Cell type diversity in a developing octopus brain

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Nov. 30, 2022

Abstract Octopuses are mollusks that have evolved intricate neural systems comparable with vertebrates in terms of cell number, complexity and size. The brain types control their sophisticated behavioral repertoire still unknown. Here, we profile the diversity paralarval Octopus vulgaris to build a type atlas comprises mostly cells, but also multiple glial subtypes, endothelial cells fibroblasts. We spatially map vertical, subesophageal optic lobes. Investigation conservation reveals shared gene signature between mouse, fly octopus. Genes related learning memory enriched vertical lobe which show molecular similarities Kenyon Drosophila . construct taxonomy revealing transcriptionally types, tend appear same region. Together, our data sheds light on evolution octopus brain.

Language: Английский

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Non-coding RNA in the wiring and remodeling of neural circuits

Neuron, Journal Year: 2023, Volume and Issue: 111(14), P. 2140 - 2154

Published: May 24, 2023

Language: Английский

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Recording electrical activity from the brain of behaving octopus

Current Biology, Journal Year: 2023, Volume and Issue: 33(6), P. 1171 - 1178.e4

Published: Feb. 23, 2023

Language: Английский

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Ancestral protein reconstruction reveals evolutionary events governing variation in Dicer helicase function

eLife, Journal Year: 2023, Volume and Issue: 12

Published: April 17, 2023

Antiviral defense in ecdysozoan invertebrates requires Dicer with a helicase domain capable of ATP hydrolysis. But despite well-conserved ATPase motifs, human is incapable hydrolysis, consistent muted role antiviral defense. To investigate this enigma, we used ancestral protein reconstruction to resurrect Dicer's animals and trace the evolutionary trajectory Biochemical assays indicated ancient possessed function, that like extant invertebrate Dicers, stimulated by dsRNA. Analyses revealed dsRNA stimulates activity increasing affinity, reflected Michaelis constants. Deuterostome Dicer-1 ancestor, while exhibiting lower retained some activity; importantly, was undetectable vertebrate which had even affinity. Reverting residues hydrolysis pocket insufficient rescue but additional substitutions distant from rescued Dicer-1's function. Our work suggests lost function ancestor due loss involving motifs active site, important for coupling binding conformation. By competing viral dsRNA, RIG-I-like receptors interferon signaling may have allowed or actively caused

Language: Английский

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Investigating Past, Present, and Future Trends on Interface Between Marine and Medical Research and Development: A Bibliometric Review

Marine Drugs, Journal Year: 2025, Volume and Issue: 23(1), P. 34 - 34

Published: Jan. 10, 2025

The convergence of marine sciences and medical studies has the potential for substantial advances in healthcare. This study uses bibliometric topic modeling to map progression research themes from 2000 2023, with an emphasis on interdisciplinary subject sciences. Building global publication output at interface between using Hierarchical Dirichlet Process, we discovered dominating topics during three periods, emphasizing shifts focus development trends. Our data show a significant rise output, indicating growing interest bioresources applications. paper identifies two main areas active research, "natural product biochemistry" "trace substance genetics", both great therapeutic potential. We used social network analysis collaborative networks identify prominent scholars institutions driving this progress. indicates important paths policy R&D management operating crossroads healthcare innovation It also underscores significance quantitative foresight methods teams identifying interpreting future scientific convergences breakthroughs.

Language: Английский

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Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine

Cell Genomics, Journal Year: 2023, Volume and Issue: 3(8), P. 100348 - 100348

Published: June 25, 2023

The annotation of microRNAs depends on the availability transcriptomics data and expert knowledge. This has led to a gap between novel genomes high-quality microRNA complements. Using >16,000 from manually curated gene database MirGeneDB, we generated trained covariance models for all conserved families. These are available in our tool MirMachine, which annotates within genomes. We successfully applied MirMachine range animal species, including those with large genome duplications extinct where small RNA sequencing is hard achieve. further describe score expected that can be used assess completeness assemblies. closes long-persisting field by facilitating automated pipelines deeper studies into evolution regulation, even organisms.

Language: Английский

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MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 53(D1), P. D116 - D128

Published: Nov. 30, 2024

Abstract We present a major update of MirGeneDB (3.0), the manually curated animal microRNA gene database. Beyond moving to new server and creation computational mirror, we have expanded database with addition 33 invertebrate species, including representatives 5 previously unsampled phyla, 6 mammal species. now contains entries for 21 822 genes (5160 these from species) belonging 1743 families. The inclusion species allowed us refine both evolutionary node appearance number genes/families, as well MirGeneDB’s phylogenetically informed nomenclature system. Updated covariance models all families, along smallRNA read data are downloadable. These enhanced annotations will allow researchers analyze properties such secondary structure features their biogenesis within robust phylogenetic context without plagued numerous false positives negatives. In light improvements, 3.0 assume responsibility naming conserved novel metazoan microRNAs. is part RNAcentral Elixir Norway publicly freely available at mirgenedb.org.

Language: Английский

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ncOrtho: efficient and reliable identification of miRNA orthologs

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 51(13), P. e71 - e71

Published: May 31, 2023

MicroRNAs (miRNAs) are post-transcriptional regulators that finetune gene expression via translational repression or degradation of their target mRNAs. Despite functional relevance, frameworks for the scalable and accurate detection miRNA orthologs missing. Consequently, there is still no comprehensive picture how miRNAs associated regulatory networks have evolved. Here we present ncOrtho, a synteny informed pipeline targeted search in unannotated genome sequences. ncOrtho matches annotations from multi-tissue transcriptomes precision, while scaling to analysis hundreds custom-selected species. The presence-absence pattern 266 human families across 402 vertebrate species reveals four bursts acquisition, which most recent event occurred last common ancestor higher primates. rarely modified lost, but notable exceptions both events exist. co-ortholog numbers faithfully indicate lineage-specific whole duplications, powerful markers phylogenomic analyses. Their exceptionally low genetic diversity makes them suitable resolve clades where phylogenetic signal blurred by incomplete lineage sorting ancestral alleles. In summary, allows routinely consider evolutionary analyses were thus far reserved protein-coding genes.

Language: Английский

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A renaissance of microRNAs as taxonomic and phylogenetic markers in animals

Zoologica Scripta, Journal Year: 2024, Volume and Issue: 53(6), P. 754 - 762

Published: June 21, 2024

Abstract Molecular markers for tracing animal sample origins and compositions are critical applications such as parasite detection, contamination screening, authentication. Among these, microRNAs have emerged promising candidates due to their deep conservation, near‐hierarchical evolution, stability. I here review the suitability of taxonomic also phylogenetic show how careful annotation efforts establishment curated microRNA gene database MirGeneDB tools like MirMachine revitalized research. These advancements enable accurate studies, highlighting microRNAs' potential in resolving long‐standing questions relationships extending ancient DNA environmental RNA analysis. Future research must focus on expanding complements across all Metazoa further improving methodologies.

Language: Английский

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Noncoding RNAs: Emerging regulators of behavioral complexity

Wiley Interdisciplinary Reviews - RNA, Journal Year: 2024, Volume and Issue: 15(3)

Published: May 1, 2024

Abstract The mammalian genome encodes thousands of non−coding RNAs (ncRNAs), ranging in size from about 20 nucleotides (microRNAs or miRNAs) to kilobases (long lncRNAs). ncRNAs contribute a layer gene regulation that could explain the evolution massive phenotypic complexity even as number protein‐coding genes remains unaltered. We propose low conservation, poor expression, and highly restricted spatiotemporal expression patterns—conventionally considered may affect behavior through direct, rapid, often sustained at transcriptional, post‐transcriptional, translational levels. Besides these direct roles, their effect during neurodevelopment manifest behavioral changes later organism's life, especially when exposed environmental cues like stress seasonal changes. lncRNAs diverse mechanisms sponging miRNAs, recruitment chromatin modifiers, alternative splicing. highlight need for synthesis between rigorously designed paradigms model organisms wide diversity behaviors documented by ethologists field studies on exquisitely adapted niche. Comparative genomics latest advancements transcriptomics provide an unprecedented scope merging lab non−model shed light role driving responses individuals groups. touch upon technical challenges contentious issues must be resolved fully understand regulating complex traits. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches >

Language: Английский

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