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Supplementary material 2 from: Petersen M, Hoffmann J, Glöckler F (2019) Access to Geosciences – Ways and Means to share and publish collection data. Research Ideas and Outcomes 5: e32987. https://doi.org/10.3897/rio.5.e32987
Results of the survey on geoscientific collection data. Names, institutions and contact details are anonymized
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, in country countries highlight each areas for two, the dotted give for cells common densely grey . and in in respectively figures species Sparsely, .) of) The 1 Uganda . number Group Africa ( and from show area data cells rainforest Congo. R white. D original , in Republic and Figures Guineo-Congolian published . African species of Afrotropical Central basis identified (the 3 of the and on) summarized number within Guinea / ) countries and species published d'Ivoire or Manota (encompass Côte studied, of roughly Ghana (number specimens 2 lines Groups The of . Dashed 1 number TABLE . distribution the focus
Data to be published
<p>Different datasets for hydroclimate analysis of drought over Europe</p>
Supporting data and code for the published paper: Machine Learning Nonadiabatic Dynamics: Eliminating Phase Freedom of Nonadiabatic Couplings with the State-Interaction State-Averaged Spin-Restricted Ensemble-Referenced Kohn–Sham Approach
Open the record for dataset details and reuse information.
Figure 6 in Karyotypes of water scavenger beetles (Coleoptera: Hydrophilidae): new data and review of published records
Figure 6. Karyotypes of the Hydrophilini. A–C, Hydrophilus, mitotic karyotype from embryo (A–B, Hydrophilus piceus; C, Hydrophilus pistaceus). D–H, Hydrochara: (D–F) Hydrochara caraboides, mitotic karyotype, embryo; (G–H) Hydrochara flavipes, mitotic karyotype, midgut. I–J, Sternolophus solieri (I, male mitotic karyotype; J, meiotic first metaphase from testes). A, C, D, G, I, without treatment. B, E, F, H, C-banded. Habitus figures: (K) Sternolophus solieri; (L) Hydrochara caraboides; (M) Hydrophilus piceus, from Short & Fikáček (2013).
Figure 5 in Karyotypes of water scavenger beetles (Coleoptera: Hydrophilidae): new data and review of published records
Figure 5. Karyotypes of the Hydrobiusini. A–D, Limnohydrobius convexus: (A–B) mitosis, midgut; (C–D): testis, prometaphase. F–J, Limnoxenus niger: (F–H) midgut; (I–J) meiotic metaphase I, testes. A–C, E–F, I, without treatment. D, G, H, J, C-banded. Habitus figures: (E) Limnohydrobius convexus; (K) Limnoxenus niger.
Figure 3 in Karyotypes of water scavenger beetles (Coleoptera: Hydrophilidae): new data and review of published records
Figure 3. Karyotypes of the Laccobiini, without treatment. A–H, Paracymus: (A–B) Paracymus aeneus, mitotic metaphase from midgut; (C–D) Paracymus scutellaris (C, spermatogonial mitosis, metaphase; D, mitotic metaphase from midgut.); (E–G) meiotic metaphase I from testes (E, Paracymus aeneus; F–G, Paracymus scutellaris). I–M, Tormus, mitotic metaphase from midgut: (I, K) Tormus posticalis; (J, L) Tormus helmsi. Habitus figures: (G) Paracymus scutellaris; (M) Tormus helmsi, from Fikáček et al. (2013).
Figure 1 in Karyotypes of water scavenger beetles (Coleoptera: Hydrophilidae): new data and review of published records
Figure 1. Tissues of hydrophiloid beetles used for chromosome preparations (as dissected, without any additional treatment, (B–E) in dorsal view; (A) Helophorus grandis; (B, C, I) Laccobius bipunctatus; (D–H) Coelostoma orbiculare). A, egg with a developing embryo. B–C, internal organs of the same male specimen in translucent light (B) and on black background (C). D, internal organs of a female with digestive system pulled aside. E, internal organs of male specimen. F, details of ovarioles and associated accessory glands. G–I, detail of midgut structure on black background (G) and in translucent light (H, I). Abbreviations: accg, accessory glands; aed, aedeagus; hg, hindgut; mg, midgut; Mt, Malpighian tubes; oo, ovarioles; ovi, ovipositor; rc, regeneration crypts; tes, testes. Not to scale.
Figure 2 in Karyotypes of water scavenger beetles (Coleoptera: Hydrophilidae): new data and review of published records
Figure 2. Karyotypes of the Amphiopini and Laccobiini. A–E, Amphiops mater, mitotic methaphase from midgut. F–L, Laccobius decorus, mitotic metaphase from midgut. A, C, F, H, J, without treatment. B, D, G, I, K, C-banded. Habitus figures: (E) Amphiops mater; (L) Laccobius decorus.
Figure 13 in Karyotypes of water scavenger beetles (Coleoptera: Hydrophilidae): new data and review of published records
Figure 13. Karyotypes of the Cylominae, without treatment. A, D, Exydrus gibbosus, mitosis, midgut. B–C, E, Tormissus magnulus, mitosis, midgut. F–H, Rygmodus modestus (F–G, meiotic metaphase I, testes; H, mitotic karyotype, midgut). Habitus figures: (I) Exydrus gibbosus; (J) Rygmodus modestus, from Minoshima et al. (2018).
Figure 14 in Karyotypes of water scavenger beetles (Coleoptera: Hydrophilidae): new data and review of published records
Figure 14. Karyotypes of the Omicrini and Sphaeridiini, without treatment. A–F, Omicrini: (A–B) Noteropagus sp. from Taiwan, meiotic karyotypes from testes; (C–D) Omicrogiton insularis, mitotic karyotype, midgut; (E–F) Paromicrus sp. from Taiwan, mitotic karyotype, midgut. G–I, habitus of examined specimens: (G) Noteropagus sp.; (H) Omicrogiton insularis; (I) Paromicrus sp. J–P, Sphaeridiini: Sphaeridium; (J–K) Sphaeridium lunatum (J, testes, mitosis; K, midgut, mitosis); (L) Sphaeridium scarabaeoides, mitosis, midgut; (M) Sphaeridium bipustulatum, mitosis, midgut; (N–P) meiosis, metaphase I, testes: (N) Sphaeridium scarabaeoides; (O) Sphaeridium bipustulatum; (P) Sphaeridium lunatum. Q, habitus of Sphaeridium scarabaeoides.
Figure 12 in Karyotypes of water scavenger beetles (Coleoptera: Hydrophilidae): new data and review of published records
Figure 12. Karyotypes of the Cylominae, without treatment. A–B, Adolopus sp., mitosis from midgut. D, Cyloma guttulatus, mitosis from midgut. E–G, Cyloma sp. (E–F, meiotic first metaphase; G, testes, mitosis;). I–M, Cylomissus glabratus: (I–J) mitotic metaphase from midgut; (K–M) meiotic metaphase I from testes. Habitus figures: (C) Adolopus sp.; (H) Cyloma sp., specimen collected with karyotyped voucher; (N) Cylomissus glabratus, from Minoshima et al. (2015).
Figure 11 in Karyotypes of water scavenger beetles (Coleoptera: Hydrophilidae): new data and review of published records
Figure 11. Karyotypes of the Acidocerinae. A–C, Agraphydrus, mitotic metaphase, midgut: (A–B) Agraphydrus decipiens; (C) Agraphydrus variabilis. D–L, Helochares: (D–E) Helochares lividus, mitosis, midgut; (F) Helochares obscurus, mitosis, midgut; (G–H) Helochares punctatus, mitosis, midgut; (I) Helochares punctatus, karyotype of male embryo with multiple y-chromosomes; (J–K) meiotic metaphase I from testes (J, Helochares punctatus; K, Helochares lividus); (L) Helochares sauteri, mitosis, midgut. A, D, F, G, I–L, without treatment. B, C, E, H, C-banded. Habitus figures: (M) Agraphydrus decipiens, from Minoshima, Komarek, & Ȏhara 2015; (N) Helochares obscurus.
Figure 10 in Karyotypes of water scavenger beetles (Coleoptera: Hydrophilidae): new data and review of published records
Figure 10. Karyotypes of Enochrus (Lumetus). A–C, Enochrus quadripunctatus, mitosis, midgut. D–K, Enochrus fuscipennis, mitosis, midgut (H–I, specimens from Denmark, Rømø Island with the karyotypes indicating their hybrid origin). L–N, meiotic metaphase I from testes (L, Enochrus quadripunctatus, UK: East Walton, Norfolk; M–N, Enochrus fuscipennis, Denmark: Rømø Island). O–P, Enochrus fuscipennis, testes, mitotic metaphase from the same specimens as in (H–I). A, B, D, E, H, I, J, M–P, without treatment. C, F, G, K, L, C-banded.
Figure 9 in Karyotypes of water scavenger beetles (Coleoptera: Hydrophilidae): new data and review of published records
Figure 9. Karyotypes of Enochrus (Lumetus), mitosis from embryos. A, Enochrus bicolor. B–C, Enochrus ochropterus. D–E, Enochrus testaceus. F–K, Enochrus halophilus. A, B, D, F, H, I, without treatment. C, E, G, K, C-banded. Habitus figures: (L) Enochrus (Lumetus) testaceus; (M) Enochrus (Lumetus) halophilus.
Figure 8 in Karyotypes of water scavenger beetles (Coleoptera: Hydrophilidae): new data and review of published records
Figure 8. Mitotic karyotypes of the Enochrinae. A, Cymbiodyta marginella, embryo. B–D, European usual-looking species of Enochrus (Methydrus) from embryos: (B) Enochrus affinis; (C) Enochrus coarctatus; (D–E) Enochrus nigritus. F–G, unusual species assigned at the moment to Enochrus (Methydrus): (F) Enochrus morenae, midgut; (G) Enochrus sauteri, midgut. H, Enochrus (s.s.) melanocephalus, embryo. A–G, without treatment. H, C-banded. Habitus figures: (I) Cymbiodyta marginella; (J) Enochrus morenae.
Figure 17 in Karyotypes of water scavenger beetles (Coleoptera: Hydrophilidae): new data and review of published records
Figure 17. Mitotic karyotypes of Cercyon from midgut. (A) Cercyon marinus; (B–E) Cercyon lateralis; (F–G) Cercyon obsoletus; (H) Cercyon impressus; (I–K) Cercyon haemorrhoidalis; (L–N) Cercyon melanocephalus. A, B, D, F, H, I, K, L, N, without treatment. C, E, G, J, M, C-banded. Habitus figures: (O) Cercyon marinus; (P) Cercyon impressus; (Q) Cercyon haemorrhoidalis, from Fikáček (2019).
Figure 15 in Karyotypes of water scavenger beetles (Coleoptera: Hydrophilidae): new data and review of published records
Figure 15. Karyotypes of the Coelostomatini and Protosternini. A–C, Coelostoma orbiculare, embryo (A, with B-chromosomes; B–C, without B-chromosomes). D–F, Dactylosternum flavicorne, embryo. G, Dactylosternum corbetti, mitosis, midgut. J–K, Protosternum abnormale, meiotic nuclei from testes. A–F, J, K, without treatment. G, C-banded. Habitus figures: (H) Coelostoma orbiculare; (I) Dactylosternum corbetti; (L) Protosternum abnormale, from Fikáček et al. (2018).
All data support published article "Function of four tryptophan residues on Cel7A catalytic efficiency: insight into cellulase screening strategy based on natural cellulose or cellulose analogs"
<p>There is a high level of conservation of tryptophans within the active site architecture of the cellulase family, whereas the function of the four tryptophans in the catalytic domain of Cel7A is unclear. By mutating four tryptophan residues in the catalytic domain of Cel7A from <em>Penicillium piceum</em> (PpCel7A), the binding affinity between PpCel7A and <em>p-</em>nitrophenol-D-cellobioside (<em>p</em>NPC) was reduced as determined by Michaelis–Menten constants, molecular dynamics simulations, and fluorescence spectroscopy. Furthermore, PpCel7A variants showed a reduced level of cellobiohydrolase activity against cellulose analogs or natural cellulose. Therefore, it could be concluded four tryptophan residues in Cel7A played a critical role in substrate binding. Mutagenesis results indicated that the W390 stacking interactions at the -2 site played an essential role in facilitating substrate distortion to the -1 site. As soon as the function was altered, the mutation would inevitably affect the catalytic activity against the natural substrate. Interestingly, no clear relationship was found between the cellobiohydrolase activity of PpCel7A variants against <em>p</em>NPC and Avicel. <em>p</em>NP contains many electrophilic groups that may result in overestimation of the binding constant between tryptophan residues and <em>p</em>NPC in comparison to the natural substrate. Consequently, screening improved cellulase using cellulose analogs would divert attention from the target direction for lignocellulose biorefinery. Clarifying mechanism of catalytic diversity on the natural cellulose or cellulose analogs may give better insight into cellulase screening and selecting strategy.</p>
All data support the published articel "Loop-optimization of Trichoderma reesei endoglucanases for balancing the activity–stability trade-off through cross-strategy between machine learning and the B-factor analysis"
<p><em>Trichoderma reesei</em> endoglucanases (EGs) have limited industrial applications due to its low thermostability and activity. Here, we aimed to improve the thermostability of EGs from<em> T.reesei</em> without reducing its activity counteracting the activity-stability trade-off. A cross-strategy combination of machine learning and B-factor analysis was used to predict beneficial amino acid substitution in EG loop optimization. Experimental validation showed single-site mutated EG concomitantly improved enzymatic activity and thermal properties by 17.21%–18.06% and 49.85%–62.90%, respectively, compared with wild-type EGs. Furthermore, the mechanism explained mutant variants had lower RMSD values and a more stable overall structure than the wild type. According to this study, EGs loop optimization is crucial for balancing the activity-stability trade-off, which may provide new insights into how loop region function interacts with enzymatic characteristics. Moreover, the cross-strategy between machine learning and B-factor analysis improved superior enzyme activity-stability performance, which integrated structure-dependent and sequence-dependent information.</p>
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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.