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opencc-by-4.0May 2020View details →

The Unfolding Journey of Superoxide Dismutase 1 Barrels Under Crowding: Atomistic Simulations Shed Light on Intermediate States and Their Interactions With Crowders

This data accompanies the article entitled The Unfolding Journey of Superoxide Dismutase 1 Barrels Under Crowding: Atomistic Simulations Shed Light on Intermediate States and Their Interactions With Crowders, published in J. Phys. Chem. Lett. (<a href="https://doi.org/10.1021/acs.jpclett.0c00699">https://doi.org/10.1021/acs.jpclett.0c00699</a>). 01_SOD1bar_unfolding_REST2.zip: The zip archive includes REST2 trajectories for the three systems investigated in the paper: 1:1 packing, 2:1 packing, and the dilute case. The trajectories are saved in the GROMACS XTC file format, separately for each temperature (i=0,...,23). Given the large trajectory sizes, only protein coordinates (SOD1bar + crowders) are reported, and the output frequency is reduced to 100 ps. A starting geometry (in the Gromos87 GRO format) after equilibration of the initial packing is provided for each REST2 simulation (conf_prot.gro). Moreover, for each REST2 simulation, an xarray (http://xarray.pydata.org) dataset, saved in the netCDF file format, is included with computed fraction of native contacts, secondary structure content, and the Calpha RMSD of the barrel core (beta sheets beta1 - beta8) with respect to the crystal structure. 02_SOD1bar_geometries_representative_unfolding.zip: Representative SOD1bar geometries along the unfolding pathway (presented in Figure 3 of the paper). 03_SOD1bar_geometries_loopVII.zip: SOD1bar geometries with varying loop VII conformation which were isolated from dilute REST2 and which are presented in Figure S9 of the paper.

opencc-by-4.0Aug 2023View details →

Phlorest phylogeny derived from Sagart et al. 2019 'Dated language phylogenies shed light on the ancestry of Sino-Tibetan'

Cite the source of the dataset as: <blockquote> Sagart L, Jacques G, Lai Y, Ryder RJ, Thouzeau V, Greenhill SJ, List J- M. 2019 Dated language phylogenies shed light on the ancestry of Sino-Tibetan. Proceedings of the National Academy of Sciences, 201817972. </blockquote>

opencc-by-4.0Aug 2023View details →

Phlorest phylogeny derived from Chacon & List 2015 'Improved computational models of sound change shed light on the history of the Tukanoan languages'

Cite the source of the dataset as: <blockquote> Chacon TC, List J-M (2015) Improved computational models of sound change shed light on the history of the Tukanoan languages. Journal of Language Relationship, 3:177–203. </blockquote>

opencc-by-4.0Oct 2019View details →

The terrestrial carnivorous plant Utricularia reniformis sheds light on environmental and life-form genome plasticity: Annotation, Gene Ontology and raw data

Description:  In this work, we deeply sequenced (genome and transcriptome of different organs), assembled, and analyzed the 311-Mbp genome of the terrestrial carnivorous plant U. reniformis (Lentibulariaceae). This project presents great importance to the understanding of genomic, evolutive and functional aspects of U. reniformis, which may, with the next-generation sequencing and computational biology approaches shed light to a better understanding not only for the biology and evolution of Utricularia genus, but also for other genera and lineages of the Lentibulariaceae family.  Here we present all the raw data generated, including annotation and gene ontology files. External Information <a href="https://genomevolution.org/coge/GenomeInfo.pl?gid=54799">Genome Browser</a> avaliable at CoGe Portal (https://genomevolution.org/coge/GenomeInfo.pl?gid=54799) <a href="http://https://www.ncbi.nlm.nih.gov/bioproject/290588">GenBank </a><a href="http://https://www.ncbi.nlm.nih.gov/bioproject/290588">Bioproject</a> (https://www.ncbi.nlm.nih.gov/bioproject/290588) for raw genomic and transcriptomic reads <a href="https://bv.fapesp.br/en/auxilios/84264/genomics-and-transcriptomics-of-utricularia-reniformis-lentibulariaceae-an-evolutive-and-function/">FAPESP grant website</a> contaning the project abstract and other information. Papers published related to Utricularia reniformis genome <pre>[1] Silva SR, Diaz YC, Penha HA, Pinheiro DG, Fernandes CC, Miranda VF, MichaelTP, Varani AM. The Chloroplast Genome of Utricularia reniformis Sheds Light on the Evolution of the ndh Gene Complex of Terrestrial Carnivorous Plants from the Lentibulariaceae Family. PLoS One. 2016 Oct 20;11(10):e0165176. doi:<a href="https://www.ncbi.nlm.nih.gov/pubmed/27764252">10.1371/journal.pone.0165176</a>. </pre> <pre>[2] Silva SR, Alvarenga DO, Aranguren Y, Penha HA, Fernandes CC, Pinheiro DG, Oliveira MT, Michael TP, Miranda VFO, Varani AM. The mitochondrial genome of the terrestrial carnivorous plant Utricularia reniformis (Lentibulariaceae): Structure, comparative analysis and evolutionary landmarks. PLoS One. 2017 Jul19;12(7):e0180484. doi: <a href="https://www.ncbi.nlm.nih.gov/pubmed/28723946">10.1371/journal.pone.0180484</a>.</pre> <pre>[3] Silva SR, Moraes AP, Penha HA, Julião MHM, Domingues DS, Michael TP, Miranda VFO, Varani AM. The Terrestrial Carnivorous Plant Utricularia reniformis Sheds Light on Environmental and Life-Form Genome Plasticity. Int J Mol Sci. 2019 Dec 18;21(1). pii: E3. doi: <a href="https://www.ncbi.nlm.nih.gov/pubmed/31861318">10.3390/ijms21010003</a>.</pre> Acknowledgements This work was supported by Sao Paulo Research Foundation FAPESP, Grant ID: [1325164-6]   --------------------------------------------------------- FILES DESCRIPTION --------------------------------------------------------- ---------------- ANNOT-vFinal.sql: MySQL database containing all integrated annotation information of Urenif and Ugibba ---------------- TABLE fields description gene_name            gene name generated by EVidence Modeler + PASA length                     gene lenght status                     duplicate_gene_classifier status (0:singleton, 1:dispersed, 2:proximal, 3: tandem, 4:WGD) product                   gene product     GOterms                 Blast2GO/OmicsBox GOterms GO_mapping           Blast2GO/OmicsBox GOterms derived from direct mapping (UniProt) GO_annotation        Blast2GO/OmicsBox annotated GOterms GO_interpro             Blast2GO/OmicsBox derived from InterProScan EC                            Blast2GO/OmicsBox EC number EC_name                 Blast2GO/OmicsBox enzyme name NOG_annot              EggNOG annotation description NOG_EC                   EggNOG EC number NOG_GO                  EggNOG GOterms NOG_class               EggNOG COG/KOG classfication KEGG_Pathway        EggNOG KEGG pathyways KEGG_ko                  EggNOG KEGG ko CAZy                        EggNOG CAZy enzymes TAIR_gene                Closest A. thaliana gene name (homologous) TAIR database lasted version TAIR_annot               Closest A. thaliana gene product (homologous) TAIR database lasted version     ortho                     MCL clustering among Vvinifera, Athaliana, and Slycopersicum (S:singleton, C: clustered, Y: shared) ortho_two                 MCL clustering among Urenif and Ugibba (S:singleton, C: clustered, Y: shared) - - ---------------- CEGs.zip                336 shared and concatenated CEGs from Urenif, U. gibba, Genlisea nigrocaulis, G. hispidula, G. aurea, G. pygmaea, and G. repens. ---------------- ProcessRepeats_mod     Modified version of RepeatMasker, ProcessRepeats script for detection of plant evolutionary lineages ---------------- ---------------------------------------------------------------------------------------------------------------------------------------------- Utricularia gibba files ---------------------------------------------------------------------------------------------------------------------------------------------- Ugibba-no-masked.fa       Ugibba genome excluding organellar genomes (provided by Lan et al., 2017) Ugibba-softmasked.fa     Ugibba genome RepeatMasker softmasked and excluding organellar genomes (provided by Lan et al., 2017) Ug.collinearity                  MCScanX collinearity file Ug-duplicates.txt             MCScanX duplicate_gene_classifier short report Ug.gene_type                  MCScanX duplicate_gene_classifier full report Ug.tandem                       Ugibba tandem genes generated by MCScanX tool Ugibba_annot.annot        Blast2GO/OmicsBox annotation file (eudicotyledons filtered and Viridiplantae GOSlim)  Ugibba_annot-noclean.annot        Blast2GO/OmicsBox annotation file (not filtered) Ugibba.cDNA                Ugibba cDNAs fasta file Ugibba.CDS                   Ugibba CDSs fasta file Ugibba-EVM.all-no-TEs-PASA-ANNOTATED.gff3    Ugibba GFF3 file fully annotated (including gene products and GO terms) Ugibba-EVM.all-no-TEs-PASA.gff3    Ugibba GFF3 file fully annotated (genes only) Ugibba_export.txt            Blast2GO/OmicsBox full exported table Ugibba_fasta.fasta            Blast2GO/OmicsBox Ugibba fasta proteins containg annotation (product and GO terms) ugibba_frozen_cleaned-validated.box        Full Blast2GO/OmicsBox file ugibba_frozen.box   Full Blast2GO/OmicsBox file (containing TEs genes annotation) ugibba_nogs_emapper_annotations.box   Full Blast2GO/OmicsBox EggNOG file (containing TEs genes annotation) Ugibba_GAF.txt            GAF file Ugibba.gene                Ugibba gene fasta file Ugibba_GOstat.txt            GOstat file Ugibba-PASA-assemblies.fasta        Ugibba PASA assemblies Ugibba-PASA.stats            Ugibba annotation STATS Ugibba.prot                Ugibba protein fasta file Ugibba-RepeatMasker.gff            Ugibba RepeatMasker gff file Ugibba-RepeatMasker.gff3        Ugibba RepeatMasker gff3 file Ugibba-RepeatMasker.tbl            Ugibba RepeatMasker results Ugibba-RepeatMasker-v2.gff3        Ugibba RepeatMasker gff3 second version file Ugibba-RNAseq-assembled.fasta        Ugibba RNAseq assembled transcriptome (Trinity) Ugibba_TEs_DANTE_2019.fa        Ugibba TEs library, detected by REPET and annotated by PASTEC and DANTE Ugibba_WEGO.txt            WEGO file ---------------------------------------------------------------------------------------------------------------------------------------------- Utricularia reniformis files ---------------------------------------------------------------------------------------------------------------------------------------------- Urenif-no-masked.fa            Urenif genome excluding organellar genomes Urenif-softmasked.fa            Urenif genome RepeatMasker softmasked and excluding organellar genomes Ur.collinearity            MCScanX collinearity file Ur-duplicates.txt            MCScanX duplicate_gene_classifier short report Ur.gene_type            MCScanX duplicate_gene_classifier full report Ur.tandem                Urenif tandem genes generated by MCScanX tool Urenif_annot.annot            Blast2GO/OmicsBox annotation file (eudicotyledons filtered and Viridiplantae GOSlim) Urenif_annot-noclean.annot        Blast2GO/OmicsBox annotation file (not filtered) Urenif.cDNA                Urenif cDNAs fasta file Urenif.CDS                Urenif cDNAs fasta file Urenif-EVM.all-no-TEs-PASA-ANNOTATED.gff3    Urenif GFF3 file fully annotated (including gene products and GO terms) Urenif-EVM.all-no-TEs-PASA.gff3    Urenif GFF3 file fully annotated (genes only) Urenif_export.txt            Blast2GO/OmicsBox full exported table Urenif_fasta.fasta            Blast2GO/OmicsBox Urenif fasta proteins containg annotation (product and GO terms) urenif_frozen_cleaned-validated.box        Full Blast2GO/OmicsBox file urenif_frozen.box   Full Blast2GO/OmicsBox file (containing TEs genes annotation) urenif_nogs_emapper_annotations.box   Full Blast2GO/OmicsBox EggNOG file (containing TEs genes annotation) Urenif_GAF.txt            GAF file Urenif.gene                Urenif gene fasta file Urenif_GOStat.txt            GOstat file Urenif-PASA-assemblies.fasta        Urenif PASA assemblies Urenif-PASA.stats            Urenif annotation STATS Urenif.prot                Urenif protein fasta file Urenif-RepeatMasker.gff            Urenif RepeatMasker gff file Urenif-RepeatMasker.gff3        Urenif RepeatMasker gff3 file Urenif-RepeatMasker.tbl            Urenif RepeatMasker results Urenif-RepeatMasker-v2.gff3        Urenif RepeatMasker gff3 second version file Urenif-RNAseq-assembled.fasta        Urenif RNAseq assembled transcriptome (Trinity) Urenif_TEs_DANTE_2019.fa        Urenif TEs library, detected by REPET and annotated by PASTEC and DANTE Urenif_WEGO.txt            WEGO file ---------------------------------------------------------------------------------------------------------------------------------------------- ----------------------------------------------------------------------------------------------------------------------------------------------

FIG. 15 in New remains of kollpaniine "condylarths" (Panameriungulata) from the early Palaeocene of Bolivia shed light on hypocone origins and molar proportions among ungulate-like placentals

FIG. 15. — Upper molar proportions in Euungulata, "Condylarthra", SANUs, and the kollpaniines from Tiupampa described here. Molar proportions are plotted in the developmental 'morphospace' (Kavanagh et al. 2007; Polly 2007) where the white region is consistent with the IC model; the broken line is the relationship predicted for lower molar of murine rodents (see Material and methods and Table 8). Abbreviations: Kalith., Kalitherium.

FIG. 11 in New remains of kollpaniine "condylarths" (Panameriungulata) from the early Palaeocene of Bolivia shed light on hypocone origins and molar proportions among ungulate-like placentals

FIG. 11. — Pucanodus gagnieri: partial right mandible with m2-3 (MHNC 13869): A, stereophotograph of occlusal view; B, the same in labial view. Scale bar: 5 mm.

FIG. 4 in New remains of kollpaniine "condylarths" (Panameriungulata) from the early Palaeocene of Bolivia shed light on hypocone origins and molar proportions among ungulate-like placentals

FIG. 4. — Molinodus suarezi: partial maxilla (MHNC 13870) with incomplete M1-2 and complete M3. Stereophotograph of occusal view. Scale bar: 5 mm.

FIG. 7 in New remains of kollpaniine "condylarths" (Panameriungulata) from the early Palaeocene of Bolivia shed light on hypocone origins and molar proportions among ungulate-like placentals

FIG. 7. — Simoclaenus sylvaticus: partial right mandible with alveolus of p1, root of p2-3, p4 and m1 (MHNC 13872): A, stereophotographs of occlusal view; B, the same in lateral view; C, the same in medial view. Scale bar: 5 mm.

FIG. 2 in New remains of kollpaniine "condylarths" (Panameriungulata) from the early Palaeocene of Bolivia shed light on hypocone origins and molar proportions among ungulate-like placentals

FIG. 2. — Partial left mandible of Molinodus suarezi (MHNC 13867) bearing p3-m3: A, stereophotographs of the occlusal view; B, lingual view; C, labial view. Scale bar: 5 mm.

FIG. 13. — A, B in New remains of kollpaniine "condylarths" (Panameriungulata) from the early Palaeocene of Bolivia shed light on hypocone origins and molar proportions among ungulate-like placentals

FIG. 13. — A, B, Lamegoia conodonta; C, didolodontidae indet.; A, occlusal view of a left m2 of Lamegoia conodonta (cast of holotype MNRJ 1463-V); B, occlusal view of a right M2 (reversed) of Lamegoia conodonta (cast of MNRJ 1465-V); C, occlusal view of a left M2 (cast of MNRJ 1464-V) of and undetermined didolodont (referred by Paula Couto [1952a] to L. conodonta). Scale bar: 5 mm.

FIG. 5 in New remains of kollpaniine "condylarths" (Panameriungulata) from the early Palaeocene of Bolivia shed light on hypocone origins and molar proportions among ungulate-like placentals

FIG. 5. — Molinodus suarezi: partial maxilla (MHNC 13870): A, occlusal view; B, lingual view. Scale bar: 5 mm.

opencc-by-4.0Jul 2020View details →

Fig. 3 in New acoustic and molecular data shed light on the poorly known Amazonian frog Adenomera simonstuarti (Leptodactylidae): implications for distribution and conservation

Fig. 3. Preserved male of nominal Adenomera simonstuarti (Angulo & Icochea, 2010) (= genetic lineage 3): call voucher INPA-H 40967 (SVL = 23.4 mm) from the upper Juruá River, in Tarauacá, Brazilian state of Acre. This specimen corresponds to a call voucher (see Fig. 5). A−B. Body in dorsal and ventral views, not to scale. C−D. Detail of the ventral surface of right foot and hand, respectively. Note the nearly solid, dark-colored stripe along the underside of the forearm. Photographs by J. Magnusson. Scale bar = 5 mm.

opencc-zeroOct 2016View details →

Leaf growth response to mild drought: natural variation sheds light on trait architecture

Plant growth and crop yield are negatively affected by a reduction in water availability. However, a clear understanding of how growth is regulated under non-lethal drought conditions is lacking. Recent advances in genomics, phenomics and transcriptomics allow in-depth analysis of natural variation. In this study, we conducted a detailed screening of leaf growth responses to mild drought in a worldwide collection of Arabidopsis thaliana accessions. The raw phenotyping can be found in: - cellularData.txt -> mature (23 days after stratification; DAS) leaf epidermis (third leaf) analysed for cell area, cell number, pavement cell area, pavement cell number, stomatal index and leaf area of the analysed leaf. - leaf3AreaMaturity.txt -> area of the third leaf at maturity (23DAs) in mm2. - leaf3AreaProliferation.txt -> area of the third leaf at proliferation (last day of full cell proliferation; 8-10 DAS) in mm2. - rosetteArea Maturity.txt -> projected rosette area at maturity (22DAS) The phenotyping results have been normalised for batch effects ('experiment' in raw data) - allPhenotypesNormalised.txt -> contains the normalised data for all the measured phenotypes All datafiles indicate the accession name ('Accession'), the unique identifier for each accessions ('Ecotype_ID') as used in the 1001genomes project (www.1001genomes.org) and the treatment ('C' indicate well-watered plants, 'S' the mild-drought treated plants). These results and methodological results are described in Clauw et al. (2016, The Plant Cell). Citation: Clauw, Pieter, Frederik Coppens, Arthur Korte, Dorota Herman, Bram Slabbinck, Stijn Dhondt, Twiggy Van Daele, et al. 2016. “Leaf Growth Response to Mild Drought: Natural Variation in Arabidopsis Sheds Light on Trait Architecture.” The Plant Cell, October. doi:10.1105/tpc.16.00483.

Documentation of a Pyu inscription (PYU012) kept at the main inscription shed on the grounds of the former royal palace in Mandalay

This data set includes photographs (.jpg), an RTI (.ptm), and related files documenting the Pyu inscription (inventory number PYU012) kept at the main inscription shed on the grounds of former royal palace in Mandalay. The photographer was James Miles or Archeovision, working on behalf of the Pyu epigraphy sub-project (PI, Nathan W. Hill of SOAS University of London) of the ERC synergy grant "Beyond Boundaries: Religion, Region, Language and the State" (Identifier: ASIA 609823) in collaboration with the project "From Vijayapuri to Sriksetra? The Beginnings of Buddhist Exchange across the Bay of Bengal as Witnessed by Inscriptions from Andhra Pradesh and Myanmar" (PI Arlo Giffiths of the EFEO) funded by The Robert H. N. Ho Family Foundation.

Documentation of a Pyu inscription (PYU027) kept in the inscription shed outside the Archaeological Museum at Halin

This data set includes photographs (.jpg), an RTI (.ptm), and related files documenting the Pyu inscription (inventory number PYU027) kept in the inscription shed outside the Archaeological Museum at Halin. The photographer was James Miles or Archeovision, working on behalf of the Pyu epigraphy sub-project (PI, Nathan W. Hill of SOAS University of London) of the ERC synergy grant "Beyond Boundaries: Religion, Region, Language and the State" (Identifier: ASIA 609823) in collaboration with the project "From Vijayapuri to Sriksetra? The Beginnings of Buddhist Exchange across the Bay of Bengal as Witnessed by Inscriptions from Andhra Pradesh and Myanmar" (PI Arlo Giffiths of the EFEO) funded by The Robert H. N. Ho Family Foundation.

Documentation of a Pyu inscription (PYU064) kept at the main inscription shed on the grounds of the former royal palace in Mandalay

This data set includes photographs (.jpg), an RTI (.ptm), and related files documenting the Pyu inscription (inventory number PYU064) kept at the main inscription shed on the grounds of former royal palace in Mandalay. The photographer was James Miles or Archeovision, working on behalf of the Pyu epigraphy sub-project (PI, Nathan W. Hill of SOAS University of London) of the ERC synergy grant "Beyond Boundaries: Religion, Region, Language and the State" (Identifier: ASIA 609823) in collaboration with the project "From Vijayapuri to Sriksetra? The Beginnings of Buddhist Exchange across the Bay of Bengal as Witnessed by Inscriptions from Andhra Pradesh and Myanmar" (PI Arlo Giffiths of the EFEO) funded by The Robert H. N. Ho Family Foundation.

Documentation of a Pyu inscriptions (PYU017) kept in the inscription shed outside the Archaeological Museum at Halin

This data set includes photographs (.jpg), an RTI (.ptm), and related files documenting a Pyu inscription (inventory number PYU017) kept in the inscription shed outside the Archaeological Museum at Halin. The photographer was James Miles or Archeovision, working on behalf of the Pyu epigraphy sub-project (PI, Nathan W. Hill of SOAS University of London) of the ERC synergy grant "Beyond Boundaries: Religion, Region, Language and the State" (Identifier: ASIA 609823) in collaboration with the project "From Vijayapuri to Sriksetra? The Beginnings of Buddhist Exchange across the Bay of Bengal as Witnessed by Inscriptions from Andhra Pradesh and Myanmar" (PI Arlo Giffiths of the EFEO) funded by The Robert H. N. Ho Family Foundation.