-01-01
Tropical dry forests (TDFs) have been widely transformed by human activities worldwide and the ecosystem services they provide are diminishing. There has been an urgent call for conservation and restoration of the degraded lands previously occupied by TDFs. Restoration experiences aim to recover species diversity and ecological functions. Different restoration strategies have been used to maximize plant performance including weeding, planting or using artificial mulching. In this investigation, we evaluated whether different restoration practices influence animal arrival and the reestablishment of biotic interactions. We particularly evaluated lepidopteran larvae diversity and caterpillar predation on plants established under different restoration treatments (mulching, weeding and control) in the Pacific West Coast of México. This study corroborated the importance of plant host identity for lepidopteran presence in a particular area. Lepidopteran diversity and herbivory rates were not affected by the restoration treatment but they were related to tree species. In contrast, caterpillar predation marks were affected by restoration treatment, with a greater number of predation marks in control plots, while caterpillar predation marks among plant species were not significantly different. This study highlights the importance of considering the introduction of high plant species diversity when planning TDF restoration to maximize lepidopteran diversity and ecosystem functioning. PMID:28560101
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Mass Transport: Circulatory System with Emphasis on Nonendothermic Species.
Crossley, Dane A; Burggren, Warren W; Reiber, Carl L; Altimiras, Jordi; Rodnick, Kenneth J
2016-12-06
Mass transport can be generally defined as movement of material matter. The circulatory system then is a biological example given its role in the movement in transporting gases, nutrients, wastes, and chemical signals. Comparative physiology has a long history of providing new insights and advancing our understanding of circulatory mass transport across a wide array of circulatory systems. Here we focus on circulatory function of nonmodel species. Invertebrates possess diverse convection systems; that at the most complex generate pressures and perform at a level comparable to vertebrates. Many invertebrates actively modulate cardiovascular function using neuronal, neurohormonal, and skeletal muscle activity. In vertebrates, our understanding of cardiac morphology, cardiomyocyte function, and contractile protein regulation by Ca2+ highlights a high degree of conservation, but differences between species exist and are coupled to variable environments and body temperatures. Key regulators of vertebrate cardiac function and systemic blood pressure include the autonomic nervous system, hormones, and ventricular filling. Further chemical factors regulating cardiovascular function include adenosine, natriuretic peptides, arginine vasotocin, endothelin 1, bradykinin, histamine, nitric oxide, and hydrogen sulfide, to name but a few. Diverse vascular morphologies and the regulation of blood flow in the coronary and cerebral circulations are also apparent in nonmammalian species. Dynamic adjustments of cardiovascular function are associated with exercise on land, flying at high altitude, prolonged dives by marine mammals, and unique morphology, such as the giraffe. Future studies should address limits of gas exchange and convective transport, the evolution of high arterial pressure across diverse taxa, and the importance of the cardiovascular system adaptations to extreme environments. © 2017 American Physiological Society. Compr Physiol 7:17-66, 2017. Copyright © 2017 John Wiley & Sons, Inc.
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Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages
Aguirre, Luis F.; Montaño-Centellas, Flavia A.; Gavilanez, M. Mercedes; Stevens, Richard D.
2016-01-01
Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups). Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement) was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia) create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for patterns of functional diversity, highlighting the need for examining different dimensions of biodiversity of bats in hyperdiverse ecosystems. PMID:27384441
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Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages.
Aguirre, Luis F; Montaño-Centellas, Flavia A; Gavilanez, M Mercedes; Stevens, Richard D
2016-01-01
Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups). Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement) was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia) create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for patterns of functional diversity, highlighting the need for examining different dimensions of biodiversity of bats in hyperdiverse ecosystems.
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Functional Diversity of Fungal Communities in Soil Contaminated with Diesel Oil.
Borowik, Agata; Wyszkowska, Jadwiga; Oszust, Karolina
2017-01-01
The widespread use and consumption of crude oil draws the public's attention to the fate of petroleum hydrocarbons in the environment, as they can permeate the soil environment in an uncontrollable manner. Contamination of soils with petroleum products, including diesel oil (DO), can cause changes in the microbiological soil properties. The effect of diesel oil on the functional diversity of fungi was tested in a model experiment during 270 days. Fungi were isolated from soil and identified. The functional diversity of fungal communities was also determined. Fungi were identified with the MALDI-TOF method, while the functional diversity was determined using FF-plates made by Biolog ® , with 95 carbon sources. Moreover, the diesel oil degradation dynamics was assessed. The research showed that soil contaminated with diesel oil is characterized by a higher activity of oxireductases and a higher number of fungi than soil not exposed to the pressure of this product. The DO pollution has an adverse effect on the diversity of fungal community. This is proved by significantly lower values of the Average Well-Color Development, substrates Richness (R) and Shannon-Weaver (H) indices at day 270 after contamination. The consequences of DO affecting soil not submitted to remediation are persistent. After 270 days, only 64% of four-ringed, 28% of five-ringed, 21% of 2-3-ringed and 16% of six-ringed PAHs underwent degradation. The lasting effect of DO on communities of fungi led to a decrease in their functional diversity. The assessment of the response of fungi to DO pollution made on the basis of the development of colonies on Petri dishes [Colony Development (CD) and Eco-physiological Diversity (EP) indices] is consistent with the analysis based on the FF MicroPlate system by Biolog ® . Thus, a combination of the FF MicroPlate system by Biolog ® with the simultaneous calculation of CD and EP indices alongside the concurrent determination of the content of PAHs and activity of oxireductases provides an opportunity to achieve relatively complete characterization of the consequences of a long-term impact of diesel oil on soil fungi.
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Functional Diversity of Fungal Communities in Soil Contaminated with Diesel Oil
Borowik, Agata; Wyszkowska, Jadwiga; Oszust, Karolina
2017-01-01
The widespread use and consumption of crude oil draws the public’s attention to the fate of petroleum hydrocarbons in the environment, as they can permeate the soil environment in an uncontrollable manner. Contamination of soils with petroleum products, including diesel oil (DO), can cause changes in the microbiological soil properties. The effect of diesel oil on the functional diversity of fungi was tested in a model experiment during 270 days. Fungi were isolated from soil and identified. The functional diversity of fungal communities was also determined. Fungi were identified with the MALDI-TOF method, while the functional diversity was determined using FF-plates made by Biolog®, with 95 carbon sources. Moreover, the diesel oil degradation dynamics was assessed. The research showed that soil contaminated with diesel oil is characterized by a higher activity of oxireductases and a higher number of fungi than soil not exposed to the pressure of this product. The DO pollution has an adverse effect on the diversity of fungal community. This is proved by significantly lower values of the Average Well-Color Development, substrates Richness (R) and Shannon–Weaver (H) indices at day 270 after contamination. The consequences of DO affecting soil not submitted to remediation are persistent. After 270 days, only 64% of four-ringed, 28% of five-ringed, 21% of 2–3-ringed and 16% of six-ringed PAHs underwent degradation. The lasting effect of DO on communities of fungi led to a decrease in their functional diversity. The assessment of the response of fungi to DO pollution made on the basis of the development of colonies on Petri dishes [Colony Development (CD) and Eco-physiological Diversity (EP) indices] is consistent with the analysis based on the FF MicroPlate system by Biolog®. Thus, a combination of the FF MicroPlate system by Biolog® with the simultaneous calculation of CD and EP indices alongside the concurrent determination of the content of PAHs and activity of oxireductases provides an opportunity to achieve relatively complete characterization of the consequences of a long-term impact of diesel oil on soil fungi. PMID:29021782
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Contrasting responses of functional diversity to major losses in taxonomic diversity.
Edie, Stewart M; Jablonski, David; Valentine, James W
2018-01-23
Taxonomic diversity of benthic marine invertebrate shelf species declines at present by nearly an order of magnitude from the tropics to the poles in each hemisphere along the latitudinal diversity gradient (LDG), most steeply along the western Pacific where shallow-sea diversity is at its tropical maximum. In the Bivalvia, a model system for macroevolution and macroecology, this taxonomic trend is accompanied by a decline in the number of functional groups and an increase in the evenness of taxa distributed among those groups, with maximum functional evenness (FE) in polar waters of both hemispheres. In contrast, analyses of this model system across the two era-defining events of the Phanerozoic, the Permian-Triassic and Cretaceous-Paleogene mass extinctions, show only minor declines in functional richness despite high extinction intensities, resulting in a rise in FE owing to the persistence of functional groups. We hypothesize that the spatial decline of taxonomic diversity and increase in FE along the present-day LDG primarily reflect diversity-dependent factors, whereas retention of almost all functional groups through the two mass extinctions suggests the operation of diversity-independent factors. Comparative analyses of different aspects of biodiversity thus reveal strongly contrasting biological consequences of similarly severe declines in taxonomic diversity and can help predict the consequences for functional diversity among different drivers of past, present, and future biodiversity loss.
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The many blades of the β-propeller proteins: conserved but versatile.
Chen, Cammy K-M; Chan, Nei-Li; Wang, Andrew H-J
2011-10-01
The β-propeller is a highly symmetrical structure with 4-10 repeats of a four-stranded antiparallel β-sheet motif. Although β-propeller proteins with different blade numbers all adopt disc-like shapes, they are involved in a diverse set of functions, and defects in this family of proteins have been associated with human diseases. However, it has remained ambiguous how variations in blade number could alter the function of β-propellers. In addition to the regularly arranged β-propeller topology, a recently discovered β-pinwheel propeller has been found. Here, we review the structural and functional diversity of β-propeller proteins, including β-pinwheels, as well as recent advances in the typical and atypical propeller structures. Copyright © 2011 Elsevier Ltd. All rights reserved.
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2016-04-01
compared to 50 healthy veteran controls in a protocol that includes physical and neuropsychological evaluations, neuroimaging (MRI, fMRI, DTI), adrenal...SUBJECT TERMS Gulf War illness, neuroimaging, neuropsychological testing, immune function, hypothalamic-pituitary-adrenal testing 16. SECURITY... neuropsychological evaluations, assessment of hypothalamic-pituitary-adrenal function, standard clinical diagnostic laboratory tests, and research
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Liujing Huang; Hongfeng Chen; Hai Ren; Jun Wang; Qinfeng Guo
2013-01-01
We investigated the effects of major environmental drivers associated with urbanization on species diversity and plant functional traits (PFTs) in the remnant subtropical evergreen broad-leaved forests in Metropolitan Guangzhou (Guangdong, China). Twenty environmental factors including topography, light, and soil properties were used to quantify the effects of...
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Eosinophils in mucosal immune responses
Travers, J; Rothenberg, M E
2015-01-01
Eosinophils, multifunctional cells that contribute to both innate and adaptive immunity, are involved in the initiation, propagation and resolution of immune responses, including tissue repair. They achieve this multifunctionality by expression of a diverse set of activation receptors, including those that directly recognize pathogens and opsonized targets, and by their ability to store and release preformed cytotoxic mediators that participate in host defense, to produce a variety of de novo pleotropic mediators and cytokines and to interact directly and indirectly with diverse cell types, including adaptive and innate immunocytes and structural cells. Herein, we review the basic biology of eosinophils and then focus on new emerging concepts about their role in mucosal immune homeostasis, particularly maintenance of intestinal IgA. We review emerging data about their development and regulation and describe new concepts concerning mucosal eosinophilic diseases. We describe recently developed therapeutic strategies to modify eosinophil levels and function and provide collective insight about the beneficial and detrimental functions of these enigmatic cells. PMID:25807184
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Mori, Akira S; Ota, Aino T; Fujii, Saori; Seino, Tatsuyuki; Kabeya, Daisuke; Okamoto, Toru; Ito, Masamichi T; Kaneko, Nobuhiro; Hasegawa, Motohiro
2015-10-01
The compositional characteristics of ecological assemblages are often simplified; this process is termed "biotic homogenization." This process of biological reorganization occurs not only taxonomically but also functionally. Testing both aspects of homogenization is essential if ecosystem functioning supported by a diverse mosaic of functional traits in the landscape is concerned. Here, we aimed to infer the underlying processes of taxonomic/functional homogenization at the local scale, which is a scale that is meaningful for this research question. We recorded species of litter-dwelling oribatid mites along a gradient of forest conversion from a natural forest to a monoculture larch plantation in Japan (in total 11 stands), and collected data on the functional traits of the recorded species to quantify functional diversity. We calculated the taxonomic and functional β-diversity, an index of biotic homogenization. We found that both the taxonomic and functional β-diversity decreased with larch dominance (stand homogenization). After further deconstructing β-diversity into the components of turnover and nestedness, which reflect different processes of community organization, a significant decrease in the response to larch dominance was observed only for the functional turnover. As a result, there was a steeper decline in the functional β-diversity than the taxonomic β-diversity. This discordance between the taxonomic and functional response suggests that species replacement occurs between species that are functionally redundant under environmental homogenization, ultimately leading to the stronger homogenization of functional diversity. The insights gained from community organization of oribatid mites suggest that the functional characteristics of local assemblages, which support the functionality of ecosystems, are of more concern in human-dominated forest landscapes.
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Shen, Congcong; Shi, Yu; Ni, Yingying; Deng, Ye; Van Nostrand, Joy D; He, Zhili; Zhou, Jizhong; Chu, Haiyan
2016-01-01
The elevational and latitudinal diversity patterns of microbial taxa have attracted great attention in the past decade. Recently, the distribution of functional attributes has been in the spotlight. Here, we report a study profiling soil microbial communities along an elevation gradient (500-2200 m) on Changbai Mountain. Using a comprehensive functional gene microarray (GeoChip 5.0), we found that microbial functional gene richness exhibited a dramatic increase at the treeline ecotone, but the bacterial taxonomic and phylogenetic diversity based on 16S rRNA gene sequencing did not exhibit such a similar trend. However, the β-diversity (compositional dissimilarity among sites) pattern for both bacterial taxa and functional genes was similar, showing significant elevational distance-decay patterns which presented increased dissimilarity with elevation. The bacterial taxonomic diversity/structure was strongly influenced by soil pH, while the functional gene diversity/structure was significantly correlated with soil dissolved organic carbon (DOC). This finding highlights that soil DOC may be a good predictor in determining the elevational distribution of microbial functional genes. The finding of significant shifts in functional gene diversity at the treeline ecotone could also provide valuable information for predicting the responses of microbial functions to climate change.
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Seeleuthner, Yoann; Mondy, Samuel; Lombard, Vincent; Carradec, Quentin; Pelletier, Eric; Wessner, Marc; Leconte, Jade; Mangot, Jean-François; Poulain, Julie; Labadie, Karine; Logares, Ramiro; Sunagawa, Shinichi; de Berardinis, Véronique; Salanoubat, Marcel; Dimier, Céline; Kandels-Lewis, Stefanie; Picheral, Marc; Searson, Sarah; Pesant, Stephane; Poulton, Nicole; Stepanauskas, Ramunas; Bork, Peer; Bowler, Chris; Hingamp, Pascal; Sullivan, Matthew B; Iudicone, Daniele; Massana, Ramon; Aury, Jean-Marc; Henrissat, Bernard; Karsenti, Eric; Jaillon, Olivier; Sieracki, Mike; de Vargas, Colomban; Wincker, Patrick
2018-01-22
Single-celled eukaryotes (protists) are critical players in global biogeochemical cycling of nutrients and energy in the oceans. While their roles as primary producers and grazers are well appreciated, other aspects of their life histories remain obscure due to challenges in culturing and sequencing their natural diversity. Here, we exploit single-cell genomics and metagenomics data from the circumglobal Tara Oceans expedition to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles. Based on the available data, each sequenced genome or genotype appears to have a specific oceanic distribution, principally correlated with water temperature and depth. The genome content provides hypotheses for specialization in terms of cell motility, food spectra, and trophic stages, including the potential impact on their lifestyles of horizontal gene transfer from prokaryotes. Our results support the idea that prominent heterotrophic marine protists perform diverse functions in ocean ecology.
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Metagenomics for mining new genetic resources of microbial communities.
Ferrer, Manuel; Beloqui, Ana; Timmis, Kenneth N; Golyshin, Peter N
2009-01-01
Recent progress has revealed that the capture of genetic resources of complex microbial communities in metagenome libraries allows the discovery of a richness of new enzymatic diversity that had not previously been imagined. Activity-based screening of such libraries has demonstrated that this new diversity is not simply variations on known sequence themes, but rather the existence of entirely new sequence classes and novel functionalities. This new diversity, the surface of which has thus far only been scratched, constitutes potential for a wealth of new and improved applications in industry, medicine, agriculture, etc., and promises to facilitate in a significant manner our transition to a sustainable society, by contributing to the transition to renewable sources of energy, chemicals and materials, the lowering of pollutant burdens, lower processes energies, etc. Current bottlenecks in metagenomics include insufficient functional characterization and amplifying non-validated annotations of proteins in databases. Copyright (c) 2008 S. Karger AG, Basel.
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Rychtecká, Terezie; Lanta, Vojtěch; Weiterová, Iva; Lepš, Jan
2014-08-01
Biodiversity-ecosystem functioning experiments (BEF) typically manipulate sown species richness and composition of experimental communities to study ecosystem functioning as a response to changes in diversity. If sown species richness is taken as a measure of diversity and aboveground biomass production as a measure of community functioning, then this relationship is usually found to be positive. The sown species richness can be considered the equivalent of a local species pool in natural communities. However, in addition to species richness, realized diversity is also an important community diversity component. Realized diversity is affected by environmental filtering and biotic interactions operating within a community. As both sown species richness and the realized diversity in BEF studies (as well as local species pool vs observed realized richness in natural communities) can differ markedly, so can their effects on the community functioning. We tested this assumption using two data sets: data from a short-term pot experiment and data from the long-term Jena biodiversity plot experiment. We considered three possible predictors of community functioning (aboveground biomass production): sown species richness, realized diversity (defined as inverse of Simpson dominance index), and survivor species richness. Sown species richness affected biomass production positively in all cases. Realized diversity as well as survivor species richness had positive effects on biomass in approximately half of cases. When realized diversity or survivor species richness was tested together with sown species richness, their partial effects were none or negative. Our results suggest that we can expect positive diversity-productivity relationship when the local species pool size is the decisive factor determining realized observed diversity; in other cases, the shape of the diversity-functioning relationship may be quite opposite.
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The Yin and Yang of YY1 in the nervous system
He, Ye; Casaccia-Bonnefil, Patrizia
2008-01-01
The transcription factor Yin Yang 1 (YY1) is a multifunctional protein that can activate or repress gene expression depending on the cellular context. YY1 is ubiquitously expressed and highly conserved between species. However its role varies in diverse cell types and includes proliferation, differentiation and apoptosis. This review will focus on the function of YY1 in the nervous system including its role in neural development, neuronal function, developmental myelination and neurological disease. The multiple functions of YY1 in distinct cell types are reviewed and the possible mechanisms underlying the cell specificity for these functions are discussed. PMID:18485096
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Wei, Sean T S; Lacap-Bugler, Donnabella C; Lau, Maggie C Y; Caruso, Tancredi; Rao, Subramanya; de Los Rios, Asunción; Archer, Stephen K; Chiu, Jill M Y; Higgins, Colleen; Van Nostrand, Joy D; Zhou, Jizhong; Hopkins, David W; Pointing, Stephen B
2016-01-01
The McMurdo Dry Valleys of Antarctica are an extreme polar desert. Mineral soils support subsurface microbial communities and translucent rocks support development of hypolithic communities on ventral surfaces in soil contact. Despite significant research attention, relatively little is known about taxonomic and functional diversity or their inter-relationships. Here we report a combined diversity and functional interrogation for soil and hypoliths of the Miers Valley in the McMurdo Dry Valleys of Antarctica. The study employed 16S rRNA fingerprinting and high throughput sequencing combined with the GeoChip functional microarray. The soil community was revealed as a highly diverse reservoir of bacterial diversity dominated by actinobacteria. Hypolithic communities were less diverse and dominated by cyanobacteria. Major differences in putative functionality were that soil communities displayed greater diversity in stress tolerance and recalcitrant substrate utilization pathways, whilst hypolithic communities supported greater diversity of nutrient limitation adaptation pathways. A relatively high level of functional redundancy in both soil and hypoliths may indicate adaptation of these communities to fluctuating environmental conditions.
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CRISPR-Cas Adaptive Immune Systems of the Sulfolobales: Unravelling Their Complexity and Diversity
Garrett, Roger A.; Shah, Shiraz A.; Erdmann, Susanne; Liu, Guannan; Mousaei, Marzieh; León-Sobrino, Carlos; Peng, Wenfang; Gudbergsdottir, Soley; Deng, Ling; Vestergaard, Gisle; Peng, Xu; She, Qunxin
2015-01-01
The Sulfolobales have provided good model organisms for studying CRISPR-Cas systems of the crenarchaeal kingdom of the archaea. These organisms are infected by a wide range of exceptional archaea-specific viruses and conjugative plasmids, and their CRISPR-Cas systems generally exhibit extensive structural and functional diversity. They carry large and multiple CRISPR loci and often multiple copies of diverse Type I and Type III interference modules as well as more homogeneous adaptation modules. These acidothermophilic organisms have recently provided seminal insights into both the adaptation process, the diverse modes of interference, and their modes of regulation. The functions of the adaptation and interference modules tend to be loosely coupled and the stringency of the crRNA-DNA sequence matching during DNA interference is relatively low, in contrast to some more streamlined CRISPR-Cas systems of bacteria. Despite this, there is evidence for a complex and differential regulation of expression of the diverse functional modules in response to viral infection. Recent work also supports critical roles for non-core Cas proteins, especially during Type III-directed interference, and this is consistent with these proteins tending to coevolve with core Cas proteins. Various novel aspects of CRISPR-Cas systems of the Sulfolobales are considered including an alternative spacer acquisition mechanism, reversible spacer acquisition, the formation and significance of antisense CRISPR RNAs, and a novel mechanism for avoidance of CRISPR-Cas defense. Finally, questions regarding the basis for the complexity, diversity, and apparent redundancy, of the intracellular CRISPR-Cas systems are discussed. PMID:25764276
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Bryant, Jessica A; Stewart, Frank J; Eppley, John M; DeLong, Edward F
2012-07-01
Oxygen minimum zones (OMZs) are natural physical features of the world's oceans. They create steep physiochemical gradients in the water column, which most notably include a dramatic draw down in oxygen concentrations over small vertical distances (<100 m). Microbial communities within OMZs play central roles in ocean and global biogeochemical cycles, yet we still lack a fundamental understanding of how microbial biodiversity is distributed across OMZs. Here, we used metagenomic sequencing to investigate microbial diversity across a vertical gradient in the water column during three seasons in the Eastern Tropical South Pacific (ETSP) OMZ. Based on analysis of small subunit ribosomal RNA (SSU rRNA) gene fragments, we found that both taxonomic and phylogenetic diversity declined steeply along the transition from oxygen-rich surface water to the permanent OMZ. We observed similar declines in the diversity of protein-coding gene categories, suggesting a decrease in functional (trait) diversity with depth. Metrics of functional and trait dispersion indicated that microbial communities are phylogenetically and functionally more overdispersed in oxic waters, but clustered within the OMZ. These dispersion patterns suggest that community assembly drivers (e.g., competition, environmental filtering) vary strikingly across the oxygen gradient. To understand the generality of our findings, we compared OMZ results to two marine depth gradients in subtropical oligotrophic sites and found that the oligotrophic sites did not display similar patterns, likely reflecting unique features found in the OMZ. Finally, we discuss how our results may relate to niche theory, diversity-energy relationships and stress gradients.
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Sex in the brain: hormones and sex differences.
Marrocco, Jordan; McEwen, Bruce S
2016-12-01
Contrary to popular belief, sex hormones act throughout the entire brain of both males and females via both genomic and nongenomic receptors. Many neural and behavioral functions are affected by estrogens, including mood, cognitive function, blood pressure regulation, motor coordination, pain, and opioid sensitivity. Subtle sex differences exist for many of these functions that are developmentally programmed by hormones and by not yet precisely defined genetic factors, including the mitochondrial genome. These sex differences, and responses to sex hormones in brain regions and upon functions not previously regarded as subject to such differences, indicate that we are entering a new era in our ability to understand and appreciate the diversity of gender-related behaviors and brain functions.
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Algorithms for Learning Preferences for Sets of Objects
NASA Technical Reports Server (NTRS)
Wagstaff, Kiri L.; desJardins, Marie; Eaton, Eric
2010-01-01
A method is being developed that provides for an artificial-intelligence system to learn a user's preferences for sets of objects and to thereafter automatically select subsets of objects according to those preferences. The method was originally intended to enable automated selection, from among large sets of images acquired by instruments aboard spacecraft, of image subsets considered to be scientifically valuable enough to justify use of limited communication resources for transmission to Earth. The method is also applicable to other sets of objects: examples of sets of objects considered in the development of the method include food menus, radio-station music playlists, and assortments of colored blocks for creating mosaics. The method does not require the user to perform the often-difficult task of quantitatively specifying preferences; instead, the user provides examples of preferred sets of objects. This method goes beyond related prior artificial-intelligence methods for learning which individual items are preferred by the user: this method supports a concept of setbased preferences, which include not only preferences for individual items but also preferences regarding types and degrees of diversity of items in a set. Consideration of diversity in this method involves recognition that members of a set may interact with each other in the sense that when considered together, they may be regarded as being complementary, redundant, or incompatible to various degrees. The effects of such interactions are loosely summarized in the term portfolio effect. The learning method relies on a preference representation language, denoted DD-PREF, to express set-based preferences. In DD-PREF, a preference is represented by a tuple that includes quality (depth) functions to estimate how desired a specific value is, weights for each feature preference, the desired diversity of feature values, and the relative importance of diversity versus depth. The system applies statistical concepts to estimate quantitative measures of the user s preferences from training examples (preferred subsets) specified by the user. Once preferences have been learned, the system uses those preferences to select preferred subsets from new sets. The method was found to be viable when tested in computational experiments on menus, music playlists, and rover images. Contemplated future development efforts include further tests on more diverse sets and development of a sub-method for (a) estimating the parameter that represents the relative importance of diversity versus depth, and (b) incorporating background knowledge about the nature of quality functions, which are special functions that specify depth preferences for features.
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Discovery and Characterization of Chromatin States for Systematic Annotation of the Human Genome
NASA Astrophysics Data System (ADS)
Ernst, Jason; Kellis, Manolis
A plethora of epigenetic modifications have been described in the human genome and shown to play diverse roles in gene regulation, cellular differentiation and the onset of disease. Although individual modifications have been linked to the activity levels of various genetic functional elements, their combinatorial patterns are still unresolved and their potential for systematic de novo genome annotation remains untapped. Here, we use a multivariate Hidden Markov Model to reveal chromatin states in human T cells, based on recurrent and spatially coherent combinations of chromatin marks.We define 51 distinct chromatin states, including promoter-associated, transcription-associated, active intergenic, largescale repressed and repeat-associated states. Each chromatin state shows specific enrichments in functional annotations, sequence motifs and specific experimentally observed characteristics, suggesting distinct biological roles. This approach provides a complementary functional annotation of the human genome that reveals the genome-wide locations of diverse classes of epigenetic function.
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Neuroscience and the fallacies of functionalism.
Reddy, William M
2010-01-01
Smail's "On Deep History and the Brain" is rightly critical of the functionalist fallacies that have plagued evolutionary theory, sociobiology, and evolutionary psychology. However, his attempt to improve on these efforts relies on functional explanations that themselves oversimplify the lessons of neuroscience. In addition, like explanations in evolutionary psychology, they are highly speculative and cannot be confirmed or disproved by evidence. Neuroscience research is too diverse to yield a single picture of brain functioning. Some recent developments in neuroscience research, however, do suggest that cognitive processing provides a kind of “operating system” that can support a great diversity of cultural material. These developments include evidence of “top-down” processing in motor control, in visual processing, in speech recognition, and in “emotion regulation.” The constraints that such a system may place on cultural learning and transmission are worth investigating. At the same time, historians are well advised to remain wary of the pitfalls of functionalism.
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Regulation of Tissue Growth by the Mammalian Hippo Signaling Pathway
Watt, Kevin I.; Harvey, Kieran F.; Gregorevic, Paul
2017-01-01
The integrative control of diverse biological processes such as proliferation, differentiation, apoptosis and metabolism is essential to maintain cellular and tissue homeostasis. Disruption of these underlie the development of many disease states including cancer and diabetes, as well as many of the complications that arise as a consequence of aging. These biological outputs are governed by many cellular signaling networks that function independently, and in concert, to convert changes in hormonal, mechanical and metabolic stimuli into alterations in gene expression. First identified in Drosophila melanogaster as a powerful mediator of cell division and apoptosis, the Hippo signaling pathway is a highly conserved regulator of mammalian organ size and functional capacity in both healthy and diseased tissues. Recent studies have implicated the pathway as an effector of diverse physiological cues demonstrating an essential role for the Hippo pathway as an integrative component of cellular homeostasis. In this review, we will: (a) outline the critical signaling elements that constitute the mammalian Hippo pathway, and how they function to regulate Hippo pathway-dependent gene expression and tissue growth, (b) discuss evidence that shows this pathway functions as an effector of diverse physiological stimuli and (c) highlight key questions in this developing field. PMID:29225579
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Heinz, Eva; Lithgow, Trevor
2014-01-01
Members of the Omp85/TpsB protein superfamily are ubiquitously distributed in Gram-negative bacteria, and function in protein translocation (e.g., FhaC) or the assembly of outer membrane proteins (e.g., BamA). Several recent findings are suggestive of a further level of variation in the superfamily, including the identification of the novel membrane protein assembly factor TamA and protein translocase PlpD. To investigate the diversity and the causal evolutionary events, we undertook a comprehensive comparative sequence analysis of the Omp85/TpsB proteins. A total of 10 protein subfamilies were apparent, distinguished in their domain structure and sequence signatures. In addition to the proteins FhaC, BamA, and TamA, for which structural and functional information is available, are families of proteins with so far undescribed domain architectures linked to the Omp85 β-barrel domain. This study brings a classification structure to a dynamic protein superfamily of high interest given its essential function for Gram-negative bacteria as well as its diverse domain architecture, and we discuss several scenarios of putative functions of these so far undescribed proteins. PMID:25101071
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Using Signature Genes as Tools To Assess Environmental Viral Ecology and Diversity
Adriaenssens, Evelien M.
2014-01-01
Viruses (including bacteriophages) are the most abundant biological entities on the planet. As such, they are thought to have a major impact on all aspects of microbial community structure and function. Despite this critical role in ecosystem processes, the study of virus/phage diversity has lagged far behind parallel studies of the bacterial and eukaryotic kingdoms, largely due to the absence of any universal phylogenetic marker. Here we review the development and use of signature genes to investigate viral diversity, as a viable strategy for data sets of specific virus groups. Genes that have been used include those encoding structural proteins, such as portal protein, major capsid protein, and tail sheath protein, auxiliary metabolism genes, such as psbA, psbB, and phoH, and several polymerase genes. These marker genes have been used in combination with PCR-based fingerprinting and/or sequencing strategies to investigate spatial, temporal, and seasonal variations and diversity in a wide range of habitats. PMID:24837394
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Villéger, Sébastien; Ramos Miranda, Julia; Flores Hernández, Domingo; Mouillot, David
2010-09-01
Human activities have strong impacts on ecosystem functioning through their effect on abiotic factors and on biodiversity. There is also growing evidence that species functional traits link changes in species composition and shifts in ecosystem processes. Hence, it appears to be of utmost importance to quantify modifications in the functional structure of species communities after human disturbance in addition to changes in taxonomic structure. Despite this fact, there is still little consensus on the actual impacts of human-mediated habitat alteration on the components of biodiversity, which include species functional traits. Therefore, we studied changes in taxonomic diversity (richness and evenness), in functional diversity, and in functional specialization of estuarine fish communities facing drastic environmental and habitat alterations. The Terminos Lagoon (Gulf of Mexico) is a tropical estuary of primary concern for its biodiversity, its habitats, and its resource supply, which have been severely impacted by human activities. Fish communities were sampled in four zones of the Terminos Lagoon 18 years apart (1980 and 1998). Two functions performed by fish (food acquisition and locomotion) were studied through the measurement of 16 functional traits. Functional diversity of fish communities was quantified using three independent components: richness, evenness, and divergence. Additionally, we measured the degree of functional specialization in fish communities. We used a null model to compare the functional and the taxonomic structure of fish communities between 1980 and 1998. Among the four largest zones studied, three did not show strong functional changes. In the northern part of the lagoon, we found an increase in fish richness but a significant decrease of functional divergence and functional specialization. We explain this result by a decline of specialized species (i.e., those with particular combinations of traits), while newly occurring species are redundant with those already present. The species that decreased in abundance have functional traits linked to seagrass habitats that regressed consecutively to increasing eutrophication. The paradox found in our study highlights the need for a multifaceted approach in the assessment of biodiversity changes in communities under pressure.
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Ecological-network models link diversity, structure and function in the plankton food-web
NASA Astrophysics Data System (ADS)
D'Alelio, Domenico; Libralato, Simone; Wyatt, Timothy; Ribera D'Alcalà, Maurizio
2016-02-01
A planktonic food-web model including sixty-three functional nodes (representing auto- mixo- and heterotrophs) was developed to integrate most trophic diversity present in the plankton. The model was implemented in two variants - which we named ‘green’ and ‘blue’ - characterized by opposite amounts of phytoplankton biomass and representing, respectively, bloom and non-bloom states of the system. Taxonomically disaggregated food-webs described herein allowed to shed light on how components of the plankton community changed their trophic behavior in the two different conditions, and modified the overall functioning of the plankton food web. The green and blue food-webs showed distinct organizations in terms of trophic roles of the nodes and carbon fluxes between them. Such re-organization stemmed from switches in selective grazing by both metazoan and protozoan consumers. Switches in food-web structure resulted in relatively small differences in the efficiency of material transfer towards higher trophic levels. For instance, from green to blue states, a seven-fold decrease in phytoplankton biomass translated into only a two-fold decrease in potential planktivorous fish biomass. By linking diversity, structure and function in the plankton food-web, we discuss the role of internal mechanisms, relying on species-specific functionalities, in driving the ‘adaptive’ responses of plankton communities to perturbations.
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Friedman, Naomi P; Miyake, Akira
2017-01-01
Executive functions (EFs) are high-level cognitive processes, often associated with the frontal lobes, that control lower level processes in the service of goal-directed behavior. They include abilities such as response inhibition, interference control, working memory updating, and set shifting. EFs show a general pattern of shared but distinct functions, a pattern described as "unity and diversity". We review studies of EF unity and diversity at the behavioral and genetic levels, focusing on studies of normal individual differences and what they reveal about the functional organization of these cognitive abilities. In particular, we review evidence that across multiple ages and populations, commonly studied EFs (a) are robustly correlated but separable when measured with latent variables; (b) are not the same as general intelligence or g; (c) are highly heritable at the latent level and seemingly also highly polygenic; and (d) activate both common and specific neural areas and can be linked to individual differences in neural activation, volume, and connectivity. We highlight how considering individual differences at the behavioral and neural levels can add considerable insight to the investigation of the functional organization of the brain, and conclude with some key points about individual differences to consider when interpreting neuropsychological patterns of dissociation. Copyright © 2016 Elsevier Ltd. All rights reserved.
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DISC1 Causes Associative Memory and Neurodevelopmental Defects in Fruit Flies
Furukubo-Tokunaga, Katsuo; Kurita, Kazuki; Honjo, Ken; Pandey, Himani; Ando, Tetsuya; Takayama, Kojiro; Arai, Yuko; Mochizuki, Hiroaki; Ando, Mai; Kamiya, Atsushi; Sawa, Akira
2016-01-01
Originally found in a Scottish family with diverse mental disorders, the DISC1 protein has been characterized as an intracellular scaffold protein that associates with diverse binding partners in neural development. To explore its functions in a genetically tractable system, we expressed the human DISC1 in fruit flies (Drosophila melanogaster). As in mammalian neurons, DISC1 is localized to diverse subcellular domains of developing fly neurons including the nuclei, axons and dendrites. Overexpression of DISC1 impairs associative memory. Experiments with deletion/mutation constructs have revealed the importance of amino terminal domain (46–290) for memory suppression whereas carboxyl domain (598–854) and the amino terminal residues (1–45) including the nuclear localization signal (NLS1) are dispensable. DISC1 overexpression also causes suppression of axonal and dendritic branching of mushroom body neurons, which mediate a variety of cognitive functions in the fly brain. Analyses with deletion constructs reveal that protein domains 598–854 and 349–402 are both required for the suppression of axonal branching while amino-terminal domains including NLS1 are dispensable. In contrast, NLS1 was required for the suppression of dendritic branching, suggesting a mechanism involving gene expression. Moreover, domain 403–596 is also required for the suppression of dendritic branching. We also show that overexpression of DISC1 suppresses glutamatergic synaptogenesis in developing neuromuscular junctions. Deletion/mutation experiments have revealed the importance of protein domains 403–596 and 349–402 for synaptic suppression, while amino terminal domains including NLS1 are dispensable. Finally, we show that DISC1 functionally interacts with the fly homolog of Dysbindin (DTNBP1) via direct protein-protein interaction in developing synapses. PMID:26976042
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Jung, Jaejoon; Philippot, Laurent; Park, Woojun
2016-03-14
The relationship between microbial biodiversity and soil function is an important issue in ecology, yet most studies have been performed in pristine ecosystems. Here, we assess the role of microbial diversity in ecological function and remediation strategies in diesel-contaminated soils. Soil microbial diversity was manipulated using a removal by dilution approach and microbial functions were determined using both metagenomic analyses and enzymatic assays. A shift from Proteobacteria- to Actinobacteria-dominant communities was observed when species diversity was reduced. Metagenomic analysis showed that a large proportion of functional gene categories were significantly altered by the reduction in biodiversity. The abundance of genes related to the nitrogen cycle was significantly reduced in the low-diversity community, impairing denitrification. In contrast, the efficiency of diesel biodegradation was increased in the low-diversity community and was further enhanced by addition of red clay as a stimulating agent. Our results suggest that the relationship between microbial diversity and ecological function involves trade-offs among ecological processes, and should not be generalized as a positive, neutral, or negative relationship.
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Jung, Jaejoon; Philippot, Laurent; Park, Woojun
2016-01-01
The relationship between microbial biodiversity and soil function is an important issue in ecology, yet most studies have been performed in pristine ecosystems. Here, we assess the role of microbial diversity in ecological function and remediation strategies in diesel-contaminated soils. Soil microbial diversity was manipulated using a removal by dilution approach and microbial functions were determined using both metagenomic analyses and enzymatic assays. A shift from Proteobacteria- to Actinobacteria-dominant communities was observed when species diversity was reduced. Metagenomic analysis showed that a large proportion of functional gene categories were significantly altered by the reduction in biodiversity. The abundance of genes related to the nitrogen cycle was significantly reduced in the low-diversity community, impairing denitrification. In contrast, the efficiency of diesel biodegradation was increased in the low-diversity community and was further enhanced by addition of red clay as a stimulating agent. Our results suggest that the relationship between microbial diversity and ecological function involves trade-offs among ecological processes, and should not be generalized as a positive, neutral, or negative relationship. PMID:26972977
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Polychaete functional diversity in shallow habitats: Shelter from the storm
NASA Astrophysics Data System (ADS)
Wouters, Julia M.; Gusmao, Joao B.; Mattos, Gustavo; Lana, Paulo
2018-05-01
Innovative approaches are needed to help understanding how species diversity is related to the latitudinal gradient at large or small scales. We have applied a novel approach, by combining morphological and biological traits, to assess the relative importance of the large scale latitudinal gradient and regional morphodynamic drivers in shaping the functional diversity of polychaete assemblages in shallow water habitats, from exposed to estuarine sandy beaches. We used literature data on polychaetes from beaches along the southern and southeastern Brazilian coast together with data on beach types, slope, grain size, temperature, salinity, and chlorophyll a concentration. Generalized linear models on the FDis index for functional diversity calculated for each site and a combined RLQ and fourth-corner analysis were used to investigate relationships between functional traits and environmental variables. Functional diversity was not related to the latitudinal gradient but negatively correlated with grain size and beach slope. Functional diversity was highest in flat beaches with small grain size, little wave exposure and enhanced primary production, indicating that small scale morphodynamic conditions are the primary drivers of polychaete functional diversity.
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Maintenance of soil functioning following erosion of microbial diversity.
Wertz, Sophie; Degrange, Valérie; Prosser, James I; Poly, Franck; Commeaux, Claire; Freitag, Thomas; Guillaumaud, Nadine; Roux, Xavier Le
2006-12-01
The paradigm that soil microbial communities, being very diverse, have high functional redundancy levels, so that erosion of microbial diversity is less important for ecosystem functioning than erosion of plant or animal diversity, is often taken for granted. However, this has only been demonstrated for decomposition/respiration functions, performed by a large proportion of the total microbial community, but not for specialized microbial groups. Here, we determined the impact of a decrease in soil microbial diversity on soil ecosystem processes using a removal approach, in which less abundant species were removed preferentially. This was achieved by inoculation of sterile soil microcosms with serial dilutions of a suspension obtained from the same non-sterile soil and subsequent incubation, to enable recovery of community size. The sensitivity to diversity erosion was evaluated for three microbial functional groups with known contrasting taxonomic diversities (ammonia oxidizers < denitrifiers < heterotrophs). Diversity erosion within each functional group was characterized using molecular fingerprinting techniques: ribosomal intergenic spacer analysis (RISA) for the eubacterial community, denaturing gradient gel electrophoresis (DGGE) analysis of nirK genes for denitrifiers, and DGGE analysis of 16S rRNA genes for betaproteobacterial ammonia oxidizers. In addition, we simulated the impact of the removal approach by dilution on the number of soil bacterial species remaining in the inoculum using values of abundance distribution of bacterial species reported in the literature. The reduction of the diversity of the functional groups observed from genetic fingerprints did not impair the associated functioning of these groups, i.e. carbon mineralization, denitrification and nitrification. This was remarkable, because the amplitude of diversity erosion generated by the dilution approach was huge (level of bacterial species loss was estimated to be around 99.99% for the highest dilution). Our results demonstrate that the vast diversity of the soil microbiota makes soil ecosystem functioning largely insensitive to biodiversity erosion even for functions performed by specialized groups.
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Donna Vizian manages essential support functions, including human resources management, diversity and inclusion, acquisition (contracts), grants management, and the protection of EPA’s facilities and other critical assets nationwide.
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A functional genomics screen in planarians reveals regulators of whole-brain regeneration
Roberts-Galbraith, Rachel H; Brubacher, John L; Newmark, Phillip A
2016-01-01
Planarians regenerate all body parts after injury, including the central nervous system (CNS). We capitalized on this distinctive trait and completed a gene expression-guided functional screen to identify factors that regulate diverse aspects of neural regeneration in Schmidtea mediterranea. Our screen revealed molecules that influence neural cell fates, support the formation of a major connective hub, and promote reestablishment of chemosensory behavior. We also identified genes that encode signaling molecules with roles in head regeneration, including some that are produced in a previously uncharacterized parenchymal population of cells. Finally, we explored genes downregulated during planarian regeneration and characterized, for the first time, glial cells in the planarian CNS that respond to injury by repressing several transcripts. Collectively, our studies revealed diverse molecules and cell types that underlie an animal’s ability to regenerate its brain. DOI: http://dx.doi.org/10.7554/eLife.17002.001 PMID:27612384
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Rivadeneira, Marcelo M; Nielsen, Sven N
2017-01-01
Functional diversity based on species traits is a powerful tool to investigate how changes in species richness and composition affect ecosystem functioning. However, studies aimed at understanding changes in functional diversity over large temporal and spatial scales are still scant. Here we evaluate the combined effect of diversification and species sorting on functional diversity of fossil marine gastropods during the Pliocene-Quaternary transition in the Pacific coast of South America. We analyzed a total of 172 species in 29 Pliocene and 97 Quaternary sites. Each species was characterized according to six functional traits: body size, feeding type, mobility, attachment, life-habit, and larval mode. Functional diversity was estimated according to four indexes (functional richness, evenness, divergence and dispersion) based on functional traits measured. Extrapolated species richness showed a slight yet not significant decrease from the Pliocene to the Quaternary despite the fact that a large faunal turnover took place; furthermore, a large extinction of Pliocene species (61-76%) was followed by a high pulse of appearances (49-56%) during the Quaternary. Three out of four indices of functional diversity (evenness, divergence and dispersion) increased significantly towards the Quaternary which is more than expected under a random turnover of species. The increase in functional diversity is associated with a loss of large-sized carnivore forms, which tended to be replaced by small-sized grazers. Hence, this trait-selective species turnover, even in the absence of significant changes in species richness, likely had a large effect and has shaped the functional diversity of present-day assemblages.
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Spasojevic, Marko J.; Grace, James B.; Harrison, Susan; Damschen, Ellen Ingman
2013-01-01
1. The physiological tolerance hypothesis proposes that plant species richness is highest in warm and/or wet climates because a wider range of functional strategies can persist under such conditions. Functional diversity metrics, combined with statistical modeling, offer new ways to test whether diversity-environment relationships are consistent with this hypothesis. 2. In a classic study by R. H. Whittaker (1960), herb species richness declined from mesic (cool, moist, northerly) slopes to xeric (hot, dry, southerly) slopes. Building on this dataset, we measured four plant functional traits (plant height, specific leaf area, leaf water content and foliar C:N) and used them to calculate three functional diversity metrics (functional richness, evenness, and dispersion). We then used a structural equation model to ask if ‘functional diversity’ (modeled as the joint responses of richness, evenness, and dispersion) could explain the observed relationship of topographic climate gradients to species richness. We then repeated our model examining the functional diversity of each of the four traits individually. 3. Consistent with the physiological tolerance hypothesis, we found that functional diversity was higher in more favorable climatic conditions (mesic slopes), and that multivariate functional diversity mediated the relationship of the topographic climate gradient to plant species richness. We found similar patterns for models focusing on individual trait functional diversity of leaf water content and foliar C:N. 4. Synthesis. Our results provide trait-based support for the physiological tolerance hypothesis, suggesting that benign climates support more species because they allow for a wider range of functional strategies.
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Liebergesell, Mario; Stahl, Ulrike; Freiberg, Martin; Welk, Erik; Kattge, Jens; Cornelissen, J. Hans C.; Peñuelas, Josep
2016-01-01
Future global change scenarios predict a dramatic loss of biodiversity for many regions in the world, potentially reducing the resistance and resilience of ecosystem functions. Once before, during Plio-Pleistocene glaciations, harsher climatic conditions in Europe as compared to North America led to a more depauperate tree flora. Here we hypothesize that this climate driven species loss has also reduced functional diversity in Europe as compared to North America. We used variation in 26 traits for 154 North American and 66 European tree species and grid-based co-occurrences derived from distribution maps to compare functional diversity patterns of the two continents. First, we identified similar regions with respect to contemporary climate in the temperate zone of North America and Europe. Second, we compared the functional diversity of both continents and for the climatically similar sub-regions using the functional dispersion-index (FDis) and the functional richness index (FRic). Third, we accounted in these comparisons for grid-scale differences in species richness, and, fourth, investigated the associated trait spaces using dimensionality reduction. For gymnosperms we find similar functional diversity on both continents, whereas for angiosperms functional diversity is significantly greater in Europe than in North America. These results are consistent across different scales, for climatically similar regions and considering species richness patterns. We decomposed these differences in trait space occupation into differences in functional diversity vs. differences in functional identity. We show that climate-driven species loss on a continental scale might be decoupled from or at least not linearly related to changes in functional diversity. This might be important when analyzing the effects of climate-driven biodiversity change on ecosystem functioning. PMID:26848836
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Wilkinson, D.L.; Schneller-McDonald, K.; Olson, R.W.; Auble, G.T.
1987-01-01
Bottomland hardwood wetlands are the natural cover type of many floodplain ecosystems in the southeastern United States. They are dynamic, productive systems that depend on intermittent flooding and moving water for maintenance of structure and function. Many of the diverse functions performed by bottomland hardwoods (e.g., flood control, sediment trapping, fish and wildlife habitat) are directly or indirectly valued by humans. Balanced decisions regarding bottomland hardwoods are often hindered by a limited ability to accurately specify the functions being performed by these systems and, furthermore, by an inability to evaluate these functions in economic terms. This report addresses these informational needs. It focuses on the bottomland hardwoods of eastern Texas and Oklahoma, serving as an introduction and entry to the literature. It is not intended to serve as a substitute for reference to the original literature. The first section of the report is a review of the major functions of bottomland hardwoods, grouped under the headings of hydrology, water quality, productivity, detritus, nutrients, and habitat. Although the hydrology of these areas is diverse and complex, especially with respect to groundwater, water storage at high flows can clearly function to attenuate peak flows, with possible reductions in downstream flooding damage. Water moving through a bottomland hardwood system carries with it various organic and inorganic constituents, including sediment, organic matter, nutrients, and pollutants. When waterborne materials are introduced to bottomland hardwoods (from river flooding or upland runoff), they may be retained, transformed, or transported. As a result, water quality may be significantly altered and improved. The fluctuating and flowing water regime of bottomland hardwoods is associated with generally high net primary productivity and rapid fluxes of organic matter and nutrients. These, in turn, support secondary productivity in the bottomland hardwoods and downstream through detrital export. A large number of studies detail the extensive utilization of bottomland hardwoods by animals. Several basic habitat components contribute to this support function, including: 1. Fluctuating water levels and permanent bodies of water, 2. Hard mast (e.g., acorns), 3. Dens and cavities, 4. High soil fertility, 5. Diversity of food and cover, 6. Predominance of woody plant communities, 7. Close proximity of diverse structural features, and 8. Linear features providing movement corridors. The second section of the report focuses on the bottomlands of eastern Texas and Oklahoma, including topics such as climate, soils, water resources, historical perspective, vegetation, and fauna. Considerable attention is given to structural characteristics in this section, in order to provide contrasts with bottomland hardwood ecosystems in other areas. In general, the bottomland hardwoods of eastern Texas and Oklahoma are very similar to those elsewhere in the southeastern United States. Differences include the occurrence and relative importance of some community types and plant species and the greater importance of reservoir construction as a source of bottomland hardwoods loss in eastern Texas and Oklahoma. Again, information on faunal utilization is extensive relative to the information available concerning other functions.
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2017-01-01
While the positive relationship between avian diversity and habitat heterogeneity is widely accepted, it is primarily based on observed species richness without accounting for imperfect detection. Other facets of diversity such as functional diversity are also rarely explored. We investigated the avian diversity-landscape heterogeneity relationship in agricultural landscapes by considering two aspects of diversity: taxonomic diversity (species richness) estimated from a multi-species dynamic occupancy model, and functional diversity (functional evenness [FEve] and divergence [FDiv]) based on traits of occurring species. We also assessed how agricultural lands enrolled in a conservation program managed on behalf of declining early successional bird species (hereafter CP38 fields, an agri-environment scheme) influenced avian diversity. We analyzed breeding bird data collected at CP38 fields in Mississippi, USA, during 2010–2012, and two principal components of environmental variables: a gradient of heterogeneity (Shannon’s landscape diversity index) and of the amount of CP38 fields (percent cover of CP38 fields; CP38). FEve did not show significant responses to environmental variables, whereas FDiv responded positively to heterogeneity and negatively to CP38. However, most FDiv values did not significantly differ from random expectations along an environmental gradient. When there was a significant difference, FDiv was lower than that expected. Unlike functional diversity, species richness showed a clear pattern. Species richness increased with increasing landscape heterogeneity but decreased with increasing amounts of CP38 fields. Only one species responded negatively to heterogeneity and positively to CP38. Our results suggest that the relationships between avian diversity and landscape heterogeneity may vary depending on the aspect of diversity considered: strong positive effects of heterogeneity on taxonomic diversity, but weakly positive or non-significant effects on functional diversity. Our results also indicate that effectiveness of CP38 in conserving avian diversity, particularly, taxonomic diversity, could be limited without the consideration of landscape heterogeneity. PMID:28125653
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Lee, Myung-Bok; Martin, James A
2017-01-01
While the positive relationship between avian diversity and habitat heterogeneity is widely accepted, it is primarily based on observed species richness without accounting for imperfect detection. Other facets of diversity such as functional diversity are also rarely explored. We investigated the avian diversity-landscape heterogeneity relationship in agricultural landscapes by considering two aspects of diversity: taxonomic diversity (species richness) estimated from a multi-species dynamic occupancy model, and functional diversity (functional evenness [FEve] and divergence [FDiv]) based on traits of occurring species. We also assessed how agricultural lands enrolled in a conservation program managed on behalf of declining early successional bird species (hereafter CP38 fields, an agri-environment scheme) influenced avian diversity. We analyzed breeding bird data collected at CP38 fields in Mississippi, USA, during 2010-2012, and two principal components of environmental variables: a gradient of heterogeneity (Shannon's landscape diversity index) and of the amount of CP38 fields (percent cover of CP38 fields; CP38). FEve did not show significant responses to environmental variables, whereas FDiv responded positively to heterogeneity and negatively to CP38. However, most FDiv values did not significantly differ from random expectations along an environmental gradient. When there was a significant difference, FDiv was lower than that expected. Unlike functional diversity, species richness showed a clear pattern. Species richness increased with increasing landscape heterogeneity but decreased with increasing amounts of CP38 fields. Only one species responded negatively to heterogeneity and positively to CP38. Our results suggest that the relationships between avian diversity and landscape heterogeneity may vary depending on the aspect of diversity considered: strong positive effects of heterogeneity on taxonomic diversity, but weakly positive or non-significant effects on functional diversity. Our results also indicate that effectiveness of CP38 in conserving avian diversity, particularly, taxonomic diversity, could be limited without the consideration of landscape heterogeneity.
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Adam, Thomas C; Kelley, Megan; Ruttenberg, Benjamin I; Burkepile, Deron E
2015-12-01
The recent loss of key consumers to exploitation and habitat degradation has significantly altered community dynamics and ecosystem function across many ecosystems worldwide. Predicting the impacts of consumer losses requires knowing the level of functional diversity that exists within a consumer assemblage. In this study, we document functional diversity among nine species of parrotfishes on Caribbean coral reefs. Parrotfishes are key herbivores that facilitate the maintenance and recovery of coral-dominated reefs by controlling algae and provisioning space for the recruitment of corals. We observed large functional differences among two genera of parrotfishes that were driven by differences in diet. Fishes in the genus Scarus targeted filamentous algal turf assemblages, crustose coralline algae, and endolithic algae and avoided macroalgae, while fishes in the genus Sparisoma preferentially targeted macroalgae. However, species with similar diets were dissimilar in other attributes, including the habitats they frequented, the types of substrate they fed from, and the spatial scale at which they foraged. These differences indicate that species that appear to be functionally redundant when looking at diet alone exhibit high levels of complementarity when we consider multiple functional traits. By identifying key functional differences among parrotfishes, we provide critical information needed to manage parrotfishes to enhance the resilience of coral-dominated reefs and reverse phase shifts on algal-dominated reefs throughout the wider Caribbean. Further, our study provides a framework for predicting the impacts of consumer losses in other species rich ecosystems.
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Crustose coralline algae increased framework and diversity on ancient coral reefs.
Weiss, Anna; Martindale, Rowan C
2017-01-01
Crustose coralline algae (CCA) are key producers of carbonate sediment on reefs today. Despite their importance in modern reef ecosystems, the long-term relationship of CCA with reef development has not been quantitatively assessed in the fossil record. This study includes data from 128 Cenozoic coral reefs collected from the Paleobiology Database, the Paleoreefs Database, as well as the original literature and assesses the correlation of CCA abundance with taxonomic diversity (both corals and reef dwellers) and framework of fossil coral reefs. Chi-squared tests show reef type is significantly correlated with CCA abundance and post-hoc tests indicate higher involvement of CCA is associated with stronger reef structure. Additionally, general linear models show coral reefs with higher amounts of CCA had a higher diversity of reef-dwelling organisms. These data have important implications for paleoecology as they demonstrate that CCA increased building capacity, structural integrity, and diversity of ancient coral reefs. The analyses presented here demonstrate that the function of CCA on modern coral reefs is similar to their function on Cenozoic reefs; thus, studies of ancient coral reef collapse are even more meaningful as modern analogues.
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Evolution and Diversity of the Ras Superfamily of Small GTPases in Prokaryotes
Wuichet, Kristin; Søgaard-Andersen, Lotte
2015-01-01
The Ras superfamily of small GTPases are single domain nucleotide-dependent molecular switches that act as highly tuned regulators of complex signal transduction pathways. Originally identified in eukaryotes for their roles in fundamental cellular processes including proliferation, motility, polarity, nuclear transport, and vesicle transport, recent studies have revealed that single domain GTPases also control complex functions such as cell polarity, motility, predation, development and antibiotic resistance in bacteria. Here, we used a computational genomics approach to understand the abundance, diversity, and evolution of small GTPases in prokaryotes. We collected 520 small GTPase sequences present in 17% of 1,611 prokaryotic genomes analyzed that cover diverse lineages. We identified two discrete families of small GTPases in prokaryotes that show evidence of three distinct catalytic mechanisms. The MglA family includes MglA homologs, which are typically associated with the MglB GTPase activating protein, whereas members of the Rup (Ras superfamily GTPase of unknown function in prokaryotes) family are not predicted to interact with MglB homologs. System classification and genome context analyses support the involvement of small GTPases in diverse prokaryotic signal transduction pathways including two component systems, laying the foundation for future experimental characterization of these proteins. Phylogenetic analysis of prokaryotic and eukaryotic GTPases supports that the last universal common ancestor contained ancestral MglA and Rup family members. We propose that the MglA family was lost from the ancestral eukaryote and that the Ras superfamily members in extant eukaryotes are the result of vertical and horizontal gene transfer events of ancestral Rup GTPases. PMID:25480683
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Chong, Chun Wie; Ahmad, Arine Fadzlun; Lim, Yvonne Ai Lian; Teh, Cindy Shuan Ju; Yap, Ivan Kok Seng; Lee, Soo Ching; Chin, Yuee Teng; Loke, P’ng; Chua, Kek Heng
2015-01-01
Gut microbiota plays an important role in mammalian host metabolism and physiological functions. The functions are particularly important in young children where rapid mental and physical developments are taking place. Nevertheless, little is known about the gut microbiome and the factors that contribute to microbial variation in the gut of South East Asian children. Here, we compared the gut bacterial richness and composition of pre-adolescence in Northern Malaysia. Our subjects covered three distinct ethnic groups with relatively narrow range of socioeconomic discrepancy. These included the Malays (n = 24), Chinese (n = 17) and the Orang Asli (indigenous) (n = 20). Our results suggested a strong ethnicity and socioeconomic-linked bacterial diversity. Highest bacterial diversity was detected from the economically deprived indigenous children while the lowest diversity was recorded from the relatively wealthy Chinese children. In addition, predicted functional metagenome profiling suggested an over-representation of pathways pertinent to bacterial colonisation and chemotaxis in the former while the latter exhibited enriched gene pathways related to sugar metabolism. PMID:26290472
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Diversity amongst trigeminal neurons revealed by high throughput single cell sequencing
Nguyen, Minh Q.; Wu, Youmei; Bonilla, Lauren S.; von Buchholtz, Lars J.
2017-01-01
The trigeminal ganglion contains somatosensory neurons that detect a range of thermal, mechanical and chemical cues and innervate unique sensory compartments in the head and neck including the eyes, nose, mouth, meninges and vibrissae. We used single-cell sequencing and in situ hybridization to examine the cellular diversity of the trigeminal ganglion in mice, defining thirteen clusters of neurons. We show that clusters are well conserved in dorsal root ganglia suggesting they represent distinct functional classes of somatosensory neurons and not specialization associated with their sensory targets. Notably, functionally important genes (e.g. the mechanosensory channel Piezo2 and the capsaicin gated ion channel Trpv1) segregate into multiple clusters and often are expressed in subsets of cells within a cluster. Therefore, the 13 genetically-defined classes are likely to be physiologically heterogeneous rather than highly parallel (i.e., redundant) lines of sensory input. Our analysis harnesses the power of single-cell sequencing to provide a unique platform for in silico expression profiling that complements other approaches linking gene-expression with function and exposes unexpected diversity in the somatosensory system. PMID:28957441
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Regulatory T Cells: Differentiation and Function.
Plitas, George; Rudensky, Alexander Y
2016-09-02
The immune system of vertebrate animals has evolved to mount an effective defense against a diverse set of pathogens while minimizing transient or lasting impairment in tissue function that could result from the inflammation caused by immune responses to infectious agents. In addition, misguided immune responses to "self" and dietary antigens, as well as to commensal microorganisms, can lead to a variety of inflammatory disorders, including autoimmunity, metabolic syndrome, allergies, and cancer. Regulatory T cells expressing the X chromosome-linked transcription factor Foxp3 suppress inflammatory responses in diverse biological settings and serve as a vital mechanism of negative regulation of immune-mediated inflammation. Cancer Immunol Res; 4(9); 721-5. ©2016 AACR. ©2016 American Association for Cancer Research.
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Sankar, Muthukumar G.; Roy, Sayantani; Tran, Tuyen Thi Ngoc; Wittstein, Kathrin; Bauer, Jonathan O.; Strohmann, Carsten; Ziegler, Slava
2018-01-01
Abstract Complexity‐generating chemical transformations that afford novel molecular scaffolds enriched in sp 3 character are highly desired. Here, we present a highly stereoselective scaffold diversity synthesis approach that utilizes cascade double‐annulation reactions of diverse pairs of zwitterionic and non‐zwitterionic partners with 3‐formylchromones to generate highly complex tetracyclic benzopyrones. Each pair of annulation partners adds to the common chroman‐4‐one scaffold to build two new rings, supporting up to four contiguous chiral centers that include an all‐carbon quaternary center. Differently ring‐fused benzopyrones display different biological activities, thus demonstrating their immense potential in medicinal chemistry and chemical biology research. PMID:29721402
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Venkatachalam, S; Ranjan, K; Prasanna, R; Ramakrishnan, B; Thapa, S; Kanchan, A
2016-07-01
The diversity and abundance of culturable microbiome members of the rice phyllosphere was investigated using cv. Pusa Punjab Basmati 1509. Both diversity and species richness of bacteria were significantly higher in plants in pots in a semi-controlled environment than those in fields. Application of fertilisers reduced both diversity and species richness in field-grown plants under a conventional flooded system of rice intensification (SRI) and in dry-seeded rice (DSR) modes. Sequence analyses of 16S rDNA of culturable bacteria, those selected after amplified ribosomal DNA restriction analysis (ARDRA), showed the dominance of α-proteobacteria (35%) and actinobacteria (38%); Pantoea, Exiguobacterium and Bacillus were common among the culturable phyllospheric bacteria. About 34% of 83 culturable bacterial isolates had higher potential (>2 μg·ml(-1) ) for indole acetic acid production in the absence of tryptophan. Interestingly, the phyllosphere bacterial isolates from the pot experiment had significantly higher potential for nitrogen fixation than isolates from the field experiment. Enrichment for cyanobacteria showed both unicellular forms and non-heterocystous filaments under aerobic as well as anaerobic conditions. PCR-DGGE analysis of these showed that aerobic and anaerobic conditions as well as the three modes of cultivation of rice in the field strongly influenced the number and abundance of phylotypes. The adaptability and functional traits of these culturable microbiome members suggest enormous diversity in the phyllosphere, including potential for plant growth promotion, which was also significantly influenced by the different methods of growing rice. © 2016 German Botanical Society and The Royal Botanical Society of the Netherlands.
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Mendes, Lucas William; Tsai, Siu Mui
2018-01-01
Soil microorganisms play crucial roles in ecosystem functioning, and the central goal in microbial ecology studies is to elucidate which factors shape community structure. A better understanding of the relationship between microbial diversity, functions and environmental parameters would increase our ability to set conservation priorities. Here, the bacterial and archaeal community structure in Atlantic Forest, restinga and mangrove soils was described and compared based on shotgun metagenomics. We hypothesized that each distinct site would harbor a distinct taxonomic and functional soil community, which is influenced by environmental parameters. Our data showed that the microbiome is shaped by soil properties, with pH, base saturation, boron and iron content significantly correlated to overall community structure. When data of specific phyla were correlated to specific soil properties, we demonstrated that parameters such as boron, copper, sulfur, potassium and aluminum presented significant correlation with the most number of bacterial groups. Mangrove soil was the most distinct site and presented the highest taxonomic and functional diversity in comparison with forest and restinga soils. From the total 34 microbial phyla identified, 14 were overrepresented in mangrove soils, including several archaeal groups. Mangrove soils hosted a high abundance of sequences related to replication, survival and adaptation; forest soils included high numbers of sequences related to the metabolism of nutrients and other composts; while restinga soils included abundant genes related to the metabolism of carbohydrates. Overall, our finds show that the microbial community structure and functional potential were clearly different across the environmental gradient, followed by functional adaptation and both were related to the soil properties.
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Plant-Pollinator Coextinctions and the Loss of Plant Functional and Phylogenetic Diversity
Vieira, Marcos Costa; Cianciaruso, Marcus Vinicius; Almeida-Neto, Mário
2013-01-01
Plant-pollinator coextinctions are likely to become more frequent as habitat alteration and climate change continue to threaten pollinators. The consequences of the resulting collapse of plant communities will depend partly on how quickly plant functional and phylogenetic diversity decline following pollinator extinctions. We investigated the functional and phylogenetic consequences of pollinator extinctions by simulating coextinctions in seven plant-pollinator networks coupled with independent data on plant phylogeny and functional traits. Declines in plant functional diversity were slower than expected under a scenario of random extinctions, while phylogenetic diversity often decreased faster than expected by chance. Our results show that plant functional diversity was relatively robust to plant-pollinator coextinctions, despite the underlying rapid loss of evolutionary history. Thus, our study suggests the possibility of uncoupled responses of functional and phylogenetic diversity to species coextinctions, highlighting the importance of considering both dimensions of biodiversity explicitly in ecological studies and when planning for the conservation of species and interactions. PMID:24312281
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Dysbiosis of the microbiome in gastric carcinogenesis.
Castaño-Rodríguez, Natalia; Goh, Khean-Lee; Fock, Kwong Ming; Mitchell, Hazel M; Kaakoush, Nadeem O
2017-11-21
The gastric microbiome has been proposed as an etiological factor in gastric carcinogenesis. We compared the gastric microbiota in subjects presenting with gastric cancer (GC, n = 12) and controls (functional dyspepsia (FD), n = 20) from a high GC risk population in Singapore and Malaysia. cDNA from 16S rRNA transcripts were amplified (515F-806R) and sequenced using Illumina MiSeq 2 × 250 bp chemistry. Increased richness and phylogenetic diversity but not Shannon's diversity was found in GC as compared to controls. nMDS clustered GC and FD subjects separately, with PERMANOVA confirming a significant difference between the groups. H. pylori serological status had a significant impact on gastric microbiome α-diversity and composition. Several bacterial taxa were enriched in GC, including Lactococcus, Veilonella, and Fusobacteriaceae (Fusobacterium and Leptotrichia). Prediction of bacterial metabolic contribution indicated that serological status had a significant impact on metabolic function, while carbohydrate digestion and pathways were enriched in GC. Our findings highlight three mechanisms of interest in GC, including enrichment of pro-inflammatory oral bacterial species, increased abundance of lactic acid producing bacteria, and enrichment of short chain fatty acid production pathways.
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The Biochemical Toxin Arsenal from Ant Venoms
Touchard, Axel; Aili, Samira R.; Fox, Eduardo Gonçalves Paterson; Escoubas, Pierre; Orivel, Jérôme; Nicholson, Graham M.; Dejean, Alain
2016-01-01
Ants (Formicidae) represent a taxonomically diverse group of hymenopterans with over 13,000 extant species, the majority of which inject or spray secretions from a venom gland. The evolutionary success of ants is mostly due to their unique eusociality that has permitted them to develop complex collaborative strategies, partly involving their venom secretions, to defend their nest against predators, microbial pathogens, ant competitors, and to hunt prey. Activities of ant venom include paralytic, cytolytic, haemolytic, allergenic, pro-inflammatory, insecticidal, antimicrobial, and pain-producing pharmacologic activities, while non-toxic functions include roles in chemical communication involving trail and sex pheromones, deterrents, and aggregators. While these diverse activities in ant venoms have until now been largely understudied due to the small venom yield from ants, modern analytical and venomic techniques are beginning to reveal the diversity of toxin structure and function. As such, ant venoms are distinct from other venomous animals, not only rich in linear, dimeric and disulfide-bonded peptides and bioactive proteins, but also other volatile and non-volatile compounds such as alkaloids and hydrocarbons. The present review details the unique structures and pharmacologies of known ant venom proteinaceous and alkaloidal toxins and their potential as a source of novel bioinsecticides and therapeutic agents. PMID:26805882
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Chlorella vulgaris: A Multifunctional Dietary Supplement with Diverse Medicinal Properties.
Panahi, Yunes; Darvishi, Behrad; Jowzi, Narges; Beiraghdar, Fatemeh; Sahebkar, Amirhossein
2016-01-01
Chlorella vulgaris is a green unicellular microalgae with biological and pharmacological properties important for human health. C. vulgaris has a long history of use as a food source and contains a unique and diverse composition of functional macro- and micro-nutrients including proteinsChlorella vulgaris is a green unicellular microalgae with biological and pharmacological properties important for human health. C. vulgaris has a long history of use as a food source and contains a unique and diverse composition of functional macro- and micro-nutrients including proteins, omega-3 polyunsaturated fatty acids, polysaccharides, vitamins and minerals. Clinical trials have suggested that supplementation with C. vulgaris can ameliorate amelioration hyperlipidemia and hyperglycemia, and protect against oxidative stress, cancer and chronic obstructive pulmonary disease. In this review, we summarize the findings on the health benefits of Chlorella supplementation and the molecular mechanisms underlying these effects., omega-3 polyunsaturated fatty acids, polysaccharides, vitamins and minerals. Clinical trials have suggested that supplementation with C. vulgaris can ameliorate amelioration hyperlipidemia and hyperglycemia, and protect against oxidative stress, cancer and chronic obstructive pulmonary disease. In this review, we summarize the findings on the health benefits of Chlorella supplementation and the molecular mechanisms underlying these effects.
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Shen, Congcong; Shi, Yu; Ni, Yingying; Deng, Ye; Van Nostrand, Joy D.; He, Zhili; Zhou, Jizhong; Chu, Haiyan
2016-01-01
The elevational and latitudinal diversity patterns of microbial taxa have attracted great attention in the past decade. Recently, the distribution of functional attributes has been in the spotlight. Here, we report a study profiling soil microbial communities along an elevation gradient (500–2200 m) on Changbai Mountain. Using a comprehensive functional gene microarray (GeoChip 5.0), we found that microbial functional gene richness exhibited a dramatic increase at the treeline ecotone, but the bacterial taxonomic and phylogenetic diversity based on 16S rRNA gene sequencing did not exhibit such a similar trend. However, the β-diversity (compositional dissimilarity among sites) pattern for both bacterial taxa and functional genes was similar, showing significant elevational distance-decay patterns which presented increased dissimilarity with elevation. The bacterial taxonomic diversity/structure was strongly influenced by soil pH, while the functional gene diversity/structure was significantly correlated with soil dissolved organic carbon (DOC). This finding highlights that soil DOC may be a good predictor in determining the elevational distribution of microbial functional genes. The finding of significant shifts in functional gene diversity at the treeline ecotone could also provide valuable information for predicting the responses of microbial functions to climate change. PMID:27524983
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Functional diversity response to hardwood forest management varies across taxa and spatial scales.
Murray, Bryan D; Holland, Jeffrey D; Summerville, Keith S; Dunning, John B; Saunders, Michael R; Jenkins, Michael A
2017-06-01
Contemporary forest management offers a trade-off between the potential positive effects of habitat heterogeneity on biodiversity, and the potential harm to mature forest communities caused by habitat loss and perforation of the forest canopy. While the response of taxonomic diversity to forest management has received a great deal of scrutiny, the response of functional diversity is largely unexplored. However, functional diversity may represent a more direct link between biodiversity and ecosystem function. To examine how forest management affects diversity at multiple spatial scales, we analyzed a long-term data set that captured changes in taxonomic and functional diversity of moths (Lepidoptera), longhorned beetles (Coleoptera: Cerambycidae), and breeding birds in response to contemporary silvicultural systems in oak-hickory hardwood forests. We used these data sets to address the following questions: how do even- and uneven-aged silvicultural systems affect taxonomic and functional diversity at the scale of managed landscapes compared to the individual harvested and unharvested forest patches that comprise the landscapes, and how do these silvicultural systems affect the functional similarity of assemblages at the scale of managed landscapes and patches? Due to increased heterogeneity within landscapes, we expected even-aged silviculture to increase and uneven-aged silviculture to decrease functional diversity at the landscape level regardless of impacts at the patch level. Functional diversity responses were taxon-specific with respect to the direction of change and time since harvest. Responses were also consistent across patch and landscape levels within each taxon. Moth assemblage species richness, functional richness, and functional divergence were negatively affected by harvesting, with stronger effects resulting from uneven-aged than even-aged management. Longhorned beetle assemblages exhibited a peak in species richness two years after harvesting, while functional diversity metrics did not differ between harvested and unharvested patches and managed landscapes. The species and functional richness of breeding bird assemblages increased in response to harvesting with more persistent effects in uneven- than in even-aged managed landscapes. For moth and bird assemblages, species turnover was driven by species with more extreme trait combinations. Our study highlights the variability of multi-taxon functional diversity in response to forest management across multiple spatial scales. © 2017 by the Ecological Society of America.
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Effects of loss of lateral hydrological connectivity on fish functional diversity.
Liu, Xueqin; Wang, Hongzhu
2018-05-26
Loss of lateral hydrological connectivity (LHC) is a major cause of biodiversity decline in river floodplains, yet little is known about its effects on aquatic functional diversity in these ecosystems. We quantified functional alpha and beta diversity of fish assemblages in Yangtze River floodplain lakes, and explored their responses to loss of LHC using generalized linear mixed models. Functional richness was much lower in river disconnected lakes where functional evenness and divergence were higher. LHC was the most important factor shaping fish diversity patterns in this region. The predicted reduction due to loss of LHC was higher in functional richness (0.47-0.82) than in taxonomic richness (0.32) of all species assemblages in contrast to non-migratory species assemblages. It seemed that functional strategies were highly unevenly distributed between migratory and non-migratory fishes in the floodplain. Taxonomic beta diversity was much higher than functional beta diversity. The former was contributed mainly by spatial turnover component (73.6-83.8%) suggesting that dissimilarity among fish assemblages was largely induced by species replacement, while the latter was induced by nestedness-resultant component (70.7-86.0%) indicating a stronger role of function loss without replacement. Both taxonomic and functional beta diversity were higher in disconnected lakes, where they were significantly correlated with fishing activity and water quality. Our study determined for the first time the effects of loss of LHC on fish functional diversity in large river floodplains. We highlight the serious decline of fish functional richness in a large floodplain, and functional diversity remained highly vulnerable to loss of LHC even in such a species rich ecosystem. Our results provide important implications regarding biodiversity conservation and LHC restoration in large river floodplains. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
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ERIC Educational Resources Information Center
Grace, George W.
The Pacific area is generally acknowledged to manifest great linguistic diversity. Such diversity is generally assumed to be dysfunctional, an obstacle to efficient functioning of society. Such diversity must, however, have its functions at least in the circumstances in which it arose. It is also generally assumed that such diversity is the result…
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Regulation and physiological functions of mammalian phospholipase C.
Nakamura, Yoshikazu; Fukami, Kiyoko
2017-04-01
Phospholipase C (PLC) is a key enzyme in phosphoinositide metabolism. PLC hydrolyses phosphatidylinositol 4,5-bis-phosphate to generate two second messengers, inositol 1,4,5-trisphosphate and diacylglycerol, that generate diverse cellular responses. PLC is activated by various signalling molecules, including Ca2+, heterometric G proteins, small G proteins, and receptor/non-receptor tyrosine kinases. In addition to their enzymatic activity, some PLC subtypes also function as a guanine nucleotide exchange factor, GTPase-activating protein, and adaptor protein, independent of their lipase activity. There are 13 PLC isozymes in mammals, and they are categorized into six classes based on structure. Generation and analysis of genetically modified mice has revealed the unexpectedly diverse physiological functions of PLC isozymes. Although all PLC isozymes catalyze the same reaction, each PLC isozyme has unique physiological functions. This review focuses on the regulation and physiological functions of PLCs. © The Authors 2017. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.
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Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides
Geiselman, Gina M; Ito, Masakazu; Mondo, Stephen J; Reilly, Morgann C; Cheng, Ya-Fang; Bauer, Stefan; Grigoriev, Igor V; Gladden, John M; Simmons, Blake A; Brem, Rachel B
2018-01-01
The basidiomycete yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded Agrobacterium tumefaciens T-DNA insertions. We identified 1,337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted function in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, and genes of unknown function. These results greatly advance our understanding of lipid metabolism in this oleaginous species and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi. PMID:29521624
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Functional-diversity indices can be driven by methodological choices and species richness.
Poos, Mark S; Walker, Steven C; Jackson, Donald A
2009-02-01
Functional diversity is an important concept in community ecology because it captures information on functional traits absent in measures of species diversity. One popular method of measuring functional diversity is the dendrogram-based method, FD. To calculate FD, a variety of methodological choices are required, and it has been debated about whether biological conclusions are sensitive to such choices. We studied the probability that conclusions regarding FD were sensitive, and that patterns in sensitivity were related to alpha and beta components of species richness. We developed a randomization procedure that iteratively calculated FD by assigning species into two assemblages and calculating the probability that the community with higher FD varied across methods. We found evidence of sensitivity in all five communities we examined, ranging from a probability of sensitivity of 0 (no sensitivity) to 0.976 (almost completely sensitive). Variations in these probabilities were driven by differences in alpha diversity between assemblages and not by beta diversity. Importantly, FD was most sensitive when it was most useful (i.e., when differences in alpha diversity were low). We demonstrate that trends in functional-diversity analyses can be largely driven by methodological choices or species richness, rather than functional trait information alone.
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Rappoport, Nadav; Linial, Michal
2015-08-07
Insects belong to a class that accounts for the majority of animals on earth. With over one million identified species, insects display a huge diversity and occupy extreme environments. At present, there are dozens of fully sequenced insect genomes that cover a range of habitats, social behavior and morphologies. In view of such diverse collection of genomes, revealing evolutionary trends and charting functional relationships of proteins remain challenging. We analyzed the relatedness of 17 complete proteomes representative of proteomes from insects including louse, bee, beetle, ants, flies and mosquitoes, as well as an out-group from the crustaceans. The analyzed proteomes mostly represented the orders of Hymenoptera and Diptera. The 287,405 protein sequences from the 18 proteomes were automatically clustered into 20,933 families, including 799 singletons. A comprehensive analysis based on statistical considerations identified the families that were significantly expanded or reduced in any of the studied organisms. Among all the tested species, ants are characterized by an exceptionally high rate of family gain and loss. By assigning annotations to hundreds of species-specific families, the functional diversity among species and between the major clades (Diptera and Hymenoptera) is revealed. We found that many species-specific families are associated with receptor signaling, stress-related functions and proteases. The highest variability among insects associates with the function of transposition and nucleic acids processes (collectively coined TNAP). Specifically, the wasp and ants have an order of magnitude more TNAP families and proteins relative to species that belong to Diptera (mosquitoes and flies). An unsupervised clustering methodology combined with a comparative functional analysis unveiled proteomic signatures in the major clades of winged insects. We propose that the expansion of TNAP families in Hymenoptera potentially contributes to the accelerated genome dynamics that characterize the wasp and ants.
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Microbial and physical properties as indicators of sandy soil quality under cropland and grassland
NASA Astrophysics Data System (ADS)
Frac, Magdalena; Lipiec, Jerzy; Usowicz, Boguslaw; Oszust, Karolina; Brzezinska, Malgorzata
2017-04-01
Land use is one of the key factor driving changes in soil properties influencing on soil health and quality. Microbial diversity and physical properties are sensitive indicators for assessing soil health and quality. The alterations of microbial diversity and physical properties following land use changes have not been sufficiently elucidated, especially for sandy soils. We investigated microbial diversity indicators including fungal communities composition and physical properties of sandy acid soil under cropland and more than 20-yr-old grassland (after cropland) in Trzebieszów, Podlasie Region, Poland (N 51° 59' 24", E 22° 33' 37"). The study included four depths within 0-60 cm. Microbial genetic diversity was assessed by terminal restriction fragment length polymorphism (t-RFLP) analysis, fungal community composition was evaluated by next generation sequencing (NGS) analysis and functional diversity was determined by Biolog EcoPlate method. Overall microbial activity was assessed by soil enzymes (dehydrogenases, β-glucosidase) and respiration test. At the same places soil texture, organic carbon content, pH, bulk density, water holding capacity were determined. Our results showed that grassland soil was characterized by higher activity of soil enzymes than cropland. The average well color development of soil microorganisms, the microbial functional diversity and the number of carbon source utilization were significantly affected by land use type and were differentiated among soil depths. In grassland compared to cropland soil a significant increase of carboxylic acids and decrease of amino acids utilization was observed. The quantitative and qualitative differences were found in community of ammonia oxidizing archaea in cropland and grassland soil. The results of fungal community composition help to explain the soil health of grassland and cropland based on the appearance of phytopathogenic and antagonistic fungi. In general bulk density and field water capacity were greater and saturated hydraulic conductivity was lower under grassland than cropland soil. The study was funded by HORIZON 2020, European Commission, Programme: H2020-SFS-4-2014: Soil quality and function, project No. 635750, Interactive Soil Quality Assessment in Europe and China for Agricultural Productivity and Environmental Resilience (iSQAPER, 2015-2020).
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Estaki, Mehrbod; Pither, Jason; Baumeister, Peter; Little, Jonathan P; Gill, Sandeep K; Ghosh, Sanjoy; Ahmadi-Vand, Zahra; Marsden, Katelyn R; Gibson, Deanna L
2016-08-08
Reduced microbial diversity in human intestines has been implicated in various conditions such as diabetes, colorectal cancer, and inflammatory bowel disease. The role of physical fitness in the context of human intestinal microbiota is currently not known. We used high-throughput sequencing to analyze fecal microbiota of 39 healthy participants with similar age, BMI, and diets but with varying cardiorespiratory fitness levels. Fecal short-chain fatty acids were analyzed using gas chromatography. We showed that peak oxygen uptake (VO2peak), the gold standard measure of cardiorespiratory fitness, can account for more than 20 % of the variation in taxonomic richness, after accounting for all other factors, including diet. While VO2peak did not explain variation in beta diversity, it did play a significant role in explaining variation in the microbiomes' predicted metagenomic functions, aligning positively with genes related to bacterial chemotaxis, motility, and fatty acid biosynthesis. These predicted functions were supported by measured increases in production of fecal butyrate, a short-chain fatty acid associated with improved gut health, amongst physically fit participants. We also identified increased abundances of key butyrate-producing taxa (Clostridiales, Roseburia, Lachnospiraceae, and Erysipelotrichaceae) amongst these individuals, which likely contributed to the observed increases in butyrate levels. Results from this study show that cardiorespiratory fitness is correlated with increased microbial diversity in healthy humans and that the associated changes are anchored around a set of functional cores rather than specific taxa. The microbial profiles of fit individuals favor the production of butyrate. As increased microbiota diversity and butyrate production is associated with overall host health, our findings warrant the use of exercise prescription as an adjuvant therapy in combating dysbiosis-associated diseases.
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Zhou, Xichun; Turchi, Craig; Wang, Denong
2009-01-01
We reported here a novel, ready-to-use bioarray platform and methodology for construction of sensitive carbohydrate cluster microarrays. This technology utilizes a 3-dimensional (3-D) poly(amidoamine) starburst dendrimer monolayer assembled on glass surface, which is functionalized with terminal aminooxy and hydrazide groups for site-specific coupling of carbohydrates. A wide range of saccharides, including monosaccharides, oligosaccharides and polysaccharides of diverse structures, are applicable for the 3-D bioarray platform without prior chemical derivatization. The process of carbohydrate coupling is effectively accelerated by microwave radiation energy. The carbohydrate concentration required for microarray fabrication is substantially reduced using this technology. Importantly, this bioarray platform presents sugar chains in defined orientation and cluster configurations. It is, thus, uniquely useful for exploration of the structural and conformational diversities of glyco-epitope and their functional properties. PMID:19791771
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Retinoid-Related Orphan Receptor β and Transcriptional Control of Neuronal Differentiation.
Liu, Hong; Aramaki, Michihiko; Fu, Yulong; Forrest, Douglas
2017-01-01
The ability to generate neuronal diversity is central to the function of the nervous system. Here we discuss the key neurodevelopmental roles of retinoid-related orphan receptor β (RORβ) encoded by the Rorb (Nr1f2) gene. Recent studies have reported loss of function of the human RORB gene in cases of familial epilepsy and intellectual disability. Principal sites of expression of the Rorb gene in model species include sensory organs, the spinal cord, and brain regions that process sensory and circadian information. Genetic analyses in mice have indicated functions in circadian behavior, vision, and, at the cellular level, the differentiation of specific neuronal cell types. Studies in the retina and sensory areas of the cerebral cortex suggest that this orphan nuclear receptor acts at decisive steps in transcriptional hierarchies that determine neuronal diversity. 2017 Published by Elsevier Inc.
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Nocturnality constrains morphological and functional diversity in the eyes of reef fishes.
Schmitz, Lars; Wainwright, Peter C
2011-11-19
Ambient light levels are often considered to drive the evolution of eye form and function. Diel activity pattern is the main mechanism controlling the visual environment of teleost reef fish, with day-active (diurnal) fish active in well-illuminated conditions, whereas night-active (nocturnal) fish cope with dim light. Physiological optics predicts several specific evolutionary responses to dim-light vision that should be reflected in visual performance features of the eye. We analyzed a large comparative dataset on morphological traits of the eyes in 265 species of teleost reef fish in 43 different families. The eye morphology of nocturnal reef teleosts is characterized by a syndrome that indicates better light sensitivity, including large relative eye size, high optical ratio and large, rounded pupils. Improved dim-light image formation comes at the cost of reduced depth of focus and reduction of potential accommodative lens movement. Diurnal teleost reef fish, released from the stringent functional requirements of dim-light vision have much higher morphological and optical diversity than nocturnal species, with large ranges of optical ratio, depth of focus, and lens accommodation. Physical characteristics of the environment are an important factor in the evolution and diversification of the vertebrate eye. Both teleost reef fish and terrestrial amniotes meet the functional requirements of dim-light vision with a similar evolutionary response of morphological and optical modifications. The trade-off between improved dim-light vision and reduced optical diversity may be a key factor in explaining the lower trophic diversity of nocturnal reef teleosts.
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Diversity and function in microbial mats from the Lucky Strike hydrothermal vent field.
Crépeau, Valentin; Cambon Bonavita, Marie-Anne; Lesongeur, Françoise; Randrianalivelo, Henintsoa; Sarradin, Pierre-Marie; Sarrazin, Jozée; Godfroy, Anne
2011-06-01
Diversity and function in microbial mats from the Lucky Strike hydrothermal vent field (Mid-Atlantic Ridge) were investigated using molecular approaches. DNA and RNA were extracted from mat samples overlaying hydrothermal deposits and Bathymodiolus azoricus mussel assemblages. We constructed and analyzed libraries of 16S rRNA gene sequences and sequences of functional genes involved in autotrophic carbon fixation [forms I and II RuBisCO (cbbL/M), ATP-citrate lyase B (aclB)]; methane oxidation [particulate methane monooxygenase (pmoA)] and sulfur oxidation [adenosine-5'-phosphosulfate reductase (aprA) and soxB]. To gain new insights into the relationships between mats and mussels, we also used new domain-specific 16S rRNA gene primers targeting Bathymodiolus sp. symbionts. All identified archaeal sequences were affiliated with a single group: the marine group 1 Thaumarchaeota. In contrast, analyses of bacterial sequences revealed much higher diversity, although two phyla Proteobacteria and Bacteroidetes were largely dominant. The 16S rRNA gene sequence library revealed that species affiliated to Beggiatoa Gammaproteobacteria were the dominant active population. Analyses of DNA and RNA functional gene libraries revealed a diverse and active chemolithoautotrophic population. Most of these sequences were affiliated with Gammaproteobacteria, including hydrothermal fauna symbionts, Thiotrichales and Methylococcales. PCR and reverse transcription-PCR using 16S rRNA gene primers targeted to Bathymodiolus sp. symbionts revealed sequences affiliated with both methanotrophic and thiotrophic endosymbionts. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.
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Soil fertility and plant diversity enhance microbial performance in metal-polluted soils.
Stefanowicz, Anna M; Kapusta, Paweł; Szarek-Łukaszewska, Grażyna; Grodzińska, Krystyna; Niklińska, Maria; Vogt, Rolf D
2012-11-15
This study examined the effects of soil physicochemical properties (including heavy metal pollution) and vegetation parameters on soil basal respiration, microbial biomass, and the activity and functional richness of culturable soil bacteria and fungi. In a zinc and lead mining area (S Poland), 49 sites were selected to represent all common plant communities and comprise the area's diverse soil types. Numerous variables describing habitat properties were reduced by PCA to 7 independent factors, mainly representing subsoil type (metal-rich mining waste vs. sand), soil fertility (exchangeable Ca, Mg and K, total C and N, organic C), plant species richness, phosphorus content, water-soluble heavy metals (Zn, Cd and Pb), clay content and plant functional diversity (based on graminoids, legumes and non-leguminous forbs). Multiple regression analysis including these factors explained much of the variation in most microbial parameters; in the case of microbial respiration and biomass, it was 86% and 71%, respectively. The activity of soil microbes was positively affected mainly by soil fertility and, apparently, by the presence of mining waste in the subsoil. The mining waste contained vast amounts of trace metals (total Zn, Cd and Pb), but it promoted microbial performance due to its inherently high content of macronutrients (total Ca, Mg, K and C). Plant species richness had a relatively strong positive effect on all microbial parameters, except for the fungal component. In contrast, plant functional diversity was practically negligible in its effect on microbes. Other explanatory variables had only a minor positive effect (clay content) or no significant influence (phosphorus content) on microbial communities. The main conclusion from this study is that high nutrient availability and plant species richness positively affected the soil microbes and that this apparently counteracted the toxic effects of metal contamination. Copyright © 2012 Elsevier B.V. All rights reserved.
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[Research on functional diversity of microorganisms on jujube fruit surface in storage].
Sha, Yuexia
2009-10-01
Disease during storage caused by microbial infection is a serious problem of jujube fruits. The aim of the study was to characterize the microbial diversity in stored jujube fruits. I used Biolog in experiment. The types of micro-plates were Filamentous Fungi micro-plate and Economicmicro-plate. There was much difference in microbial functional diversity on the surface of stored jujube fruit. The microbial functional diversity of stored 30 days was richer than it of stored 15 days. The diversity, homogeneity and average well color development of jujube used by fruit perservatives were lower than it not used by fruit preservatives. There were six kinds of the characteristic carbon. Our study firstly showed microbial diversity on the surface of stored jujube fruit. Biolog could be applied in the research on microbial functional diversity of fruit surface.
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Habitat diversity and ecosystem multifunctionality—The importance of direct and indirect effects
Alsterberg, Christian; Roger, Fabian; Sundbäck, Kristina; Juhanson, Jaanis; Hulth, Stefan; Hallin, Sara; Gamfeldt, Lars
2017-01-01
Ecosystems worldwide are facing habitat homogenization due to human activities. Although it is commonly proposed that such habitat homogenization can have negative repercussions for ecosystem functioning, this question has yet to receive explicit scientific attention. We expand on the framework for evaluating the functional consequences of biodiversity loss by scaling up from the level of species to the level of the entire habitats. Just as species diversity generally fosters ecosystem functioning through positive interspecies interactions, we hypothesize that different habitats within ecosystems can facilitate each other through structural complementarity and through exchange of material and energy across habitats. We show that experimental ecosystems comprised of a diversity of habitats show higher levels of multiple ecosystem functions than ecosystems with low habitat diversity. Our results demonstrate that the effect of habitat diversity on multifunctionality varies with season; it has direct effects on ecosystem functioning in summer and indirect effects, via changes in species diversity, in autumn, but no effect in spring. We propose that joint consideration of habitat diversity and species diversity will prove valuable for both environmental management and basic research. PMID:28246634
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Mouchet, Maud A; Bouvier, Corinne; Bouvier, Thierry; Troussellier, Marc; Escalas, Arthur; Mouillot, David
2012-03-01
Considering the major involvement of gut microflora in the digestive function of various macro-organisms, bacterial communities inhabiting fish guts may be the main actors of organic matter degradation by fish. Nevertheless, the extent and the sources of variability in the degradation potential of gut bacterial communities are largely overlooked. Using Biolog Ecoplate™ and denaturing gradient gel electrophoresis (DGGE), we explored functional (i.e. the ability to degrade organic matter) and genetic (i.e. identification of DGGE banding patterns) diversity of fish gut bacterial communities, respectively. Gut bacterial communities were extracted from fish species characterized by different diets sampled along a salinity gradient in the Patos-Mirim lagoons complex (Brazil). We found that functional diversity was surprisingly unrelated to genetic diversity of gut bacterial communities. Functional diversity was not affected by the sampling site but by fish species and diet, whereas genetic diversity was significantly influenced by all three factors. Overall, the functional diversity was consistently high across fish individuals and species, suggesting a wide functional niche breadth and a high potential of organic matter degradation. We conclude that fish gut bacterial communities may strongly contribute to nutrient cycling regardless of their genetic diversity and environment. © European Union 2011.
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Functional Diversity of Microbial Communities in Sludge-Amended Soils
NASA Astrophysics Data System (ADS)
Sun, Y. H.; Yang, Z. H.; Zhao, J. J.; Li, Q.
The BIOLOG method was applied to exploration of functional diversity of soil microbial communities in sludge-amended soils sampled from the Yangtze River Delta. Results indicated that metabolic profile, functional diversity indexes and Kinetic parameters of the soil microbial communities changed following soil amendment with sewage sludge, suggesting that the changes occurred in population of the microbes capable of exploiting carbon substrates and in this capability as well. The kinetic study of the functional diversity revealed that the metabolic profile of the soil microbial communities exhibited non-linear correlation with the incubation time, showing a curse of sigmoid that fits the dynamic model of growth of the soil microbial communities. In all the treatments, except for treatments of coastal fluvo-aquic soil amended with fresh sludge and dried sludge from Hangzhou, kinetic parameters K and r of the functional diversity of the soil microbial communities decreased significantly and parameter S increased. Changes in characteristics of the functional diversity well reflected differences in C utilizing capacity and model of the soil microbial communities in the sludge-amended soils, and changes in functional diversity of the soil microbial communities in a particular eco-environment, like soil amended with sewage sludge.
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Yang, Jie; Swenson, Nathan G; Zhang, Guocheng; Ci, Xiuqin; Cao, Min; Sha, Liqing; Li, Jie; Ferry Slik, J W; Lin, Luxiang
2015-08-03
The relative degree to which stochastic and deterministic processes underpin community assembly is a central problem in ecology. Quantifying local-scale phylogenetic and functional beta diversity may shed new light on this problem. We used species distribution, soil, trait and phylogenetic data to quantify whether environmental distance, geographic distance or their combination are the strongest predictors of phylogenetic and functional beta diversity on local scales in a 20-ha tropical seasonal rainforest dynamics plot in southwest China. The patterns of phylogenetic and functional beta diversity were generally consistent. The phylogenetic and functional dissimilarity between subplots (10 × 10 m, 20 × 20 m, 50 × 50 m and 100 × 100 m) was often higher than that expected by chance. The turnover of lineages and species function within habitats was generally slower than that across habitats. Partitioning the variation in phylogenetic and functional beta diversity showed that environmental distance was generally a better predictor of beta diversity than geographic distance thereby lending relatively more support for deterministic environmental filtering over stochastic processes. Overall, our results highlight that deterministic processes play a stronger role than stochastic processes in structuring community composition in this diverse assemblage of tropical trees.
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2017-01-01
We assessed changes in phylogenetic diversity of angiosperm flora on six oceanic islands located in the southeastern Pacific Ocean, by comparing flora from two periods: the pre-European colonization of islands and current times. We hypothesize that, in the time between these periods, extinction of local plant species and addition of exotic plants modified phylogenetic-α-diversity at different levels (deeper and terminal phylogeny) and increased phylo-β-diversity among islands. Based on floristic studies, we assembled a phylogenetic tree from occurrence data that includes 921 species, of which 165 and 756 were native or exotic in origin, respectively. Then, we studied change in the phylo-α-diversity and phylo-β-diversity (1 –Phylosor) by comparing pre-European and current times. Despite extinction of 18 native angiosperm species, an increase in species richness and phylo-α-diversity was observed for all islands studied, attributed to introduction of exotic plants (between 6 to 477 species per island). We did not observe significant variation of mean phylogenetic distance (MPD), a measure of the ‘deeper’ phylogenetic diversity of assemblages (e.g., orders, families), suggesting that neither extinctions nor introductions altered phylogenetic structure of the angiosperms of these islands. In regard to phylo-β-diversity, we detected temporal turnover (variation in phylogenetic composition) between periods to flora (0.38 ± 0.11). However, when analyses were performed only considering native plants, we did not observe significant temporal turnover between periods (0.07 ± 0.06). These results indicate that introduction of exotic angiosperms has contributed more notably than extinctions to the configuration of plant assemblages and phylogenetic diversity on the studied islands. Because phylogenetic diversity is closely related to functional diversity (species trait variations and roles performed by organisms), our results suggests that the introduction of exotic plants to these islands could have detrimental impacts for ecosystem functions and ecosystem services that islands provide (e.g. productivity). PMID:28763508
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Human-mediated loss of phylogenetic and functional diversity in coral reef fishes.
D'agata, Stéphanie; Mouillot, David; Kulbicki, Michel; Andréfouët, Serge; Bellwood, David R; Cinner, Joshua E; Cowman, Peter F; Kronen, Mecki; Pinca, Silvia; Vigliola, Laurent
2014-03-03
Beyond the loss of species richness, human activities may also deplete the breadth of evolutionary history (phylogenetic diversity) and the diversity of roles (functional diversity) carried out by species within communities, two overlooked components of biodiversity. Both are, however, essential to sustain ecosystem functioning and the associated provision of ecosystem services, particularly under fluctuating environmental conditions. We quantified the effect of human activities on the taxonomic, phylogenetic, and functional diversity of fish communities in coral reefs, while teasing apart the influence of biogeography and habitat along a gradient of human pressure across the Pacific Ocean. We detected nonlinear relationships with significant breaking points in the impact of human population density on phylogenetic and functional diversity of parrotfishes, at 25 and 15 inhabitants/km(2), respectively, while parrotfish species richness decreased linearly along the same population gradient. Over the whole range, species richness decreased by 11.7%, while phylogenetic and functional diversity dropped by 35.8% and 46.6%, respectively. Our results call for caution when using species richness as a benchmark for measuring the status of ecosystems since it appears to be less responsive to variation in human population densities than its phylogenetic and functional counterparts, potentially imperiling the functioning of coral reef ecosystems. Copyright © 2014 Elsevier Ltd. All rights reserved.
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Cesar Hinojo Hinojo; Alejandro E. Castellanos; Jose M. Llano Sotelo
2013-01-01
Although the Sonoran Desert does not have the highest plant species richness, it has been documented with the highest growth form diversity from the North American deserts. It is not known if this high growth form diversity could also harbor a high functional diversity. In this study we characterize the ecophysiological functional traits of photosynthetic capacity,...
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Lipskaya-Velikovsky, Lena; Jarus, Tal; Kotler, Moshe
2017-06-01
Participation in day-to-day activities of people with schizophrenia is restricted, causing concern to them, their families, service providers and the communities at large. Participation is a significant component of health and recovery; however, factors predicting participation are still not well established. This study examines whether the parameters obtained during acute hospitalization can predict the intensity and diversity of participation in day-to-day activities six months after discharge. In-patients with chronic schizophrenia (N = 104) were enrolled into the study and assessed for cognitive functioning, functional capacity in instrumental activities of daily living (IADL), and symptoms. Six months after discharge, the intensity and diversity of participation in day-to-day activities were evaluated (N = 70). Multiple correlations were found between parameters obtained during hospitalization and participation diversity, but not participation intensity. The model that is better suited to the prediction of participation diversity contains cognitive ability of construction, negative symptoms and number of previous hospitalizations. The total explained variance is 37.8% (F 3,66 = 14.99, p < 0.001). This study provides evidence for ecological validity of the in-patient evaluation process for the prediction of participation diversity in day-to-day activities six months after discharge. Participation diversity is best predicted through a set of factors reflecting personal and environmental indicators. Implications for rehabilitation Results of in-patient evaluations can predict the diversity of participation in day-to-day activities six months after discharge. Higher prediction of participation diversity is obtained using a holistic evaluation model that includes assessments for cognitive abilities, negative symptoms severity and number of hospitalizations.
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Ordonez, Alejandro; Svenning, Jens-Christian
2017-02-23
Current and historical environmental conditions are known to determine jointly contemporary species distributions and richness patterns. However, whether historical dynamics in species distributions and richness translate to functional diversity patterns remains, for the most part, unknown. The geographic patterns of plant functional space size (richness) and packing (dispersion) for six widely distributed orders of European angiosperms were estimated using atlas distribution data and trait information. Then the relative importance of late-Quaternary glacial-interglacial climate change and contemporary environmental factors (climate, productivity, and topography) as determinants of functional diversity of evaluated orders was assesed. Functional diversity patterns of all evaluated orders exhibited prominent glacial-interglacial climate change imprints, complementing the influence of contemporary environmental conditions. The importance of Quaternary glacial-interglacial climate change factors was comparable to that of contemporary environmental factors across evaluated orders. Therefore, high long-term paleoclimate variability has imposed consistent supplementary constraints on functional diversity of multiple plant groups, a legacy that may permeate to ecosystem functioning and resilience. These findings suggest that strong near-future anthropogenic climate change may elicit long-term functional disequilibria in plant functional diversity.
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Frontiers in research on biodiversity and disease.
Johnson, Pieter T J; Ostfeld, Richard S; Keesing, Felicia
2015-10-01
Global losses of biodiversity have galvanised efforts to understand how changes to communities affect ecological processes, including transmission of infectious pathogens. Here, we review recent research on diversity-disease relationships and identify future priorities. Growing evidence from experimental, observational and modelling studies indicates that biodiversity changes alter infection for a range of pathogens and through diverse mechanisms. Drawing upon lessons from the community ecology of free-living organisms, we illustrate how recent advances from biodiversity research generally can provide necessary theoretical foundations, inform experimental designs, and guide future research at the interface between infectious disease risk and changing ecological communities. Dilution effects are expected when ecological communities are nested and interactions between the pathogen and the most competent host group(s) persist or increase as biodiversity declines. To move beyond polarising debates about the generality of diversity effects and develop a predictive framework, we emphasise the need to identify how the effects of diversity vary with temporal and spatial scale, to explore how realistic patterns of community assembly affect transmission, and to use experimental studies to consider mechanisms beyond simple changes in host richness, including shifts in trophic structure, functional diversity and symbiont composition. © 2015 John Wiley & Sons Ltd/CNRS.
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Radziwiłłowicz, Wioletta; Lewandowska, Magdalena
2017-04-30
The aim of the study was to analyze the relationships between clinical variables (the severity of depression symptoms, feelings towards the body, dissociation, number and type of traumatic events) and deliberate self-injury functions. Moreover, we investigated whether the of group self-mutilating adolescents is internally diverse in terms of how important individual functions of self-mutilation are, and whether the subgroups singled out by these functions differ between each other in terms of clinical variables. The Inventory of Statements about Self-Injury was used. Characterizations of examined individuals and other research tools are included in our previous article (year, issue, pages). Associated with negative feelings towards the body are the functions of self-injuries (anti-dissociation, self-punishment) that can be described as interpersonal. High levels of depression symptoms (self-depreciation included) are mainly associated with the self-injury functions: self-punishment, anti-dissociation, establishing interpersonal boundaries. Affect regulation becomes more important as a function of self-inflicted injuries in cases of biological dysregulation and intense dissociative symptoms. The adolescents psychiatric inpatients are internally diverse in terms of dominant functions of self-injuries, which can be categorized into intra- and interpersonal. Intrapersonal functions dominate when an individual experiences severe depression, dissociative symptoms, and negative feelings towards the body. In cases of moderate intensity of depression, dissociative symptoms and negative feelings towards the body, both intrapersonal and interpersonal functions of self-mutilation are similarly important. Further research is required to explain the lowest severity of depression symptoms, dissociative symptoms and negative feelings towards the body co-occurs with no awareness of self-injuries functions.
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Luckett, Brian G; DeClerck, Fabrice A J; Fanzo, Jessica; Mundorf, Adrienne R; Rose, Donald
2015-09-01
Dietary diversity is associated with nutrient adequacy and positive health outcomes but indicators to measure diversity have focused primarily on consumption, rather than sustainable provisioning of food. The Nutritional Functional Diversity score was developed by ecologists to describe the contribution of biodiversity to sustainable diets. We have employed this tool to estimate the relative contribution of home production and market purchases in providing nutritional diversity to agricultural households in Malawi and examine how food system provisioning varies by time, space and socio-economic conditions. A secondary analysis of nationally representative household consumption data to test the applicability of the Nutritional Functional Diversity score. The data were collected between 2010 and 2011 across the country of Malawi. Households (n 11 814) from predominantly rural areas of Malawi. Nutritional Functional Diversity varied demographically, geographically and temporally. Nationally, purchased foods contributed more to household nutritional diversity than home produced foods (mean score=17·5 and 7·8, respectively). Households further from roads and population centres had lower overall diversity (P<0·01) and accessed relatively more of their diversity from home production than households closer to market centres (P<0·01). Nutritional diversity was lowest during the growing season when farmers plant and tend crops (P<0·01). The present analysis demonstrates that the Nutritional Functional Diversity score is an effective indicator for identifying populations with low nutritional diversity and the relative roles that markets, agricultural extension and home production play in achieving nutritional diversity. This information may be used by policy makers to plan agricultural and market-based interventions that support sustainable diets and local food systems.
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Chen, Chuanrui; Karshalev, Emil; Guan, Jianguo; Wang, Joseph
2018-06-01
The new capabilities and functionalities of synthetic micro/nanomotors open up considerable opportunities for diverse environmental and biomedical applications. Water-powered micromachines are particularly attractive for realizing many of these applications. Magnesium-based motors directly use water as fuel to generate hydrogen bubbles for their propulsion, eliminating the requirement of common toxic fuels. This Review highlights the development of new Mg-based micromotors and discusses the chemistry that makes it extremely attractive for micromotor applications. Understanding these Mg properties and its transient nature is essential for controlling the propulsion efficiency, lifetime, and overall performance. The unique and attractive behavior of Mg offers significant advantages, including efficient water-powered movement, remarkable biocompatibility, controlled degradation, convenient functionalization, and built-in acid neutralization ability, and has paved the way for multifunctional micromachines for diverse real-life applications, including operation in living animals. A wide range of such Mg motor-based applications, including the detection and destruction of environmental threats, effective in-vivo cargo delivery, and autonomous release, have been demonstrated. In conclusion, the current challenges, future opportunities, and performance improvements of the Mg-based micromotors are discussed. With continuous innovation and attention to key challenges, it is expected that Mg-based motors will have a profound impact on diverse biomedical and environmental applications. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Phylogenetic and functional diversity in large carnivore assemblages
Dalerum, F.
2013-01-01
Large terrestrial carnivores are important ecological components and prominent flagship species, but are often extinction prone owing to a combination of biological traits and high levels of human persecution. This study combines phylogenetic and functional diversity evaluations of global and continental large carnivore assemblages to provide a framework for conservation prioritization both between and within assemblages. Species-rich assemblages of large carnivores simultaneously had high phylogenetic and functional diversity, but species contributions to phylogenetic and functional diversity components were not positively correlated. The results further provide ecological justification for the largest carnivore species as a focus for conservation action, and suggests that range contraction is a likely cause of diminishing carnivore ecosystem function. This study highlights that preserving species-rich carnivore assemblages will capture both high phylogenetic and functional diversity, but that prioritizing species within assemblages will involve trade-offs between optimizing contemporary ecosystem function versus the evolutionary potential for future ecosystem performance. PMID:23576787
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77 FR 48553 - Notice of Intent To Seek Approval To Establish an Information Collection
Federal Register 2010, 2011, 2012, 2013, 2014
2012-08-14
... functions of the Foundation, including whether the information will have practical utility; (b) the accuracy.... Our goal is to gain an understanding of the climate of diversity within the ERCs. Need and Use of...
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Gagic, Vesna; Bartomeus, Ignasi; Jonsson, Tomas; Taylor, Astrid; Winqvist, Camilla; Fischer, Christina; Slade, Eleanor M.; Steffan-Dewenter, Ingolf; Emmerson, Mark; Potts, Simon G.; Tscharntke, Teja; Weisser, Wolfgang; Bommarco, Riccardo
2015-01-01
Drastic biodiversity declines have raised concerns about the deterioration of ecosystem functions and have motivated much recent research on the relationship between species diversity and ecosystem functioning. A functional trait framework has been proposed to improve the mechanistic understanding of this relationship, but this has rarely been tested for organisms other than plants. We analysed eight datasets, including five animal groups, to examine how well a trait-based approach, compared with a more traditional taxonomic approach, predicts seven ecosystem functions below- and above-ground. Trait-based indices consistently provided greater explanatory power than species richness or abundance. The frequency distributions of single or multiple traits in the community were the best predictors of ecosystem functioning. This implies that the ecosystem functions we investigated were underpinned by the combination of trait identities (i.e. single-trait indices) and trait complementarity (i.e. multi-trait indices) in the communities. Our study provides new insights into the general mechanisms that link biodiversity to ecosystem functioning in natural animal communities and suggests that the observed responses were due to the identity and dominance patterns of the trait composition rather than the number or abundance of species per se. PMID:25567651
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Response Diversity and Resilience in Social-Ecological Systems
Leslie, Paul; McCabe, J. Terrence
2013-01-01
Recent work in ecology suggests that the diversity of responses to environmental change among species contributing to the same ecosystem function can strongly influence ecosystem resilience. To render this important realization more useful for understanding coupled human-natural systems, we broaden the concept of response diversity to include heterogeneity in human decisions and action. Simply put, not all actors respond the same way to challenges, opportunities, and risks. The range, prevalence, and spatial and temporal distributions of different responses may be crucial to the resilience or the transformation of a social-ecological system, and thus have a bearing on human vulnerability and well-being in the face of environmental, socioeconomic, and political change. Response diversity can be seen at multiple scales (e.g., household, village, region) and response diversity at one scale may act synergistically with or contrary to the effects of diversity at another scale. Although considerable research on the sources of response diversity has been done, our argument is that the consequences of response diversity warrant closer attention. We illustrate this argument with examples drawn from our studies of two East African pastoral populations and discuss the relationship of response diversity to characteristics of social-ecological systems that can promote or diminish resilience. PMID:24855324
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Functional Redundancy Patterns Reveal Non-Random Assembly Rules in a Species-Rich Marine Assemblage
Guillemot, Nicolas; Kulbicki, Michel; Chabanet, Pascale; Vigliola, Laurent
2011-01-01
The relationship between species and the functional diversity of assemblages is fundamental in ecology because it contains key information on functional redundancy, and functionally redundant ecosystems are thought to be more resilient, resistant and stable. However, this relationship is poorly understood and undocumented for species-rich coastal marine ecosystems. Here, we used underwater visual censuses to examine the patterns of functional redundancy for one of the most diverse vertebrate assemblages, the coral reef fishes of New Caledonia, South Pacific. First, we found that the relationship between functional and species diversity displayed a non-asymptotic power-shaped curve, implying that rare functions and species mainly occur in highly diverse assemblages. Second, we showed that the distribution of species amongst possible functions was significantly different from a random distribution up to a threshold of ∼90 species/transect. Redundancy patterns for each function further revealed that some functions displayed fast rates of increase in redundancy at low species diversity, whereas others were only becoming redundant past a certain threshold. This suggested non-random assembly rules and the existence of some primordial functions that would need to be fulfilled in priority so that coral reef fish assemblages can gain a basic ecological structure. Last, we found little effect of habitat on the shape of the functional-species diversity relationship and on the redundancy of functions, although habitat is known to largely determine assemblage characteristics such as species composition, biomass, and abundance. Our study shows that low functional redundancy is characteristic of this highly diverse fish assemblage, and, therefore, that even species-rich ecosystems such as coral reefs may be vulnerable to the removal of a few keystone species. PMID:22039543
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ERIC Educational Resources Information Center
Bailey, Christopher A.; Ostrov, Jamie M.
2008-01-01
The purpose of this study was to extend the current literature on forms (i.e., physical and relational) and functions (i.e., proactive and reactive) of participants' cognitions and beliefs about aggressive behavior. Participants included an ethnically diverse group of emerging adults (N = 165; M = 19.05 years; SD = 1.55) and completed a battery of…
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Sitters, Holly; York, Alan; Swan, Matthew; Christie, Fiona; Di Stefano, Julian
2016-01-01
Disturbance regimes are changing worldwide, and the consequences for ecosystem function and resilience are largely unknown. Functional diversity (FD) provides a surrogate measure of ecosystem function by capturing the range, abundance and distribution of trait values in a community. Enhanced understanding of the responses of FD to measures of vegetation structure at landscape scales is needed to guide conservation management. To address this knowledge gap, we used a whole-of-landscape sampling approach to examine relationships between bird FD, vegetation diversity and time since fire. We surveyed birds and measured vegetation at 36 landscape sampling units in dry and wet forest in southeast Australia during 2010 and 2011. Four uncorrelated indices of bird FD (richness, evenness, divergence and dispersion) were derived from six bird traits, and we investigated responses of these indices and species richness to both vertical and horizontal vegetation diversity using linear mixed models. We also considered the extent to which the mean and diversity of time since fire were related to vegetation diversity. Results showed opposing responses of FD to vegetation diversity in dry and wet forest. In dry forest, where fire is frequent, species richness and two FD indices (richness and dispersion) were positively related to vertical vegetation diversity, consistent with theory relating to environmental variation and coexistence. However, in wet forest subject to infrequent fire, the same three response variables were negatively associated with vertical diversity. We suggest that competitive dominance by species results in lower FD as vegetation diversity increases in wet forest. The responses of functional evenness were opposite to those of species richness, functional richness and dispersion in both forest types, highlighting the value of examining multiple FD metrics at management-relevant scales. The mean and diversity of time since fire were uncorrelated with vegetation diversity in wet forest, but positively correlated with vegetation diversity in dry forest. We therefore suggest that protection of older vegetation is important, but controlled application of low-severity fire in dry forest may sustain ecosystem function by enhancing different elements of FD.
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York, Alan; Swan, Matthew; Christie, Fiona; Di Stefano, Julian
2016-01-01
Disturbance regimes are changing worldwide, and the consequences for ecosystem function and resilience are largely unknown. Functional diversity (FD) provides a surrogate measure of ecosystem function by capturing the range, abundance and distribution of trait values in a community. Enhanced understanding of the responses of FD to measures of vegetation structure at landscape scales is needed to guide conservation management. To address this knowledge gap, we used a whole-of-landscape sampling approach to examine relationships between bird FD, vegetation diversity and time since fire. We surveyed birds and measured vegetation at 36 landscape sampling units in dry and wet forest in southeast Australia during 2010 and 2011. Four uncorrelated indices of bird FD (richness, evenness, divergence and dispersion) were derived from six bird traits, and we investigated responses of these indices and species richness to both vertical and horizontal vegetation diversity using linear mixed models. We also considered the extent to which the mean and diversity of time since fire were related to vegetation diversity. Results showed opposing responses of FD to vegetation diversity in dry and wet forest. In dry forest, where fire is frequent, species richness and two FD indices (richness and dispersion) were positively related to vertical vegetation diversity, consistent with theory relating to environmental variation and coexistence. However, in wet forest subject to infrequent fire, the same three response variables were negatively associated with vertical diversity. We suggest that competitive dominance by species results in lower FD as vegetation diversity increases in wet forest. The responses of functional evenness were opposite to those of species richness, functional richness and dispersion in both forest types, highlighting the value of examining multiple FD metrics at management-relevant scales. The mean and diversity of time since fire were uncorrelated with vegetation diversity in wet forest, but positively correlated with vegetation diversity in dry forest. We therefore suggest that protection of older vegetation is important, but controlled application of low-severity fire in dry forest may sustain ecosystem function by enhancing different elements of FD. PMID:27741290
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Hisano, Masumi; Searle, Eric B; Chen, Han Y H
2018-02-01
Forest ecosystems are critical to mitigating greenhouse gas emissions through carbon sequestration. However, climate change has affected forest ecosystem functioning in both negative and positive ways, and has led to shifts in species/functional diversity and losses in plant species diversity which may impair the positive effects of diversity on ecosystem functioning. Biodiversity may mitigate climate change impacts on (I) biodiversity itself, as more-diverse systems could be more resilient to climate change impacts, and (II) ecosystem functioning through the positive relationship between diversity and ecosystem functioning. By surveying the literature, we examined how climate change has affected forest ecosystem functioning and plant diversity. Based on the biodiversity effects on ecosystem functioning (B→EF), we specifically address the potential for biodiversity to mitigate climate change impacts on forest ecosystem functioning. For this purpose, we formulate a concept whereby biodiversity may reduce the negative impacts or enhance the positive impacts of climate change on ecosystem functioning. Further B→EF studies on climate change in natural forests are encouraged to elucidate how biodiversity might influence ecosystem functioning. This may be achieved through the detailed scrutiny of large spatial/long temporal scale data sets, such as long-term forest inventories. Forest management strategies based on B→EF have strong potential for augmenting the effectiveness of the roles of forests in the mitigation of climate change impacts on ecosystem functioning. © 2017 Cambridge Philosophical Society.
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Degradation in landscape matrix has diverse impacts on diversity in protected areas
Brotons, Lluís; Rajasärkkä, Ari; Tornberg, Risto
2017-01-01
Introduction A main goal of protected areas is to maintain species diversity and the integrity of biological assemblages. Intensifying land use in the matrix surrounding protected areas creates a challenge for biodiversity conservation. Earlier studies have mainly focused on taxonomic diversity within protected areas. However, functional and especially phylogenetic diversities are less studied phenomena, especially with respect to the impacts of the matrix that surrounds protected areas. Phylogenetic diversity refers to the range of evolutionary lineages, the maintenance of which ensures that future evolutionary potential is safeguarded. Functional diversity refers to the range of ecological roles that members of a community perform. For ecosystem functioning and long-term resilience, they are at least as important as taxonomic diversity. Aim We studied how the characteristics of protected areas and land use intensity in the surrounding matrix affect the diversity of bird communities in protected boreal forests. We used line-transect count and land-cover data from 91 forest reserves in Northern Finland, and land-cover data from buffer zones surrounding these reserves. We studied if habitat diversity and productivity inside protected areas, and intensity of forest management in the matrix have consistent effects on taxonomic, functional and phylogenetic diversities, and community specialization. Results We found that habitat diversity and productivity inside protected areas have strong effects on all diversity metrics, but matrix effects were inconsistent. The proportion of old forest in the matrix, reflecting low intensity forest management, had positive effects on community specialization. Interestingly, functional diversity increased with increasing logging intensity in the matrix. Conclusions Our results indicate that boreal forest reserves are not able to maintain their species composition and abundances if embedded in a severely degraded matrix. Our study also highlights the importance of focusing on different aspects of biodiversity. PMID:28950017
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Plant Diversity Impacts Decomposition and Herbivory via Changes in Aboveground Arthropods
Ebeling, Anne; Meyer, Sebastian T.; Abbas, Maike; Eisenhauer, Nico; Hillebrand, Helmut; Lange, Markus; Scherber, Christoph; Vogel, Anja; Weigelt, Alexandra; Weisser, Wolfgang W.
2014-01-01
Loss of plant diversity influences essential ecosystem processes as aboveground productivity, and can have cascading effects on the arthropod communities in adjacent trophic levels. However, few studies have examined how those changes in arthropod communities can have additional impacts on ecosystem processes caused by them (e.g. pollination, bioturbation, predation, decomposition, herbivory). Therefore, including arthropod effects in predictions of the impact of plant diversity loss on such ecosystem processes is an important but little studied piece of information. In a grassland biodiversity experiment, we addressed this gap by assessing aboveground decomposer and herbivore communities and linking their abundance and diversity to rates of decomposition and herbivory. Path analyses showed that increasing plant diversity led to higher abundance and diversity of decomposing arthropods through higher plant biomass. Higher species richness of decomposers, in turn, enhanced decomposition. Similarly, species-rich plant communities hosted a higher abundance and diversity of herbivores through elevated plant biomass and C:N ratio, leading to higher herbivory rates. Integrating trophic interactions into the study of biodiversity effects is required to understand the multiple pathways by which biodiversity affects ecosystem functioning. PMID:25226237
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Bacterial dynamics in steady-state biofilters: beyond functional stability.
Cabrol, Léa; Malhautier, Luc; Poly, Franck; Lepeuple, Anne-Sophie; Fanlo, Jean-Louis
2012-01-01
The spatial and temporal dynamics of microbial community structure and function were surveyed in duplicated woodchip-biofilters operated under constant conditions for 231 days. The contaminated gaseous stream for treatment was representative of composting emissions, included ammonia, dimethyl disulfide and a mixture of five oxygenated volatile organic compounds. The community structure and diversity were investigated by denaturing gradient gel electrophoresis on 16S rRNA gene fragments. During the first 42 days, microbial acclimatization revealed the influence of operating conditions and contaminant loading on the biofiltration community structure and diversity, as well as the limited impact of inoculum compared to the greater persistence of the endogenous woodchip community. During long-term operation, a high and stable removal efficiency was maintained despite a highly dynamic microbial community, suggesting the probable functional redundancy of the community. Most of the contaminant removal occurred in the first compartment, near the gas inlet, where the microbial diversity was the highest. The stratification of the microbial structures along the filter bed was statistically correlated to the longitudinal distribution of environmental conditions (selective pressure imposed by contaminant concentrations) and function (contaminant elimination capacity), highlighting the central role of the bacterial community. The reproducibility of microbial succession in replicates suggests that the community changes were presumably driven by a deterministic process.
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Jassey, Vincent E J; Lamentowicz, Mariusz; Bragazza, Luca; Hofsommer, Maaike L; Mills, Robert T E; Buttler, Alexandre; Signarbieux, Constant; Robroek, Bjorn J M
2016-09-01
Soil microbial communities significantly contribute to global fluxes of nutrients and carbon. Their response to climate change, including winter warming, is expected to modify these processes through direct effects on microbial functions due to osmotic stress, and changing temperature regimes. Using four European peatlands reflecting different frequencies of frost events, we show that peatland testate amoeba communities diverge among sites with different winter climates, and that this is reflected through contrasting functions. We found that exposure to harder soil frost promoted species β-diversity (species turnover) thus shifting the community composition of testate amoebae. In particular, we found that harder soil frost, and lower water-soluble phenolic compounds, induced functional turnover through the decrease of large species (-68%, >80μm) and the increase of small-bodied mixotrophic species (i.e. Archerella flavum; +79%). These results suggest that increased exposure to soil frost could be highly limiting for large species while smaller species are more resistant. Furthermore, we found that β-glucosidase enzymatic activity, in addition to soil temperature, strongly depended of the functional diversity of testate amoebae (R 2 =0.95, ANOVA). Changing winter conditions can therefore strongly impact peatland decomposition process, though it remains unclear if these changes are carried-over to the growing season. Copyright © 2016 Elsevier GmbH. All rights reserved.
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Metagenomics and the protein universe
Godzik, Adam
2011-01-01
Metagenomics sequencing projects have dramatically increased our knowledge of the protein universe and provided over one-half of currently known protein sequences; they have also introduced a much broader phylogenetic diversity into the protein databases. The full analysis of metagenomic datasets is only beginning, but it has already led to the discovery of thousands of new protein families, likely representing novel functions specific to given environments. At the same time, a deeper analysis of such novel families, including experimental structure determination of some representatives, suggests that most of them represent distant homologs of already characterized protein families, and thus most of the protein diversity present in the new environments are due to functional divergence of the known protein families rather than the emergence of new ones. PMID:21497084
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Functional implications of Major Histocompatibility (MH) variation using estuarine fish populations.
Cohen, Sarah; Tirindelli, Joëlle; Gomez-Chiarri, Marta; Nacci, Diane
2006-12-01
Recently, there has been a dramatic expansion of studies of major histocompatibility complex (MHC) variation aimed at discovering functional differences in immunity across wild populations of diverse vertebrate species. Some species with relatively low genetic diversity or under strong directional selection by pathogens have revealed fascinating cases of MHC allelic disease linkage. More generally in genetically diverse species, however, these linkages may be hard to find. In this paper, we review approaches for assessing functional variation in MHC and discuss their potential use for discovering smaller-scale intraspecific spatial and temporal patterns of MHC variation. Then, we describe and illustrate an approach using the structural model to produce a population composite of variation in antigen-binding regions by mapping population-specific substitutions onto functional regions of the molecule. We are producing models of variation in major histocompatibility (MH) loci for populations of non-migratory fish (killifish, Fundulus heteroclitus) resident at sites that vary dramatically in environmental quality. We discuss the goal of relating MH population variation to functional differences in disease susceptibility such as those inferred by observations of parasitic infection and direct measurement of bacterial challenges in the laboratory. Our study has focused on relatively well-studied killifish populations, including those resident in a highly disturbed, chemically contaminated estuary and nearby less contaminated sites. Population-specific genetic changes at MHC antigen-binding loci are described, and evidence relevant to functional implications of these changes is reviewed. Population-specific patterns of variation in antigen-binding regions in combination with a range of assessments of immune function will provide a powerful new approach to reveal functional changes in MHC.
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Biological diversity can be divided into: alpha (α, local), beta (β, difference in assemblage composition among locals), and gamma (γ, total diversity). We assessed the partitioning of taxonomic diversity of Ephemeroptera, Plecoptera and Trichoptera (EPT) and of functional feedin...
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CONFIG: Integrated engineering of systems and their operation
NASA Technical Reports Server (NTRS)
Malin, Jane T.; Ryan, Dan; Fleming, Land
1994-01-01
This article discusses CONFIG 3, a prototype software tool that supports integrated conceptual design evaluation from early in the product life cycle, by supporting isolated or integrated modeling, simulation, and analysis of the function, structure, behavior, failures and operations of system designs. Integration and reuse of models is supported in an object-oriented environment providing capabilities for graph analysis and discrete event simulation. CONFIG supports integration among diverse modeling approaches (component view, configuration or flow path view, and procedure view) and diverse simulation and analysis approaches. CONFIG is designed to support integrated engineering in diverse design domains, including mechanical and electro-mechanical systems, distributed computer systems, and chemical processing and transport systems.
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Silva, Cynthia C; Hayden, Helen; Sawbridge, Tim; Mele, Pauline; Kruger, Ricardo H; Rodrigues, Marili Vn; Costa, Gustavo Gl; Vidal, Ramon O; Sousa, Maíra P; Torres, Ana Paula R; Santiago, Vânia Mj; Oliveira, Valéria M
2012-03-27
In petrochemical refinery wastewater treatment plants (WWTP), different concentrations of pollutant compounds are received daily in the influent stream, including significant amounts of phenolic compounds, creating propitious conditions for the development of particular microorganisms that can rapidly adapt to such environment. In the present work, the microbial sludge from a refinery WWTP was enriched for phenol, cloned into fosmid vectors and pyrosequenced. The fosmid libraries yielded 13,200 clones and a comprehensive bioinformatic analysis of the sequence data set revealed a complex and diverse bacterial community in the phenol degrading sludge. The phylogenetic analyses using MEGAN in combination with RDP classifier showed a massive predominance of Proteobacteria, represented mostly by the genera Diaphorobacter, Pseudomonas, Thauera and Comamonas. The functional classification of phenol degrading sludge sequence data set generated by MG-RAST showed the wide metabolic diversity of the microbial sludge, with a high percentage of genes involved in the aerobic and anaerobic degradation of phenol and derivatives. In addition, genes related to the metabolism of many other organic and xenobiotic compounds, such as toluene, biphenyl, naphthalene and benzoate, were found. Results gathered herein demonstrated that the phenol degrading sludge has complex phylogenetic and functional diversities, showing the potential of such community to degrade several pollutant compounds. This microbiota is likely to represent a rich resource of versatile and unknown enzymes which may be exploited for biotechnological processes such as bioremediation.
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Diversity of terrestrial mammal seed dispersers along a lowland Amazon forest regrowth gradient
Arévalo-Sandi, Alexander; Bobrowiec, Paulo Estefano D.; Rodriguez Chuma, Victor Juan Ulises
2018-01-01
There is increasing interest in the restoration/regeneration of degraded tropical habitats yet the potential role of natural regenerators remains unclear. We test the hypothesis that the richness and functional diversity of terrestrial mammals differs between forest regrowth stages. We quantified the richness and functional diversity of eight terrestrial mammal seed-disperser species across a forest regrowth gradient in the eastern Brazilian Amazon. We installed camera-traps in 15 sites within small-holder properties with forest regrowth stage classified into three groups, with five sites each of: late second-regrowth forest, early second-regrowth forest and abandoned pasture. Species richness and functional dispersion from the regrowth sites were compared with 15 paired forest control sites. Multi model selection showed that regrowth class was more important for explaining patterns in richness and functional diversity than other variables from three non-mutually exclusive hypotheses: hunting (distance to house, distance to river, distance to town, small holder residence), land cover (% forest cover within 50 meters, 1 kilometer and 5 kilometers) and land use (regrowth class, time since last use). Differences in functional diversity were most strongly explained by a loss of body mass. We found that diversity in regrowth sites could be similar to control sites even in some early-second regrowth areas. This finding suggests that when surrounded by large intact forest areas the richness and functional diversity close to human small-holdings can return to pre-degradation values. Yet we also found a significant reduction in richness and functional diversity in more intensely degraded pasture sites. This reduction in richness and functional diversity may limit the potential for regeneration and increase costs for ecological regeneration and restoration actions around more intense regrowth areas. PMID:29547648
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Medrano, Mónica; Herrera, Carlos M; Bazaga, Pilar
2014-10-01
The ecological significance of epigenetic variation has been generally inferred from studies on model plants under artificial conditions, but the importance of epigenetic differences between individuals as a source of intraspecific diversity in natural plant populations remains essentially unknown. This study investigates the relationship between epigenetic variation and functional plant diversity by conducting epigenetic (methylation-sensitive amplified fragment length polymorphisms, MSAP) and genetic (amplified fragment length polymorphisms, AFLP) marker-trait association analyses for 20 whole-plant, leaf and regenerative functional traits in a large sample of wild-growing plants of the perennial herb Helleborus foetidus from ten sampling sites in south-eastern Spain. Plants differed widely in functional characteristics, and exhibited greater epigenetic than genetic diversity, as shown by per cent polymorphism of MSAP fragments (92%) or markers (69%) greatly exceeding that for AFLP ones (41%). After controlling for genetic structuring and possible cryptic relatedness, every functional trait considered exhibited a significant association with at least one AFLP or MSAP marker. A total of 27 MSAP (13.0% of total) and 12 AFLP (4.4%) markers were involved in significant associations, which explained on average 8.2% and 8.0% of trait variance, respectively. Individual MSAP markers were more likely to be associated with functional traits than AFLP markers. Between-site differences in multivariate functional diversity were directly related to variation in multilocus epigenetic diversity after multilocus genetic diversity was statistically accounted for. Results suggest that epigenetic variation can be an important source of intraspecific functional diversity in H. foetidus, possibly endowing this species with the capacity to exploit a broad range of ecological conditions despite its modest genetic diversity. © 2014 John Wiley & Sons Ltd.
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Eisenhauer, Nico; Milcu, Alexandru; Sabais, Alexander C. W.; Bessler, Holger; Brenner, Johanna; Engels, Christof; Klarner, Bernhard; Maraun, Mark; Partsch, Stephan; Roscher, Christiane; Schonert, Felix; Temperton, Vicky M.; Thomisch, Karolin; Weigelt, Alexandra; Weisser, Wolfgang W.; Scheu, Stefan
2011-01-01
Background One of the most significant consequences of contemporary global change is the rapid decline of biodiversity in many ecosystems. Knowledge of the consequences of biodiversity loss in terrestrial ecosystems is largely restricted to single ecosystem functions. Impacts of key plant functional groups on soil biota are considered to be more important than those of plant diversity; however, current knowledge mainly relies on short-term experiments. Methodology/Principal Findings We studied changes in the impacts of plant diversity and presence of key functional groups on soil biota by investigating the performance of soil microorganisms and soil fauna two, four and six years after the establishment of model grasslands. The results indicate that temporal changes of plant community effects depend on the trophic affiliation of soil animals: plant diversity effects on decomposers only occurred after six years, changed little in herbivores, but occurred in predators after two years. The results suggest that plant diversity, in terms of species and functional group richness, is the most important plant community property affecting soil biota, exceeding the relevance of plant above- and belowground productivity and the presence of key plant functional groups, i.e. grasses and legumes, with the relevance of the latter decreasing in time. Conclusions/Significance Plant diversity effects on biota are not only due to the presence of key plant functional groups or plant productivity highlighting the importance of diverse and high-quality plant derived resources, and supporting the validity of the singular hypothesis for soil biota. Our results demonstrate that in the long term plant diversity essentially drives the performance of soil biota questioning the paradigm that belowground communities are not affected by plant diversity and reinforcing the importance of biodiversity for ecosystem functioning. PMID:21249208
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Diversity of terrestrial mammal seed dispersers along a lowland Amazon forest regrowth gradient.
Arévalo-Sandi, Alexander; Bobrowiec, Paulo Estefano D; Rodriguez Chuma, Victor Juan Ulises; Norris, Darren
2018-01-01
There is increasing interest in the restoration/regeneration of degraded tropical habitats yet the potential role of natural regenerators remains unclear. We test the hypothesis that the richness and functional diversity of terrestrial mammals differs between forest regrowth stages. We quantified the richness and functional diversity of eight terrestrial mammal seed-disperser species across a forest regrowth gradient in the eastern Brazilian Amazon. We installed camera-traps in 15 sites within small-holder properties with forest regrowth stage classified into three groups, with five sites each of: late second-regrowth forest, early second-regrowth forest and abandoned pasture. Species richness and functional dispersion from the regrowth sites were compared with 15 paired forest control sites. Multi model selection showed that regrowth class was more important for explaining patterns in richness and functional diversity than other variables from three non-mutually exclusive hypotheses: hunting (distance to house, distance to river, distance to town, small holder residence), land cover (% forest cover within 50 meters, 1 kilometer and 5 kilometers) and land use (regrowth class, time since last use). Differences in functional diversity were most strongly explained by a loss of body mass. We found that diversity in regrowth sites could be similar to control sites even in some early-second regrowth areas. This finding suggests that when surrounded by large intact forest areas the richness and functional diversity close to human small-holdings can return to pre-degradation values. Yet we also found a significant reduction in richness and functional diversity in more intensely degraded pasture sites. This reduction in richness and functional diversity may limit the potential for regeneration and increase costs for ecological regeneration and restoration actions around more intense regrowth areas.
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Changes in tree functional composition amplify the response of forest biomass to climate variability
NASA Astrophysics Data System (ADS)
Lichstein, Jeremy; Zhang, Tao; Niinemets, Ulo; Sheffield, Justin
2017-04-01
The response of forest carbon storage to climate change is highly uncertain, contributing substantially to the divergence among global climate model projections. Numerous studies have documented responses of forest ecosystems to climate change and variability, including drought-induced increases in tree mortality rates. However, the sensitivity of forests to climate variability - in terms of both biomass carbon storage and functional components of tree species composition - has yet to be quantified across a large region using systematically sampled data. Here, we combine systematic forest inventories across the eastern USA with a species-level drought-tolerance index, derived from a meta-analysis of published literature, to quantify changes in forest biomass and community-mean-drought-tolerance in one-degree grid cells from the 1980s to 2000s. We show that forest biomass responds to decadal-scale changes in water deficit and that this biomass response is amplified by concurrent changes in community-mean-drought-tolerance. The amplification of the direct effects of water stress on biomass occurs because water stress tends to induce a shift in tree species composition towards more drought-tolerant but lower-biomass species. Multiple plant functional traits are correlated with the above species-level drought-tolerance index, and likely contribute to the decrease in biomass with increasing drought-tolerance. These traits include wood density and P50 (the xylem water potential at which a plant loses 50% of its hydraulic conductivity). Simulations with a trait- and competition-based dynamic global vegetation model suggest that species differences in plant carbon allocation to wood, leaves, and fine roots also likely contribute to the observed decrease in biomass with increasing drought-tolerance, because competition drives plants to over-invest in fine roots when water is limiting. Thus, the most competitive species under dry conditions have greater root allocation but lower total biomass than productivity-maximizing plants. Amplification of the biomass-climate response due to shifts in species functional composition (temporal beta diversity) contrasts with evidence that local (alpha) diversity increases ecosystem stability, including increased resistance to climate extremes. These contrasting effects of alpha and beta diversity highlight the need to better understand how different components of biodiversity, including changes in the functional traits of the dominant plant species, affect ecosystem functioning.
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Functional group diversity is key to Southern Ocean benthic carbon pathways
Sands, Chester J.
2017-01-01
High latitude benthos are globally important in terms of accumulation and storage of ocean carbon, and the feedback this is likely to have on regional warming. Understanding this ecosystem service is important but difficult because of complex taxonomic diversity, history and geography of benthic biomass. Using South Georgia as a model location (where the history and geography of benthic biology is relatively well studied) we investigated whether the composition of functional groups were critical to benthic accumulation, immobilization and burial pathway to sequestration–and also aid their study through simplification of identification. We reclassified [1], [2]) morphotype and carbon mass data to 13 functional groups, for each sample of 32 sites around the South Georgia continental shelf. We investigated the influence on carbon accumulation, immobilization and sequestration estimate by multiple factors including the compositions of functional groups. Functional groups showed high diversity within and between sites, and within and between habitat types. Carbon storage was not linked to a functional group in particular but accumulation and immobilization increased with the number of functional groups present and the presence of hard substrata. Functional groups were also important to carbon burial rate, which increased with the presence of mixed (hard and soft substrata). Functional groups showed high surrogacy for taxonomic composition and were useful for examining contrasting habitat categorization. Functional groups not only aid marine carbon storage investigation by reducing time and the need for team size and speciality, but also important to benthic carbon pathways per se. There is a distinct geography to seabed carbon storage; seabed boulder-fields are hotspots of carbon accumulation and immobilization, whilst the interface between such boulder-fields and sediments are key places for burial and sequestration. PMID:28654664
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Immune and stress responses in oysters with insights on adaptation.
Guo, Ximing; He, Yan; Zhang, Linlin; Lelong, Christophe; Jouaux, Aude
2015-09-01
Oysters are representative bivalve molluscs that are widely distributed in world oceans. As successful colonizers of estuaries and intertidal zones, oysters are remarkably resilient against harsh environmental conditions including wide fluctuations in temperature and salinity as well as prolonged air exposure. Oysters have no adaptive immunity but can thrive in microbe-rich estuaries as filter-feeders. These unique adaptations make oysters interesting models to study the evolution of host-defense systems. Recent advances in genomic studies including sequencing of the oyster genome have provided insights into oyster's immune and stress responses underlying their amazing resilience. Studies show that the oyster genomes are highly polymorphic and complex, which may be key to their resilience. The oyster genome has a large gene repertoire that is enriched for immune and stress response genes. Thousands of genes are involved in oyster's immune and stress responses, through complex interactions, with many gene families expanded showing high sequence, structural and functional diversity. The high diversity of immune receptors and effectors may provide oysters with enhanced specificity in immune recognition and response to cope with diverse pathogens in the absence of adaptive immunity. Some members of expanded immune gene families have diverged to function at different temperatures and salinities or assumed new roles in abiotic stress response. Most canonical innate immunity pathways are conserved in oysters and supported by a large number of diverse and often novel genes. The great diversity in immune and stress response genes exhibited by expanded gene families as well as high sequence and structural polymorphisms may be central to oyster's adaptation to highly stressful and widely changing environments. Copyright © 2015 Elsevier Ltd. All rights reserved.
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Eisenhauer, Nico; Dobies, Tomasz; Cesarz, Simone; Hobbie, Sarah E.; Meyer, Ross J.; Worm, Kally; Reich, Peter B.
2013-01-01
Recent metaanalyses suggest biodiversity loss affects the functioning of ecosystems to a similar extent as other global environmental change agents. However, the abundance and functioning of soil organisms have been hypothesized to be much less responsive to such changes, particularly in plant diversity, than aboveground variables, although tests of this hypothesis are extremely rare. We examined the responses of soil food webs (soil microorganisms, nematodes, microarthropods) to 13-y manipulation of multiple environmental factors that are changing at global scales—specifically plant species richness, atmospheric CO2, and N deposition—in a grassland experiment in Minnesota. Plant diversity was a strong driver of the structure and functioning of soil food webs through several bottom-up (resource control) effects, whereas CO2 and N only had modest effects. We found few interactions between plant diversity and CO2 and N, likely because of weak interactive effects of those factors on resource availability (e.g., root biomass). Plant diversity effects likely were large because high plant diversity promoted the accumulation of soil organic matter in the site’s sandy, organic matter–poor soils. Plant diversity effects were not explained by the presence of certain plant functional groups. Our results underline the prime importance of plant diversity loss cascading to soil food webs (density and diversity of soil organisms) and functions. Because the present results suggest prevailing plant diversity effects and few interactions with other global change drivers, protecting plant diversity may be of high priority to maintain the biodiversity and functioning of soils in a changing world. PMID:23576722
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Xia, Wei; Bai, Yingguo; Cui, Ying; Xu, Xinxin; Qian, Lichun; Shi, Pengjun; Zhang, Wei; Luo, Huiying; Zhan, Xiuan; Yao, Bin
2016-01-01
The fungus Humicola insolens is one of the most powerful decomposers of crystalline cellulose. However, studies on the β-glucosidases from this fungus remain insufficient, especially on glycosyl hydrolase family 3 enzymes. In the present study, we analyzed the functional diversity of three distant family 3 β-glucosidases from Humicola insolens strain Y1, which belonged to different evolutionary clades, by heterogeneous expression in Pichia pastoris strain GS115. The recombinant enzymes shared similar enzymatic properties including thermophilic and neutral optima (50–60 °C and pH 5.5–6.0) and high glucose tolerance, but differed in substrate specificities and kinetics. HiBgl3B was solely active towards aryl β-glucosides while HiBgl3A and HiBgl3C showed broad substrate specificities including both disaccharides and aryl β-glucosides. Of the three enzymes, HiBgl3C exhibited the highest specific activity (158.8 U/mg on pNPG and 56.4 U/mg on cellobiose) and catalytic efficiency and had the capacity to promote cellulose degradation. Substitutions of three key residues Ile48, Ile278 and Thr484 of HiBgl3B to the corresponding residues of HiBgl3A conferred the enzyme activity towards sophorose, and vice versa. This study reveals the functional diversity of GH3 β-glucosidases as well as the key residues in recognizing +1 subsite of different substrates. PMID:27271847
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Xia, Wei; Bai, Yingguo; Cui, Ying; Xu, Xinxin; Qian, Lichun; Shi, Pengjun; Zhang, Wei; Luo, Huiying; Zhan, Xiuan; Yao, Bin
2016-06-08
The fungus Humicola insolens is one of the most powerful decomposers of crystalline cellulose. However, studies on the β-glucosidases from this fungus remain insufficient, especially on glycosyl hydrolase family 3 enzymes. In the present study, we analyzed the functional diversity of three distant family 3 β-glucosidases from Humicola insolens strain Y1, which belonged to different evolutionary clades, by heterogeneous expression in Pichia pastoris strain GS115. The recombinant enzymes shared similar enzymatic properties including thermophilic and neutral optima (50-60 °C and pH 5.5-6.0) and high glucose tolerance, but differed in substrate specificities and kinetics. HiBgl3B was solely active towards aryl β-glucosides while HiBgl3A and HiBgl3C showed broad substrate specificities including both disaccharides and aryl β-glucosides. Of the three enzymes, HiBgl3C exhibited the highest specific activity (158.8 U/mg on pNPG and 56.4 U/mg on cellobiose) and catalytic efficiency and had the capacity to promote cellulose degradation. Substitutions of three key residues Ile48, Ile278 and Thr484 of HiBgl3B to the corresponding residues of HiBgl3A conferred the enzyme activity towards sophorose, and vice versa. This study reveals the functional diversity of GH3 β-glucosidases as well as the key residues in recognizing +1 subsite of different substrates.
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Circular RNAs: diversity of form and function.
Lasda, Erika; Parker, Roy
2014-12-01
It is now clear that there is a diversity of circular RNAs in biological systems. Circular RNAs can be produced by the direct ligation of 5' and 3' ends of linear RNAs, as intermediates in RNA processing reactions, or by "backsplicing," wherein a downstream 5' splice site (splice donor) is joined to an upstream 3' splice site (splice acceptor). Circular RNAs have unique properties including the potential for rolling circle amplification of RNA, the ability to rearrange the order of genomic information, protection from exonucleases, and constraints on RNA folding. Circular RNAs can function as templates for viroid and viral replication, as intermediates in RNA processing reactions, as regulators of transcription in cis, as snoRNAs, and as miRNA sponges. Herein, we review the breadth of circular RNAs, their biogenesis and metabolism, and their known and anticipated functions. © 2014 Lasda and Parker; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
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Circular RNAs: diversity of form and function
Lasda, Erika
2014-01-01
It is now clear that there is a diversity of circular RNAs in biological systems. Circular RNAs can be produced by the direct ligation of 5′ and 3′ ends of linear RNAs, as intermediates in RNA processing reactions, or by “backsplicing,” wherein a downstream 5′ splice site (splice donor) is joined to an upstream 3′ splice site (splice acceptor). Circular RNAs have unique properties including the potential for rolling circle amplification of RNA, the ability to rearrange the order of genomic information, protection from exonucleases, and constraints on RNA folding. Circular RNAs can function as templates for viroid and viral replication, as intermediates in RNA processing reactions, as regulators of transcription in cis, as snoRNAs, and as miRNA sponges. Herein, we review the breadth of circular RNAs, their biogenesis and metabolism, and their known and anticipated functions. PMID:25404635
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HnRNP-like proteins as post-transcriptional regulators.
Yeap, Wan-Chin; Namasivayam, Parameswari; Ho, Chai-Ling
2014-10-01
Plant cells contain a diverse repertoire of RNA-binding proteins (RBPs) that coordinate a network of post-transcriptional regulation. RBPs govern diverse developmental processes by modulating the gene expression of specific transcripts. Recent gene annotation and RNA sequencing clearly showed that heterogeneous nuclear ribonucleoprotein (hnRNP)-like proteins which form a family of RBPs, are also expressed in higher plants and serve specific plant functions. In addition to their involvement in post-transcriptional regulation from mRNA capping to translation, they are also involved in telomere regulation, gene silencing and regulation in chloroplast. Here, we review the involvement of plant hnRNP-like proteins in post-transcription regulation of RNA processes and their functional roles in control of plant developmental processes especially plant-specific functions including flowering, chloroplastic-specific mRNA regulation, long-distance phloem transportation and plant responses to environmental stresses. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.
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Molecular Characteristics and Biological Functions of Surface-Active and Surfactant Proteins.
Sunde, Margaret; Pham, Chi L L; Kwan, Ann H
2017-06-20
Many critical biological processes take place at hydrophobic:hydrophilic interfaces, and a wide range of organisms produce surface-active proteins and peptides that reduce surface and interfacial tension and mediate growth and development at these boundaries. Microorganisms produce both small lipid-associated peptides and amphipathic proteins that allow growth across water:air boundaries, attachment to surfaces, predation, and improved bioavailability of hydrophobic substrates. Higher-order organisms produce surface-active proteins with a wide variety of functions, including the provision of protective foam environments for vulnerable reproductive stages, evaporative cooling, and gas exchange across airway membranes. In general, the biological functions supported by these diverse polypeptides require them to have an amphipathic nature, and this is achieved by a diverse range of molecular structures, with some proteins undergoing significant conformational change or intermolecular association to generate the structures that are surface active.
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Breast Milk Oligosaccharides: Structure-Function Relationships in the Neonate
Smilowitz, Jennifer T.; Lebrilla, Carlito B.; Mills, David A.; German, J. Bruce; Freeman, Samara L.
2015-01-01
In addition to providing complete postnatal nutrition, breast milk is a complex biofluid that delivers bioactive components for the growth and development of the intestinal and immune systems. Lactation is a unique opportunity to understand the role of diet in shaping the intestinal environment including the infant microbiome. Of considerable interest is the diversity and abundance of milk glycans that are energetically costly for the mammary gland to produce yet indigestible by infants. Milk glycans comprise free oligosaccharides, glycoproteins, glycopeptides, and glycolipids. Emerging technological advances are enabling more comprehensive, sensitive, and rapid analyses of these different classes of milk glycans. Understanding the impact of inter- and intraindividual glycan diversity on function is an important step toward interventions aimed at improving health and preventing disease. This review discusses the state of technology for glycan analysis and how specific structure-function knowledge is enhancing our understanding of early nutrition in the neonate. PMID:24850388
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Tröbs, R-B; Heinecke, K; Elouahidi, T; Nounla, J; Kluge, R
2006-01-01
We examined renal function and urinary drainage of children with primary megaureter (PMU) in dependence on conservative or operative treatment. The retrospective analysis covering the years 1994 to 2000 comprised children at an age of 0-7 years with 35 PMU. Sonography, dynamic MAG3 renography as well as endogenic creatinine clearance (GFR) were used to assess drainage and the renal function. Temporary urinary diversion was established in fourteen patients of both groups. In 14 children with 16 PMU a ureteroneocystostomy (UNC) was performed. The average observation period was 30 months (11-108). The children of the UNC group differed from the non-neoimplanted group in the age at diagnosis (10.5 vs. < 1 months), higher degrees of hydronephrosis on average, a more distinct dilatation of the ureter as well as renographically significant obstruction. Children of the non-UNC group, including four children with a type B drainage curve (O'Reilly), had an unimpaired differential renal function or improved during the observation period (initially 51% vs. 50.5% at the end). In neoimplantation group the differential function improved from 32.5% to 38.5% (p < 0.05) and obstruction resolved with one exception. Given a higher-grade PMU with a reduced function of the kidneys and a significant impaired drainage pattern and/or symptoms, neoimplantation without temporary diversion has proved to be an efficient renoprotective method. Furthermore, data clearly justify a conservative approach without urinary diversion in infants with large asymptomatic PMU.
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Beta-diversity of ectoparasites at two spatial scales: nested hierarchy, geography and habitat type.
Warburton, Elizabeth M; van der Mescht, Luther; Stanko, Michal; Vinarski, Maxim V; Korallo-Vinarskaya, Natalia P; Khokhlova, Irina S; Krasnov, Boris R
2017-06-01
Beta-diversity of biological communities can be decomposed into (a) dissimilarity of communities among units of finer scale within units of broader scale and (b) dissimilarity of communities among units of broader scale. We investigated compositional, phylogenetic/taxonomic and functional beta-diversity of compound communities of fleas and gamasid mites parasitic on small Palearctic mammals in a nested hierarchy at two spatial scales: (a) continental scale (across the Palearctic) and (b) regional scale (across sites within Slovakia). At each scale, we analyzed beta-diversity among smaller units within larger units and among larger units with partitioning based on either geography or ecology. We asked (a) whether compositional, phylogenetic/taxonomic and functional dissimilarities of flea and mite assemblages are scale dependent; (b) how geographical (partitioning of sites according to geographic position) or ecological (partitioning of sites according to habitat type) characteristics affect phylogenetic/taxonomic and functional components of dissimilarity of ectoparasite assemblages and (c) whether assemblages of fleas and gamasid mites differ in their degree of dissimilarity, all else being equal. We found that compositional, phylogenetic/taxonomic, or functional beta-diversity was greater on a continental rather than a regional scale. Compositional and phylogenetic/taxonomic components of beta-diversity were greater among larger units than among smaller units within larger units, whereas functional beta-diversity did not exhibit any consistent trend regarding site partitioning. Geographic partitioning resulted in higher values of beta-diversity of ectoparasites than ecological partitioning. Compositional and phylogenetic components of beta-diversity were higher in fleas than mites but the opposite was true for functional beta-diversity in some, but not all, traits.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Sun, Jianwei; Remsing, Richard C.; Zhang, Yubo
2016-06-13
One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and vanmore » der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.« less
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2011 Plant Lipids: Structure, Metabolism, & Function Gordon Research Conference
DOE Office of Scientific and Technical Information (OSTI.GOV)
Christopher Benning
2011-02-04
This is the second Gordon Research Conference on 'Plant Lipids: Structure, Metabolism & Function'. It covers current topics in lipid structure, metabolism and function in eukaryotic photosynthetic organisms including seed plants, algae, mosses and ferns. Work in photosynthetic bacteria is considered as well as it serves the understanding of specific aspects of lipid metabolism in plants. Breakthroughs are discussed in research on plant lipids as diverse as glycerolipids, sphingolipids, lipids of the cell surface, isoprenoids, fatty acids and their derivatives. The program covers nine concepts at the forefront of research under which afore mentioned plant lipid classes are discussed. Themore » goal is to integrate areas such as lipid signaling, basic lipid metabolism, membrane function, lipid analysis, and lipid engineering to achieve a high level of stimulating interaction among diverse researchers with interests in plant lipids. One Emphasis is on the dynamics and regulation of lipid metabolism during plant cell development and in response to environmental factors.« less
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Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides
DOE Office of Scientific and Technical Information (OSTI.GOV)
Coradetti, Samuel T.; Pinel, Dominic; Geiselman, Gina M.
The basidiomycete yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded Agrobacterium tumefaciens T-DNA insertions. We identified 1,337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted functionmore » in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, and genes of unknown function. Lastly, these results greatly advance our understanding of lipid metabolism in this oleaginous species and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi.« less
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Sun, Jianwei; Remsing, Richard C; Zhang, Yubo; Sun, Zhaoru; Ruzsinszky, Adrienn; Peng, Haowei; Yang, Zenghui; Paul, Arpita; Waghmare, Umesh; Wu, Xifan; Klein, Michael L; Perdew, John P
2016-09-01
One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and van der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.
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Armitage, David W
2017-11-01
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. These included mid-successional peaks in bacterial diversity and metabolic substrate use, predictable and parallel successional trajectories among microbial communities, and convergence giving way to divergence in community composition and carbon substrate use. Bacterial composition, biomass, and diversity positively influenced the rate of prey decomposition, which was in turn positively associated with a host leaf's nitrogen uptake efficiency. Overall digestive performance was greatest during late summer. These results highlight links between community succession and ecosystem functioning and extend succession theory to host-associated microbial communities.
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Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides
Coradetti, Samuel T.; Pinel, Dominic; Geiselman, Gina M.; ...
2018-03-09
The basidiomycete yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded Agrobacterium tumefaciens T-DNA insertions. We identified 1,337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted functionmore » in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, and genes of unknown function. Lastly, these results greatly advance our understanding of lipid metabolism in this oleaginous species and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi.« less
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Predator-Prey Dynamics Driven by Feedback between Functionally Diverse Trophic Levels
Wirtz, Kai; Gaedke, Ursula
2011-01-01
Neglecting the naturally existing functional diversity of communities and the resulting potential to respond to altered conditions may strongly reduce the realism and predictive power of ecological models. We therefore propose and study a predator-prey model that describes mutual feedback via species shifts in both predator and prey, using a dynamic trait approach. Species compositions of the two trophic levels were described by mean functional traits—prey edibility and predator food-selectivity—and functional diversities by the variances. Altered edibility triggered shifts in food-selectivity so that consumers continuously respond to the present prey composition, and vice versa. This trait-mediated feedback mechanism resulted in a complex dynamic behavior with ongoing oscillations in the mean trait values, reflecting continuous reorganization of the trophic levels. The feedback was only possible if sufficient functional diversity was present in both trophic levels. Functional diversity was internally maintained on the prey level as no niche existed in our system, which was ideal under any composition of the predator level due to the trade-offs between edibility, growth and carrying capacity. The predators were only subject to one trade-off between food-selectivity and grazing ability and in the absence of immigration, one predator type became abundant, i.e., functional diversity declined to zero. In the lack of functional diversity the system showed the same dynamics as conventional models of predator-prey interactions ignoring the potential for shifts in species composition. This way, our study identified the crucial role of trade-offs and their shape in physiological and ecological traits for preserving diversity. PMID:22096560
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spads 1.0: a toolbox to perform spatial analyses on DNA sequence data sets.
Dellicour, Simon; Mardulyn, Patrick
2014-05-01
SPADS 1.0 (for 'Spatial and Population Analysis of DNA Sequences') is a population genetic toolbox for characterizing genetic variability within and among populations from DNA sequences. In view of the drastic increase in genetic information available through sequencing methods, spads was specifically designed to deal with multilocus data sets of DNA sequences. It computes several summary statistics from populations or groups of populations, performs input file conversions for other population genetic programs and implements locus-by-locus and multilocus versions of two clustering algorithms to study the genetic structure of populations. The toolbox also includes two MATLAB and r functions, GDISPAL and GDIVPAL, to display differentiation and diversity patterns across landscapes. These functions aim to generate interpolating surfaces based on multilocus distance and diversity indices. In the case of multiple loci, such surfaces can represent a useful alternative to multiple pie charts maps traditionally used in phylogeography to represent the spatial distribution of genetic diversity. These coloured surfaces can also be used to compare different data sets or different diversity and/or distance measures estimated on the same data set. © 2013 John Wiley & Sons Ltd.
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The Epigenomic Landscape of Prokaryotes
Blow, Matthew J.; Clark, Tyson A.; Daum, Chris G.; ...
2016-02-12
DNA methylation acts in concert with restriction enzymes to protect the integrity of prokaryotic genomes. Studies in a limited number of organisms suggest that methylation also contributes to prokaryotic genome regulation, but the prevalence and properties of such non-restriction-associated methylation systems remain poorly understood. Here, we used single molecule, real-time sequencing to map DNA modifications including m6A, m4C, and m5C across the genomes of 230 diverse bacterial and archaeal species. We observed DNA methylation in nearly all (93%) organisms examined, and identified a total of 834 distinct reproducibly methylated motifs. This data enabled annotation of the DNA binding specificities ofmore » 620 DNA Methyltransferases (MTases), doubling known specificities for previously hard to study Type I, IIG and III MTases, and revealing their extraordinary diversity. Strikingly, 48% of organisms harbor active Type II MTases with no apparent cognate restriction enzyme. These active ‘orphan’ MTases are present in diverse bacterial and archaeal phyla and show motif specificities and methylation patterns consistent with functions in gene regulation and DNA replication. Our results reveal the pervasive presence of DNA methylation throughout the prokaryotic kingdoms, as well as the diversity of sequence specificities and potential functions of DNA methylation systems.« less
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The Epigenomic Landscape of Prokaryotes
DOE Office of Scientific and Technical Information (OSTI.GOV)
Blow, Matthew J.; Clark, Tyson A.; Daum, Chris G.
DNA methylation acts in concert with restriction enzymes to protect the integrity of prokaryotic genomes. Studies in a limited number of organisms suggest that methylation also contributes to prokaryotic genome regulation, but the prevalence and properties of such non-restriction-associated methylation systems remain poorly understood. Here, we used single molecule, real-time sequencing to map DNA modifications including m6A, m4C, and m5C across the genomes of 230 diverse bacterial and archaeal species. We observed DNA methylation in nearly all (93%) organisms examined, and identified a total of 834 distinct reproducibly methylated motifs. This data enabled annotation of the DNA binding specificities ofmore » 620 DNA Methyltransferases (MTases), doubling known specificities for previously hard to study Type I, IIG and III MTases, and revealing their extraordinary diversity. Strikingly, 48% of organisms harbor active Type II MTases with no apparent cognate restriction enzyme. These active ‘orphan’ MTases are present in diverse bacterial and archaeal phyla and show motif specificities and methylation patterns consistent with functions in gene regulation and DNA replication. Our results reveal the pervasive presence of DNA methylation throughout the prokaryotic kingdoms, as well as the diversity of sequence specificities and potential functions of DNA methylation systems.« less
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Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.
Fierer, Noah; Leff, Jonathan W; Adams, Byron J; Nielsen, Uffe N; Bates, Scott Thomas; Lauber, Christian L; Owens, Sarah; Gilbert, Jack A; Wall, Diana H; Caporaso, J Gregory
2012-12-26
For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant-free cold desert soils typically had the lowest levels of functional diversity (diversity of protein-coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the metric used. The desert communities had higher relative abundances of genes associated with osmoregulation and dormancy, but lower relative abundances of genes associated with nutrient cycling and the catabolism of plant-derived organic compounds. Antibiotic resistance genes were consistently threefold less abundant in the desert soils than in the nondesert soils, suggesting that abiotic conditions, not competitive interactions, are more important in shaping the desert microbial communities. As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes.
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Fungal diversity in deep-sea sediments of a hydrothermal vent system in the Southwest Indian Ridge
NASA Astrophysics Data System (ADS)
Xu, Wei; Gong, Lin-feng; Pang, Ka-Lai; Luo, Zhu-Hua
2018-01-01
Deep-sea hydrothermal sediment is known to support remarkably diverse microbial consortia. In deep sea environments, fungal communities remain less studied despite their known taxonomic and functional diversity. High-throughput sequencing methods have augmented our capacity to assess eukaryotic diversity and their functions in microbial ecology. Here we provide the first description of the fungal community diversity found in deep sea sediments collected at the Southwest Indian Ridge (SWIR) using culture-dependent and high-throughput sequencing approaches. A total of 138 fungal isolates were cultured from seven different sediment samples using various nutrient media, and these isolates were identified to 14 fungal taxa, including 11 Ascomycota taxa (7 genera) and 3 Basidiomycota taxa (2 genera) based on internal transcribed spacers (ITS1, ITS2 and 5.8S) of rDNA. Using illumina HiSeq sequencing, a total of 757,467 fungal ITS2 tags were recovered from the samples and clustered into 723 operational taxonomic units (OTUs) belonging to 79 taxa (Ascomycota and Basidiomycota contributed to 99% of all samples) based on 97% sequence similarity. Results from both approaches suggest that there is a high fungal diversity in the deep-sea sediments collected in the SWIR and fungal communities were shown to be slightly different by location, although all were collected from adjacent sites at the SWIR. This study provides baseline data of the fungal diversity and biogeography, and a glimpse to the microbial ecology associated with the deep-sea sediments of the hydrothermal vent system of the Southwest Indian Ridge.
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Nadrowski, Karin; Pietsch, Katherina; Baruffol, Martin; Both, Sabine; Gutknecht, Jessica; Bruelheide, Helge; Heklau, Heike; Kahl, Anja; Kahl, Tiemo; Niklaus, Pascal; Kröber, Wenzel; Liu, Xiaojuan; Mi, Xiangcheng; Michalski, Stefan; von Oheimb, Goddert; Purschke, Oliver; Schmid, Bernhard; Fang, Teng; Welk, Erik; Wirth, Christian
2014-01-01
Future climates are likely to include extreme events, which in turn have great impacts on ecological systems. In this study, we investigated possible effects that could mitigate stem breakage caused by a rare and extreme ice storm in a Chinese subtropical forest across a gradient of forest diversity. We used Bayesian modeling to correct stem breakage for tree size and variance components analysis to quantify the influence of taxon, leaf and wood functional traits, and stand level properties on the probability of stem breakage. We show that the taxon explained four times more variance in individual stem breakage than did stand level properties; trees with higher specific leaf area (SLA) were less susceptible to breakage. However, a large part of the variation at the taxon scale remained unexplained, implying that unmeasured or undefined traits could be used to predict damage caused by ice storms. When aggregated at the plot level, functional diversity and wood density increased after the ice storm. We suggest that for the adaption of forest management to climate change, much can still be learned from looking at functional traits at the taxon level. PMID:24879434
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Perron, Gabriel G.; Whyte, Lyle; Turnbaugh, Peter J.; Goordial, Jacqueline; Hanage, William P.; Dantas, Gautam; Desai, Michael M.
2015-01-01
Using functional metagenomics to study the resistomes of bacterial communities isolated from different layers of the Canadian high Arctic permafrost, we show that microbial communities harbored diverse resistance mechanisms at least 5,000 years ago. Among bacteria sampled from the ancient layers of a permafrost core, we isolated eight genes conferring clinical levels of resistance against aminoglycoside, β-lactam and tetracycline antibiotics that are naturally produced by microorganisms. Among these resistance genes, four also conferred resistance against amikacin, a modern semi-synthetic antibiotic that does not naturally occur in microorganisms. In bacteria sampled from the overlaying active layer, we isolated ten different genes conferring resistance to all six antibiotics tested in this study, including aminoglycoside, β-lactam and tetracycline variants that are naturally produced by microorganisms as well as semi-synthetic variants produced in the laboratory. On average, we found that resistance genes found in permafrost bacteria conferred lower levels of resistance against clinically relevant antibiotics than resistance genes sampled from the active layer. Our results demonstrate that antibiotic resistance genes were functionally diverse prior to the anthropogenic use of antibiotics, contributing to the evolution of natural reservoirs of resistance genes. PMID:25807523
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Diversity-dependent temporal divergence of ecosystem functioning in experimental ecosystems.
Guerrero-Ramírez, Nathaly R; Craven, Dylan; Reich, Peter B; Ewel, John J; Isbell, Forest; Koricheva, Julia; Parrotta, John A; Auge, Harald; Erickson, Heather E; Forrester, David I; Hector, Andy; Joshi, Jasmin; Montagnini, Florencia; Palmborg, Cecilia; Piotto, Daniel; Potvin, Catherine; Roscher, Christiane; van Ruijven, Jasper; Tilman, David; Wilsey, Brian; Eisenhauer, Nico
2017-11-01
The effects of biodiversity on ecosystem functioning generally increase over time, but the underlying processes remain unclear. Using 26 long-term grassland and forest experimental ecosystems, we demonstrate that biodiversity-ecosystem functioning relationships strengthen mainly by greater increases in functioning in high-diversity communities in grasslands and forests. In grasslands, biodiversity effects also strengthen due to decreases in functioning in low-diversity communities. Contrasting trends across grasslands are associated with differences in soil characteristics.
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Nocturnality constrains morphological and functional diversity in the eyes of reef fishes
2011-01-01
Background Ambient light levels are often considered to drive the evolution of eye form and function. Diel activity pattern is the main mechanism controlling the visual environment of teleost reef fish, with day-active (diurnal) fish active in well-illuminated conditions, whereas night-active (nocturnal) fish cope with dim light. Physiological optics predicts several specific evolutionary responses to dim-light vision that should be reflected in visual performance features of the eye. Results We analyzed a large comparative dataset on morphological traits of the eyes in 265 species of teleost reef fish in 43 different families. The eye morphology of nocturnal reef teleosts is characterized by a syndrome that indicates better light sensitivity, including large relative eye size, high optical ratio and large, rounded pupils. Improved dim-light image formation comes at the cost of reduced depth of focus and reduction of potential accommodative lens movement. Diurnal teleost reef fish, released from the stringent functional requirements of dim-light vision have much higher morphological and optical diversity than nocturnal species, with large ranges of optical ratio, depth of focus, and lens accommodation. Conclusions Physical characteristics of the environment are an important factor in the evolution and diversification of the vertebrate eye. Both teleost reef fish and terrestrial amniotes meet the functional requirements of dim-light vision with a similar evolutionary response of morphological and optical modifications. The trade-off between improved dim-light vision and reduced optical diversity may be a key factor in explaining the lower trophic diversity of nocturnal reef teleosts. PMID:22098687
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Yeats, Trevor H.; Buda, Gregory J.; Wang, Zhonghua; Chehanovsky, Noam; Moyle, Leonie C.; Jetter, Reinhard; Schaffer, Arthur A.; Rose, Jocelyn K.C.
2013-01-01
Summary The cuticle covers the aerial epidermis of land plants and plays a primary role in water regulation and protection from external stresses. Remarkable species diversity in the structure and composition of its components, cutin and wax, have been catalogued, but few functional or genetic correlations have emerged. Tomato (Solanum lycopersicum) is part of a complex of closely related wild species endemic to the northern Andes and the Galapagos Islands (Solanum Sect. Lycopersicon). Although sharing an ancestor less than seven million years ago, these species are found in diverse environments and are subject to unique selective pressures. Furthermore, they are genetically tractable, since they can be crossed with S. lycopersicum, which has a sequenced genome. With the aim of evaluating the relationships between evolution, structure and function of the cuticle, we characterized the morphological and chemical diversity of fruit cuticles of seven species from Solanum Sect. Lycopersicon. Striking differences in cuticular architecture and quantities of cutin and waxes were observed, with wild species wax coverage exceeding that of S. lycopersicum by up to seven fold. Wax composition varied in the occurrence of wax esters and triterpenoid isomers. Using a S. habrochaites introgression line population, we mapped triterpenoid differences to a genomic region that includes two S. lycopersicum triterpene synthases. Based on known metabolic pathways for acyl wax compounds, hypotheses are discussed to explain the appearance of wax esters with atypical chain lengths. These results establish a model system for understanding the ecological and evolutionary functional genomics of plant cuticles. PMID:22007785
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Wu, Ping; Ng, Chen Siang; Yan, Jie; Lai, Yung-Chih; Chen, Chih-Kuan; Lai, Yu-Ting; Wu, Siao-Man; Chen, Jiun-Jie; Luo, Weiqi; Widelitz, Randall B.; Li, Wen-Hsiung; Chuong, Cheng-Ming
2015-01-01
Avian integumentary organs include feathers, scales, claws, and beaks. They cover the body surface and play various functions to help adapt birds to diverse environments. These keratinized structures are mainly composed of corneous materials made of α-keratins, which exist in all vertebrates, and β-keratins, which only exist in birds and reptiles. Here, members of the keratin gene families were used to study how gene family evolution contributes to novelty and adaptation, focusing on tissue morphogenesis. Using chicken as a model, we applied RNA-seq and in situ hybridization to map α- and β-keratin genes in various skin appendages at embryonic developmental stages. The data demonstrate that temporal and spatial α- and β-keratin expression is involved in establishing the diversity of skin appendage phenotypes. Embryonic feathers express a higher proportion of β-keratin genes than other skin regions. In feather filament morphogenesis, β-keratins show intricate complexity in diverse substructures of feather branches. To explore functional interactions, we used a retrovirus transgenic system to ectopically express mutant α- or antisense β-keratin forms. α- and β-keratins show mutual dependence and mutations in either keratin type results in disrupted keratin networks and failure to form proper feather branches. Our data suggest that combinations of α- and β-keratin genes contribute to the morphological and structural diversity of different avian skin appendages, with feather-β-keratins conferring more possible composites in building intrafeather architecture complexity, setting up a platform of morphological evolution of functional forms in feathers. PMID:26598683
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Diversity and regulation of plant Ca2+ pumps: insights from expression in yeast
NASA Technical Reports Server (NTRS)
Sze, H.; Liang, F.; Hwang, I.; Curran, A. C.; Harper, J. F.; Evans, M. L. (Principal Investigator)
2000-01-01
The spatial and temporal regulation of calcium concentration in plant cells depends on the coordinate activities of channels and active transporters located on different organelles and membranes. Several Ca2+ pumps have been identified and characterized by functional expression of plant genes in a yeast mutant (K616). This expression system has opened the way to a genetic and biochemical characterization of the regulatory and catalytic features of diverse Ca2+ pumps. Plant Ca(2+)-ATPases fall into two major types: AtECA1 represents one of four or more members of the type IIA (ER-type) Ca(2+)-ATPases in Arabidopsis, and AtACA2 is one of seven or more members of the type IIB (PM-type) Ca(2+)-ATPases that are regulated by a novel amino terminal domain. Type IIB pumps are widely distributed on membranes, including the PM (plasma membrane), vacuole, and ER (endoplasmic reticulum). The regulatory domain serves multiple functions, including autoinhibition, calmodulin binding, and sites for modification by phosphorylation. This domain, however, is considerably diverse among several type IIB ATPases, suggesting that the pumps are differentially regulated. Understanding of Ca2+ transporters at the molecular level is providing insights into their roles in signaling networks and in regulating fundamental processes of cell biology.
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A Comparison of Two Measures of HIV Diversity in Multi-Assay Algorithms for HIV Incidence Estimation
Cousins, Matthew M.; Konikoff, Jacob; Sabin, Devin; Khaki, Leila; Longosz, Andrew F.; Laeyendecker, Oliver; Celum, Connie; Buchbinder, Susan P.; Seage, George R.; Kirk, Gregory D.; Moore, Richard D.; Mehta, Shruti H.; Margolick, Joseph B.; Brown, Joelle; Mayer, Kenneth H.; Kobin, Beryl A.; Wheeler, Darrell; Justman, Jessica E.; Hodder, Sally L.; Quinn, Thomas C.; Brookmeyer, Ron; Eshleman, Susan H.
2014-01-01
Background Multi-assay algorithms (MAAs) can be used to estimate HIV incidence in cross-sectional surveys. We compared the performance of two MAAs that use HIV diversity as one of four biomarkers for analysis of HIV incidence. Methods Both MAAs included two serologic assays (LAg-Avidity assay and BioRad-Avidity assay), HIV viral load, and an HIV diversity assay. HIV diversity was quantified using either a high resolution melting (HRM) diversity assay that does not require HIV sequencing (HRM score for a 239 base pair env region) or sequence ambiguity (the percentage of ambiguous bases in a 1,302 base pair pol region). Samples were classified as MAA positive (likely from individuals with recent HIV infection) if they met the criteria for all of the assays in the MAA. The following performance characteristics were assessed: (1) the proportion of samples classified as MAA positive as a function of duration of infection, (2) the mean window period, (3) the shadow (the time period before sample collection that is being assessed by the MAA), and (4) the accuracy of cross-sectional incidence estimates for three cohort studies. Results The proportion of samples classified as MAA positive as a function of duration of infection was nearly identical for the two MAAs. The mean window period was 141 days for the HRM-based MAA and 131 days for the sequence ambiguity-based MAA. The shadows for both MAAs were <1 year. Both MAAs provided cross-sectional HIV incidence estimates that were very similar to longitudinal incidence estimates based on HIV seroconversion. Conclusions MAAs that include the LAg-Avidity assay, the BioRad-Avidity assay, HIV viral load, and HIV diversity can provide accurate HIV incidence estimates. Sequence ambiguity measures obtained using a commercially-available HIV genotyping system can be used as an alternative to HRM scores in MAAs for cross-sectional HIV incidence estimation. PMID:24968135
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2014-01-01
Background African Americans have been treated as a representative population for African ancestry for many purposes, including pharmacogenomic studies. However, the contribution of European ancestry is expected to result in considerable differences in the genetic architecture of African American individuals compared with an African genome. In particular, the genetic admixture influences the genomic diversity of drug metabolism-related genes, and may cause high heterogeneity of drug responses in admixed populations such as African Americans. Results The genomic ancestry information of African-American (ASW) samples was obtained from data of the 1000 Genomes Project, and local ancestral components were also extracted for 32 core genes and 252 extended genes, which are associated with drug absorption, distribution, metabolism, and excretion (ADME) genes. As expected, the global genetic diversity pattern in ASW was determined by the contributions of its putative ancestral source populations, and the whole profiles of ADME genes in ASW are much closer to those in YRI than in CEU. However, we observed much higher diversity in some functionally important ADME genes in ASW than either CEU or YRI, which could be a result of either genetic drift or natural selection, and we identified some signatures of the latter. We analyzed the clinically relevant polymorphic alleles and haplotypes, and found that 28 functional mutations (including 3 missense, 3 splice, and 22 regulator sites) exhibited significantly higher differentiation between the three populations. Conclusions Analysis of the genetic diversity of ADME genes showed differentiation between admixed population and its ancestral source populations. In particular, the different genetic diversity between ASW and YRI indicated that the ethnic differences in pharmacogenomic studies are broadly existed despite that African ancestry is dominant in Africans Americans. This study should advance our understanding of the genetic basis of the drug response heterogeneity between populations, especially in the case of population admixture, and have significant implications for evaluating potential inter-population heterogeneity in drug treatment effects. PMID:24884825
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USDA-ARS?s Scientific Manuscript database
Phytoplasmas are unculturable, cell wall-less bacteria that parasitize plants and insects. This transkingdom life cycle requires rapid responses to vastly different environments including transitions from plant phloem sieve elements to various insect tissues and alterations of diverse plant hosts. ...
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Vegetation community response to tidal marsh restoration of a large river estuary
Belleveau, Lisa J.; Takekawa, John Y.; Woo, Isa; Turner, Kelley L.; Barham, Jesse B.; Takekawa, Jean E.; Ellings, Christopher S.; Chin-Leo, Gerardo
2015-01-01
Estuaries are biologically productive and diverse ecosystems that provide ecosystem services including protection of inland areas from flooding, filtering freshwater outflows, and providing habitats for fish and wildlife. Alteration of historic habitats, including diking for agriculture, has decreased the function of many estuarine systems, and recent conservation efforts have been directed at restoring these degraded areas to reestablish their natural resource function. The Nisqually Delta in southern Puget Sound is an estuary that has been highly modified by restricting tidal flow, and recent restoration of the delta contributed to one of the largest tidal salt marsh restorations in the Pacific Northwest. We correlated the response of nine major tidal marsh species to salinities at different elevation zones. Our results indicated that wetland species richness was not related to soil pore-water salinity (R2 = 0.03), but were stratified into different elevation zones (R2 = 0.47). Thus, restoration that fosters a wide range of elevations will provide the most diverse plant habitat, and potentially, the greatest resilience to environmental change.
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Escher, Fabian; Seiffge-Krenke, Inge
2013-09-01
Studies are lacking that analyze how clinically referred adolescents and healthy adolescents cope with everyday stressors. Clinically referred adolescents from three problematic domains (diverse disorders including delinquency, drug abuse, and depression) were compared to healthy adolescents using the Coping Across Situations Questionnaire (Seiffge-Krenke, 1995) and a short version of the Youth Self-Report (Achenbach, 1991). The different clinical groups (n = 469) showed unique patterns concerning their coping styles. The group of depressed youth altogether showed lower coping activities. The youth from institutions for drug abusive youth used more dysfunctional coping. The adolescents from youth welfare services (diverse disorders including delinquency) were more active in both dysfunctional and functional coping than the other two clinically referred groups. The control group showed more functional and less dysfunctional coping. The clinically referred adolescents did not differentiate in their coping behavior, depending on the type of stressor. Gender effects were apparent, albeit negligible. Clinically referred youth are unable to adapt their coping behavior according to the given situation.
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Mechanical design of translocating motor proteins.
Hwang, Wonmuk; Lang, Matthew J
2009-01-01
Translocating motors generate force and move along a biofilament track to achieve diverse functions including gene transcription, translation, intracellular cargo transport, protein degradation, and muscle contraction. Advances in single molecule manipulation experiments, structural biology, and computational analysis are making it possible to consider common mechanical design principles of these diverse families of motors. Here, we propose a mechanical parts list that include track, energy conversion machinery, and moving parts. Energy is supplied not just by burning of a fuel molecule, but there are other sources or sinks of free energy, by binding and release of a fuel or products, or similarly between the motor and the track. Dynamic conformational changes of the motor domain can be regarded as controlling the flow of free energy to and from the surrounding heat reservoir. Multiple motor domains are organized in distinct ways to achieve motility under imposed physical constraints. Transcending amino acid sequence and structure, physically and functionally similar mechanical parts may have evolved as nature's design strategy for these molecular engines.
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Mechanical Design of Translocating Motor Proteins
Lang, Matthew J.
2013-01-01
Translocating motors generate force and move along a biofilament track to achieve diverse functions including gene transcription, translation, intracellular cargo transport, protein degradation, and muscle contraction. Advances in single molecule manipulation experiments, structural biology, and computational analysis are making it possible to consider common mechanical design principles of these diverse families of motors. Here, we propose a mechanical parts list that include track, energy conversion machinery, and moving parts. Energy is supplied not just by burning of a fuel molecule, but there are other sources or sinks of free energy, by binding and release of a fuel or products, or similarly between the motor and the track. Dynamic conformational changes of the motor domain can be regarded as controlling the flow of free energy to and from the surrounding heat reservoir. Multiple motor domains are organized in distinct ways to achieve motility under imposed physical constraints. Transcending amino acid sequence and structure, physically and functionally similar mechanical parts may have evolved as nature’s design strategy for these molecular engines. PMID:19452133
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Cork, Sarah M.
2011-01-01
While G-protein-coupled receptors (GPCRs) have received considerable attention for their biological activity in a diversity of physiological functions and have become targets for therapeutic intervention in many diseases, the function of the cell adhesion subfamily of GPCRs remains poorly understood. Within this group, the family of brain angiogenesis inhibitor molecules (BAI1-3) has become increasingly appreciated for their diverse roles in biology and disease. In particular, recent findings suggest emerging roles for BAI1 in the regulation of phenomena including phagocytosis, synaptogenesis, and the inhibition of tumor growth and angiogenesis via the processing of its extracellular domain into secreted vasculostatins. Here we summarize the known biological features of the BAI proteins, including their structure, proteolysis events, and interacting partners, and their recently identified ability to regulate certain signaling pathways. Finally, we discuss the potential of the BAIs as therapeutics or targets for diseases as varied as cancer, stroke, and schizophrenia. PMID:21509575
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Decarboxylative Trifluoromethylation of Aliphatic Carboxylic Acids.
Kautzky, Jacob A; Wang, Tao; Evans, Ryan W; MacMillan, David W C
2018-05-14
Herein we disclose an efficient method for the conversion of carboxylic acids to trifluoromethyl groups via the combination of photoredox and copper catalysis. This transformation tolerates a wide range of functionality including heterocycles, olefins, alcohols, and strained ring systems. To demonstrate the broad potential of this new methodology for late-stage functionalization, we successfully converted a diverse array of carboxylic acid-bearing natural products and medicinal agents to the corresponding trifluoromethyl analogues.
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Raeber, Alexandra E; Wong, Bryan M
2015-05-12
We present a detailed analysis of several time-dependent DFT (TD-DFT) methods, including conventional hybrid functionals and two types of nonempirically tuned range-separated functionals, for predicting a diverse set of electronic excitations in DNA nucleobase monomers and dimers. This large and extensive set of excitations comprises a total of 50 different transitions (for each tested DFT functional) that includes several n → π and π → π* valence excitations, long-range charge-transfer excitations, and extended Rydberg transitions (complete with benchmark calculations from high-level EOM-CCSD(T) methods). The presence of localized valence excitations as well as extreme long-range charge-transfer excitations in these systems poses a serious challenge for TD-DFT methods that allows us to assess the importance of both short- and long-range exchange contributions for simultaneously predicting all of these various transitions. In particular, we find that functionals that do not have both short- and full long-range exchange components are unable to predict the different types of nucleobase excitations with the same accuracy. Most importantly, the current study highlights the importance of both short-range exchange and a nonempirically tuned contribution of long-range exchange for accurately predicting the diverse excitations in these challenging nucleobase systems.
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Lin, Xiaodong; Liu, Yaqing; Deng, Jiankang; Lyu, Yanlong; Qian, Pengcheng; Li, Yunfei; Wang, Shuo
2018-02-21
The integration of multiple DNA logic gates on a universal platform to implement advance logic functions is a critical challenge for DNA computing. Herein, a straightforward and powerful strategy in which a guanine-rich DNA sequence lighting up a silver nanocluster and fluorophore was developed to construct a library of logic gates on a simple DNA-templated silver nanoclusters (DNA-AgNCs) platform. This library included basic logic gates, YES, AND, OR, INHIBIT, and XOR, which were further integrated into complex logic circuits to implement diverse advanced arithmetic/non-arithmetic functions including half-adder, half-subtractor, multiplexer, and demultiplexer. Under UV irradiation, all the logic functions could be instantly visualized, confirming an excellent repeatability. The logic operations were entirely based on DNA hybridization in an enzyme-free and label-free condition, avoiding waste accumulation and reducing cost consumption. Interestingly, a DNA-AgNCs-based multiplexer was, for the first time, used as an intelligent biosensor to identify pathogenic genes, E. coli and S. aureus genes, with a high sensitivity. The investigation provides a prototype for the wireless integration of multiple devices on even the simplest single-strand DNA platform to perform diverse complex functions in a straightforward and cost-effective way.
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Oxidative Modulation of Voltage-Gated Potassium Channels
Sahoo, Nirakar; Hoshi, Toshinori
2014-01-01
Abstract Significance: Voltage-gated K+ channels are a large family of K+-selective ion channel protein complexes that open on membrane depolarization. These K+ channels are expressed in diverse tissues and their function is vital for numerous physiological processes, in particular of neurons and muscle cells. Potentially reversible oxidative regulation of voltage-gated K+ channels by reactive species such as reactive oxygen species (ROS) represents a contributing mechanism of normal cellular plasticity and may play important roles in diverse pathologies including neurodegenerative diseases. Recent Advances: Studies using various protocols of oxidative modification, site-directed mutagenesis, and structural and kinetic modeling provide a broader phenomenology and emerging mechanistic insights. Critical Issues: Physicochemical mechanisms of the functional consequences of oxidative modifications of voltage-gated K+ channels are only beginning to be revealed. In vivo documentation of oxidative modifications of specific amino-acid residues of various voltage-gated K+ channel proteins, including the target specificity issue, is largely absent. Future Directions: High-resolution chemical and proteomic analysis of ion channel proteins with respect to oxidative modification combined with ongoing studies on channel structure and function will provide a better understanding of how the function of voltage-gated K+ channels is tuned by ROS and the corresponding reducing enzymes to meet cellular needs. Antioxid. Redox Signal. 21, 933–952. PMID:24040918
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Chen, Hongmei; Oram, Natalie J; Barry, Kathryn E; Mommer, Liesje; van Ruijven, Jasper; de Kroon, Hans; Ebeling, Anne; Eisenhauer, Nico; Fischer, Christine; Gleixner, Gerd; Gessler, Arthur; González Macé, Odette; Hacker, Nina; Hildebrandt, Anke; Lange, Markus; Scherer-Lorenzen, Michael; Scheu, Stefan; Oelmann, Yvonne; Wagg, Cameron; Wilcke, Wolfgang; Wirth, Christian; Weigelt, Alexandra
2017-11-01
Plant diversity influences many ecosystem functions including root decomposition. However, due to the presence of multiple pathways via which plant diversity may affect root decomposition, our mechanistic understanding of their relationships is limited. In a grassland biodiversity experiment, we simultaneously assessed the effects of three pathways-root litter quality, soil biota, and soil abiotic conditions-on the relationships between plant diversity (in terms of species richness and the presence/absence of grasses and legumes) and root decomposition using structural equation modeling. Our final structural equation model explained 70% of the variation in root mass loss. However, different measures of plant diversity included in our model operated via different pathways to alter root mass loss. Plant species richness had a negative effect on root mass loss. This was partially due to increased Oribatida abundance, but was weakened by enhanced root potassium (K) concentration in more diverse mixtures. Equally, grass presence negatively affected root mass loss. This effect of grasses was mostly mediated via increased root lignin concentration and supported via increased Oribatida abundance and decreased root K concentration. In contrast, legume presence showed a net positive effect on root mass loss via decreased root lignin concentration and increased root magnesium concentration, both of which led to enhanced root mass loss. Overall, the different measures of plant diversity had contrasting effects on root decomposition. Furthermore, we found that root chemistry and soil biota but not root morphology or soil abiotic conditions mediated these effects of plant diversity on root decomposition.
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Debouk, Haifa; de Bello, Francesco; Sebastià, Maria-Teresa
2015-01-01
Plant functional traits underlie vegetation responses to environmental changes such as global warming, and consequently influence ecosystem processes. While most of the existing studies focus on the effect of warming only on species diversity and productivity, we further investigated (i) how the structure of community plant functional traits in temperate grasslands respond to experimental warming, and (ii) whether species and functional diversity contribute to a greater stability of grasslands, in terms of vegetation composition and productivity. Intact vegetation turves were extracted from temperate subalpine grassland (highland) in the Eastern Pyrenees and transplanted into a warm continental, experimental site in Lleida, in Western Catalonia (lowland). The impacts of simulated warming on plant production and diversity, functional trait structure, and vegetation compositional stability were assessed. We observed an increase in biomass and a reduction in species and functional diversity under short-term warming. The functional structure of the grassland communities changed significantly, in terms of functional diversity and community-weighted means (CWM) for several traits. Acquisitive and fast-growing species with higher SLA, early flowering, erect growth habit, and rhizomatous strategy became dominant in the lowland. Productivity was significantly positively related to species, and to a lower extent, functional diversity, but productivity and stability after warming were more dependent on trait composition (CWM) than on diversity. The turves with more acquisitive species before warming changed less in composition after warming. Results suggest that (i) the short-term warming can lead to the dominance of acquisitive fast growing species over conservative species, thus reducing species richness, and (ii) the functional traits structure in grassland communities had a greater influence on the productivity and stability of the community under short-term warming, compared to diversity effects. In summary, short-term climate warming can greatly alter vegetation functional structure and its relation to productivity.
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Debouk, Haifa; de Bello, Francesco; Sebastià, Maria-Teresa
2015-01-01
Plant functional traits underlie vegetation responses to environmental changes such as global warming, and consequently influence ecosystem processes. While most of the existing studies focus on the effect of warming only on species diversity and productivity, we further investigated (i) how the structure of community plant functional traits in temperate grasslands respond to experimental warming, and (ii) whether species and functional diversity contribute to a greater stability of grasslands, in terms of vegetation composition and productivity. Intact vegetation turves were extracted from temperate subalpine grassland (highland) in the Eastern Pyrenees and transplanted into a warm continental, experimental site in Lleida, in Western Catalonia (lowland). The impacts of simulated warming on plant production and diversity, functional trait structure, and vegetation compositional stability were assessed. We observed an increase in biomass and a reduction in species and functional diversity under short-term warming. The functional structure of the grassland communities changed significantly, in terms of functional diversity and community-weighted means (CWM) for several traits. Acquisitive and fast-growing species with higher SLA, early flowering, erect growth habit, and rhizomatous strategy became dominant in the lowland. Productivity was significantly positively related to species, and to a lower extent, functional diversity, but productivity and stability after warming were more dependent on trait composition (CWM) than on diversity. The turves with more acquisitive species before warming changed less in composition after warming. Results suggest that (i) the short-term warming can lead to the dominance of acquisitive fast growing species over conservative species, thus reducing species richness, and (ii) the functional traits structure in grassland communities had a greater influence on the productivity and stability of the community under short-term warming, compared to diversity effects. In summary, short-term climate warming can greatly alter vegetation functional structure and its relation to productivity. PMID:26513148
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Kelvin Lee, Kai Wei; Hoong Yam, Joey Kuok; Mukherjee, Manisha; Periasamy, Saravanan; Steinberg, Peter D; Kjelleberg, Staffan; Rice, Scott A
2016-01-01
Diversity has a key role in the dynamics and resilience of communities and both interspecific (species) and intraspecific (genotypic) diversity can have important effects on community structure and function. However, a critical and unresolved question for understanding the ecology of a community is to what extent these two levels of diversity are functionally substitutable? Here we show, for a mixed-species biofilm community composed of Pseudomonas aeruginosa, P. protegens and Klebsiella pneumoniae, that increased interspecific diversity reduces and functionally substitutes for intraspecific diversity in mediating tolerance to stress. Biofilm populations generated high percentages of genotypic variants, which were largely absent in biofilm communities. Biofilms with either high intra- or interspecific diversity were more tolerant to SDS stress than biofilms with no or low diversity. Unexpectedly, genotypic variants decreased the tolerance of biofilm communities when experimentally introduced into the communities. For example, substituting P. protegens wild type with its genotypic variant within biofilm communities decreased SDS tolerance by twofold, apparently due to perturbation of interspecific interactions. A decrease in variant frequency was also observed when biofilm populations were exposed to cell-free effluents from another species, suggesting that extracellular factors have a role in selection against the appearance of intraspecific variants. This work demonstrates the functional substitution of inter- and intraspecific diversity for an emergent property of biofilms. It also provides a potential explanation for a long-standing paradox in microbiology, in which morphotypic variants are common in laboratory grown biofilm populations, but are rare in diverse, environmental biofilm communities. PMID:26405829
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Social network types and functional dependency in older adults in Mexico.
Doubova Dubova, Svetlana Vladislavovna; Pérez-Cuevas, Ricardo; Espinosa-Alarcón, Patricia; Flores-Hernández, Sergio
2010-02-27
Social networks play a key role in caring for older adults. A better understanding of the characteristics of different social networks types (TSNs) in a given community provides useful information for designing policies to care for this age group. Therefore this study has three objectives: 1) To derive the TSNs among older adults affiliated with the Mexican Institute of Social Security; 2) To describe the main characteristics of the older adults in each TSN, including the instrumental and economic support they receive and their satisfaction with the network; 3) To determine the association between functional dependency and the type of social network. Secondary data analysis of the 2006 Survey of Autonomy and Dependency (N = 3,348). The TSNs were identified using the structural approach and cluster analysis. The association between functional dependency and the TSNs was evaluated with Poisson regression with robust variance analysis in which socio-demographic characteristics, lifestyle and medical history covariates were included. We identified five TSNs: diverse with community participation (12.1%), diverse without community participation (44.3%); widowed (32.0%); nonfriends-restricted (7.6%); nonfamily-restricted (4.0%). Older adults belonging to widowed and restricted networks showed a higher proportion of dependency, negative self-rated health and depression. Older adults with functional dependency more likely belonged to a widowed network (adjusted prevalence ratio 1.5; 95%CI: 1.1-2.1). The derived TSNs were similar to those described in developed countries. However, we identified the existence of a diverse network without community participation and a widowed network that have not been previously described. These TSNs and restricted networks represent a potential unmet need of social security affiliates.
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Valencia-Gómez, Enrique; Maestre, Fernando T.; Le Bagousse-Pinguet, Yoann; Quero, José Luis; Tamme, Riin; Börger, Luca; García-Gómez, Miguel; Gross, Nicolas
2015-01-01
SUMMARY We used a functional trait-based approach to assess the impacts of aridity and shrub encroachment on the functional structure of Mediterranean dryland communities (functional diversity and community-weighted mean trait values [CWM]), and to evaluate how these functional attributes ultimately affect multifunctionality (i.e., the provision of several ecosystem functions simultaneously). Shrub encroachment (the increase in the abundance/cover of shrubs) is a major land cover change that is taking place in grasslands worldwide. Studies conducted on drylands have reported positive or negative impacts of shrub encroachment depending on the functions and the traits of the sprouting or non-sprouting shrub species considered. Functional diversity and CWM were equally important as drivers of multifunctionality responses to both aridity and shrub encroachment. Size traits (e.g., vegetative height or lateral spread) and leaf traits (e.g., specific leaf area and leaf dry matter content) captured the effect of shrub encroachment on multifunctionality with a relative high accuracy (r2=0.63). Functional diversity also improved the resistance of multifunctionality along the aridity gradient studied. Maintaining and enhancing functional diversity in plant communities may help to buffer negative effects of ongoing global environmental change on dryland multifunctionality. PMID:25615801
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Shifts in diversity and function of lake bacterial communities upon glacier retreat.
Peter, Hannes; Sommaruga, Ruben
2016-07-01
Global climate change is causing a wastage of glaciers and threatening biodiversity in glacier-fed ecosystems. The high turbidity typically found in those ecosystems, which is caused by inorganic particles and result of the erosive activity of glaciers is a key environmental factor influencing temperature and light availability, as well as other factors in the water column. Once these lakes loose hydrological connectivity to glaciers and turn clear, the accompanying environmental changes could represent a potential bottleneck for the established local diversity with yet unknown functional consequences. Here, we study three lakes situated along a turbidity gradient as well as one clear unconnected lake and evaluate seasonal changes in their bacterial community composition and diversity. Further, we assess potential consequences for community functioning. Glacier runoff represented a diverse source community for the lakes and several taxa were able to colonize downstream turbid habitats, although they were not found in the clear lake. Operational taxonomic unit-based alpha diversity and phylogenetic diversity decreased along the turbidity gradient, but metabolic functional diversity was negatively related to turbidity. No evidence for multifunctional redundancy, which may allow communities to maintain functioning upon alterations in diversity, was found. Our study gives a first view on how glacier-fed lake bacterial communities are affected by the melting of glaciers and indicates that diversity and community composition significantly change when hydrological connectivity to the glacier is lost and lakes turn clear.
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Vertebrate LTR retrotransposons of the Tf1/sushi group.
Butler, M; Goodwin, T; Simpson, M; Singh, M; Poulter, R
2001-03-01
LTR retrotransposons of the Tf1/sushi group from a diversity of vertebrates, including fish, amphibians, and mammals (humans, mice, and others), are described as full-length or partial elements. These elements are compared, and the mechanisms involved in self-priming of reverse transcriptase and programmed phase shifting are inferred. Evidence is presented that in mammals these elements are still transcriptionally active and are represented as proteins. This suggests that members of the Tf1/sushi group are present as functional elements (or incorporated as partial elements into host genes) in diverse vertebrate lineages.
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[Advance in molecular biology of Dendrobium (Orchidaceae)].
Li, Qing; Li, Biao; Guo, Shun-Xing
2016-08-01
With the development of molecular biology, the process in molecular biology research of Dendrobium is going fast. Not only did it provide new ways to identify Dendrobium quickly, reveal the genetic diversity and relationship of Dendrobium, but also lay the vital foundation for explaining the mechanism of Dendrobium growth and metabolism. The present paper reviews the recent process in molecular biology research of Dendrobium from three aspects, including molecular identification, genetic diversity and functional genes. And this review will facilitate the development of this research area and Dendrobium. Copyright© by the Chinese Pharmaceutical Association.
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Mason, Chase M; Goolsby, Eric W; Davis, Kaleigh E; Bullock, Devon V; Donovan, Lisa A
2017-05-01
Trait-based plant ecology attempts to use small numbers of functional traits to predict plant ecological strategies. However, a major gap exists between our understanding of organ-level ecophysiological traits and our understanding of whole-plant fitness and environmental adaptation. In this gap lie whole-plant organizational traits, including those that describe how plant biomass is allocated among organs and the timing of plant reproduction. This study explores the role of whole-plant organizational traits in adaptation to diverse environments in the context of life history, growth form and leaf economic strategy in a well-studied herbaceous system. A phylogenetic comparative approach was used in conjunction with common garden phenotyping to assess the evolution of biomass allocation and reproductive timing across 83 populations of 27 species of the diverse genus Helianthus (the sunflowers). Broad diversity exists among species in both relative biomass allocation and reproductive timing. Early reproduction is strongly associated with resource-acquisitive leaf economic strategy, while biomass allocation is less integrated with either reproductive timing or leaf economics. Both biomass allocation and reproductive timing are strongly related to source site environmental characteristics, including length of the growing season, temperature, precipitation and soil fertility. Herbaceous taxa can adapt to diverse environments in many ways, including modulation of phenology, plant architecture and organ-level ecophysiology. Although leaf economic strategy captures one key aspect of plant physiology, on their own leaf traits are not particularly predictive of ecological strategies in Helianthus outside of the context of growth form, life history and whole-plant organization. These results highlight the importance of including data on whole-plant organization alongside organ-level ecophysiological traits when attempting to bridge the gap between functional traits and plant fitness and environmental adaptation. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com
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Goolsby, Eric W.; Davis, Kaleigh E.; Bullock, Devon V.; Donovan, Lisa A.
2017-01-01
Abstract Background and Aims Trait-based plant ecology attempts to use small numbers of functional traits to predict plant ecological strategies. However, a major gap exists between our understanding of organ-level ecophysiological traits and our understanding of whole-plant fitness and environmental adaptation. In this gap lie whole-plant organizational traits, including those that describe how plant biomass is allocated among organs and the timing of plant reproduction. This study explores the role of whole-plant organizational traits in adaptation to diverse environments in the context of life history, growth form and leaf economic strategy in a well-studied herbaceous system. Methods A phylogenetic comparative approach was used in conjunction with common garden phenotyping to assess the evolution of biomass allocation and reproductive timing across 83 populations of 27 species of the diverse genus Helianthus (the sunflowers). Key Results Broad diversity exists among species in both relative biomass allocation and reproductive timing. Early reproduction is strongly associated with resource-acquisitive leaf economic strategy, while biomass allocation is less integrated with either reproductive timing or leaf economics. Both biomass allocation and reproductive timing are strongly related to source site environmental characteristics, including length of the growing season, temperature, precipitation and soil fertility. Conclusions Herbaceous taxa can adapt to diverse environments in many ways, including modulation of phenology, plant architecture and organ-level ecophysiology. Although leaf economic strategy captures one key aspect of plant physiology, on their own leaf traits are not particularly predictive of ecological strategies in Helianthus outside of the context of growth form, life history and whole-plant organization. These results highlight the importance of including data on whole-plant organization alongside organ-level ecophysiological traits when attempting to bridge the gap between functional traits and plant fitness and environmental adaptation. PMID:28203721
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Mason-Romo, Edgard David; Farías, Ariel A; Ceballos, Gerardo
2017-01-01
Understanding the effects of global climate disruption on biodiversity is important to future conservation efforts. While taxonomic diversity is widely studied, functional diversity of plants, and recently animals, is receiving increasing attention. Most studies of mammals are short-term, focus on temperate habitats, and rely on traits described in the literature rather than generating traits from observations. Unlike previous studies, this long-term field study assessed the factors driving the functional and taxonomic diversity of small-mammal assemblages in dry tropical forests using both traits recorded from literature and a demographic database. We assessed the drivers (abundance and biomass, temperature and rainfall) of taxonomic richness and functional diversity for two rain-driven seasons in two adjacent but distinct forests-upland and lowland (arroyo or riparian) forests. Our analysis found that rainfall, both seasonal and atypical, was the primary factor driving functional and taxonomic diversity of small-mammal assemblages. Functional responses differed between the two types of forests, however, with effects being stronger in the harsher conditions of the upland forests than in the less severe conditions prevailing in the arroyo (riparian) forest. The latter also supports a richer, more diverse, and more stable small-mammal assemblage. These findings highlight the importance of climate to tropical biological diversity, as extreme climate events (hurricanes, droughts and floods) and disruption of rainfall patterns were shown to decrease biodiversity. They also support the need to preserve these habitats, as their high taxonomic diversity and functional redundancy makes them resilient against global climate disruption and local extreme events. Tropical dry forests constitute a potential reservoir for biodiversity and the ecosystem services they provide. Unfortunately, these forests are among the most endangered terrestrial ecosystems because of deforestation and the likely impacts of global climate disruption.
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Luiz, Amom Mendes; Sawaya, Ricardo J.
2018-01-01
Ecological communities are complex entities that can be maintained and structured by niche-based processes such as environmental conditions, and spatial processes such as dispersal. Thus, diversity patterns may be shaped simultaneously at different spatial scales by very distinct processes. Herein we assess whether and how functional, taxonomic, and phylogenetic beta diversities of frog tadpoles are explained by environmental and/or spatial predictors. We implemented a distance–based redundancy analysis to explore variation in components of beta diversity explained by pure environmental and pure spatial predictors, as well as their interactions, at both fine and broad spatial scales. Our results indicated important but complex roles of spatial and environmental predictors in structuring phylogenetic, taxonomic and functional beta diversities. The pure fine-scales spatial fraction was more important in structuring all beta diversity components, especially to functional and taxonomical spatial turnover. Environmental variables such as canopy cover and vegetation structure were important predictors of all components, but especially to functional and taxonomic beta diversity. We emphasize that distinct factors related to environment and space are affecting distinct components of beta diversity in different ways. Although weaker, phylogenetic beta diversity, which is structured more on biogeographical scales, and thus can be represented by spatially structured processes, was more related to broad spatial processes than other components. However, selected fine-scale spatial predictors denoted negative autocorrelation, which may be revealing the existence of differences in unmeasured habitat variables among samples. Although overall important, local environmental-based processes explained better functional and taxonomic beta diversity, as these diversity components carry an important ecological value. We highlight the importance of assessing different components of diversity patterns at different scales by spatially explicit models in order to improve our understanding of community structure and help to unravel the complex nature of biodiversity. PMID:29672575
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Yang, Jinny Wu; Wu, Wenxue; Chung, Chih-Ching; Chiang, Kuo-Ping; Gong, Gwo-Ching; Hsieh, Chih-Hao
2018-06-01
The importance of biodiversity effects on ecosystem functioning across trophic levels, especially via predatory-prey interactions, is receiving increased recognition. However, this topic has rarely been explored for marine microbes, even though microbial biodiversity contributes significantly to marine ecosystem function and energy flows. Here we examined diversity and biomass of bacteria (prey) and nanoflagellates (predators), as well as their effects on trophic transfer efficiency in the East China Sea. Specifically, we investigated: (i) predator diversity effects on prey biomass and trophic transfer efficiency (using the biomass ratio of predator/prey as a proxy), (ii) prey diversity effects on predator biomass and trophic transfer efficiency, and (iii) the relationship between predator and prey diversity. We found higher prey diversity enhanced both diversity and biomass of predators, as well as trophic transfer efficiency, which may arise from more balanced diet and/or enhanced niche complementarity owing to higher prey diversity. By contrast, no clear effect was detected for predator diversity on prey biomass and transfer efficiency. Notably, we found prey diversity effects on predator-prey interactions; whereas, we found no significant diversity effect on biomass within the same trophic level. Our findings highlight the importance of considering multi-trophic biodiversity effects on ecosystem functioning in natural ecosystems.
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Shen, Yong; Yu, Shixiao; Lian, Juyu; Shen, Hao; Cao, Honglin; Lu, Huanping; Ye, Wanhui
2016-01-01
Tropical forests play a disproportionately important role in the global carbon (C) cycle, but it remains unclear how local environments and functional diversity regulate tree aboveground C storage. We examined how three components (environments, functional dominance and diversity) affected C storage in Dinghushan 20-ha plot in China. There was large fine-scale variation in C storage. The three components significantly contributed to regulate C storage, but dominance and diversity of traits were associated with C storage in different directions. Structural equation models (SEMs) of dominance and diversity explained 34% and 32% of variation in C storage. Environments explained 26–44% of variation in dominance and diversity. Similar proportions of variation in C storage were explained by dominance and diversity in regression models, they were improved after adding environments. Diversity of maximum diameter was the best predictor of C storage. Complementarity and selection effects contributed to C storage simultaneously, and had similar importance. The SEMs disengaged the complex relationships among the three components and C storage, and established a framework to show the direct and indirect effects (via dominance and diversity) of local environments on C storage. We concluded that local environments are important for regulating functional diversity and C storage. PMID:27278688
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The Plant Peptidome: An Expanding Repertoire of Structural Features and Biological Functions[OPEN
Tavormina, Patrizia; De Coninck, Barbara; Nikonorova, Natalia; De Smet, Ive; Cammue, Bruno P.A.
2015-01-01
Peptides fulfill a plethora of functions in plant growth, development, and stress responses. They act as key components of cell-to-cell communication, interfere with signaling and response pathways, or display antimicrobial activity. Strikingly, both the diversity and amount of plant peptides have been largely underestimated. Most characterized plant peptides to date acting as small signaling peptides or antimicrobial peptides are derived from nonfunctional precursor proteins. However, evidence is emerging on peptides derived from a functional protein, directly translated from small open reading frames (without the involvement of a precursor) or even encoded by primary transcripts of microRNAs. These novel types of peptides further add to the complexity of the plant peptidome, even though their number is still limited and functional characterization as well as translational evidence are often controversial. Here, we provide a comprehensive overview of the reported types of plant peptides, including their described functional and structural properties. We propose a novel, unifying peptide classification system to emphasize the enormous diversity in peptide synthesis and consequent complexity of the still expanding knowledge on the plant peptidome. PMID:26276833
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[Soil microbial functional diversity of different altitude Pinus koraiensis forests].
Han, Dong-xue; Wang, Ning; Wang, Nan-nan; Sun, Xue; Feng, Fu-juan
2015-12-01
In order to comprehensively understand the soil microbial carbon utilization characteristics of Pinus koraiensis forests, we took the topsoil (0-5 cm and 5-10 cm) along the 700-1100 m altitude in Changbai Mountains and analyzed the vertical distributed characteristics and variation of microbial functional diversity along the elevation gradient by Biolog microplate method. The results showed that there were significant differences in functional diversity of microbial communities at different elevations. AWCD increased with the extension of incubation time and AWCD at the same soil depth gradually decreased along with increasing altitude; Shannon, Simpson and McIntosh diversity index also showed the same trend with AWCD and three different diversity indices were significantly different along the elevation gradient; Species diversity and functional diversity showed the same variation. The utilization intensities of six categories carbon sources had differences while amino acids were constantly the most dominant carbon source. Principal component analysis (PCA) identified that soil microbial carbon utilization at different altitudes had obvious spatial differentiation, as reflected in the use of carbohydrates, amino acids and carboxylic acids. In addition, the cluster of the microbial diversity indexes and AWCD values of different altitudes showed that the composition of vegetation had a significant impact on soil microbial composition and functional activity.
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Seasonal cycles, phylogenetic assembly, and functional diversity of orchid bee communities.
Ramírez, Santiago R; Hernández, Carlos; Link, Andres; López-Uribe, Margarita M
2015-05-01
Neotropical rainforests sustain some of the most diverse terrestrial communities on Earth. Euglossine (or orchid) bees are a diverse lineage of insect pollinators distributed throughout the American tropics, where they provide pollination services to a staggering diversity of flowering plant taxa. Elucidating the seasonal patterns of phylogenetic assembly and functional trait diversity of bee communities can shed new light into the mechanisms that govern the assembly of bee pollinator communities and the potential effects of declining bee populations. Male euglossine bees collect, store, and accumulate odoriferous compounds (perfumes) to subsequently use during courtship display. Thus, synthetic chemical baits can be used to attract and monitor euglossine bee populations. We conducted monthly censuses of orchid bees in three sites in the Magdalena valley of Colombia - a region where Central and South American biotas converge - to investigate the structure, diversity, and assembly of euglossine bee communities through time in relation to seasonal climatic cycles. In particular, we tested the hypothesis that phylogenetic community structure and functional trait diversity changed in response to seasonal rainfall fluctuations. All communities exhibited strong to moderate phylogenetic clustering throughout the year, with few pronounced bursts of phylogenetic overdispersion that coincided with the transition from wet-to-dry seasons. Despite the heterogeneous distribution of functional traits (e.g., body size, body mass, and proboscis length) and the observed seasonal fluctuations in phylogenetic diversity, we found that functional trait diversity, evenness, and divergence remained constant during all seasons in all communities. However, similar to the pattern observed with phylogenetic diversity, functional trait richness fluctuated markedly with rainfall in all sites. These results emphasize the importance of considering seasonal fluctuations in community assembly and provide a glimpse to the potential effects that climatic alterations may have on both pollinator communities and the ecosystem services they provide.
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Bengtsson, Mia M; Wagner, Karoline; Schwab, Clarissa; Urich, Tim; Battin, Tom J
2018-04-21
Phototrophic biofilms are ubiquitous in freshwater and marine environments where they are critical for biogeochemical cycling, food webs and in industrial applications. In streams, phototrophic biofilms dominate benthic microbial life and harbor an immense prokaryotic and eukaryotic microbial biodiversity with biotic interactions across domains and trophic levels. Here, we examine how community structure and function of these biofilms respond to varying light availability, as the crucial energy source for phototrophic biofilms. Using metatranscriptomics, we found that under light limitation dominant phototrophs, including diatoms and cyanobacteria, displayed a remarkable plasticity in their photosynthetic machinery manifested as higher abundance of messenger RNAs (mRNAs) involved in photosynthesis and chloroplast ribosomal RNA. Under higher light availability, bacterial mRNAs involved in phosphorus metabolism, mainly from Betaproteobacteria and Cyanobacteria, increased, likely compensating for nutrient depletion in thick biofilms with high biomass. Consumers, including diverse ciliates, displayed community shifts indicating preferential grazing on algae instead of bacteria under higher light. For the first time, we show that the functional integrity of stream biofilms under variable light availability is maintained by structure-function adaptations on several trophic levels. Our findings shed new light on complex biofilms, or "microbial jungles", where in analogy to forests, diverse and multi-trophic level communities lend stability to ecosystem functioning. This multi-trophic level perspective, coupling metatranscriptomics to process measurements, could advance understanding of microbial-driven ecosystems beyond biofilms, including planktonic and soil environments. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
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Deciphering Diversity Indices for a Better Understanding of Microbial Communities.
Kim, Bo-Ra; Shin, Jiwon; Guevarra, Robin; Lee, Jun Hyung; Kim, Doo Wan; Seol, Kuk-Hwan; Lee, Ju-Hoon; Kim, Hyeun Bum; Isaacson, Richard
2017-12-28
The past decades have been a golden era during which great tasks were accomplished in the field of microbiology, including food microbiology. In the past, culture-dependent methods have been the primary choice to investigate bacterial diversity. However, using cultureindependent high-throughput sequencing of 16S rRNA genes has greatly facilitated studies exploring the microbial compositions and dynamics associated with health and diseases. These culture-independent DNA-based studies generate large-scale data sets that describe the microbial composition of a certain niche. Consequently, understanding microbial diversity becomes of greater importance when investigating the composition, function, and dynamics of the microbiota associated with health and diseases. Even though there is no general agreement on which diversity index is the best to use, diversity indices have been used to compare the diversity among samples and between treatments with controls. Tools such as the Shannon- Weaver index and Simpson index can be used to describe population diversity in samples. The purpose of this review is to explain the principles of diversity indices, such as Shannon- Weaver and Simpson, to aid general microbiologists in better understanding bacterial communities. In this review, important questions concerning microbial diversity are addressed. Information from this review should facilitate evidence-based strategies to explore microbial communities.
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MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution
Boeuf, Dominique; Audic, Stéphane; Brillet-Guéguen, Loraine; Caron, Christophe; Jeanthon, Christian
2015-01-01
Microbial rhodopsins are a diverse group of photoactive transmembrane proteins found in all three domains of life and in viruses. Today, microbial rhodopsin research is a flourishing research field in which new understandings of rhodopsin diversity, function and evolution are contributing to broader microbiological and molecular knowledge. Here, we describe MicRhoDE, a comprehensive, high-quality and freely accessible database that facilitates analysis of the diversity and evolution of microbial rhodopsins. Rhodopsin sequences isolated from a vast array of marine and terrestrial environments were manually collected and curated. To each rhodopsin sequence are associated related metadata, including predicted spectral tuning of the protein, putative activity and function, taxonomy for sequences that can be linked to a 16S rRNA gene, sampling date and location, and supporting literature. The database currently covers 7857 aligned sequences from more than 450 environmental samples or organisms. Based on a robust phylogenetic analysis, we introduce an operational classification system with multiple phylogenetic levels ranging from superclusters to species-level operational taxonomic units. An integrated pipeline for online sequence alignment and phylogenetic tree construction is also provided. With a user-friendly interface and integrated online bioinformatics tools, this unique resource should be highly valuable for upcoming studies of the biogeography, diversity, distribution and evolution of microbial rhodopsins. Database URL: http://micrhode.sb-roscoff.fr. PMID:26286928
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MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution.
Boeuf, Dominique; Audic, Stéphane; Brillet-Guéguen, Loraine; Caron, Christophe; Jeanthon, Christian
2015-01-01
Microbial rhodopsins are a diverse group of photoactive transmembrane proteins found in all three domains of life and in viruses. Today, microbial rhodopsin research is a flourishing research field in which new understandings of rhodopsin diversity, function and evolution are contributing to broader microbiological and molecular knowledge. Here, we describe MicRhoDE, a comprehensive, high-quality and freely accessible database that facilitates analysis of the diversity and evolution of microbial rhodopsins. Rhodopsin sequences isolated from a vast array of marine and terrestrial environments were manually collected and curated. To each rhodopsin sequence are associated related metadata, including predicted spectral tuning of the protein, putative activity and function, taxonomy for sequences that can be linked to a 16S rRNA gene, sampling date and location, and supporting literature. The database currently covers 7857 aligned sequences from more than 450 environmental samples or organisms. Based on a robust phylogenetic analysis, we introduce an operational classification system with multiple phylogenetic levels ranging from superclusters to species-level operational taxonomic units. An integrated pipeline for online sequence alignment and phylogenetic tree construction is also provided. With a user-friendly interface and integrated online bioinformatics tools, this unique resource should be highly valuable for upcoming studies of the biogeography, diversity, distribution and evolution of microbial rhodopsins. Database URL: http://micrhode.sb-roscoff.fr. © The Author(s) 2015. Published by Oxford University Press.
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INVASIVE PLANTS HARBOR HUNGRY DETRITIVORES THAT ALTER ECOSYSTEM FUNCTION
Ecosystems are expected to function more efficiently in response to a diverse community of inhabitants. However, biological invasions may change expected relationships between ecosystem function and diversity. We observed increased decomposition, a measure of ecosystem function...
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Monitoring biological diversity: strategies, tools, limitations, and challenges
Beever, E.A.
2006-01-01
Monitoring is an assessment of the spatial and temporal variability in one or more ecosystem properties, and is an essential component of adaptive management. Monitoring can help determine whether mandated environmental standards are being met and can provide an early-warning system of ecological change. Development of a strategy for monitoring biological diversity will likely be most successful when based upon clearly articulated goals and objectives and may be enhanced by including several key steps in the process. Ideally, monitoring of biological diversity will measure not only composition, but also structure and function at the spatial and temporal scales of interest. Although biodiversity monitoring has several key limitations as well as numerous theoretical and practical challenges, many tools and strategies are available to address or overcome such challenges; I summarize several of these. Due to the diversity of spatio-temporal scales and comprehensiveness encompassed by existing definitions of biological diversity, an effective monitoring design will reflect the desired sampling domain of interest and its key stressors, available funding, legal requirements, and organizational goals.
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Reaves, B J; Wolstenholme, A J
2007-02-01
TRP (transient receptor potential) cationic channels are key molecules that are involved in a variety of diverse biological processes ranging from fertility to osmosensation and nociception. Increasing our knowledge of these channels will help us to understand a range of physiological and pathogenic processes, as well as highlighting potential therapeutic drug targets. The founding members of the TRP family, Drosophila TRP and TRPL (TRP-like) proteins, were identified within the last two decades and there has been a subsequent explosion in the number and type of TRP channel described. Although information is accumulating as to the function of some of the TRP channels, the activation and inactivation mechanisms, structure, and interacting proteins of many, if not most, are awaiting elucidation. The Cell and Molecular Biology of TRP Channels Meeting held at the University of Bath included speakers working on a number of the different subfamilies of TRP channels and provided a basis for highlighting both similarities and differences between these groups. As the TRP channels mediate diverse functions, this meeting also brought together an audience with wide-ranging research interests, including biochemistry, cell biology, physiology and neuroscience, and inspired lively discussion on the issues reviewed herein.
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Comparative genomics reveals tissue-specific regulation of prolactin receptor gene expression
USDA-ARS?s Scientific Manuscript database
Prolactin (PRL), acting via the prolactin receptor, fulfills a diversity of biological functions including the maintenance of solute balance and mineral homeostasis via tissues such as the heart, kidneys and intestine. Expression and activity of the prolactin receptor (PRLR) is regulated by various ...
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Chemical toxicity can arise from disruption of specific biomolecular functions or through more generalized cell stress and cytotoxicity-mediated processes. Here, concentration-dependent responses of 1063 chemicals including pharmaceuticals, natural products, pesticidals, consumer...
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University-Community Engagement in Australia: Practice, Policy and Public Good
ERIC Educational Resources Information Center
Winter, Alexandra; Wiseman, John; Muirhead, Bruce
2006-01-01
The rise of a community engagement movement offers a range of possibilities for universities to function as "sites of citizenship". These include contributing to community social and economic infrastructure, supporting equity and diversity within higher education, and education for democratic citizenship. This article provides an…
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Diverse structures, functions and uses of FK506 binding proteins.
Bonner, Julia Maeve; Boulianne, Gabrielle L
2017-10-01
FK506 (Tacrolimus), isolated from Streptomyces tsukubaenis is a powerful immunosuppressant shown to inhibit T cell activation. FK506 mediated immunosuppression requires the formation of a complex between FK506, a FK506 binding protein (FKBP) and calcineurin. Numerous FKBPs have been identified in a wide range of species, from single celled organisms to humans. FKBPs show peptidylprolyl cis/trans isomerase (PPIase) activity and have been shown to affect a wide range of cellular processes including protein folding, receptor signaling and apoptosis. FKBPs also affect numerous biological functions in addition to immunosuppression including regulation of cardiac function, neuronal function and development and have been implicated in several diseases including cardiac disease, cancer and neurodegenerative diseases such as Alzheimer's disease. More recently, FKBPs have proven useful as molecular tools for studying protein interactions, localization and functions. This review provides an overview of the current state of knowledge of FKBPs and their numerous biological functions and uses. Copyright © 2017 Elsevier Inc. All rights reserved.
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van Egmond, Jeroen C; Breugem, Stefan J M; Driessen, Marcel; Bruijn, Daniel J
2015-06-01
Plantar fasciitis is the most common cause of heel pain. Diverse non-operative treatment options are available. The purpose of this study was to determine if a single platelet-rich-plasma injection at the origin of the plantar fascia in patients with plantar fasciitis gives a functional improvement. Patients with plantar fasciitis and failed conservative treatment were included in this retrospective study. Included patients were sent four questionnaires after platelet-rich-plasma injection. Primary outcome is functional improvement, determined by foot function index in which lower scores correlates with a better foot function. A total of 61 feet in 58 patients were included. The median foot function index before treatment was 69.4 and after treatment 31.8, which is a significant decrease. In 80.3% of the patients the foot function index decreased. Therefore platelet-rich-plasma injection seems to be effective in treatment of patients with plantar fasciitis when conservative treatment failed.
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Chao, Anne; Chiu, Chun-Huo; Colwell, Robert K; Magnago, Luiz Fernando S; Chazdon, Robin L; Gotelli, Nicholas J
2017-11-01
Estimating the species, phylogenetic, and functional diversity of a community is challenging because rare species are often undetected, even with intensive sampling. The Good-Turing frequency formula, originally developed for cryptography, estimates in an ecological context the true frequencies of rare species in a single assemblage based on an incomplete sample of individuals. Until now, this formula has never been used to estimate undetected species, phylogenetic, and functional diversity. Here, we first generalize the Good-Turing formula to incomplete sampling of two assemblages. The original formula and its two-assemblage generalization provide a novel and unified approach to notation, terminology, and estimation of undetected biological diversity. For species richness, the Good-Turing framework offers an intuitive way to derive the non-parametric estimators of the undetected species richness in a single assemblage, and of the undetected species shared between two assemblages. For phylogenetic diversity, the unified approach leads to an estimator of the undetected Faith's phylogenetic diversity (PD, the total length of undetected branches of a phylogenetic tree connecting all species), as well as a new estimator of undetected PD shared between two phylogenetic trees. For functional diversity based on species traits, the unified approach yields a new estimator of undetected Walker et al.'s functional attribute diversity (FAD, the total species-pairwise functional distance) in a single assemblage, as well as a new estimator of undetected FAD shared between two assemblages. Although some of the resulting estimators have been previously published (but derived with traditional mathematical inequalities), all taxonomic, phylogenetic, and functional diversity estimators are now derived under the same framework. All the derived estimators are theoretically lower bounds of the corresponding undetected diversities; our approach reveals the sufficient conditions under which the estimators are nearly unbiased, thus offering new insights. Simulation results are reported to numerically verify the performance of the derived estimators. We illustrate all estimators and assess their sampling uncertainty with an empirical dataset for Brazilian rain forest trees. These estimators should be widely applicable to many current problems in ecology, such as the effects of climate change on spatial and temporal beta diversity and the contribution of trait diversity to ecosystem multi-functionality. © 2017 by the Ecological Society of America.
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Atopic Dermatitis Susceptibility Variants in Filaggrin Hitchhike Hornerin Selective Sweep
Eaaswarkhanth, Muthukrishnan; Xu, Duo; Flanagan, Colin; Rzhetskaya, Margarita; Hayes, M. Geoffrey; Blekhman, Ran; Jablonski, Nina G.; Gokcumen, Omer
2016-01-01
Human skin has evolved rapidly, leaving evolutionary signatures in the genome. The filaggrin (FLG) gene is widely studied for its skin-barrier function in humans. The extensive genetic variation in this gene, especially common loss-of-function (LoF) mutations, has been established as primary risk factors for atopic dermatitis. To investigate the evolution of this gene, we analyzed 2,504 human genomes and genotyped the copy number variation of filaggrin repeats within FLG in 126 individuals from diverse ancestral backgrounds. We were unable to replicate a recent study claiming that LoF of FLG is adaptive in northern latitudes with lower ultraviolet light exposure. Instead, we present multiple lines of evidence suggesting that FLG genetic variation, including LoF variants, have little or no effect on fitness in modern humans. Haplotype-level scrutinization of the locus revealed signatures of a recent selective sweep in Asia, which increased the allele frequency of a haplotype group (Huxian haplogroup) in Asian populations. Functionally, we found that the Huxian haplogroup carries dozens of functional variants in FLG and hornerin (HRNR) genes, including those that are associated with atopic dermatitis susceptibility, HRNR expression levels and microbiome diversity on the skin. Our results suggest that the target of the adaptive sweep is HRNR gene function, and the functional FLG variants that involve susceptibility to atopic dermatitis, seem to hitchhike the selective sweep on HRNR. Our study presents a novel case of a locus that harbors clinically relevant common genetic variation with complex evolutionary trajectories. PMID:27678121
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Grate, Jay W.; Mo, Kai -For; Daily, Michael D.
2016-02-10
Sequence control in polymers, well-known in nature, encodes structure and functionality. Here we introduce a new architecture, based on the nucleophilic aromatic substitution chemistry of cyanuric chloride, that creates a new class of sequence-defined polymers dubbed TZPs. Proof of concept is demonstrated with two synthesized hexamers, having neutral and ionizable side chains. Molecular dynamics simulations show backbone–backbone interactions, including H-bonding motifs and pi–pi interactions. This architecture is arguably biomimetic while differing from sequence-defined polymers having peptide bonds. In conclusion, the synthetic methodology supports the structural diversity of side chains known in peptides, as well as backbone–backbone hydrogen-bonding motifs, and willmore » thus enable new macromolecules and materials with useful functions.« less
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Grate, Jay W; Mo, Kai-For; Daily, Michael D
2016-03-14
Sequence control in polymers, well-known in nature, encodes structure and functionality. Here we introduce a new architecture, based on the nucleophilic aromatic substitution chemistry of cyanuric chloride, that creates a new class of sequence-defined polymers dubbed TZPs. Proof of concept is demonstrated with two synthesized hexamers, having neutral and ionizable side chains. Molecular dynamics simulations show backbone-backbone interactions, including H-bonding motifs and pi-pi interactions. This architecture is arguably biomimetic while differing from sequence-defined polymers having peptide bonds. The synthetic methodology supports the structural diversity of side chains known in peptides, as well as backbone-backbone hydrogen-bonding motifs, and will thus enable new macromolecules and materials with useful functions. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Grate, Jay W.; Mo, Kai -For; Daily, Michael D.
Sequence control in polymers, well-known in nature, encodes structure and functionality. Here we introduce a new architecture, based on the nucleophilic aromatic substitution chemistry of cyanuric chloride, that creates a new class of sequence-defined polymers dubbed TZPs. Proof of concept is demonstrated with two synthesized hexamers, having neutral and ionizable side chains. Molecular dynamics simulations show backbone–backbone interactions, including H-bonding motifs and pi–pi interactions. This architecture is arguably biomimetic while differing from sequence-defined polymers having peptide bonds. In conclusion, the synthetic methodology supports the structural diversity of side chains known in peptides, as well as backbone–backbone hydrogen-bonding motifs, and willmore » thus enable new macromolecules and materials with useful functions.« less
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Ice-binding proteins: a remarkable diversity of structures for stopping and starting ice growth.
Davies, Peter L
2014-11-01
Antifreeze proteins (AFPs) were discovered in marine fishes that need protection from freezing. These ice-binding proteins (IBPs) are widespread across biological kingdoms, and their functions include freeze tolerance and ice adhesion. Consistent with recent independent evolution, AFPs have remarkably diverse folds that rely heavily on hydrogen- and disulfide-bonding. AFP ice-binding sites are typically flat, extensive, relatively hydrophobic, and are thought to organize water into an ice-like arrangement that merges and freezes with the quasi-liquid layer next to the ice lattice. In this article, the roles, properties, and structure-function interactions of IBPs are reviewed, and their relationship to ice nucleation proteins, which promote freezing at high subzero temperatures, is explored. Copyright © 2014 Elsevier Ltd. All rights reserved.
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Gagic, Vesna; Bartomeus, Ignasi; Jonsson, Tomas; Taylor, Astrid; Winqvist, Camilla; Fischer, Christina; Slade, Eleanor M; Steffan-Dewenter, Ingolf; Emmerson, Mark; Potts, Simon G; Tscharntke, Teja; Weisser, Wolfgang; Bommarco, Riccardo
2015-02-22
Drastic biodiversity declines have raised concerns about the deterioration of ecosystem functions and have motivated much recent research on the relationship between species diversity and ecosystem functioning. A functional trait framework has been proposed to improve the mechanistic understanding of this relationship, but this has rarely been tested for organisms other than plants. We analysed eight datasets, including five animal groups, to examine how well a trait-based approach, compared with a more traditional taxonomic approach, predicts seven ecosystem functions below- and above-ground. Trait-based indices consistently provided greater explanatory power than species richness or abundance. The frequency distributions of single or multiple traits in the community were the best predictors of ecosystem functioning. This implies that the ecosystem functions we investigated were underpinned by the combination of trait identities (i.e. single-trait indices) and trait complementarity (i.e. multi-trait indices) in the communities. Our study provides new insights into the general mechanisms that link biodiversity to ecosystem functioning in natural animal communities and suggests that the observed responses were due to the identity and dominance patterns of the trait composition rather than the number or abundance of species per se. © 2015 The Author(s) Published by the Royal Society. All rights reserved.
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Li, Ying Hong; Xu, Jing Yu; Tao, Lin; Li, Xiao Feng; Li, Shuang; Zeng, Xian; Chen, Shang Ying; Zhang, Peng; Qin, Chu; Zhang, Cheng; Chen, Zhe; Zhu, Feng; Chen, Yu Zong
2016-01-01
Knowledge of protein function is important for biological, medical and therapeutic studies, but many proteins are still unknown in function. There is a need for more improved functional prediction methods. Our SVM-Prot web-server employed a machine learning method for predicting protein functional families from protein sequences irrespective of similarity, which complemented those similarity-based and other methods in predicting diverse classes of proteins including the distantly-related proteins and homologous proteins of different functions. Since its publication in 2003, we made major improvements to SVM-Prot with (1) expanded coverage from 54 to 192 functional families, (2) more diverse protein descriptors protein representation, (3) improved predictive performances due to the use of more enriched training datasets and more variety of protein descriptors, (4) newly integrated BLAST analysis option for assessing proteins in the SVM-Prot predicted functional families that were similar in sequence to a query protein, and (5) newly added batch submission option for supporting the classification of multiple proteins. Moreover, 2 more machine learning approaches, K nearest neighbor and probabilistic neural networks, were added for facilitating collective assessment of protein functions by multiple methods. SVM-Prot can be accessed at http://bidd2.nus.edu.sg/cgi-bin/svmprot/svmprot.cgi.
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Gu, Yunfu; D. Van Nostrand, Joy; Wu, Liyou; He, Zhili; Qin, Yujia; Zhao, Fang-Jie; Zhou, Jizhong
2017-01-01
To understand how soil microbial communities and arsenic (As) functional genes respond to soil arsenic (As) contamination, five soils contaminated with As at different levels were collected from diverse geographic locations, incubated for 54 days under flooded conditions, and examined by both MiSeq sequencing of 16S rRNA gene amplicons and functional gene microarray (GeoChip 4.0). The results showed that both bacterial community structure and As functional gene structure differed among geographical locations. The diversity of As functional genes correlated positively with the diversity of 16S rRNA genes (P< 0.05). Higher diversities of As functional genes and 16S rRNA genes were observed in the soils with higher available As. Soil pH, phosphate-extractable As, and amorphous Fe content were the most important factors in shaping the bacterial community structure and As transformation functional genes. Geographic location was also important in controlling both the bacterial community and As transformation functional potential. These findings provide insights into the variation of As transformation functional genes in soils contaminated with different levels of As at different geographic locations, and the impact of environmental As contamination on the soil bacterial community. PMID:28475654
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Reconstruction of facial nerve injuries in children.
Fattah, Adel; Borschel, Gregory H; Zuker, Ron M
2011-05-01
Facial nerve trauma is uncommon in children, and many spontaneously recover some function; nonetheless, loss of facial nerve activity leads to functional impairment of ocular and oral sphincters and nasal orifice. In many cases, the impediment posed by facial asymmetry and reduced mimetic function more significantly affects the child's psychosocial interactions. As such, reconstruction of the facial nerve affords great benefits in quality of life. The therapeutic strategy is dependent on numerous factors, including the cause of facial nerve injury, the deficit, the prognosis for recovery, and the time elapsed since the injury. The options for treatment include a diverse range of surgical techniques including static lifts and slings, nerve repairs, nerve grafts and nerve transfers, regional, and microvascular free muscle transfer. We review our strategies for addressing facial nerve injuries in children.
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Regional zooplankton dispersal provides spatial insurance for ecosystem function.
Symons, Celia C; Arnott, Shelley E
2013-05-01
Changing environmental conditions are affecting diversity and ecosystem function globally. Theory suggests that dispersal from a regional species pool may buffer against changes in local community diversity and ecosystem function after a disturbance through the establishment of functionally redundant tolerant species. The spatial insurance provided by dispersal may decrease through time after environmental change as the local community monopolizes resources and reduces community invasibility. To test for evidence of the spatial insurance hypothesis and to determine the role dispersal timing plays in this response we conducted a field experiment using crustacean zooplankton communities in a subarctic region that is expected to be highly impacted by climate change - Churchill, Canada. Three experiments were conducted where nutrients, salt, and dispersal were manipulated. The three experiments differed in time-since-disturbance that the dispersers were added. We found that coarse measures of diversity (i.e. species richness, evenness, and Shannon-Weiner diversity) were generally resistant to large magnitude disturbances, and that dispersal had the most impact on diversity when dispersers were added shortly after disturbance. Ecosystem functioning (chl-a) was degraded in disturbed communities, but dispersal recovered ecosystem function to undisturbed levels. This spatial insurance for ecosystem function was mediated through changes in community composition and the relative abundance of functional groups. Results suggest that regional diversity and habitat connectivity will be important in the future to maintain ecosystem function by introducing functionally redundant species to promote compensatory dynamics. © 2012 Blackwell Publishing Ltd.
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Plant-soil feedback and the maintenance of diversity in Mediterranean-climate shrublands.
Teste, François P; Kardol, Paul; Turner, Benjamin L; Wardle, David A; Zemunik, Graham; Renton, Michael; Laliberté, Etienne
2017-01-13
Soil biota influence plant performance through plant-soil feedback, but it is unclear whether the strength of such feedback depends on plant traits and whether plant-soil feedback drives local plant diversity. We grew 16 co-occurring plant species with contrasting nutrient-acquisition strategies from hyperdiverse Australian shrublands and exposed them to soil biota from under their own or other plant species. Plant responses to soil biota varied according to their nutrient-acquisition strategy, including positive feedback for ectomycorrhizal plants and negative feedback for nitrogen-fixing and nonmycorrhizal plants. Simulations revealed that such strategy-dependent feedback is sufficient to maintain the high taxonomic and functional diversity characterizing these Mediterranean-climate shrublands. Our study identifies nutrient-acquisition strategy as a key trait explaining how different plant responses to soil biota promote local plant diversity. Copyright © 2017, American Association for the Advancement of Science.
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Jeong, Jaeyoung; Kim, Juho; Song, Kwangsun; Autumn, Kellar; Lee, Jongho
2014-01-01
Developing electronics in unconventional forms provides opportunities to expand the use of electronics in diverse applications including bio-integrated or implanted electronics. One of the key challenges lies in integrating semiconductor microdevices onto unconventional substrates without glue, high pressure or temperature that may cause damage to microdevices, substrates or interfaces. This paper describes a solution based on natural gecko setal arrays that switch adhesion mechanically on and off, enabling pick and place manipulation of thin microscale semiconductor materials onto diverse surfaces including plants and insects whose surfaces are usually rough and irregular. A demonstration of functional ‘geckoprinted’ microelectronic devices provides a proof of concept of our results in practical applications. PMID:25056216
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Lu, Zhenmei; He, Zhili; Parisi, Victoria A.; Kang, Sanghoon; Deng, Ye; Van Nostrand, Joy D.; Masoner, Jason R.; Cozzarelli, Isabelle M.; Suflita, Joseph M.; Zhou, Jizhong
2012-01-01
The functional gene diversity and structure of microbial communities in a shallow landfill leachate-contaminated aquifer were assessed using a comprehensive functional gene array (GeoChip 3.0). Water samples were obtained from eight wells at the same aquifer depth immediately below a municipal landfill or along the predominant downgradient groundwater flowpath. Functional gene richness and diversity immediately below the landfill and the closest well were considerably lower than those in downgradient wells. Mantel tests and canonical correspondence analysis (CCA) suggested that various geochemical parameters had a significant impact on the subsurface microbial community structure. That is, leachate from the unlined landfill impacted the diversity, composition, structure, and functional potential of groundwater microbial communities as a function of groundwater pH, and concentrations of sulfate, ammonia, and dissolved organic carbon (DOC). Historical geochemical records indicate that all sampled wells chronically received leachate, and the increase in microbial diversity as a function of distance from the landfill is consistent with mitigation of the impact of leachate on the groundwater system by natural attenuation mechanisms.
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Functional diversity of aquatic ciliates.
Weisse, Thomas
2017-10-01
This paper first reviews the concept of functional diversity in general terms and then applies it to free-living aquatic ciliates. Ciliates are extremely versatile organisms and display an enormous functional diversity as key elements of pelagic food webs, acting as predators of bacteria, algae, other protists and even some metazoans. Planktonic ciliates are important food for zooplankton, and mixotrophic and functionally autotrophic species may significantly contribute to primary production in the ocean and in lakes. The co-occurrence of many ciliate species in seemingly homogenous environments indicates a wide range of their ecological niches. Variation in space and time may foster co-occurrence and prevent violating the competitive exclusion principle among ciliates using the same resources. Considering that many ciliates may be dormant and/or rare in many habitats, ciliate species diversity must be higher than can be deduced from simple sampling techniques; molecular methods of identification clearly point to this hidden diversity. From a functional point of view, the question is how much of this diversity represents redundancy. A key challenge for future research is to link the ecophysiological performance of naturally co-occurring ciliates to their functional genes. To this end, more experimental research is needed with with functionally different species. Copyright © 2017 The Author. Published by Elsevier GmbH.. All rights reserved.
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Patoine, Guillaume; Thakur, Madhav P; Friese, Julia; Nock, Charles; Hönig, Lydia; Haase, Josephine; Scherer-Lorenzen, Michael; Eisenhauer, Nico
2017-11-01
A better understanding of the mechanisms driving litter diversity effects on decomposition is needed to predict how biodiversity losses affect this crucial ecosystem process. In a microcosm study, we investigated the effects of litter functional diversity and two major groups of soil macro-detritivores on the mass loss of tree leaf litter mixtures. Furthermore, we tested the effects of litter trait community means and dissimilarity on litter mass loss for seven traits relevant to decomposition. We expected macro-detritivore effects on litter mass loss to be most pronounced in litter mixtures of high functional diversity. We used 24 leaf mixtures differing in functional diversity, which were composed of litter from four species from a pool of 16 common European tree species. Earthworms, isopods, or a combination of both were added to each litter combination for two months. Litter mass loss was significantly higher in the presence of earthworms than in that of isopods, whereas no synergistic effects of macro-detritivore mixtures were found. The effect of functional diversity of the litter material was highest in the presence of both macro-detritivore groups, supporting the notion that litter diversity effects are most pronounced in the presence of different detritivore species. Species-specific litter mass loss was explained by nutrient content, secondary compound concentration, and structural components. Moreover, dissimilarity in N concentrations increased litter mass loss, probably because detritivores having access to nutritionally diverse food sources. Furthermore, strong competition between the two macro-detritivores for soil surface litter resulted in a decrease of survival of both macro-detritivores. These results show that the effects of litter functional diversity on decomposition are contingent upon the macro-detritivore community and composition. We conclude that the temporal dynamics of litter trait diversity effects and their interaction with detritivore diversity are key to advancing our understanding of litter mass loss in nature.
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Patoine, Guillaume; Thakur, Madhav P.; Friese, Julia; Nock, Charles; Hönig, Lydia; Haase, Josephine; Scherer-Lorenzen, Michael; Eisenhauer, Nico
2017-01-01
A better understanding of the mechanisms driving litter diversity effects on decomposition is needed to predict how biodiversity losses affect this crucial ecosystem process. In a microcosm study, we investigated the effects of litter functional diversity and two major groups of soil macro-detritivores on the mass loss of tree leaf litter mixtures. Furthermore, we tested the effects of litter trait community means and dissimilarity on litter mass loss for seven traits relevant to decomposition. We expected macro-detritivore effects on litter mass loss to be most pronounced in litter mixtures of high functional diversity. We used 24 leaf mixtures differing in functional diversity, which were composed of litter from four species from a pool of 16 common European tree species. Earthworms, isopods, or a combination of both were added to each litter combination for two months. Litter mass loss was significantly higher in the presence of earthworms than in that of isopods, whereas no synergistic effects of macro-detritivore mixtures were found. The effect of functional diversity of the litter material was highest in the presence of both macro-detritivore groups, supporting the notion that litter diversity effects are most pronounced in the presence of different detritivore species. Species-specific litter mass loss was explained by nutrient content, secondary compound concentration, and structural components. Moreover, dissimilarity in N concentrations increased litter mass loss, probably because detritivores having access to nutritionally diverse food sources. Furthermore, strong competition between the two macro-detritivores for soil surface litter resulted in a decrease of survival of both macro-detritivores. These results show that the effects of litter functional diversity on decomposition are contingent upon the macro-detritivore community and composition. We conclude that the temporal dynamics of litter trait diversity effects and their interaction with detritivore diversity are key to advancing our understanding of litter mass loss in nature. PMID:29180828
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Old and new challenges in using species diversity for assessing biodiversity
Chiarucci, Alessandro; Bacaro, Giovanni; Scheiner, Samuel M.
2011-01-01
Although the maintenance of diversity of living systems is critical for ecosystem functioning, the accelerating pace of global change is threatening its preservation. Standardized methods for biodiversity assessment and monitoring are needed. Species diversity is one of the most widely adopted metrics for assessing patterns and processes of biodiversity, at both ecological and biogeographic scales. However, those perspectives differ because of the types of data that can be feasibly collected, resulting in differences in the questions that can be addressed. Despite a theoretical consensus on diversity metrics, standardized methods for its measurement are lacking, especially at the scales needed to monitor biodiversity for conservation and management purposes. We review the conceptual framework for species diversity, examine common metrics, and explore their use for biodiversity conservation and management. Key differences in diversity measures at ecological and biogeographic scales are the completeness of species lists and the ability to include information on species abundances. We analyse the major pitfalls and problems with quantitative measurement of species diversity, look at the use of weighting measures by phylogenetic distance, discuss potential solutions and propose a research agenda to solve the major existing problems. PMID:21768157
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Davison, John; Moora, Mari; Öpik, Maarja; Ainsaar, Leho; Ducousso, Marc; Hiiesalu, Inga; Jairus, Teele; Johnson, Nancy; Jourand, Philippe; Kalamees, Rein; Koorem, Kadri; Meyer, Jean-Yves; Püssa, Kersti; Reier, Ülle; Pärtel, Meelis; Semchenko, Marina; Traveset, Anna; Vasar, Martti; Zobel, Martin
2018-06-08
Island biogeography theory is one of the most influential paradigms in ecology. That island characteristics, including remoteness, can profoundly modulate biological diversity has been borne out by studies of animals and plants. By contrast, the processes influencing microbial diversity in island systems remain largely undetermined. We sequenced arbuscular mycorrhizal (AM) fungal DNA from plant roots collected on 13 islands worldwide and compared AM fungal diversity on islands with existing data from mainland sites. AM fungal communities on islands (even those >6000 km from the closest mainland) comprised few endemic taxa and were as diverse as mainland communities. Thus, in contrast to patterns recorded among macro-organisms, efficient dispersal appears to outweigh the effects of taxogenesis and extinction in regulating AM fungal diversity on islands. Nonetheless, AM fungal communities on more distant islands comprised a higher proportion of previously cultured and large-spored taxa, indicating that dispersal may be human-mediated or require tolerance of significant environmental stress, such as exposure to sunlight or high salinity. The processes driving large-scale patterns of microbial diversity are a key consideration for attempts to conserve and restore functioning ecosystems in this era of rapid global change.
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2012-01-01
In petrochemical refinery wastewater treatment plants (WWTP), different concentrations of pollutant compounds are received daily in the influent stream, including significant amounts of phenolic compounds, creating propitious conditions for the development of particular microorganisms that can rapidly adapt to such environment. In the present work, the microbial sludge from a refinery WWTP was enriched for phenol, cloned into fosmid vectors and pyrosequenced. The fosmid libraries yielded 13,200 clones and a comprehensive bioinformatic analysis of the sequence data set revealed a complex and diverse bacterial community in the phenol degrading sludge. The phylogenetic analyses using MEGAN in combination with RDP classifier showed a massive predominance of Proteobacteria, represented mostly by the genera Diaphorobacter, Pseudomonas, Thauera and Comamonas. The functional classification of phenol degrading sludge sequence data set generated by MG-RAST showed the wide metabolic diversity of the microbial sludge, with a high percentage of genes involved in the aerobic and anaerobic degradation of phenol and derivatives. In addition, genes related to the metabolism of many other organic and xenobiotic compounds, such as toluene, biphenyl, naphthalene and benzoate, were found. Results gathered herein demonstrated that the phenol degrading sludge has complex phylogenetic and functional diversities, showing the potential of such community to degrade several pollutant compounds. This microbiota is likely to represent a rich resource of versatile and unknown enzymes which may be exploited for biotechnological processes such as bioremediation. PMID:22452812
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TRP channel proteins and signal transduction.
Minke, Baruch; Cook, Boaz
2002-04-01
TRP channel proteins constitute a large and diverse family of proteins that are expressed in many tissues and cell types. This family was designated TRP because of a spontaneously occurring Drosophila mutant lacking TRP that responded to a continuous light with a transient receptor potential (hence TRP). In addition to responses to light, TRPs mediate responses to nerve growth factor, pheromones, olfaction, mechanical, chemical, temperature, pH, osmolarity, vasorelaxation of blood vessels, and metabolic stress. Furthermore, mutations in several members of TRP-related channel proteins are responsible for several diseases, such as several tumors and neurodegenerative disorders. TRP-related channel proteins are found in a variety of organisms, tissues, and cell types, including nonexcitable, smooth muscle, and neuronal cells. The large functional diversity of TRPs is also reflected in their diverse permeability to ions, although, in general, they are classified as nonselective cationic channels. The molecular domains that are conserved in all members of the TRP family constitute parts of the transmembrane domains and in most members also the ankyrin-like repeats at the NH2 terminal of the protein and a "TRP domain" at the COOH terminal, which is a highly conserved 25-amino acid stretch with still unknown function. All of the above features suggest that members of the TRP family are "special assignment" channels, which are recruited to diverse signaling pathways. The channels' roles and characteristics such as gating mechanism, regulation, and permeability are determined by evolution according to the specific functional requirements.
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Kim, Mara; Cooper, Brian A.; Venkat, Rohit; Phillips, Julie B.; Eidem, Haley R.; Hirbo, Jibril; Nutakki, Sashank; Williams, Scott M.; Muglia, Louis J.; Capra, J. Anthony; Petren, Kenneth; Abbot, Patrick; Rokas, Antonis; McGary, Kriston L.
2016-01-01
Mammalian gestation and pregnancy are fast evolving processes that involve the interaction of the fetal, maternal and paternal genomes. Version 1.0 of the GEneSTATION database (http://genestation.org) integrates diverse types of omics data across mammals to advance understanding of the genetic basis of gestation and pregnancy-associated phenotypes and to accelerate the translation of discoveries from model organisms to humans. GEneSTATION is built using tools from the Generic Model Organism Database project, including the biology-aware database CHADO, new tools for rapid data integration, and algorithms that streamline synthesis and user access. GEneSTATION contains curated life history information on pregnancy and reproduction from 23 high-quality mammalian genomes. For every human gene, GEneSTATION contains diverse evolutionary (e.g. gene age, population genetic and molecular evolutionary statistics), organismal (e.g. tissue-specific gene and protein expression, differential gene expression, disease phenotype), and molecular data types (e.g. Gene Ontology Annotation, protein interactions), as well as links to many general (e.g. Entrez, PubMed) and pregnancy disease-specific (e.g. PTBgene, dbPTB) databases. By facilitating the synthesis of diverse functional and evolutionary data in pregnancy-associated tissues and phenotypes and enabling their quick, intuitive, accurate and customized meta-analysis, GEneSTATION provides a novel platform for comprehensive investigation of the function and evolution of mammalian pregnancy. PMID:26567549
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Balhana, Ricardo J C; Singla, Ashima; Sikder, Mahmudul Hasan; Withers, Mike; Kendall, Sharon L
2015-06-27
Mycobacteria inhabit diverse niches and display high metabolic versatility. They can colonise both humans and animals and are also able to survive in the environment. In order to succeed, response to environmental cues via transcriptional regulation is required. In this study we focused on the TetR family of transcriptional regulators (TFTRs) in mycobacteria. We used InterPro to classify the entire complement of transcriptional regulators in 10 mycobacterial species and these analyses showed that TFTRs are the most abundant family of regulators in all species. We identified those TFTRs that are conserved across all species analysed and those that are unique to the pathogens included in the analysis. We examined genomic contexts of 663 of the conserved TFTRs and observed that the majority of TFTRs are separated by 200 bp or less from divergently oriented genes. Analyses of divergent genes indicated that the TFTRs control diverse biochemical functions not limited to efflux pumps. TFTRs typically bind to palindromic motifs and we identified 11 highly significant novel motifs in the upstream regions of divergently oriented TFTRs. The C-terminal ligand binding domain from the TFTR complement in M. tuberculosis showed great diversity in amino acid sequence but with an overall architecture common to other TFTRs. This study suggests that mycobacteria depend on TFTRs for the transcriptional control of a number of metabolic functions yet the physiological role of the majority of these regulators remain unknown.
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Ortiz-Álvarez, Rüdiger; Fierer, Noah; de Los Ríos, Asunción; Casamayor, Emilio O; Barberán, Albert
2018-02-20
Ecologists have long studied primary succession, the changes that occur in biological communities after initial colonization of an environment. Most of this work has focused on succession in plant communities, laying the conceptual foundation for much of what we currently know about community assembly patterns over time. Because of their prevalence and importance in ecosystems, an increasing number of studies have focused on microbial community dynamics during succession. Here, we conducted a meta-analysis of bacterial primary succession patterns across a range of distinct habitats, including the infant gut, plant surfaces, soil chronosequences, and aquatic environments, to determine whether consistent changes in bacterial diversity, community composition, and functional traits are evident over the course of succession. Although these distinct habitats harbor unique bacterial communities, we were able to identify patterns in community assembly that were shared across habitat types. We found an increase in taxonomic and functional diversity with time while the taxonomic composition and functional profiles of communities became less variable (lower beta diversity) in late successional stages. In addition, we found consistent decreases in the rRNA operon copy number and in the high-efficient phosphate assimilation process (Pst system) suggesting that reductions in resource availability during succession select for taxa adapted to low-resource conditions. Together, these results highlight that, like many plant communities, microbial communities also exhibit predictable patterns during primary succession.
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Takahashi, Toshio
2013-06-01
Peptides are known to play important developmental and physiological roles in signaling. The rich diversity of peptides, with functions as diverse as intercellular communication, neurotransmission and signaling that spatially and temporally controls axis formation and cell differentiation, hints at the wealth of information passed between interacting cells. Little is known about peptides that control developmental processes such as cell differentiation and pattern formation in metazoans. The cnidarian Hydra is one of the most basic metazoans and is a key model system for study of the peptides involved in these processes. We developed a novel peptidomic approach for the isolation and identification of functional peptide signaling molecules from Hydra (the Hydra Peptide Project). Over the course of this project, a wide variety of novel neuropeptides were identified. Most of these peptides act directly on muscle cells and their functions include induction of contraction and relaxation. Some peptides are involved in cell differentiation and morphogenesis. Moreover, epitheliopeptides that are produced by epithelial cells were originally identified in Hydra. Some of these epitheliopeptides exhibit morphogen-like activities, whereas others are involved in regulating neuron differentiation, possibly through neuron-epithelial cell interactions. We also describe below our high-throughput reverse-phase nano-flow LCMALDI- TOF-MS/MS approach, which has proved a powerful tool for the discovery of novel peptide signaling molecules in Hydra.
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Shifts in diversity and function of lake bacterial communities upon glacier retreat
Peter, Hannes; Sommaruga, Ruben
2016-01-01
Global climate change is causing a wastage of glaciers and threatening biodiversity in glacier-fed ecosystems. The high turbidity typically found in those ecosystems, which is caused by inorganic particles and result of the erosive activity of glaciers is a key environmental factor influencing temperature and light availability, as well as other factors in the water column. Once these lakes loose hydrological connectivity to glaciers and turn clear, the accompanying environmental changes could represent a potential bottleneck for the established local diversity with yet unknown functional consequences. Here, we study three lakes situated along a turbidity gradient as well as one clear unconnected lake and evaluate seasonal changes in their bacterial community composition and diversity. Further, we assess potential consequences for community functioning. Glacier runoff represented a diverse source community for the lakes and several taxa were able to colonize downstream turbid habitats, although they were not found in the clear lake. Operational taxonomic unit-based alpha diversity and phylogenetic diversity decreased along the turbidity gradient, but metabolic functional diversity was negatively related to turbidity. No evidence for multifunctional redundancy, which may allow communities to maintain functioning upon alterations in diversity, was found. Our study gives a first view on how glacier-fed lake bacterial communities are affected by the melting of glaciers and indicates that diversity and community composition significantly change when hydrological connectivity to the glacier is lost and lakes turn clear. PMID:26771929
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Abia, Akebe Luther King; Alisoltani, Arghavan; Keshri, Jitendra; Ubomba-Jaswa, Eunice
2018-03-01
Water quality is an important public health issue given that the presence of pathogenic organisms in such waters can adversely affect human and animal health. Despite the numerous studies conducted to assess the quality of environmental waters in many countries, limited efforts have been put on investigating the microbial quality of the sediments in developing countries and how this relates to different land uses. The present study evaluated the bacterial diversity in water and sediments in a highly used South African river to find out how the different land uses influenced the bacterial diversity, and to verify the human diseases functional classes of the bacterial populations. Samples were collected on river stretches influenced by an informal, a peri-urban and a rural settlement. Genomic DNA was extracted from water and sediment samples and sequenced on an Illumina® MiSeq platform targeting the 16S rRNA gene variable region V3-V4 from the genomic DNA. Metagenomic data analysis revealed that there was a great diversity in the microbial populations associated with the different land uses, with the informal settlement having the most considerable influence on the bacterial diversity in the water and sediments of the Apies River. The Proteobacteria (69.8%), Cyanobacteria (4.3%), Bacteroidetes (2.7%), and Actinobacteria (2.7%) were the most abundant phyla; the Alphaproteobacteria, Betaproteobacteria and Anaerolineae were the most recorded classes. Also, the sediments had a greater diversity and abundance in bacterial population than the water column. The functional profiles of the bacterial populations revealed an association with many human diseases including cancer pathways. Further studies that would isolate these potentially pathogenic organisms in the aquatic environment are therefore needed as this would help in protecting the lives of communities using such rivers, especially against emerging bacterial pathogens. Copyright © 2017 Elsevier B.V. All rights reserved.
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Kinsman-Costello, L E; Sheik, C S; Sheldon, N D; Allen Burton, G; Costello, D M; Marcus, D; Uyl, P A Den; Dick, G J
2017-03-01
For a large part of earth's history, cyanobacterial mats thrived in low-oxygen conditions, yet our understanding of their ecological functioning is limited. Extant cyanobacterial mats provide windows into the putative functioning of ancient ecosystems, and they continue to mediate biogeochemical transformations and nutrient transport across the sediment-water interface in modern ecosystems. The structure and function of benthic mats are shaped by biogeochemical processes in underlying sediments. A modern cyanobacterial mat system in a submerged sinkhole of Lake Huron (LH) provides a unique opportunity to explore such sediment-mat interactions. In the Middle Island Sinkhole (MIS), seeping groundwater establishes a low-oxygen, sulfidic environment in which a microbial mat dominated by Phormidium and Planktothrix that is capable of both anoxygenic and oxygenic photosynthesis, as well as chemosynthesis, thrives. We explored the coupled microbial community composition and biogeochemical functioning of organic-rich, sulfidic sediments underlying the surface mat. Microbial communities were diverse and vertically stratified to 12 cm sediment depth. In contrast to previous studies, which used low-throughput or shotgun metagenomic approaches, our high-throughput 16S rRNA gene sequencing approach revealed extensive diversity. This diversity was present within microbial groups, including putative sulfate-reducing taxa of Deltaproteobacteria, some of which exhibited differential abundance patterns in the mats and with depth in the underlying sediments. The biological and geochemical conditions in the MIS were distinctly different from those in typical LH sediments of comparable depth. We found evidence for active cycling of sulfur, methane, and nutrients leading to high concentrations of sulfide, ammonium, and phosphorus in sediments underlying cyanobacterial mats. Indicators of nutrient availability were significantly related to MIS microbial community composition, while LH communities were also shaped by indicators of subsurface groundwater influence. These results show that interactions between the mats and sediments are crucial for sustaining this hot spot of biological diversity and biogeochemical cycling. © 2016 John Wiley & Sons Ltd.
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Typological diversity of tall buildings and complexes in relation to their functional structure
NASA Astrophysics Data System (ADS)
Generalov, Viktor P.; Generalova, Elena M.; Kalinkina, Nadezhda A.; Zhdanova, Irina V.
2018-03-01
The paper focuses on peculiarities of tall buildings and complexes, their typology and its formation in relation to their functional structure. The research is based on the analysis of tall buildings and complexes and identifies the following main functional elements of their formation: residential, administrative (office), hotel elements. The paper also considers the following services as «disseminated» in the space-planning structure: shops, medicine, entertainment, kids and sports facilities, etc., their location in the structure of the total bulk of the building and their impact on typological diversity. Research results include suggestions to add such concepts as «single-function tall buildings» and «mixed-use tall buildings and complexes» into the classification of tall buildings. In addition, if a single-function building or complex performs serving functions, it is proposed to add such concepts as «a residential tall building (complex) with provision of services», «an administrative (public) tall building (complex) with provision of services» into the classification of tall buildings. For mixed-use buildings and complexes the following terms are suggested: «a mixed-use tall building with provision of services», «a mixed-use tall complex with provision of services».
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High Microbial Diversity Promotes Soil Ecosystem Functioning.
Maron, Pierre-Alain; Sarr, Amadou; Kaisermann, Aurore; Lévêque, Jean; Mathieu, Olivier; Guigue, Julien; Karimi, Battle; Bernard, Laetitia; Dequiedt, Samuel; Terrat, Sébastien; Chabbi, Abad; Ranjard, Lionel
2018-05-01
In soil, the link between microbial diversity and carbon transformations is challenged by the concept of functional redundancy. Here, we hypothesized that functional redundancy may decrease with increasing carbon source recalcitrance and that coupling of diversity with C cycling may change accordingly. We manipulated microbial diversity to examine how diversity decrease affects the decomposition of easily degradable (i.e., allochthonous plant residues) versus recalcitrant (i.e., autochthonous organic matter) C sources. We found that a decrease in microbial diversity (i) affected the decomposition of both autochthonous and allochthonous carbon sources, thereby reducing global CO 2 emission by up to 40%, and (ii) shaped the source of CO 2 emission toward preferential decomposition of most degradable C sources. Our results also revealed that the significance of the diversity effect increases with nutrient availability. Altogether, these findings show that C cycling in soil may be more vulnerable to microbial diversity changes than expected from previous studies, particularly in ecosystems exposed to nutrient inputs. Thus, concern about the preservation of microbial diversity may be highly relevant in the current global-change context assumed to impact soil biodiversity and the pulse inputs of plant residues and rhizodeposits into the soil. IMPORTANCE With hundreds of thousands of taxa per gram of soil, microbial diversity dominates soil biodiversity. While numerous studies have established that microbial communities respond rapidly to environmental changes, the relationship between microbial diversity and soil functioning remains controversial. Using a well-controlled laboratory approach, we provide empirical evidence that microbial diversity may be of high significance for organic matter decomposition, a major process on which rely many of the ecosystem services provided by the soil ecosystem. These new findings should be taken into account in future studies aimed at understanding and predicting the functional consequences of changes in microbial diversity on soil ecosystem services and carbon storage in soil. Copyright © 2018 American Society for Microbiology.
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[Diversity of parasitic protozoan mitochondria and adaptive evolution].
Tian, Hai-Feng; Wen, Jian-Fan
2010-02-01
Eukaryotic mitochondrion generally possess a definite and canonical structure and function. However, in the unicellular parasitic protozoa, various atypical mitochondria with respect to the number, structure, and function, have been discovered consecutively, revealing the variability, plasticity and rich diversity of mitochondrion. Here, we review the mitochondrial diversity in diverse parasitic protozoa, and the underlying reason for such diversity--the adaptive evolution of mitochondrion to the micro-oxygen or anaero parasitic environment of these parasites is also analyzed and discussed.
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Biodiversity-ecosystem functioning relationships in a long-term non-weeded field experiment.
Veen, Ciska G F; van der Putten, Wim H; Bezemer, T Martijn
2018-05-30
Many grassland biodiversity experiments show a positive relationship between biodiversity and ecosystem functioning, however, in most these experiments plant communities are established by sowing and natural colonization is prevented by selective weeding of non-sown species. During ecosystem restoration, for example on abandoned fields, plant communities start on bare soil, and diversity is often manipulated in a single sowing event. How such initial plant diversity manipulations influence plant biodiversity development and ecosystem functioning is not well understood. We examined how relationships between taxonomic and functional diversity, biomass production and stability develop over 16 years in non-weeded plots sown with 15 species, 4 species, or that were not sown. We found that sown plant communities become functionally similar to unsown, naturally colonized plant communities. However, initial sowing treatments had long-lasting effects on species composition and taxonomic diversity. We found only few relationships between biomass production, or stability in biomass production, and functional or taxonomic diversity, and the ones we observed were negative. In addition, the cover of dominant plant species was positively related to biomass production and stability. We conclude that effects of introducing plant species at the start of secondary succession can persist for a long time, and that in secondary succession communities with natural plant species dynamics diversity-functioning relationships can be weak or negative. Moreover, our findings indicate that in systems where natural colonization of species is allowed effects of plant dominance may underlie diversity-functioning relationships. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
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Drury, Crawford; Schopmeyer, Stephanie; Goergen, Elizabeth; Bartels, Erich; Nedimyer, Ken; Johnson, Meaghan; Maxwell, Kerry; Galvan, Victor; Manfrino, Carrie; Lirman, Diego
2017-08-01
Threatened Caribbean coral communities can benefit from high-resolution genetic data used to inform management and conservation action. We use Genotyping by Sequencing (GBS) to investigate genetic patterns in the threatened coral, Acropora cervicornis , across the Florida Reef Tract (FRT) and the western Caribbean. Results show extensive population structure at regional scales and resolve previously unknown structure within the FRT. Different regions also exhibit up to threefold differences in genetic diversity (He), suggesting targeted management based on the goals and resources of each population is needed. Patterns of genetic diversity have a strong spatial component, and our results show Broward and the Lower Keys are among the most diverse populations in Florida. The genetic diversity of Caribbean staghorn coral is concentrated within populations and within individual reefs (AMOVA), highlighting the complex mosaic of population structure. This variance structure is similar over regional and local scales, which suggests that in situ nurseries are adequately capturing natural patterns of diversity, representing a resource that can replicate the average diversity of wild assemblages, serving to increase intraspecific diversity and potentially leading to improved biodiversity and ecosystem function. Results presented here can be translated into specific goals for the recovery of A. cervicornis , including active focus on low diversity areas, protection of high diversity and connectivity, and practical thresholds for responsible restoration.
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Fourie, Nicolaas H.; Wang, Dan; Abey, Sarah K.; Creekmore, Amy L.; Hong, Shuangsong; Martin, Christiana G.; Wiley, John W.
2017-01-01
ABSTRACT Stress is known to perturb the microbiome and exacerbate irritable bowel syndrome (IBS) associated symptoms. Characterizing structural and functional changes in the microbiome is necessary to understand how alterations affect the biomolecular environment of the gut in IBS. Repeated water avoidance (WA) stress was used to induce IBS-like symptoms in rats. The colon-mucosa associated microbiome was characterized in 13 stressed and control animals by 16S sequencing. In silico analysis of the functional domains of microbial communities was done by inferring metagenomic profiles from 16S data. Microbial communities and functional profiles were compared between conditions. WA animals exhibited higher α-diversity and moderate divergence in community structure (β-diversity) compared with controls. Specific clades and taxa were consistently and significantly modified in the WA animals. The WA microbiome was particularly enriched in Proteobacteria and depleted in several beneficial taxa. A decreased capacity in metabolic domains, including energy- and lipid-metabolism, and an increased capacity for fatty acid and sulfur metabolism was inferred for the WA microbiome. The stressed condition favored the proliferation of a greater diversity of microbes that appear to be functionally similar, resulting in a functionally poorer microbiome with implications for epithelial health. Taxa, with known beneficial effects, were found to be depleted, which supports their relevance as therapeutic agents to restore microbial health. Microbial sulfur metabolism may form a key component of visceral nerve sensitization pathways and is therefore of interest as a target metabolic domain in microbial ecological restoration. PMID:28059627
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Modeling Forest Structure and Vascular Plant Diversity in Piedmont Forests
NASA Astrophysics Data System (ADS)
Hakkenberg, C.
2014-12-01
When the interacting stressors of climate change and land cover/land use change (LCLUC) overwhelm ecosystem resilience to environmental and climatic variability, forest ecosystems are at increased risk of regime shifts and hyperdynamism in process rates. To meet the growing range of novel biotic and environmental stressors on human-impacted ecosystems, the maintenance of taxonomic diversity and functional redundancy in metacommunities has been proposed as a risk spreading measure ensuring that species critical to landscape ecosystem functioning are available for recruitment as local systems respond to novel conditions. This research is the first in a multi-part study to establish a dynamic, predictive model of the spatio-temporal dynamics of vascular plant diversity in North Carolina Piedmont mixed forests using remotely sensed data inputs. While remote sensing technologies are optimally suited to monitor LCLUC over large areas, direct approaches to the remote measurement of plant diversity remain a challenge. This study tests the efficacy of predicting indices of vascular plant diversity using remotely derived measures of forest structural heterogeneity from aerial LiDAR and high spatial resolution broadband optical imagery in addition to derived topo-environmental variables. Diversity distribution modelling of this sort is predicated upon the idea that environmental filtering of dispersing species help define fine-scale (permeable) environmental envelopes within which biotic structural and compositional factors drive competitive interactions that, in addition to background stochasticity, determine fine-scale alpha diversity. Results reveal that over a range of Piedmont forest communities, increasing structural complexity is positively correlated with measures of plant diversity, though the nature of this relationship varies by environmental conditions and community type. The diversity distribution model is parameterized and cross-validated using three high quality vegetation survey datasets, including Duke Forest Korstian permanent plots, Forest Inventory Analysis (FIA), and the scale transgressive, nested module Carolina Vegetation Survey (CVS).
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Activation and Function of the MAPKs and Their Substrates, the MAPK-Activated Protein Kinases
Cargnello, Marie; Roux, Philippe P.
2011-01-01
Summary: The mitogen-activated protein kinases (MAPKs) regulate diverse cellular programs by relaying extracellular signals to intracellular responses. In mammals, there are more than a dozen MAPK enzymes that coordinately regulate cell proliferation, differentiation, motility, and survival. The best known are the conventional MAPKs, which include the extracellular signal-regulated kinases 1 and 2 (ERK1/2), c-Jun amino-terminal kinases 1 to 3 (JNK1 to -3), p38 (α, β, γ, and δ), and ERK5 families. There are additional, atypical MAPK enzymes, including ERK3/4, ERK7/8, and Nemo-like kinase (NLK), which have distinct regulation and functions. Together, the MAPKs regulate a large number of substrates, including members of a family of protein Ser/Thr kinases termed MAPK-activated protein kinases (MAPKAPKs). The MAPKAPKs are related enzymes that respond to extracellular stimulation through direct MAPK-dependent activation loop phosphorylation and kinase activation. There are five MAPKAPK subfamilies: the p90 ribosomal S6 kinase (RSK), the mitogen- and stress-activated kinase (MSK), the MAPK-interacting kinase (MNK), the MAPK-activated protein kinase 2/3 (MK2/3), and MK5 (also known as p38-regulated/activated protein kinase [PRAK]). These enzymes have diverse biological functions, including regulation of nucleosome and gene expression, mRNA stability and translation, and cell proliferation and survival. Here we review the mechanisms of MAPKAPK activation by the different MAPKs and discuss their physiological roles based on established substrates and recent discoveries. PMID:21372320
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Flavonoid concentration diversity of 3 different species in the phaseoleae tribe
USDA-ARS?s Scientific Manuscript database
The functional vegetable species including Lablab purpureus L. Sweet, Macrotyloma uniflorum (Lam.) Verdc., and Teramnus labialis (L.f.) Spreng are in the Phaseoleae tribe. Seeds from 10 L. purpureus and 7 M. uniflorum accessions originated from the field during 2009 and 2009 to 2010, respectively at...
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Phenotypic diversity of anthocyanins in sorghum accessions with various pericarp pigments
USDA-ARS?s Scientific Manuscript database
Anthocyanins, a sub-class of flavonoids, are natural pigments known to have functional health benefits. Sorghum is a rich source of various phytochemicals including anthocyanins. This study was to identify and quantify the profiles of anthocyanins by HPLC-DAD in the selected 25 sorghum accessions wi...
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Genome wide association studies on yield components using a lentil genetic diversity panel
USDA-ARS?s Scientific Manuscript database
The cool season food legume research community are now at the threshold of deploying the cutting-edge molecular genetics and genomics tools that have led to significant and rapid expansion of gene discovery, knowledge of gene function (including tolerance to biotic and abiotic stresses) and genetic ...
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Chemical ecology of the Thysanoptera
Murray S. Blum
1991-01-01
The chemical ecology of the Thysanoptera is identified with a variety of natural products discharged in anal droplets during confrontations with adversaries. These exudates are fortified with defensive allomones that may function as repellents, contact irritants, or in some cases, fumigants. Thrips synthesize a large diversity of allomonal products that include...
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USDA-ARS?s Scientific Manuscript database
Wetlands provide essential functions to the ecosphere that range from water filtration to flood control. Current methods of evaluating the quality of wetlands include assessing vegetation, soil type, and period of inundation. With recent advances in molecular and bioinformatic techniques, measuremen...
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Publishing: The Creative Business.
ERIC Educational Resources Information Center
Bohne, Harald; Van Ierssel, Harry
This book offers guidelines to emerging and would-be publishers, whether they plan to enter publishing as a career, a sideline, or a diversion. It stresses the business aspects of publishing and emphasizes the major housekeeping functions encountered in the business, except methods of sales and distribution. Contents include "The Mechanics of…
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A Teachers' Guide to the Whales of the Gulf of Maine.
ERIC Educational Resources Information Center
Elk, Catherine Kiorpes; Lignell, Kathleen, Ed.
This guide provides: (1) background information for teachers on whales; (2) 10 interdisciplinary activities; (3) teacher resources; (4) a bibliography; and (5) "pocket materials." Topic areas addressed in the first section include evolution and adaptation to an aquatic environment, diversity of whales, functional anatomy of feeding and…
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Federal Register 2010, 2011, 2012, 2013, 2014
2011-03-18
... Networks Security--Isolation or Protection From Unauthorized Passenger Domain Systems Access AGENCY... systems and data networks. The applicable airworthiness regulations do not contain adequate or appropriate... connected networks. The network architecture would be used for a diverse set of functions, including: 1...
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NASA Astrophysics Data System (ADS)
Silva-Júnior, C. A. B.; Mérigot, B.; Lucena-Frédou, F.; Ferreira, B. P.; Coxey, M. S.; Rezende, S. M.; Frédou, T.
2017-11-01
Environmental changes and human activities may have strong impacts on biodiversity and ecosystem functioning. While biodiversity is traditionally based on species richness and composition, there is a growing concern to take into account functional diversity to assess and manage species communities. In spite of their economic importance, functional diversity quantified by a traits-based approach is still poorly documented in tropical estuaries. In this study, the functional diversity of fishes was investigated within four estuaries in Pernambuco state, northeast of Brazil. These areas are subject to different levels of human impact (e.g. mangrove deforestation, shrimp farming, fishing etc.) and environmental conditions. Fishes were collected during 34 scientific surveys. A total of 122 species were identified and 12 functional traits were quantified describing two main functions: food acquisition and locomotion. Fish abundance and functional dissimilarities data were combined into a multivariate analysis, the Double Principal Coordinate Analysis, to identify the functional typology of fish assemblages according to the estuary. Results showed that Itapissuma, the largest estuary with a wider mangrove forest area, differs from the other three estuaries, showing higher mean values per samples of species richness S and quadratic entropy Q. Similarly, it presented a different functional typology (the first two axes of the DPCoA account for 68.7% of total inertia, while those of a traditional PCA based solely on species abundances provided only 17.4%). Conversely, Suape, Sirinhaém, and to a lower extent Rio Formoso, showed more similarity in their diversity. This result was attributed to their predominantly marine influenced hydrological features, and similar levels of species abundances and in morphological traits. Overall, this study, combining diversity indices and a recent multivariate analysis to access species contribution to functional typology, allows to deepen diversity assessment by providing additional information regarding the functional pattern of fish assemblages.
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Hagar, J.C.
2007-01-01
Non-coniferous vegetation, including herbs, shrubs, and broad-leaved trees, makes a vital contribution to ecosystem function and diversity in Pacific Northwest conifer forests. However, forest management has largely been indifferent or detrimental to shrubs and trees that have low commercial value, in spite of a paradigm shift towards more holistic management in recent decades. Forest management practices that are detrimental to broad-leaved trees and shrubs are likely to decrease habitat diversity for wildlife, but the number of species that may be affected has not previously been enumerated. I reviewed life history accounts for forest-dwelling vertebrate wildlife species and derived a list of 78 species in Oregon and Washington that are associated with non-coniferous vegetation. The diversity of direct and indirect food resources provided was the primary functional basis for associations of most species with non-coniferous vegetation. Thus, a diversity of herbs and broad-leaved trees and shrubs provides the foundation for food webs that contribute to diversity at multiple trophic levels in Pacific Northwest conifer forests. Given the number of species associated with non-coniferous vegetation in conifer-dominated forests, maintaining habitats that support diverse plant communities, particularly broad-leaved trees and shrubs, will be an important component of management strategies intended to foster biodiversity. Silvicultural practices such as modified planting densities, and pre-commercial and commercial thinning, can be used to control stand density in order to favor the development of understory herbs, shrubs, and a diversity of tree species within managed stands. Allowing shrubs and hardwood trees to develop and persist in early seral stands by curtailing vegetation control also would benefit many species associated with non-coniferous vegetation.
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Diversity of the soil biota in burned areas of southern taiga forests (Tver oblast)
NASA Astrophysics Data System (ADS)
Gongalsky, K. B.; Zaitsev, A. S.; Korobushkin, D. I.; Saifutdinov, R. A.; Yazrikova, T. E.; Benediktova, A. I.; Gorbunova, A. Yu.; Gorshkova, I. A.; Butenko, K. O.; Kosina, N. V.; Lapygina, E. V.; Kuznetsova, D. M.; Rakhleeva, A. A.; Shakhab, S. V.
2016-03-01
Relations between soil biota diversity and its contribution to the performance of some ecosystem functions were assessed based on the results obtained in undisturbed and burned spruce forests near the Central Forest Nature Biosphere Reserve (Tver oblast). In August 2014, in two 4-year-old burned areas, abiotic parameters of the soils, indicators of the state of the microbial communities, the number, taxonomic diversity, and the abundance of the main groups of soil invertebrates (testate amoebae, nematodes, enchytraeids, mites, collembolans, and the mesofauna as a whole) were determined. In the soils of the burned areas, higher CO2, CH4, and N2O emissions were observed. The number of bacterial cells remained similar, and the total length of active mycelium was not significantly different. All this implies a certain intensification of biogenic processes promoting the mobilization of carbon and nitrogen after fire. The number of most of the groups of soil animals was lower (not always significantly) in the burned area than that in the soils of the undisturbed forests. The changes in the taxonomic diversity were specific for each taxon studied. Overall, the diversity of invertebrates was related to the litter thickness. However, the high taxonomic diversity of soil fauna did not always correspond to the active functioning of the ecosystem. Thus, for some taxa, a quite close correlation was found, for instance, between the total number of species (of testate amoebae in particular) and the berry crop, as well as between the soil mesofauna population and the dead wood stock. The total diversity of the investigated taxa included in the detrital trophic web was the most reliable indicator of the carbon stock in the burned areas.
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Sivadas, A; Salleh, M Z; Teh, L K; Scaria, V
2017-10-01
Expanding the scope of pharmacogenomic research by including multiple global populations is integral to building robust evidence for its clinical translation. Deep whole-genome sequencing of diverse ethnic populations provides a unique opportunity to study rare and common pharmacogenomic markers that often vary in frequency across populations. In this study, we aim to build a diverse map of pharmacogenetic variants in South East Asian (SEA) Malay population using deep whole-genome sequences of 100 healthy SEA Malay individuals. We investigated the allelic diversity of potentially deleterious pharmacogenomic variants in SEA Malay population. Our analysis revealed 227 common and 466 rare potentially functional single nucleotide variants (SNVs) in 437 pharmacogenomic genes involved in drug metabolism, transport and target genes, including 74 novel variants. This study has created one of the most comprehensive maps of pharmacogenetic markers in any population from whole genomes and will hugely benefit pharmacogenomic investigations and drug dosage recommendations in SEA Malays.
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Price, S A; Holzman, R; Near, T J; Wainwright, P C
2011-05-01
Although coral reefs are renowned biodiversity hotspots it is not known whether they also promote the evolution of exceptional ecomorphological diversity. We investigated this question by analysing a large functional morphological dataset of trophic characters within Labridae, a highly diverse group of fishes. Using an analysis that accounts for species relationships, the time available for diversification and model uncertainty we show that coral reef species have evolved functional morphological diversity twice as fast as non-reef species. In addition, coral reef species occupy 68.6% more trophic morphospace than non-reef species. Our results suggest that coral reef habitats promote the evolution of both trophic novelty and morphological diversity within fishes. Thus, the preservation of coral reefs is necessary, not only to safeguard current biological diversity but also to conserve the underlying mechanisms that can produce functional diversity in future. © 2011 Blackwell Publishing Ltd/CNRS.
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Patterns of bird functional diversity on land-bridge island fragments.
Ding, Zhifeng; Feeley, Kenneth J; Wang, Yanping; Pakeman, Robin J; Ding, Ping
2013-07-01
The loss of species diversity due to habitat fragmentation has been extensively studied. In contrast, the impacts of habitat fragmentation on functional diversity remains relatively poorly understood. We conducted bird functional diversity studies on a set of 41 recently isolated land-bridge islands in the Thousand Island Lake, China. We analysed differences in bird species richness and a recently developed suite of complementary functional diversity indices (FRic, volume of functional space occupied; FEve, evenness of abundance distribution in the functional trait space; FDiv, divergence in the distribution of abundance in the trait volume) across different gradients (island area and isolation). We found no correlations between FRic and FEve or FEve and FDiv, but negative correlations between FRic and FDiv. As predicted, island area accounted for most of the variation in bird species richness, whereas isolation explained most of the variation in species evenness (decreasing species evenness with increasing isolation). Functional diversity appears to be more strongly influenced by habitat filtering as opposed to limiting similarity. More specifically, across all islands, both FRic and FEve were significantly lower than expected for randomly assembled communities, but FDiv showed no clear patterns. FRic increased with island area, FEve decreased with island area and FDiv showed no clear patterns. Our finding that FEve decreases with island area at TIL may indicate low functional stability on such islands, and as such large islands and habitat patches may deserve extra attention and/or protection. These results help to demonstrate the importance of considering the effects of fragmentation on functional diversity in habitat management and reserve design plans. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.
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Metagenomic Exploration of Viruses throughout the Indian Ocean
Lorenzi, Hernan A.; Fadrosh, Douglas W.; Brami, Daniel; Thiagarajan, Mathangi; McCrow, John P.; Tovchigrechko, Andrey; Yooseph, Shibu; Venter, J. Craig
2012-01-01
The characterization of global marine microbial taxonomic and functional diversity is a primary goal of the Global Ocean Sampling Expedition. As part of this study, 19 water samples were collected aboard the Sorcerer II sailing vessel from the southern Indian Ocean in an effort to more thoroughly understand the lifestyle strategies of the microbial inhabitants of this ultra-oligotrophic region. No investigations of whole virioplankton assemblages have been conducted on waters collected from the Indian Ocean or across multiple size fractions thus far. Therefore, the goals of this study were to examine the effect of size fractionation on viral consortia structure and function and understand the diversity and functional potential of the Indian Ocean virome. Five samples were selected for comprehensive metagenomic exploration; and sequencing was performed on the microbes captured on 3.0-, 0.8- and 0.1 µm membrane filters as well as the viral fraction (<0.1 µm). Phylogenetic approaches were also used to identify predicted proteins of viral origin in the larger fractions of data from all Indian Ocean samples, which were included in subsequent metagenomic analyses. Taxonomic profiling of viral sequences suggested that size fractionation of marine microbial communities enriches for specific groups of viruses within the different size classes and functional characterization further substantiated this observation. Functional analyses also revealed a relative enrichment for metabolic proteins of viral origin that potentially reflect the physiological condition of host cells in the Indian Ocean including those involved in nitrogen metabolism and oxidative phosphorylation. A novel classification method, MGTAXA, was used to assess virus-host relationships in the Indian Ocean by predicting the taxonomy of putative host genera, with Prochlorococcus, Acanthochlois and members of the SAR86 cluster comprising the most abundant predictions. This is the first study to holistically explore virioplankton dynamics across multiple size classes and provides unprecedented insight into virus diversity, metabolic potential and virus-host interactions. PMID:23082107
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Inskeep, William P.; Rusch, Douglas B.; Jay, Zackary J.; Herrgard, Markus J.; Kozubal, Mark A.; Richardson, Toby H.; Macur, Richard E.; Hamamura, Natsuko; Jennings, Ryan deM.; Fouke, Bruce W.; Reysenbach, Anna-Louise; Roberto, Frank; Young, Mark; Schwartz, Ariel; Boyd, Eric S.; Badger, Jonathan H.; Mathur, Eric J.; Ortmann, Alice C.; Bateson, Mary; Geesey, Gill; Frazier, Marvin
2010-01-01
The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14–15,000 Sanger reads per site) was obtained for five high-temperature (>65°C) chemotrophic microbial communities sampled from geothermal springs (or pools) in Yellowstone National Park (YNP) that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved oxygen and ferrous iron. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3) Fe-oxyhydroxide mat, where a higher O2 influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H2-oxidation, and aerobic respiration (terminal oxidation) provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, Fe, O2) control microbial community structure and function in YNP geothermal springs. PMID:20333304
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NASA Astrophysics Data System (ADS)
Powell, T.; Kueppers, L. M.; Koven, C.; Johnson, D. J.; Faybishenko, B.; McDowell, N. G.; Chambers, J. Q.
2016-12-01
Land surface models that include demographic and plant hydrodynamic processes are promising tools for characterizing how different drought scenarios may affect carbon cycling of tropical forests. The Ecosystem Demography (ED2) model, now formulated with such features, was used to evaluate how different drought scenarios affect mortality patterns, functional diversity and coexistence of four plant functional types (PFTs) of tropical trees at Barro Colorado Island (BCI), Panama. The four PFTs simulated were early- versus late-successional groups subdivided into drought-tolerant versus -intolerant groups. The hydrodynamic formulation enables the four PFTs to compete mechanistically along two largely orthogonal resource gradients of water and light. The model simulations produced considerable differences in the aboveground biomass response to contrasting drying scenarios that included longer dry seasons, El Nino related droughts, and drier dry seasons. The emergent mortality dynamics reflect the physiological trade-off between water-use and carbon fixation formulated by the hydrodynamic regulation over stomatal conductance. During dry periods, the model predicts increased mortality rates of pioneer trees compared to generalists and drought-intolerant trees compared to -tolerant trees. The model also predicts that surviving cohorts in the smallest size classes of drought-intolerant trees are occasionally primed for release from competition following acute droughts. Observations at BCI showed increased mortality rates for large trees (i.e. >30 cm dbh) during the 1982 El Nino drought, but not subsequent El Nino related droughts. The causes of the elevated mortality rates are explored with the model. Coexistence of four plant functional types in the model is highly sensitive to the parameterization of stem hydraulic conductivity; but, surprisingly not very sensitive to shifts in rainfall patterns. These results demonstrate (a) that plant hydrodynamics are critical for simulating dynamic mortality patterns between drought-tolerant and -intolerant PFTs in order to increase representation of functional diversity in land surface models, and (b) that more demographic, plant hydraulic and deeper soil moisture observations are required to constrain hydrodynamic parameter selection.
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Functional richness: Overview of indices and underlying concepts
NASA Astrophysics Data System (ADS)
Legras, G.; Loiseau, N.; Gaertner, J.-C.
2018-02-01
Functional richness, currently defined as the amount of niche space occupied by the species within a community, is one of the three major components of functional diversity. Different indices have been developed in order to quantify this component. However, the range of indices available for assessing functional richness, often mathematically complex and based on different rationales, can cause confusion for field ecologists and lead to misinterpretation of the results obtained. In this context, we have provided the first study exclusively focused on the comparison of the definitions, advantages and drawbacks of a large set of functional richness indices. The first part of this work is focused on four indices (FDP&G, FRic, TOP and N-hypervolumes indices) that are currently the most commonly used for assessing functional richness. We have completed our study by including recently developed indices that enable us to take into account the intraspecific trait variability (i.e. FRim index and TDP framework), because there is currently a growing scientific consensus regarding the necessity of including this aspect in the assessment of the functional diversity of communities. We demonstrate that although authors have argued that their index describes the functional richness, each of them describes only part of it, and this part may strongly differ from one index to another. Rather than advocating the general use of a single index and/or systematically avoiding others, our study highlights the need for selecting indices in close relation with the context, the available data and the aims of each study. Such a strategy is an essential preliminary step for preventing misunderstanding and artefactual controversies. Along these lines, we propose some guidelines to help users in selecting the most appropriate indices according both to the facet of functional richness on which they wish to focus and to the characteristics of the available data.
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Maintaining ecosystem function and services in logged tropical forests.
Edwards, David P; Tobias, Joseph A; Sheil, Douglas; Meijaard, Erik; Laurance, William F
2014-09-01
Vast expanses of tropical forests worldwide are being impacted by selective logging. We evaluate the environmental impacts of such logging and conclude that natural timber-production forests typically retain most of their biodiversity and associated ecosystem functions, as well as their carbon, climatic, and soil-hydrological ecosystem services. Unfortunately, the value of production forests is often overlooked, leaving them vulnerable to further degradation including post-logging clearing, fires, and hunting. Because logged tropical forests are extensive, functionally diverse, and provide many ecosystem services, efforts to expand their role in conservation strategies are urgently needed. Key priorities include improving harvest practices to reduce negative impacts on ecosystem functions and services, and preventing the rapid conversion and loss of logged forests. Copyright © 2014 Elsevier Ltd. All rights reserved.
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NASA Astrophysics Data System (ADS)
Gadeken, K.; Dorgan, K. M.; Moore, J.; Berke, S. K.
2016-02-01
Evolutionary relationships may shed light on observed patterns of diversity and functional traits when viewed through the lens of phylogeny. The potential for phylogenetic information to be used to explain patterns in community structure, such as niche partitioning and responses to stress, is extensive. Differential distribution of related species with similar functional traits suggests niche partitioning, and local redundancy in functional traits may indicate the potential for interspecific competition. In this study, we investigated phylogenetic and functional diversity as a function of habitat for sites with varying levels of oil contamination in the Northern Gulf of Mexico. Our study was conducted in a shallow benthic community at the Chandeleur Islands, a group of uninhabited barrier islands. Infauna were sampled from seagrass (Halodule wrightii) and bare sediment at three sites along the island chain that experienced variable levels of oil impact from the Deepwater Horizon oil spill. Individuals were preserved and 18S and COI genes sequenced, and a phylogenetic tree was constructed of the local community using maximum likelihood. Phylogenetic diversity and evenness were quantified. Ecologically important functional traits were then compiled into respective distance matrices, evaluated through different functional diversity indices, and assessed for correlation with the phylogeny. This integration of functional and phylogenetic diversity has the potential to provide greater insight into factors driving community structure than either metric alone. Determining relevant metrics of diversity is critical to understanding the ecological effects of major disturbances such as oil spills.
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Turnover of plant lineages shapes herbivore phylogenetic beta diversity along ecological gradients.
Pellissier, Loïc; Ndiribe, Charlotte; Dubuis, Anne; Pradervand, Jean-Nicolas; Salamin, Nicolas; Guisan, Antoine; Rasmann, Sergio
2013-05-01
Understanding drivers of biodiversity patterns is of prime importance in this era of severe environmental crisis. More diverse plant communities have been postulated to represent a larger functional trait-space, more likely to sustain a diverse assembly of herbivore species. Here, we expand this hypothesis to integrate environmental, functional and phylogenetic variation of plant communities as factors explaining the diversity of lepidopteran assemblages along elevation gradients in the Swiss Western Alps. According to expectations, we found that the association between butterflies and their host plants is highly phylogenetically structured. Multiple regression analyses showed the combined effect of climate, functional traits and phylogenetic diversity in structuring butterfly communities. Furthermore, we provide the first evidence that plant phylogenetic beta diversity is the major driver explaining butterfly phylogenetic beta diversity. Along ecological gradients, the bottom up control of herbivore diversity is thus driven by phylogenetically structured turnover of plant traits as well as environmental variables. © 2013 Blackwell Publishing Ltd/CNRS.
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Boyle, Patricia A.; Yu, Lei; Wilson, Robert S.; Segawa, Eisuke; Buchman, Aron S.; Bennett, David A.
2013-01-01
Literacy is an important determinant of health and well-being across the lifespan but is critical in aging, when many influential health and financial decisions are made. Prior studies suggest that older persons exhibit lower literacy than younger persons, particularly in the domains of financial and health literacy, but the reasons why remain unknown. The objectives of this study were to: a) examine pathways linking diverse resources (i.e., education, word knowledge, cognitive function, and decision making style) to health and financial literacy among older persons and determine the extent to which the relation of age with literacy represents a direct effect versus an indirect effect due to decrements in specific cognitive functions (i.e., executive functions and episodic memory), and b) test the hypothesis that declines in executive function and episodic memory are associated with lower literacy among older persons without dementia. 645 community-based older persons without dementia underwent detailed assessments of diverse resources, including education, word knowledge, cognitive function (i.e., executive function, episodic memory) and decision making style (i.e., risk aversion), and completed a measure of literacy that included items similar to those assessed in the Health and Retirement Study, such as numeracy, financial concepts such as compound inflation and knowledge of stocks and bonds, and important health concepts such as understanding of drug risk and Medicare Part D. Path analysis revealed a strong effect of age on literacy, with about half of the effect of age on literacy due to decrements in executive functions and episodic memory. In addition, executive function had an indirect effect on literacy via decision making style (i.e., risk aversion), and education and word knowledge had independent effects on literacy. Finally, among (n=447) persons with repeated cognitive assessments available for up to 14 years, regression analysis supported the association of multiple resources with literacy; moreover, more rapid declines in executive function and episodic memory over an average of 6.4 years prior to the literacy assessment predicted lower literacy scores (p’s<0.02), but rate of decline in word knowledge did not. These findings suggest that diverse individual resources contribute to financial and health literacy and lower literacy in old age is partially due to declines in executive function and episodic memory. PMID:23957225
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Boyle, Patricia A; Yu, Lei; Wilson, Robert S; Segawa, Eisuke; Buchman, Aron S; Bennett, David A
2013-09-01
Literacy is an important determinant of health and well-being across the life span but is critical in aging, when many influential health and financial decisions are made. Prior studies suggest that older persons exhibit lower literacy than younger persons, particularly in the domains of financial and health literacy, but the reasons why remain unknown. The objectives of this study were to: (a) examine pathways linking diverse resources (i.e., education, word knowledge, cognitive function, and decision making style) to health and financial literacy among older persons and determine the extent to which the relation of age with literacy represents a direct effect versus an indirect effect due to decrements in specific cognitive functions (i.e., executive functions and episodic memory); and (b) test the hypothesis that declines in executive function and episodic memory are associated with lower literacy among older persons without dementia. Six-hundred and forty-five community-based older persons without dementia underwent detailed assessments of diverse resources, including education, word knowledge, cognitive function (i.e., executive function, episodic memory) and decision making style (i.e., risk aversion), and completed a measure of literacy that included items similar to those used in the Health and Retirement Study, such as numeracy, financial concepts such as compound inflation and knowledge of stocks and bonds, and important health concepts such as understanding of drug risk and Medicare Part D. Path analysis revealed a strong effect of age on literacy, with about half of the effect of age on literacy due to decrements in executive functions and episodic memory. In addition, executive function had an indirect effect on literacy via decision making style (i.e., risk aversion), and education and word knowledge had independent effects on literacy. Finally, among (n = 447) persons with repeated cognitive assessments available for up to 14 years, regression analysis supported the association of multiple resources with literacy; moreover, more rapid declines in executive function and episodic memory over an average of 6.4 years prior to the literacy assessment predicted lower literacy scores (ps < 0.02), but rate of decline in word knowledge did not. These findings suggest that diverse individual resources contribute to financial and health literacy and lower literacy in old age is partially due to declines in executive function and episodic memory.
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Contrasting species and functional beta diversity in montane ant assemblages.
Bishop, Tom R; Robertson, Mark P; van Rensburg, Berndt J; Parr, Catherine L
2015-09-01
Beta diversity describes the variation in species composition between sites and can be used to infer why different species occupy different parts of the globe. It can be viewed in a number of ways. First, it can be partitioned into two distinct patterns: turnover and nestedness. Second, it can be investigated from either a species identity or a functional-trait point of view. We aim to document for the first time how these two aspects of beta diversity vary in response to a large environmental gradient. Maloti-Drakensberg Mountains, southern Africa. We sampled ant assemblages along an extensive elevational gradient (900-3000 m a.s.l.) twice yearly for 7 years, and collected functional-trait information related to the species' dietary and habitat-structure preferences. We used recently developed methods to partition species and functional beta diversity into their turnover and nestedness components. A series of null models were used to test whether the observed beta diversity patterns differed from random expectations. Species beta diversity was driven by turnover, but functional beta diversity was composed of both turnover and nestedness patterns at different parts of the gradient. Null models revealed that deterministic processes were likely to be responsible for the species patterns but that the functional changes were indistinguishable from stochasticity. Different ant species are found with increasing elevation, but they tend to represent an increasingly nested subset of the available functional strategies. This finding is unique and narrows down the list of possible factors that control ant existence across elevation. We conclude that diet and habitat preferences have little role in structuring ant assemblages in montane environments and that some other factor must be driving the non-random patterns of species turnover. This finding also highlights the importance of distinguishing between different kinds of beta diversity.
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Pimentel, Harold; Parra, Marilyn; Gee, Sherry L.; ...
2015-11-03
Differentiating erythroblasts execute a dynamic alternative splicing program shown here to include extensive and diverse intron retention (IR) events. Cluster analysis revealed hundreds of developmentallydynamic introns that exhibit increased IR in mature erythroblasts, and are enriched in functions related to RNA processing such as SF3B1 spliceosomal factor. Distinct, developmentally-stable IR clusters are enriched in metal-ion binding functions and include mitoferrin genes SLC25A37 and SLC25A28 that are critical for iron homeostasis. Some IR transcripts are abundant, e.g. comprising ~50% of highly-expressed SLC25A37 and SF3B1 transcripts in late erythroblasts, and thereby limiting functional mRNA levels. IR transcripts tested were predominantly nuclearlocalized. Splicemore » site strength correlated with IR among stable but not dynamic intron clusters, indicating distinct regulation of dynamically-increased IR in late erythroblasts. Retained introns were preferentially associated with alternative exons with premature termination codons (PTCs). High IR was observed in disease-causing genes including SF3B1 and the RNA binding protein FUS. Comparative studies demonstrated that the intron retention program in erythroblasts shares features with other tissues but ultimately is unique to erythropoiesis. Finally, we conclude that IR is a multi-dimensional set of processes that post-transcriptionally regulate diverse gene groups during normal erythropoiesis, misregulation of which could be responsible for human disease.« less
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Immunoglobulin superfamily members encoded by viruses and their multiple roles in immune evasion.
Farré, Domènec; Martínez-Vicente, Pablo; Engel, Pablo; Angulo, Ana
2017-05-01
Pathogens have developed a plethora of strategies to undermine host immune defenses in order to guarantee their survival. For large DNA viruses, these immune evasion mechanisms frequently rely on the expression of genes acquired from host genomes. Horizontally transferred genes include members of the immunoglobulin superfamily, whose products constitute the most diverse group of proteins of vertebrate genomes. Their promiscuous immunoglobulin domains, which comprise the building blocks of these molecules, are involved in a large variety of functions mediated by ligand-binding interactions. The flexible structural nature of the immunoglobulin domains makes them appealing targets for viral capture due to their capacity to generate high functional diversity. Here, we present an up-to-date review of immunoglobulin superfamily gene homologs encoded by herpesviruses, poxviruses, and adenoviruses, that include CD200, CD47, Fc receptors, interleukin-1 receptor 2, interleukin-18 binding protein, CD80, carcinoembryonic antigen-related cell adhesion molecules, and signaling lymphocyte activation molecules. We discuss their distinct structural attributes, binding properties, and functions, shaped by evolutionary pressures to disarm specific immune pathways. We include several novel genes identified from extensive genome database surveys. An understanding of the properties and modes of action of these viral proteins may guide the development of novel immune-modulatory therapeutic tools. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Pimentel, Harold; Parra, Marilyn; Gee, Sherry L.
Differentiating erythroblasts execute a dynamic alternative splicing program shown here to include extensive and diverse intron retention (IR) events. Cluster analysis revealed hundreds of developmentallydynamic introns that exhibit increased IR in mature erythroblasts, and are enriched in functions related to RNA processing such as SF3B1 spliceosomal factor. Distinct, developmentally-stable IR clusters are enriched in metal-ion binding functions and include mitoferrin genes SLC25A37 and SLC25A28 that are critical for iron homeostasis. Some IR transcripts are abundant, e.g. comprising ~50% of highly-expressed SLC25A37 and SF3B1 transcripts in late erythroblasts, and thereby limiting functional mRNA levels. IR transcripts tested were predominantly nuclearlocalized. Splicemore » site strength correlated with IR among stable but not dynamic intron clusters, indicating distinct regulation of dynamically-increased IR in late erythroblasts. Retained introns were preferentially associated with alternative exons with premature termination codons (PTCs). High IR was observed in disease-causing genes including SF3B1 and the RNA binding protein FUS. Comparative studies demonstrated that the intron retention program in erythroblasts shares features with other tissues but ultimately is unique to erythropoiesis. Finally, we conclude that IR is a multi-dimensional set of processes that post-transcriptionally regulate diverse gene groups during normal erythropoiesis, misregulation of which could be responsible for human disease.« less
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Mueller, Kevin E; Hobbie, Sarah E; Tilman, David; Reich, Peter B
2013-04-01
The effects of global environmental changes on soil nitrogen (N) pools and fluxes have consequences for ecosystem functions such as plant productivity and N retention. In a 13-year grassland experiment, we evaluated how elevated atmospheric carbon dioxide (CO2 ), N fertilization, and plant species richness alter soil N cycling. We focused on soil inorganic N pools, including ammonium and nitrate, and two N fluxes, net N mineralization and net nitrification. In contrast with existing hypotheses, such as progressive N limitation, and with observations from other, often shorter, studies, elevated CO2 had relatively static and small, or insignificant, effects on soil inorganic N pools and fluxes. Nitrogen fertilization had inconsistent effects on soil N transformations, but increased soil nitrate and ammonium concentrations. Plant species richness had increasingly positive effects on soil N transformations over time, likely because in diverse subplots the concentrations of N in roots increased over time. Species richness also had increasingly positive effects on concentrations of ammonium in soil, perhaps because more carbon accumulated in soils of diverse subplots, providing exchange sites for ammonium. By contrast, subplots planted with 16 species had lower soil nitrate concentrations than less diverse subplots, especially when fertilized, probably due to greater N uptake capacity of subplots with 16 species. Monocultures of different plant functional types had distinct effects on N transformations and nitrate concentrations, such that not all monocultures differed from diverse subplots in the same manner. The first few years of data would not have adequately forecast the effects of N fertilization and diversity on soil N cycling in later years; therefore, the dearth of long-term manipulations of plant species richness and N inputs is a hindrance to forecasting the state of the soil N cycle and ecosystem functions in extant plant communities. © 2012 Blackwell Publishing Ltd.
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Frontiers in research on biodiversity and disease
Johnson, Pieter T. J.; Ostfeld, Richard S.; Keesing, Felicia
2016-01-01
Global losses of biodiversity have galvanised efforts to understand how changes to communities affect ecological processes, including transmission of infectious pathogens. Here, we review recent research on diversity–disease relationships and identify future priorities. Growing evidence from experimental, observational and modelling studies indicates that biodiversity changes alter infection for a range of pathogens and through diverse mechanisms. Drawing upon lessons from the community ecology of free-living organisms, we illustrate how recent advances from biodiversity research generally can provide necessary theoretical foundations, inform experimental designs, and guide future research at the interface between infectious disease risk and changing ecological communities. Dilution effects are expected when ecological communities are nested and interactions between the pathogen and the most competent host group(s) persist or increase as biodiversity declines. To move beyond polarising debates about the generality of diversity effects and develop a predictive framework, we emphasise the need to identify how the effects of diversity vary with temporal and spatial scale, to explore how realistic patterns of community assembly affect transmission, and to use experimental studies to consider mechanisms beyond simple changes in host richness, including shifts in trophic structure, functional diversity and symbiont composition. PMID:26261049
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Kröber, Wenzel; Li, Ying; Härdtle, Werner; Ma, Keping; Schmid, Bernhard; Schmidt, Karsten; Scholten, Thomas; Seidler, Gunnar; von Oheimb, Goddert; Welk, Erik; Wirth, Christian; Bruelheide, Helge
2015-09-01
While functional diversity (FD) has been shown to be positively related to a number of ecosystem functions including biomass production, it may have a much less pronounced effect than that of environmental factors or species-specific properties. Leaf and wood traits can be considered particularly relevant to tree growth, as they reflect a trade-off between resources invested into growth and persistence. Our study focussed on the degree to which early forest growth was driven by FD, the environment (11 variables characterizing abiotic habitat conditions), and community-weighted mean (CWM) values of species traits in the context of a large-scale tree diversity experiment (BEF-China). Growth rates of trees with respect to crown diameter were aggregated across 231 plots (hosting between one and 23 tree species) and related to environmental variables, FD, and CWM, the latter two of which were based on 41 plant functional traits. The effects of each of the three predictor groups were analyzed separately by mixed model optimization and jointly by variance partitioning. Numerous single traits predicted plot-level tree growth, both in the models based on CWMs and FD, but none of the environmental variables was able to predict tree growth. In the best models, environment and FD explained only 4 and 31% of variation in crown growth rates, respectively, while CWM trait values explained 42%. In total, the best models accounted for 51% of crown growth. The marginal role of the selected environmental variables was unexpected, given the high topographic heterogeneity and large size of the experiment, as was the significant impact of FD, demonstrating that positive diversity effects already occur during the early stages in tree plantations.
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Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens
Silby, Mark W; Cerdeño-Tárraga, Ana M; Vernikos, Georgios S; Giddens, Stephen R; Jackson, Robert W; Preston, Gail M; Zhang, Xue-Xian; Moon, Christina D; Gehrig, Stefanie M; Godfrey, Scott AC; Knight, Christopher G; Malone, Jacob G; Robinson, Zena; Spiers, Andrew J; Harris, Simon; Challis, Gregory L; Yaxley, Alice M; Harris, David; Seeger, Kathy; Murphy, Lee; Rutter, Simon; Squares, Rob; Quail, Michael A; Saunders, Elizabeth; Mavromatis, Konstantinos; Brettin, Thomas S; Bentley, Stephen D; Hothersall, Joanne; Stephens, Elton; Thomas, Christopher M; Parkhill, Julian; Levy, Stuart B; Rainey, Paul B; Thomson, Nicholas R
2009-01-01
Background Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species. Results Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome. Conclusions P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome. PMID:19432983
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Kröber, Wenzel; Li, Ying; Härdtle, Werner; Ma, Keping; Schmid, Bernhard; Schmidt, Karsten; Scholten, Thomas; Seidler, Gunnar; von Oheimb, Goddert; Welk, Erik; Wirth, Christian; Bruelheide, Helge
2015-01-01
While functional diversity (FD) has been shown to be positively related to a number of ecosystem functions including biomass production, it may have a much less pronounced effect than that of environmental factors or species-specific properties. Leaf and wood traits can be considered particularly relevant to tree growth, as they reflect a trade-off between resources invested into growth and persistence. Our study focussed on the degree to which early forest growth was driven by FD, the environment (11 variables characterizing abiotic habitat conditions), and community-weighted mean (CWM) values of species traits in the context of a large-scale tree diversity experiment (BEF-China). Growth rates of trees with respect to crown diameter were aggregated across 231 plots (hosting between one and 23 tree species) and related to environmental variables, FD, and CWM, the latter two of which were based on 41 plant functional traits. The effects of each of the three predictor groups were analyzed separately by mixed model optimization and jointly by variance partitioning. Numerous single traits predicted plot-level tree growth, both in the models based on CWMs and FD, but none of the environmental variables was able to predict tree growth. In the best models, environment and FD explained only 4 and 31% of variation in crown growth rates, respectively, while CWM trait values explained 42%. In total, the best models accounted for 51% of crown growth. The marginal role of the selected environmental variables was unexpected, given the high topographic heterogeneity and large size of the experiment, as was the significant impact of FD, demonstrating that positive diversity effects already occur during the early stages in tree plantations. PMID:26380685
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Global Diversity and Phylogeny of the Asteroidea (Echinodermata)
Mah, Christopher L.; Blake, Daniel B.
2012-01-01
Members of the Asteroidea (phylum Echinodermata), popularly known as starfish or sea stars, are ecologically important and diverse members of marine ecosystems in all of the world's oceans. We present a comprehensive overview of diversity and phylogeny as they have figured into the evolution of the Asteroidea from Paleozoic to the living fauna. Living post-Paleozoic asteroids, the Neoasteroidea, are morphologically separate from those in the Paleozoic. Early Paleozoic asteroid faunas were diverse and displayed morphology that foreshadowed later living taxa. Preservation presents significant difficulties, but fossil occurrence and current accounts suggests a diverse Paleozoic fauna, which underwent extinction around the Permian-Triassic interval was followed by re-diversification of at least one surviving lineage. Ongoing phylogenetic classification debates include the status of the Paxillosida and the Concentricycloidea. Fossil and molecular evidence has been and continues to be part of the ongoing evolution of asteroid phylogenetic research. The modern lineages of asteroids include the Valvatacea, the Forcipulatacea, the Spinlosida, and the Velatida. We present an overview of diversity in these taxa, as well as brief notes on broader significance, ecology, and functional morphology of each. Although much asteroid taxonomy is stable, many new taxa remain to be discovered with many new species currently awaiting description. The Goniasteridae is currently one of the most diverse families within the Asteroidea. New data from molecular phylogenetics and the advent of global biodiversity databases, such as the World Asteroidea Database (http://www.marinespecies.org/Asteroidea/) present important new springboards for understanding the global biodiversity and evolution of asteroids. PMID:22563389
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Identifying taxonomic and functional surrogates for spring biodiversity conservation.
Jyväsjärvi, Jussi; Virtanen, Risto; Ilmonen, Jari; Paasivirta, Lauri; Muotka, Timo
2018-02-27
Surrogate approaches are widely used to estimate overall taxonomic diversity for conservation planning. Surrogate taxa are frequently selected based on rarity or charisma, whereas selection through statistical modeling has been applied rarely. We used boosted-regression-tree models (BRT) fitted to biological data from 165 springs to identify bryophyte and invertebrate surrogates for taxonomic and functional diversity of boreal springs. We focused on these 2 groups because they are well known and abundant in most boreal springs. The best indicators of taxonomic versus functional diversity differed. The bryophyte Bryum weigelii and the chironomid larva Paratrichocladius skirwithensis best indicated taxonomic diversity, whereas the isopod Asellus aquaticus and the chironomid Macropelopia spp. were the best surrogates of functional diversity. In a scoring algorithm for priority-site selection, taxonomic surrogates performed only slightly better than random selection for all spring-dwelling taxa, but they were very effective in representing spring specialists, providing a distinct improvement over random solutions. However, the surrogates for taxonomic diversity represented functional diversity poorly and vice versa. When combined with cross-taxon complementarity analyses, surrogate selection based on statistical modeling provides a promising approach for identifying groundwater-dependent ecosystems of special conservation value, a key requirement of the EU Water Framework Directive. © 2018 Society for Conservation Biology.
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Diversity in GABAergic signaling.
Vogt, Kaspar
2015-01-01
GABA(A) receptor-mediated synaptic transmission is responsible for inhibitory control of neural function in the brain. Recent progress has shown that GABA(A) receptors also provide a wide range of additional functions beyond simple inhibition. This diversity of functions is mediated by a large variety of different interneuron classes acting on a diverse population of receptor subtypes. Here, I will focus on an additional source of GABAergic signaling diversity, caused by the highly variable ion signaling mechanism of GABA(A) receptors. In concert with the other two sources of GABAergic heterogeneity, this variability in signaling allows for a wide array of GABAergic effects that are crucial for the development of the brain and its function. © 2015 Elsevier Inc. All rights reserved.
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Walker, Peter J; Dietzgen, Ralf G; Joubert, D Albert; Blasdell, Kim R
2011-12-01
The Rhabdoviridae is one of the most ecologically diverse families of RNA viruses with members infecting a wide range of organisms including placental mammals, marsupials, birds, reptiles, fish, insects and plants. The availability of complete nucleotide sequences for an increasing number of rhabdoviruses has revealed that their ecological diversity is reflected in the diversity and complexity of their genomes. The five canonical rhabdovirus structural protein genes (N, P, M, G and L) that are shared by all rhabdoviruses are overprinted, overlapped and interspersed with a multitude of novel and diverse accessory genes. Although not essential for replication in cell culture, several of these genes have been shown to have roles associated with pathogenesis and apoptosis in animals, and cell-to-cell movement in plants. Others appear to be secreted or have the characteristics of membrane-anchored glycoproteins or viroporins. However, most encode proteins of unknown function that are unrelated to any other known proteins. Understanding the roles of these accessory genes and the strategies by which rhabdoviruses use them to engage, divert and re-direct cellular processes will not only present opportunities to develop new anti-viral therapies but may also reveal aspects of cellar function that have broader significance in biology, agriculture and medicine. Crown Copyright © 2011. Published by Elsevier B.V. All rights reserved.
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2017-01-01
Understanding the effects of global climate disruption on biodiversity is important to future conservation efforts. While taxonomic diversity is widely studied, functional diversity of plants, and recently animals, is receiving increasing attention. Most studies of mammals are short-term, focus on temperate habitats, and rely on traits described in the literature rather than generating traits from observations. Unlike previous studies, this long-term field study assessed the factors driving the functional and taxonomic diversity of small-mammal assemblages in dry tropical forests using both traits recorded from literature and a demographic database. We assessed the drivers (abundance and biomass, temperature and rainfall) of taxonomic richness and functional diversity for two rain-driven seasons in two adjacent but distinct forests—upland and lowland (arroyo or riparian) forests. Our analysis found that rainfall, both seasonal and atypical, was the primary factor driving functional and taxonomic diversity of small-mammal assemblages. Functional responses differed between the two types of forests, however, with effects being stronger in the harsher conditions of the upland forests than in the less severe conditions prevailing in the arroyo (riparian) forest. The latter also supports a richer, more diverse, and more stable small-mammal assemblage. These findings highlight the importance of climate to tropical biological diversity, as extreme climate events (hurricanes, droughts and floods) and disruption of rainfall patterns were shown to decrease biodiversity. They also support the need to preserve these habitats, as their high taxonomic diversity and functional redundancy makes them resilient against global climate disruption and local extreme events. Tropical dry forests constitute a potential reservoir for biodiversity and the ecosystem services they provide. Unfortunately, these forests are among the most endangered terrestrial ecosystems because of deforestation and the likely impacts of global climate disruption. PMID:29228017
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Yin, DeLu (Tyler); Urresti, Saioa; Lafond, Mickael; Johnston, Esther M.; Derikvand, Fatemeh; Ciano, Luisa; Berrin, Jean-Guy; Henrissat, Bernard; Walton, Paul H.; Davies, Gideon J.; Brumer, Harry
2015-01-01
Alcohol oxidases, including carbohydrate oxidases, have a long history of research that has generated fundamental biological understanding and biotechnological applications. Despite a long history of study, the galactose 6-oxidase/glyoxal oxidase family of mononuclear copper-radical oxidases, Auxiliary Activity Family 5 (AA5), is currently represented by only very few characterized members. Here we report the recombinant production and detailed structure–function analyses of two homologues from the phytopathogenic fungi Colletotrichum graminicola and C. gloeosporioides, CgrAlcOx and CglAlcOx, respectively, to explore the wider biocatalytic potential in AA5. EPR spectroscopy and crystallographic analysis confirm a common active-site structure vis-à-vis the archetypal galactose 6-oxidase from Fusarium graminearum. Strikingly, however, CgrAlcOx and CglAlcOx are essentially incapable of oxidizing galactose and galactosides, but instead efficiently catalyse the oxidation of diverse aliphatic alcohols. The results highlight the significant potential of prospecting the evolutionary diversity of AA5 to reveal novel enzyme specificities, thereby informing both biology and applications. PMID:26680532
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Aharon, Yael; Pasternak, Zohar; Ben Yosef, Michael; Behar, Adi; Lauzon, Carol; Yuval, Boaz
2013-01-01
The Mediterranean fruit fly (medfly) (Ceratitis capitata) lays eggs in fruits, where larvae subsequently develop, causing large-scale agricultural damage. Within its digestive tract, the fly supports an extended bacterial community that is composed of multiple strains of a variety of enterobacterial species. Most of these bacteria appear to be functionally redundant, with most strains sustaining diazotrophy and/or pectinolysis. At least some of these bacteria were shown to be vertically inherited, but colonization, structural, and metabolic aspects of the community's dynamics have not been investigated. We used fluorescent in situ hybridization, metabolic profiling, plate cultures, and pyrosequencing to show that an initial, egg-borne, diverse community expands throughout the fly's life cycle. While keeping “core” diazotrophic and pectinolytic functions, it also harbors diverse and fluctuating populations that express varied metabolic capabilities. We suggest that the metabolic and compositional plasticity of the fly's microbiota provides potential adaptive advantages to the medfly host and that its acquisition and dynamics are affected by mixed processes that include stochastic effects, host behavior, and molecular barriers. PMID:23104413
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Consumers control diversity and functioning of a natural marine ecosystem.
Altieri, Andrew H; Trussell, Geoffrey C; Ewanchuk, Patrick J; Bernatchez, Genevieve; Bracken, Matthew E S
2009-01-01
Our understanding of the functional consequences of changes in biodiversity has been hampered by several limitations of previous work, including limited attention to trophic interactions, a focus on species richness rather than evenness, and the use of artificially assembled communities. In this study, we manipulated the density of an herbivorous snail in natural tide pools and allowed seaweed communities to assemble in an ecologically relevant and non-random manner. Seaweed species evenness and biomass-specific primary productivity (mg O(2) h(-1) g(-1)) were higher in tide pools with snails because snails preferentially consumed an otherwise dominant seaweed species that can reduce biomass-specific productivity rates of algal assemblages. Although snails reduced overall seaweed biomass in tide pools, they did not affect gross primary productivity at the scale of tide pools (mg O(2) h(-1) pool(-1) or mg O(2) h(-1) m(-2)) because of the enhanced biomass-specific productivity associated with grazer-mediated increases in algal evenness. Our results suggest that increased attention to trophic interactions, diversity measures other than richness, and particularly the effects of consumers on evenness and primary productivity, will improve our understanding of the relationship between diversity and ecosystem functioning and allow more effective links between experimental results and real-world changes in biodiversity.
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Consumers Control Diversity and Functioning of a Natural Marine Ecosystem
Altieri, Andrew H.; Trussell, Geoffrey C.; Ewanchuk, Patrick J.; Bernatchez, Genevieve; Bracken, Matthew E. S.
2009-01-01
Background Our understanding of the functional consequences of changes in biodiversity has been hampered by several limitations of previous work, including limited attention to trophic interactions, a focus on species richness rather than evenness, and the use of artificially assembled communities. Methodology and Principal Findings In this study, we manipulated the density of an herbivorous snail in natural tide pools and allowed seaweed communities to assemble in an ecologically relevant and non-random manner. Seaweed species evenness and biomass-specific primary productivity (mg O2 h−1 g−1) were higher in tide pools with snails because snails preferentially consumed an otherwise dominant seaweed species that can reduce biomass-specific productivity rates of algal assemblages. Although snails reduced overall seaweed biomass in tide pools, they did not affect gross primary productivity at the scale of tide pools (mg O2 h−1 pool−1 or mg O2 h−1 m−2) because of the enhanced biomass-specific productivity associated with grazer-mediated increases in algal evenness. Significance Our results suggest that increased attention to trophic interactions, diversity measures other than richness, and particularly the effects of consumers on evenness and primary productivity, will improve our understanding of the relationship between diversity and ecosystem functioning and allow more effective links between experimental results and real-world changes in biodiversity. PMID:19384410
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Wang, Fan; Zhao, Hongwei; Xiang, Haiying; Wu, Lijun; Men, Xiao; Qi, Chang; Chen, Guoqiang; Zhang, Haibo; Wang, Yi; Xian, Mo
2018-06-05
Microbes on aging flue-cured tobaccos (ATFs) improve the aroma and other qualities desirable in products. Understanding the relevant organisms would picture microbial community diversity, metabolic potential, and their applications. However, limited efforts have been made on characterizing the microbial quality and functional profiling. Herein, we present our investigation of the bacterial diversity and predicted potential genetic capability of the bacteria from two AFTs using 16S rRNA gene sequences and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) software. The results show that dominant bacteria from AFT surfaces were classified into 48 genera, 36 families, and 7 phyla. In addition, Bacillus spp. was found prevalent on both ATFs. Furthermore, PICRUSt predictions of bacterial community functions revealed many attractive metabolic capacities in the AFT microbiota, including several involved in the biosynthesis of flavors and fragrances and the degradation of harmful compounds, such as nicotine and nitrite. These results provide insights into the importance of AFT bacteria in determining product qualities and indicate specific microbial species with predicted enzymatic capabilities for the production of high-efficiency flavors, the degradation of undesirable compounds, and the provision of nicotine and nitrite tolerance which suggest fruitful areas of investigation into the manipulation of AFT microbiota for AFT and other product improvements.
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Yeast diversity of sourdoughs and associated metabolic properties and functionalities.
De Vuyst, Luc; Harth, Henning; Van Kerrebroeck, Simon; Leroy, Frédéric
2016-12-19
Together with acidifying lactic acid bacteria, yeasts play a key role in the production process of sourdough, where they are either naturally present or added as a starter culture. Worldwide, a diversity of yeast species is encountered, with Saccharomyces cerevisiae, Candida humilis, Kazachstania exigua, Pichia kudriavzevii, Wickerhamomyces anomalus, and Torulaspora delbrueckii among the most common ones. Sourdough-adapted yeasts are able to withstand the stress conditions encountered during their growth, including nutrient starvation as well as the effects of acidic, oxidative, thermal, and osmotic stresses. From a technological point of view, their metabolism primarily contributes to the leavening and flavour of sourdough products. Besides ethanol and carbon dioxide, yeasts can produce metabolites that specifically affect flavour, such as organic acids, diacetyl, higher alcohols from branched-chain amino acids, and esters derived thereof. Additionally, several yeast strains possess functional properties that can potentially lead to nutritional and safety advantages. These properties encompass the production of vitamins, an improvement of the bioavailability of phenolic compounds, the dephosphorylation of phytic acid, the presence of probiotic potential, and the inhibition of fungi and their mycotoxin production. Strains of diverse species are new candidate functional starter cultures, offering opportunities beyond the conventional use of baker's yeast. Copyright © 2016 Elsevier B.V. All rights reserved.
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Strains, functions, and dynamics in the expanded Human Microbiome Project
Lloyd-Price, Jason; Mahurkar, Anup; Rahnavard, Gholamali; Crabtree, Jonathan; Orvis, Joshua; Hall, A. Brantley; Brady, Arthur; Creasy, Heather H.; McCracken, Carrie; Giglio, Michelle G.; McDonald, Daniel; Franzosa, Eric A.; Knight, Rob; White, Owen; Huttenhower, Curtis
2018-01-01
Summary The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, microbial population diversity, biogeography, and molecular function. The NIH Human Microbiome Project (HMP) has provided one of the broadest such characterizations to date. Here, we introduce an expanded second phase of the study, abbreviated HMP1-II, comprising 1,631 new metagenomic samples (2,355 total) targeting diverse body sites with multiple time points in 265 individuals. We applied updated profiling and assembly methods to these data to provide new characterizations of microbiome personalization. Strain identification revealed distinct subspecies clades specific to body sites; it also quantified species with phylogenetic diversity under-represented in isolate genomes. Body-wide functional profiling classified pathways into universal, human-enriched, and body site-enriched subsets. Finally, temporal analysis decomposed microbial variation into rapidly variable, moderately variable, and stable subsets. This study furthers our knowledge of baseline human microbial diversity, thus enabling an understanding of personalized microbiome function and dynamics. PMID:28953883
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Diversity of respiratory impedance based on quantitative computed tomography in patients with COPD.
Wada, Yosuke; Kitaguchi, Yoshiaki; Yasuo, Masanori; Ueno, Fumika; Kawakami, Satoshi; Fukushima, Kiyoyasu; Fujimoto, Keisaku; Hanaoka, Masayuki
2018-01-01
This study was conducted in order to investigate the diversity of respiratory physiology, including the respiratory impedance and reversibility of airway obstruction, based on quantitative computed tomography (CT) in patients with COPD. Medical records of 174 stable COPD patients were retrospectively reviewed to obtain the patients' clinical data, including the pulmonary function and imaging data. According to the software-based quantification of the degree of emphysema and airway wall thickness, the patients were classified into the "normal by CT" phenotype, the airway-dominant phenotype, the emphysema-dominant phenotype, and the mixed phenotype. The pulmonary function, including the respiratory impedance evaluated by using the forced oscillation technique (FOT) and the reversibility of airway obstruction in response to inhaled short-acting β 2 -agonists, was then compared among the four phenotypes. The respiratory system resistance at 5 and 20 Hz (R5 and R20) was significantly higher, and the respiratory system reactance at 5 Hz (X5) was significantly more negative in the airway-dominant and mixed phenotypes than in the other phenotypes. The within-breath changes of X5 (ΔX5) were significantly greater in the mixed phenotype than in the "normal by CT" and emphysema-dominant phenotypes. The FOT parameters (R5, R20, and X5) were significantly correlated with indices of the degree of airway wall thickness and significantly but weakly correlated with the reversibility of airway obstruction. There was no significant correlation between the FOT parameters (R5, R20, and X5) and the degree of emphysema. There is a diversity of respiratory physiology, including the respiratory impedance and reversibility of airway obstruction, based on quantitative CT in patients with COPD. The FOT measurements may reflect the degree of airway disease and aid in detecting airway remodeling in patients with COPD.
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Flórez, Karen R; Richardson, Andrea S; Ghosh-Dastidar, Madhumita Bonnie; Troxel, Wendy; DeSantis, Amy; Colabianchi, Natalie; Dubowitz, Tamara
2018-04-01
Social support and social networks can elucidate important structural and functional aspects of social relationships that are associated with health-promoting behaviors, including Physical Activity (PA) and weight. A growing number of studies have investigated the relationship between social support, social networks, PA and obesity specifically among African Americans; however, the evidence is mixed and many studies focus exclusively on African American women. Most studies have also focused on either functional or structural aspects of social relationships (but not both) and few have objectively measured moderate-to-vigorous physical activity (MVPA) and body mass index (BMI). Cross-sectional surveys of adult African American men and women living in two low-income predominantly African American neighborhoods in Pittsburgh, PA (N = 799) measured numerous structural features as well as functional aspects of social relationships. Specifically, structural features included social isolation, and social network size and diversity. Functional aspects included perceptions of social support for physical activity from the social network in general as well as from family and friends specifically. Height, weight, and PA were objectively measured. From these, we derived Body Mass Index (BMI) and moderate-to-vigorous physical activity (MVPA). All regression models were stratified by gender, and included age, income, education, employment, marital status, physical limitations, and a neighborhood indicator. Greater social isolation was a significant predictor of lower BMI among men only. Among women only, social isolation was significantly associated with increased MVPA whereas, network diversity was significantly associated with reduced MVPA. Future research would benefit from in-depth qualitative investigations to understand how social networks may act to influence different types of physical activity among African Americans, as well as understand how they can be possible levers for health promotion and prevention.
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Transdiagnostic dimensions of anxiety: Neural mechanisms, executive functions, and new directions.
Sharp, Paul B; Miller, Gregory A; Heller, Wendy
2015-11-01
Converging neuroscientific and psychological evidence points to several transdiagnostic factors that cut across DSM-defined disorders, which both affect and are affected by executive dysfunction. Two of these factors, anxious apprehension and anxious arousal, have helped bridge the gap between psychological and neurobiological models of anxiety. The present integration of diverse findings advances an understanding of the relationships between these transdiagnostic anxiety dimensions, their interactions with each other and executive function, and their neural mechanisms. Additionally, a discussion is provided concerning how these constructs fit within the Research Domain Criteria (RDoC) matrix developed by the National Institutes of Mental Health and how they relate to other anxiety constructs studied with different methods and at other units of analysis. Suggestions for future research are offered, including how to (1) improve measurement and delineation of these constructs, (2) use new neuroimaging methods and theoretical approaches of how the brain functions to build neural mechanistic models of these constructs, and (3) advance understanding of the relationships of these constructs to diverse emotional phenomena and executive functions. Copyright © 2015 Elsevier B.V. All rights reserved.
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Morris, Aaron; Guégan, Jean-François; Benbow, M Eric; Williamson, Heather; Small, Pamela L C; Quaye, Charles; Boakye, Daniel; Merritt, Richard W; Gozlan, Rodolphe E
2016-09-01
Emerging infectious disease outbreaks are increasingly suspected to be a consequence of human pressures exerted on natural ecosystems. Previously, host taxonomic communities have been used as indicators of infectious disease emergence, and the loss of their diversity has been implicated as a driver of increased presence. The mechanistic details in how such pathogen-host systems function, however, may not always be explained by taxonomic variation or loss. Here we used machine learning and methods based on Gower's dissimilarity to quantify metrics of invertebrate functional diversity, in addition to functional groups and their taxonomic diversity at sites endemic and non-endemic for the model generalist pathogen Mycobacterium ulcerans, the causative agent of Buruli ulcer. Changes in these metrics allowed the rapid categorisation of the ecological niche of the mycobacterium's hosts and the ability to relate specific host traits to its presence in aquatic ecosystems. We found that taxonomic diversity of hosts and overall functional diversity loss and evenness had no bearing on the mycobacterium's presence, or whether the site was in an endemic area. These findings, however, provide strong evidence that generalist environmentally persistent bacteria such as M. ulcerans can be associated with specific functional traits rather than taxonomic groups of organisms, increasing our understanding of emerging disease ecology and origin.
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Yoon, Ki-Young; Dong, Guangbin
2018-05-23
Herein, we report the palladium/norbornene cooperatively catalyzed polymerization, which simplifies synthesis of functional aromatic polymers, including conjugated polymers. Specifically, an A2B2C-type multicomponent polymerization is developed using ortho-amination/ipso-alkynylation reaction for preparing various amine-functionalized arylacetylene-containing polymers. Within a single catalytic cycle, the amine side-chains are site-selectively installed in situ via C-H activation during the polymerization process, which represents a major difference from conventional cross-coupling polymerizations. This in situ-functionalization strategy enables modular incorporation of functional side-chains from simple monomers, thereby conveniently affording a diverse range of functional polymers. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Addition of Rubber to soil damages the functional diversity of soil.
Goswami, Madhurankhi; Bhattacharyya, Purnita; Tribedi, Prosun
2017-07-01
Rubber is a polymer of isoprene, consisting mainly of cis-1,4-polyisoprene units. The unmanageable production and its irresponsible disposal pose severe threats to environmental ecology. Therefore, the current study focuses extensively on the ill-effects of Rubber disposal on soil microbial functional diversity as it reflects the health of ecosystem by acting as a key component in ecosystem productivity. To investigate the effect of Rubber on soil microbial functional diversity, soil samples were collected from landfill sites and three different soil microcosms (Rubber treated, untreated, and sterile soil) were prepared. The soil enzymatic activity was determined by fluorescein diacetate hydrolysis followed by the determination of the microbial metabolic potential and functional diversity by average well color development and Shannon-Weaver index (H), respectively. BiOLOG ECO plates were used for determining the microbial functional diversity of the soil microcosms. Higher heterotrophic microbial count as well as higher soil microbial activity was observed in Rubber untreated soil than Rubber treated soil microcosm. The result indicated that the addition of Rubber to soil reduced soil heterotrophic microbial count and soil microbial activity considerably. Similarly, soil microbial metabolic potential as well as microbial functional diversity of soil had been decreased by the addition of Rubber gloves in it. Variation in soil microbial metabolic spectrum between Rubber treated and untreated microcosm was confirmed by multivariate analysis. Collectively, all the results demonstrated that the addition of Rubber to soil reduced the soil microbial functional diversity considerably. Therefore, it is necessary for the commission of serious steps regarding Rubber disposal and protection of the environment from serious environmental issues.
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Multifunctional Mitochondrial AAA Proteases
Glynn, Steven E.
2017-01-01
Mitochondria perform numerous functions necessary for the survival of eukaryotic cells. These activities are coordinated by a diverse complement of proteins encoded in both the nuclear and mitochondrial genomes that must be properly organized and maintained. Misregulation of mitochondrial proteostasis impairs organellar function and can result in the development of severe human diseases. ATP-driven AAA+ proteins play crucial roles in preserving mitochondrial activity by removing and remodeling protein molecules in accordance with the needs of the cell. Two mitochondrial AAA proteases, i-AAA and m-AAA, are anchored to either face of the mitochondrial inner membrane, where they engage and process an array of substrates to impact protein biogenesis, quality control, and the regulation of key metabolic pathways. The functionality of these proteases is extended through multiple substrate-dependent modes of action, including complete degradation, partial processing, or dislocation from the membrane without proteolysis. This review discusses recent advances made toward elucidating the mechanisms of substrate recognition, handling, and degradation that allow these versatile proteases to control diverse activities in this multifunctional organelle. PMID:28589125
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Multifunctional Mitochondrial AAA Proteases.
Glynn, Steven E
2017-01-01
Mitochondria perform numerous functions necessary for the survival of eukaryotic cells. These activities are coordinated by a diverse complement of proteins encoded in both the nuclear and mitochondrial genomes that must be properly organized and maintained. Misregulation of mitochondrial proteostasis impairs organellar function and can result in the development of severe human diseases. ATP-driven AAA+ proteins play crucial roles in preserving mitochondrial activity by removing and remodeling protein molecules in accordance with the needs of the cell. Two mitochondrial AAA proteases, i-AAA and m-AAA, are anchored to either face of the mitochondrial inner membrane, where they engage and process an array of substrates to impact protein biogenesis, quality control, and the regulation of key metabolic pathways. The functionality of these proteases is extended through multiple substrate-dependent modes of action, including complete degradation, partial processing, or dislocation from the membrane without proteolysis. This review discusses recent advances made toward elucidating the mechanisms of substrate recognition, handling, and degradation that allow these versatile proteases to control diverse activities in this multifunctional organelle.
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Intermediate Filaments and the Regulation of Cell Motility during Regeneration and Wound Healing.
Cheng, Fang; Eriksson, John E
2017-09-01
SUMMARYIntermediate filaments (IFs) comprise a diverse group of flexible cytoskeletal structures, the assembly, dynamics, and functions of which are regulated by posttranslational modifications. Characteristically, the expression of IF proteins is specific for tissues, differentiation stages, cell types, and functional contexts. Recent research has rapidly expanded the knowledge of IF protein functions. From being regarded as primarily structural proteins, it is now well established that IFs act as powerful modulators of cell motility and migration, playing crucial roles in wound healing and tissue regeneration, as well as inflammatory and immune responses. Although many of these IF-associated functions are essential for tissue repair, the involvement of IF proteins has been established in many additional facets of tissue healing and regeneration. Here, we review the recent progress in understanding the multiple functions of cytoplasmic IFs that relate to cell motility in the context of wound healing, taking examples from studies on keratin, vimentin, and nestin. Wound healing and regeneration include orchestration of a broad range of cellular processes, including regulation of cell attachment and migration, proliferation, differentiation, immune responses, angiogenesis, and remodeling of the extracellular matrix. In this respect, IF proteins now emerge as multifactorial and tissue-specific integrators of tissue regeneration, thereby acting as essential guardian biopolymers at the interface between health and disease, the failing of which contributes to a diverse range of pathologies. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.
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Bioinformatic Characterization of Glycyl Radical Enzyme-Associated Bacterial Microcompartments
Zarzycki, Jan; Erbilgin, Onur
2015-01-01
Bacterial microcompartments (BMCs) are proteinaceous organelles encapsulating enzymes that catalyze sequential reactions of metabolic pathways. BMCs are phylogenetically widespread; however, only a few BMCs have been experimentally characterized. Among them are the carboxysomes and the propanediol- and ethanolamine-utilizing microcompartments, which play diverse metabolic and ecological roles. The substrate of a BMC is defined by its signature enzyme. In catabolic BMCs, this enzyme typically generates an aldehyde. Recently, it was shown that the most prevalent signature enzymes encoded by BMC loci are glycyl radical enzymes, yet little is known about the function of these BMCs. Here we characterize the glycyl radical enzyme-associated microcompartment (GRM) loci using a combination of bioinformatic analyses and active-site and structural modeling to show that the GRMs comprise five subtypes. We predict distinct functions for the GRMs, including the degradation of choline, propanediol, and fuculose phosphate. This is the first family of BMCs for which identification of the signature enzyme is insufficient for predicting function. The distinct GRM functions are also reflected in differences in shell composition and apparently different assembly pathways. The GRMs are the counterparts of the vitamin B12-dependent propanediol- and ethanolamine-utilizing BMCs, which are frequently associated with virulence. This study provides a comprehensive foundation for experimental investigations of the diverse roles of GRMs. Understanding this plasticity of function within a single BMC family, including characterization of differences in permeability and assembly, can inform approaches to BMC bioengineering and the design of therapeutics. PMID:26407889
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Unrecognized coral species diversity masks differences in functional ecology
Boulay, Jennifer N.; Hellberg, Michael E.; Cortés, Jorge; Baums, Iliana B.
2014-01-01
Porites corals are foundation species on Pacific reefs but a confused taxonomy hinders understanding of their ecosystem function and responses to climate change. Here, we show that what has been considered a single species in the eastern tropical Pacific, Porites lobata, includes a morphologically similar yet ecologically distinct species, Porites evermanni. While P. lobata reproduces mainly sexually, P. evermanni dominates in areas where triggerfish prey on bioeroding mussels living within the coral skeleton, thereby generating asexual coral fragments. These fragments proliferate in marginal habitat not colonized by P. lobata. The two Porites species also show a differential bleaching response despite hosting the same dominant symbiont subclade. Thus, hidden diversity within these reef-builders has until now obscured differences in trophic interactions, reproductive dynamics and bleaching susceptibility, indicative of differential responses when confronted with future climate change. PMID:24335977
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Unrecognized coral species diversity masks differences in functional ecology.
Boulay, Jennifer N; Hellberg, Michael E; Cortés, Jorge; Baums, Iliana B
2014-02-07
Porites corals are foundation species on Pacific reefs but a confused taxonomy hinders understanding of their ecosystem function and responses to climate change. Here, we show that what has been considered a single species in the eastern tropical Pacific, Porites lobata, includes a morphologically similar yet ecologically distinct species, Porites evermanni. While P. lobata reproduces mainly sexually, P. evermanni dominates in areas where triggerfish prey on bioeroding mussels living within the coral skeleton, thereby generating asexual coral fragments. These fragments proliferate in marginal habitat not colonized by P. lobata. The two Porites species also show a differential bleaching response despite hosting the same dominant symbiont subclade. Thus, hidden diversity within these reef-builders has until now obscured differences in trophic interactions, reproductive dynamics and bleaching susceptibility, indicative of differential responses when confronted with future climate change.
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Functional diversity of soil invertebrates: a potential tool to explain N2O emission?
NASA Astrophysics Data System (ADS)
Lubbers, Ingrid; De Deyn, Gerlinde; Drake, Harold; Hunger, Sindy; Oppermann, Timo; van Groenigen, Jan Willem
2017-04-01
Soil biota play a crucial role in the mineralization of nutrients from organic material. However, they can thereby increase emissions of the potent greenhouse gas nitrous oxide (N2O). Our current lack of understanding of the factors controlling N2O production and emission is impeding the development of effective mitigation strategies. It is the challenge to control N2O emissions from production systems without reducing crop yield, and diversity of soil fauna may play a key role. A high functional diversity of soil invertebrates is known to stimulate nitrogen mineralization and thereby plant growth, however, it is unknown whether a high functional diversity of soil invertebrates can concurrently diminish N2O emissions. We hypothesized that increased functional diversity of soil invertebrates reduces faunal-induced N2O emissions by facilitating more complete denitrification through (i) stimulating the activity of denitrifying microbes, and (ii) affecting the distribution of micro and macro pores, creating more anaerobic reaction sites. Using state-of-the-art X-ray tomography and next-generation sequencing, we studied effects of functional diversity on soil structural properties and the diversity of the microbial community (16S rRNA genes and 16S rRNA), and linked these to soil N2O emissions. In a 120-day study we found that the functional composition of the soil invertebrate community determined N2O emissions: earthworm activity was key to faunal-induced N2O emissions (a 32-fold increase after 120 days, P<0.001). No proof was found to explain faunal-induced N2O emissions through differences in stimulated microbial activity. On the other hand, soil structural properties (mean pore size, pore size distribution) were found to be radically altered by earthworm activity. We conclude that the presence of a few functional groups (ecosystem engineers) is more important than overall increased functional diversity in explaining faunal-affected N2O emissions.
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Microbial diversity and metabolic networks in acid mine drainage habitats
Méndez-García, Celia; Peláez, Ana I.; Mesa, Victoria; Sánchez, Jesús; Golyshina, Olga V.; Ferrer, Manuel
2015-01-01
Acid mine drainage (AMD) emplacements are low-complexity natural systems. Low-pH conditions appear to be the main factor underlying the limited diversity of the microbial populations thriving in these environments, although temperature, ionic composition, total organic carbon, and dissolved oxygen are also considered to significantly influence their microbial life. This natural reduction in diversity driven by extreme conditions was reflected in several studies on the microbial populations inhabiting the various micro-environments present in such ecosystems. Early studies based on the physiology of the autochthonous microbiota and the growing success of omics-based methodologies have enabled a better understanding of microbial ecology and function in low-pH mine outflows; however, complementary omics-derived data should be included to completely describe their microbial ecology. Furthermore, recent updates on the distribution of eukaryotes and archaea recovered through sterile filtering (herein referred to as filterable fraction) in these environments demand their inclusion in the microbial characterization of AMD systems. In this review, we present a complete overview of the bacterial, archaeal (including filterable fraction), and eukaryotic diversity in these ecosystems, and include a thorough depiction of the metabolism and element cycling in AMD habitats. We also review different metabolic network structures at the organismal level, which is necessary to disentangle the role of each member of the AMD communities described thus far. PMID:26074887
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Schuldt, Andreas; Baruffol, Martin; Bruelheide, Helge; Chen, Simon; Chi, Xiulian; Wall, Marcus; Assmann, Thorsten
2014-09-01
Global change is predicted to cause non-random species loss in plant communities, with consequences for ecosystem functioning. However, beyond the simple effects of plant species richness, little is known about how plant diversity and its loss influence higher trophic levels, which are crucial to the functioning of many species-rich ecosystems. We analyzed to what extent woody plant phylogenetic diversity and species richness contribute to explaining the biomass and abundance of herbivorous and predatory arthropods in a species-rich forest in subtropical China. The biomass and abundance of leaf-chewing herbivores, and the biomass dispersion of herbivores within plots, increased with woody plant phylogenetic diversity. Woody plant species richness had much weaker effects on arthropods, but interacted with plant phylogenetic diversity to negatively affect the ratio of predator to herbivore biomass. Overall, our results point to a strong bottom-up control of functionally important herbivores mediated particularly by plant phylogenetic diversity, but do not support the general expectation that top-down predator effects increase with plant diversity. The observed effects appear to be driven primarily by increasing resource diversity rather than diversity-dependent primary productivity, as the latter did not affect arthropods. The strong effects of plant phylogenetic diversity and the overall weaker effects of plant species richness show that the diversity-dependence of ecosystem processes and interactions across trophic levels can depend fundamentally on non-random species associations. This has important implications for the regulation of ecosystem functions via trophic interaction pathways and for the way species loss may impact these pathways in species-rich forests.
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Biodiversity, ecosystem functioning, and classical biological control.
Evans, Edward W
Increasing concern over worldwide loss of biodiversity has led ecologists to focus intently on how ecosystem functioning may depend on diversity. In applied entomology, there is longstanding interest in the issue, especially as regards the importance of natural enemy diversity for pest control. Here I review parallels in interest, conceptual framework, and conclusions concerning biodiversity as it affects ecosystem functioning in general and classical biological control in particular. Whereas the former focuses on implications of loss of diversity, the latter focuses on implications of increase in diversity as additional species of natural enemies are introduced to novel communities in new geographic regions for insect pest and weed control. Many field studies now demonstrate that ecosystem functioning, e.g., as reflected in primary productivity, is enhanced and stabilized over time by high diversity as the community increases in its efficiency in exploiting available resources. Similarly, there is growing field support for the generalization that increasing species and functional diversity of natural enemies leads to increasing pest suppression. Nonetheless a central concern of classical biological control in particular, as it seeks to minimize non-target effects, remains as to whether one or a few species of natural enemies can provide sufficient pest control.
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Influence of Altered Gut Microbiota Composition on Aging and Aging-Related Diseases
Choi, Jeonghyun; Hur, Tai-Young; Hong, Yonggeun
2018-01-01
The gut microbiota forms a large community that coexists with all species, including humans and rodents. Genome projects have been conducted by many researchers in nearly every country to better understand and treat diseases that lead to death in humans. However, the gut microbiota is known as a “second genome” because it includes microbes, genomic DNA, proteins, and metabolites. A large number of studies have revealed the importance of the gut microbiota. In elderly people, the diversity of the gut microbiota is reduced and there is an increased incidence of degenerative diseases, including Alzheimer’s and Parkinson’s, and decreased cognitive and memory functions. However, the administration of pre/probiotics can help to improve the symptoms of these diseases. Therefore, we believe that the gut microbiota is important for maintaining homeostasis and diversity, as well as for avoiding gastrointestinal tract-derived diseases and improving health in the elderly population. PMID:29581954
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Approach to Peripheral Neuropathy for the Primary Care Clinician.
Doughty, Christopher T; Seyedsadjadi, Reza
2018-02-02
Peripheral neuropathy is commonly encountered in the primary care setting and is associated with significant morbidity, including neuropathic pain, falls, and disability. The clinical presentation of neuropathy is diverse, with possible symptoms including weakness, sensory abnormalities, and autonomic dysfunction. Accordingly, the primary care clinician must be comfortable using the neurologic examination-including the assessment of motor function, multiple sensory modalities, and deep tendon reflexes-to recognize and characterize neuropathy. Although the causes of peripheral neuropathy are numerous and diverse, careful review of the medical and family history coupled with limited, select laboratory testing can often efficiently lead to an etiologic diagnosis. This review offers an approach for evaluating suspected neuropathy in the primary care setting. It will describe the most common causes, suggest an evidence-based workup to aid in diagnosis, and highlight recent evidence that allows for selection of symptomatic treatment of patients with neuropathy. Copyright © 2018 Elsevier Inc. All rights reserved.
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NASA Astrophysics Data System (ADS)
Chen, Bingzhang; Smith, Sherwood Lan
2018-02-01
Diversity plays critical roles in ecosystem functioning, but it remains challenging to model phytoplankton diversity in order to better understand those roles and reproduce consistently observed diversity patterns in the ocean. In contrast to the typical approach of resolving distinct species or functional groups, we present a ContInuous TRAiT-basEd phytoplankton model (CITRATE) that focuses on macroscopic system properties such as total biomass, mean trait values, and trait variance. This phytoplankton component is embedded within a nitrogen-phytoplankton-zooplankton-detritus-iron model that itself is coupled with a simplified one-dimensional ocean model. Size is used as the master trait for phytoplankton. CITRATE also incorporates
trait diffusion
for sustaining diversity and simple representations of physiological acclimation, i.e., flexible chlorophyll-to-carbon and nitrogen-to-carbon ratios. We have implemented CITRATE at two contrasting stations in the North Pacific where several years of observational data are available. The model is driven by physical forcing including vertical eddy diffusivity imported from three-dimensional general ocean circulation models (GCMs). One common set of model parameters for the two stations is optimized using the Delayed-Rejection Adaptive Metropolis-Hasting Monte Carlo (DRAM) algorithm. The model faithfully reproduces most of the observed patterns and gives robust predictions on phytoplankton mean size and size diversity. CITRATE is suitable for applications in GCMs and constitutes a prototype upon which more sophisticated continuous trait-based models can be developed. -
Ohm, Robin A.; Feau, Nicolas; Henrissat, Bernard; Schoch, Conrad L.; Horwitz, Benjamin A.; Barry, Kerrie W.; Condon, Bradford J.; Copeland, Alex C.; Dhillon, Braham; Glaser, Fabian; Hesse, Cedar N.; Kosti, Idit; LaButti, Kurt; Lindquist, Erika A.; Lucas, Susan; Salamov, Asaf A.; Bradshaw, Rosie E.; Ciuffetti, Lynda; Hamelin, Richard C.; Kema, Gert H. J.; Lawrence, Christopher; Scott, James A.; Spatafora, Joseph W.; Turgeon, B. Gillian; de Wit, Pierre J. G. M.; Zhong, Shaobin; Goodwin, Stephen B.; Grigoriev, Igor V.
2012-01-01
The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress. PMID:23236275
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Ohm, Robin A.; Feau, Nicolas; Henrissat, Bernard
The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appearsmore » to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress.« less
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NASA Astrophysics Data System (ADS)
de Mar Alguacil, Maria; Torrecillas, Emma; Garcia-Orenes, Fuensanta; Torres, Maria Pilar; Roldan, Antonio
2013-04-01
The arbuscular mycorrhizal fungi (AMF) are a key, integral component of the stability, sustainability and functioning of ecosystems. In this study a field experiment was performed at the El Teularet-Sierra de Enguera Experimental Station (eastern Spain) to assess the influence during a 6-yr period of different agricultural practices on the diversity of arbuscular mycorrhizal fungi (AMF). The management practices included residual herbicide use, ploughing, ploughing + oats, addition of oat straw mulch and a control (land abandonment). Adjacent soil under natural vegetation was used as a reference for local, high-quality soil and as a control for comparison with the agricultural soils under different management practices. The AM fungal small-subunit (SSU) rRNA genes were subjected to PCR, cloning, sequencing and phylogenetic analyses. Thirty-six different phylotypes were identified, which were grouped in four families: Glomeraceae, Paraglomeraceae, Ambisporaceae and Claroideoglomeraceae. The first results showed significant differences in the distribution of the AMF phylotypes as consequence of the difference between agricultural management practices. Thus, the lowest diversity was observed for the plot that was treated with herbicide. The management practices including ploughing and ploughing + oats had similar AMF diversity. Oat straw mulching yielded the highest number of different AMF sequence types and showed the highest diversity index. Thus, this treatment could be more suitable in sustainable soil use and therefore protection of biodiversity.
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Dunfield, Kari E; King, Gary M
2004-07-01
Genomic DNA extracts from four sites at Kilauea Volcano were used as templates for PCR amplification of the large subunit (coxL) of aerobic carbon monoxide dehydrogenase. The sites included a 42-year-old tephra deposit, a 108-year-old lava flow, a 212-year-old partially vegetated ash-and-tephra deposit, and an approximately 300-year-old forest. PCR primers amplified coxL sequences from the OMP clade of CO oxidizers, which includes isolates such as Oligotropha carboxidovorans, Mycobacterium tuberculosis, and Pseudomonas thermocarboxydovorans. PCR products were used to create clone libraries that provide the first insights into the diversity and phylogenetic affiliations of CO oxidizers in situ. On the basis of phylogenetic and statistical analyses, clone libraries for each site were distinct. Although some clone sequences were similar to coxL sequences from known organisms, many sequences appeared to represent phylogenetic lineages not previously known to harbor CO oxidizers. On the basis of average nucleotide diversity and average pairwise difference, a forested site supported the most diverse CO-oxidizing populations, while an 1894 lava flow supported the least diverse populations. Neither parameter correlated with previous estimates of atmospheric CO uptake rates, but both parameters correlated positively with estimates of microbial biomass and respiration. Collectively, the results indicate that the CO oxidizer functional group associated with recent volcanic deposits of the remote Hawaiian Islands contains substantial and previously unsuspected diversity.
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Dunfield, Kari E.; King, Gary M.
2004-01-01
Genomic DNA extracts from four sites at Kilauea Volcano were used as templates for PCR amplification of the large subunit (coxL) of aerobic carbon monoxide dehydrogenase. The sites included a 42-year-old tephra deposit, a 108-year-old lava flow, a 212-year-old partially vegetated ash-and-tephra deposit, and an approximately 300-year-old forest. PCR primers amplified coxL sequences from the OMP clade of CO oxidizers, which includes isolates such as Oligotropha carboxidovorans, Mycobacterium tuberculosis, and Pseudomonas thermocarboxydovorans. PCR products were used to create clone libraries that provide the first insights into the diversity and phylogenetic affiliations of CO oxidizers in situ. On the basis of phylogenetic and statistical analyses, clone libraries for each site were distinct. Although some clone sequences were similar to coxL sequences from known organisms, many sequences appeared to represent phylogenetic lineages not previously known to harbor CO oxidizers. On the basis of average nucleotide diversity and average pairwise difference, a forested site supported the most diverse CO-oxidizing populations, while an 1894 lava flow supported the least diverse populations. Neither parameter correlated with previous estimates of atmospheric CO uptake rates, but both parameters correlated positively with estimates of microbial biomass and respiration. Collectively, the results indicate that the CO oxidizer functional group associated with recent volcanic deposits of the remote Hawaiian Islands contains substantial and previously unsuspected diversity. PMID:15240307
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Lynch-Jordan, Anne M; Sil, Soumitri; Bromberg, Maggie; Ting, Tracy V; Kashikar-Zuck, Susmita
2015-11-01
Juvenile-onset fibromyalgia (JFM) affects physical, social, and emotional functioning. Little is known about how social support and social interactions are impacted in the transition to young adulthood for patients diagnosed with JFM. Young adults (Mage = 21.6) diagnosed with JFM during adolescence (N = 94) and matched healthy controls (N = 33) completed measures of social network size and diversity, perceived social support, physical functioning, and depressive symptoms as part of a cross-sectional survey study. No difference in social network diversity was found, although JFM patients reported fewer total people within their social networks. JFM patients reported poorer emotional and tangible support and fewer positive social interactions than healthy controls. After controlling for condition and pain intensity, the level of perceived social support was a significant predictor of physical functioning and depressive symptoms, whereas social network size also contributed uniquely to physical functioning. Given the developmental importance of social support in adolescence and young adulthood, interventions should include methods of improving social support into fibromyalgia management. Copyright © 2015 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.
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Pillarisetti, Sivaram; Alexander, Christopher W; Khanna, Ish
2009-12-01
Fatty acid amide hydrolase (FAAH) is responsible for the hydrolysis of several important endogenous fatty acid amides (FAAs), including anandamide, oleoylethanolamide and palmitoylethanolamide. Because specific FAAs interact with cannabinoid and vanilloid receptors, they are often referred to as 'endocannabinoids' or 'endovanilloids'. Initial interest in this area, therefore, has focused on developing FAAH inhibitors to augment the actions of FAAs and reduce pain. However, recent literature has shown that these FAAs - through interactions with unique receptors (extracellular and intracellular) - can induce a diverse array of effects that include appetite suppression, modulation of lipid and glucose metabolism, vasodilation, cardiac function and inflammation. This review gives an overview of FAAs and diverse FAAH inhibitors and their potential therapeutic utility in pain and non-pain indications.
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Context-Based Questions: Optics in Animal Eyes
ERIC Educational Resources Information Center
Kaltakci, Derya; Eryilmaz, Ali
2011-01-01
Context is important as a motivational factor for student involvement with physics. The diversity in the types and the functions of animal eyes is an excellent context in which to achieve this goal. There exists a range of subtopics in optics including pinhole, reflection, refraction, and superposition that can be discussed in the context of the…
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Teachers and External Curriculum Consultants: Can They Function Effectively Together?
ERIC Educational Resources Information Center
Mahan, James; And Others
This paper reports on a 2-year field investigation of the frequency and content of interactions between curriculum consultants and elementary school teachers involved in implementing an inquiry-oriented curriculum. The report includes data generated by 45 consultants and 600 teachers in 53 diverse schools. The types of questions teachers ask…
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Adolescents' Anxiety in Dating Situations: The Potential Role of Friends and Romantic Partners
ERIC Educational Resources Information Center
La Greca, Annette M.; Mackey, Eleanor Race
2007-01-01
This study examined adolescents' interpersonal functioning, including the qualities of their closest friendships and romantic relationships, as predictors of dating/heterosocial anxiety. An ethnically diverse sample of 781 adolescents (57% girls; ages 15-19 years) completed measures that assessed the number and type of close friends, the presence…
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ERIC Educational Resources Information Center
La Greca, Annette M.; Harrison, Hannah Moore
2005-01-01
This study examined multiple levels of adolescents' interpersonal functioning, including general peer relations (peer crowd affiliations, peer victimization), and qualities of best friendships and romantic relationships as predictors of symptoms of depression and social anxiety. An ethnically diverse sample of 421 adolescents (57% girls; 14 to 19…
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USDA-ARS?s Scientific Manuscript database
Applications of nanomaterials, including carbon nanotubes (CNTs), are increasing; however, their impact on the environment is still not well understood. A semi-arid soil was treated with multi-walled carbon nanotubes (MWCNTs) at four different concentrations (10-10000 mgMWCNTs kg-1soil), and incubat...
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USDA-ARS?s Scientific Manuscript database
The Middle East-Asia Minor 1 (MEAM1) whitefly, Bemisia tabaci (Gennadius) is an economically important pest of food, fiber, and ornamental crops. This pest has evolved a number of adaptations to overcome physiological challenges, including 1) the ability to regulate osmotic stress between gut lumen ...
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USDA-ARS?s Scientific Manuscript database
The Arthropods are a diverse group of organisms including Chelicerata (ticks, mites, spiders), Crustacea (crabs, shrimps), and Insecta (flies, mosquitoes, beetles, silkworm). The cattle tick, Rhipicephalus (Boophilus) microplus, is an economically significant ectoparasite of cattle affecting cattle...
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Portable Technology Comes of Age
ERIC Educational Resources Information Center
Wangemann, Paul; Lewis, Nina; Squires, David A.
2003-01-01
The PDA was originally conceived of as a portable handheld electronic device that provided a user with a tool to organize his or her life through easy access to a personal calendar, daily planner, and address book. Over the years, these devices have expanded to include many new functions, which have helped more applications in diverse fields. This…
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ERIC Educational Resources Information Center
Parker, Jennifer S.; Benson, Mark J.
2004-01-01
The present study examined parental support and monitoring as they relate to adolescent outcomes. It was hypothesized that support and monitoring would be associated with higher self-esteem and less risky behavior during adolescence. The diverse sample included 16,749 adolescents assessed as part of the National Educational Longitudinal Study.…
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Federal Register 2010, 2011, 2012, 2013, 2014
2013-10-25
... the individual sending the comment (or signing the comment for an association, business, labor union... rudder, controlled by the pilot or copilot sidestick. The digital systems architecture for the Embraer... architecture is used for a diverse set of functions, including: Flight-safety related control and navigation...
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Strategic Engagement: New Models of Relationship Management for Academic Librarians
ERIC Educational Resources Information Center
Eldridge, Jeanette; Fraser, Katie; Simmonds, Tony; Smyth, Neil
2016-01-01
How do we best bridge the gap between the Library and the diverse academic communities it serves? Librarians need new strategies for engagement. Traditional models of liaison, aligning solutions to disciplines, are yielding to functional specialisms, including a focus on building partnerships. This paper offers a snapshot of realignment across the…
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What North America's skeleton crew of megafauna tells us about community disassembly
2017-01-01
Functional trait diversity is increasingly used to model future changes in community structure despite a poor understanding of community disassembly's effects on functional diversity. By tracking the functional diversity of the North American large mammal fauna through the End-Pleistocene megafaunal extinction and up to the present, I show that contrary to expectations, functionally unique species are no more likely to go extinct than functionally redundant species. This makes total functional richness loss no worse than expected given similar taxonomic richness declines. However, where current species sit in functional space relative to pre-anthropogenic baselines is not random and likely explains ecosystem functional changes better than total functional richness declines. Prehistoric extinctions have left many extant species functionally isolated and future extinctions will cause even more rapid drops in functional richness. PMID:28077767