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Figure 5 from: Bulbul MZH, Chowdhury TS, Misbah MMH, Ferdous J, Dey S, Hasan I, Fujii Y, Ozeki Y, Kawsar SMA (2021) Synthesis of new series of pyrimidine nucleoside derivatives bearing the acyl moieties as potential antimicrobial agents. Pharmacia 68(1): 23-34. https://doi.org/10.3897/pharmacia.68.e56543
Figure 5 Percentage zone of mycelial growth inhibition for compounds 3 and 11 against A. niger (A and B, respectively). DMSO represents the negative control, whereas nystatin is the positive control.
Figure 2 from: Bulbul MZH, Chowdhury TS, Misbah MMH, Ferdous J, Dey S, Hasan I, Fujii Y, Ozeki Y, Kawsar SMA (2021) Synthesis of new series of pyrimidine nucleoside derivatives bearing the acyl moieties as potential antimicrobial agents. Pharmacia 68(1): 23-34. https://doi.org/10.3897/pharmacia.68.e56543
Figure 2 Percentage of inhibition observed for A) B. subtilis by compounds 7, 9, and 8; B) E. coli by compounds 2, 4, and 9; C) S. abony by compounds 7, 9, and 14; and D) S. aureus by compounds 7, 9, and 14. DMSO was the negative control, whereas azithromycin represented the positive control.
Figure 7 from: Bulbul MZH, Chowdhury TS, Misbah MMH, Ferdous J, Dey S, Hasan I, Fujii Y, Ozeki Y, Kawsar SMA (2021) Synthesis of new series of pyrimidine nucleoside derivatives bearing the acyl moieties as potential antimicrobial agents. Pharmacia 68(1): 23-34. https://doi.org/10.3897/pharmacia.68.e56543
Figure 7 Percentage growth inhibition observed for various concentrations of compound 9. Right figure 96-well flat-bottom experiment.
Figure 3 from: Demchenko SА, Fedchenkova YА, Yeromina HО, Herashenko IV, Berdnyk OH, Demchenko AM (2021) The synthesis of N-(4-aryl-thiazol-2-yl)-N1-(4,5,6,7-tetrahydro-3H-azepin-2-yl)-hydrazine hydrobromides and the cardioprotective activity of (41-methoxyphenyl-thiazol-2-yl) derivative. Pharmacia 68(1): 141-146. https://doi.org/10.3897/pharmacia.68.e58788
Figure 3 Smooth muscle preparations miographic study methodic scheme, where: 1 peristaltic pump 2 thermostat 3 amplifier 4 Capacitive tensometric sensor 5 work chamber (heated wtih thermostat) 6 analog-to-digital converter 7 personal computer.
Figure 1 from: Demchenko SА, Fedchenkova YА, Yeromina HО, Herashenko IV, Berdnyk OH, Demchenko AM (2021) The synthesis of N-(4-aryl-thiazol-2-yl)-N1-(4,5,6,7-tetrahydro-3H-azepin-2-yl)-hydrazine hydrobromides and the cardioprotective activity of (41-methoxyphenyl-thiazol-2-yl) derivative. Pharmacia 68(1): 141-146. https://doi.org/10.3897/pharmacia.68.e58788
Figure 1 Structural formulas for active components of Levocarnitin (а), Mildronate (b) and N-[4-(41-methoxyphenyl)-thiazol-2-yl]-N1-(4,5,6,7-tetrahydro-3H-azepin-2-yl)-hydrazine hydrobromide (5 b)
Scheme 1 from: Demchenko SА, Fedchenkova YА, Yeromina HО, Herashenko IV, Berdnyk OH, Demchenko AM (2021) The synthesis of N-(4-aryl-thiazol-2-yl)-N1-(4,5,6,7-tetrahydro-3H-azepin-2-yl)-hydrazine hydrobromides and the cardioprotective activity of (41-methoxyphenyl-thiazol-2-yl) derivative. Pharmacia 68(1): 141-146. https://doi.org/10.3897/pharmacia.68.e58788
Scheme 1 Synthesis of N-(4-aryl-thiazol-2-yl)-N1-(4,5,6,7-tetrahydro-3Н-azepin-2-yl)-hydrazine hydrobromides (5 a–d). Where: 1, 3, 5: a) R=R1=H b) R=OCH3, R1=H; c) R=Cl, R1=H; d) RR1=-OCH2CH2O-.
Figure 1 from: Proskurina K, Yevtifieieva O, Mala O, Mashtaler V (2021) Development of the method for standardization of the medicinal plant raw material of Cichorium intybus L. herb by the total amount of hydroxycinnamic acid derivatives. Pharmacia 68(1): 167-173. https://doi.org/10.3897/pharmacia.68.e49273
Figure 1 The TLC chromatogram of hydroxycinnamic acids in ethanolic extracts of different samples of chicory herb originating from Ukraine. S1–3: chlorogenic acid, caffeic acid and ferulic acid as references; for plant extracts, see abbreviations in Table 3.
Figure 2 from: Proskurina K, Yevtifieieva O, Mala O, Mashtaler V (2021) Development of the method for standardization of the medicinal plant raw material of Cichorium intybus L. herb by the total amount of hydroxycinnamic acid derivatives. Pharmacia 68(1): 167-173. https://doi.org/10.3897/pharmacia.68.e49273
Figure 2 The absorption spectrum of ethanol (50 per cent V/V) chicory herb extracts for 8 sample of the raw plant material. See abbreviations in Table 3. UV/Vis absorption spectra of chlorogenic acid chemical standard at 10.08 µg/ml in ethanol (50 per cent V/V).
Figure 3 from: Proskurina K, Yevtifieieva O, Mala O, Mashtaler V (2021) Development of the method for standardization of the medicinal plant raw material of Cichorium intybus L. herb by the total amount of hydroxycinnamic acid derivatives. Pharmacia 68(1): 167-173. https://doi.org/10.3897/pharmacia.68.e49273
Figure 3 Absorbance values of chlorogenic acid as a function of the solution concentrations. The data correlation was calculated by a linear fit.
The Molecular Diversity Scope of Oxindole Derivatives in Organic Synthesis
<p>The role of oxindole derivatives is discussed as starting materials in diverse organic reactions including two and more components between the years 2014 until 2020. Oxindoles are famous because of their biological properties for instance chromanone-fused polycyclic pyrrolidinyl-dispirooxindoles, functionalized polycyclic spiro-fused carbocyclicoxindole, and 3,3-disubstituted oxindoles have anti-cancer, anti-tumor, and anti-microbial properties, respectively. Therefore, various methods for synthesizing the oxindole structures have received more attention in organic chemistry.</p>
Data from: Functional role of phenylacetic acid from metapleural gland secretions in controlling fungal pathogens in evolutionarily derived leafcutter ants
Fungus-farming ant colonies vary four to five orders of magnitude in size. They employ compounds from actinomycete bacteria and exocrine glands as antimicrobial agents. Atta colonies have millions of ants and are particularly relevant for understanding hygienic strategies as they have abandoned their ancestors' prime dependence on antibiotic-based biological control in favour of using metapleural gland (MG) chemical secretions. Atta MGs are unique in synthesizing large quantities of phenylacetic acid (PAA), a known but little investigated antimicrobial agent. We show that particularly the smallest workers greatly reduce germination rates of Escovopsis and Metarhizium spores after actively applying PAA to experimental infection targets in garden fragments and transferring the spores to the ants' infrabuccal cavities. In vitro assays further indicated that Escovopsis strains isolated from evolutionarily derived leaf-cutting ants are less sensitive to PAA than strains from phylogenetically more basal fungus-farming ants, consistent with the dynamics of an evolutionary arms race between virulence and control for Escovopsis, but not Metarhizium. Atta ants form larger colonies with more extreme caste differentiation relative to other attines, in societies characterized by an almost complete absence of reproductive conflicts. We hypothesize that these changes are associated with unique evolutionary innovations in chemical pest management that appear robust against selection pressure for resistance by specialized mycopathogens.
Data from: A fat-derived metabolite regulates a peptidergic feeding circuit in Drosophila
Here, we show that the enzymatic cofactor tetrahydrobiopterin (BH4) inhibits feeding in Drosophila. BH4 biosynthesis requires the sequential action of the conserved enzymes Punch, Purple, and Sepiapterin Reductase (Sptr). Although we observe increased feeding upon loss of Punch and Purple in the adult fat body, loss of Sptr must occur in the brain. We found Sptr expression is required in four adult neurons that express neuropeptide F (NPF), the fly homologue of the vertebrate appetite regulator neuropeptide Y (NPY). As expected, feeding flies BH4 rescues the loss of Punch and Purple in the fat body and the loss of Sptr in NPF neurons. Mechanistically, we found BH4 deficiency reduces NPF staining, likely by promoting its release, while excess BH4 increases NPF accumulation without altering its expression. We thus show that, because of its physically distributed biosynthesis, BH4 acts as a fat-derived signal that induces satiety by inhibiting the activity of the NPF neurons.
Data from: Mechanistic insights into landscape genetic structure of two tropical amphibians using field-derived resistance surfaces
Conversion of forests to agriculture often fragments distributions of forest species and can disrupt gene flow. We examined effects of prevalent land uses on genetic connectivity of two amphibian species in northeastern Costa Rica. We incorporated data from field surveys and experiments to develop resistance surfaces that represent local mechanisms hypothesized to modify dispersal success of amphibians, such as habitat-specific predation and desiccation risk. Because time lags can exist between forest conversion and genetic responses, we evaluated landscape effects using land-cover data from different time periods. Populations of both species were structured at similar spatial scales but exhibited differing responses to landscape features. Litter frog population differentiation was significantly related to landscape resistances estimated from abundance and experiment data. Model support was highest for experiment-derived surfaces that represented responses to microclimate variation. Litter frog genetic variation was best explained by contemporary landscape configuration, indicating rapid population response to land-use change. Poison frog genetic structure was strongly associated with geographic isolation, which explained up to 45% of genetic variation, and long-standing barriers, such as rivers and mountains. However, there was also partial support for abundance and microclimate response derived resistances. Differences in species responses to landscape features may be explained by overriding effects of population size on patterns of differentiation for poison frogs, but not litter frogs. In addition, pastures are likely semi-permeable to poison frog gene flow because the species is known to use pastures when remnant vegetation is present, but litter frogs do not. Ongoing reforestation efforts will likely increase connectivity in the region by increasing tree cover and reducing area of pastures.
Data from: Diurnal transcriptional regulation of endosymbiotically derived genes in the chlorarachniophyte Bigelowiella natans
Chlorarachniophyte algae possess complex plastids acquired by the secondary endosymbiosis of a green alga, and the plastids harbor a relict nucleus of the endosymbiont, the so-called nucleomorph. Due to massive gene transfer from the endosymbiont to the host, many proteins involved in plastid and nucleomorph are encoded by the nuclear genome. Genome sequences have provided a blueprint for the fate of endosymbiotically derived genes; however, transcriptional regulation of these genes remains poorly understood. To gain insight into the evolution of endosymbiotic genes, we performed genome-wide transcript profiling along the cell cycle of the chlorarachniophyte Bigelowiella natans, synchronized by light and dark cycles. Our comparative analyses demonstrated that transcript levels of 7,751 nuclear genes (35.7% of 21,706 genes) significantly oscillated along the diurnal/cell cycles, and those included 780 and 147 genes for putative plastid and nucleomorph-targeted proteins, respectively. Clustering analysis of those genes revealed the existence of transcriptional networks related to specific biological processes such as photosynthesis, carbon metabolism, translation, and DNA replication. Interestingly, transcripts of many plastid-targeted proteins in B. natans were induced before dawn, unlike other photosynthetic organisms. In contrast to nuclear genes, 99% nucleomorph genes were found to be constitutively expressed during the cycles. We also found that the nucleomorph DNA replication would be controlled by a nucleus-encoded viral-like DNA polymerase. The results of this study suggest that nucleomorph genes have lost transcriptional regulation along the diurnal cycles, and nuclear genes exert control over the complex plastid including the nucleomorph.
Data from: Bioclimatic variables derived from remote sensing: assessment and application for species distribution modeling
Remote sensing techniques offer an opportunity to improve biodiversity modeling and prediction worldwide. Yet, to date, the weather-station based WorldClim dataset has been the primary source of temperature and precipitation information used in correlative species distribution models. WorldClim consists of grids interpolated from in situ station data recorded primarily from 1960 to 1990. Those datasets suffer from uneven geographic coverage, with many areas of Earth poorly represented. Here, we compare two remote sensing data sources for the purposes of biodiversity prediction: MERRA climate reanalysis data and AMSR-E, a pure remote sensing data source. We use these data to generate novel temperature-based bioclimatic information and to model the distributions of 20 species of vertebrates endemic to four regions of South America: Amazonia, the Atlantic Forest, the Cerrado, and Patagonia. We compare the bioclimatic datasets derived from MERRA and AMSR-E information with in situ station data, and contrast species distribution models based on these two products to models built with WorldClim. Surface temperature estimates provided by MERRA and AMSR-E showed warm temperature biases relative to the in situ data fields, but the reliability of these datasets varied in geographic space. Species distribution models derived from the MERRA data performed equally well (in Cerrado, Amazonia, and Patagonia) or better (Atlantic Forest) than models built with the WorldClim data. In contrast, the performance of models constructed with the AMSR-E data was similar to (Amazonia, Atlantic Forest, Cerrado) or worse than (Patagonia) that of models built with WorldClim data. Whereas this initial comparison assessed only temperature fields, efforts to estimate precipitation from remote sensing information hold great promise; furthermore, other environmental datasets with higher spatial and temporal fidelity may improve upon these results.
Data from: Functional and mechanistic neurotoxicity profiling using human iPSC–derived neural 3D cultures
Neurological disorders affect millions of people worldwide and appear to be on the rise. While the reason for this increase remains unknown, environmental factors are a suspected contributor. Hence, there is an urgent need to develop more complex, biologically relevant, and predictive in vitro assays to screen larger sets of compounds with the potential for neurotoxicity. Here, we employed a human induced pluripotent stem cell (iPSC)-based 3D neural platform composed of mature cortical neurons and astrocytes as a model for this purpose. The iPSC-derived human 3D cortical neuron/astrocyte co-cultures (3D neural cultures) present spontaneous synchronized, readily detectable calcium oscillations. This advanced neural platform was optimized for high-throughput screening in 384-well plates and displays highly consistent, functional performance across different wells and plates. Characterization of oscillation profiles in 3D neural cultures was performed through multi-parametric analysis that included the calcium oscillation rate and peak width, amplitude, and waveform irregularities. Cellular and mitochondrial toxicity were assessed by high-content imaging. For assay characterization, we used a set of neuromodulators with known mechanisms of action. We then explored the neurotoxic profile of a library of 87 compounds that included pharmaceutical drugs, pesticides, flame retardants, and other chemicals. Our results demonstrated that 57% of the tested compounds exhibited effects in the assay. The compounds were then ranked according to their effective concentrations based on in vitro activity. Our results show that a human iPSC-derived 3D neural culture assay platform is a promising biologically-relevant tool to assess the neurotoxic potential of drugs and environmental toxicants.
Data from: In silico site-directed mutagenesis informs species-specific predictions of chemical susceptibility derived from the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool
Chemical hazard assessment requires extrapolation of information from model organisms to all species of concern. The Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool was developed as a rapid, cost effective method to aid cross-species extrapolation of susceptibility to chemicals acting on specific protein targets through evaluation of protein structural similarities and differences. The greatest resolution for extrapolation of chemical susceptibility across species involves comparisons of individual amino acid residues at key positions involved in protein-chemical interactions. However, a lack of understanding of whether specific amino acid substitutions among species at key positions in proteins affect interaction with chemicals made manual interpretation of alignments time consuming and potentially inconsistent. Therefore, this study used in silico site-directed mutagenesis coupled with docking simulations of computational models for acetylcholinesterase (AChE) and ecdysone receptor (EcR) to investigate how specific amino acid substitutions impact protein-chemical interaction. This study found that computationally derived substitutions in identities of key amino acids caused no change in protein-chemical interaction if residues share the same side chain functional properties and have comparable molecular dimensions, while differences in these characteristics can change protein-chemical interaction. These findings were considered in the development of capabilities for automatically generated species-specific predictions of chemical susceptibility in SeqAPASS. These predictions for AChE and EcR were shown to agree with SeqAPASS predictions comparing the primary sequence and functional domain sequence of proteins for more than 90 % of the investigated species, but also identified dramatic species-specific differences in chemical susceptibility that align with results from standard toxicity tests. These results provide a compelling line-of-evidence for use of SeqAPASS in deriving screening level, species-specific, susceptibility predictions across broad taxonomic groups for application to human and ecological hazard assessment.
Data from: Nɛ-acetyl lysine derivatives with zinc binding groups as novel HDAC inhibitors
HDAC inhibitors have been developed very rapidly in clinical trials and even in approvals for treating several cancers. However, there are few reported HDAC inhibitors designed from Nε-acetyl lysine. In current study, we raised a novel design, which is about Nε-acetyl lysine analogues containing amide acetyl groups with the hybridization of ZBG groups as novel HDAC inhibitors.
Data from: Green approach for synthesis of bioactive Hantzsch 1,4-dihydropyridine derivatives based on thiophene moiety via multicomponent reaction
A novel green and efficient one-pot multicomponent reaction of dihydropyridine derivatives was reported as having good to excellent yield. In the presence of the catalyst ceric ammonium nitrate (CAN), different 1,3-diones and same starting materials as 5-bromothiophene-2-carboxaldehyde and ammonium acetate were used at room temperature under solvent-free condition for the Hantzsch pyridine synthesis within a short period of time. All compounds were evaluated for their in vitro antibacterial and antifungal activity and, interestingly, we found that 5(b–f) show excellent activity compared with Ampicillin, whereas only the 5e compound shows excellent antifungal activity against Candida albicans compared with griseofulvin. The cytotoxicity of all compounds has been assessed against breast tumour cell lines (BT-549), but no activity was found. The X-ray structure of one such compound, 5a, viewed as a colourless block crystal, corresponded accurately to a primitive monoclinic cell.
Data from: Synthesis of gypsogenin derivatives with capabilities to arrest cell cycle and induce apoptosis in human cancer cells
Thirty-two gypsogenin derivatives were synthesized and screened for their cytotoxic activities. Their structures were established using IR, 1H NMR, 13C NMR, and LC-MS spectroscopic data. In MTT assays nearly all the compounds displayed good cytotoxicity in the low μM range for several human tumour cell lines (A549, LOVO, SKOV3 and HepG2). Low IC50 values were obtained especially for the carboxamides 7a–7j, for an oxime derivative 3 and a (2,4-dinitrophenyl)hydrazono derivative 4. In particular, the IC50 values of compounds 4 (IC50 = 2.97 ± 1.13 µΜ) and 7 g (IC50 = 3.59 ± 2.04 µΜ) against LOVO cells were found to be much lower than those of the other derivatives and parent compound. These compounds were submitted to an extensive biological testing and proved compounds 4 and 7 g to act mainly by an arrest of the tumour cells in the S phase of the cell cycle. In addition, compounds 4 and 7 g triggered the apoptotic pathway in cancer cells, showing high apoptosis ratios.
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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.