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2,315 results for “Comparative analysis”
Comparative Analysis of Complete Chloroplast Genomes of 13 Species in Epilobium, Circaea, and Chamaenerion and Insights into Phylogenetic Relationships of Onagraceae
<p>This is all the alignments which used to constructed a phylogenetic tree in our study about Onagraceae. The evening primrose family, Onagraceae, is a well defined family of the order Myrtales, which comprises 22 genera widely distributed from boreal to tropical areas. In the present study, we report and characterize the complete chloroplast genome sequences of 13 species in <em>Circaea</em>,<em> Chamaenerion</em>, and <em>Epilobium</em> using a next-generation sequencing method. We also retrieved plastome sequences from two other Onagraceae genera to characterize the chloroplast genome of the family. The complete plastomes of Onagraceae showed a typical quadripartite structure and encoded an identical set of 112 genes (with exclusion of duplication), including 78 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs. The results show that chloroplast genomes are basically conserved in gene arrangement across the family. Whereas, a large segment of inversion was detected in the LSC region of all samples in the<em> Oenothera </em>subsect. <em>Oenothera</em>. An inverted repeat (IR) contraction was found in <em>Circaea</em> and<em> Ludwigia </em>samples. We also compared chloroplast genomes across the Onagraceae samples and revealed similarities in some features, including nucleotide content, codon usage, RNA editing sites, and simple sequence repeats (SSRs). Phylogeny was inferred by the chloroplast genome data using maximum-likelihood (ML) and Bayesian inference (BI) methods. The generic relationship of Onagraceae was well resolved by the complete plastome sequences, showing potential value in inferring phylogeny within the family. <em>Oenothera </em>phylogeny was better resolved than other densely sampled genera. Biparental transmission may be the main cause of higher variation in the genus<em> Oenothera</em>.</p>
Comparative karyotype analysis in chickpea (Cicer arietinum L.) using oligo painting FISH
<p>Chickpea (<i>Cicer arietinum</i> L.) is one of the main sources of plant proteins in the Indian subcontinent and West Asia, where two different morphotypes, desi and kabuli, are grown. Despite the progress in genome mapping and sequencing, the knowledge of chickpea genome at chromosomal level, including the long-range molecular chromosome organization is limited. Earlier cytogenetic studies in chickpea suffered from limited number of cytogenetic landmarks and did not permit to identify individual chromosomes in the metaphase spreads or to anchor pseudomolecules to chromosomes <i>in situ</i>. In this study, we developed a system for fast molecular karyotyping for both morphotypes of cultivated chickpea<i>. </i>We demonstrate that even draft genome sequences are adequate to develop oligo-FISH barcodes for identification of chromosomes and comparative analysis among closely related chickpea genotypes. Our results show the potential of oligo-FISH barcoding for identification of structural changes in chromosomes, which accompanied genome diversification among chickpea cultivars. Moreover, oligo-FISH barcoding in chickpea pointed out some problematic, most probably wrongly assembled regions of the pseudomolecules of both, kabuli and desi reference genomes. Thus, oligo painting appears as a powerful tool not only for comparative karyotyping, but also for validation of genome assemblies.</p>
FIGURE 12 in Comparative mitogenome analysis and phylogenetic inference of the genus Ultragryllacris (Orthoptera: Gryllacrididae)
FIGURE 12. Ultragryllacris pulchra rubricapitis Bin & Bian, 2021. A. habitus in lateral view; B–E. tegmina in dorsal view: B, D. left tegmen, C, E. right tegmen; A–C. male; D–E. female.
FIGURE 11 in Comparative mitogenome analysis and phylogenetic inference of the genus Ultragryllacris (Orthoptera: Gryllacrididae)
FIGURE 11. Ultragryllacris pulchra rubricapitis Bin & Bian, 2021. Female: A. head in frontal view; B–C. head and pronotum: B. dorsal view, C. lateral view; D. second and third abdominal tergites in lateral view; E–G. apex of abdomen: E. dorsal view, F. lateral view, G. ventral view; H. apices of ovipositor in lateral view.
FIGURE 8 in Comparative mitogenome analysis and phylogenetic inference of the genus Ultragryllacris (Orthoptera: Gryllacrididae)
FIGURE 8. NJ tree constructed based on cob genes. ABGD method is indicated with dark gray bars and jMOTU with light gray bars.
FIGURE 4. The secondary structures for 22 in Comparative mitogenome analysis and phylogenetic inference of the genus Ultragryllacris (Orthoptera: Gryllacrididae)
FIGURE 4. The secondary structures for 22 tRNA genes of the Ultragryllacris pulchra rubricapitis XZ273.
FIGURE 10 in Comparative mitogenome analysis and phylogenetic inference of the genus Ultragryllacris (Orthoptera: Gryllacrididae)
FIGURE 10. Ultragryllacris pulchra rubricapitis Bin & Bian, 2021. Male: A–B. head in frontal view; C–E. head and pronotum: C–D. dorsal view, E. lateral view; F–G, I. apex of abdomen: F. lateral view, G. apico-dorsal view, I. ventral view; H. ninth abdominal tergite in ventral view.
FIGURE 3. The secondary structures for 22 in Comparative mitogenome analysis and phylogenetic inference of the genus Ultragryllacris (Orthoptera: Gryllacrididae)
FIGURE 3. The secondary structures for 22 tRNA genes of the Ultragryllacris pulchra rubricapitis XZ267.
FIGURE 7 in Comparative mitogenome analysis and phylogenetic inference of the genus Ultragryllacris (Orthoptera: Gryllacrididae)
FIGURE 7. NJ tree constructed based on cox1 genes. ABGD method is indicated with dark gray bars and jMOTU with light gray bars.
FIGURE 5. The secondary structures for 22 in Comparative mitogenome analysis and phylogenetic inference of the genus Ultragryllacris (Orthoptera: Gryllacrididae)
FIGURE 5. The secondary structures for 22 tRNA genes of the Ultragryllacris pulchra rubricapitis XZ506.
Supplementary material 1 from: Luo X-X, Li Q-Q, Zamani A, Che Y-L, Wang Z-Q (2023) Redescription of Periplaneta arabica (Bey-Bienko, 1938) (Blattodea, Blattidae), with a comparative analysis of three species of Periplaneta Burmeister, 1838 (sensu stricto). ZooKeys 1146: 165-183. https://doi.org/10.3897/zookeys.1146.90817
Genetic divergence of distances calculated by K2P model method using cytochrome c oxidase subunit I (COI) gene sequences in MEGA
Supplementary material 4 from: She C-W, Jiang X-H, He C-P (2023) Comparative karyotype analysis of eight Cucurbitaceae crops using fluorochrome banding and 45S rDNA-FISH. Comparative Cytogenetics 17(1): 31-58. https://doi.org/10.3897/compcytogen.v17.i1.99236
The correlational analysis between the difference in TCL and the change in nuclear DNA content within the eight Cucurbitaceae crops using the SPSS 25.0 software
Supplementary material 2 from: Luo X-X, Li Q-Q, Zamani A, Che Y-L, Wang Z-Q (2023) Redescription of Periplaneta arabica (Bey-Bienko, 1938) (Blattodea, Blattidae), with a comparative analysis of three species of Periplaneta Burmeister, 1838 (sensu stricto). ZooKeys 1146: 165-183. https://doi.org/10.3897/zookeys.1146.90817
Interspecific genetic divergence of distances calculated by K2P model method using cytochrome c oxidase subunit I (COI) gene sequences in MEGA
A Machine Learning based approach to osteoporosis classification: correlational and comparative analysis between Osseus and DXA exams
<p>The osseus dataset is composed of data from 505 individuals who underwent the osseus triage and DXA exam at the University Hospital Onofre Lopes of Federal University of Rio Grande do Norte, Brazil. This dataset provides elementary data to analyze the prediction of changes in bone mineral density by Osseus using supervised classification algorithms. Supplementary file presents the dictionary used during the data analysis.</p>
Data from: Comparative studies on water- and vapor-based hydrothermal carbonization: process analysis
<p>Hydrothermal carbonization (HTC) reactor systems used to convert wet organic wastes into value-added hydrochar are generally classified in the literature as liquid water-based (HTC) or vapor-based (VTC). However, the distinction between the two is often ambiguous. In this paper, we theoretically developed models for predicting reactor pressure, volume fraction of liquid water, and water distribution between phases as a function of temperature.</p>
Lifestyle and sense of coherence: A comparative analysis among university students in different areas of knowledge
<p>Background: The concept of health has undergone profound changes. Lifestyle Medicine (LSM) consists of therapeutic approaches that focus on the prevention and treatment of diseases. It follows that the quality of life of university students directly affects their health and educational progress.</p> <p>Experimental Methodology: Socioeconomic, lifestyle (LS), and sense of coherence (SOC) questionnaires were administered to college students from three different areas. The results were analyzed for normality and homogeneity, followed by ANOVA variance analysis and Dunn and Tukey post hoc test for multiple comparisons. Spearman's correlation coefficient evaluated the correlation between lifestyle and sense of coherence; p values < 0.05 were considered statistically significant. </p> <p>Results: The correlation between LS and SOC was higher among males and higher among Medical and Human sciences students compared to Exact sciences. Medical students' scores were higher than Applied sciences and Human sciences students on the LS questionnaire. Exact science students' scores on the SOC questionnaire were higher than Human sciences students. In the LS areas related to alcohol intake, sleeping quality, and behavior, there were no differences between the areas. However, women scored better in the nutrition domain and alcohol intake. The SOC was also higher in men compared to women. </p> <p>Conclusion: The results obtained demonstrate in an unprecedented way in the literature that the correlation between the LS and SOC of college students varies according to gender and areas of knowledge, reflecting the importance of actions on improving students' quality of life and enabling better academic performance.</p>
Fig. 2 in Comparative analysis of cyclotide-producing plant cell suspensions presents opportunities for cyclotide plant molecular farming
Fig. 2. Cyclotide profiles in O. affinis cultures. A Relative quantification by MALDI-TOF-MS of cyclotides from in vitro grown organs, calli, and suspension cells of O. affinis. B Amino acid alignment of partial coding sequences encoding cyO2 derived from transcriptome sequencing of H. enneaspermus and a Sanger sequence-validated O. affinis transcript. Amino acid differences only exist within the N-terminal repeat (NTR) and C-terminal propeptide (CTPP) regions, whilst the coding sequence but not the peptide sequence differs between the two species. C Comparison of previously described kalata B18 (kB18) (Seydel et al., 2007) and Sanger sequence validated kalata B23 (kB23) presented in this work.
Fig. 3 in Comparative analysis of cyclotide-producing plant cell suspensions presents opportunities for cyclotide plant molecular farming
Fig. 3. Relative quantification by MALDI-TOF-MS of cyclotides from in vitro grown organs, calli, and suspension cells of A C. ternatea and B H. enneaspermus. Relative quantification was achieved by comparing the MS signal ratio between peptides of interest to that of an internally spiked peptide control using MALDITOF-MS.
Fig. 1 in Comparative analysis of cyclotide-producing plant cell suspensions presents opportunities for cyclotide plant molecular farming
Fig. 1. Example calli grown on optimal media formulations of A C. ternatea and B H. enneaspermus. Growth curves of suspension cultures (n = 3 for each media formulation) grown in media formulations for C C. ternatea and D H. enneaspermus. Growth was recorded relative to starting packed cell volume.
Fig. 5 in Comparative analysis of cyclotide-producing plant cell suspensions presents opportunities for cyclotide plant molecular farming
Fig. 5. Assessment of transcript or peptide levels present in O. affinis leaf, calli, and suspension cells at days 1, 14, 21 and 28. A Relative transcript expression determined by qPCR (n = 4) of asparaginyl endopeptidases OaAEP1, OaAEP2 and OaAEP3. B Relative transcript expression determined by qPCR (n = 4) of select cyclotide precursors Oak1 encoding kB1, Oak4 encoding kB2, and OaCyO2 encoding cyO2. C Relative peptide levels determined by MALDI-TOFMS (n = 4) of O. affinis cyclotides.
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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.
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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.