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Fig. 4 in Increase in isoflavonoid content in Glycine max cells transformed by the constitutively active Ca independent form of the AtCPK1 gene
Fig. 4. Expression of the G. max genes (a) - of the upstream enzymes - 4- coumarate:CoA ligase (4CL), (b) – of the downstream enzymes - isoflavones synthase (IFS) and the final step of daidzein and genistein biosynthesis - 2- hydroxyisoflavanone dehydratase (HID) and (c) - enzymes involve in prenilation of daidzein and coumestrol - isoflavone dimethylallyltransferase (IDT1) and coumestrol 4-dimethylallyltransferase (C4DT) in the control callus culture (Gm) and callus line transformed with the constitutively active AtCPK1 (GmCa1 and GmCa2). Data (mean ± standard error) represent measurements of three independent replicates from two different RNA isolations and are presented as relative expression levels normalized to the expression of the G. max housekeeping genes. Different letters above the bars indicate statistically significant differences of means (P <0.05), Fisher's LSD.
Fig. 2. A in Increase in isoflavonoid content in Glycine max cells transformed by the constitutively active Ca independent form of the AtCPK1 gene
Fig. 2. A representative HPLC-UV profile of the AtCPK1-transformed callus culture of G. max – GmCa2 (A) and the control callus culture Gm (B). The callus tissue extracts recorded at 254 nm. Peak numbers correspond to each of the identified components and are listed in Table 3.
Fig. 3 in Increase in isoflavonoid content in Glycine max cells transformed by the constitutively active Ca independent form of the AtCPK1 gene
Fig. 3. Content (mg/g DW) of isoflavones-aglycones (a) and their glucosides and malonyl-glucosides derivatives (b–d) and prenylated isoflavones (e) in the control calli (Gm) and the AtCPK-transformed callus cultures - GmCa1 and GmCa2. Data are presented as the mean ± SE from four subcultures (biological replicates) with two technical replicates for each experiment. Different letters above the bars indicate statistically significant differences of means (P <0.05), Fisher's LSD.
Fig. 1 in Increase in isoflavonoid content in Glycine max cells transformed by the constitutively active Ca independent form of the AtCPK1 gene
Fig. 1. The branch of phenylpropanoid pathway leading to flavonoids. PAL, phenylalanine ammonia-lyase; C4H, cinnamate 4-hydroxylase; CHS, chalkone synthase; CHR, chalkone reductase; CHI, chalkone isomerase; FN3H, flavanone 3-hydroxylase; IFS, isoflavone synthase; HID, 2-hydroxyisoflavanone dehydratase, IDT1, isoflavone dimethylallyltransferase 1; IDT2, isoflavone dimethylallyltransferase 2; C4DT, coumestrol 4-dimethylallyltransferase.
Simulation Dataset: The antimicrobial fibupeptide lugdunin forms water-filled channel structures in lipid membranes
<p>The Zenodo repository contains data to the molecular dynamics simulations in the following manuscript: </p> <p><strong>The antimicrobial fibupeptide lugdunin forms water-filled channel structures in lipid membranes </strong></p> <p>by</p> <p>Dominik Ruppelt, Marius F. W. Trollmann, Taulant Dema, Sebastian N. Wirtz, Hendrik <br>Flegel, Sophia Mönnikes, Stephanie Grond, Rainer A. Böckmann*, Claudia Steinem*</p> <p>0) Lugdunin-parameterization</p> <p>1) Lugdunin-stack-stability</p> <p> - trans_configuration.gro: Artifical lugdunin stack in trans configuration (see SFig. 23 a).</p> <p> - gauche_configuration.gro: Artifical lugdunin stack in gauche configuration (see SFig. 23 b)</p> <p> - DMPC</p> <p> - DOPC</p> <p> - POPC</p> <p> - POPC_CHOL</p> <p>2) Partitioning-of-Lugdunin-in-Membranes</p> <p> - POPC</p> <p> - POPC_CHOL</p> <p> - GRAMPOS</p> <p>3) PMF-calculations</p> <p> - GRAMPOS_WT</p> <p> - POPC_CHOL_MUT</p> <p> - POPC_CHOL_WT</p> <p> - POPC_MUT</p> <p> - POPC_WT</p>
Dataset : Acute kidney injury complicating critical forms of COVID-19: risk factors and prognostic impact
<p><span><span>We aimed to assess the incidence, risk factors and prognostic impact of AKI complicating critical forms of COVID-19. Thus we conducted a</span> retrospective descriptive case/control monocentric study conducted in a medical intensive care unit of a tertiary teaching hospital over a period of 18 months.</span></p>
Pappulab/N130-Liquid-Structure: Biomolecular condensates form spatially inhomogeneous network fluids
<p>This repository contains the data for the Nature Communications manuscript, "Biomolecular condensates form spatially inhomogeneous network fluids" by F. Dar†, S. R. Cohen†, D. M. Mitrea, A. H. Phillips, G. Nagy, W. C. Leite, C. B. Stanley, J-M. Choi†,§, R. W. Kriwacki§, R. V. Pappu§. (†Equal contributors; §Co-corresponding authors). (2024). <a href="https://doi.org/10.1038/s41467-024-47602-z" target="_blank" rel="noopener">https://doi.org/10.1038/s41467-024-47602-z</a></p> <p>For accompanying analysis scripts, please consult: <a href="https://github.com/Pappulab/n130-liquid-structure" target="_blank" rel="noopener">https://github.com/Pappulab/n130-liquid-structure</a>.</p>
Figures for Development, retainment, and assessment of the graphite-electrolyte interphase in Li-ion batteries regarding the functionality of SEI-forming additives
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Data from: Genomic signatures of adaptation to wine biological aging conditions in biofilm-forming flor yeasts
The molecular and evolutionary processes underlying fungal domestication remain largely unknown despite the importance of fungi to bioindustry and for comparative adaptation genomics in eukaryotes. Wine fermentation and biological aging are performed by strains of S. cerevisiae with, respectively, pelagic fermentative growth on glucose, and biofilm aerobic growth utilizing ethanol. Here, we use environmental samples of wine and flor yeasts to investigate the genomic basis of yeast adaptation to contrasted anthropogenic environments. Phylogenetic inference and population structure analysis based on single nucleotide polymorphisms (SNPs) revealed a group of flor yeasts separated from wine yeasts. A combination of methods revealed several highly differentiated regions between wine and flor yeasts, and analyses using codon-substitution models for detecting molecular adaptation identified sites under positive selection in the high affinity transporter gene ZRT1. The Cross Population Composite Likelihood Ratio (XP-CLR) revealed selective sweeps at three regions, including in the hexose transporter gene HXT7, the yapsin gene YPS6 and the membrane protein coding gene MTS27. Our analyses also revealed that the biological aging environment has led to the accumulation of numerous mutations in proteins from several networks, including Flo11 regulation and divalent metal transport. Together, our findings suggest that the tuning of FLO11 expression and zinc transport networks are a distinctive feature of the genetic changes underlying the domestication of flor yeasts. Our study highlights the multiplicity of genomic changes underlying yeast adaptation to man-made habitats, and reveals that flor/wine yeast lineage can serve as a useful model for studying the genomics of adaptive divergence.
raw data - Association between Bristol Stool Form Scale and the risk of colorectal polyp recurrence: A retrospective cohort study
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High-speed video observation of needles formed during the leader stage in a positive cloud-to-ground flash
<p>The data supports the manuscript entitled “<span>High-speed video observation</span><span> of needles formed during </span><span><span>the </span></span><span><span><span>leader</span></span></span><span><span><span> </span></span></span><span><span><span>stage</span></span></span><span> in a positive cloud-to-ground flash</span>”. The high-speed video data files of the positive cloud-to-ground lightning of *.cihx and *.avi can be opened by Photron Camera Control software (Photron Fastcam Viewer) that can be download from this link: https://photron.com/photron-support/</p> <p>In addition, MATLAB can open the *.mat file (electric field change data), and Microsoft Excel can open the *.xlsx file (Guangdong-Hong Kong-Macao Lightning Location data.</p> <p>The data can be used freely for scientific purposes with the appropriate citation.</p>
Cataloged fresh craters of "Subsurface heterogeneity of light plains formed by the Orientale basin"
<p>This dataset includes all the fresh impact craters observed in the work. The craters in each region are stored as a separate shapefile. In the attribute table, the "Rock" field is marked as "1" for observed excavated boulders and "0" for no observed boulders. The "Diameter" field represents the crater diameter in meters, and the "Max_EXdepth" field indicates the excavation depth of the crater, also in meters.</p>
Figure 7. Phylogeny. A in The evolutionary diversity of barnacles, with an updated classification of fossil and living forms
Figure 7. Phylogeny. A summary of the phylogenetic relationships amongst the Thecostraca families, with major groups labelled on the right and on the branches within the Thoracica. All families are considered monophyletic, except where specifically noted in the text. In Rhizocephala, families with an akentrogonid type of host invasion are coloured blue. Drawings representing the different groups are, from the top: Facetotectan y-cyprid; Dendrogaster; Trypetesa; Clistosaccus; Sacculina; Ibla; Pollicipes; Lepas; Neolepas; Verruca; Catophragmus; Xenobalanus; Balanus.
Figure 6. Fossil Thoracica. A in The evolutionary diversity of barnacles, with an updated classification of fossil and living forms
Figure 6. Fossil Thoracica. A, Stramentum pulchellum, Stramentidae, Upper Cretaceous, Turonian, UK. B, Archaeolepas redtenbacheri, Archaeolepadidae, Upper Jurassic, Tithonian, Germany. C, Eolepas bathonica, Eolepadidae, Middle Jurassic, France. D, E, Witherscalpellum aptiensis, Cretiscalpellidae, Lower Cretaceous, UK; capitulum, in lateral (D) and dorsal (E) views. F, G, Brachylepas naissanti, Brachylepadidae, Upper Cretaceous, UK, in apical (F) and lateral (G) views. H, Etcheslepas durotrigensis, Zeugmatolepadidae, Upper Jurassic, UK. I, J, Proverruca vinculum, Proverrucidae, Upper Cretaceous, UK, in apical (I) and lateral (J) views. K, L, Q, R, Eoverruca hewitti, Eoverrucidae, Upper Cretaceous, UK; K, L, calcified basis with imbricating scales; and Q, R, fixed and moveable scuta. M–P, Myolepas scanica, Myolepadidae, Upper Cretaceous, Sweden; external (M) and internal (O) views of tergum; and external (N) and internal (P) views of scutum. S–AE, fossil whale barnacles, Coronula. Scale bars: 5 mm in A–H; 2 mm in M–P; 1 mm in I–L; 0.5 mm in Q, R, AE.
Figure 9 in The evolutionary diversity of barnacles, with an updated classification of fossil and living forms
Figure 9. Timeline of Thoracican evolution. Generic diversity of the Thoracica from the latest Triassic to the present. Early forms are entirely phosphatic, followed by calcitic pedunculated forms. Balanomorphans (acorn barnacles) appeared in the Cretaceous, but they radiated only after a low-diversity period following the Cretaceous– Palaeogene (K–Pg) extinction. The diversification starting in the Neogene is still ongoing. Living genera shown include only forms with shell plates, in order to compare with the fossil record. Further explanation is given in the main text. (1) Eolepadomorpha, Eolepadidae, Eolepas; (2) Eolepadomorpha, Eolepadidae, Toarcolepas; (3) Pollicipedomorpha, Zeugmatolepadidae, Concinnalepas; (4) Archaeolepadomorpha, Archaeolepadidae, Archaeolepas; (5) Calanticomorpha, Cretiscalpellidae, Witherscalpellum; (6) Scalpelloidea, Scalpellidae, Arcoscalpellum; (7) Brachylepadomorpha, Brachylepadidae, Pycnolepas; (8) Verrucomorpha, Verrucidae, Altiverruca; (9) Balanomorpha, Catophragmidae, Catomerus; (10) Lepadoidea, Lepadidae, Lepas; (11) Neolepadomorpha, Neolepadidae, Stipilepas.
Figure 2. Ascothoracida. A–D in The evolutionary diversity of barnacles, with an updated classification of fossil and living forms
Figure 2. Ascothoracida. A–D, larval diversity of selected Ascothoracida. A, an early, live Baccalaureus nauplius larva. B, an early, live Zibrowia nauplius larva. C, D, a Tessmann's larva or a-cypris (C), with hooked antennules (D). E–N, adult diversity of selected Ascothoracida. E–G, the coral Turbinaria, showing the galls formed by the ascothoracidan Petrarca. Insert in E shows the galls in cross-section, with red Petrarca inside the coral skeleton. F, Petrarca. G, magnified view of Petrarca. H, Synagoga arabesque, with extended, hooked first antennules. I, J, Ascothorax rybakovi on the brittle star Ophiacantha pacifica. K, a free Dengrogaster sp. L–N, the zoanthid Palythoa with Baccalaureus sp. inside. Abbreviation: a1, first antennule. Fig 2C photographed by ND and Dr. Jørgen Olesen, Natural History Museum of Denmark.
Figure 5. Thoracica. A in The evolutionary diversity of barnacles, with an updated classification of fossil and living forms
Figure 5. Thoracica. A, nauplius larva of Balanus improvisus. Note the presence of frontal horns. B, cypris larva of Amphibalanus amphitrite, showing the pair of extended first antennules and six pairs of thoracopods. C, Anelasma squalicola, a parasite of deep-sea lantern sharks (Etmopterus). The cirri are rudimentary, and the base of the peduncle has a root-like structure embedded inside the tissue of the shark to absorb nutrients. D, Fistulobalanus albicostatus, common on mangrove tree trunks. E, the family Pyrgomatidae are associated with scleratinian corals, and the bases are embedded in the coral skeleton. Cantellius sp. extending the cirri. F, Ibla cumingi, which is located at the most basal position on the molecular phylogenetic tree of thoracican barnacles. G, Megabalanus, Amphibalanus and Lepas inhabiting the capitulum of a penduculated barnacle. H, Capitulum mitella, a stalked barnacle inhabiting rocky shores. In molecular phylogenetic analyses, it is the sister to Anelasma (see C). I, Conchoderma, a stalked barnacle with reduced shell plates, epibiotic on many marine taxa, mostly crabs and whales. J, An early dwarf male settled on the surface of an adult Heteralepas. K, Octolasmis cor lives exclusively on the surface of crab gills. L, Scalpellum scalpellum, a stalked barnacle epibiotic with hydroids. The inserts in LM (upper) and SEM (lower) shows the hermaphrodite receptacles, which can house dwarf males. Inserts show a dwarf male with extended penis (upper) and an SEM micrograph of the receptacle structure. M, Waikalasma is a deep-sea inhabitant, having a row of imbricating plates on the base of shells. N, Chthamalus malayensis is common on intertidal shores. O, Tetraclita, with four shell plates, common on rocky and tropical shores.
Figure 8 in The evolutionary diversity of barnacles, with an updated classification of fossil and living forms
Figure 8. Thoracica phylogenetic hypotheses. Comparison of four recent hypotheses on the phylogenetic relationships among recent Thoracica. Note the overall similarity in topology. Major discordances are highlighted by colour. Note especially the difference in the precise position of the genera Capitulum, Lithotrya and Pollicipes, but also that these taxa always appear 'close together' (highlighted in yellow) in the trees. In the analysis by Herrera et al. (2015), these genera are nested inside the Balanomorpha (dotted square). See detailed explanation in the main text.
Figure 4. Rhizocephala. A–H in The evolutionary diversity of barnacles, with an updated classification of fossil and living forms
Figure 4. Rhizocephala. A–H, life cycle stages and larval morphology of selected Rhizocephala. A, nauplius larva of Sacculina carcini. B, male cyprid of S. carcini. C, settled male cyprid of Lernaeodiscus porcellanae in the mantle aperture of a virginal female reproductive body (externa). Box D indicates the receptacle holding the trichogon. D, male trichogon of S. carcini dissected from the mantle cavity of a virginal female externa. E, female cypris of S. carcini. F, kentrogon of S. carcini, inside the empty cuticle of the spent female cyprid, in the process of injecting the primordial parasite. G, vermigon of Loxothylacus panopaei. H, scanning electron micrograph of Peltogaster curvata, showing the reproductive sac (externa) connected to the ramified internal root system. I–P, diversity of selected Rhizocephala externae. I, Peltogasterella sulcata on its host, Pagurus cuanensis. J, Briarosaccus auratum on its host, Lithodes aequispinus. K, Parthenopea subterranea on its host, Calianassa subterranea. L, Sacculina carcini on its host, Carcinus manaeas. M, Thompsonia sp. on its host, Thyraplax truncata, courtesey of Peter Castro. N, Sylon hippolytes on its host, Spirontocaris lilljeborgi. O, Heterosaccus dollfusi on its host, Charybdis longicollis. P, Polyascus gregarius on its host, Eriocheir japonica.
Figure 11 in The evolutionary diversity of barnacles, with an updated classification of fossil and living forms
Figure 11. Moulting and growth in Thoracica. Moulting occurs in the cuticular zones separating shell plates. A, new cuticle is formed by infolded epidermis in a narrow growth zone between two adjacent shell plates. B, old cuticle is shed only above the growth zone. The broken-off cuticle leaves distinct growth lines on either side of the growth zone. C, the new cuticle expands by outfolding; the growth zone is not distinct during intermoults. D, a new growth zone forms for the next moult; the shell plate can now expand laterally under the cuticle; older growth lines can thereby be included on top of the plate. Constructed from descriptions by Mahmoud (1959, 1960), Bourget & Crisp (1975) and Blomsterberg et al. (2004).
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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.