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352 results for “Data Enrichment”
Data from: A phylogenomic approach based on PCR target enrichment and high throughput sequencing: resolving the diversity within the South American species of Bartsia l. (Orobanchaceae)
Advances in high-throughput sequencing (HTS) have allowed researchers to obtain large amounts of biological sequence information at speeds and costs unimaginable only a decade ago. Phylogenetics, and the study of evolution in general, is quickly migrating towards using HTS to generate larger and more complex molecular datasets. In this paper, we present a method that utilizes microfluidic PCR and HTS to generate large amounts of sequence data suitable for phylogenetic analyses. The approach uses the Fluidigm Access Array System (Fluidigm, San Francisco, CA, USA) and two sets of PCR primers to simultaneously amplify 48 target regions across 48 samples, incorporating sample-specific barcodes and HTS adapters (2,304 unique amplicons per Access Array). The final product is a pooled set of amplicons ready to be sequenced, and thus, there is no need to construct separate, costly genomic libraries for each sample. Further, we present a bioinformatics pipeline to process the raw HTS reads to either generate consensus sequences (with or without ambiguities) for every locus in every sample or—more importantly—recover the separate alleles from heterozygous target regions in each sample. This is important because it adds allelic information that is well suited for coalescent-based phylogenetic analyses that are becoming very common in conservation and evolutionary biology. To test our approach and bioinformatics pipeline, we sequenced 576 samples across 96 target regions belonging to the South American clade of the genus Bartsia L. in the plant family Orobanchaceae. After sequencing cleanup and alignment, the experiment resulted in ~25,300bp across 486 samples for a set of 48 primer pairs targeting the plastome, and ~13,500bp for 363 samples for a set of primers targeting regions in the nuclear genome. Finally, we constructed a combined concatenated matrix from all 96 primer combinations, resulting in a combined aligned length of ~40,500bp for 349 samples.
Data from: Trait identity and functional diversity co-drive response of ecosystem productivity to nitrogen enrichment
1. Exploring the mechanisms underlying the change in ecosystem productivity under anthropogenic nitrogen (N) inputs is of fundamental ecological interest. It has been proposed that functional traits, environmental factors, and species richness are central drivers linking ecosystem productivity with environmental change. However, few studies have considered the joint effects of functional traits, environmental factors, and species richness on ecosystem productivity under increasing N inputs. 2. We established a N-manipulation experiment in a Tibetan alpine steppe in 2013. Using structural equation models, we assessed the effects of N-induced changes in environmental factors, species richness, and trait metrics (the mean, variance, skewness and kurtosis of trait distribution) on gross ecosystem productivity as well as three resource use efficiencies (water, light, and phosphorus (P) use efficiencies), based on measurements during the peak growing season in 2016. 3. We found that both light and P use efficiencies decreased under N enrichment, largely due to the N-induced decline in functional diversity of leaf P concentration. However, both gross ecosystem productivity and water use efficiency exhibited initial increases and subsequent slight decreases with N addition. These nonlinear patterns were closely associated with both the increased morphological trait (i.e., mean-leaf area) and decreased diversity of leaf P concentration. 4. Synthesis. Our results illustrate how N-induced changes in functional traits may have dual effects on ecosystem productivity: the stimulating effects of the dominant trait identity via increasing canopy light interception vs. the inhibiting effect of decreasing trait diversity via declining resource use efficiencies. Our results highlight the importance of including functional traits in land surface models to improve predictions of the response of ecosystem function to N inputs.
Data from: Urine is an important nitrogen source for plants irrespective of vegetation composition in an Arctic tundra: insights from a 15N-enriched urea tracer experiment
1. Mammalian herbivores can strongly influence nitrogen (N) cycling and herbivore urine could be a central component of the N cycle in grazed ecosystems. Despite its potential role for ecosystem productivity and functioning, the fate of N derived from urine has rarely been investigated in grazed ecosystems. 2. This study explored the fate of <sup>15</sup>N-enriched urea in tundra sites that have been either lightly or intensively grazed by reindeer for more than 50 years. We followed the fate of the <sup>15</sup>N applied to the plant canopy, at 2 weeks and 1 year after tracer addition, in the different ecosystem N pools. 3. <sup>15</sup>N-urea was rapidly incorporated in cryptogams and in aboveground parts of vascular plants, while the soil microbial pool and plant roots sequestered only a marginal proportion. Further, the litter layer constituted a large sink for the <sup>15</sup>N-urea, at least in the short term, indicating a high biological activity in the litter layer and high immobilization in the first phases of organic matter decomposition. 4. Mosses and lichens still constituted the largest sink for the <sup>15</sup>N-urea 1 year after tracer addition at both levels of grazing intensity demonstrating their large ability to capture and retain N from urine. Despite large fundamental differences in their traits, deciduous and evergreen shrubs were just as efficient as graminoids in taking up the <sup>15</sup>N-urea. The total recovery of <sup>15</sup>N-urea was lower in the intensively grazed sites, suggesting that reindeer reduce ecosystem N retention. 5. <i>Synthesis</i> The rapid incorporation of the applied <sup>15</sup>N-urea indicates that arctic plants can take advantage of a pulse of incoming N from urine. In addition, δ <sup>15</sup>N values of all taxa in the heavily grazed sites converged towards the δ <sup>15</sup>N values for urine, bringing further evidence that urine is an important N source for plants in grazed tundra ecosystems.
Data from: Effects of chronic consumption of sugar-enriched diets on brain metabolism and insulin sensitivity in adult Yucatan Minipigs
Excessive sugar intake might increase the risk to develop eating disorders via an altered reward circuitry, but it remains unknown whether different sugar sources induce different neural effects and whether these effects are dependent from body weight. Therefore, we compared the effects of three high-fat and isocaloric diets varying only in their carbohydrate sources on brain activity of reward-related regions, and assessed whether brain activity is dependent on insulin sensitivity. Twenty-four minipigs underwent 18FDG PET brain imaging following 7-month intake of high-fat diets of which 20% in dry matter weight (36.3% of metabolisable energy) was provided by starch, glucose or fructose (n = 8 per diet). Animals were then subjected to a euglycemic hyperinsulinemic clamp to determine peripheral insulin sensitivity. After a 7-month diet treatment, all groups had substantial increases in body weight (from 36.02±0.85 to 63.33±0.81 kg; P<0.0001), regardless of the diet. All groups presented similar insulin sensitivity index (ISI = 1.39±0.10 mL·min-1·μUI·kg). Compared to starch, chronic exposure to fructose and glucose induced bilateral brain activations, i.e. increased basal cerebral glucose metabolism, in several reward-related brain regions including the anterior and dorsolateral prefrontal cortex, the orbitofrontal cortex, the anterior cingulate cortex, the caudate and putamen. The lack of differences in insulin sensitivity index and body weight suggests that the observed differences in basal brain glucose metabolism are not related to differences in peripheral insulin sensitivity and weight gain. The differences in basal brain metabolism in reward-related brain areas suggest the onset of cerebral functional alterations induced by chronic consumption of dietary sugars. Further studies should explore the underlying mechanisms, such as the availability of intestinal and brain sugar transporter, or the appearance of addictive-like behavioral correlates of these brain functional characteristics.
Data from: An experimental test of the effects of dispersal and the paradox of enrichment on metapopulation persistence
Many species exhibit high-amplitude, extinction-prone cycles, for instance due to resource enrichment (called the paradox of enrichment). How do such species manage to persist? One possibility is metapopulation dynamics, but it is unclear if these can mitigate the paradox of enrichment. The paradox of enrichment might increase local population extinction rates, and might also increase the spatial synchrony of population fluctuations because population cycles are easily synchronized by even low rates of dispersal. Spatially-synchronous population fluctuations would leave no scope for rescue effects, and spatially-synchronous local extinctions would leave no source for recolonization. We conducted a protist microcosm experiment to test how dispersal and enrichment affect the persistence of predator-prey metapopulations by altering spatial synchrony. We assembled 54, 4-patch metapopulations of the protist predator Euplotes patella and its protist prey Tetrahymena pyriformis. Each metapopulation experienced one of nine dispersal rates, crossed with one of 6 enrichment levels. We tested the effects of enrichment and dispersal on predator-prey cycle amplitude, predator population extinction risk, spatial synchrony of predator population fluctuations, and predator metapopulation persistence time. Enrichment increased predator-prey cycle amplitude but had no detectable effect on population extinction risk. Dispersal had no effect on predator-prey cycle amplitude. Spatial synchrony increased with enrichment and dispersal. Metapopulation persistence decreased with enrichment and spatial synchrony. We conclude that increasing enrichment reduced metapopulation persistence primarily by increasing spatial synchrony of local extinctions, rather than by increasing their frequency. These results highlight the importance of synchrony-preventing mechanisms for metapopulation persistence.
Data from: Direct and indirect effects of nitrogen enrichment on soil organisms and carbon and nitrogen mineralization in a semi‐arid grassland
1. Semi-arid grasslands on the Mongolian Plateau are expected to experience high inputs of anthropogenic reactive nitrogen in this century. It remains unclear, however, how soil organisms and nutrient cycling are directly affected by N enrichment (i.e., without mediation by plant input to soil) vs. indirectly affected via changes in plant-related inputs to soils resulting from N enrichment. 2. To test the direct and indirect effects of N enrichment on soil organisms (bacteria, fungi, and nematodes) and their associated C and N mineralization, in 2010 we designated two subplots (with plants and without plants) in every plot of a six-level N-enrichment experiment established in 1999 in a semi-arid grassland. 3. In 2014, 4 years after subplots with and without plant were established, N enrichment had substantially altered the soil bacterial, fungal, and nematode community structures due to declines in biomass or abundance whether plants had been removed or not. N enrichment also reduced the diversity of these groups (except for fungi) and the soil C mineralization rate and induced a hump-shaped response of soil N mineralization. As expected, plant removal decreased the biomass or abundance of soil organisms and C and N mineralization rates due to declines in soil substrates or food resources. 4. Analyses of plant removal-induced changes (ratios of without- to with-plant subplots) showed that microorganisms and C and N mineralization rates were not enhanced as N enrichment increased but that nematodes were enhanced as N enrichment increased, indicating that the effects of plant removal on soil organisms and mineralization depended on trophic level and nutrient status.5. Surprisingly, there was no statistical interaction between N enrichment and plant removal for most variables, indicating that plant-related inputs did not qualitatively change the effects of N enrichment on soil organisms or mineralization. Structural equation modeling confirmed that changes in soil communities and mineralization rates were more affected by the direct effects of N enrichment (via soil acidification and increased N availability) than by plant-related indirect effects. Our results provide insight into how future changes in N-deposition and vegetation may modify below-ground communities and processes in grassland ecosystems.
Data from: A target enrichment method for gathering phylogenetic information from hundreds of loci: an example from the Compositae
Premise of the study: The Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. Methods and Results: We designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family. Conclusions: These methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families.
Data from: Contrasting effects of nutrient enrichment on below-ground biomass in coastal wetlands
Anthropogenically-enhanced nutrient availability is often cited among the most important drivers of altered ecosystem function and loss of services worldwide. Although the above-ground consequences of nutrient enrichment on plant growth patterns are numerous and well-documented, below-ground impacts are less clear but nonetheless critical from a global change perspective. In coastal wetlands, for example, plant-soil-nutrient dynamics directly affect the capacity to sequester carbon as soil organic matter, keep pace with sea level rise, and resist storm-induced erosion. Here, we investigate the effects of excess nutrient loading on below-ground plant growth in an oligohaline marsh fertilized for seven years with a factorial combination of nitrogen (N) and phosphorus (P). We used two common assessment procedures, the ingrowth and standing crop methods, to simultaneously quantify distinct aspects of below-ground plant growth: 1) below-ground biomass accumulation into unexploited open resource space, and 2) in situ, or maintenance, below-ground biomass of plants in equilibrium with their environment, respectively. Our objective was to determine if plant growth responses to nutrient enrichment differed depending on process and/or biomass component measured. We show that excess N concurrently increased live root biomass accumulation in ingrowth cores and reduced in situ live root standing crop. Similar, albeit non-significant, response trajectories were apparent for other below-ground biomass pools using both methods, excepting dead biomass and total standing crop. A review of previously published research supports our results and suggests that nutrient enrichment consistently has contrasting effects on below-ground plant growth depending on whether biomass accumulation or standing crop is measured, and that living biomass components are most responsive to enhanced nutrient availability. Synthesis. We conclude that eutrophic conditions can be both beneficial and detrimental to ecosystem function by either stimulating below-ground biomass accumulation in unexploited soil or reducing the below-ground standing crop required to sustain the nutritional needs of established plants in mature communities. Thus, nutrient enrichment may, in the short-term, contribute to soil organic matter (i.e., carbon) accumulation by increasing below-ground growth as plants exploit new resource space. Over the long-term, however, nutrient enrichment has the potential to negatively impact soil organic matter content as plants equilibrate to excess nutrient availability by down-regulating below-ground standing crop.
Data from: Enriched rearing environment and wild genetic background can enhance survival and disease resistance of salmonid fishes during parasite epidemics
The importance and volume of aquaculture is increasing world-wide. Rearing practices play a key role in determining growth rate, survival and disease resistance in aquaculture fishes. Recent evidence suggests that in comparison with a standard stimulus-poor rearing environment, an enriched or variable rearing environment has significant positive effects on several traits underlying growth and well-being of fish. However, the effect of enriched rearing on one of the most important threats for aquaculture development, occurrence of parasitic infections, remains unknown. We used surveillance data of experimental salmonid populations of wild and hatchery origin under semi-natural parasite exposure to explore effects of enriched rearing on outbreaks of important aquaculture pathogens and associated fish mortalities in production-scale fish densities. We also conducted controlled parasite exposures to investigate if enriched rearing reduces susceptibility of fish to infection in comparison with standard rearing conditions. We found evidence of enriched rearing influencing survival and disease resistance of aquaculture fish during parasite epidemics. Essentially, populations from enriched rearing had a higher survival rate, lower parasite occurrence and greater resistance to most infections compared to fish held in standard rearing conditions. Similarly, fish of wild genetic background had lower mortality during some of the epidemics compared to fish of hatchery origin. However, we also demonstrate significant variation in these patterns and in some cases a tendency for opposite effects of enriched rearing and genetic background depending on the fish species and nature of the epidemic. Synthesis and applications. Our results suggest that parasitic infections and epidemics can be managed through enriched rearing conditions. This may have important implications for economically and ecologically sustainable parasite and disease prevention strategies in aquaculture.
Data from: Anchored hybrid enrichment for massively high-throughput phylogenomics
The field of phylogenetics is on the cusp of a major revolution, enabled by new methods of data collection that leverage both genomic resources and recent advances in DNA sequencing. Previous phylogenetic work has required labor-intensive marker development coupled with single-locus PCR and DNA sequencing on a clade-by-clade and marker-by-marker basis. Here, we present a new, cost-efficient, and rapid approach to obtaining data from hundreds of genes for potentially hundreds of individuals for deep and shallow phylogenetic studies. Specifically, we designed probes for target enrichment of >500 loci in highly-conserved anchor regions of vertebrate genomes (flanked by less conserved regions) from five model species and tested enrichment efficiency in non-model species up to 254 million years divergent from the nearest model. We found that hybrid enrichment using conserved probes (anchored enrichment) can recover a large number of unlinked loci that are useful at a diversity of phylogenetic timescales. This new approach has the potential to not only expedite resolution of deep-scale portions of the Tree of Life but also to greatly accelerate resolution of the large number of shallow clades that remain unresolved. The combination of low cost (~1% of the cost of traditional Sanger sequencing and ~3.5% of the cost of high-throughput amplicon sequencing for projects on the scale of 500 loci x 100 individuals) and rapid data collection (~2 weeks of laboratory time) are expected to make this approach tractable even for researchers working on systems with limited or non-existent genomic resources.
Data from: Soil acidification exerts a greater control on soil respiration than soil nitrogen availability in grasslands subjected to long-term nitrogen enrichment
Terrestrial ecosystems worldwide are receiving increasing amounts of biologically reactive nitrogen (N) as a consequence of anthropogenic activities. This intended or unintended fertilization can have a wide-range of impacts on biotic communities and hence on soil respiration. Reduction in below-ground carbon (C) allocation induced by high N availability has been assumed to be a major mechanism determining the effects of N enrichment on soil respiration. In addition to increasing available N, however, N enrichment causes soil acidification, which may also affect root and microbial activities. The relative importance of increased N availability vs. soil acidification on soil respiration in natural ecosystems experiencing N enrichment is unclear. We conducted a 12-year N enrichment experiment and a 4-year complementary acid addition experiment in a semi-arid Inner Mongolian grassland. We found that N enrichment had contrasting effects on root and microbial respiration. N enrichment significantly increased root biomass, root N content and specific root respiration, thereby promoting root respiration. In contrast, N enrichment significantly suppressed microbial respiration likely by reducing total microbial biomass and changing the microbial community composition. The effect on root activities was due to both soil acidity and increased available N, while the effect on microbes primarily stemmed from soil acidity, which was further confirmed by results from the acid addition experiment. Our results indicate that soil acidification exerts a greater control than soil N availability on soil respiration in grasslands experiencing long-term N enrichment. These findings suggest that N-induced soil acidification should be included in predicting terrestrial ecosystem C balance under future N deposition scenarios.
Data from: PCR-Free enrichment of mitochondrial DNA from human blood and cell lines for high quality next-generation DNA sequencing
Recent advances in sequencing technology allow for accurate detection of mitochondrial sequence variants, even those in low abundance at heteroplasmic sites. Considerable sequencing cost savings can be achieved by enriching samples for mitochondrial (relative to nuclear) DNA. Reduction in nuclear DNA (nDNA) content can also help to avoid false positive variants resulting from nuclear mitochondrial sequences (numts). We isolate intact mitochondrial organelles from both human cell lines and blood components using two separate methods: a magnetic bead binding protocol and differential centrifugation. DNA is extracted and further enriched for mitochondrial DNA (mtDNA) by an enzyme digest. Only 1 ng of the purified DNA is necessary for library preparation and next generation sequence (NGS) analysis. Enrichment methods are assessed and compared using mtDNA (versus nDNA) content as a metric, measured by using real-time quantitative PCR and NGS read analysis. Among the various strategies examined, the optimal is differential centrifugation isolation followed by exonuclease digest. This strategy yields >35% mtDNA reads in blood and cell lines, which corresponds to hundreds-fold enrichment over baseline. The strategy also avoids false variant calls that, as we show, can be induced by the long-range PCR approaches that are the current standard in enrichment procedures. This optimization procedure allows mtDNA enrichment for efficient and accurate massively parallel sequencing, enabling NGS from samples with small amounts of starting material. This will decrease costs by increasing the number of samples that may be multiplexed, ultimately facilitating efforts to better understand mitochondria-related diseases.
Data from: Environmental enrichment normalizes hippocampal timing coding in a malformed hippocampus
Neurodevelopmental insults leading to malformations of cortical development (MCD) are a common cause of psychiatric disorders, learning impairments and epilepsy. In the methylazoxymethanol (MAM) model of MCDs, animals have impairments in spatial cognition that, remarkably, are improved by post-weaning environmental enrichment (EE). To establish how EE impacts network-level mechanisms of spatial cognition, hippocampal in vivo single unit recordings were performed in freely moving animals in an open arena. We took a generalized linear modeling approach to extract fine spike timing (FST) characteristics and related these to place cell fidelity used as a surrogate of spatial cognition. We find that MAM disrupts FST and place-modulated rate coding in hippocampal CA1 and that EE improves many FST parameters towards normal. Moreover, FST parameters predict spatial coherence of neurons, suggesting that mechanisms determining altered FST are responsible for impaired cognition in MCDs. This suggests that FST parameters could represent a therapeutic target to improve cognition even in the context of a brain that develops with a structural abnormality.
Data from: Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite
Background: Phylogenetic heterogeneity across Pseudomonas genus is complemented by its diverse genome architecture enriched by accessory genetic elements (plasmids, transposons, and integrons) conferring resistance across this genus. Here, we sequenced a stress tolerant genotype i.e. Pseudomonas sp. strain RL isolated from a hexachlorocyclohexane (HCH) contaminated pond (45 mg of total HCH g−1 sediment) and further compared its gene repertoire with 17 reference ecotypes belonging to P. stutzeri, P. mendocina, P. aeruginosa, P. psychrotolerans and P. denitrificans, representing metabolically diverse ecosystems (i.e. marine, clinical, and soil/sludge). Metagenomic data from HCH contaminated pond sediment and similar HCH contaminated sites were further used to analyze the pan-genome dynamics of Pseudomonas genotypes enriched across increasing HCH gradient. Results: Although strain RL demonstrated clear species demarcation (ANI ≤ 80.03%) from the rest of its phylogenetic relatives, it was found to be closest to P. stutzeri clade which was further complemented functionally. Comparative functional analysis elucidated strain specific enrichment of metabolic pathways like α-linoleic acid degradation and carbazole degradation in Pseudomonas sp. strain RL and P. stutzeri XLDN-R, respectively. Composition based methods (%codon bias and %G + C difference) further highlighted the significance of horizontal gene transfer (HGT) in evolution of nitrogen metabolism, two-component system (TCS) and methionine metabolism across the Pseudomonas genomes used in this study. An intact mobile class-I integron (3,552 bp) with a captured gene cassette encoding for dihydrofolate reductase (dhfra1) was detected in strain RL, distinctly demarcated from other integron harboring species (i.e. P. aeruginosa, P. stutzeri, and P. putida). Mobility of this integron was confirmed by its association with Tnp21-like transposon (95% identity) suggesting stress specific mobilization across HCH contaminated sites. Metagenomics data from pond sediment and recently surveyed HCH adulterated soils revealed the in situ enrichment of integron associated transposase gene (TnpA6100) across increasing HCH contamination (0.7 to 450 mg HCH g−1 of soil). Conclusions: Unlocking the potential of comparative genomics supplemented with metagenomics, we have attempted to resolve the environment and strain specific demarcations across 18 Pseudomonas gene complements. Pan-genome analyses of these strains indicate at astoundingly diverse metabolic strategies and provide genetic basis for the cosmopolitan existence of this taxon.
Data from: A long PCR based approach for DNA enrichment prior to next-generation sequencing for systematic studies
Premise of the study: We present an alternative approach for molecular systematic studies that combines long PCR and next-generation sequencing (NGS). Our approach can be used to generate templates from any DNA source for NGS. Here we test our approach by amplifying complete chloroplast genomes and we present a set of 58 potentially universal primers for angiosperms to do so. Additionally, this approach is likely to be particularly useful for nuclear regions. Methods and Results: Chloroplast genomes of 30 species across angiosperms were amplified to test our approach. Amplification success varied depending on whether PCR conditions were optimized for a given taxon. To further test our approach, some amplicons were sequenced on an Illumina HiSeq 2000. Conclusions: Although here we tested this approach by sequencing plastomes, long PCR amplicons could be generated using DNA from any genome, expanding the possibilities of this approach for molecular systematic studies.
Data from: Identifying conserved genomic elements and designing universal bait sets to enrich them
Targeted enrichment of conserved genomic regions is a popular method for collecting large amounts of sequence data from non-model taxa for phylogenetic, phylogeographic and population genetic studies. For example, two available bait sets each allow enrichment of thousands of orthologous loci from >20 000 species (Faircloth et al. Systematic Biology, 61, 717–726, 2012; Molecular Ecology Resources, 15, 489–501, 2015). Unfortunately, few open-source workflows are available to identify conserved genomic elements shared among divergent taxa and to design enrichment baits targeting these regions. Those that do exist require extensive bioinformatics expertise and significant amounts of time to use. These shortcomings limit the application of targeted enrichment methods to additional organismal groups. Here, I describe a universal workflow for identifying conserved genomic regions in available genomic data and for designing targeted enrichment baits to collect data from these conserved regions. These methods require less expertise, less time and better use commonly available information to identify conserved loci and design baits to capture them. I apply this computational approach to the understudied arthropod groups Arachnida, Coleoptera, Diptera, Hemiptera or Lepidoptera to identify thousands of conserved loci in each group and design target enrichment baits to capture these loci. I then use in silico analyses to demonstrate that targeted enrichment of the conserved loci can be used to reconstruct the accepted relationships among genome sequences from the focal arthropod orders. The software workflow I created allowed me to identify thousands of conserved loci in five diverse arthropod groups and design sequence capture baits to target them. This suite of capture bait designs should enable collection of phylogenomic data from >900 000 arthropod species. Although the examples in this manuscript focus on understudied arthropod groups, the approach I describe is applicable to all organismal groups having some form of pre-existing genomic information (e.g. other invertebrates, plants, fungi and microbes). Finally, the documentation, design steps, software code and bait sets developed here are available under an open-source license for restriction-free testing, use, and additional modification by any research group.
Data from: Nitrogen enrichment and warming shift community functional composition via distinct mechanisms: the role of intraspecific trait variability and species turnover
<p>1. Global change factors may shift community functional composition by driving species turnover (species occurrence and species relative abundance) and intraspecific trait variability. However, their relative contribution in determining the functional response of community to global change, especially nitrogen enrichment and warming, remains unclear.</p> <p>2. We conducted a fully factorial field experiment in a Tibetan alpine meadow to examine responses of plant community functional composition to nitrogen enrichment and warming by quantifying seven plant functional traits in each plot. Using the sum of squares decomposition, we further disentangled the relative contribution of intraspecific trait variability and species turnover to changes in community functional composition.</p> <p>3. We found that nitrogen enrichment caused a shift of plant community toward a more resource-acquisitive strategy, while warming resulted in a shift toward a more resource-conservative strategy. Plant intraspecific trait variability controls shifts in community functional composition in response to nitrogen enrichment, whereas species turnover (especially change in species relative abundance) mainly explains warming-induced shifts. Nitrogen enrichment and warming did not show significant interactive effects on plant functional composition.</p> <p>4. These findings suggest that nitrogen enrichment and warming can alter community functional composition of alpine meadow through distinct mechanisms. Plant intraspecific trait variability confers functional resilience of Tibetan alpine meadows under nitrogen enrichment, but warming could induce significant turnover of species that pronouncedly impacts community functioning in this highland ecosystem.</p>
Aurora Publications 2022 | 700.000+ records | Enriched with data measuring Societal Relevance, Societal Impact and Scientific Impact, using SDG's, Unpaywall, Altmetric, Scite and Scival
<p>This data set contains 700.000+ publications from all Aurora Universities in the period from the early1700's till mid 2022.</p> <p>Additional tables are added with enrichment data:</p> <ul> <li>Societal Relevance data: <ul> <li>SDG probabilities,</li> </ul> </li> <li>Societal Impact data: <ul> <li>Altmetric Mentions in News, Policy and Patents,</li> <li>Unpaywall Open Access Status,</li> </ul> </li> <li>Scientific Impact data: <ul> <li>Scival Field Weighted Citation Impact</li> <li>Scite Citation Sentiment</li> </ul> </li> </ul> <p>The enrichment tables can be connected to the master table with the publications by DOI, row numbers, university name and SDG label, as follows:</p> <p><a href="https://zenodo.org/api/files/07fb51a8-5b1c-4a2e-8d94-6b9dd540832f/aurora-connecting-tables.png">https://zenodo.org/api/files/07fb51a8-5b1c-4a2e-8d94-6b9dd540832f/aurora-connecting-tables.png</a></p>
Data from: Ultraconserved elements anchor thousands of genetic markers for target enrichment spanning multiple evolutionary timescales
Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota, because UCEs and phylogenetic relationships are well known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2,030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2,386 UCE-anchored loci from nine, non-model avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels.
Data from: Protective role of nano-selenium-enriched Bifidobacterium longum in delaying the onset of streptozotocin-induced diabetes
Bifidobacterium longum (B. longum) could accumulate Selenium (Se) and nano-Se in the form of Se-B. longum and Nano-Se-B. longum, respectively. In this study, the effect of Nano-Se-B. longum in diabetic mice was evaluated. Physiological and metabolic parameters such as blood glucose, body weight, serum insulin level, intraperitoneal glucose tolerance test (IPGTT), food intake, water consumption, and urine output were evaluated. The expression of insulin signaling pathway-related proteins was evaluated by western blotting. Hematoxylin and eosin (H&E) was used for histological examination of the liver, pancreas, and kidney sections. Creatinine levels in serum (SCr) and blood urea nitrogen (BUN) were measured. Nano-Se-B. longum was the best in terms of delaying the onset of diabetes. Nano-Se-B. longum decreased blood glucose and body weight compared with those noted for the model group. IPGTT, food intake, water consumption, and urine output significantly increased and serum insulin levels significantly decreased in the model group compared with those in all the Nano-Se-B. longum-treated mice. Histological results showed that the Nano-Se-B. longum-treated mice were better than the model group mice in terms of pathological changes. The expression of insulin signaling pathway-related proteins was upregulated in the Nano-Se-B. longum-treated groups. A significant increase in SCr and BUN levels was noted in the model group. This study for the first time reported the dose-dependent preventive effect of Nano-Se-B. longum on the onset of diabetes and renal damage. The mechanism may be related to changes in insulin signaling.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.