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237 results for “trypanosoma”
X-ray diffraction images for L-threonine dehydrogenase from Trypanosoma brucei with NAD and pyruvate bound.
<p>X-ray diffraction images which were collected at ESRF (Grenoble) using an ADSC 315r CCD detector on beamline ID29 on 11th November 2009. More details are given in the uploaded notes. </p>
Trypanosoma Epitope Dataset: Valid Epitopes and Randomly Generated Peptides with Biochemical Metrics and AI-Generated Scores
<p>This dataset contains information about valid linear B-Cell epitopes from the Trypanosoma genus, as well as randomly generated peptides. It includes biochemical metrics generated by the EpiBuilder-1.0 tool and scores generated by the BepiPred-3.0 software. The data was originally collected from the IEDB and UniProtKB platforms and has been processed and enhanced with these informations for researchers interested in understanding the molecular interactions between Trypanosoma protozoans and the immune system.</p>
Fig. 3 in Trypanosoma madeirae sp. n.: A species of the clade T. cruzi associated with the neotropical common vampire bat Desmodus rotundus
Fig. 3. Phylogenetic positioning of T. rotundus in the clade T. cruzi. ML phylogenetic analysis based on the concatenated sequences of V7V8 SSU rRNA and gGAPDH genes (1.690 characters, –Ln = 8768.346166) from ten isolates of T. rotundus, other 29 bat trypanosomes, and 21 trypanosomes from other mammals. T. lewisi was used as outgroup. The numbers at the nodes correspond respectively to P, ML (500 replicates) and BI support values.
Fig. 2 in Trypanosoma madeirae sp. n.: A species of the clade T. cruzi associated with the neotropical common vampire bat Desmodus rotundus
Fig. 2. Barcoding (V7-V8 SSU rRNA sequences) of T. rotundus from cultures and bat blood samples, and its related species of the clade T. cruzi. Phylogenetic tree inferred by Parsimony using 93 (∼800 bp) of V7-V8 SSU rRNA sequences. The node numbers are bootstrap values derived from 500 replicates.
Fig. 1 in Trypanosoma madeirae sp. n.: A species of the clade T. cruzi associated with the neotropical common vampire bat Desmodus rotundus
Fig. 1. Geographical origin of Trypanosoma rotundus n. sp. isolates obtained by hemoculturing and archived blood samples from Desmodus rotundus captured in the following Brazilian states: PA, Pará; MG, Minas Gerais; ES, Espírito Santo; RJ, Rio de Janeiro; SP, São Paulo and SC, Santa Catarina.
Fig. 4 in Trypanosoma madeirae sp. n.: A species of the clade T. cruzi associated with the neotropical common vampire bat Desmodus rotundus
Fig. 4. Photomicrographs illustrative of the morphological diversity of culture forms of T. madeirae (isolate M3-209). (a) rosetes of epimastigotes, (b-d) flagellates resembling promastigotes forms, (d-h) epimastigotes (7 days), (i-k) large epimastigote forms under division, (l-m), large trypomastigotes, and (n) slender trypomastigotes (10 days). Giemsa stained. 1000x. K, kinetoplast, N, nucleus, F, flagellum. The scale bar indicates 10 μm.
Trypanosoma cruzi DM28c_2018 annotation with UTR
<p>UTR regions were annotated to the T. cruzi genome 2018 (https://tritrypdb.org/common/downloads/release-68/TcruziDm28c2018/gff/data/). We used custom script for the 5' UTR and peaks2UTR - https://academic.oup.com/bioinformatics/article/39/3/btad112/7067741 for the process. </p>
Microscopy Imaging Dataset: Trypanosoma brucei Bloodstream Form Classification Using Deep Learning
<p>This dataset provides a comprehensive collection of microscopic images and associated labels, specifically designed to facilitate the automated classification of <em>Trypanosoma brucei</em> bloodstream forms—slender and stumpy. Accurate differentiation of these life cycle stages is vital for understanding the parasite's biology, transmission dynamics, and adaptation mechanisms in its mammalian host.</p> <p><strong>Contents:</strong></p> <ul> <li><strong>Image Data</strong>: Microscopic images of <em>T. brucei</em> bloodstream forms captured under standard imaging conditions, encompassing a broad array of image quality, cellular arrangements, and morphological characteristics.</li> <li><strong>Label Data</strong>: Annotation files for each image, specifying cellular forms as slender or stumpy, essential for supervised machine learning applications.</li> <li><strong>Supplementary Files</strong>: Additional Excel files providing information on training, testing, and validation splits, alongside test results for model evaluation.</li> </ul> <p><strong>Purpose:</strong></p> <p>This dataset serves as a valuable resource for researchers in parasitology, machine learning, and computational biology. It supports investigations into the biology and life cycle of <em>T. brucei</em>, while also providing a robust testbed for developing, validating, and benchmarking image processing and classification algorithms tailored to parasite morphology.</p> <p><strong>Data Collection and Methodology:</strong></p> <p>The dataset was compiled using advanced deep learning techniques, integrating the Cellpose segmentation algorithm with a custom-trained Xception model optimized for classifying <em>T. brucei</em> forms. The model achieved 97% classification accuracy, demonstrating effective application in handling complex cell images and distinguishing between slender and stumpy forms in challenging imaging conditions.</p> <p><strong>Usage:</strong></p> <p>Researchers are encouraged to use this dataset to:</p> <ul> <li>Analyze and classify the life cycle stages of <em>T. brucei</em> bloodstream forms in microscopic images.</li> <li>Develop and test deep learning models for single-cell image segmentation and classification.</li> <li>Explore cellular morphology patterns and refine machine learning approaches for other single-cell imaging applications.</li> </ul> <p><strong>Citation:</strong></p> <p>Please cite the original dataset if you utilize this resource in your research to acknowledge its contribution to the field.</p> <p><strong>Access and Availability:</strong></p> <p>This dataset is openly available through Zenodo, enabling researchers to download, explore, and apply it in various fields, from parasitology to advanced computational biology.</p>
Figure 7. T in Bioinformatics and expression analysis of the Xeroderma Pigmentosum complementation group C (XPC) of Trypanosoma evansi in Trypanosoma cruzi cells
Figure 7. T. cruzi growth assessment after cisplatin treatment (300 ΜM). (a) Wild type (WT). (b) TcXPC superexpressor (Tc-TcXPC). (c) TevXPC expressor (Tc-TevXPC). The solid lines represent the untreated cells, while the dotted lines represent the cells treated with cisplatin. Statistical student's t test: (*) On that point, cells treated with cisplatin presented a statistically significant lower growth in relation to untreated cells (p <0.05). Representative results of three independent experiments.
Figure 6 in Bioinformatics and expression analysis of the Xeroderma Pigmentosum complementation group C (XPC) of Trypanosoma evansi in Trypanosoma cruzi cells
Figure 6. Growth assessment of T. cruzi: wild type (WT), TcXPC superexpressor (Tc-TcXPC) and TevXPC expressor (Tc-TevXPC). Statistical student's t test: (*) On that point, only Tc-TevXPC presented a statistically significant lower growth in relation to WT (p <0.05); (**) On that point, both Tc-TcXPC and Tc-TevXPC presented a significant lower growth in relation to WT (p <0.05). All parasites were at same initial concentration, grown on LIT medium and were counted daily. Representative results of three independent experiments.
Figure 5 in Bioinformatics and expression analysis of the Xeroderma Pigmentosum complementation group C (XPC) of Trypanosoma evansi in Trypanosoma cruzi cells
Figure 5. TevXPC amplification by RT-PCR with the cDNA from cell cultures. Lanes: (1) 1Kb DNA Ladder; (2) WT; (3) Tc-TcXPC; (4 and 5) Tc-TevXPC; (6) positive control (DNA from T. evansi); (7) negative control.
Figure 4 in Bioinformatics and expression analysis of the Xeroderma Pigmentosum complementation group C (XPC) of Trypanosoma evansi in Trypanosoma cruzi cells
Figure 4. (a) TcXPB-R protein model. (b) TevXPB-R protein model. (c) TcXPB-R (blue) and TevXPB-R (orange) models overlay.
Figure 2 in Bioinformatics and expression analysis of the Xeroderma Pigmentosum complementation group C (XPC) of Trypanosoma evansi in Trypanosoma cruzi cells
Figure 2. (a) Alignment between TcXPC and TevXPC proteins (mismatches highlighted) and its domains. Green: RAD4/PNGase transglutaminase-like fold. Blue: RAD4 beta-hairpin domain 1. Red: RAD4 beta-hairpin domain 2. Yellow: RAD4 beta-hairpin domain 3. (b) Candidate sequence motif involved in p62 interaction (highlighted by brown rectangle) found in TcXPC and TevXPC. This sequence is suggested based on the sequence motif described for Human XPC and yeast RAD4: D/E-F/W-E-D/E-V.
Figure 1 in Bioinformatics and expression analysis of the Xeroderma Pigmentosum complementation group C (XPC) of Trypanosoma evansi in Trypanosoma cruzi cells
Figure 1. (a) TcXPC protein model. (b) TevXPC protein model. (c) TbXPC protein model (d) Model of TevXPC protein bound to a mismatch DNA. (e) TcXPC (red), TevXPC (blue) and TbXPC (green) models overlay. (f) Crystal structure of Rad4-Rad23 bound to a mismatched DNA performed by Min and Pavletich (2007).
Figure 3 in Bioinformatics and expression analysis of the Xeroderma Pigmentosum complementation group C (XPC) of Trypanosoma evansi in Trypanosoma cruzi cells
Figure 3. (a) TcXPB protein model. (b) TevXPB protein model. (c) TcXPB (green) and TevXPB (red) models overlay.
Fig. 2 in Trypanosoma brucei: trypanocidal and cell swelling activities of lasalocid acid
Fig. 2 Effect of lasalocid acid and salinomycin on the growth of bloodstream forms of T. brucei and human myeloid leukaemia HL-60 cell. Trypanosomes (circles) and HL-60 cells (squares) were incubated with varying concentration of lasalocid acid (closed symbols) or salinomycin (open symbols). After 72 h of culture, cell viability and proliferation were determined with the colorimetric dye resazurin. The experiment was repeated three times and mean values ± SD of three experiments are shown
Fig. 3 in Trypanosoma brucei: trypanocidal and cell swelling activities of lasalocid acid
Fig. 3 Effect of polyether ionophore antibiotics on the cell volume of bloodstream forms of T. brucei. a Trypanosomes (5 × 107 cell/ml) were incubated with 100 μM lasalocid acid (triangles) or salinomycin (squares) in Baltz medium in the presence of 1% DMSO. Controls (circles) were incubated with 1% DMSO. Every 10 min, the absorbance at 490 nm was measured. Mean values ± SD of three experiments are shown. Except for the time point 0 min at all other time points, the absorbance values were statistically significantly different from each other (One-way ANOVA test, p <0.01). b Trypanosomes (5 × 107 cell/ml) were incubated with 100 μM lasalocid acid in the absence (closed circles, solid line) or presence of 6 mM EDTA (open squares, dashed line) in Baltz medium containing 1% DMSO. Every 10 min, the absorbance at 490 nm was measured. Mean values of three experiments are shown. For clarity, the standard deviations were omitted. The standard deviations ranged between 17.5–25.1% of the mean values. At each time point, the data points of the two curves were statistically not significantly different (p = 0.465–0.977, Student's t test)
Fig. 1 in Trypanosoma brucei: trypanocidal and cell swelling activities of lasalocid acid
Fig. 1 Structure of lasalocid acid. The PubChem compound identifier (CID) for the compound is shown in parentheses
Fig. 3 A in Comparative analysis of metacyclogenesis and infection curves in different discrete typing units of Trypanosoma cruzi
Fig. 3 A The production of amastigotes per cell in T. cruzi infections provides insight into the intracellular dynamics of T. cruzi within host cells. B Percentage of uninfected cells observed along the infection curves, susceptibility dynamics, and infection progression, highlighting variations in the percentage of uninfected cells throughout the experimental period. C Release of cell-derived trypomastigotes during infection of Vero cells, Neubauer chamber count
Fig. 1 A in Comparative analysis of metacyclogenesis and infection curves in different discrete typing units of Trypanosoma cruzi
Fig. 1 A Microphotographs of 10-day incubation cultures of Trypanosoma cruzi epimastigotes in LIT medium with Field's staining and magnification (100 ×), metacyclic forms are indicated by red arrows. B Epimastigote production, evaluated for 12 days in a LIT medium. C Metacyclogenetic curve representing the dynamic process of metacyclic trypomastigote formation in T. cruzi. In x is the time (days) while the y-axis indicates the number of metacyclic trypomastigotes (MT) per milliliter. The data points provide information on the efficacy and kinetics of metacyclic trypomastigote production. D Dynamics of metacyclogenesis in T. cruzi, capturing both the starting point and the peak of the process. The data presented provide a better understanding of the timing and efficiency of metacyclic trypomastigote production. E This comparative approach uses brackets to indicate statistically significant differences (p <0.05) between DTUs in both the onset and peak phases of metacyclogenesis. In this graph, it can be seen whether there are DTUs with noticeable variations during the kinetics of metacyclogenesis
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.