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Dataset of "Liquid-Jet Photoemission Spectroscopy as a Structural Tool: Site-Specific Acid-Base Chemistry of Vitamin C"
<p>Liquid-jet photoemission spectroscopy (LJ-PES) directly probes the electronic structure of solutes<br>and solvents. It also emerges as a novel tool to explore chemical structure in aqueous solutions, yet<br>the scope of the approach has to be examined. Here, we present a pH-dependent liquid-jet photoelectron<br>spectroscopic investigation of ascorbic acid (vitamin C). We combine core-level photoelectron<br>spectroscopy and ab initio calculations, allowing us to site-specifically explore the acid-base chemistry<br>of the biomolecule. For the first time, we demonstrate the capability of the method to simultaneously<br>assign two deprotonation sites within the molecule. We show that a large change in chemical shift<br>appears even for atoms distant several bonds from the chemically modified group. Furthermore, we<br>present a highly efficient and accurate computational protocol based on a single structure using the<br>maximum overlap method for modeling core-level photoelectron spectra in aqueous environments.<br>This work poses a broader question: To what extent can LJ-PES complement established structural<br>techniques such as nuclear magnetic resonance? Answering this question is highly relevant in view<br>of the large number of incorrect molecular structures published.</p>
Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice: dataset bone marrow HbAA mice injected or not with heme
<p>The objective of this experiment was to explore the transcriptome of the HbSS Townes mouse model of sickle cell disease. Townes model mice carry several human hemoglobin knock-in genes replacing the endogenous mouse genes and may be useful in studying sickle cell disease. All mice were genotyped, age- and sex-matched littermates. All HbAA (control, normal human hemoglobin) vs HbSS (sickle cell disease, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group heterogeneity. Hemin (Ferriprotoporphyrin IX) was purchased from Frontiers Scientific and injected intravenously (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received PBS instead. Mice were anesthetized with isoflurane 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection.</p> <p>This dataset contains the results of the HbAA mice with and without heme.</p> <p>The corresponding HbSS mice with and without heme are deposited under number 10.5281/zenodo.10962782</p> <p>Bone marrow RNA was extracted by Macherey Nagel kit, according to the manufacturer’s instructions. The quality and quantity of mRNA were evaluated using a 2100<br>bioanalyzer with TNA 6000 NanoKits (all Agilent Technologies, Palo Alto, CA, USA). RNA Integrity Numbers superior to 7 were eligible for subsequent reverse transcription into cDNA. RNAseq was performed at the GenomIC plateform Cochin Institute INSERM U1016. After RNA extraction, RNA quality (RNA integrity number) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (Illumina) according to manufacturer instructions. Briefly, purified poly-A containing mRNA molecules were fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the cDNA was followed by ligation of Illumina adapters.<br>Libraries were quantified by qPCR using KAPA Library Quantification Kits for Illumina Libraries (KapaBiosystems, Wilmington, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode. After sequencing, primary analysis based on AOZAN software (ENS, Paris), was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5).</p> <p>The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA PBS, HbAA heme, HbSS PBS, HbSS heme. </p> <p> </p>
Economical routes to size-specific assembly of self-closing structures
<p>This data contains images related to a publication on the self-assembly of DNA origami particles (<a href="https://www.science.org/doi/10.1126/sciadv.ado5979">https://www.science.org/doi/10.1126/sciadv.ado5979</a>). In this work, we conduct self-assembly experiments with various unique subunit types that target two different diameters of tubule structures.</p> <p>We provide image data of tubules that are associated with the probability distributions reported across several figures in the main text. Images of tubules are in the ZIP archives and show the section of tubules we analyzed to produce the probability distributions in the manuscript. Each folder of images has an associated CSV file that relates an image name to the type of tubule that the image was identified as. Tubule types have "m" and "n" values.</p> <p>We provide full tomogram reconstruction data for the multicomponent tubules that are shown in Figure 2 of the main text. In the ZIP archive, each tubule image has two files associated with it: a REC file that contains the tomogram reconstruction data and an MDOC file that contains imaging metadata. REC files can be opened with the open-source software IMOD.</p> <p>We provide raw image data of pitch- and width-controlled tubules that have been labeled with gold nanoparticles. These accompany the representative images in Figure 4 in the main text. (Pitch Controlled 4-color with GNPs.zip, Width Controlled 4-color with GNPs.zip).</p> <p>We provide raw image data of length-controlled tubules. These images accompany Figure 5 in the main text. (Length Controlled Tubule Images.zip)</p> <p><strong>Associated publication citation:</strong></p> <div> <p><span>Thomas E. Videbæk <em>et al., </em></span><span>Economical routes to size-specific assembly of self-closing structures. </span><span><em>Sci. Adv. </em></span><span><strong>10</strong>, </span><span>eado5979 </span><span>(2024). </span><span>DOI:<a href="https://doi.org/10.1126/sciadv.ado5979">10.1126/sciadv.ado5979</a></span></p> </div>
Island-specific evolution of a sex-primed autosome in the planarian Schmidtea mediterranea
<p>The sexual strain of the planarian <em>Schmidtea mediterranea </em>is a hermaphrodite indigenous to Tunisia and several Mediterranean islands. Here, we isolated individual chromosomes and used sequencing, Hi-C and linkage mapping to assemble a chromosome-scale genome reference. The linkage map revealed an extremely low rate of recombination on chromosome 1. We confirmed suppression of recombination on chromosome 1 by genotyping of individual sperm and oocytes. We showed that previously identified genomic regions that maintain heterozygosity even after prolonged inbreeding comprise essentially all of chromosome 1. Genome sequencing of individuals isolated in the wild indicated that this phenomenon has evolved specifically in populations from Sardinia and Corsica. We found that most known master regulators of the reproductive system are located on chromosome 1. We used RNA interference to knock down a gene with haplotype-biased expression and observed that this led to the formation of a more pronounced female mating organ. Based on these observations, we propose that chromosome 1 is a sex-primed autosome primed for evolution into a sex chromosome.</p>
A blood atlas of COVID-19 defines hallmarks of disease severity and specificity: Associated data
<p>This dataset contains raw and processed data from the COvid-19 Multi-omics Blood ATlas (COMBAT) consortium. Data are divided into 26 datasets representing anonymised raw and processed data from deep immune phenotyping of peripheral blood from COVID-19 patients. </p> <p>In addition to the data listed below, some datasets are available through other repositories: </p> <ul> <li> <p>Proteomics data (CBD-KEY-PROTEOMICS) is available at PRIDE</p> <ul> <li> <p>Accession number: PDX023175</p> </li> <li> <p>Contact: Roman Fischer</p> </li> </ul> </li> </ul> <ul> <li> <p>Genetic data and detailed clinical information are available via a data access agreement through EGA</p> <ul> <li> <p>Study accession: EGAS00001005493 </p> </li> </ul> </li> </ul> <p>For further information regarding specific datasets, please contact the individuals listed in Dataset_descriptions.pdf through <a href="mailto:contact@combat.ox.ac.uk">contact@combat.ox.ac.uk</a>. </p>
Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo'orea and their symbionts (Symbiodiniaceae)
<p>GENERAL INFORMATION</p> <p>1. Title of Dataset: Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo'orea and their symbionts (Symbiodiniaceae)</p> <p>2. Author Information<br> A. Principal Investigator Contact Information<br> Name: Scott Burgess<br> Institution: Florida State University<br> Address: 319 Stadium Drive, Tallahassee, FL, USA 32306<br> Email: sburgess@bio.fsu.edu</p> <p><br> 3. Date of data collection (single date, range, approximate date): 2019-08</p> <p>4. Geographic location of data collection: Moorea, French Polynesia</p> <p>5. Information about funding sources that supported the collection of the data: National Science Foundation (NSF; OCE-1829867)</p> <p> </p> <p><br> DATA & FILE OVERVIEW</p> <p>1. File List:<br> Figure 2 Make.R<br> Figure 4 Make.R<br> Figure 5b Make.R<br> Figure 6 Make.R</p> <p>Figure 1 SNAPP species tree.xml<br> Figure 2.txt<br> Figure 2.vcf<br> Figure 3b - Pocillopora mt genomes.nex<br> Figure 4 and 6 data.csv<br> Figure 4 colors.csv<br> Figure 5a - Cladocopium_psbA.nex<br> Figure 5b - Clad clades.csv<br> Figure 5b_Cladocopium.nex<br> Figure 5b_Pocillopora.nex<br> Figure 5b.csv</p> <p><br> 2. Relationship between files:<br> Figure 2 Make.R uses Figure 2.txt and Figure 2.vcf<br> Figure 4 Make.R uses Figure 4 and 6 data.csv and Figure 4 colors.csv<br> Figure 5b Make.R uses Figure 5b - Clad clades.csv, Figure 5b_Cladocopium.nex, Figure 5b_Pocillopora.nex, and Figure 5b.csv<br> Figure 6 Make.R Figure 4 and 6 data.csv</p> <p> </p> <p>3. Metadata</p> <p>Figure 2 Make.R:<br> R code to produce Figure 2, and the accompanying analyses presented in the text, in:<br> Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae).<br> Uses 'Figure 2.txt', 'Figure 2.vcf'</p> <p><br> Figure 4 Make.R:<br> R code to produce Figure 4, and the accompanying analyses presented in the text, in:<br> Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae).<br> Uses 'Figure 4 and 4 data.csv', 'Figure 4 colors'</p> <p><br> Figure 5b Make.R:<br> R code to produce Figure 5b, and the accompanying analyses presented in the text, in:<br> Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae).<br> Uses 'Figure 5b - Clad clades.csv', 'Figure 5b_Cladocopium.nex', 'Figure 5b_Pocillopora.nex', 'Figure 5b.csv'</p> <p><br> Figure 6 Make.R:<br> R code to produce Figure 6, and the accompanying analyses presented in the text, in:<br> Johnston EC, Cunning, Burgess SC. Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo’orea and their symbionts (Symbiodiniaceae).<br> Uses 'Figure 4 and 6 data.csv'</p> <p><br> Figure 1 SNAPP species tree.xml:<br> Data for species tree used in Figure 1</p> <p>Figure 2.txt:<br> Metadata<br> Sample_ID: Sample ID<br> Hap_Spp: Pocillopora species or haplotype</p> <p>Figure 2.vcf:<br> Linked dataset of 7,887 SNPs</p> <p>Figure 3b - Pocillopora mt genomes.nex:<br> Nexus tree of Pocillopora mitochondrial genomes used in Figure 3b</p> <p><br> Figure 4 and 6 data.csv:<br> Metadata<br> Species.haplotype: Pocillopora species or haplotype<br> Depth.m: Sampling depth in meters<br> Site: Sampling site, label corresponds to the site used in the Moorea Coral Reef Long-Term Ecological Research (MCR-LTER) program.<br> Coral.ID: Coral colony identifier<br> Type_profile: ITS2 type profile generated by SymPortal<br> Type_profile_Prop: Proportion of that given ITS2 type profile in colony sampled<br> Remaining columns: Proportion of ITS2 sequences in colony sampled</p> <p>Figure 4 colors.csv:<br> Metadata<br> my_colors: Custom colors for each ITS2 sequence<br> Symbio.clade: ITS2 sequences</p> <p>Figure 5a - Cladocopium_psbA.nex:<br> Nexus tree of Cladocopium taxa in figure 5a</p> <p>Figure 5b - Clad clades.csv:<br> Metadata<br> UCI_links: Sample ID that contains Pocillopora species or haplotype, sample ID, and ITS2 type profile<br> Clad_clades: Clade assignment from figure 5a</p> <p>Figure 5b_Cladocopium.nex:<br> Nexus tree of Cladocopium taxa in Figure 5b</p> <p>Figure 5b_Pocillopora.nex:<br> Nexus tree of Pocillopora taxa used in PACo analysis, Figure 5b</p> <p>Figure 5b.csv:<br> Matrix of Pocillopora host and Cladocopium symbiont links</p>
The pan-genome of Aspergillus fumigatus provides a high-resolution view of its population structure revealing high-levels of lineage-specific diversity driven by recombination
<p><em>Aspergillus fumigatus </em>is a deadly agent of human fungal disease, where virulence heterogeneity is thought to be at least partially structured by genetic variation between strains. While population genomic analyses based on reference genome alignments offer valuable insights into how gene variants are distributed across populations, these approaches fail to capture intraspecific variation in genes absent from the reference genome. Pan-genomic analyses based on <em>de novo</em> assemblies offer a promising alternative to reference-based genomics, with the potential to address the full genetic repertoire of a species. Here, we use a combination of population genomics, phylogenomics, and pan-genomics to assess population structure and recombination frequency, phylogenetically structured gene presence-absence variation, evidence for metabolic specificity, and the distribution of putative antifungal resistance genes in <em>A. fumigatus</em>. We provide evidence for three distinct populations of <em>A. fumigatus</em>, structured by both gene variation (SNPs and indels) and distinct gene presence-absence variation with unique suites of accessory genes present exclusively in each clade. Accessory genes displayed functional enrichment for nitrogen and carbohydrate metabolism, hinting that populations may be stratified by environmental niche specialization. Similarly, the distribution of antifungal resistance genes and resistance alleles were often structured by phylogeny. Despite low levels of outcrossing, <em>A. fumigatus</em> demonstrated a large pan-genome including many genes unrepresented in the Af293 reference genome. These results highlight the inadequacy of relying on a single-reference based approach for evaluating intraspecific variation, and the power of combined genomic approaches to elucidate population structure, genetic diversity, and the putative ecological drivers of clinically relevant fungi.</p> <p>Accompanying manuscript is available as preprint at <a href="https://dx.doi.org/10.1101/2021.12.12.472145">https://dx.doi.org/10.1101/2021.12.12.472145</a> </p> <p>Lotus A. Lofgren, Brandon S. Ross, Robert A. Cramer, Jason E. Stajich. Combined Pan-, Population-, and Phylo-Genomic Analysis of <em>Aspergillus fumigatus</em> Reveals Population Structure and Lineage-Specific Diversity bioRxiv 2021.12.12.472145; doi: https://doi.org/10.1101/2021.12.12.472145</p>
Review of existing modelling studies focusing on specific soil-based ecosystem services (SES) and threats (ST) including climate change, management and land use change scenarios.
<p><span>We </span><span>reviewed existing modelling studies focusing on soil ecosystem services (SES) and soil threats (ST) including climate change, land use change and management scenarios. A publication has been submitted and is currently being reviewed. The title of the manuscript is: </span><span>Assessing and mapping soil ecosystem services and soil threats changes in agroecosystems through scenario-based approaches – a systematic review. </span></p> <p><span>Work was split between various authors. All Co-authors were working on either one or more SES or one ST. Excel sheets were prepared by INRA and BFW to ensure the comparability of results that members extracted from the papers found. Literature search was done in Scopus and Web of Science. The final list of related publications is reported here. <br></span></p>
Crop-specific global fertilizer application rates from "Closing yield gaps through nutrient and water management"
<p>Crop-specific global maps of N, P2O5, and K2O fertilizer application rates circa the year 2000 from the following paper:</p> <p>Mueller, ND, JS Gerber, M Johnston, DK Ray, N Ramankutty, and JA Foley. 2012. Closing yield gaps through nutrient and water management. <em>Nature</em> <strong>490</strong>: 254–257</p> <p>Data are provided at five arc-minute resolution and are saved as netcdf files. Fertilizer application rates are estimated from reconciling various national and subnational data sources. See the Supplementary Information from the 2012 paper for a full description of data sources and methods. Data quality for each grid cell is described in a map layer. Files containing the text "totalcons" sum nutrient consumption across crops per grid cell, using crop harvested areas from Monfreda et al. 2008 Global Biogeochemical Cycles. For maize, wheat, and soybean N application rates, additional maps and csv files (containing the text "politboundaries") identify the political units around the world containing unique information. Crops and crop group categories are consistent with those utilized in Monfreda et al. 2008 Global Biogeochemical Cycles.</p>
Single-molecule DNA methylation patterns of full-length human-specific LINE-1 (L1HS) retrotransposons in a panel of cell lines.
<p>We used bs-ATLAS-seq to comprehensively map the genomic location and assess the DNA methylation status of full-length human-specific LINE-1 elements (L1HS). The approach capture region 1-210 of L1HS elements, which corresponds to the most 5' end of its promoter sequence. This was performed in a panel of 12 human primary or transformed cell lines (BJ, IMR90, MRC5, H1, K562, HCT116, HeLa S3, HepG2, MCF7, HEK-293, HEK-293T, 2102Ep), many being shared with the encode project.</p> <p>These datasets provide a visualization for DNA methylation patterns at the single molecule level for each L1HS loci.</p>
Data set for the journal article: Site-Specific Protein Ubiquitylation Using an Engineered, Chimeric E1 Activating Enzyme and E2 SUMO Conjugating Enzyme Ubc9
<p>Mutations observed in evolved chimeric E1 variants. Top row (1.X to 4.X) describes rounds of evolutions with respective variants in the round. </p> <p>Residues that appear to be enriched are highlighted with gray fill. Star (★) marks residues subjected to saturation mutagenesis in the round 4.</p>
Identification of microbial exopolymer producers in sandy and muddy intertidal sediments by compound-specific isotope analysis.
<p>This dataset supports the version 2 of the paper entitled <em>Identification of microbial exopolymer producers in sandy and muddy intertidal sediments by compound-specific isotope analysis :</em></p> <p><em>Hubas, Cédric; Gaubert-Boussarie, Julie; D’Hondt, An-Sofie; Jesus, Bruno; Lamy, Dominique; Meleder, Vona; Prins, Antoine; Rosa, Philippe; Stock, Willem; Sabbe, Koen. Identification of microbial exopolymer producers in sandy and muddy intertidal sediments by compound-specific isotope analysis. Peer Community Journal, Volume 3 (2023), article no. e104. doi : <a href="https://doi.org/10.24072/pcjournal.336">10.24072/pcjournal.336</a>. <a href="https://peercommunityjournal.org/articles/10.24072/pcjournal.336/">https://peercommunityjournal.org/articles/10.24072/pcjournal.336/</a></em></p>
Augmented emission maps: several petrol and diesel (Euro 5 - 6d-Temp) vehicle-specific augmented emission maps
<p>In order to enable the sharing of data the emission data for vehicles is standardized. The data exchange format contains all data that is applicable for a specific engine taxonomy code.</p> <p>The standardized emission map has a “.map.txt” extension and is also human readable. The files starts with metadata which contains information about:</p> <ul> <li>the engine taxonomy code,</li> <li>total driven kilometers over which the data was gathered,</li> <li>total time in hours over which the data was gathered,</li> <li>the number of vehicles which were tested to create the emission map,</li> <li>the DOI (Digital Object Identifier) reference,</li> <li>Which emission maps are available in the file.</li> </ul> <p>The DOI <a href="http://doi.org/10.5281/zenodo.4268034">10.5281/zenodo</a> refers to a meta-data document that provides the full description of the standardized emission map</p>
Aligned bam files for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits"
<p>Aligned bam files used for analysis in "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits".</p> <p>This is an accompanying dataset to Datasets and code for "Phylogenetic modeling of enhancer shifts in mole-rats reveals regulatory changes associated with tissue-specific traits" (https://zenodo.org/record/7442105).</p>
Phylogenetic and epidemiologic data relating to age-specific HIV incidence and transmission in Rakai, Uganda, 2003-2018.
<p>This repository contains the data for the analyses presented in the paper Growing gender inequity in HIV infection in Africa: sources and policy implications by M. Monod, A. Brizzi, R. Galiwango, R. Ssekubugu, Y. Chen, X. Xi et al. available in the pre-print <a href="https://doi.org/10.1101/2023.03.16.23287351">https://doi.org/10.1101/2023.03.16.23287351</a> </p> <p>We thank all contributors, program staff and participants to the Rakai Community Cohort Study; all members of the PANGEA-HIV consortium, the <a href="https://www.rhsp.org/index.php">Rakai Health Sciences Program</a>, and CDC Uganda for comments on an earlier version of the manuscript.</p> <p>We also extend our gratitude to the <a href="https://doi.org/10.14469/hpc/2232">Imperial College Research Computing Service</a> and the <a href="https://www.bdi.ox.ac.uk/about/biomedical-research-computing">Biomedical Research Computing Cluster</a> at the University of Oxford for providing the computational resources to perform this study. Additionally, we thank the Office of Cyberinfrastructure and Computational Biology at the <a href="https://www.niaid.nih.gov/">National Institute for Allergy and Infectious Diseases</a> for data management support; and Zulip for sponsoring team communications through the Zulip Cloud Standard chat app. </p> <p>All analysis code is available from <a href="https://github.com/MLGlobalHealth/phyloSI-RakaiAgeGender">https://github.com/MLGlobalHealth/phyloSI-RakaiAgeGender</a>.</p>
Allele-specific quantitation of ATXN3 and HTT transcripts in polyQ disease models.
<p>Precise values obtained during the research that led to the publishing of scientific paper entitled 'Allele-specific quantitation of ATXN3 and HTT transcripts in polyQ disease models'.</p>
Measurements of water column specific conductivity, salinity, dissolved oxygen, chlorophyll, temperature, and pH by deployed datasondes every 20 minutes for several periods during the summertime in 2017-2020
West Falmouth Harbor (West Falmouth, MA, USA) has been experiencing a dramatic increase in nitrogen loading from an upgradient municipal wastewater treatment facility since the early 2000's. As part of a long-term study into the effects of this nitrogen enrichment, we have measured water column parameters at 20 minute intervals in two locations within West Falmouth Harbor (West Falmouth, MA, USA), one in the well-flushed outer basin and one in the inner basin closer to the dominant groundwater N source. The goal of this dataset is to compare conditions at the two sites, as well as to derive rates of metabolism. Parameters measured include temperature, specific conductivity, salinity, dissolved oxygen, chlorophyll, and pH. YSI Datasondes were deployed during 4 periods ranging from 6 to 11 days in July and August, suspended vertically from a surface buoy. Over all deployments, instruments passed all QA checks, and average differences between the two instruments over all deployments were less than 0.06 degrees C (temperature), 0.3 (salinity), 0.05 (pH), 1.0 µg/L (chlorophyll), 1.5 (%DO Saturation). Data provided here are not corrected for drift, and chlorophyll data are uncorrected as reported by the instruments. Chlorophyll reported is uncorrected from the YSI calculation based on in-situ fluorescence and calibration with a single-point using deionized water. Lab fluorometric analysis checks show that the YSI chlorophyll is over-reporting by at least 20% at low concentrations, and high concentrations were not able to be validated. Methodology details and analysis of earlier data can be found in Howarth et al 2014, "Metabolism of a nitrogen-enriched coastal marine lagoon during the summertime," doi:10.1007/s10533-013-9901-x
Carbon dioxide response curve, dark respiration, specific leaf area, and leaf nitrogen data for the 2014 Eriophorum vaginatum reciprocal transplant gardens at Toolik Lake and Sagwon, AK, collected in 2016.
Transplant gardens at Toolik Lake and Sagwon were established in 2014. At each location, 60 tussocks each from ecotypes of Eriophorum vaginatum from Coldfoot (CF, 67°15′32″N, 150°10′12″W), Toolik Lake (TL, 68°37′44″N, 149°35′0″W), and Sagwon (SAG, 69°25′26″N, 148°42′49″W) were transplanted. Half the transplanted tussocks were grown under ambient conditions, while the other half were exposed to passive warming supplied by open-top chambers (OTC). Data were collected in late June through July 2016 include carbon dioxide response curve data, dark respiration, specific leaf area, and leaf nitrogen content.
Sex-specific relationships between urbanization, parasitism, and plumage coloration in house finches
Historically, studies of condition-dependent signals in animals have been male-centric, but recent work suggests that female ornaments can also communicate individual quality (e.g., disease state, fecundity). There also has been a surge of interest in how urbanization alters signaling traits, but we know little about if and how cities affect signal expression in female animals. We present data of carotenoid-based plumage coloration and coccidian (Isospora spp.) parasite burden in desert and city populations of house finches Haemorhous mexicanus to examine links between urbanization, health state, and feather pigmentation in males and females. In earlier work, we showed that male house finches are less colorful and more parasitized in the city, and we again detected such patterns in this study for males; however, urban females were less colorful, but not more parasitized, than rural females. Moreover, contrary to rural populations, we found that urban birds (regardless of sex) with larger patches of carotenoid coloration were also more heavily infected with coccidia. These results show that urban environments can disrupt condition-dependent color expression and highlight the need for more studies on how cities affect disease and signaling traits in both male and female animals.
SMB01 Variation in soil respiration and bacterial community due to species-specific plant-soil history at konza prairie
We conducted a “home vs. away” plant-soil feedback greenhouse experiment using two C3 grass species (Bromus inermis and Pascopyrum smithii) grown in soil collected from Konza Prairie. We used a closed-circuit CO2 trapping method and isotopic analysis to differentiate between root-derived and SOM-derived CO2 production. We investigated how soil chemistry and soil bacterial communities differed in soils with a history of B. inermis vs soils with a history of P. smithii.
ScienceDex guides
Understand access before you commit
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.