Find research datasets worth reusing

Fig. 20 in The Indo-Pacific Amalda (Neogastropoda, Olivoidea, Ancillariidae) revisited with molecular data, with special emphasis on New Caledonia

Fig. 20. Radulae of species of Amalda H. Adams & A. Adams, 1853. A. Amalda sp., MNHN IM-2013- 63891 (shell on Fig. 19A–B). B, E. A. monilifera (Reeve, 1864), MNHN IM-2013-63898 (shell on Fig. 19F–G). C–D. A. contusa, MNHN IM-2009-22264, SL 22.7 mm. F–I. A. hayashii Ninomiya, 1988. F–G. MNHN IM-2013-44413 (shell on Fig. 19J–K). H. MNHN IM-2013-44432. I. MNHN IM-2013- 44457, SL 38.2 mm. J–K. A. hinomotoensis (Yokoyama, 1922), MNHN IM-2019-619, SL 38.5 mm.

Fig. 18. A–E. A in The Indo-Pacific Amalda (Neogastropoda, Olivoidea, Ancillariidae) revisited with molecular data, with special emphasis on New Caledonia

Fig. 18. A–E. A. fuscolingua Kilburn & Bouchet, 1988. A–B. Holotype, MNHN IM-2000-1439, SL 30.6 mm. C. MNHN IM-2007-43643, SL 26.6 mm (sequenced specimen). D–E. MNHN IM-2007- 43649, SL 30.2 mm (sequenced specimen). F–J. A. coriolis Kilburn & Bouchet, 1988. F–G. Holotype, MNHN IM-2000-1393, SL 40.1 mm. H–I. MNHN IM-2013-63899, SL 40.4 mm (sequenced specimen). J. Coral Sea, Capel Bank, KANADEEP, stn DW4944, 25°21′ S, 159°45′ E, 235–242 m, SL 37.3 mm. A–E = at the same scale; F–J = at the same scale.

Fig. 12 in The Indo-Pacific Amalda (Neogastropoda, Olivoidea, Ancillariidae) revisited with molecular data, with special emphasis on New Caledonia

Fig. 12. Amalda montrouzieri (Souverbie, 1860), southern New Caledonia. A–C. Syntype MNHN IM-2000-1475, SL 41.4 mm. D–E. MNHN IM-2013-80199, SL 18.7 mm (sequenced specimen). F. Secteur Île Ouen-Baie du Prony, LAGON, stn DW98, 22°35.7′ S, 166°31.8′ E, 15 m, SL 25.6 mm. G. Grand Récif Sud, LAGON, stn DW334, 22°38′ S, 166°53.6′ E, 47–48 m, SL 26.6 mm (illustrated by Kilburn & Bouchet 1988: fig. 14). H. Secteur de Nouméa. LAGON, stn DW51, 22°14.7′ S, 166°11.1′ E, 10 m, SL 27.6 mm. I. Grand Récif Sud, LAGON, stn DW544, 22°50.8′ S, 166°48.5′ E, 25 m, SL 25.4 mm. J–K. A. cf. montrouzieri. Deep-water morph, SMIB2, stn DW23, 22°31′ S, 167°37′ E, 410–420 m, SL 30.2 mm (specimen illustrated by Kilburn & Bouchet 1988: figs 5–6). All specimens except D–E not sequenced. Shells at the same scale.

Fig. 11 in The Indo-Pacific Amalda (Neogastropoda, Olivoidea, Ancillariidae) revisited with molecular data, with special emphasis on New Caledonia

Fig. 11. Amalda cacao sp. nov. A–E. Holotype, MNHN IM-2000-35296, SL 74.9 mm (D–E = enlarged apical and lateral views of the protoconch), specimen not sequenced. F. MNHN IM-2007-33287, SL 61 mm, sequenced specimen. G. KANADEEP 1, stn DW4951, 25°29′ S, 159°49′ E, 310–320 m, Capel Bank, SL 50 mm, specimen not sequenced. H. NORFOLK 1, stn CP1676, 24°44′ S, 168°09′ E, 227–232 m, Norfolk Ridge, SL 67.1 mm, specimen not sequenced. Shells at the same scale.

Fig. 6 in The Indo-Pacific Amalda (Neogastropoda, Olivoidea, Ancillariidae) revisited with molecular data, with special emphasis on New Caledonia

Fig. 6. Amalda hilgendorfi (von Martens, 1897). Southern New Caledonia morph. A–D and E–H belong to two molecularly distinct subclades. A–B. MNHN IM-2007-43664, SL 30.6 mm. C. MNHN IM-2007-43673, SL 34.2 mm. D. MNHN IM-2009-11964, SL 15.2 mm. E–F. MNHN IM-2007-43671, SL 33.8 mm. G. MNHN IM-2007-43674, SL 34.7 mm. H. MNHN IM-2009-11945, SL 31.6 mm. I. Norfolk Ridge, Banc Éponge, NORFOLK 1, stn DW 1693, 24°55′ S, 168°21′ E, 564–1144 m, SL 61 mm, specimen not sequenced, shell not to scale. Shells (except I, reduced) at the same scale.

Fig. 17 in The Indo-Pacific Amalda (Neogastropoda, Olivoidea, Ancillariidae) revisited with molecular data, with special emphasis on New Caledonia

Fig. 17. Comparison of Amalda allaryi Bozzetti, 2007 with A. montrouzieri (Souverbie, 1860). A–B. A. allaryi, MNHN IM-2013-68272, SL 26.2 mm, specimen not sequenced. C–D. A. montrouzieri, LAGON, stn DW51, Nouméa Sector, 22°15′ S, 166°11′ E, 10 m, SL 27.6 mm, specimen not sequenced.

Input Data for "Molecular Lignin Solubility and Structure in Organic Solvents"

Input structures for a manuscript, along with selected output data and structures. This directory structure contains a cut-down copy of the directories used to generate the simulation data and the analysis. In order to make this fit into the 50GB Zenodo limit, it was constructed with the following tar command: `tar -zcvf ligninsolvationstudy.tar.gz --exclude="*BAK" --exclude="*#" --exclude="*xtc" --exclude="*gro" --exclude="*log" --exclude="*[0-9].out" --exclude="*npz" --exclude="*pkl" --exclude="*npy" --exclude="*png" --exclude="*bmim*" --exclude="*old" --exclude="*dcd" --exclude="*tmp" --exclude="*xst" --exclude="*edr" --exclude="*txt" --exclude="*state_prev.cpt" LigninSolvation`, which intentionally excludes large files. The full dataset is available upon request. Directory Descriptions BuildSolventBoxes contains the scripts and inputs needed to make the solvent boxes suitable for use with the VMD solvate plugin. BuildSystems assembles the lignin polymers and solvates them into a complete simulation system. Depends on the outputs from [LigninBuilder](https://github.com/jvermaas/LigninBuilder). Equilibrium has all the equilibrium trajectories and the scripts needed to set them up. FEP has the free energy perturbation calculation key outputs (the fepout files) and the scripts needed to set up the calculation and analyze them. The scripts are mostly python scripts, but some are also in tcl, and have the appropriate file endings. GROMACS run input files (.tpr) and namd configuration files (.namd) may also be of general interest.

Fig. 7 in Eight new species of the genus Anaplecta Burmeister, 1838 (Blattodea: Blattoidea: Anaplectidae) from China based on molecular and morphological data

Fig. 7. Anaplecta cruciata Deng & Che sp. nov., holotype, ♂ (SWU). A. Habitus, dorsal view. B. Habitus, ventral view. C. Head, ventral view. D. Pronotum, dorsal view. E. Tegmina. F. Tegmina vein. G. Maxillary palp. H. Front femur, ventral view. I. Wings. J. Supra-anal plate, dorsal view. K. Subgenital plate, ventral view. L. Hook, ventral view. M. Left phallomere, ventral view. N. Right phallomere, ventral view. Scale bars: A–C = 1 mm; D–F, I–K = 0.5 mm; G–H = 0.2 mm; L–N = 0.25 mm.

Fig. 5 in Eight new species of the genus Anaplecta Burmeister, 1838 (Blattodea: Blattoidea: Anaplectidae) from China based on molecular and morphological data

Fig. 5. Anaplecta strigata Deng & Che sp. nov., holotype, ♂ (SWU). A. Habitus, dorsal view. B. Habitus, ventral view. C. Head, ventral view. D. Pronotum, dorsal view. E. Tegmina. F. Tegmina vein. G. Maxillary palp. H. Front femur, ventral view. I. Wings. J. Supra-anal plate, dorsal view. K. Subgenital plate, ventral view. L. Hook, ventral view. M. Left phallomere, ventral view. N. Right phallomere, ventral view. Scale bars: A–B = 2 mm; C, E–F, I = 1 mm; D, G–H, J–K, M–N = 0.5 mm; L = 0.25 mm.

Fig. 10. A–B, E in Eight new species of the genus Anaplecta Burmeister, 1838 (Blattodea: Blattoidea: Anaplectidae) from China based on molecular and morphological data

Fig. 10. A–B, E. Anaplecta omei Bey-Bienko, 1958. A. Habitus, dorsal view. B. Habitus, ventral view. E. Supra-anal plate, dorsal view. – C–D. Anaplecta basalis Bey-Bienko, 1969. C. Habitus, dorsal view. D. Habitus, ventral view. – F–I. Comparison of R1 of A. corneola Deng & Che sp. nov. from different localities. F. Guangdong Prov., Zhaoqing City (ZQ). G. Hainan Prov., Ledong County, Mt. Jianfengling (JFL1). H. Hunan Prov., Chenzhou City, Yizhang County, Mangshan National Forest Park (MS). I. Fujian Prov., Wuyishan City, (WY). Scale bars: A–B = 2 mm; C–D = 1 mm; E = 0.5 mm; F–I = 0.25 mm.

Fig. 4 in Eight new species of the genus Anaplecta Burmeister, 1838 (Blattodea: Blattoidea: Anaplectidae) from China based on molecular and morphological data

Fig. 4. Anaplecta arcuata Deng & Che sp. nov., holotype, ♂ (SWU). A. Habitus, dorsal view. B. Habitus, ventral view. C. Head, ventral view. D. Pronotum, dorsal view. E. Maxillary palp. F. Front femur, ventral view. G. Tegmina. H. Wings. I. Supra-anal plate, dorsal view. J. Subgenital plate, ventral view. K. Hook, ventral view. L. Left phallomere, ventral view. Scale bars: A–B, G–H = 2 mm; C = 1 mm; D–F, I–J = 0.5 mm; K–L = 0.1 mm.

Fig. 1 in Eight new species of the genus Anaplecta Burmeister, 1838 (Blattodea: Blattoidea: Anaplectidae) from China based on molecular and morphological data

Fig. 1. Maximum-likelihood (ML) tree derived from COI gene analysis following GTR GAMMA model with 1000 bootstrap replicates. Colored bars in red refer to the morphospecies, those in blue to MOTUs in ABGD and those in purple to MOTUs in GMYC.

Fig. 6 in Eight new species of the genus Anaplecta Burmeister, 1838 (Blattodea: Blattoidea: Anaplectidae) from China based on molecular and morphological data

Fig. 6. Anaplecta furcata Deng & Che sp. nov., holotype, ♂ (SWU). A. Habitus, dorsal view. B. Habitus, ventral view. C. Head, ventral view. D. Pronotum, dorsal view. E. Tegmina. F. Tegmina vein. G. Maxillary palp. H. Front femur, ventral view. I. Wings. J. Supra-anal plate, dorsal view. K. Supra-anal plate. L. Subgenital plate, ventral view. M. Hook, ventral view. N. Left and right phallomere, ventral view. Scale bars: A–B = 1 mm; C–F, H–N = 0.5 mm; G = 0.25 mm.

Fig. 3 in Eight new species of the genus Anaplecta Burmeister, 1838 (Blattodea: Blattoidea: Anaplectidae) from China based on molecular and morphological data

Fig. 3. Anaplecta staminiformis Deng & Che sp. nov. A–M. Holotype, ♂ (SWU). A. Habitus, dorsal view. B. Habitus, ventral view. C. Head, ventral view. D. Pronotum, dorsal view. E. Maxillary palp. F. Front femur, ventral view. G. Tegmina. H. Wings. I. Supra-anal plate, dorsal view. J. Subgenital plate, ventral view. K. Hook, ventral view. L. Left phallomere, ventral view. M. Right phallomere, ventral view. – N–P. Paratype, ♂, samples from LMS (SWU). N. Hook, ventral view. O. Left phallomere, ventral view. P. Right phallomere, ventral view. Scale bars: A–B, G–H = 2 mm; C, E–F = 1 mm; D, I–J, L–M, O–P = 0.5 mm; K, N = 0.25 mm.

opencc-by-4.0Nov 2020View details →

Dataset related to the article "Clinical and Molecular Data Define a Diagnosis of Arrhythmogenic Cardiomyopathy in a Carrier of a Brugada-Syndrome-Associated PKP2 Mutation"

This record contains raw data related to the article “ Molecular Data Define a Diagnosis of Arrhythmogenic Cardiomyopathy in a Carrier of a Brugada-Syndrome-Associated PKP2 Mutation”.  Plakophilin-2 (PKP2) is the most frequently mutated desmosomal gene in arrhythmogenic cardiomyopathy (ACM), a disease characterized by structural and electrical alterations predominantly affecting the right ventricular myocardium. Notably, ACM cases without overt structural alterations are frequently reported, mainly in the early phases of the disease. Recently, the PKP2 p.S183N mutation was found in a patient affected by Brugada syndrome (BS), an inherited arrhythmic channelopathy most commonly caused by sodium channel gene mutations. We here describe a case of a patient carrier of the same BS-related PKP2 p.S183N mutation but with a clear diagnosis of ACM. Specifically, we report how clinical and molecular investigations can be integrated for diagnostic purposes, distinguishing between ACM and BS, which are increasingly recognized as syndromes with clinical and genetic overlaps. This observation is fundamentally relevant in redefining the role of genetics in the approach to the arrhythmic patient, progressing beyond the concept of "one mutation, one disease", and raising concerns about the most appropriate approach to patients affected by structural/electrical cardiomyopathy. The merging of genetics, electroanatomical mapping, and tissue and cell characterization summarized in our patient seems to be the most complete diagnostic algorithm, favoring a reliable diagnosis.

opencc-by-4.0Dec 2020View details →

Data for the article: "Molecular Modelling Reveals Eight Novel Druggable Binding Sites in SARS-CoV-2's Spike Protein" by Ilke Ugur and Antoine Marion

This upload contains data related to the article published as a preprint on ChemRxiv with DOI https://doi.org/10.26434/chemrxiv.13292768 "Molecular Modelling Reveals Eight Novel Druggable Binding Sites in SARS-CoV-2's Spike Protein" by Ilke Ugur and Antoine Marion (2020) Department of Chemistry, Middle East Technical University, Ankara, Turkey. For further information, please contact: ilkeugur@metu.edu.tr ; amarion@metu.edu.tr The manuscript is currently under peer-review. Content: Library of molecules derived from DrugBank v 5.1.5: - DrugBank_2020_5.1.5/        # All necessary files for the docking and refinement of the library of molecules. -- DB_5.1.5_pH7.4_pdbqt/      ## PDBQT readily usable for docking with AutoDock Vina. -- DB_5.1.5_pH7.4_mol2amber/  ## mol2 files containing assigned GAFF atom types and Gasteiger atomic charges. -- DB_5.1.5_pH7.4_frcmod/     ## frcmod files containing missing molecular mechanics parameters -- dbID_name.dat              ## DrugBank ID to generic name dictionary Note: The files were prepared automatically via a series of operations handling openbabel and antechamber.       The protonation state of ionizable groups as well as Gasteiger atomic charges were assigned by openbabel for a pH of 7.4       mol2 and frcmod files can be used readily via the tleap module of AmberTools to produce topology files. Receptor structures: - receptors/                  # PDB files for the four structures of the spike protein considered in this work -- CS00ns.pdb                 ## Closed state after the remodelling of missing loops (PDB ID 6vxx) -- OS00ns.pdb                 ## Open   state after the remodelling of missing loops (PDB ID 6vyb) -- CS25ns.pdb                 ## Closed state after 25 ns of molecular dynamics in explicit water -- OS25ns.pdb                 ## Open   state after 25 ns of molecular dynamics in explicit water Note: All structures are aligned to CS00ns.pdb and can be converted to pdbqt for docking with AutoDock Vina Docking grid centers: - dockingCenters/             # XYZ files containing the coordinates of each docking grid center considered in this work Note: The coordinates are given in the same frame as that of the four structures of the receptor. Binding sites: - bindingSites/               # XYZ files with the coordinates of the representative atomic centres                               # of each binding site identified in this work (A-H). Note: These files can be used to get a clearer picture of the binding sites within the structures       of the spike protein shared in the receptors directory. Final modelling results: - allData.txt                 # data for all molecules in the set (approved and investigational) - appData.txt                 # data for approved molecules only - data.xlsx                   # data for all molecules in the set (approved and investigational)                               # as a formatted excel spreadsheet Note: The columns are delimited with semi-colons ";".       The files contain the results for the best pose of all approved molecules for which       molecular mechanics-based geometry optimization succeeded, regardless of their score.       For other molecules, the result of their best pose is reported only for those complexes       having MM interaction energy lower or equal to -22.00 kcal/mol. Visualization: - bs.pse                      # pymol session representing the binding sites within the                               # closed state structure of the spike protein (CS00ns) - pt.pse                      # pymol session representing the docking grid centres within                               # closed statestructure of the spike protein (CS00ns) Note: the PSE files should be compatible with version 7.0 of pymol and later

dryad40/100

Data from: Natural selection and repeated patterns of molecular evolution following allopatric divergence

Background: Geographic speciation is a major force in generating biodiversity. However, how genomes diverge over time after geographic isolation has halted gene flow has remained unclear. We examine genome-wide divergence of putatively single-copy orthologous genes (POGs) from transcriptomes in 20 allopatric species/variety pairs from diverse angiosperm clades. Sixteen of these pairs reflect the well-known eastern Asia – eastern North America floristic disjunction; these species have been isolated for different lengths of time, from the Miocene to Pleistocene. Results: Molecular evolutionary analyses revealed that >90% of the genes examined are under purifying selection and <10% are under positive selection, and this pattern was observed for all taxon pairs, despite differences in divergence time. The divergence level at synonymous sites shared by most POGs in each taxon pair predicts the divergence time between the species/varieties. Divergence time estimates were positively correlated with abundance of genes under moderate purifying selection, but negatively correlated with abundance of genes under strong purifying selection. We identified 200 genes under strong positive selection across the species pairs, with 14 shared by 10-15 pairs and one shared by all taxon pairs. An additional 15 loci annotated to biological processes responding to various stimuli were present in 1-3 pairs.Conclusions: Our results suggest a common "most genes conserved–few genes adaptive" genomic architecture for the taxon pairs, which may be a key for maintaining a balance between the ability to conserve ancestral functions and the ability to evolve new features beneficial for new adaptations. As geographic isolation proceeds through time, the evolutionary trajectory of some genes changed from strong purifying selection to more relaxed selection. The allopatric divergence of these taxon pairs involved both neutral and adaptive evolution of functional genes.

opencc-zeroAug 2019View details →

opencc-by-4.0Jun 2021View details →

Data for: Faster rates of molecular sequence evolution in reproduction-related genes and in species with hypodermic sperm morphologies

This repository contains a record of analysis scripts and sequence alignments used for the analyses presented in the manuscript. Some of the R scripts depend on supplementary tables associated with the manuscript.

dryad40/100

Data from: Drift happens: molecular genetic diversity and differentiation among populations of jewelweed (Impatiens capensis Meerb.) reflect fragmentation of floodplain forests

Landscape features often shape patterns of gene flow and genetic differentiation in plant species. Populations that are small and isolated enough also become subject to genetic drift. We examined patterns of gene flow and differentiation among 12 floodplain populations of the selfing annual jewelweed (Impatiens capensis Meerb.) nested within four river systems and two major watersheds in Wisconsin, USA. Floodplain forests and marshes provide a model system for assessing the effects of habitat fragmentation within agricultural/urban landscapes and for testing whether rivers act to genetically connect dispersed populations. We generated a panel of 12,856 single nucleotide polymorphisms and assessed genetic diversity, differentiation, gene flow, and drift. Clustering methods revealed strong population genetic structure with limited admixture and highly differentiated populations (mean multilocus FST = 0.32, FST' = 0.33). No signals of isolation by geographic distance or environment emerged, but alleles may flow along rivers given that genetic differentiation increased with river distance. Differentiation also increased in populations with fewer private alleles (R2 = 0.51) and higher local inbreeding (R2 = 0.22). Populations varied greatly in levels of local inbreeding (FIS = 0.2 to 0.9) and FIS declined in smaller, more isolated populations. These results suggest that genetic drift dominates other forces in structuring these Impatiens populations. In rapidly changing environments, species must migrate or genetically adapt. Habitat fragmentation limits both processes, potentially compromising the ability of species to persist in fragmented landscapes.

opencc-zeroDec 2018View details →