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Fig. 19. Relief low, blunt cusps. A in Functional Characterization of Ungulate Molars Using the Abrasion-Attrition Wear Gradient: A New Method for Reconstructing Paleodiets
Fig. 19. Relief low, blunt cusps. A: Equus grevyi AMNH 277427, right M1-M3; B: Equus burchelli AMNH 83601, left M1; C: 27749, right M1-M3; D: 165064, left M1; E: 82313, left M1- M3; F: 182315, right M1; G: 82316, left M2-M3; H: 82314, left M2-M3.
Fig. 18. Relief low, blunt cusps. A in Functional Characterization of Ungulate Molars Using the Abrasion-Attrition Wear Gradient: A New Method for Reconstructing Paleodiets
Fig. 18. Relief low, blunt cusps. A: Ceratotherium simum TE 5919, left M2; B: 5926, left M2; C: 5923, right M1; D: Equus burchelli AMNH 82036, right M2-M3; E: 82037, left M1; F: 119669, left M3; G: 54247, right M3; H: 119669, left M1; I: 165065, right M1-M2; J: 16062, left M1.
Figure 1 in Chromosomal and genetic characterization of four Caribbean Prioninae (Coleoptera: Cerambycidae) species with notes on biogeography
Figure 1. Schematic representation of the Lesser Antilles and photography of the insects under study.
Figure 10 in Chromosomal and genetic characterization of four Caribbean Prioninae (Coleoptera: Cerambycidae) species with notes on biogeography
Figure 10. Phylogenetic tree resulting from the Bayesian analysis, clustering the different haplotypes of Prioninae retrieved from the Genbank with those assessed of this study as compressed subtree (red triangle). Expansion of the subtree and phylogenetic relationships between the different haplotypes is also shown. The topology of the clusters was similar for the UPGMA and NJ trees. Numbers above branches of the major clusters correspond to posterior probabilities from the Bayesian analysis. TdeH and TdeB: Terre-de-Haut and Terre-de-Bas islands from Les Saintes.
Figures 6-9 in Chromosomal and genetic characterization of four Caribbean Prioninae (Coleoptera: Cerambycidae) species with notes on biogeography
Figures 6-9. Karyotypes of Solenoptera and Hovorodon species. 6) Giemsa stained karyotype of S. touroulti exhibiting three pairs (# 1, 2 and 4) of sub-metacentric autosomes. 7) Karyotype of a spermatocyte I at pachynema of S. touroulti, after Giemsa (left) and silver (right) stainings. Notice the lack of synapsis at the NOR locus (arrow) and the silver staining of nucleoli. 8) Giemsa stained karyotype of H. maxillosum exhibiting 10 pairs of sub-metacentric autosomes. 9) Karyotype of a spermatocyte I at pachynema of H. maxillosum, after Giemsa (left) and silver (right) stainings. Arrow: NOR on bivalent 12. Bars = 10μm.
Figures 2-5 in Chromosomal and genetic characterization of four Caribbean Prioninae (Coleoptera: Cerambycidae) species with notes on biogeography
Figures 2-5. Karyotypes of Solenoptera species. 2) Giemsa stained male karyotype of S. canaliculata. The arrows on chromosome 4 indicate an elongated region, which is the only region stained by C-banding. Bar = 10 μm, as in other figures. 3) Karyotype of a spermatocyte I at pachynema of S. canaliculata, after Giemsa (left) and silver (right) stainings. The NOR on bivalent 4 looks elongated, and is surrounded by nucleoli after silver staining. 4) Giemsa stained XYY karyotype of S. quadrilineata. Chromosome 4 is elongated at the same position as in S. canaliculata (arrow), which indicates the position of the NOR. 5) Giemsa stained metaphase I of the XYY male of S. quadrilineata exhibiting a parachute sex trivalent. Arrows point out the two Ys. The accidental presence of two Ys in male beetles was estimated to about 1 per cent (Dutrillaux and Dutrillaux 2011). Bars = 10μm.
Recombination and In-silico protein modelling and functional characterization of copLAB genes from Trinidadian Xanthomonas campestris and melonis isolates
<p>RDP, GARD, RaptorX and InterProScan outputs relating to the publication tentatively titled "Heavy metal resistance islands associated with a putative Tn in Trinidadian copper resistant <em>Xanthomonas campestris </em>and <em>melonis </em>strains are strongly linked to homologs from the <em>Stenotrophomonas </em>genus"</p>
Figure 1 in Biological characterization of the obligate symbiosis between Acropyga sauteri Forel (Hymenoptera: Formicidae) and Eumyrmococcus smithii Silvestri (Hemiptera: Pseudococcidae: Rhizoecinae) on Okinawa Island, southern Japan
Figure 1. Schematic design of cubic clod sampling. (a) Protocol for sampling in June 2002; (b) protocol for sampling in January 2002. At each sampling event we randomly chose a ground surface area for sampling clods, from which individuals of Acropyga sauteri and its symbiont Eumyrmococcus smithii were collected. The dates of sampling events and the numbers and sizes of areas and cubic clods are listed in Table I.
Figure 10 in Biological characterization of the obligate symbiosis between Acropyga sauteri Forel (Hymenoptera: Formicidae) and Eumyrmococcus smithii Silvestri (Hemiptera: Pseudococcidae: Rhizoecinae) on Okinawa Island, southern Japan
Figure 10. Seasonal changes in the average numbers (with SE) of individuals of Eumyrmococcus smithii per colony and the age structure (percentage of components). Numerals above the bars indicate the sample size (presumed number of ant colonies). ''Pupa'' here includes pupae of both sexes and male prepupa, which were difficult to discriminate when not on slides.
Figure 13 in Biological characterization of the obligate symbiosis between Acropyga sauteri Forel (Hymenoptera: Formicidae) and Eumyrmococcus smithii Silvestri (Hemiptera: Pseudococcidae: Rhizoecinae) on Okinawa Island, southern Japan
Figure 13. First-instar nymph, right side shows venter of the nymph; left side shows dorsum of the nymph. Anal lobe setae are long, but here only a part of the setae are drawn. Scale bar: 0.1 mm.
Figure 4 in Biological characterization of the obligate symbiosis between Acropyga sauteri Forel (Hymenoptera: Formicidae) and Eumyrmococcus smithii Silvestri (Hemiptera: Pseudococcidae: Rhizoecinae) on Okinawa Island, southern Japan
Figure 4. Schematic illustration of the presumed life cycle of Eumyrmococcus smithii. The first-instar nymph is followed by the pupa and adult in the female and by the prepupa, pupa, and adult in the male.
Figure 12 in Biological characterization of the obligate symbiosis between Acropyga sauteri Forel (Hymenoptera: Formicidae) and Eumyrmococcus smithii Silvestri (Hemiptera: Pseudococcidae: Rhizoecinae) on Okinawa Island, southern Japan
Figure 12. (a) Female pupa; (b) male prepupa; (c) male pupa. Right sides show venter of the prepupal or pupal stages; left sides show dorsum of the prepupal or pupal stages. Scale bars: 0.2 mm.
Figure 6 in Biological characterization of the obligate symbiosis between Acropyga sauteri Forel (Hymenoptera: Formicidae) and Eumyrmococcus smithii Silvestri (Hemiptera: Pseudococcidae: Rhizoecinae) on Okinawa Island, southern Japan
Figure 6. Average numbers (with SD) of workers of Acropyga sauteri in clods with Eumyrmococcus smithii (open area) or without E. smithii (shaded area) in August and June. Numerals above the bars indicate the sample size (number of cubic clods).
Figure 9 in Biological characterization of the obligate symbiosis between Acropyga sauteri Forel (Hymenoptera: Formicidae) and Eumyrmococcus smithii Silvestri (Hemiptera: Pseudococcidae: Rhizoecinae) on Okinawa Island, southern Japan
Figure 9. Seasonal changes in the average numbers (with SE) of individuals of Acropyga sauteri per colony and the age structure (percentage of components). Numerals above the bars indicate the sample size (presumed number of ant colonies).
Figure 8 in Biological characterization of the obligate symbiosis between Acropyga sauteri Forel (Hymenoptera: Formicidae) and Eumyrmococcus smithii Silvestri (Hemiptera: Pseudococcidae: Rhizoecinae) on Okinawa Island, southern Japan
Figure 8. Distribution of the numbers of alate female ants (a) and alate male ants (b) per colony of Acropyga sauteri. A plot represents the variable for a colony or the average for multiple colonies in the vicinity. When multiple queens were sampled from certain clods in the vicinity, we estimated the average numbers of the reproductives by dividing the total number of queens into the total numbers of the reproductives. Numerals above the solid circles indicate the number of colonies used for the average estimation.
Figure 5 in Biological characterization of the obligate symbiosis between Acropyga sauteri Forel (Hymenoptera: Formicidae) and Eumyrmococcus smithii Silvestri (Hemiptera: Pseudococcidae: Rhizoecinae) on Okinawa Island, southern Japan
Figure 5. Percentage of clods containing more than five workers of Acropyga sauteri across depths. Numerals above the bars indicate the sample size (number of cubic clods).
Figure 11 in Biological characterization of the obligate symbiosis between Acropyga sauteri Forel (Hymenoptera: Formicidae) and Eumyrmococcus smithii Silvestri (Hemiptera: Pseudococcidae: Rhizoecinae) on Okinawa Island, southern Japan
Figure 11. Adult male, right side shows venter of the adult male; left side shows dorsum of the adult male. (a) Lateral view of genitalia of the adult male; (b) ventral view of genitalia of the adult male. Scale bar: 0.1 mm.
Figure 2 in Biological characterization of the obligate symbiosis between Acropyga sauteri Forel (Hymenoptera: Formicidae) and Eumyrmococcus smithii Silvestri (Hemiptera: Pseudococcidae: Rhizoecinae) on Okinawa Island, southern Japan
Figure 2. Schematic illustration of the method used to determine colony identity. (a) Distance (D) between two particular ant aggregations was defined as the distance between the centre of the two clods containing the two aggregations; (b) five workers were placed in a plastic cup covered with black paper; (c) an ant worker was introduced into another cup (of recipient workers); (d) the contact behaviour of recipient and introduced workers was observed; (e) the trial ended after contact had occurred two or three times, after which the introduced worker was returned to the original cup. In a match between two aggregations, the method described from (c) to (e) was repeated five times.
TEST DATA for Enhanced protein isoform characterization through long-read proteogenomics
<p>Test data for The detection of physiologically relevant protein isoforms encoded by the human genome is critical to biomedicine. Mass spectrometry (MS)-based proteomics is the preeminent method for protein detection, but isoform-resolved proteomic analysis relies on accurate reference databases that match the sample; neither a subset nor a superset database is ideal. Long-read RNA sequencing (e.g. PacBio, Oxford Nanopore) provides full-length transcript sequencing, which can be used to predict full-length proteins. Here, we describe a long-read proteogenomics approach for integrating matched long-read RNA-seq and MS-based proteomics data to enhance isoform characterization. We introduce a classification scheme for protein isoforms, discover novel protein isoforms, and present the first protein inference algorithm for the direct incorporation of long-read transcriptome data in protein inference to enable detection of protein isoforms that are intractable to MS detection. We have released an open-source Nextflow pipeline that integrates long-read sequencing in a proteomic workflow for isoform-resolved analysis.</p> <p>Companion Repositories:</p> <ol> <li><a href="https://doi.org/10.5281/zenodo.5920817">Long-Read-Proteogenomics Workflow GitHub Repository Release</a></li> <li><a href="https://doi.org/10.5281/zenodo.5920847">Long-Read-Proteogenomics Analysis GitHub Repository Release</a></li> </ol> <p>Companion Datasets</p> <ol> <li><a href="https://zenodo.org/deposit/5703754">Jurkat Samples and Reference Data</a></li> <li><a href="http://10.5281/zenodo.5920920">Long-Read-Proteogenomics Workflow Results using Jurkat Sample data</a></li> </ol> <p>This Repository contains the test data, specifically:</p> <p><a href="https://doi.org/10.5281/zenodo.5234651">TEST Data for Long-Read-Proteogenomics Workflow GitHub Actions</a></p>
Fig. 3 a-h in Ecological characterization of habitats colonized by the freshwater gastropod Viviparus contectus (MILLET, 1813) (Gastropoda, Prosobranchia) - Theoretical and experimental data
Fig. 3 a-h: Logistic regression models of the single environmental variables for the presentation of eventual habitat preferences of V. contectus. For a validation of the models experimental data from diverse field studies were used (e.g., PATZNER & ISARCH 1999, STURM 2000a).
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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.
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.