cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28606844.v1
title: Germline expression of Imp-L2 in Drosophila females enhances reproductive activity and longevity

description: The Imaginal morphogenesis protein-Late 2 (Imp-L2) in <i>Drosophila</i> is recognized as a functional homolog of the insulin-like growth factor (IGF) binding protein family. In this study, we report that Imp-L2 expression in germline cells during oogenesis simultaneously enhances both fecundity and lifespan in female <i>Drosophila</i>. Loss of Imp-L2, either through knockout or germline-specific knockdown, resulted in decreased reproductive activity, as evidenced by reduced ovary size and fecundity, along with a higher proportion of infertile flies. Conversely, overexpression of Imp-L2 specifically in germline cells enhanced reproductive activity. Imp-L2 appears to regulate germline stem cell proliferation and differentiation independently of IGF signaling. Interestingly, germline-specific knockdown of <i>Imp-L2</i> shortened the lifespan of female flies, whereas its overexpression extended it. Thus, Imp-L2 expression in the germline promotes both reproductive activity and longevity, presenting an exception to the typical trade-off between reproduction and lifespan.
DOI: 10.3535/vjv-y39-rb1
title: Xestia ashworthii subsp. Xestia ashworthii jotunensis (Schoyen, 1887)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.6084/m9.figshare.28235109
title: Adaptation responses to salt stress in the gut of <i>Poecilia reticulata</i>

description: Osmoregulation is essential for the survival of aquatic organisms, particularly teleost fish facing osmotic challenges in environments characterized by variable salinity. While the gills are known for ion exchange, the intestine’s role in water and salt absorption is gaining attention. Here, we investigated the adaptive responses of the intestine to salinity stress in guppies (<i>Poecilia reticulata</i>), observing significant morphological and transcriptomic alterations. Guppies showed superior salt tolerance compared to zebrafish (<i>Danio rerio</i>). Increasing salinity reduced villus length and intestinal diameter in guppies, while zebrafish exhibited damage to villus structure and loss of goblet cells. Transcriptomic analysis identified key genes involved in osmoregulation, tissue remodeling, and immune modulation. Upregulated genes included the solute carrier transporters <i>slc2al</i> and <i>slc3al</i>, which facilitate ion and water transport, as well as a transcription factor AP-1 subunit and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta, both of which participate in tissue repair and growth responses. In contrast, many genes related to the innate immune system (such as <i>Tnfaip6</i>) were downregulated, suggesting a shift toward the prioritization of osmoregulatory functions over immune responses. Interestingly, the differential expression of adaptation genes was linked to variations in epigenetic modifications and transcription factor activity. Transcription factors crucial for adapting to salt stress, such as <i>bhlhe40</i>, <i>cebpd</i>, and <i>gata6,</i> were progressively upregulated in guppies but remained downregulated in zebrafish. Our findings highlight the intricate mechanisms of adaptation to salinity stress in <i>P. reticulata</i>, providing insights into osmoregulatory mechanisms involving the intestine in aquatic organisms.
DOI: 10.6084/m9.figshare.28235109.v1
title: Adaptation responses to salt stress in the gut of <i>Poecilia reticulata</i>

description: Osmoregulation is essential for the survival of aquatic organisms, particularly teleost fish facing osmotic challenges in environments characterized by variable salinity. While the gills are known for ion exchange, the intestine’s role in water and salt absorption is gaining attention. Here, we investigated the adaptive responses of the intestine to salinity stress in guppies (<i>Poecilia reticulata</i>), observing significant morphological and transcriptomic alterations. Guppies showed superior salt tolerance compared to zebrafish (<i>Danio rerio</i>). Increasing salinity reduced villus length and intestinal diameter in guppies, while zebrafish exhibited damage to villus structure and loss of goblet cells. Transcriptomic analysis identified key genes involved in osmoregulation, tissue remodeling, and immune modulation. Upregulated genes included the solute carrier transporters <i>slc2al</i> and <i>slc3al</i>, which facilitate ion and water transport, as well as a transcription factor AP-1 subunit and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta, both of which participate in tissue repair and growth responses. In contrast, many genes related to the innate immune system (such as <i>Tnfaip6</i>) were downregulated, suggesting a shift toward the prioritization of osmoregulatory functions over immune responses. Interestingly, the differential expression of adaptation genes was linked to variations in epigenetic modifications and transcription factor activity. Transcription factors crucial for adapting to salt stress, such as <i>bhlhe40</i>, <i>cebpd</i>, and <i>gata6,</i> were progressively upregulated in guppies but remained downregulated in zebrafish. Our findings highlight the intricate mechanisms of adaptation to salinity stress in <i>P. reticulata</i>, providing insights into osmoregulatory mechanisms involving the intestine in aquatic organisms.
DOI: 10.3535/l70-qja-cwa
title: Leucodonta bicoloria ([Denis & Schiffermüller], 1775)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.6084/m9.figshare.28169041
title: Loss of neuronal βPix isoforms impairs neuronal morphology in the hippocampus and causes behavioral defects

description: βPix is a guanine nucleotide exchange factor for the Rac1 and Cdc42 small GTPases, which play important roles in dendritic spine morphogenesis by modulating actin cytoskeleton organization. The formation and plasticity of the dendritic spines are essential for normal brain function. Among the alternatively spliced βPix isoforms, βPix-b and βPix-d are expressed specifically in neurons. Our previous studies using cultured hippocampal neurons identified the roles of βPix-b and βPix-d in spine formation and neurite development, respectively. Here, we analyzed the <i>in vivo</i> role of the neuronal βPix isoforms in brain development and function by using βPix neuronal isoform knockout (βPix-NIKO) mice, in which the expression of the βPix-b and βPix-d isoforms is blocked, while the expression of the ubiquitous βPix-a isoform is maintained. Loss of the neuronal βPix isoforms leads to reduced activity of Rac1 and Cdc42, decreased dendritic complexity and spine density, and increased GluN2B and Ca<sup>2+</sup>/calmodulin-dependent protein kinase IIα expression in the hippocampus. The defects in neurite development, dendritic spine maturation, and synaptic density in cultured βPix-NIKO hippocampal neurons were rescued by the expression of βPix-b or βPix-d. In behavioral studies, βPix-NIKO mice exhibited robust deficits in novel object recognition and decreased anxiety levels. Our findings suggest that neuronal morphogenetic signaling by the neuronal βPix isoforms contributes to normal behaviors.
DOI: 10.6084/m9.figshare.28169041.v1
title: Loss of neuronal βPix isoforms impairs neuronal morphology in the hippocampus and causes behavioral defects

description: βPix is a guanine nucleotide exchange factor for the Rac1 and Cdc42 small GTPases, which play important roles in dendritic spine morphogenesis by modulating actin cytoskeleton organization. The formation and plasticity of the dendritic spines are essential for normal brain function. Among the alternatively spliced βPix isoforms, βPix-b and βPix-d are expressed specifically in neurons. Our previous studies using cultured hippocampal neurons identified the roles of βPix-b and βPix-d in spine formation and neurite development, respectively. Here, we analyzed the <i>in vivo</i> role of the neuronal βPix isoforms in brain development and function by using βPix neuronal isoform knockout (βPix-NIKO) mice, in which the expression of the βPix-b and βPix-d isoforms is blocked, while the expression of the ubiquitous βPix-a isoform is maintained. Loss of the neuronal βPix isoforms leads to reduced activity of Rac1 and Cdc42, decreased dendritic complexity and spine density, and increased GluN2B and Ca<sup>2+</sup>/calmodulin-dependent protein kinase IIα expression in the hippocampus. The defects in neurite development, dendritic spine maturation, and synaptic density in cultured βPix-NIKO hippocampal neurons were rescued by the expression of βPix-b or βPix-d. In behavioral studies, βPix-NIKO mice exhibited robust deficits in novel object recognition and decreased anxiety levels. Our findings suggest that neuronal morphogenetic signaling by the neuronal βPix isoforms contributes to normal behaviors.
DOI: 10.3535/hf7-k4q-9b3
title: Colocasia coryli (Linnaeus, 1758)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.6084/m9.figshare.28089785
title: <i>Drosophila miR-263b-5p</i> controls wing developmental growth by targeting <i>Akt</i>

description: Tissue growth is controlled by various signaling pathways, such as the insulin/IGF-signaling (IIS) pathway. Although IIS activation is regulated by a complex regulatory network, the mechanism underlying miRNA-based regulation of the IIS pathway in <i>Drosophila</i> wing development remains unclear. In this study, we found that the wing size of adult flies was negatively affected by miR-263b expression. The miR-263b-mediated alteration in wing size was linked to a reduction in wing cell number. Additionally, <i>miR-263b</i> overexpression in <i>Drosophila</i> S2 cells decreased cell proliferation and increased cell death. Consequently, we identified <i>Akt</i> as a direct target of miR-263b-5p and found that miR-263b-mediated wing growth regulation was due to changes in <i>Akt</i> expression. Co-expression of <i>Akt</i> in <i>miR-263b</i>-overexpressing wings rescued the <i>miR-263b</i> overexpression-mediated reduction in wing growth. These results enhance our understanding of the crucial role of miRNAs in growth regulation during <i>Drosophila</i> wing development.
DOI: 10.6084/m9.figshare.28089785.v1
title: <i>Drosophila miR-263b-5p</i> controls wing developmental growth by targeting <i>Akt</i>

description: Tissue growth is controlled by various signaling pathways, such as the insulin/IGF-signaling (IIS) pathway. Although IIS activation is regulated by a complex regulatory network, the mechanism underlying miRNA-based regulation of the IIS pathway in <i>Drosophila</i> wing development remains unclear. In this study, we found that the wing size of adult flies was negatively affected by miR-263b expression. The miR-263b-mediated alteration in wing size was linked to a reduction in wing cell number. Additionally, <i>miR-263b</i> overexpression in <i>Drosophila</i> S2 cells decreased cell proliferation and increased cell death. Consequently, we identified <i>Akt</i> as a direct target of miR-263b-5p and found that miR-263b-mediated wing growth regulation was due to changes in <i>Akt</i> expression. Co-expression of <i>Akt</i> in <i>miR-263b</i>-overexpressing wings rescued the <i>miR-263b</i> overexpression-mediated reduction in wing growth. These results enhance our understanding of the crucial role of miRNAs in growth regulation during <i>Drosophila</i> wing development.
DOI: 10.3535/6bt-htx-rld
title: Caradrina (Caradrina) morpheus (Hufnagel, 1766)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/7mf-yk7-n5l
title: Orthosia (Cororthosia) opima Hübner

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/nbf-hy4-zvh
title: Orthosia (Cororthosia) opima Hübner

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/x4j-4ne-11v
title: Nyea lurideola (Zincken, 1817)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.6084/m9.figshare.29448560
title: Holoprosencephaly and cyclopia in <i>bmp7b</i> and <i>bmpr1ba</i> Crispant zebrafish

description: Holoprosencephaly (HPE) is the most frequent developmental disorder of the forebrain. In HPE, the early single anlage of the forebrain, the anterior neural plate (ANP) which encompasses the future telencephalon and eye field, fails to divide. BMP signaling and antagonism are overall important for nervous system development. The focus of this study was on the role of the ligand <i>bmp7b</i> and the receptor <i>bmpr1ba</i> during forebrain development. The zebrafish loci of <i>bmp7b</i> and <i>bmpr1ba</i> were targeted transiently with CRISPR/Ca9. Crispants for both <i>bmp7b</i> and <i>bmpr1ba</i> presented HPE and cyclopia, one central eye. Subsequently, the ANP was addressed in <i>bmp7b</i> Crispants. The morphology of the eye field was affected, with important markers, <i>rx3</i>, <i>six3b</i> and <i>cxcr4a</i> expressed condensed at the midline. Induced expression of <i>bmp4</i> is also known to result in HPE. Such <i>bmp4</i> induction altered the expression of <i>bmpr1ba</i>. Zebrafish Crispants for <i>bmp7b</i> and <i>bmpr1ba</i> can be used as a novel HPE model. A challenge in future analyses will be the penetrance of phenotypes in Crispants. The advantages are, however, that analyses can be conducted anywhere, without the need of mutant lines. One important aspect for future analysis will be the role of individual bmp ligands, receptors and antagonists in forebrain development.
DOI: 10.6084/m9.figshare.29448560.v1
title: Holoprosencephaly and cyclopia in <i>bmp7b</i> and <i>bmpr1ba</i> Crispant zebrafish

description: Holoprosencephaly (HPE) is the most frequent developmental disorder of the forebrain. In HPE, the early single anlage of the forebrain, the anterior neural plate (ANP) which encompasses the future telencephalon and eye field, fails to divide. BMP signaling and antagonism are overall important for nervous system development. The focus of this study was on the role of the ligand <i>bmp7b</i> and the receptor <i>bmpr1ba</i> during forebrain development. The zebrafish loci of <i>bmp7b</i> and <i>bmpr1ba</i> were targeted transiently with CRISPR/Ca9. Crispants for both <i>bmp7b</i> and <i>bmpr1ba</i> presented HPE and cyclopia, one central eye. Subsequently, the ANP was addressed in <i>bmp7b</i> Crispants. The morphology of the eye field was affected, with important markers, <i>rx3</i>, <i>six3b</i> and <i>cxcr4a</i> expressed condensed at the midline. Induced expression of <i>bmp4</i> is also known to result in HPE. Such <i>bmp4</i> induction altered the expression of <i>bmpr1ba</i>. Zebrafish Crispants for <i>bmp7b</i> and <i>bmpr1ba</i> can be used as a novel HPE model. A challenge in future analyses will be the penetrance of phenotypes in Crispants. The advantages are, however, that analyses can be conducted anywhere, without the need of mutant lines. One important aspect for future analysis will be the role of individual bmp ligands, receptors and antagonists in forebrain development.
DOI: 10.3535/l5s-ffc-0v6
title: Apamea (Apamea) monoglypha (Hufnagel, 1766)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/y0w-xfh-y1n
title: Chrysoteuchia culmella Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.6084/m9.figshare.28557783
title: Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas

description: Gene co-expression network inference from bulk tissue samples often misses cell-type-specific interactions, which can be detected through single-cell gene expression data. However, the noise and sparsity of single-cell data challenge the inference of these networks. We developed scNET, a framework for integrative cell-type-specific co-expression network inference from single-cell transcriptome data, demonstrating its utility in augmenting the human interactome for more accurate disease gene prediction. We address the limitations of <i>de novo</i> network inference from single-cell expression data through dropout imputation, metacell formation, and data transformation. Employing this data preprocessing pipeline, we inferred cell-type-specific co-expression links from single-cell atlas data, covering various cell types and tissues, and integrated over 850K of these inferred links into a preexisting human interactome, HumanNet, resulting in HumanNet-plus. This integration notably enhanced the accuracy of network-based disease gene prediction. These findings suggest that with proper data preprocessing, network inference from single-cell gene expression data can be highly effective, potentially enriching the human interactome and advancing the field of network medicine.
DOI: 10.6084/m9.figshare.28557783.v1
title: Augmenting the human interactome for disease prediction through gene networks inferred from human cell atlas

description: Gene co-expression network inference from bulk tissue samples often misses cell-type-specific interactions, which can be detected through single-cell gene expression data. However, the noise and sparsity of single-cell data challenge the inference of these networks. We developed scNET, a framework for integrative cell-type-specific co-expression network inference from single-cell transcriptome data, demonstrating its utility in augmenting the human interactome for more accurate disease gene prediction. We address the limitations of <i>de novo</i> network inference from single-cell expression data through dropout imputation, metacell formation, and data transformation. Employing this data preprocessing pipeline, we inferred cell-type-specific co-expression links from single-cell atlas data, covering various cell types and tissues, and integrated over 850K of these inferred links into a preexisting human interactome, HumanNet, resulting in HumanNet-plus. This integration notably enhanced the accuracy of network-based disease gene prediction. These findings suggest that with proper data preprocessing, network inference from single-cell gene expression data can be highly effective, potentially enriching the human interactome and advancing the field of network medicine.
DOI: 10.6084/m9.figshare.29078831
title: Early postnatal exposure to bicuculline modulates E/I balance and induces ASD-like behavioral phenotypes in mice

description: Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by social interaction deficits and repetitive behaviors. While precise causes of ASD remain elusive, growing evidence highlights that an imbalance in excitatory and inhibitory (E/I) signaling is a pivotal factor in ASD development and modulation. Balanced E/I neurotransmission is critical for circuit formation, synaptic plasticity, and developmental timing. However, key questions persist, including the critical perturbation window, neurological and neurodevelopmental effects, and clinical implications of E/I imbalance. This study investigated early-life modulation of the GABAergic system’s impact on E/I balance and ASD-like behaviors in mice. Mice were treated with bicuculline, a GABAA receptor antagonist, from postnatal days 7–11, and behavioral tests were conducted during adolescence. Results revealed deficits in social interaction in both male and female mice and increased repetitive behaviors in bicuculline-treated male mice. Electrophysiological recordings in the mPFC indicated reduced resting membrane potential, heightened neuronal excitability, and a shift in the E/I ratio. In the hippocampus, recordings displayed enhanced LTP and altered synaptic plasticity. DEG analysis of the PFC in bicuculline-treated mice unveiled aberrant gene profiles related to the regulation of synaptic function. Clinical significance and underlying mechanisms of abnormal brain activity, neurodevelopment, and ASD-related behaviors prompted by neonatal bicuculline treatment require further investigation. Nevertheless, these results suggest that GABAergic signaling disruption during the neonatal period might contribute to ASD-related brain pathophysiological changes.
DOI: 10.6084/m9.figshare.29078831.v1
title: Early postnatal exposure to bicuculline modulates E/I balance and induces ASD-like behavioral phenotypes in mice

description: Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by social interaction deficits and repetitive behaviors. While precise causes of ASD remain elusive, growing evidence highlights that an imbalance in excitatory and inhibitory (E/I) signaling is a pivotal factor in ASD development and modulation. Balanced E/I neurotransmission is critical for circuit formation, synaptic plasticity, and developmental timing. However, key questions persist, including the critical perturbation window, neurological and neurodevelopmental effects, and clinical implications of E/I imbalance. This study investigated early-life modulation of the GABAergic system’s impact on E/I balance and ASD-like behaviors in mice. Mice were treated with bicuculline, a GABAA receptor antagonist, from postnatal days 7–11, and behavioral tests were conducted during adolescence. Results revealed deficits in social interaction in both male and female mice and increased repetitive behaviors in bicuculline-treated male mice. Electrophysiological recordings in the mPFC indicated reduced resting membrane potential, heightened neuronal excitability, and a shift in the E/I ratio. In the hippocampus, recordings displayed enhanced LTP and altered synaptic plasticity. DEG analysis of the PFC in bicuculline-treated mice unveiled aberrant gene profiles related to the regulation of synaptic function. Clinical significance and underlying mechanisms of abnormal brain activity, neurodevelopment, and ASD-related behaviors prompted by neonatal bicuculline treatment require further investigation. Nevertheless, these results suggest that GABAergic signaling disruption during the neonatal period might contribute to ASD-related brain pathophysiological changes.
DOI: 10.3535/4pn-1vc-mkl
title: Conistra (Conistra) vaccinii (Linnaeus, 1761)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/85n-jmq-8tc
title: Trisateles emortualis ([Denis & Schiffermüller], 1775)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.
DOI: 10.3535/l7s-xbq-s5d
title: Caradrina (Caradrina) morpheus (Hufnagel, 1766)

description: Digital Specimen for the physical specimen hosted at Finnish Museum of Natural History.