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Fig. 1. Neighbour-joining phylogenetic tree derived using 16S rRNA gene sequences, showing the relationships between strain HNM0687T in Gordonia mangrovi sp. nov., a novel actinobacterium isolated from mangrove soil in Hainan
Fig. 1. Neighbour-joining phylogenetic tree derived using 16S rRNA gene sequences, showing the relationships between strain HNM0687T and other type strains of the genus Gordonia. Only values above 50% are shown. Asterisks represent clades that were also recovered by the maximum-likelihood and maximum-parsimony methods. Bar, one nucleotide substitution per 100 nucleotides.
Genome sequences of Rhizopogon roseolus, Mariannaea elegans, Myrothecium verrucaria, and Sphaerostilbella broomeana and the identification of biosynthetic gene clusters for fungal peptide natural products
<p>Data to accompany the paper, detailed in manifest.txt</p>
The cDNA sequence data of hox genes in Daphnia similoides sinensis
<p><span><span><span><span><span><span><span><span><span><span><span>Hox genes are important regulatory factors of transcription in metazoans, and are involved in the growth and development of organisms. In this study, the effects of <i><span>Microcystis aeruginosa </span></i>on Hox gene expression in the mothers and offspring of <i><span>Daphnia similoides sinensis</span></i> were investigated using a mixed diet of <i><span>M. aeruginosa</span></i> and <i><span>Scenedesmus obliquus</span></i><i> </i>in two clones. The 14 Hox genes sequence were identified in D<i><span>. similoides sinensisare </span></i>through the previous transcriptome data (Zhang et al., 2016. DOI: 10.1038/srep34241).</span></span></span></span></span></span></span></span></span></span></span></p>
FIGURE 3 in Life-stage association of black flies, using a fast-evolving nuclear gene sequence, and description of the larva of Simulium lampangense Takaoka & Choochote (Diptera: Simuliidae) from Thailand
FIGURE 3. Larva of Simulium lampangense. A. Cephalic apotome, dorsal view. B. Mandible, apex. C. Hypostoma. D. Head capsule showing postgenal cleft, ventral view. Scale bars = 0.1 mm for A and D and 0.05 mm for B and C.
FIGURE 2. Bayesian tree for nuclear elongation complex protein 1 in Life-stage association of black flies, using a fast-evolving nuclear gene sequence, and description of the larva of Simulium lampangense Takaoka & Choochote (Diptera: Simuliidae) from Thailand
FIGURE 2. Bayesian tree for nuclear elongation complex protein 1 (ECP1) sequences of five nominal species and unknown (Unk) larvae in the Simulium multistriatum species group in Thailand. Bootstrap values for neighbor-joining and maximum likelihood and posterior probability of Bayesian analysis are shown above or near the branches. -- denotes bootstrap support less than 50%. Scale bar represents 0.03 substitutions per nucleotide position.
FIGURE 1 in Life-stage association of black flies, using a fast-evolving nuclear gene sequence, and description of the larva of Simulium lampangense Takaoka & Choochote (Diptera: Simuliidae) from Thailand
FIGURE 1. Bayesian tree based on cytochrome c oxidase subunit I (COI) sequences of six nominal species and unknown (Unk) larvae in the Simulium multistriatum species group in Thailand. Bootstrap values for neighbor-joining and maximum likelihood (ML) and posterior probability of Bayesian analysis are shown above or near the branches. -- denotes bootstrap support less than 50%. Scale bar represents 0.03 substitutions per nucleotide position.
Supplementary material 1 from: Yuhui X, Lijun Z, Yue H, Xiaoqi W, Chen Z, Huilun Z, Ruoran W, Da P, Hongying S (2017) Complete mitochondrial genomes from two species of Chinese freshwater crabs of the genus Sinopotamon recovered using next-generation sequencing reveal a novel gene order (Brachyura, Potamidae). ZooKeys 705: 41-60. https://doi.org/10.3897/zookeys.705.11852
Figure S1 : Explanation note: Comparisons of the consensus sequence and variable sites in the entire mNCR for Sinopotamon yaanense, S. yangtsekiense and S. xiushuiense. The conserved central domain is grey shaded, and the extended termination associated sequences (ETAS) is underlined.
Gene annotation of complete genome sequence of Achromobacter sp. strain E1
Open the record for dataset details and reuse information.
Transposon DNA sequences facilitate the tissue-specific gene transfer of circulating tumor DNA between human cells
<p><strong><span>nuc_ctDNA_process</span></strong></p> <p><span>ImageJ 1.x macros and Matlab code for processing 3D nuclear classification and quantification. This repo is designed to help you recreate the methods use in the associated publication. Please don't hesitate to contact if you have questions. Happy to debug, update, etc if there's need.</span></p> <p><strong><span>Lif files:</span></strong></p> <p><span>Use ImageJ 1.x macro in fiji folder to process lif files for subsequent ilastik and Matlab processing. Works with 3 channel data (DAPI, DIC, Rh-Red-X) and 4 channel data (DAPI, Cy5, Rh-Red-X, DIC). Generates .h5 or .tif files for ilastik raining, .jpgs for visualization and ROI overlays, and raw tif files for Matlab analysis.</span></p> <p><strong><span>Macro Usage</span></strong></p> <p><span>Drag and drop; click Run and select .lif of interest. Only 3D data will be included, single layer images will be noted in output. A table of dimensions and max intensities is also created. Save .csv image info, and .txt output log for reference.</span></p> <p><strong><span>Organize Folder Structure</span></strong></p> <p><span>Folders: </span></p> <ul> <li><span>Ilastik output</span></li> <li><span>Nuc</span></li> <li><span>Raw</span></li> <li><span>Roi</span></li> </ul> <p><span> ------------</span></p> <ul> <li><span>Place .h5 nuclear, or .tif nuclear and DIC, and .jpg thumbnail data in subfolder called “nuc”</span></li> <li><span>Place .tif raw data export into subfolder called “raw”</span></li> <li><span>Create subfolders “ilastik output” and “roi”</span></li> <li><span>Ilastik (version 1.3.2post1) trained with ~10-20% of datasets </span></li> <ul> <li><span>Ilastik side note: currently don't know how to share Ilastik projects without getting errors on loading for the given files and filepaths present during creation. You will need to train your own models. See NoPhotonLeftBehind for Ilastik series that includes training tips and details of features used for these data. <a href="https://www.youtube.com/channel/UCRVa5DSphB5gHMaFKPgyKSQ"><span>https://www.youtube.com/channel/UCRVa5DSphB5gHMaFKPgyKSQ</span></a></span></li> </ul> <li><span>Models trained as Pixel Classifications – two classes, background and nucleus</span></li> <li><span>Ilsatik model trained to classify nuclear vs non nuclear – classical thresholding methods found to be less effective due to varying amounts on cytoplasmic DNA stain present.</span></li> <li><span>Single match and mismatch trained using nuclear channel only; double mismatch trained using nuclear and DIC channels together</span></li> <li><span>Data separated and models trained for each cell type due to distinct morphologies, e.g. MM1S model, HCT116 model, etc etc</span></li> <li><span>Probability density files </span></li> <ul> <li><span>Matlab looks for “*_nrmNuc.tiff“ in relative folder “.\ilastik output”, and this is the suffix added in the Fiji macro</span></li> <li><span>In ilastik, set output format to multipage tiff, and select path to .{nickname}.tiff. Note, use path of .{nickname}_nrmNuc.tiff if _nrmNuc is not added during your file collation and logistics to this point. Also note .tiff not .tif</span></li> <li><span>Leave image export settings as default; shape here is, for example, 16, 512, 512, 1, with axis order zyxc and data type float32</span></li> <li><span>In Batch Processing section, select all of the .h5 or .tif files in the “nuc” folder and Process all files</span></li> </ul> <li><span>Matlab UI </span></li> <ul> <li><span>Files Tab: </span></li> <ul> <li><span>Set Root – select folder containing “ilastik output”, “raw”, “roi”, and “nuc”</span></li> <li><span>Filename list will propagate, and Overview text at the top will highlight red if the correct number of files are not present in all folders. (TODO: - run test on error scenario to get instructions)</span></li> <li><span>Sig Num Chns – the total number of channels in the raw data tif files</span></li> <li><span>Rh/Cy5 Sig Chn – the 1 to N based index of the channel to measure inside the nucleus</span></li> <li><span>Rh/Cy5 Bkgd – the number of counts considered as background/cell autoflourescene/non-specific signal during measurements; only voxels with counts above this level will be included in the measurements</span></li> <li><span>ROI Num Chns – total number of channels in the ilastik probability density tiff files</span></li> <li><span>ROI Chn – 1 to N based index of channel to use for generating nuclear 3D ROIs</span></li> <li><span>Thumbnails on/off toggle when selecting images in list</span></li> <li><span>Currently only single or double channel analyses available (signal is measured inside and outside of nucleus 3D ROI)</span></li> <li><span>Click on files to view the nuc jpgs. Click Processing tab to experiment with settings. Note, above channel totals and indices do not currently have error checking. Check correct combinations if you receive tif read errors. Jpgs are loaded on each click, and raw is loaded on switching to Processing tab; expect short delay depending on file size and available disk read speeds.</span></li> <li><span>Open in Explorer button – no prizes for guessing that it opens the selected file in explorer. It defaults to the raw data.</span></li> <li><span>Process All button runs all the files using the settings in place in the Processing Tab. </span></li> <ul> <li><span>A dated folder in roi is created. Inside this folder there are four different types of output file:</span></li> </ul> </ul> <li><span>.bin – a binary mask of the 3D ROI</span></li> <li><span>_dims.bin – the dimensions of the binary mask</span></li> <li><span>.jpg – a thumbnail of ROI overlays</span></li> <li><span>.mat – parameters used for generating the ROIs (open .mat files, and click on the params variable in the Import Wizard to quickly view the relevant parameters) </span></li> <ul> <li><span>Use Masks dropdown: </span></li> <ul> <li><span>For faster re-processing of data with differing minimum number of voxels existing binary masks can be used</span></li> <li><span>Note, resulting .mat file in subsequent output will not reflect the parameters used to generate the binary masks – refer to the original folder (this is noted and will be added to newer versions)</span></li> </ul> <li><span> </span></li> </ul> <li><span>Processing tab: </span></li> <ul> <li><span>FFT % is the amount of Fourier space to keep; lower values retain low frequencies only – empirically determined for best resulting nuclear shape</span></li> <li><span>FFT Smooth value is Gaussian smoothing value in pixels applied to the ellipsoid mask used to retain the central region of Fourier space. Ringing can be seen for values close to 0, increase as needed.</span></li> <li><span>Gauss Smooth is the Gaussian smoothing applied to the raw prob data prior to Otsu thresholding. In noisy classifications thresholding leads to multiple fragmented regions; some smoothing prior to thresholding helps to ‘fuse’ these fragmented regions, prior to 3D FFT spatial filtering to smooth based on size.</span></li> <li><span>FFT xz factor is used to avoid smoothing nuclei in the z direction more than x and y. This value affects the ratio of xy and z of the 3D ellipsoid used to mask Fourier space. Set empirically; Click Run and then View Volume to inspect the z ‘stretch’.</span></li> <li><span>Button group options to apply different combinations of smoothing and FFT spatial filters: </span></li> <ul> <li><span>Gauss – uses Gauss Smooth value above; applied to raw prob data</span></li> <li><span>Otsu – Otsu binary threshold</span></li> <li><span>Fill – Binary fill applied after smooth and binarization</span></li> <li><span>FFT – 3D spatial filtering based on % of Fourier space</span></li> </ul> <li><span>Run, well, runs the analysis</span></li> <li><span>View Volume displays 3D viewer for resulting data set</span></li> <li><span>Min volume slider and value are used to exclude all 3D ROIs smaller than specified value; in voxels. Note slider is linear and plot is log.</span></li> </ul> <li><span>Notes: </span></li> <ul> <li><span>Requires Matlab 2018a or newer</span></li> <li><span>Requires Parallel Computing Toolbox for parfor loop in function ProcessAllButtonPushed. Change parfor to for if not available.</span></li> <li><span> </span></li> </ul> </ul> <li><span>Matlab filelist: </span></li> <ul> <li><span>*.mlapp</span></li> <li><span>import_tif.m</span></li> <li><span>bw_outline_p.m</span></li> <li><span>smth_otsu_fill_p.m</span></li> <li><span>LPFFT3D_p.m</span></li> <li><span>otsu_bw.m</span></li> <li><span>makepsd3.m</span></li> <li><span>ellipsoid_mask.m</span></li> <li><span>bin_load_mask.m</span></li> <li><span>process_ctDNA_table.m</span></li> <li><span>_p refers to passed param struct: </span></li> <ul> <li><span>wid = 3; % width of dilation in outline overlay</span></li> <li><span>pc; % percent of Fourier space to keep - smaller numbers -> more blurred out larger images</span></li> <li><span>pad = 1; % pad Fourier space to the next power of 2</span></li> <li><span>umpx = 0.09; % image pix size</span></li> <li><span>umpz = 0.3; % again in z</span></li> <li><span>fft_smth; % smoothing of the eliptical Fourier space mask</span></li> <li><span>gauss_smth; % sigma of Guass smooth for Guass, Otsu, Fill, BW</span></li> <li><span>scl = [1 1 1/0.3]; % scale ratios for volume viewer</span></li> <li><span>fft_xz_factor; % factor to increase or decrease the amount of z FFT smoothing compared to xy</span></li> <li><span>minvol = 0;</span></li> </ul> </ul> </ul>
Mutant Harmonia axyridis raw sequencing data of CRISPR/Cas9 induced mutations in the genes laccase2 and scarlet
<p><em>Harmonia axyridis</em> (Pallas), commonly known as the Asian lady beetle, is a native insect species of Asia that has been intentionally introduced to various regions for biocontrol purposes. However, its widespread presence beyond its original release sites suggests a high degree of invasiveness. In this study, we utilized the CRISPR-Cas9 approach to achieve precise genome editing in <em>H. axyridis</em>. Specifically, we targeted two genes in <em>H. axyridis</em>, <em>laccase2</em> and <em>scarlet</em>, knockdown of which orthologs in other insects showed visible phenotypic changes. The knockout <em>laccase2</em> resulted in an early-detectable phenotype but also in lethality. However, we successfully established a viable and genetically stable mutant colony by disrupting the <em>scarlet </em>gene, resulting in beetles with white eyes. Our findings contribute to the expanding knowledge of genetic manipulation in <em>H. axyridis</em> and provide insights into its potential for future research and practical applications for biocontrol and invasive species management.</p>
Sequencing data for "Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays"
<p>Illumina and Oxford Nanopore sequencing datasets (in FASTQ format) generated for the manuscript "Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays." Paired-end Illumina MiSeq data are uploaded as two separate files ("r1" and "r2") for each passaged population. BAM files, filtered to exclude reads that did not align to K3L, are provided for passaged populations analyzed in the manuscript.</p>
FIGURE 6 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 6. Distribution of the five species of the N. melanoleuca complex. A full list of voucher specimens beyond those included in multivariate analyses and Appendix 2 is available on request from the first author.
FIGURE 1 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 1. Maximum likelihood mitochondrial phylogeny of the Naja melanoleuca complex. Node support values indicate % bootstrap support; support values for the most distal nodes not shown. Country abbreviations: CAR = Central African Republic, DRC = Democratic Republic of Congo, KZN = KwaZulu-Natal Province, South Africa, RoC = Republic of Congo. Mitochondrial candidate species (CS) are shown in the same colours as in Figures 2–4. For specimen information see Appendix 1.
FIGURE 5 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 5. Naja (Boulengerina) guineensis sp. nov. Left and top right: holotype, MNHN 1921.0485, dorsal and ventral view and side view of head. Note extensive mottling of throat and anterior ventral side and limited posterior extent of lighter ventral markings. Bottom right: live adult specimen measuring approximately 200 cm total length, from Sekondi-Takoradi, Western Region, Ghana, displaying dark suffusion of throat and anterior venter (not preserved; photo L. Chirio).
FIGURE 4 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 4. Ordination of individual specimens and OTU centroids of four of the mitochondrially defined candidate species of the N. melanoleuca complex along the first two canonical variates. CS5-peroescobari was omitted due to the small available sample size. Canonical variates 1 and 2 account for 57.9 and 22.8% of total variance, respectively. Enlarged symbols indicate OTU centroids.
FIGURE 3 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 3. Ordination of individual specimens in a Principal Coordinates Analysis of standardised multilocus distances of PRLR and UBN1 scnDNA sequence data. (a) All specimens; (b) Analysis repeated under exclusion of CS2 and CS3.
FIGURE 8 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 8. Naja (Boulengerina) melanoleuca. Adult specimens from Yaoundé, Cameroon (left—photo J.-F. Trape) and Tsibilé, Gabon (right—photo L. Chirio). Note the diffuse but distinct hood mark that is often present in this species, and the combination of broad main bands and narrow accessory bands on the ventral side.
FIGURE 9 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 9. Naja (Boulengerina) subfulva. Variation in colour and pattern. Top left: specimen from Kakamega, western Kenya, illustrating the typically deep black and white specimens with strong facial markings from the periphery of Lake Victoria. Bottom left: specimen from Chuka, Mount Kenya, Kenya, illustrating an extreme of the brown forebody and reduced facial pigmentation typical of the species in much of its range. Photos W. Wüster, courtesy Royjan Taylor / Bio-Ken snake farm live collection, Watamu, Kenya. Right: specimen from Bamenda, Cameroon, representing the form described by Stucki-Stirn (1979) as Naja melanoleuca aurata. Note the indistinct ventral bands and the lack of accessory ventral bands, as is typical of this species. Photo J.-F. Trape.
FIGURE 7 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 7. Naja (Boulengerina) savannula sp. nov. Top row and bottom left: holotype, MNHN 2018.0002. Bottom right: live specimen from Kindia, Guinea, showing conspicuous, broad dorsal bands and ventral banding, including narrow accessory bands (not vouchered). Photos J.-F. Trape.
FIGURE 2 in Integration of nuclear and mitochondrial gene sequences and morphology reveals unexpected diversity in the forest cobra (Naja melanoleuca) species complex in Central and West Africa (Serpentes: Elapidae)
FIGURE 2. Haplotype networks for single copy nuclear loci. (a) PRLR; (b) UBN1. Small black circles indicate unsampled haplotypes.
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.