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Gut microbiome composition associated with Plasmodium infection in the Eurasian tree sparrow
<p>Recent expansion of microbiome research has uncovered connections between resident microbial communities and blood parasite risk, establishing the potential for microbial disease treatments such as probiotics in the future. However, this field has largely focused on humans and model organisms, leaving much unknown about how microbial communities might directly or indirectly impact parasite infection in wild populations and non-mammals. To contribute to this knowledge base in wild birds, we collected fecal and blood samples from wild Eurasian tree sparrows (<em>Passer montanus</em>) in the United States to test for associations between blood parasite infection and the gut microbiome. We used a widespread molecular approach to test 81 samples from peripheral blood for <em>Plasmodium</em> and <em>Haemoproteus</em>, and we characterized the gut microbiome using fecal samples as a proxy. Neither alpha nor beta diversity significantly varied with detected <em>Plasmodium</em> infection. However, differential abundance analysis highlighted a number of significantly varying bacteria, with the greatest representation within the phyla <em>Proteobacteria</em> and <em>Firmicutes</em> in <em>Plasmodium</em>-infected birds. These differentially abundant taxa offer a starting point for experimental work establishing the relationship between microbial abundance and <em>Plasmodium</em> infection.</p>
Supplementary data of the paper 'Adaptive trends of sequence compositional complexity over pandemic time in the SARS CoV 2 coronavirus'
<p>Supplement of the paper<br> "Adaptive trends of sequence compositional complexity over pandemic time in the SARS-CoV-2 coronavirus”<br> During the spread of the COVID-19 pandemic, the SARS-CoV-2 coronavirus underwent mutation and recombination events that altered its genome compositional structure, thus providing an unprecedented opportunity to check an evolutionary process in real time. The mutation rate is known to be lower than expected for neutral evolution, suggesting natural selection and convergent evolution. We begin by summarizing the compositional heterogeneity of each viral genome by computing its Sequence Compositional Complexity (SCC). To analyze the full range of SCC diversity, we select random samples of high quality coronavirus genomes covering the full span of the pandemic. We then search for evolutionary trends that could inform us on the adaptive process of the virus to its human host by computing the phylogenetic ridge regression of SCC against time (i.e., the collection date of each viral isolate). In early samples, we find no statistical support for any trend in SCC values, although the viral genome appears to evolve faster than Brownian Motion (BM) expectation. However, in samples taken after the emergence of high fitness variants, and despite the brief time span elapsed, a driven decreasing trend for SCC and an increasing one for its absolute evolutionary rate are detected, pointing to a role for selection in the evolution of SCC in the coronavirus. We conclude that the higher fitness of variant genomes may have leads to adaptive trends of SCC over pandemic time in the coronavirus.</p> <p>Supplementary files</p> <table> <tbody> <tr> <td> <p><strong>File</strong></p> </td> <td> <p><strong>Description</strong></p> </td> </tr> <tr> <td> <p>SupplementaryTables S1-S19.zip</p> </td> <td> <p>Excel supplementary tables: The strain name, the collection date, and the SCC values for each analyzed genome.</p> </td> </tr> <tr> <td>nextstrain_ncov_open_global_timetree.nwk</td> <td>ML phylodynamic tree for the Nextstrain sample</td> </tr> <tr> <td> <p>SupplementaryTable S20.pdf</p> </td> <td> <p>A complete list acknowledging the authors, originating and submitting laboratories of the genetic sequences we used for the analysis of the Nextstrain sample.</p> </td> </tr> <tr> <td>Nextstrain_sample_fasta_3059.zip</td> <td>Nextstrain sample (sequences in Fasta format)</td> </tr> <tr> <td> <p>PhylogeneticTimetrees_NewickFormat.zip</p> </td> <td> <p>Phylogenetic timetrees (Newick format).</p> </td> </tr> </tbody> </table> <p> </p>
Fungal community composition and genetic potential regulate fine root decay in northern temperate forests
<p>Understanding how genetic differences among soil microorganisms regulate spatial patterns in litter decay remains a persistent challenge in ecology. Despite fine root litter accounting for ~50% of total litter production in forest ecosystems, far less is known about the microbial decay of fine roots relative to aboveground litter. Here, we evaluated whether fine root decay occurred more rapidly where fungal communities have a greater genetic potential for litter decay. Additionally, we tested if linkages between decay and fungal genes can be adequately captured by delineating saprotrophic and ectomycorrhizal fungal functional groups based on whether they have genes encoding certain ligninolytic class II peroxidase enzymes, which oxidize lignin and polyphenolic compounds. To address these ideas, we used a litterbag study paired with fungal DNA barcoding to characterize fine root decay rates and fungal community composition at the landscape scale in northern temperate forests, and we estimated the genetic potential of fungal communities for litter decay using publicly available genomes. Fine root decay occurred more rapidly where fungal communities had a greater genetic potential for decay, especially of cellulose and hemicellulose. Fine root decay was positively correlated with ligninolytic saprotrophic fungi and negatively correlated with ECM fungi with ligninolytic peroxidases, likely because these saprotrophic and ectomycorrhizal functional groups had the highest and lowest genetic potentials for plant cell wall degradation, respectively. These fungal variables overwhelmed direct environmental controls, suggesting fungal community composition and genetic variation are primary controls over fine root decay in temperate forests at regional scales.</p>
NIR-MFCO dataset: Near-infrared-based false-color images of post-consumer plastics at different material flow compositions and material flow presentations
<p>Determining mass-based material flow compositions (MFCOs) is crucial for assessing and optimizing the recycling of post-consumer plastics. Currently, MFCOs in plastic recycling are mostly determined through manual sorting analysis, but the use of inline near-infrared (NIR) sensors holds potential to automate the characterization process, paving the way for novel sensor-based material flow characterization (SBMC) applications. The NIR-MFCO dataset aims to expedite SBMC research by providing NIR-based false-color images of plastic material flows with their corresponding MFCOs. The false-color images were created through the pixel-based classification of binary material mixtures using a hyperspectral imaging camera (EVK HELIOS NIR G2-320; 990 nm – 1678 nm wavelength range) and the on-chip classification algorithm (CLASS 32). The resulting NIR-MFCO dataset includes <em>n</em> = 880 false-color images from three test series: (T1) high-density polyethylene (HDPE) and polyethylene terephthalate (PET) flakes, (T2a) post-consumer HDPE packaging and PET bottles, and (T2b) post-consumer HDPE packaging and beverage cartons for <em>n</em> = 11 different HDPE shares (0% - 50%) at four different material flow presentations (singled, monolayer, bulk height H1, bulk height H2). The dataset can be used, e.g., to train machine learning algorithms, evaluate the accuracy of inline SBMC applications, and deepen the understanding of segregation effects of anthropogenic material flows, thus further advancing SBMC research and enhancing post-consumer plastic recycling.</p>
Figs 8–10 in A new family Tritogeniidae for the genera Tritogenia and Michalakus, earlier accredited to the composite Microchaetidae (Annelida: Oligochaeta)
Figs 8–10. Tritogenia species: (8) T. shawi Plisko & Zicsi, 1991, material from the area adjacent to the type locality; (9) T. tetrata Plisko, 2003, paratype; (10) T. zuluensis (Beddard, 1907), syntype. Scale bars = 1 cm.
Figs 4–7 in A new family Tritogeniidae for the genera Tritogenia and Michalakus, earlier accredited to the composite Microchaetidae (Annelida: Oligochaeta)
Figs 4–7. Paratypes of (4) Tritogenia curta Plisko & Zicsi, 1991; (5) T. hiltonia Plisko, 2003; (6) T. insolita Plisko, 1997; and (7) T. koilia Plisko, 1997. Scale bars = 1 cm.
Fig. 3 in A new family Tritogeniidae for the genera Tritogenia and Michalakus, earlier accredited to the composite Microchaetidae (Annelida: Oligochaeta)
Fig. 3. Tritogenia sp., live specimens: (A) juvenile; (B) specimen developing tubercula pubertatis. (Photo by H. Grobler)
Fig. 1. Tritogenia sulcata Kinberg, 1867 in A new family Tritogeniidae for the genera Tritogenia and Michalakus, earlier accredited to the composite Microchaetidae (Annelida: Oligochaeta)
Fig. 1. Tritogenia sulcata Kinberg, 1867, type material fragments (NHRS 157; photo by E. Sigvaldadóttir).
Dataset from: The effects of crop type, landscape composition and agroecological practices on biodiversity and ecosystem services in tropical smallholder farms
<p>1. In the tropics, smallholder farming characterizes some of the world's most biodiverse landscapes. Agroecology as a pathway to sustainable agriculture has been proposed and implemented in sub-Saharan Africa, but the effects of agricultural practices in smallholder agriculture on biodiversity and ecosystem services are understudied. Similarly, the contribution of different landscape elements, such as shrubland or grassland cover, on biodiversity and ecosystem services to fields remains unknown.</p> <p>2. We selected 24 villages situated in landscapes with varying shrubland and grassland cover in Malawi. In each village, we assessed biodiversity of eight taxa and ecosystem services in relation to crop type, shrubland and grassland cover and the number of agroecological pest and soil management practices on smallholder's fields of different crop types (bean monoculture, maize-bean intercrop, and maize monoculture).</p> <p>3. Increasing shrubland cover altered carabid and soil bacteria communities. Carabid abundance increased in maize but decreased in intercrop and bean fields with increasing shrubland cover. Carabid abundance and richness and wasp abundance increased with soil management practices. Carabid, spider, and parasitoid abundances were higher in bean monocultures, but this was modulated by surrounding shrubland cover. Natural enemy abundances in beans were especially high in landscapes with little shrubland, possibly leading to lower bean damage in monocultures compared to intercropped fields, whereas maize monocultures had higher damage. In maize, grassland cover and pest management practices were positively related to damage. Carabid abundance was higher in fields with high bean damage and increased carabid richness in fields with high maize damage. Parasitoid abundance was negatively associated with bean damage.</p> <p>4. <em>Synthesis and application:</em> Our results suggest that maintaining biodiversity and ecosystem services on smallholder farms is not achievable with a "one size fits all" approach but should instead be adapted to the landscape context and the priorities of smallholders. Shrubland is important to maintain carabid and soil bacterial diversity, but legume cultivation beneficial to natural enemies could complement pest management in landscapes with a low shrubland cover. An increased number of agroecological soil management practices can lead to improved pest control whilst the effectiveness of agroecological pest management practices needs to be re-evaluated.</p>
IODP Expedition 385 Interstitial water composite report
<p>This composite report includes data from numerous interstitial water (IW) analyses (e.g., ICP-LIQUIDS and IONCHROM) in a variable set of columns. Each row combines the data from several tests (groups of measurements made on the same sample at the same time) for a particular IW sample. If data do not exist for a particular expedition, the column does not appear. To identify individual samples and tests, see each separate analysis (ALKALINITY, ICP-LIQUIDS, IONCHROM, SALINITY, SPEC, TITRATOR, and potentially others). Major and minor elements were determined by inductively coupled plasma-atomic emission spectrocsopy (ICP-LIQUIDS). Cations and anions were measured by ion chromatography (IONCHROM). Complex ions were measured by colorimetric measurements using a UV-VIS spectrometer (SPEC). Alkalinity and chloride was measured by titration (ALKALINITY and TITRATOR). Dissolved carbon (DC), dissolved inorganic carbon (DIC), and dissolved organic carbon (DOC) were measured by combustion in a total organic carbon (TOC) analyzer. Salinity was measured by refractometer (SALINITY). pH was measured by ion-selective electrode as part of the alkalinity procedure and is reported in the ALKALINITY analysis.</p>
IODP Expedition 385 Carbonates composite report
<p>This composite report includes data from two analyses (total carbon from Elemental analysis [CHNS], and inorganic carbon from [Coulometer]). Each row combines the CHNS and Coulometer data from measurements made on the same sample at the same time for a particular section and section offset (depth). If data do not exist for a particular expedition, the column does not appear. To identify individual samples and tests, see each separate data type (Elemental analysis and Coulometer). If the same sample was measured multiple times by any of the methods, results in the report will be combined on one line where possible. Each additional replicate result will be shown in subsequent rows and will be combined where possible. Report includes results for carbon forms: total, inorganic, calcium carbonate, and organic by difference, along with total hydrogen, nitrogen, and sulfur.</p>
IODP Expedition 385 Core composite images
<p>A digital composite image (PNG) is made for each core comprising core sections scanned using a line-scan camera. The composite layout is equivalent to traditional core table photos. Top left is top of core; color and meter rule references are included.</p>
IODP Expedition 385 Whole-round core section composite 360 degree images
<p>Images of the outside of hard rock whole-round sections were acquired using a linescan imager (Section Half Imaging Logger [SHIL]) and a special holder that allows each 90 degree segment of the outer surface to be positioned properly. The images were taken at a resolution of 20 lines/mm (50 micropixels). JRSO staff take these quadrant images and compile them into a side-by-side rollout photograph of the section. Composite images are available as both JPG and TIF image formats. Individual quadrant images are available as JPG images only through this report; contact the <a href="mailto:database@iodp.tamu.edu">IODP-JRSO Data Librarian</a> if quadrant TIF files (~160 MB) are needed.</p>
Compositionally constrained sites drive long branch attraction
<p>Accurate phylogenies are fundamental to our understanding of the pattern and process of evolution. Yet, phylogenies at deep evolutionary timescales, with correspondingly long branches, have been fraught with controversy resulting from conflicting estimates from models with varying complexity and goodness of fit. Analyses of historical as well as current empirical datasets, such as alignments including Microsporidia, Nematoda or Platyhelminthes, have demonstrated that inadequate modeling of across-site compositional heterogeneity, which is the result of biochemical constraints that lead to varying patterns of accepted amino acids along sequences, can lead to erroneous topologies that are strongly supported. Unfortunately, models that adequately account for across-site compositional heterogeneity remain computationally challenging or intractable for an increasing fraction of contemporary datasets. Here, we introduce "compositional constraint analysis", a method to investigate the effect of site-specific amino acid diversity on phylogenetic inference, and show that more constrained sites with lower diversity and less constrained sites with higher diversity exhibit ostensibly conflicting signal under models ignoring across-site compositional heterogeneity and thus contribute to topological bias and long branch attraction artifacts. We demonstrate that more complex models accounting for across-site compositional heterogeneity can ameliorate this bias. We present CAT-PMSF, a pipeline for diagnosing and resolving phylogenetic bias resulting from inadequate modeling of across-site compositional heterogeneity based on the CAT model. CAT-PMSF is robust against long branch attraction in all alignments we have examined. We suggest using CAT-PMSF when convergence of the CAT model cannot be assured. We find evidence that compositionally constrained sites are driving long branch attraction in two metazoan datasets and recover evidence for Porifera as the sister group to all other animals.</p>
Data from: The spatial patterns of community composition, their environmental drivers and their spatial scale dependence vary markedly between fungal ecological guilds
<p><strong><span>Aim</span></strong></p> <p><span>How community composition varies in space and what governs the variation has been extensively investigated in macroorganisms. However, we have only limited knowledge for microorganisms, especially fungi, despite their ecological and economic significance. Based on previous research, we define and test a series of hypotheses regarding the composition of fungal communities, its most influential drivers and their spatial scale dependence. </span></p> <p><strong><span>Location</span></strong></p> <p><span>Czech Republic.</span></p> <p><strong><span>Time period</span></strong></p> <p><span>Present.</span></p> <p><strong><span>Taxa studied</span></strong></p> <p><span>Fungi.</span></p> <p><strong><span>Methods</span></strong></p> <p><span>We analyzed the distance decay relationships, community composition and its drivers (physical distance, litter and soil chemistry, tree composition, climate) in fungi, using multivariate analyses. We compared the results across three fungal ecological guilds (ectomycorrhizal fungi, saprotrophs and yeasts), two forest microhabitats (litter and bulk soil) and six spatial scales (from 5 m to 80 km) that comprehensively cover the Czech Republic.</span></p> <p><strong><span>Results</span></strong></p> <p><span>We found that, similar to macroorganisms, the ectomycorrhizal fungi and saprotrophs showed marked distance-decay relationships</span><span>,</span><span> and their community composition was driven mainly by vegetation and dispersal at local scales, but at regional scales, by environmental effects. In contrast, the third fungal guild, the unicellular yeasts, showed little distance decay, suggesting extraordinary spatial homogeneity, as often seen in microorganisms, such as bacteria.</span></p> <p><strong><span>Main conclusions</span></strong></p> <p><span>Our results underscore the remarkable variation in the community ecology of fungi, which seems to range well-known patterns both from the macro- and the microworld. Knowledge of these patterns advances our understanding of the ecology of fungi, rather understudied organisms of significant ecological and economic importance, which our findings identify as a potentially suitable model for bridging the gaps between the biogeography of micro- and macroorganisms. </span></p>
Cellular composition and circuit organization of mouse locus coeruleus
<p>The locus coeruleus (LC) houses the vast majority of noradrenergic neurons in the brain and regulates many fundamental functions including fight and flight response, attention control, and sleep/wake cycles. While efferent projections of the LC have been extensively investigated, little is known about its local circuit organization. Here, we performed large-scale multi-patch recordings of noradrenergic neurons in adult mouse LC to profile their morpho-electric properties while simultaneously examining their interactions. LC noradrenergic neurons are diverse and could be classified into two major morpho-electric types. While fast excitatory synaptic transmission among LC noradrenergic neurons was not observed in our preparation, these mature LC neurons connected via gap junction at a rate similar to their early developmental stage and comparable to other brain regions. Most electrical connections form between dendrites and are restricted to narrowly spaced pairs or small clusters of neurons of the same type. In addition, more than two electrically coupled cell pairs were often identified across a cohort of neurons from individual multi-cell recording sets that followed a chain-like organizational pattern. The assembly of LC noradrenergic neurons thus follows a spatial and cell type-specific wiring principle that may be imposed by a unique chain-like rule.</p>
A 5 m multi-scale topographic position color composite (MTPCC) across France
<p>The multi-scale topographic position color composite (MTPCC) describes the position of a pixel relative to its neighborhood at several spatial scales. It was derived from the national airborne DTM (RGE ALTI ®) at 5 m spatial resolution, which is available from the website of the French National Geographic Institute (IGN) (<a href="https://geoservices.ign.fr/">https://geoservices.ign.fr/</a>).</p> <p>Dataset includes:</p> <ul> <li>280 GeoTIFF raster files (MTPCC_000.tif) projected in the French Lambert-93 system (EPSG code 2154), each file corresponding to a 50 x 50 km tile. The number indicates the tile of interest ;</li> <li>1 vector tile index at Google Earth format (tile_index.kmz) showing the location of each tile. This file has been created to facilitate download layer only on area of interest.</li> </ul> <p>To reduce storage space and download time, each raster file has been packed at 7-Zip freeware format.</p> <p>A complete description of the dataset can be found in Panhelleux, L., Rapinel, S., Lemercier, B., Gayet, G., Hubert-Moy, L., 2023. A 5 m dataset of digital terrain model derivatives across mainland France. Data in Brief 109369. https://doi.org/10.1016/j.dib.2023.109369</p>
IODP Expedition 396 Carbonates composite report
<p>This composite report includes data from two analyses (total carbon from Elemental analysis [CHNS], and inorganic carbon from [Coulometer]). Each row combines the CHNS and Coulometer data from measurements made on the same sample at the same time for a particular section and section offset (depth). If data do not exist for a particular expedition, the column does not appear. To identify individual samples and tests, see each separate data type (Elemental analysis and Coulometer). If the same sample was measured multiple times by any of the methods, results in the report will be combined on one line where possible. Each additional replicate result will be shown in subsequent rows and will be combined where possible. Report includes results for carbon forms: total, inorganic, calcium carbonate, and organic by difference, along with total hydrogen, nitrogen, and sulfur.</p>
IODP Expedition 396 Interstitial water composite report
<p>This composite report includes data from numerous interstitial water (IW) analyses (e.g., ICP-LIQUIDS and IONCHROM) in a variable set of columns. Each row combines the data from several tests (groups of measurements made on the same sample at the same time) for a particular IW sample. If data do not exist for a particular expedition, the column does not appear. To identify individual samples and tests, see each separate analysis (ALKALINITY, ICP-LIQUIDS, IONCHROM, SALINITY, SPEC, TITRATOR, and potentially others). Major and minor elements were determined by inductively coupled plasma-atomic emission spectrocsopy (ICP-LIQUIDS). Cations and anions were measured by ion chromatography (IONCHROM). Complex ions were measured by colorimetric measurements using a UV-VIS spectrometer (SPEC). Alkalinity and chloride was measured by titration (ALKALINITY and TITRATOR). Dissolved carbon (DC), dissolved inorganic carbon (DIC), and dissolved organic carbon (DOC) were measured by combustion in a total organic carbon (TOC) analyzer. Salinity was measured by refractometer (SALINITY). pH was measured by ion-selective electrode as part of the alkalinity procedure and is reported in the ALKALINITY analysis.</p>
IODP Expedition 396 Core composite images
<p>A digital composite image (PNG) is made for each core comprising core sections scanned using a line-scan camera. The composite layout is equivalent to traditional core table photos. Top left is top of core; color and meter rule references are included.</p>
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.