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50 pages, 7974 KiB  
Article
Multiple Histories of Russian Occultism and the Unfinished Modernity: Imperial Esoterica Versus Modernizations of Avant-Garde Conceptualism
by Dennis Ioffe
Histories 2025, 5(3), 34; https://doi.org/10.3390/histories5030034 - 29 Jul 2025
Viewed by 1125
Abstract
The essay offers an expansive and multi-stratified investigation into the role of esoteric traditions within the development of Russian modernity, reframing occultism not as an eccentric deviation but as a foundational epistemological regime integral to Russia’s aesthetic, philosophical, and political evolution. By analyzing [...] Read more.
The essay offers an expansive and multi-stratified investigation into the role of esoteric traditions within the development of Russian modernity, reframing occultism not as an eccentric deviation but as a foundational epistemological regime integral to Russia’s aesthetic, philosophical, and political evolution. By analyzing the arc from Petrine-era alchemical statecraft to the techno-theurgical aspirations of Russian Cosmism and the esoteric visual regimes of the avant-garde, this essay discloses the deep ontological entanglement between sacral knowledge and modernist radical experimentation. The work foregrounds figures such as Jacob Bruce, Wassily Kandinsky, and Kazimir Malevich, situating them within broader transnational currents of Hermeticism, Theosophy, and Rosicrucianism, while interrogating the role of occult infrastructures in both late-imperial and Soviet paradigms. Drawing on recent theoretical frameworks in the global history of esotericism and modernist studies, the long-read article elucidates the metaphysical substrata animating Russian Symbolism, Abstraction, Malevich’s non-Euclidian Suprematism and Moscow Conceptualism. This study contends that esotericism in Russia—far from marginal—served as a generative matrix for radical aesthetic innovation and ideological reconfiguration. It proposes a reconceptualization of Russian cultural history as a palimpsest of submerged sacral structures, where utopia and apocalypse, magic and technology, converge in a distinctively Russian cosmopoietic horizon. Ultimately, this essay reframes Russian and European occultism as an alternate technology of cognition and a performative semiotic universe shaping not only artistic modernism but also the very grammar of Russian historical imagination. Full article
(This article belongs to the Section Cultural History)
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18 pages, 1956 KiB  
Article
Panel-Based Genetic Testing in a Consecutive Series of Individuals with Inherited Retinal Diseases in Australia: Identifying Predictors of a Diagnosis
by Alexis Ceecee Britten-Jones, Doron G. Hickey, Thomas L. Edwards and Lauren N. Ayton
Genes 2025, 16(8), 888; https://doi.org/10.3390/genes16080888 - 27 Jul 2025
Viewed by 375
Abstract
Background/Objectives: Genetic testing is important for diagnosing inherited retinal diseases (IRDs), but further evidence is needed on the utility of singleton genetic testing in an Australian cohort. Methods: A consecutive series of individuals with clinically diagnosed IRDs without prior genetic testing [...] Read more.
Background/Objectives: Genetic testing is important for diagnosing inherited retinal diseases (IRDs), but further evidence is needed on the utility of singleton genetic testing in an Australian cohort. Methods: A consecutive series of individuals with clinically diagnosed IRDs without prior genetic testing underwent commercial panel-based sequencing (Invitae or Blueprint Genetics), clinical assessment, and multimodal imaging. Retinal images were graded using the Human Phenotype Ontology terms. Binary logistic regression was used to evaluate clinical predictors of a positive molecular diagnosis. Results: Among 140 participants (mean age 49 ± 19 years), genetic testing was undertaken, on average, 23 ± 17 years after the initial clinical IRD diagnosis. Of the 60% who received a probable molecular diagnosis, 40% require further phase testing, highlighting the limitations of singleton genetic testing. USH2A, ABCA4, and RPGR were the most common encountered genes; 67% of the probably solved participants had causative genes with targeted experimental treatments in ongoing human clinical trials. Symptom onset before the age of 30 (OR = 3.06 [95% CI: 1.34–7.18]) and a positive IRD family history (OR = 2.87 [95% CI: 1.27–6.78]) were each associated with higher odds of receiving a molecular diagnosis. Diagnostic rates were comparable across retinal imaging phenotypes (atrophy and autofluorescence patterns in widespread IRD, and the extent of dystrophy in macular IRDs). Conclusions: In an Australian IRD population without prior genetic testing, commercial panels yielded higher diagnostic rates in individuals with IRD onset before the age of 30 and those with an IRD family history. Further research is needed to understand the genetic basis of IRDs, especially isolated and late-onset cases, to improve diagnosis and access to emerging therapies. Full article
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17 pages, 1840 KiB  
Article
Epigenomic Interactions Between Chronic Pain and Recurrent Pressure Injuries After Spinal Cord Injury
by Letitia Y. Graves, Melissa R. Alcorn, E. Ricky Chan, Katelyn Schwartz, M. Kristi Henzel, Marinella Galea, Anna M. Toth, Christine M. Olney and Kath M. Bogie
Epigenomes 2025, 9(3), 26; https://doi.org/10.3390/epigenomes9030026 - 23 Jul 2025
Viewed by 306
Abstract
Background/Objectives: This study investigated variations in DNA methylation patterns associated with chronic pain and propensity for recurrent pressure injuries (PrI) in persons with spinal cord injury (SCI). Methods: Whole blood was collected from 81 individuals with SCI. DNA methylation was quantified using Illumina [...] Read more.
Background/Objectives: This study investigated variations in DNA methylation patterns associated with chronic pain and propensity for recurrent pressure injuries (PrI) in persons with spinal cord injury (SCI). Methods: Whole blood was collected from 81 individuals with SCI. DNA methylation was quantified using Illumina genome-wide arrays (EPIC and EPICv2). Comprehensive clinical profiles collected included secondary health complications, in particular current PrI and chronic pain. Relationships between recurrent PrI and chronic pain and whether the co-occurrence of both traits was mediated by changes in DNA methylation were investigated using R packages limma, DMRcate and mCSEA. Results: Three differentially methylated positions (DMPs) (cg09867095, cg26559694, cg24890286) and one region in the micro-imprinted locus for BLCAP/NNAT are associated with chronic pain in persons with SCI. The study cohort was stratified by PrI status to identify any sites associated with chronic pain and while the same three sites and region were replicated in the group with no recurrent PrI, two novel, hypermethylated (cg21756558, cg26217441) sites and one region in the protein-coding gene FDFT1 were identified in the group with recurrent PrI. Gene enrichment and genes associated with specific promoters using MetaScape identified several shared disorders and ontology terms between independent phenotypes of pain and recurrent PrI and interactive sub-groups. Conclusions: DMR analysis using mCSEA identified several shared genes, promoter-associated regions and CGI associated with overall pain and PrI history, as well as sub-groups based on recurrent PrI history. These findings suggest that a much larger gene regulatory network is associated with each phenotype. These findings require further validation. Full article
(This article belongs to the Special Issue Features Papers in Epigenomes 2025)
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12 pages, 229 KiB  
Article
Difficulties of Difference
by Rachel Cecília de Oliveira
Arts 2025, 14(4), 79; https://doi.org/10.3390/arts14040079 - 21 Jul 2025
Viewed by 243
Abstract
This article examines the persistent conceptual and structural obstacles that pluralism faces within the Euro-United-Statesian art system, particularly in the fields of criticism, art history, and aesthetics. The study situates its inquiry within broader debates around the politics of difference and the decolonization [...] Read more.
This article examines the persistent conceptual and structural obstacles that pluralism faces within the Euro-United-Statesian art system, particularly in the fields of criticism, art history, and aesthetics. The study situates its inquiry within broader debates around the politics of difference and the decolonization of knowledge, aiming to understand how theoretical frameworks historically incorporated plurality in ways that ultimately neutralize its disruptive potential. Methodologically, the article combines philosophical analysis with a critical rereading of canonical texts by figures such as Clement Greenberg and Arthur Danto, juxtaposed with insights from Indigenous, Black, and decolonial thinkers. The findings suggest that pluralism, while rhetorically embraced, is frequently rendered compatible with a teleological and universalizing narrative that privileges Western aesthetic trajectories. As a result, forms of difference are tolerated only insofar as they can be translated into hegemonic terms. The article concludes by advocating for critical practices that sustain rather than resolve difference, calling for frameworks capable of embracing dissonance, incommensurability, and multiple ontologies without collapsing them into sameness. In doing so, it repositions the contemporary struggle over meaning in art not as a problem to be overcome, but as a necessary symptom of epistemic plurality. Full article
(This article belongs to the Section Visual Arts)
24 pages, 3832 KiB  
Article
Stitching History into Semantics: LLM-Supported Knowledge Graph Engineering for 19th-Century Greek Bookbinding
by Dimitrios Doumanas, Efthalia Ntalouka, Costas Vassilakis, Manolis Wallace and Konstantinos Kotis
Mach. Learn. Knowl. Extr. 2025, 7(3), 59; https://doi.org/10.3390/make7030059 - 24 Jun 2025
Viewed by 786
Abstract
Preserving cultural heritage can be efficiently supported by structured and semantic representation of historical artifacts. Bookbinding, a critical aspect of book history, provides valuable insights into past craftsmanship, material use, and conservation practices. However, existing bibliographic records often lack the depth needed to [...] Read more.
Preserving cultural heritage can be efficiently supported by structured and semantic representation of historical artifacts. Bookbinding, a critical aspect of book history, provides valuable insights into past craftsmanship, material use, and conservation practices. However, existing bibliographic records often lack the depth needed to analyze bookbinding techniques, provenance, and preservation status. This paper presents a proof-of-concept system that explores how Large Language Models (LLMs) can support knowledge graph engineering within the context of 19th-century Greek bookbinding (1830–1900), and as a result, generate a domain-specific ontology and a knowledge graph. Our ontology encapsulates materials, binding techniques, artistic styles, and conservation history, integrating metadata standards like MARC and Dublin Core to ensure interoperability with existing library and archival systems. To validate its effectiveness, we construct a Neo4j knowledge graph, based on the generated ontology and utilize Cypher Queries—including LLM-generated queries—to extract insights about bookbinding practices and trends. This study also explores how semantic reasoning over the knowledge graph can identify historical binding patterns, assess book conservation needs, and infer relationships between bookbinding workshops. Unlike previous bibliographic ontologies, our approach provides a comprehensive, semantically rich representation of bookbinding history, methods and techniques, supporting scholars, conservators, and cultural heritage institutions. By demonstrating how LLMs can assist in ontology/KG creation and query generation, we introduce and evaluate a semi-automated pipeline as a methodological demonstration for studying historical bookbinding, contributing to digital humanities, book conservation, and cultural informatics. Finally, the proposed approach can be used in other domains, thus, being generally applicable in knowledge engineering. Full article
(This article belongs to the Special Issue Knowledge Graphs and Large Language Models)
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19 pages, 291 KiB  
Article
Prolegomena to Agapeology: Reflections on Love as Panexperiential Phenomenon
by Lenart Škof
Religions 2025, 16(6), 733; https://doi.org/10.3390/rel16060733 - 6 Jun 2025
Viewed by 801
Abstract
This paper is an attempt to reflect upon the hidden or mysterious logic of love as an ontological and panexperiential phenomenon. In our attempt, we are crossing the fields of philosophy, spirituality, and contemporary research in psi phenomena (also known as paranormal phenomena) [...] Read more.
This paper is an attempt to reflect upon the hidden or mysterious logic of love as an ontological and panexperiential phenomenon. In our attempt, we are crossing the fields of philosophy, spirituality, and contemporary research in psi phenomena (also known as paranormal phenomena) and investigating some historical conditions of margins and disputes between the disciplines based on David Ray Griffin’s work, Parapsychology, Philosophy, and Spirituality. In the main part of this paper, we present the aesthetic theory of force by Christoph Menke and follow his rich analyses on the hidden, obscure layers of the soul. Based on these analyses, we present our own thesis on agapeology as being related both to psi phenomena and aesthetic phenomena. Throughout the history of religion and Western science, magical and miraculous events were too often relegated to the domain of faith or superstition and dismissed almost entirely. In the final parts of this paper, we aim to show that using the approaches of synchronicity (C.G. Jung) and ontology of the ground (F.W.J., Schelling) and acknowledging the phenomena known as quantum entanglement (C. Keller), we can postulate an underlying nexus, providing us with an access to the agapeistic effects of what we idiosyncratically call the phenomenon of dark love. Full article
(This article belongs to the Special Issue Between Philosophy and Theology: Liminal and Contested Issues)
37 pages, 13139 KiB  
Article
Digital Humanities for Increasing Disaster Resilience in Art Nouveau and Modernist Buildings
by Maria Bostenaru Dan and Adrian Ibric
Sustainability 2025, 17(3), 1328; https://doi.org/10.3390/su17031328 - 6 Feb 2025
Viewed by 1741
Abstract
The paper will focus on the topic of adapting digital humanities methods from architectural history to technical history, considering mapping and image analysis for increasing disaster resilience in Art Nouveau and Modernist buildings in different geographical areas—including lessons from Europe to the USA. [...] Read more.
The paper will focus on the topic of adapting digital humanities methods from architectural history to technical history, considering mapping and image analysis for increasing disaster resilience in Art Nouveau and Modernist buildings in different geographical areas—including lessons from Europe to the USA. The project proposes the transformation of the collection of photographs of early 20th-century architecture gathered by the applicant over about 30 years of travel into a database by answering the research question on how threats from the hazards of earthquakes, floods, and fires can be answered by taking into account the local culture in the European countries covered, for buildings from a period when the architecture styles were already global at that time. For this purpose, digital humanities methods of image annotation (including architectural volumetric analysis) and mapping are employed. From the knowledge gathered and the resulting database, a prototyping ontology and taxonomy is derived. This outcome can be further developed into a set of evaluation criteria, considering the decisions that can be taken to prioritize the retrofit interventions depending on the geographic positions of the buildings. Full article
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34 pages, 379 KiB  
Article
Leibniz and the Proof of God’s Existence from Eternal Truths
by Paul Rateau
Religions 2025, 16(2), 123; https://doi.org/10.3390/rel16020123 - 23 Jan 2025
Viewed by 1232
Abstract
The aim of this article is to show how and in what stages G. W. Leibniz came to develop his proof of God’s existence from eternal truths. It begins by tracing the main stages in the history of this proof, initially forged by [...] Read more.
The aim of this article is to show how and in what stages G. W. Leibniz came to develop his proof of God’s existence from eternal truths. It begins by tracing the main stages in the history of this proof, initially forged by Augustine of Hippo, and discusses the reasons for its renewal in the last quarter of the 17th century in the post-Cartesian context. The article then shows why, despite skepticism towards this proof in his youth, Leibniz finally produced a version of it that he presents in the Monadology even before the ontological proof. My hypothesis is that the development of the proof from eternal truths is directly linked to Leibniz’s reflection on the nature of the possible, a reflection that is itself to be placed in the context of the polemic between Nicolas Malebranche and Simon Foucher after the publication of the Search after Truth. The Leibnizian proof is original in that it rests on the consideration of the reality of possibles, insofar as God is the reason for them, and on the claimed subordination of logic to ontology. Full article
31 pages, 14800 KiB  
Article
An Ontology of the Word in Catalan Romanesque Culture
by Alfons Puigarnau
Religions 2025, 16(1), 33; https://doi.org/10.3390/rel16010033 - 31 Dec 2024
Viewed by 1231
Abstract
The history of culture in Catalonia during the Romanesque period (9th–12th centuries) has often been written from a strongly positivist mentality, which is a reductionistic approach. Economic history has distorted this period’s intellectual and cultural history. This article presents a compelling analysis of [...] Read more.
The history of culture in Catalonia during the Romanesque period (9th–12th centuries) has often been written from a strongly positivist mentality, which is a reductionistic approach. Economic history has distorted this period’s intellectual and cultural history. This article presents a compelling analysis of a series of manuscripts from the monastery of Ripoll in the context of Catalonia’s visual and intellectual culture between the 10th and 12th centuries. These writings demonstrate the pivotal role of the arts of the word (dialectic, rhetoric, and grammar) in this cultural center of great European significance. They also illustrate the formative influence of this institution on Gerbert of Aurillac, who would become Pope Sylvester II and the fruitful period of Abbot Oliba. Other artworks and musical manuscripts contribute to understanding a profound ontology of the word in Catalonia and prepare the ground for its cultural renaissance in the 12th century. Full article
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26 pages, 7457 KiB  
Article
Digitalizing Material Knowledge: A Practical Framework for Ontology-Driven Knowledge Graphs in Process Chains
by Elena Garcia Trelles, Christoph Schweizer, Akhil Thomas, Philipp von Hartrott and Marina Janka-Ramm
Appl. Sci. 2024, 14(24), 11683; https://doi.org/10.3390/app142411683 - 14 Dec 2024
Cited by 1 | Viewed by 1558
Abstract
This paper proposes a robust methodology for integrating process-specific data and domain expert knowledge into linked knowledge graphs. These graphs utilize an ontology that provides a standardized vocabulary for material science and facilitates the creation of semantic models for various processes along the [...] Read more.
This paper proposes a robust methodology for integrating process-specific data and domain expert knowledge into linked knowledge graphs. These graphs utilize an ontology that provides a standardized vocabulary for material science and facilitates the creation of semantic models for various processes along the digital process chain. A generic template for structuring processes is proposed, simplifying subsequent data retrieval. The templates of specific processes are designed collaboratively by domain and ontology experts, aided by a proposed interview template that bridges the knowledge gap. Following the digitalization of material data through semantic modeling, machine-readable data with contextual metadata is stored in a graph database, which can be efficiently queried using the SPARQL language, enabling seamless integration into data pipelines. To demonstrate this approach, a knowledge graph is developed to represent the process chain of AlSi10Mg objects manufactured via permanent mold casting, capturing their complete history from the initial manufacturing step to final non-destructive testing and mechanical characterization. This methodology enhances data interoperability and accessibility while providing context-rich data for training AI models, potentially accelerating new knowledge discovery in material science. Full article
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34 pages, 12661 KiB  
Article
Discovery of Alanomyces manoharacharyi: A Novel Fungus Identified Using Genome Sequencing and Metabolomic Analysis
by Shiwali Rana and Sanjay K. Singh
J. Fungi 2024, 10(11), 791; https://doi.org/10.3390/jof10110791 - 14 Nov 2024
Cited by 1 | Viewed by 1392
Abstract
In this study, a new species of Alanomyces was isolated as an endophyte from the bark of Azadirachta indica from Mulshi, Maharashtra. The identity of this isolate was confirmed based on the asexual morphological characteristics as well as multi-gene phylogeny based on the [...] Read more.
In this study, a new species of Alanomyces was isolated as an endophyte from the bark of Azadirachta indica from Mulshi, Maharashtra. The identity of this isolate was confirmed based on the asexual morphological characteristics as well as multi-gene phylogeny based on the internal transcribed spacer (ITS) and large subunit (LSU) nuclear ribosomal RNA (rRNA) regions. As this was the second species to be reported in this genus, we sequenced the genome of this species to increase our knowledge about the possible applicability of this genus to various industries. Its genome length was found to be 35.01 Mb, harboring 7870 protein-coding genes as per Augustus and 8101 genes using GeMoMa. Many genes were annotated using the Clusters of Orthologous Groups (COGs) database, the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), Swiss-Prot, NCBI non-redundant nucleotide sequences (NTs), and NCBI non-redundant protein sequences (NRs). The number of repeating sequences was predicted using Proteinmask and RepeatMasker; tRNA were detected using tRNAscan and snRNA were predicted using rfam_scan. The genome was also annotated using the Pathogen–Host Interactions Database (PHI-base) and AntiSMASH. To confirm the evolutionary history, average nucleotide identity (ANIb), phylogeny based on orthologous proteins, and single nucleotide polymorphisms (SNPs) were carried out. Metabolic profiling of the methanolic extract of dried biomass and ethyl acetate extract of the filtrate revealed a variety of compounds of great importance in the pharmaceutical and cosmetic industry. The characterization and genomic analysis of the newly discovered species Alanomyces manoharacharyi highlights its potential applicability across multiple industries, particularly in pharmaceuticals and cosmetics due to its diverse secondary metabolites and unique genetic features it possesses. Full article
(This article belongs to the Special Issue Taxonomy, Systematics and Evolution of Forestry Fungi, 2nd Edition)
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15 pages, 283 KiB  
Article
Undisciplining the Museum: Indigenous Relationality as Religion
by Rebecca J. Mendoza
Religions 2024, 15(11), 1325; https://doi.org/10.3390/rel15111325 - 30 Oct 2024
Viewed by 1333
Abstract
What does it mean to decolonize or undiscipline the anthropology museum? What happens when the museum is confronted by Indigenous and descendant communities who demand an ethic of care rooted in relational ontologies and epistemologies? This article features Indigenous creativity as it has [...] Read more.
What does it mean to decolonize or undiscipline the anthropology museum? What happens when the museum is confronted by Indigenous and descendant communities who demand an ethic of care rooted in relational ontologies and epistemologies? This article features Indigenous creativity as it has disrupted ‘business as usual’ in anthropology museums. This is primarily evidenced by Fork Peck Tribes who confronted the University of Montana to enact a long-overdue repatriation. Additional examples from The Metropolitan Museum of Art and Peabody Museum of Archaeology and Ethnology at Harvard demonstrate diverse expressions of relationality among Indigenous and descendant communities. These interventions are analyzed through Critical Indigenous Theory to specify the ways in which Indigenous religious traditions refuse the narratives and norms of settler colonial knowledge production and undermine the imperial museological practices of preservation. Instead, relationality is prioritized in the caretaking of and connection with more-than-human entities and materials in the museum. This article emphasizes relationality and repatriation as religious acts that challenge assumptions embedded in imperial and settler colonial approaches to history and science. From various social locations and through multiple strategies, we see the active undisciplining of the museum by Indigenous and descendant communities. Full article
(This article belongs to the Special Issue Undisciplining Religion and Science: Science, Religion and Nature)
12 pages, 988 KiB  
Article
Addressing Fascism: A New Politics of Experience?
by Thaddeus D. Martin
Philosophies 2024, 9(5), 152; https://doi.org/10.3390/philosophies9050152 - 27 Sep 2024
Viewed by 1343
Abstract
(1) Background: The rise of fascism in American and, indeed, throughout the world, prompts a question: why does fascism remain persistent in human existence? The question is one that Karl Jaspers might have asked regarding the origin and goal of history. The political [...] Read more.
(1) Background: The rise of fascism in American and, indeed, throughout the world, prompts a question: why does fascism remain persistent in human existence? The question is one that Karl Jaspers might have asked regarding the origin and goal of history. The political description of fascism is not adequate to describe the lived experience of those drawn to it, and to assume such people to be irrational does not suffice. Rather, culture provides semiotic structure, which is phenomenologically embodied by people in a Mitwelt. (2) Results: Perhaps what is needed is not a political description of fascism but a communicological analysis that proceeds as a semiotic phenomenology of fascism as it is culturally embodied. Jaspers’ concept of evil frames fascism as colonialism turned against itself, disguised banally in such phenomena as Schadenfreude, as described by Lanigan. (3) I approach this question using a semiotic phenomenological method. (4) Conclusions: The fading colonial dominance in the form of cultural hegemony creates Laingian ontological insecurity and a desire for one’s inner fascist to identify itself in others. Addressing fascism requires new politics of experience. Full article
(This article belongs to the Special Issue Communicative Philosophy)
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18 pages, 1951 KiB  
Article
Dog Domestication Strongly Relied on Translation Regulation According to Differential Gene Expression Analysis
by David Jonas, Kitti Tatrai, Sara Sandor, Balazs Egyed and Eniko Kubinyi
Animals 2024, 14(18), 2655; https://doi.org/10.3390/ani14182655 - 12 Sep 2024
Cited by 1 | Viewed by 1771
Abstract
Domestication of dogs from their shared ancestors with wolves occurred more than 15,000 years ago and affected many characteristics of the species. We analyzed the blood RNA sequence data of 12 dogs and 11 wolves from Europe and Asia to shed more light [...] Read more.
Domestication of dogs from their shared ancestors with wolves occurred more than 15,000 years ago and affected many characteristics of the species. We analyzed the blood RNA sequence data of 12 dogs and 11 wolves from Europe and Asia to shed more light on the domestication history of dogs. We implemented a differential gene expression analysis, a weighted gene correlation network analysis, gene ontology and genetic pathway analyses. We found that both the sample origin (Europe or Asia) and the species had a significant effect on the blood gene expression profiles of the animals. We identified 1567 differentially expressed genes between wolves and dogs and found several significantly overrepresented gene ontology terms, such as RNA polymerase II transcription regulatory region sequence-specific DNA binding or translation. We identified 11 significant gene co-expression networks, hosting a total of 4402 genes, related to DNA replication, metabolism of RNA or metabolism of proteins, for example. Our findings suggest that gene expression regulation played a cardinal role in dog domestication. We recommend further diversifying the analyzed dog and wolf populations in the future by including individuals from different dog breeds and geographical origins, in order to enhance the specificity of detecting significant, true positive genes related to domestication as well as to reduce the false positive rate. Full article
(This article belongs to the Special Issue Genomics of Animal Domestication and Trait Evolution)
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22 pages, 4239 KiB  
Article
Proteomic Blueprint of Atlantic Cod (Gadus morhua) Otoliths Revealing Environmental Stress Insights through Label-Free Quantitative Shotgun Proteomics
by Trevena N. Youssef, Sherri L. Christian, Rick Rideout, Aaron Adamack, Pierre Thibault, Eric Bonneil, Travis D. Fridgen and Joseph Banoub
BioChem 2024, 4(2), 144-165; https://doi.org/10.3390/biochem4020008 - 19 Jun 2024
Cited by 1 | Viewed by 1845
Abstract
Otoliths of the fish’s inner ear serve as a natural chronological recorder because of their continuous formation marked by daily, monthly, and annual increments. Despite their importance, the comprehensive protein content of otoliths remains not fully identified. Using the label-free shotgun proteomics method [...] Read more.
Otoliths of the fish’s inner ear serve as a natural chronological recorder because of their continuous formation marked by daily, monthly, and annual increments. Despite their importance, the comprehensive protein content of otoliths remains not fully identified. Using the label-free shotgun proteomics method with one-dimensional liquid chromatography coupled to electrospray ionization-orbitrap tandem mass spectrometry, we quantified a broad range of proteins, with individual otoliths containing between 1341 and 1839 proteins. The identified proteins could potentially serve as a blueprint for fish growth from embryo to adult. We quantified eleven heat-shock proteins (HSPs) in both sexes and several proteins impacted by endocrine disruptors, indicating the otolith’s capacity to reflect environmental stress, potentially linked to climate change effects and altering of hormonal and neuroendocrine functions. Our bioinformatic ontology analysis confirmed the presence of proteins critical for various biological processes, including structural and enzymatic proteins. Protein–protein interaction (PPI) mapping also identified key interactions between the identified proteins. These findings significantly advance our understanding of otolith proteomics, offering a solid foundation for future work. Most of the identified proteins deposited daily and influenced by the environment were not implicated in the biomineralization of otolith, raising the potential for the otolith proteome to recreate details of fish life history at previously unrealized levels. Full article
(This article belongs to the Special Issue Feature Papers in BioChem)
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