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Figure 4 in Differential gene expression pattern and plasma sex steroids during testicular development in Genyatremus luteus (Perciforme: Haemulidae) (Bloch, 1790)
Figure 4. Principal component analysis (PCA) used to classify the influence of lhr and er gene expression, plasma steroids (11-KT, 17- OHP and E2), ichthyological parameters and GSI on male G. luteus individuals. Legend: LHR = LH receptor; ER = estrogen receptor; KT = 11-ketotestosterone; E2 = 17β-estradiol; OHP = 17-α-hydroxyprogesterone; TW = total weight; TL = total length; GW = gonad weight; GSI = gonadosomatic index.
Figure 1 in Differential gene expression pattern and plasma sex steroids during testicular development in Genyatremus luteus (Perciforme: Haemulidae) (Bloch, 1790)
Figure 1. Photomicrographs of germ cell and testes development stages of Genyatremus luteus. Stages were determined as (A) Immature, (B) Maturing, (C) Mature. Abbreviations are as follows: SPG, spermatogonia; SPC, spermatocyte; SPZ, spermatozoa. All panels were at 60x magnification.
Figure 2 in Differential gene expression pattern and plasma sex steroids during testicular development in Genyatremus luteus (Perciforme: Haemulidae) (Bloch, 1790)
Figure 2. Steroid concentrations in the blood plasma of male Genyatremus luteus individuals during their reproductive cycle. (A) 11-ketotestosterone. (B) 17 α-hidroxy progesterone. (C) 17β-estradiol. Data are represented as mean ± SEM. abc: indicates statistically significant difference (p<0.05).
Pelagomonas calceolata gene expression levels in different nitrogen conditions and differential expression analysis.
<p>These files contains the expression levels and DESeq2 results of <em>Pelagomonas calceolata</em> genes cultivated with different nitrate conditions. Two strains of <em>P. calceolata </em>(RCC100 and RCC697) were cultivated and their RNAs reads were aligned on the predicted genes of <em>P. calceolata</em> RCC100 genome: <a href="https://www.ncbi.nlm.nih.gov/Traces/wgs/CAKKNE01?display=download" rel="nofollow">https://www.ncbi.nlm.nih.gov/Traces/wgs/CAKKNE01?display=download</a></p> <p>The following culture conditions were analysed :</p> <p>882 µM of Nitrate (RCC100 and RCC697) </p> <p>441 µM of Nitrate (RCC100)</p> <p>220 µM of Nitrate (RCC100 and RCC697)</p> <p>50 µM of Nitrate (RCC697)</p> <p>882 µM Cyanate (RCC100)</p> <p>882 µM Ammonia (RCC100)</p> <p>441 µM Urea (RCC100)</p> <p><a href="../api/records/12582059/draft/files/20230427_RCC100-Nitrate_transcriptomes_rawcounts.tsv/content" target="_blank" rel="noopener noreferrer">20230427_RCC100-Nitrate_transcriptomes_rawcounts.tsv</a> : the file contains the raw read counts of RCC100 in 6 culture conditions in triplicate + the gene names = 19 columns.</p> <p><a href="../api/records/12582059/draft/files/20230427_RCC100-Nitrate_transcriptomes_TPM.tsv/content" target="_blank" rel="noopener noreferrer">20230427_RCC100-Nitrate_transcriptomes_TPM.tsv</a> : same data normalized in transcript per kb per million mapped reads (TPM).</p> <p><a href="../api/records/12582059/draft/files/20230427_RCC100-Nitrate_transcriptomes_rawcounts.tsv/content" target="_blank" rel="noopener noreferrer">20230427_RCC697-Nitrate_transcriptomes_rawcounts.tsv</a> : the file contains the raw read counts of RCC697 of 3 culture conditions in triplicate + the gene names = 10 columns.</p> <p><a href="../api/records/12582059/draft/files/20230427_RCC100-Nitrate_transcriptomes_TPM.tsv/content" target="_blank" rel="noopener noreferrer">20230427_RCC697-Nitrate_transcriptomes_TPM.tsv</a> : same data normalized in transcript per kb per million mapped reads (TPM).</p> <p><span>Differential expression analysis (DESeq2) was performed by pairwise comparisons between the standard condition (882 µM nitrate) and low-nitrate conditions (50, 220 or 441 µM nitrate) or changing nitrogen sources (882 µM ammonium, 882 µM cyanate and 441 µM urea). Each DESeq-results_RCCxxx_xxx.tsv file contains 6 columns : <em>P.calceolata </em>gene name, base Mean, log2 Fold Change, standard error value (lfcSE), pvalue and adjusted pvalue (padj).<br></span></p>
A plant virus differentially alters DNA methylation in two cryptic species of a hemipteran vector
<p>This study investigated DNA methylation patterns in two cryptic species (B and Q) of the sweet potato whitefly, <em>Bemisia tabaci</em> (Gennadius), following the acquisition of the tomato yellow curl virus, a single-stranded DNA virus. The methylation levels in genomic features such as promoters, gene bodies, and transposable elements in both cryptic species were described in this study. While overall trends were found to be similar, specific differences in methylation levels were observed. Virus-induced differentially methylated regions (DMRs) were associated with different genes in each cryptic species and were negatively correlated with differential gene expression. These DMRs were analyzed for changes in gene expression and alternative splicing, revealing clusters of hyper- and hypomethylated genes related to virus-vector interactions, immune functions, and detoxification processes. These methylation differences may help explain the distinct biological and physiological traits observed between the B and Q cryptic species.</p>
Data and code to reproduce: Host and parasite intervality in differentially human-modified habitats
<p>Data and code in:</p> <p>Llopis-Belenguer, Feijen, Morand, Chaisiri, Ribas and Jokela (2024) Host and parasite intervality in differentially human-modified habitats. Oikos. DOI: 10.1111/oik.10446</p>
Fig. 7 in Differential analysis of the cytochrome p450 acaricide-resistance genes in Panonychus citri (Trombidiformes: Tetranychidae) strains
Fig. 7. Alignment of the predicted amino acid sequences of the CYP307A1 in Panonychus citri between the hexythiazox-resistant (RR) and susceptible (SS) strains. Mazarine shading indicates identities and different color shading represents mutations. "-" represents no sequence to compare. We detected a sense amino acid mutation (14-threonine to serine).. This figure is shown in color in a supplementary document online as Suppl. Fig. 7 in Florida Entomologist 98(1) (March 2015) at http://purl.fcla.edu/fcla/entomologist/browse.
Fig. 5 in Differential analysis of the cytochrome p450 acaricide-resistance genes in Panonychus citri (Trombidiformes: Tetranychidae) strains
Fig. 5. Alignment of the predicted amino acid sequences of CYP307A1 in Panonychus citribetween the hexythiazox-resistant (RR) and susceptible (SS) strains. Mazarine shading indicates identities and different color shading represents mutations. "-" represents no sequence to compare. Only one amino acid mutation (278-lysine to glutamine) was detected.. This figure is shown in color in a supplementary document online as Suppl. Fig. 5 in Florida Entomologist 98(1) (March 2015) at http://purl.fcla.edu/fcla/entomologist/browse.
Fig. 6 in Differential analysis of the cytochrome p450 acaricide-resistance genes in Panonychus citri (Trombidiformes: Tetranychidae) strains
Fig. 6. Nucleotide sequence comparison of CYP381A2 in Panonychus citri between the hexythiazox-resistant (RR) and susceptible (SS) strains. Mazarine shading indicates identities and different color shading represents mutations. "-" represents no sequence to compare. Just one SNP site was detected. The nucleotide transition of A to T was at position 40.. This figure is shown in color in a supplementary document online as Suppl. Fig. 6 in Florida Entomologist 98(1) (March 2015) at http://purl.fcla.edu/fcla/entomologist/browse.
Fig. 4 in Differential analysis of the cytochrome p450 acaricide-resistance genes in Panonychus citri (Trombidiformes: Tetranychidae) strains
Fig. 4. Nucleotide sequence comparison of the CYP307A1 in Panonychus citri between the hexythiazox-resistant (RR) and susceptible (SS) strains. Mazarine shading indicates identities and different color shading represents mutations. "-" represents no sequence to compare. Three SNP sites were detected in all. The first nucleotide mutation (A to C) is located at 841, the second mutation is 1395-T to C, and the final mutation is 1491-T to C.. This figure is shown in color in a supplementary document online as Suppl. Fig. 4 in Florida Entomologist 98(1) (March 2015) at http://purl.fcla.edu/fcla/entomologist/browse.
Fig. 3 in Differential analysis of the cytochrome p450 acaricide-resistance genes in Panonychus citri (Trombidiformes: Tetranychidae) strains
Fig. 3. Quantitative Real-time PCR analysis of CYPs in Panonychus citri between the hexythiazox-resistant (RR) and susceptible (SS) strains. The numbers of genes down-regulated and up-regulated in the RR relative to the SS are indicated above or below the X axis. The light or dark gray was susceptible strain and resistant strain, respectively.
Fig. 1 in Differential analysis of the cytochrome p450 acaricide-resistance genes in Panonychus citri (Trombidiformes: Tetranychidae) strains
Fig. 1. Number, family and clan distribution of cytochrome P450 genes in Panonychus citri. The number shown along each column represents the P450 family and the number in parenthesis is the number of individual genes in the corresponding family. The P450 gene sequence information generated is from the VectorBase of the P. citri transcriptome sequence.
Fig. 2 in Differential analysis of the cytochrome p450 acaricide-resistance genes in Panonychus citri (Trombidiformes: Tetranychidae) strains
Fig. 2. Neighbor-joining phylogenetic analysis of cytochrome P450 from Panonychus citri and Tetranychus urticae. 4clans were observed. There are species (P. citri and T. urticae) in the phylogenetic tree. Only 10 sequences belong to T. urticae; A (Pc) before the CYP name denotes P. citri, a (Tu) before the CYP name denotes T. urticae. Numbers at nodes are bootstrap values.
Fig. 1 in Molecular diagnostic technique for the differentiation of the Formosan subterranean termite, Coptotermes formosanus (Isoptera: Rhinotermitidae) from other subterranean termites by multiplex-PCR
Fig. 1. Ethidium bromide-stained agarose gel (2%) illustrating a common amplicon of 262 bp from the mtDNA 16S gene for various termite species and unique amplicon of 221 bp specific for the Formosan subterranean termite.
Beyond gene flow: (non)-parallelism of secondary contact in a pair of highly differentiated sibling species
<p>Replicated secondary contact zones can provide insights on the barriers to gene flow that are important during speciation and can reveal to which degree secondary contact may result in similar evolutionary outcomes. Here, we studied two secondary contact zones between highly differentiated Alpine butterflies<em> </em>of the genus <em>Erebia</em> using whole-genome re-sequencing data. We assessed the genomic relationships between populations and species and find hybridization to be rare, with no to little current or historical introgression in either contact zone. There are large similarities between the contact zones, consistent with an allopatric origin of interspecific differentiation, with no indications for ongoing reinforcing selection. Consistent with expected reduced effective population size, we further find that scaffolds related to the Z-chromosome show increased differentiation compared to the already high levels across the entire genome, which could also hint towards a contribution of the Z chromosome to species divergence in this system. Finally, we detected the presence of the endosymbiont <em>Wolbachia</em>, which can cause reproductive isolation between its hosts, in all <em>E. cassioides</em>, while it appears to be fully or largely absent in contact zone populations of <em>E. tyndarus</em>. We discuss how this rare pattern may have arisen and how it may have affected the dynamics of speciation upon secondary contact.</p>
Fig. 1 in Short communication First documented observation of differential dorsoventral coat colouration in wild boar Sus scrofa (Artyodactyla: Suidae) in Italy
Fig. 1 - The juvenile wild boar object of this note showing the differential dorsoventral colouration pattern (right) next another wild-type individual (left). Additional footage available at: https://youtu.be/gTc0BFSE9kA. / Il giovane esemplare di cinghiale oggetto di questa nota in cui è visibile il pattern cromatico a demarcazione dorsoventrale (a destra) accanto a un altro individuo con la tipica colorazione marrone uniforme (a sinistra). È anche disponibile un filmato aggiuntivo: https://youtu.be/ gTc0BFSE9kA. (Photo and video: / Foto e video: Francesco Gallozzi).
Fig. 7 in Stable isotope markers differentiate between mass-reared and wild Lepidoptera in sterile insect technique programs
Fig. 7. Isotope signatures of the European grapevine moth, Lobesia botrana; error bars are 2 standard deviations of the mean.
Fig. 1 in Stable isotope markers differentiate between mass-reared and wild Lepidoptera in sterile insect technique programs
Fig. 1. Percentage of sucrose based on dry weight (DW) in popular artificial diets for mass rearing various moth species, as described by Dyck (2010).
Fig. 3 in Stable isotope markers differentiate between mass-reared and wild Lepidoptera in sterile insect technique programs
Fig. 3. Isotope signatures of the African sugarcane borer, Eldana saccharina. Wild moths developed on sugarcane at Eston, and at Tinely Manor, a 3rd group developed on papyrus at Eston and a 4th group was mass reared on an artificial diet. Error bars are 3 standard deviations of the mean.
Fig. 2 in Stable isotope markers differentiate between mass-reared and wild Lepidoptera in sterile insect technique programs
Fig. 2. Isotope signatures of cactus, a laboratory formulated diet and of cactus moths, Cactoblastis cactorum, reared on these 2 substrates; error bars are 2 standard deviations of the mean.
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.