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FIGURE 1. Schinopsis boqueronensis. A. Brachyblast with compound leaves and inflorescence. B in A new tree species of Schinopsis (Anacardiaceae) from Paraguay and Bolivia
FIGURE 1. Schinopsis boqueronensis. A. Brachyblast with compound leaves and inflorescence. B. Macroblast fragment usually found in lower positions in the tree crown, showing leaf polymorphism and spines. C. Staminate flower. D. Samara.
Screening of anti-Acinetobacter baumannii plant-based compounds, based on potential inhibition of OmpA and OmpW functions
<p><span>Considering the adverse effect of antimicrobial resistance (AMR) crisis on human life, there is an immediate need for finding new alternatives for treatment of emerging infectious diseases. Therapeutic options, including last-line or combined antibiotic therapies for <i>Acinetobacter baumannii</i>, as an emergent multi-drug resistant (MDR) human pathogen responsible for severe nosocomial and several other infections, are apparently ineffective. The outer membrane protein A (OmpA) and outer membrane protein W (OmpW) are two porins known as virulence factors with different cellular functions. Identification of natural compounds with potentials to block these putative virulence factors can possibly attenuate the growth of the bacteria and control the relating diseases. The current work aimed to screen the therapeutic potential of a library of 371 phytochemicals, as multi-blockers of OmpA and OmpW in <em>A. baumannii</em>. Although the anti-virulence activities of these biomolecules are reported previously, no evaluation on <i>A. baumannii </i>has been performed so far. Moreover, there is no safety screening and early alerts of these compounds. In this study, hits were initially selected based on their physicochemical, absorption, distribution, metabolism, excretion, and toxicity (ADMET) drug-like properties. Afterwards, the selected ligands were subjected to standard docking calculations against predicted three-dimensional structure of OmpA and OmpW in <i>A. baumannii</i>. We identified five phytochemicals (Amorphigenin (PUBCHEM CID 92207), Bisdemethoxy-curcumin (PUBCHEM CID 5315472), Dalbinol (PUBCHEM CID 44257412), Epicatechin gallate (PUBCHEM CID 72276) and Nordihydroguaiaretic acid (PUBCHEM CID 4534)) bearing appreciable binding affinity towards the selected binding pocket of OmpA and OmpW. </span></p>
Figure 32. Isolated right compound bone. A in Cranial osteology and preliminary phylogenetic assessment of Plectrurus aureus Beddome, 1880 (Squamata: Serpentes: Uropeltidae)
Figure 32. Isolated right compound bone. A, right-lateral view, anterior to the right. B, right-medial view, anterior to the left. Abbreviations: cop, coronoid process; ctf, foramen for the chorda tympani; ldp, lateral dentary process; mdbc, mandibular canal; mdbf, mandibular fossa; mdp, medial dentary process; mj, mandibular joint; rap, retroarticular process. Scale bar: 1 mm.
Measurement report: Springtime reactive Volatile Organic Compounds (VOCs) and impacts on ozone in urban areas of Yunnan-Guizhou Plateau, China: a PTR-TOF-MS study
<p>Time-varying sequence and day-to-day concentration after treatment. It includes 18 observed major VOCs [acetaldehyde, 2-acrolein, acetone, methyl ethyl ketone (MEK), methyl vinyl ketone (MVK), methacrolein (MACR), methyl isobutyl ketone (MIK), 2-pentanone, ethyl acetate, isoprene, α-pinene, benzene, toluene, styrene, C8 aromatic hydrocarbons, C9 aromatic hydrocarbons, 1,3-dichlorobenzene, naphthalene, and acetonitrile].</p>
Enhanced foliar 15N enrichment with increasing nitrogen addition rates: Role of plant species and nitrogen compounds
<p>Determining the abundance of N isotope (δ15N) in natural environments is a simple but powerful method for providing integrated information on the N cycling dynamics and status in an ecosystem under exogenous N inputs. However, whether the input of different N compounds could differently impact plant growth and their 15N signatures remains unclear. Here, the response of δ15N signatures and growth of three dominant plants (Leymus chinensis, Carex duriuscula, and Thermopsis lanceolata) to the addition of three N compounds (NH4HCO3, urea, and NH4NO3) at multiple N addition rates were assessed in a meadow steppe in Inner Mongolia. The three plants showed different initial foliar δ15N values because of differences in their N acquisition strategies. Particularly, T. lanceolata (N2-fixing species) showed significantly lower 15N signatures than L. chinensis (associated with arbuscular mycorrhizal fungi, AMF) and C. duriuscula (associated with AMF). Moreover, the foliar δ15N of all three species increased with increasing N addition rates, with a sharp increase above an N addition rate of ~10 g N m-2yr-1. Foliar δ15N values were significantly higher when NH4HCO3 and urea were added than when NH4NO3 was added, suggesting that adding weakly acidifying N compounds could result in a more open N cycle. Overall, our results imply that assessing the N transformation processes in the context of increasing global N deposition necessitates the consideration of N deposition rates, forms of the deposited N compounds, and N utilization strategies of the co-existing plant species in the ecosystem.<span> </span></p>
Compound coastal, fluvial, and pluvial flooding during historical hurricane events in the Sabine-Neches Estuary, Texas
<p>This dataset contains boundary forcing (offshore water level and river discharge), topobathy, and Manning's n roughness data used to simulate compound flooding due to historical hurricanes (Harvey, Ike, and Rita) in the Sabine-Neches Estuary in Texas. It also includes water level outputs used for the analysis presented in the manuscript entitled: <em>Compound coastal, fluvial, and pluvial flooding during historical hurricane events in the Sabine-Neches Estuary, Texas </em>(<a href="https://doi.org/10.1029/2022WR033144">https://doi.org/10.1029/2022WR033144</a>).</p>
Fig. 3 in Variation in the amino acids, volatile organic compounds and terpenes profiles in induced polyploids and in Solanum tuberosum varieties
Fig. 3. Hierarchical cluster analysis (represented by a heat-map) of amino acids content in leaves of potato allo- and autotetraploids and cultivated varieties. Dendrograms were constructed by UPGMA clustering method for 18 amino acids and 10 lines: diploid S. kurtzianum parental line (2xPL), diploid S. tuberosum x S. kurtzianum parental interspecific hybrid (2xPIH), three autotetraploids (4xAuL1, 4xAuL2 and 4xAuL3), two allotetraploids (4xAL2 and 4xAL4) and three cultivated varieties (4xCalen, 4xInnovator and 4xPampeana).
Fig. 1 in Variation in the amino acids, volatile organic compounds and terpenes profiles in induced polyploids and in Solanum tuberosum varieties
Fig. 1. Fold change of compounds content in allotetraploids (a) and autotetraploids (b) relative to their respective diploid parental line. Fold change is expressed as log10(Tetraploid/Diploid). Horizontal lines are the average of the absolute logFC for each evaluated line, letters denote differences by Duncan's multiple range test (P <0.05).
IDSL.CSA - metabolomics data matrix for annotated compound using CSA spectra for ST001000 study
<p>IDSL.CSA - metabolomics data matrix for annotated compound using CSA spectra for ST001000 study</p>
Screening of 165,988 compounds reflecting biological and chemical diversity in the Janssen Library for anti-SARS-CoV-2 activity
<p>This report describes the most relevant results of screening a diversity set of the Janssen Pharmaceutica compound collection for potential activity against SARS-CoV-2 in a stable eGFP-expressing VeroE6 cell line infected with SARS-CoV-2.</p>
Assessment of covalently binding warhead compounds in the validation of the cytomegalovirus nuclear egress complex as an antiviral target
<p>Supplementary to the publication:</p> <p>"Assessment of covalently binding warhead compounds in the validation of the cytomegalovirus nuclear egress complex as an antiviral target" (2023), published in Cells</p> <p>Raw images of the Figures 4, 10, 11 and 14</p>
Testing the effect of individual scent compounds on pollinator attraction in nature using quasi-isogenic Capsella lines
<p>Data are available in five Appendices that are presented in Word files.</p> <p>APPENDIX S1.Figure S1. Crossing scheme for construction of scent-manipulated genotypes (<em>CNL1</em>/<em>TPS2</em>, <em>CNL1</em>/<em>tps2</em>, <em>cnl1</em>/<em>TPS2</em> and <em>cnl1</em>/<em>tps2</em>).</p> <p>APPENDIX S2. Table S1. Primers for scent-manipulated individual genotyping and haplotype amplification.</p> <p>APPENDIX S3. Table S2. Peak area of BAld and β-ocimene in 3-hour floral scent and air headspace sampling. The amount of BAld and β-ocimene emitted by the flowers in flower scent samples (net emission) was calculated by subtracting the respective volatile peak area in the air samples collected on the same collection device on the same collecting date from the volatile peak area in the floral scent headspace sample. The emission rates are calculated as their net emissions divided by the number of flowers enclosed in the headspace collection chamber and the sampling time (3 hours). See more details in “Headspace floral scent collection and analysis”.</p> <p>APPENDIX S4. Table S3. Number of visits by different pollinator group to flowers of the four scent-manipulated genotypes and SC <em>Capsella grandiflora</em> in forty 15-min observation periods.</p> <p>APPENDIX S5. Figure S2. Haplotype-frequency dot plots for each amplicon. Dots with the same color between different individuals indicate the same haplotype sharing. CgCg: <em>CNL1</em>/<em>TPS2</em>, CgCr:<em> cnl1</em>/<em>TPS2</em>, CrCg: <em>CNL1</em>/<em>tps2</em>, CrCr: <em>cnl1</em>/<em>tps2</em> and SC: SC <em>C. grandiflora</em>. Numbers after genotype names indicate their individual and sampling plot number, for example, CgCg2_1 refers the individual No. 1 of <em>CNL1</em>/<em>TPS2 </em>genotype in sampling plot No. 2. Individuals with number 48/418 refer to the ones whose leaf materials were harvested to provide parental haplotype information.</p>
PubChem Compound TOC: Drug and Medication Information
<p><strong>ABSTRACT: </strong>PubChem, a widely used chemical information resource, has undergone notable transformations in the last two years. Over 120 data sources have been incorporated into PubChem, enriching its data repository. Key highlights of the updates include the integration of Google Patents data, which significantly expanded the PubChem Patent collection's coverage. Additionally, new data collections for Cell Line and Taxonomy were introduced, offering convenient access to chemical information based on specific cell lines and taxa. The bioassay data model was updated to enhance its functionality. Moreover, PubChem's programmatic access protocols, PUG-REST and PUG-View, received enhancements, including support for target-centric data download and the 'standardize' option for returning standardized chemical structures. Furthermore, PubChemRDF underwent a substantial update. This paper presents a comprehensive overview of these transformative changes.</p> <p><strong>Instruction: </strong>Data underwent a cleaning process involving the removal of duplicates. Collaboratively with my colleague, we identified and eliminated redundant columns from the dataset. Additionally, we successfully modified the names of certain columns to enhance clarity and eliminate redundancy.</p> <p><strong>Inspiration: </strong>The dataset was uploaded to UBRITE for "DGR_DEPOT" summer 2023 team project</p> <p><strong>Acknowledgements: </strong>Sunghwan Kim, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li, Benjamin A Shoemaker, Paul A Thiessen, Bo Yu, Leonid Zaslavsky, Jian Zhang, Evan E Bolton</p> <p>Kim, Sunghwan et al. “PubChem 2023 update.” <em>Nucleic Acids Res.</em> vol. 51,D1 (2023): D1373-D1380. <a href="https://doi.org/10.1093/nar/gkac956">doi:10.1093/nar/gkac956</a></p> <p><strong>UBRITE LAST UPDATED July 1, 2023</strong></p>
Fig. 2. A in Psilostachyins as trypanocidal compounds: Bioguided fractionation of Ambrosia tenuifolia chemically modified extract
Fig. 2. A) Schematic representation of bioguided separation of CH2Cl2-m-CPBA modified extract of Ambrosia tenuifolia to isolate and identify the main SLs responsible for the trypanocidal activity. B) Percentage of parasite inhibition after treatment with the pools (I-VI) and benznidazole at 5 μg/mL. Asterisks indicate significant differences between the indicated groups and the control, benznidazole (****, p <0.001), and ns indicates no significant differences. C) Percentage of parasite inhibition after treatment at different concentrations (1, 5 and 10 μg/mL) with the pure compounds obtained after chemical extract derivatization. At 1 and 5 μg/mL, only the indicated groups did not exhibit significant differences compared to the respective concentration of benznidazole (ns). At 10 μg/mL, the indicated group showed significant differences compared to benznidazole at the same concentration (****, p <0.001). The molar concentrations equivalent to 1 μg/mL of each compound are 3.8 μM (Psi C and benznidazol) and 3.6 μM (Psi A, paulitin, isopaulitin, 2 and 3), for more details see figure S8.
Phenolic compounds and Aromatic acids emission factors
<p>Primary and secondary emission data of phenolic compounds and Aromatic acids from different fuels combustion.</p>
Fig. 5 in Phenolic compounds from the flowers of Rosa hugonis Hemsl. and their neuroprotective effects
Fig. 5. Effects of compound 5 on PI3K/Akt/GSK-3β signaling pathway in 6- OHDA induced PC12 cells. The levels of total or phosphorylated PDK1, Akt and GSK-3β were identified by Western blot. β-Actin was used as a control.
Fig. 4 in Phenolic compounds from the flowers of Rosa hugonis Hemsl. and their neuroprotective effects
Fig. 4. Effects of compound 5 on 6-OHDA-induced ROS generation. (A) PC12 cell were treated with different concentration of compound 5 before exposure to 6- OHDA for 24 h. Cells were then stained with DCFH-DA. (a) Control; (b) 6-OHDA group; (c) 6-OHDA and 5 μM compound 5 treatment; (d) 6-OHDA and 10 μM compound 5 treatment. (B–C) PC12 cell were treated with different concentration of compound 5 before exposure to 6-OHDA for 24 h. The relative mRNA expression levels of SOD and CAT were determined by RT-qPCR. The values are presented as the mean ± SD (n = 3). *p <0.05 versus 6-OHDA group; #p <0.05 versus control group.
Fig. 3 in Phenolic compounds from the flowers of Rosa hugonis Hemsl. and their neuroprotective effects
Fig. 3. Effects of compound 5 on 6-OHDA-induced PC12 cell injury. (A) PC12 cells were preincubated with different concentration of compound 5 for 30 min and then exposed to 6-OHDA for 24 h. The values are presented as the mean ±SD (n =3). *p <0.05 versus 6-OHDA group; #p <0.05 versus control group. (B) PC12 cells were treated with different concentration of compound 5 for 24 h. The values are presented as the mean ± SD (n = 3). *p <0.05 versus control group. (C) The changes of morphology of PC12 cells in present of compound 5. (a) Control; (b) 6-OHDA group; (c) 6-OHDA and 5 μM compound 5 treatment; (d) 6-OHDA and 10 μM compound 5 treatment.
Fig. 4. Calculated and experimental ECD spectra for compounds 1 in Sesquiterpenoids and monoterpenoids from the water decoction of Valeriana officinalis L
Fig. 4. Calculated and experimental ECD spectra for compounds 1 (A), 3 (B), 4 (C), 5 (D, in water), 6 (E, in water), 7 (F), and 8 (G) in MeOH.
Fig. 8. Compound 14 activated Nrf2 in Diterpenoids with anti-inflammatory activity from Euphorbia wallichii
Fig. 8. Compound 14 activated Nrf2/HO-1 signaling pathway. (A–C) The expressions of Nrf2 and HO-1 were determined by Western blot analysis and the quantification of protein expression was performed by Image J. (D) The inhibitory effect of 14 (16 μM) on the nuclear translocation of Nrf2 induced by LPS via confocal laser scanning microscopy. RAW264.7 cells stained for Nrf2 (red) and nuclei (DAPI, blue) (scale bar: 10 μm). The values are presented as mean ± SD of three independent experiments, n 3. ###p <0.001, vs. the control group; **p <0.01, ***p <0.001, vs. LPS-treated group. (For interpretation of the references to color in = this figure legend, the reader is referred to the Web version of this article.)
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
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.