Find research datasets worth reusing

FIGURE 7. Bythotrephes transcaucasicus Behning, 1941 in Redescription of Bythotrephes arcticus Lilljeborg, 1901 (Crustacea: Cladocera: Onychopoda) and confirmation of an independent species status of the distant Transcaucasian populations of the genus Bythotrephes Leydig

FIGURE 7. Bythotrephes transcaucasicus Behning, 1941, parthenogenetic females, Lake Chaldyr (Turkey), 1879. A, general lateral view. B, antennule. C, upper antennal branch. D, lower antennal branch. E, apical end of upper antennal branch. F, apical end of lower antennal branch. G, thoracic limb of first pair (tl I). H, distal part of pseudognathobase of tl I. I, J, distal setae of first segment of endopodite of tl I. K, L, distal setae of second segment of endopodite of tl I. M, postabdomen and proximal part of caudal process. N, distal part of caudal process. O, apical setae of caudal process.

FIGURE 8. Bythotrephes transcaucasicus Behning, 1941 in Redescription of Bythotrephes arcticus Lilljeborg, 1901 (Crustacea: Cladocera: Onychopoda) and confirmation of an independent species status of the distant Transcaucasian populations of the genus Bythotrephes Leydig

FIGURE 8. Bythotrephes transcaucasicus Behning, 1941, parthenogenetic females, Lake Chaldyr (Turkey), 1879. A, B, outer distal parts of protopodites of tl I–tl III (from right to left). C, thoracic limb of second pair (tl II). D, pseudognathobase of tl II, E, thoracic limb of third pair (tl III). F, pseudognathobase of tl III, G, thoracic limb of fourth pair (tl IV). H, pseudognathobase of tl IV. I, J, K, claws of postabdomen and caudal spine. L, posterior part of trunk with a line separating third abdominal segment and postabdomen (arrowed).

FIGURE 9 in Redescription of Bythotrephes arcticus Lilljeborg, 1901 (Crustacea: Cladocera: Onychopoda) and confirmation of an independent species status of the distant Transcaucasian populations of the genus Bythotrephes Leydig

FIGURE 9. Geographical distribution of Bythotrephes arcticus (black circles with "?", localities with atypical specimens; SK, locality Sabanty-Kul in Northern Kazakhstan) and B. transcaucasicus (asterisk)

FIGURE 5 in Redescription of Bythotrephes arcticus Lilljeborg, 1901 (Crustacea: Cladocera: Onychopoda) and confirmation of an independent species status of the distant Transcaucasian populations of the genus Bythotrephes Leydig

FIGURE 5. Bythotrephes arcticus Lilljeborg, adult parthenogenetic females (A, lake 1 (basin of the River Tchernaya, Bol'shezemelskaya tundra, Arkhangel'skaya region, North-Eastern European Russia); B, E, Lake Sabanty Kul, Akmolinskaya region (Kazakhstan); C, lake near village Puiko, Yamal Peninsula (Western Siberia, Russia); D, F, Forellenmägen (Norway); G, Pustozersk (Arkhangel'skaya region, North-East of European Russia); H, Råbosjön (Hls, Sweden); I, tundra near mouth of the River Pechera (Bol'shezemelskaya tundra, Arkhangel'skaya region, North-Eastern European Russia); J, K, Karabel'naya bay ("Karabella"), Kola Peninsula, Russia), Lake Dubovskoi (Bol'shezemelskaya tundra, Arkhangel'skaya region, North-Eastern European Russia)). A–K, variability of postabdominal claws and claws of caudal process. L, postabdomen and proximal part of caudal process with two sclerotized sections (dotted).

FIGURE 4 in Redescription of Bythotrephes arcticus Lilljeborg, 1901 (Crustacea: Cladocera: Onychopoda) and confirmation of an independent species status of the distant Transcaucasian populations of the genus Bythotrephes Leydig

FIGURE 4. Bythotrephes arcticus Lilljeborg, adult parthenogenetic females, lake 1 (basin of the River Tchernaya, Bol'shezemelskaya tundra, Arkhangel'skaya region, North-Eastern European Russia). A, anterior seta of second segment of endopodite of thoracic limb of third pair (tl III) (C, see Fig. 2). B, proximal part of anterior terminal seta of tl III (D, see Fig. 2). C, armament of posterior subterminal seta of tl III (G, see Fig. 2). D, distal part of pseudognathobase of tl III (pore is arrowed). E, outer terminal seta of tl IV (L, see Fig. 2). F, inner terminal seta of tl IV. G, pseudognathobase of tl IV (pore is arrowed). H, distal part of mandible. I, "postabdomen" and proximal part of caudal process (abd = posterior abdominal segment, p/abd = postabdomen). J, mandibular maxillar process. K, papillae of maxillar process. Scale bars: I =250 µm; H = 50 µm; A, D, E = 25 µm; B, C, F, G =20 µm; J = 10 µm; K= 5 µm.

FIGURE 2 in Redescription of Bythotrephes arcticus Lilljeborg, 1901 (Crustacea: Cladocera: Onychopoda) and confirmation of an independent species status of the distant Transcaucasian populations of the genus Bythotrephes Leydig

FIGURE 2. Bythotrephes arcticus Lilljeborg, adult parthenogenetic females, lake 1 (basin of the River Tchernaya, Bol'shezemelskaya tundra, Arkhangel'skaya region, North-Eastern European Russia). A, thoracic limb of second pair (tl II) (small letters indicate the respective type of setae). B, anterior lateral seta of first segment of endopodite of tl II. C, anterior distal seta of second segment of endopodite of tl II. D, anterior terminal seta of endopodite of tl II. E, anterior subterminal seta of endopodite of tl II. F, posterior terminal seta of endopodite of tl II. G, posterior subterminal seta of endopodite of tl II. H, thoracic limb of third pair (tl III). I, thoracic limb of fourth pair (tl IV) (inner view). J, distal seta of protopodite of tl IV. K, inner lateral seta of distal segment of tl IV. L, outer seta of distal segment of tl IV. M, outer distal parts of protopodites of tl I–tl III.

FIGURE 6 in Redescription of Bythotrephes arcticus Lilljeborg, 1901 (Crustacea: Cladocera: Onychopoda) and confirmation of an independent species status of the distant Transcaucasian populations of the genus Bythotrephes Leydig

FIGURE 6. Bythotrephes arcticus Lilljeborg, males (A–I) and parthenogenetic female of first generation (J, K); (A, I, swamps of Kildin Island (Murmansk region, Russia); B, C, H, Lake Dubovskoi (Bol'shezemelskaya tundra, Arkhangel'skaya region, North-Eastern European Russia); D, Karesuando (Norrbotten, Sweden); E, Porsanger lake (Norway); F, Karabel'naya bay ("Karabella"), Kola Peninsula, Russia); G, Forellenmägen (Norway); J, K, Alexandrovsk (Kola Peninsula, Russia)). A, male, general lateral view. B, male's hook. C–G, claws of postabdomen and caudal spine. H, I, copulatory appendage. J, thoracic limb of first pair (tl I). K, postabdomen and caudal spine with claws.

FIGURE 1 in Redescription of Bythotrephes arcticus Lilljeborg, 1901 (Crustacea: Cladocera: Onychopoda) and confirmation of an independent species status of the distant Transcaucasian populations of the genus Bythotrephes Leydig

FIGURE 1. Bythotrephes arcticus Lilljeborg, adult parthenogenetic females and juveniles. A–G, I, K–M: lake 1 (basin of River Tchernaya, Bol'shezemelskaya tundra, Arkhangel'skaya region, North-Eastern European Russia). H: Lake Yan (basin of the River Pur, Western Siberia), J: Forelenmägen (Norway). A, general lateral view. B, antennule. C, upper lip (labrum) with anterior process. D, apical end of lower antennal branch, outer side. E, apical end of upper antennal branch, inner side. F, seta on apical end of upper antennal branch, outer side. G, distal part of caudal process. H, terminal setae of caudal process (juvenile specimen). I, thoracic limb of first pair (tl I) (C, anterior setae, see Fig. 2). J, armament of first segment and second segment of endopodite of tl I. K, distal setae of first segment of endopodite of tl I. L, distal end of second segment of endopodite of tl I. M, the same (juvenile specimen).

FIGURE 3 in Redescription of Bythotrephes arcticus Lilljeborg, 1901 (Crustacea: Cladocera: Onychopoda) and confirmation of an independent species status of the distant Transcaucasian populations of the genus Bythotrephes Leydig

FIGURE 3. Bythotrephes arcticus Lilljeborg, adult parthenogenetic females, lake 1 (basin of the River Tchernaya, Bol'shezemelskaya tundra, Arkhangel'skaya region, North-Eastern European Russia). A, thoracic limbs, general view. B, pseudognathobase of thoracic limb of first pair (tl I). C, anterior lateral setae of first segment of endopodite of tl I (C, see Fig. 2). D, armament of anterior lateral seta of first segment of endopodite of tl I (C, see Fig. 2). E, armament of posterior distal seta of first segment of endopodite of tl I. F, armament of terminal seta of tl I. G, anterior and posterior lateral setae of first segment of endopodite of thoracic limb of second pair (tl II). H, armament of distal part of anterior lateral seta of endopodite of tl II (B, see Fig. 2). I, distal anterior seta of first segment of endopodite of tl II (C, see Fig. 2). J, anterior subterminal seta of tl II (E, see Fig. 2). K, proximal part of anterior terminal seta of tl II (D, see Fig. 2). L, distal part of pseudognathobase of tl II (pore is arrowed). Scale bars: A = 250 µm; G, J = 50 µm; B, C, F, I, K, L = 25 µm; D, E, H =10 µm.

opencc-by-4.0Mar 2017View details →

Datasets for "An Evaluation of Bayesian Approaches based on Uniformly Most Powerful Tests for Detecting Violations of Local Independence"

<p>These files contain the results of the simulation studies reported in the main text. A detailed documentation is included as pdf file.</p>

opencc-by-4.0Aug 2024View details →

Family life and cadmium ingestion independently shape offspring microbiomes in a subsocial insect

<h1>READ ME</h1> <p>This repositery contains all dataset that allow to reproduce this study (16S rRNA sequences in .fastq format, the R script and the informative file related with the samples (env_succession.txt). It also contains Supplemental material to complete the related manuscript.</p> <h2>1) The file "cd_data.txt" </h2> <p>It contains the informations regarding the samples. The description of the variables follows:</p> <ul> <li>ID: The identifiant of the sample (host)</li> <li>Clutch: The name of the family</li> <li>Treatment: The cadmium doses that had been administered (0, 25 or 100 mg/L)</li> <li>Group_nymph: social environment of the nymph where nymph are either isolated, with sibling (10 nymphs) or in family (10 nymphs with their mother).</li> </ul> <h2>2) The file "Cadmium_script.R" </h2> <p>This script allows to perform all the bioinformatical process and analyses that were made for this study. It was made on R version 4.4. This script needs the source code provided by the "<strong>make_biom.R</strong>" code that will need to be downloaded in the "reference_database" the script creates (but see the Cadmium_script).</p> <h2>3) The RData objects</h2> <p>We publish the R objects (phyloseq objects) that allow to perform all statistical analyses from the initial object "<strong>ps_proka.RData</strong>" or directly after the core calculation "<strong>core.RData</strong>". It avoids to perform all bioinformatical steps to process the sequences.</p> <h2>4) The file "R1R2.zip"</h2> <p>This folder zip contains all sequence at fastq format. These sequences are from the V3-V4 of the 16S rRNA genes sequenced by Illumina MiSeq 2x250 bp.</p> <h2>5) The file "Supplemental Material.pdf"</h2> <p>This document contains all supplemental tables and figures related with our study. Specifically,</p> <ul> <li><strong>Table S1:</strong> Results of the DESeq2 analysis regarding the effects of the cadmium ingestion and the social environment.</li> <li><strong>Figure S1: </strong>Electrophoresis gel (agarose 1.5%) of the 16S rRNA amplicons.</li> <li><strong>Figure S2: </strong>Species-Abundance Distribution (SAD) patterns for the microbial ASVs of the European earwig nymphs.</li> <li><strong>Figure S3:</strong> Rarefaction curves for each nymph microbiome, depending on its social environment.</li> <li><strong>Figure S4:</strong> <span lang="EN-GB">Alpha and beta-diversity</span><span lang="EN-GB"> of the nymph microbiomes.</span></li> </ul>

opencc-by-4.0Sep 2023View details →

A histone methyltransferase-independent function of PRC2 controls small RNA dynamics during programmed DNA elimination in Paramecium

<p><span lang="EN-US">To limit transposable element (TE) mobilization, most eukaryotes have evolved small RNAs to silence TE activity via homology-dependent mechanisms. Small RNAs, 20-30 nucleotides in length, bind to PIWI proteins and guide them to nascent transcripts by sequence complementarity, triggering the recruitment of histone methyltransferase enzymes on chromatin to repress the transcriptional activity of TEs and other repeats. In<span> the ciliate <em>Paramecium tetraurelia</em>,</span> 25-nt scnRNAs corresponding to TEs recruit Polycomb Repressive Complex 2 (PRC2), and trigger their elimination during the formation of the somatic nucleus. Here, we sequenced sRNAs during the entire sexual cycle with unprecedented resolution. Our data confirmed that scnRNAs are produced from the entire germline genome, from TEs and non-TE sequences, during meiosis. Non-TE scnRNAs are selectively degraded, which results in the specific selection of TE-scnRNAs. We demonstrate that PRC2 is essential for the selective degradation of non-TE-scnRNAs, independently of its histone methyltransferase activity. We further show that the PRC2 cofactor Rf4 mediates the physical interaction between the scnRNA-binding protein Ptiwi09 and the zinc finger protein Gtsf1, pointing to an architectural role of PRC2 in scnRNA degradation.</span></p>

opencc-by-4.0Oct 2023View details →

Sequence-independent, site-specific incorporation of chemical modifications to generate light-activated plasmids (Source Data)

<p>Source data for Chemical Science paper "Sequence-independent, site-specific incorporation of chemical modifications to generate light-activated plasmids" DOI: 10.1039/D3SC02761A</p>

opencc-by-4.0Dec 2023View details →

Clustering-independent estimation of cell abundances in bulk tissues using single-cell RNA-seq data

<p>ConDecon is a clustering-independent method for inferring the likelihood for each cell in a single-cell dataset to be present in a bulk tissue. This repository contains the raw data of the benchmarking analyses presented in the original publication using the pipeline of Avila-Cobos et al. (10.1038/s41467-020-19015-1). We used this pipeline to evaluate the ability of ConDecon and 17 other deconvolution methods to infer discrete cell type abundances in bulk tissues. The compressed file in this repository contains the synthetic bulk data, ground truth cell type proportions, and the predicted cell type proportions for each method and dataset associated with these analyses. Additional details can be found in the Methods section of the ConDecon publication.</p>

opencc-by-4.0Mar 2024View details →

Independent variable importance

<p>Independe variables importances (<em>MYC</em>,<em> BCL2</em>,<em> </em>and <em>BCL6 </em>MLP analysis)</p>

Fig. 4 in Increase in isoflavonoid content in Glycine max cells transformed by the constitutively active Ca independent form of the AtCPK1 gene

Fig. 4. Expression of the G. max genes (a) - of the upstream enzymes - 4- coumarate:CoA ligase (4CL), (b) – of the downstream enzymes - isoflavones synthase (IFS) and the final step of daidzein and genistein biosynthesis - 2- hydroxyisoflavanone dehydratase (HID) and (c) - enzymes involve in prenilation of daidzein and coumestrol - isoflavone dimethylallyltransferase (IDT1) and coumestrol 4-dimethylallyltransferase (C4DT) in the control callus culture (Gm) and callus line transformed with the constitutively active AtCPK1 (GmCa1 and GmCa2). Data (mean ± standard error) represent measurements of three independent replicates from two different RNA isolations and are presented as relative expression levels normalized to the expression of the G. max housekeeping genes. Different letters above the bars indicate statistically significant differences of means (P <0.05), Fisher's LSD.

Fig. 2. A in Increase in isoflavonoid content in Glycine max cells transformed by the constitutively active Ca independent form of the AtCPK1 gene

Fig. 2. A representative HPLC-UV profile of the AtCPK1-transformed callus culture of G. max – GmCa2 (A) and the control callus culture Gm (B). The callus tissue extracts recorded at 254 nm. Peak numbers correspond to each of the identified components and are listed in Table 3.

Fig. 3 in Increase in isoflavonoid content in Glycine max cells transformed by the constitutively active Ca independent form of the AtCPK1 gene

Fig. 3. Content (mg/g DW) of isoflavones-aglycones (a) and their glucosides and malonyl-glucosides derivatives (b–d) and prenylated isoflavones (e) in the control calli (Gm) and the AtCPK-transformed callus cultures - GmCa1 and GmCa2. Data are presented as the mean ± SE from four subcultures (biological replicates) with two technical replicates for each experiment. Different letters above the bars indicate statistically significant differences of means (P <0.05), Fisher's LSD.

Fig. 1 in Increase in isoflavonoid content in Glycine max cells transformed by the constitutively active Ca independent form of the AtCPK1 gene

Fig. 1. The branch of phenylpropanoid pathway leading to flavonoids. PAL, phenylalanine ammonia-lyase; C4H, cinnamate 4-hydroxylase; CHS, chalkone synthase; CHR, chalkone reductase; CHI, chalkone isomerase; FN3H, flavanone 3-hydroxylase; IFS, isoflavone synthase; HID, 2-hydroxyisoflavanone dehydratase, IDT1, isoflavone dimethylallyltransferase 1; IDT2, isoflavone dimethylallyltransferase 2; C4DT, coumestrol 4-dimethylallyltransferase.