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490 results for “DNA integrity”
An Integrated Structural Model of the DNA Damage Responsive H3K4me3 Binding WDR76:SPIN1 Complex with the Nucleosome
<p>Serial Capture Affinity Purification (SCAP) is a powerful method to isolate a specific protein complex. When combined with cross linking mass spectrometry (XL-MS) and computational approaches one can build an integrated structural model of the isolated complex. Here, we applied SCAP to dissect a subpopulation of WDR76 in complex with SPIN1, a histone marker reader that specifically recognizes trimethylated histone H3 lysine4 (H3K4me3). In contrast to a previous SCAP analysis of the SPIN1:SPINDOC complex, histones and the H3K4me3 mark were copurified with the WDR76:SPIN1 complex. Next, interaction network analysis of copurifying proteins and microscopy analysis revealed a potential role of the WDR76:SPIN1 complex in the DNA damage response. Since we detected an extensive number of cross-linked sites were found between WDR76, SPIN1, and histones, we first built an integrated structural model of the complex which revealed that SPIN1 recognized the H3K4me3 epigenetic mark while interacting with WDR76. Finally, we then used the powerful Integrative Modeling Platform to build a structural model of WDR76 and SPIN1 bound to the nucleosome.</p>
Figures 60–65 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 60–65. Heterolepisma cooloola sp. nov. holotype ♀ (60) presternum, prothoracic sternum and PI; (61) mesothoracic sternum and PII; (62) apex of mesothoracic sternum; (63) metathoracic sternum and PIII; (64) apex of metathoracic sternum; (65) pretarsus of PIII. Scale bars = 0.1 mm.
Figures 24–31 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 24–31. Heterolepisma coorongooba sp. nov. holotype ♀ (24) presternum, prothoracic sternum and PI; (25) mesothoracic sternum; (26) metathoracic sternum and PIII; (27) urotergite III; (28) idem, sublateral comb; (29) idem, submedial comb; (30) urotergite IX, infralateral combs; (31) urotergite X. Scale bars = 0.1 mm.
Figures 15–23 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 15–23. Heterolepisma coorongooba sp. nov. holotype ♀ (15) left lateral, anterior and posterior margins of pronotum; (16) idem, detail of left anterior trichobothrial area; (17) idem, detail of right posterior trichobothrial area; (18) idem, left posterior comb of pronotum; (19) lateral margin of mesonotum; (20) idem, trichobothrial areas of right side; (21) idem, left posterior comb of mesonotum; (22) lateral margin of metanotum; (23) idem, trichobothrial areas of left side. Scale bars = 0.1 mm.
Figures 7–14 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 7–14. Heterolepisma sclerophylla Smith and Heterolepisma coorongooba sp. nov. (7) Heterolepisma sclerophylla Smith, holotype ♀, medial section of pronotal collar. (8–14) Heterolepisma coorongooba sp. nov. holotype ♀ (8) medial section of pronotal collar; (9) lateral bristlecomb of urotergite III and adjacent scale; (10) head; (11) scape, pedicel and basal interval of flagellum, from above; (12) antenna, most distal surviving annuli; (13) maxilla, only larger setae of palp illustrated; (14) labium, setae of palp not strong so not illustrated. Scale bars = 0.1 mm.
Figures 32–36 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 32–36. Heterolepisma coorongooba sp. nov. holotype ♀, unless otherwise indicated by specimen number (32) urosternite III; (33) idem, posterior comb; (34) coxites VIII and IX, ovipositor and styli; (35) coxite IX, paramere and penis (K.260993); (36) paramere (K.260993). Scale bars = 0.1 mm.
Figures 78–85 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 78–85. Heterolepisma cooloola sp. nov. holotype ♀ unless otherwise indicated by specimen number (78) stylet IX (QM 207012); (79) apex of anterior gonapophysis; (80) apex of posterior gonapophysis; (81) bases of terminal filaments; (82) most distal surviving divisions of cerci; (83) most distal surviving divisions of median filament; (84) coxites IX, styli and penis of male (QM 207012); (85) paramere. Scale bars = 0.1 mm.
Figures 49–59 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 49–59. Heterolepisma cooloola sp. nov. holotype ♀ (49) labium, only large setae of palp illustrated; (50) idem, ultimate article of palp; (51) pronotum; (52) idem, right margin; (53) idem, detail of right anterior trichobothrial area; (54) idem, detail of left posterior trichobothrial area; (55) lateral margin of mesonotum; (56) idem, posterior trichobothrial area; (57) idem, anterior trichobothrial area; (58) idem, right posterior comb; (59) lateral margin of metanotum. Scale bars = 0.1 mm.
Figure 4 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figure 4. BI tree for concatenated COI and 28S genes. BI posterior probabilities and ML bootstrap values are shown above and below branches, if ≥0.9 or ≥70%, respectively. Asterisks indicate type specimens, with a single asterisk for paratypes and a double asterisk for holotypes.
Figure 3 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figure 3. BI tree for nuclear gene 28S. BI posterior probabilities and ML bootstrap values are shown above and below branches, if ≥0.9 or ≥70%, respectively. Asterisks indicate type specimens, with a single asterisk for paratypes and a double asterisk for holotypes.
Figure 5 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figure 5. Scatterplot of principal component analysis 1. Members of lineages are indicated by a ⅔ confidence interval ellipse.
Figures 38–48 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 38–48. Heterolepisma cooloola sp. nov. holotype ♀, unless indicated otherwise by specimen number(38) habitus (K.377754); (39) posterior comb of pronotum with scale; (40) head; (41) scape, pedicel and basal intervals of flagellum, from above; (42) idem, from below; (43) antenna, most distal surviving interval; (44) mandible; (45) idem, detail of molar and incisor regions; (46) maxilla, only larger setae of palp illustrated; (47) idem, lacinia and galea (QM 207012); (48) ultimate article of maxillary palp of ♂ (QM 207012). Scale bars = 0.1 mm unless otherwise indicated.
Figures 66–77 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figures 66–77. Heterolepisma cooloola sp. nov. holotype ♀, unless otherwise indicated by specimen number (66) urotergite IV; (67) urotergite V, right lateral comb; (68) idem, left sublateral comb; (69) idem, left submedial comb; (70) right side of urotergite VIII (K.261189); (71) infralateral comb of urotergite IX; (72) urotergite X; (73) urotergite X of paratype (QM 207012); (74) urosternite IV; (75) posterior comb of urosternite V; (76) urosternites VII, VIII, IX and ovipositor; (77) base of stylus VII. Scale bars = 0.1 mm.
Figure 2 in DNA Barcoding and Integrative Taxonomy of the Heterolepisma sclerophylla species complex (Zygentoma: Lepismatidae: Heterolepismatinae) and the Description of Two New Species
Figure 2. BI trees for mitochondrial genes 16S and COI. BI posterior probabilities and ML bootstrap values are shown above and below branches, if ≥0.9 or ≥70%, respectively.Asterisks indicate type specimens, with a single asterisk for paratypes and a double asterisk for holotypes.
Figs 30–35 in Description of a new species of Loxosceles Heineken & Lowe (Araneae, Sicariidae) recluse spiders from Hidalgo, Mexico, under integrative taxonomy: morphological and DNA barcoding data (CO1 + ITS2)
Figs 30–35. Variation of the male palps, left palps, prolateral views. 30–33. Loxosceles tolantongo sp. nov. 30–32. Tourist Center Grutas de Tolantongo, Municipality of Cardonal, Hidalgo (type locality). 33. 500 m west of the entrance No. 5 to the Tourist Center Grutas de Tolantongo, Municipality of Cardonal, Hidalgo. 34–35. Loxosceles jaca Gertsch & Ennik, 1983. 2.5 km north of Jacala de Ledezma, Municipality of Jacala de Ledezma, Hidalgo. Scale bars = 0.5 mm.
Fig. 56 in Description of a new species of Loxosceles Heineken & Lowe (Araneae, Sicariidae) recluse spiders from Hidalgo, Mexico, under integrative taxonomy: morphological and DNA barcoding data (CO1 + ITS2)
Fig. 56. Maximum likelihood tree inferred from the concatenated matrix (CO1 + ITS2) of species of Loxosceles Heineken & Lowe, 1832 from Mexico. Colors of branches and bars indicate different species. Numbers above bars represent the delimitation methods: 1 = morphology (M); 2 = neighbor joining (NJ); 3 = ABGD with initial partitions (IP); 4–5 = ABGD with recursive partitions (RP); 6 = GMYC yule analysis; 7 = GMYC coalescent analysis; 8 bPTP with ML; 9 = bPTP with IB. Numbers below bars represent species recovered for each delimitation method. Red numbers correspond to Bayesian posterior probabilities, black numbers are bootstrap support values from the ML analysis.
Figs 20–25 in Description of a new species of Loxosceles Heineken & Lowe (Araneae, Sicariidae) recluse spiders from Hidalgo, Mexico, under integrative taxonomy: morphological and DNA barcoding data (CO1 + ITS2)
Figs 20–25. Loxosceles tolantongo sp. nov., ♂ holotype (CNAN-T01317). 20–22. Left palp, prolateral, dorsal and retrolateral views, respectively. 23–25. Detail of the bulb and embolus, retrolateral, dorsal and apical views, respectively. Scale bars: 20–22 = 0.5 mm; 23–25 = 0.2 mm.
Fig. 54 in Description of a new species of Loxosceles Heineken & Lowe (Araneae, Sicariidae) recluse spiders from Hidalgo, Mexico, under integrative taxonomy: morphological and DNA barcoding data (CO1 + ITS2)
Fig. 54. Maximum likelihood tree inferred from CO1 gene of species of Loxosceles Heineken & Lowe, 1832 from Mexico. Colors of branches and bars indicate different species. Numbers above bars represent the delimitation methods: 1 = morphology (M); 2 = neighbor joining (NJ); 3 = ABGD with initial partitions (IP); 4–6 = ABGD with recursive partitions (RP); 7 = GMYC yule analysis; 8 = GMYC coalescent analysis; 9 = bPTP with ML; 10 = bPTP with IB. Numbers below bars represent species recovered for each delimitation method. Red numbers on branches correspond to Bayesian posterior probabilities, black numbers are bootstrap support values from the ML analysis.
MetaCOXI: An integrated collection of metazoan cytochrome oxidase subunit-I DNA sequences
<p><strong>MetaCOXI Sequences Taxonomy and Metadata</strong></p> <p>This collection is based on the integration of the European Nucleotide Archive (ENA, release 142) and the Barcode of Life Data Systems (BOLD: <a href="http://www.boldsystems.org/">http://www.boldsystems.org/</a>) data.</p> <p><strong>CONTENT: </strong>Currently it contains 5,608,848 entries of metazoan COXI sequences and their corresponding taxonomic classification and metadata. <em>MetaCOXI_Seqs.tar.gz</em> contains the full sequence collection in 'fasta' format. <em>MetaCOXI_Taxonomy_Metadata.tar.gz</em> contains the entries-associated taxonomy path and additional metadata</p> <p>Taxonomic path are provided for the following seven levels with their NCBI-TaxIDs: Kingdom, Phylum, Class, Order, Family, Genus, Species.</p> <p>For additional information visit: https://github.com/bachob5/MetaCOXI</p>
MetaCOXI: An integrated collection of metazoan cytochrome oxidase subunit-I DNA sequences
<p><strong>MetaCOXI Sequences in fasta format</strong></p> <p>This collection is based on the integration of the European Nucleotide Archive (ENA, release 142) and the Barcode of Life Data Systems (BOLD: http://www.boldsystems.org/) data.</p> <p><strong>CONTENT: </strong>Currently it contains 5,608,848 entries of metazoan COXI sequences and their corresponding taxonomic classification and metadata. MetaCOXI_Seqs_1.tar.gz contains the full sequence collection in 'fasta' format. MetaCOXI_Taxonomy_Metadata.tar.gz contains the entries-associated taxonomy path and additional metadata</p> <p>Taxonomic path are provided for the following seven levels with their NCBI-TaxIDs: Kingdom, Phylum, Class, Order, Family, Genus, Species.</p> <p>For additional information visit: https://github.com/bachob5/MetaCOXI</p>
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
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Annotated Behaviour and Observability Dataset (ABODe)
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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.