cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30003221
title: A comparative study of capacitation-mediated changes in whole mouse sperm proteome

description: Mammalian spermatozoa acquire fertilizing ability in response to environmental factors enriched in the female reproductive tract, a process called capacitation. During capacitation, sperm undergo physiological changes that are accompanied by functional regulation of sperm proteins. However, the mechanism by which capacitation orchestrates sperm protein functions to modulate physiological characteristics remains unclear. Here, I analyzed capacitation-mediated global proteomic changes in mouse spermatozoa to unravel the underlying molecular association with the biological processes in sperm capacitation. I quantitatively compared 4,587 proteins identified by liquid chromatography-tandem mass spectrometry. Among them, the amounts of 47 and 180 proteins were reduced to over 1.5-fold (<i>p</i> &lt; 0.05) and 1.3-fold (<i>p</i> &lt; 0.1), respectively, and those of 11 and 60 proteins were increased over 1.5-fold (<i>p</i> &lt; 0.05) and 1.3-fold (<i>p</i> &lt; 0.1), respectively, in capacitated mouse sperm. Functional annotation of proteins reduced in capacitated sperm revealed that these proteins could be associated with lipid metabolism, RNA processing, and remodeling of the nuclear envelope structure. This result suggests that reactive oxygen species might be more generated for cholesterol efflux and the nucleus might undergo decondensation to form pronucleus in sperm during capacitation. In addition, functional annotation of proteins of which levels are increased in capacitated sperm represents that they could be involved in sperm structure. This study expands the molecular contribution to modulation of sperm functions and provides new insights into potential biological processes involving regulatory molecular machinery in capacitated sperm.
DOI: 10.6084/m9.figshare.30003221.v1
title: A comparative study of capacitation-mediated changes in whole mouse sperm proteome

description: Mammalian spermatozoa acquire fertilizing ability in response to environmental factors enriched in the female reproductive tract, a process called capacitation. During capacitation, sperm undergo physiological changes that are accompanied by functional regulation of sperm proteins. However, the mechanism by which capacitation orchestrates sperm protein functions to modulate physiological characteristics remains unclear. Here, I analyzed capacitation-mediated global proteomic changes in mouse spermatozoa to unravel the underlying molecular association with the biological processes in sperm capacitation. I quantitatively compared 4,587 proteins identified by liquid chromatography-tandem mass spectrometry. Among them, the amounts of 47 and 180 proteins were reduced to over 1.5-fold (<i>p</i> &lt; 0.05) and 1.3-fold (<i>p</i> &lt; 0.1), respectively, and those of 11 and 60 proteins were increased over 1.5-fold (<i>p</i> &lt; 0.05) and 1.3-fold (<i>p</i> &lt; 0.1), respectively, in capacitated mouse sperm. Functional annotation of proteins reduced in capacitated sperm revealed that these proteins could be associated with lipid metabolism, RNA processing, and remodeling of the nuclear envelope structure. This result suggests that reactive oxygen species might be more generated for cholesterol efflux and the nucleus might undergo decondensation to form pronucleus in sperm during capacitation. In addition, functional annotation of proteins of which levels are increased in capacitated sperm represents that they could be involved in sperm structure. This study expands the molecular contribution to modulation of sperm functions and provides new insights into potential biological processes involving regulatory molecular machinery in capacitated sperm.
DOI: 10.3535/46h-x5k-gvz
title: Sciota hostilis Stephens, 1834

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ydk-ygk-wqg
title: Erebidae

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/43k-d72-p5m
title: Paratalanta pandalis Hübner, 1825

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.6084/m9.figshare.28959866
title: Identification of YAP regulators through high-throughput screening and NanoBiT-based validation-drug repositioning for cancer therapy

description: Yes-associated protein (YAP), a key co-transcription factor of the Hippo pathway, is a promising drug target for cancer therapy due to its critical role in promoting cell proliferation, survival, and tumor progression when dysregulated. While most Hippo pathway-targeting drugs focus on disrupting TEAD-YAP interactions or modulating the MST or LATS kinase cascade, new approaches are needed to identify small molecules that regulate YAP activity. In this study, we conducted high-throughput screening of FDA-approved drugs to discover potential YAP modulators. Using a NanoBiT-based system, which enables real-time and quantitative measurement of protein interactions, combined with phenotype-based assays in EGFP-YAP-expressing cells, we identified compounds that activate or inhibit YAP function. Among the identified YAP regulators, the microtubule destabilizer vinorelbine promoted YAP nuclear localization and transcriptional activation, while the antipsychotic drug thioridazine enhanced YAP phosphorylation at Ser127, resulting in its cytoplasmic retention and reduced transcriptional activity, effectively suppressing cancer cell growth. These findings demonstrate the potential of FDA-approved drugs in modulating YAP activity and present a novel screening strategy for developing YAP-targeting therapeutics. Furthermore, this approach can be extended to identify modulators of other signaling pathways, advancing drug discovery for a wide range of diseases.
DOI: 10.6084/m9.figshare.28959866.v1
title: Identification of YAP regulators through high-throughput screening and NanoBiT-based validation-drug repositioning for cancer therapy

description: Yes-associated protein (YAP), a key co-transcription factor of the Hippo pathway, is a promising drug target for cancer therapy due to its critical role in promoting cell proliferation, survival, and tumor progression when dysregulated. While most Hippo pathway-targeting drugs focus on disrupting TEAD-YAP interactions or modulating the MST or LATS kinase cascade, new approaches are needed to identify small molecules that regulate YAP activity. In this study, we conducted high-throughput screening of FDA-approved drugs to discover potential YAP modulators. Using a NanoBiT-based system, which enables real-time and quantitative measurement of protein interactions, combined with phenotype-based assays in EGFP-YAP-expressing cells, we identified compounds that activate or inhibit YAP function. Among the identified YAP regulators, the microtubule destabilizer vinorelbine promoted YAP nuclear localization and transcriptional activation, while the antipsychotic drug thioridazine enhanced YAP phosphorylation at Ser127, resulting in its cytoplasmic retention and reduced transcriptional activity, effectively suppressing cancer cell growth. These findings demonstrate the potential of FDA-approved drugs in modulating YAP activity and present a novel screening strategy for developing YAP-targeting therapeutics. Furthermore, this approach can be extended to identify modulators of other signaling pathways, advancing drug discovery for a wide range of diseases.
DOI: 10.6084/m9.figshare.29820295
title: Asxl1 regulates optic cup development through interaction with Lhx2 and epigenetic modulation of Wnt signaling

description: The <i>additional sex combs-like 1</i> (<i>Asxl1</i>) gene is a chromatin regulator involved in transcriptional activation and repression. While Asxl1 plays a crucial role in various organ development, its role in ocular development remains unclear. Here, we analyzed <i>Asxl1</i> knockout (KO) mice and observed disrupted optic cup formation at embryonic day 10.5 (E10.5). RNA-seq of the E10.5 optic cup revealed dysregulation of Wnt signaling and early eye development genes. In further investigation using isolated cell from E10.5 retinal region, neuroepithelial stem cells from <i>Asxl1</i> KO embryos exhibited impaired proliferation and spheroid formation. To elucidate the transcriptional mechanism by Asxl1 in optic cup formation, biochemical assays demonstrated that Asxl1 binds the LIM domain of Lhx2, facilitating repression of Wnt1, Wnt2, and Wnt8b. Following ChIP analysis showed that the gain of function of Asxl1 increased repressive histone marks (H3K27me3, H3K9me3) and reduced active marks (H3K4me3) at Lhx2-binding motifs within the cis-regulatory regions of canonical Wnt ligand genes. These findings establish Asxl1 as a key epigenetic regulator of optic cup development by modulating Lhx2-mediated Wnt signaling, providing insights into congenital eye disorders.
DOI: 10.6084/m9.figshare.29820295.v1
title: Asxl1 regulates optic cup development through interaction with Lhx2 and epigenetic modulation of Wnt signaling

description: The <i>additional sex combs-like 1</i> (<i>Asxl1</i>) gene is a chromatin regulator involved in transcriptional activation and repression. While Asxl1 plays a crucial role in various organ development, its role in ocular development remains unclear. Here, we analyzed <i>Asxl1</i> knockout (KO) mice and observed disrupted optic cup formation at embryonic day 10.5 (E10.5). RNA-seq of the E10.5 optic cup revealed dysregulation of Wnt signaling and early eye development genes. In further investigation using isolated cell from E10.5 retinal region, neuroepithelial stem cells from <i>Asxl1</i> KO embryos exhibited impaired proliferation and spheroid formation. To elucidate the transcriptional mechanism by Asxl1 in optic cup formation, biochemical assays demonstrated that Asxl1 binds the LIM domain of Lhx2, facilitating repression of Wnt1, Wnt2, and Wnt8b. Following ChIP analysis showed that the gain of function of Asxl1 increased repressive histone marks (H3K27me3, H3K9me3) and reduced active marks (H3K4me3) at Lhx2-binding motifs within the cis-regulatory regions of canonical Wnt ligand genes. These findings establish Asxl1 as a key epigenetic regulator of optic cup development by modulating Lhx2-mediated Wnt signaling, providing insights into congenital eye disorders.
DOI: 10.3535/w1v-0pa-qyr
title: Diarsia mendica Fabricius, 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.6084/m9.figshare.30337323
title: LncRNA-mRNA integrated networks in the neuroendocrine system of bisphenol a-treated mice induce cellular dysfunctions by disrupting transcriptional homeostasis

description: Bisphenol A (BPA) is a widely used xenoestrogen that can disrupt neuroendocrine and immune regulation through multiple hormone receptors. This study investigated BPA-induced long non-coding RNA (lncRNA)-mRNA interactions in the cerebral cortex and hypothalamic-pituitary-thyroid (HPT) axis of adult male mice. Transcriptome sequencing and comprehensive lncRNA annotation identified 14,858 novel lncRNA transcripts. Integrated network analysis using weighted gene co-expression network analysis (WGCNA) revealed four distinct tissue-specific modules: neuronal signaling alterations (<i>Tac1</i>, <i>Htr1b</i>, <i>Npy</i>), RNA splicing modifications (<i>Srsf5</i>), PI3K/Akt-mediated cellular dysfunction (<i>Creb5</i>, <i>Cdkn1a</i>), and immune receptor signaling disruptions (<i>Trbv15, Fcrla</i>). These findings suggest that BPA reprograms transcriptional networks in a tissue-specific manner, potentially disrupting hormone-related neurotransmission, metabolic regulation, and immune signaling via lncRNA-mediated mechanisms. Such systems-level reprogramming of the immune-neuroendocrine network (INEN) provides novel mechanistic insights and biomarker candidates for assessing and mitigating the health impacts of environmental endocrine disruptors.
DOI: 10.6084/m9.figshare.30337323.v1
title: LncRNA-mRNA integrated networks in the neuroendocrine system of bisphenol a-treated mice induce cellular dysfunctions by disrupting transcriptional homeostasis

description: Bisphenol A (BPA) is a widely used xenoestrogen that can disrupt neuroendocrine and immune regulation through multiple hormone receptors. This study investigated BPA-induced long non-coding RNA (lncRNA)-mRNA interactions in the cerebral cortex and hypothalamic-pituitary-thyroid (HPT) axis of adult male mice. Transcriptome sequencing and comprehensive lncRNA annotation identified 14,858 novel lncRNA transcripts. Integrated network analysis using weighted gene co-expression network analysis (WGCNA) revealed four distinct tissue-specific modules: neuronal signaling alterations (<i>Tac1</i>, <i>Htr1b</i>, <i>Npy</i>), RNA splicing modifications (<i>Srsf5</i>), PI3K/Akt-mediated cellular dysfunction (<i>Creb5</i>, <i>Cdkn1a</i>), and immune receptor signaling disruptions (<i>Trbv15, Fcrla</i>). These findings suggest that BPA reprograms transcriptional networks in a tissue-specific manner, potentially disrupting hormone-related neurotransmission, metabolic regulation, and immune signaling via lncRNA-mediated mechanisms. Such systems-level reprogramming of the immune-neuroendocrine network (INEN) provides novel mechanistic insights and biomarker candidates for assessing and mitigating the health impacts of environmental endocrine disruptors.
DOI: 10.3535/4fv-n8a-05n
title: Chrysoteuchia culmella Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/hal-4b9-3lc
title: Trisateles emortualis ([Denis & Schiffermüller], 1775)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.6084/m9.figshare.28524908
title: Behind the mountains and over the sea: the Changbai Mountain Range provided <i>Rana coreana</i> with a Chinese residence permit all along

description: The Changbai Mountain Range is generally perceived as a barrier to amphibian distribution, but it might not be playing this role anymore. <i>Rana coreana</i> was first described as a Korean endemic species, split from <i>Rana amurensis</i>, which ranges at more northern latitude. The species was then found on the Shandong peninsula in China, where it was first described as <i>Rana kunyuensis</i>, before being synonymised with <i>R. coreana</i>. So far, the contact zone with <i>R. amurensis</i> was expected to be in the vicinity of Pyongyang in DPR Korea, west of the Baekdu Mountain Range. However, the species is known from a population further north, and during surveys in Dalian in Liaoning Province, China, we found <i>R. coreana</i> on the southern slopes of the Laoling Mountain Range facing the Yellow Sea. Our phylogenetic analyses based on mitochondrial ribosomal markers showed the individual to cluster with <i>R. coreana</i> samples from the Korean Peninsula. In addition, our ecological niche models showed the presence of suitable habitats outside of the known range of the species, deserving further investigation. The habitat of the species at this new locality is similar to the one known in the three range nations, and highlights the need for more surveys in northeast China as the barrier formed by the Changbai Range is more porous than originally expected.
DOI: 10.6084/m9.figshare.28524908.v1
title: Behind the mountains and over the sea: the Changbai Mountain Range provided <i>Rana coreana</i> with a Chinese residence permit all along

description: The Changbai Mountain Range is generally perceived as a barrier to amphibian distribution, but it might not be playing this role anymore. <i>Rana coreana</i> was first described as a Korean endemic species, split from <i>Rana amurensis</i>, which ranges at more northern latitude. The species was then found on the Shandong peninsula in China, where it was first described as <i>Rana kunyuensis</i>, before being synonymised with <i>R. coreana</i>. So far, the contact zone with <i>R. amurensis</i> was expected to be in the vicinity of Pyongyang in DPR Korea, west of the Baekdu Mountain Range. However, the species is known from a population further north, and during surveys in Dalian in Liaoning Province, China, we found <i>R. coreana</i> on the southern slopes of the Laoling Mountain Range facing the Yellow Sea. Our phylogenetic analyses based on mitochondrial ribosomal markers showed the individual to cluster with <i>R. coreana</i> samples from the Korean Peninsula. In addition, our ecological niche models showed the presence of suitable habitats outside of the known range of the species, deserving further investigation. The habitat of the species at this new locality is similar to the one known in the three range nations, and highlights the need for more surveys in northeast China as the barrier formed by the Changbai Range is more porous than originally expected.
DOI: 10.3535/dpd-b82-zbj
title: Brachionycha nubeculosa Esper, 1785

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/3ff-9hx-wdd
title: Apamea (Apamea) monoglypha (Hufnagel, 1766)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/b0h-geg-whv
title: Luperina testacea [Denis & Schiffermüller], 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/9s1-m6a-my0
title: Caradrina (Caradrina) morpheus (Hufnagel, 1766)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/qgn-1xm-0vw
title: Caradrina (Caradrina) morpheus (Hufnagel, 1766)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/7y7-7bn-qs5
title: Melitaea athalia von Rottemburg, 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/fxz-k0a-ev5
title: Morophaga choragella (Denis & Schiff., 1775)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/vx5-5dm-g1h
title: Agonopterix heracliana Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0ga-wwq-tfk
title: Panthea coenobita (Esper, 1785)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dvx-8gq-rzj
title: Panthea coenobita (Esper, 1785)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/sm4-75h-zf6
title: Diloba caeruleocephala (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/w20-b1k-z18
title: Laothoe populi Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/77r-e3g-6hj
title: Mecyna flavalis [Denis & Schiffermüller], 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/zma-66r-zhk
title: Conistra (Conistra) vaccinii (Linnaeus, 1761)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/fj5-d5x-ej5
title: Leucodonta bicoloria ([Denis & Schiffermüller], 1775)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/kpb-d93-m1v
title: Paratalanta pandalis Hübner, 1825

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/lz7-dqk-dya
title: Oligia Hübner, 1821

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/xce-h0f-6t5
title: Nyea lurideola (Zincken, 1817)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/lpq-9qa-94t
title: Nyea lurideola (Zincken, 1817)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/qj7-kct-sbv
title: Euclidia (Euclidia) glyphica Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/01d-4te-rv1
title: Nyea lurideola (Zincken, 1817)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/s39-xsb-8zj
title: Luperina testacea [Denis & Schiffermüller], 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/fz2-lqa-9gh
title: Saturnia (Eudia) pavonia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/h17-bwt-afr
title: Luperina testacea [Denis & Schiffermüller], 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/038-qcz-kn5
title: Conistra (Conistra) vaccinii (Linnaeus, 1761)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/0p3-9es-8cv
title: Panthea coenobita (Esper, 1785)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/rks-629-gnd
title: Cerura (Cerura) vinula (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/9a6-1we-wn2
title: Leucodonta bicoloria ([Denis & Schiffermüller], 1775)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/n78-h9g-01p
title: Trisateles emortualis ([Denis & Schiffermüller], 1775)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ar6-vat-76v
title: Conistra (Conistra) vaccinii (Linnaeus, 1761)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/8by-bth-kqx
title: Caradrina (Caradrina) morpheus (Hufnagel, 1766)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/325-y9d-fhl
title: Apamea (Apamea) furva ([Denis & Schiffermüller], 1775)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/rbh-qdg-qh1
title: Brachionycha nubeculosa Esper, 1785

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/hw0-96d-ygp
title: Euclidia (Euclidia) glyphica Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/y4r-lsk-59b
title: Melitaea athalia von Rottemburg, 1775

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/dyc-66l-yrc
title: Saturnia (Eudia) pavonia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/ydv-6nb-pxb
title: Paratalanta pandalis Hübner, 1825

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/kve-rxg-26j
title: Euclidia (Euclidia) glyphica Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.5281/zenodo.17844649
title: DynamicEntropySearch-spectra files for benchmark(2)

description: Dataset2 for DynamicEntropySearch (charge 1, batch 0-49)
DOI: 10.3535/ejq-668-7j1
title: Charanyca (Rusina) Stephens, 1829

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.5281/zenodo.17844648
title: DynamicEntropySearch-spectra files for benchmark(2)

description: Dataset2 for DynamicEntropySearch (charge 1, batch 0-49)