PubChem 2025 update

Nucleic Acids Research, Год журнала: 2024, Номер 53(D1), С. D1516 - D1525

Опубликована: Ноя. 18, 2024

Abstract PubChem (https://pubchem.ncbi.nlm.nih.gov) is a large and highly-integrated public chemical database resource at NIH. In the past two years, significant updates were made to PubChem. With additions from over 130 new sources, contains >1000 data 119 million compounds, 322 substances 295 bioactivities. New interfaces, such as consolidated literature panel patent knowledge panel, developed. The combines all references about compound into single list, allowing users easily find, sort, export relevant articles for in one place. panels given query or gene display chemicals, genes, diseases co-mentioned with documents, helping explore relationships between co-occurring entities within documents. PubChemRDF was expanded include co-occurrence underlying enabling exploit semantic web technologies entity based on co-occurrences scientific literature. usability accessibility of information chemicals non-discrete structures (e.g. biologics, minerals, polymers, UVCBs glycans) greatly improved dedicated pages that provide comprehensive view available these chemicals.

Язык: Английский

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Astrocyte-to-neuron H2O2 signalling supports long-term memory formation in Drosophila and is impaired in an Alzheimer’s disease model

Nature Metabolism, Год журнала: 2025, Номер unknown

Опубликована: Янв. 24, 2025

Abstract Astrocytes help protect neurons from potential damage caused by reactive oxygen species (ROS). While ROS can also exert beneficial effects, it remains unknown how neuronal signalling is activated during memory formation, and whether astrocytes play a role in this process. Here we discover an astrocyte-to-neuron H 2 O cascade Drosophila that essential for long-term formation. Stimulation of acetylcholine induces increase intracellular calcium ions, which triggers the generation extracellular superoxide (O • – ) astrocytic NADPH oxidase. Astrocyte-secreted dismutase 3 (Sod3) converts to hydrogen peroxide (H ), imported into olfactory centre, mushroom body, as revealed vivo imaging. Notably, Sod3 activity requires copper are supplied amyloid precursor protein. We find human amyloid-β peptide, implicated Alzheimer’s disease, inhibits nAChRα7 cholinergic receptor impairs formation preventing synthesis. These findings may have important implications understanding aetiology disease.

Язык: Английский

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CUL4-Based Ubiquitin Ligases in Chromatin Regulation: An Evolutionary Perspective

Cells, Год журнала: 2025, Номер 14(2), С. 63 - 63

Опубликована: Янв. 7, 2025

Ubiquitylation is a post-translational modification that modulates protein function and stability. It orchestrated by the concerted action of three types enzymes, with substrate specificity governed ubiquitin ligases (E3s), which may exist as single proteins or part multi-protein complexes. Although Cullin (CUL) lack intrinsic enzymatic activity, they participate in formation active ligase complexes, known Cullin-Ring Ligases (CRLs), through their association ROC1 ROC2, along adaptor receptor proteins. Mammalian genomes encode several CUL (CUL1-9), each contributing to distinct CRLs. Among these proteins, CUL1, CUL3, CUL4 are believed be most ancient evolutionarily conserved from yeast mammals, uniquely duplicated vertebrates. Genetic evidence strongly implicates CUL4-based (CRL4s) chromatin regulation across various species suggests that, vertebrates, CRL4s have also acquired cytosolic role, facilitated cytosol-localizing paralog CUL4. Substrates identified biochemical studies elucidated molecular mechanisms regulate processes. The substantial body knowledge on biology amassed over past two decades provides unique opportunity explore functional evolution CRL4. In this review, we synthesize available structural, genetic, data CRL4 model organisms discuss novel functions CRL4s.

Язык: Английский

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Cell type-specific driver lines targeting the Drosophila central complex and their use to investigate neuropeptide expression and sleep regulation

Опубликована: Янв. 21, 2025

The central complex (CX) plays a key role in many higher-order functions of the insect brain including navigation and activity regulation. Genetic tools for manipulating individual cell types, knowledge what neurotransmitters neuromodulators they express, will be required to gain mechanistic understanding how these are implemented. We generated characterized split-GAL4 driver lines that express or small subsets about half CX types. surveyed neuropeptide receptor expression using fluorescent situ hybridization. About neuropeptides we examined were expressed only few cells, while rest dozens hundreds cells. Neuropeptide receptors more broadly at lower levels. Using our GAL4 drivers mark found 51 85 types least one 21 multiple neuropeptides. Surprisingly, all co-expressed molecule neurotransmitter. Finally, used identify whose activation affects sleep, identified other link circadian clock CX. well-characterized genetic information on neurotransmitter provide should enhance studies

Язык: Английский

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Contribution of neurons that express fruitless and Clock transcription factors to behavioral rhythms and courtship

iScience, Год журнала: 2025, Номер 28(3), С. 112037 - 112037

Опубликована: Фев. 16, 2025

Animals need to integrate information across neuronal networks that direct reproductive behaviors and circadian rhythms. The Drosophila master regulatory transcription factors courtship rhythms are co-expressed. We find sex differences in the number of these fruitless (fru) Clock (Clk)-expressing neurons (fru ∩ Clk neurons) regulated by male-specific Fru. assign fru electron microscopy connectome subtypes clock neurons. discover fru-expressing post-synaptic targets Clk-expressing When activated or silenced, we observe a shortening period length. Activation also changes rate behavior is performed. examine male over 24 h activities peak at lights-on. These results reveal how subserve two processes can impact behavioral outcomes sex-specific manner.

Язык: Английский

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Cell type-specific driver lines targeting the Drosophila central complex and their use to investigate neuropeptide expression and sleep regulation

Опубликована: Фев. 28, 2025

The central complex (CX) plays a key role in many higher-order functions of the insect brain including navigation and activity regulation. Genetic tools for manipulating individual cell types, knowledge what neurotransmitters neuromodulators they express, will be required to gain mechanistic understanding how these are implemented. We generated characterized split-GAL4 driver lines that express or small subsets about half CX types. surveyed neuropeptide receptor expression using fluorescent situ hybridization. About neuropeptides we examined were expressed only few cells, while rest dozens hundreds cells. Neuropeptide receptors more broadly at lower levels. Using our GAL4 drivers mark found 51 85 types least one 21 multiple neuropeptides. Surprisingly, all co-expressed neurotransmitter. Finally, used identify whose activation affects sleep, identified other link circadian clock CX. well-characterized genetic information on neurotransmitter provide should enhance studies

Язык: Английский

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Entomophthovirus: An insect-derived iflavirus that infects a behavior-manipulating fungal pathogen of dipterans

G3 Genes Genomes Genetics, Год журнала: 2024, Номер 14(10)

Опубликована: Авг. 19, 2024

Abstract We report a virus infecting Entomophthora muscae, behavior-manipulating fungal pathogen of dipterans. The virus, which we name Berkeley Entomophthovirus, is positive-strand RNA in the iflaviridae family capsid-forming viruses, are mostly known to infect insects. viral expressed at high levels cells vitro and during vivo infections Drosophila melanogaster, particles can be seen intracellularly E. muscae. This find two closely related variants our culture also three different viruses reported from metagenomic surveys, were isolated wild dipterans, third ticks. By analyzing sequencing data these earlier reports, abundant reads aligning muscae specifically samples sequenced. These establish wide perhaps obligate association with wild, consistent laboratory that host for viruses. Because this, propose Entomophthovirus (EV) this group highly variants. As other members have been cause behavioral changes insects, speculate on possibility EV plays role manipulation flies infected

Язык: Английский

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Cell type-specific driver lines targeting the Drosophila central complex and their use to investigate neuropeptide expression and sleep regulation

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Окт. 22, 2024

The central complex (CX) plays a key role in many higher-order functions of the insect brain including navigation and activity regulation. Genetic tools for manipulating individual cell types, knowledge what neurotransmitters neuromodulators they express, will be required to gain mechanistic understanding how these are implemented. We generated characterized split-GAL4 driver lines that express or small subsets about half CX types. surveyed neuropeptide receptor expression using fluorescent

Язык: Английский

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Using Drosophila to Study the Mechanisms That Underlie Down Syndrome

Опубликована: Янв. 1, 2025

Язык: Английский

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R2DT: a comprehensive platform for visualizing RNA secondary structure

Nucleic Acids Research, Год журнала: 2025, Номер 53(4)

Опубликована: Янв. 14, 2025

RNA secondary (2D) structure visualization is an essential tool for understanding function. R2DT a software package designed to visualize 2D structures in consistent, recognizable, and reproducible layouts. The latest release, 2.0, introduces multiple significant features, including the ability display position-specific information, such as single nucleotide polymorphisms or SHAPE reactivities. It also offers new template-free mode allowing of RNAs without pre-existing templates, alongside constrained folding support animated visualizations. Users can interactively modify diagrams, either manually using natural language prompts, generate templates create publication-quality images. Additionally, features faster performance, expanded template library, growing collection compatible tools utilities. Already integrated into biological databases, has evolved comprehensive platform visualization, accessible at https://r2dt.bio.

Язык: Английский

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