Culturing protists offers a powerful approach to exploring eukaryotic diversity, especially for deep-branching lineages. In this study, we cultured and described a novel protist species, named n sp. within the poorly st...Culturing protists offers a powerful approach to exploring eukaryotic diversity, especially for deep-branching lineages. In this study, we cultured and described a novel protist species, named n sp. within the poorly studied and unclassified genus . While an SSU rDNA gene phylogeny failed to resolve its phylogenetic placement in the eukaryotic tree, a phylogenomic analysis of 340 proteins indicated as a member of the CRuMs clade. Prior to this study, this clade consisted of diverse heterotrophic amoeba and flagellates, and lacked clear synapomorphies. Ultrastructural observations revealed that shares the characteristics with some CRuMs members, including the pellicle underlying the plasma membrane and an internal sleeve surrounding the central pair of the axoneme at the flagellar transitional region. Our findings suggest potential shared characteristics and synapomorphies for CRuMs and contribute to a deeper understanding of the character evolution within this clade.
The type III secretion system (T3SS) has traditionally been studied for its role in bacterial virulence. However, recent research emphasizes its dual role in beneficial interactions between bacteria and plants. This revi...The type III secretion system (T3SS) has traditionally been studied for its role in bacterial virulence. However, recent research emphasizes its dual role in beneficial interactions between bacteria and plants. This review examines the immunomodulatory functions of T3SS beyond pathogenicity and focuses on how T3SS effectors manipulate plant immune responses to promote symbioses. By comparing T3SS mechanisms in pathogenic and non-pathogenic bacteria, we aim to understand how this system enables beneficial microbes to colonize plants and improve plant growth and stress resilience. We also investigate the potential of T3SS to trigger induced systemic resistance in plants, a mechanism that could be utilized in agriculture to improve crop resistance to pathogens. The review concludes with an outlook on future research and emphasizes the need for comprehensive studies on T3SS effectors in non-pathogenic bacteria and their interactions with plant hosts.
Novel and invasive diseases are a key threat to wildlife. The disease chytridiomycosis has had devastating global impacts, but some amphibian species can persist and even rebound after severe declines. Understanding how...Novel and invasive diseases are a key threat to wildlife. The disease chytridiomycosis has had devastating global impacts, but some amphibian species can persist and even rebound after severe declines. Understanding how these species persist is critical to discovering management techniques for supporting declining species. Here, we explored the impacts of disease on reproduction in the threatened , investigating its effect on reproductive effort and success using a combination of laboratory-based clinical trials and field sampling through capture-mark-recapture surveys. We found that male frogs are increasing various facets of their breeding effort resulting in increased offspring. Infected male frogs (i) increased vocal sac coloration, (ii) increased sperm quality, and (iii) fathered more egg masses than uninfected males. Our research demonstrates that frogs can counteract high disease-caused mortality through enhanced breeding effort, which could lead to population persistence. Mitigation for wildlife diseases often aims to directly reduce mortality, such as through increasing host resistance or decreasing environmental suitability for the pathogen. Our work indicates that reproductive output is also important and should be considered when protecting our precious amphibians.
Centrosomes are intracellular organelles traditionally recognized as the primary microtubule (MT) organizing centres (MTOCs) in the cell, playing a crucial role in organizing the cytoskeleton and forming the MT-based spi...Centrosomes are intracellular organelles traditionally recognized as the primary microtubule (MT) organizing centres (MTOCs) in the cell, playing a crucial role in organizing the cytoskeleton and forming the MT-based spindle during cell division. However, it is now well established that centrosomes also function as central hubs for a wide range of signalling pathways. In non-dividing cells, they give rise to the primary cilium, a surface antenna that serves as a key structure for signalling. Neurons are highly specialized cells with a distinctive morphology, and most neurons have cilia. During brain development, cilia regulate the self-renewal of neural progenitors, as well as the differentiation, migration and synapse formation of newly generated neurons. As a consequence, defects in cilia result in various neurodevelopmental disorders. The role of centrosomes and cilia in neurodegeneration, or the progressive loss of neurons, is less understood. Centrosomes take part in several cellular processes that are often disrupted in neurodegenerative diseases (NDDs), and many proteins associated with these conditions have been found at centrosomes or cilia suggesting a link between these organelles and the underlying mechanisms that contribute to neuronal decline. Unravelling if and how centrosome dysfunction contributes to neurodegeneration could significantly deepen our understanding of the underlying biology of these disorders. Such insights may pave the way for new therapeutic approaches to address these debilitating conditions.
Gene presence/absence variations (PAVs) have been considered as the important determinants of genome evolution and phenotypic diversity. However, studies on gene PAVs have been poorly documented, especially in fishes. In...Gene presence/absence variations (PAVs) have been considered as the important determinants of genome evolution and phenotypic diversity. However, studies on gene PAVs have been poorly documented, especially in fishes. In the present study, the pan-genome of rainbow trout was constructed based on 268 whole-genome re-sequencing accessions (4.38 Tb data). It recovered an additional 62 Mb sequences and 1288 protein-coding genes. Then, 9831 (22.77%) gene PAVs were genotyped across the 268 individuals. PAV-based PCA analysis, together with phylogenetic topology and STRUCTURE, revealed the clear separation among the different wild and selection populations. Additionally, a PAV-based genome-wide association study (GWAS) identified three candidate PAVs significantly associated with artificial selection. Meanwhile, fixation index analysis revealed 35 PAVs with significant frequency differences between wild and selection populations in Canada, while 15 candidate PAVs were detected between the populations in America. Their biological functions have been reported to participate in the regulation of growth performance and stress response. The present study deepens our understanding of widespread gene PAVs and facilitates the identification of key candidates that contribute to important traits.
Genomic data are lacking for most Antarctic marine invertebrates, predicating our ability to understand physiological adaptation and specific life-history traits, such as longevity. The environmental stress response of t...Genomic data are lacking for most Antarctic marine invertebrates, predicating our ability to understand physiological adaptation and specific life-history traits, such as longevity. The environmental stress response of the Antarctic infaunal clam is much diminished in older adult animals compared with younger juvenile individuals. However, the mechanism underlying this reduced capacity is unknown. In this study, we describe and analyse the genome of and use it as a tool to understand transcriptomic responses to shell damage across different age cohorts. Gene expression data were combined with reduced representation enzymic methyl sequencing to identify if methylation was acting as an epigenetic mechanism driving age-dependent transcriptional profiles. Our transcriptomic results demonstrated a clear bipartite molecular response in , associated with a rapid growth phase in juveniles and a stabilization phase in reproductively mature adults. Genes active in the response to damage repair in juvenile animals are silent in adults but can be reactivated after several months following damage stimulus; however, these genes were not methylated. Hence, the trigger for this critical and imprinted change in physiological state is, as yet, unknown. While epigenetics is likely involved in this process, the mechanism is unlikely to be methylation.
Understanding and treating disease depend upon our knowledge of how the body works. The biomedical approach to disease describes health purely in terms of biological factors, with a focus on the genome as the molecular b...Understanding and treating disease depend upon our knowledge of how the body works. The biomedical approach to disease describes health purely in terms of biological factors, with a focus on the genome as the molecular basis for cellular function and dysfunction in disease. However, the eukaryotic cell has evolved as a partnership between prokaryotic cells with mitochondria being crucial to this relationship. Aside from their role as bioenergetic and biosynthetic hubs, mitochondria are also involved in cell signalling and cell fate pathways, playing a multifaceted role in cell function and health. Crucially, mitochondria are implicated in most diseases. Perhaps then, visualizing biomedical function on the backdrop of endosymbiosis may provide another viewpoint for explaining and treating disease.
Sound sensitivity is a common sensory complaint for people with autism spectrum disorder (ASD). How and why sounds are perceived as overwhelming by affected people is unknown. To process sound information properly, the b...Sound sensitivity is a common sensory complaint for people with autism spectrum disorder (ASD). How and why sounds are perceived as overwhelming by affected people is unknown. To process sound information properly, the brain requires high activity and fast processing, as seen in areas like the medial nucleus of the trapezoid body (MNTB) of the auditory brainstem. Recent work has shown dysfunction in mitochondria in a genetic model of ASD, Fragile X Syndrome (FXS). Whether mitochondrial functions are also altered in sound-processing neurons has not been characterized yet. To address this question, we imaged MNTB in a mouse model of FXS. We stained MNTB brain slices from wild-type and FXS mice with two mitochondrial markers, TOMM20 and PMPCB, located on the outer mitochondrial membrane and in the matrix, respectively. Our imaging reveals significant sex-specific differences between genotypes. Colocalization analyses between TOMM20 and PMPCB show that the integrity of mitochondrial subcompartments is most disrupted in female FXS mice compared with female wild-type mice. We highlight a quantitative fluorescence microscopy pipeline to monitor mitochondrial functions in the MNTB from control or FXS mice and provide four complementary readouts, paving the way to understanding how cellular mechanisms important to sound encoding are altered in ASD.
Micronuclei exhibit defective proteomes rendering their chromatin vulnerable to fragmentation. This fragmentation process, known as chromothripsis, promotes tumorigenesis by catalysing the activation of oncogenes and the...Micronuclei exhibit defective proteomes rendering their chromatin vulnerable to fragmentation. This fragmentation process, known as chromothripsis, promotes tumorigenesis by catalysing the activation of oncogenes and the silencing of tumor suppressors. With this role in mind, micronuclei serve as promising targets for therapeutic intervention. This review will explore recent discoveries regarding how micronuclei form, their function in catalysing chromothripsis and how chromothripsis provides a selective advantage for cancer cells.
Our current understanding of the functional morphology of olfactory systems in arthropods largely relies on information obtained in hexapods. Existing analyses of the olfactory pathway in crustacean representatives have...Our current understanding of the functional morphology of olfactory systems in arthropods largely relies on information obtained in hexapods. Existing analyses of the olfactory pathway in crustacean representatives have suggested that these animals share several corresponding anatomical elements with hexapod olfactory systems but that the latter likely feature a different olfactory wiring logic from receptor to olfactory glomerulus. This study sets out to further explore the diversity of arthropod olfactory systems by presenting a detailed morphological analysis of the peripheral and central olfactory pathways in an emerging model system, the peracarid crustacean (Malacostraca). These animals feature all neuronal elements that characterize malacostracan crustacean's olfactory systems, and the simplicity of this animal's olfactory system provided the unique opportunity to quantify the numbers of olfactory sensilla and associated sensory neurons, olfactory interneurons and olfactory glomeruli. These data showed that the number of those neuronal elements is highly variable across individuals, contrasting with more stable numbers of neuronal elements in hexapod olfactory systems that typically are characterized by olfactory glomeruli with individual identities and constant numbers. We discuss the possible steps needed for an evolutionary transformation of a malacostracan crustacean type of olfactory system into a hexapod type.
Essential to much medical progress (for example, preventing AIDS, tuberculosis and cancer) is understanding how the class of immunity is controlled. Most envisage that pathogen- or danger-associated signals are critical....Essential to much medical progress (for example, preventing AIDS, tuberculosis and cancer) is understanding how the class of immunity is controlled. Most envisage that pathogen- or danger-associated signals are critical. Many classical observations, particularly on the variables of immunization affecting the class of immunity generated, are paradoxical under this dominant view, and are therefore neglected. Among these is the role of antigen dose. Plausible strategies to prevent and treat AIDS, cancer and tuberculosis are based on such neglected observations. Many suggest that the information overload stultifies the canon, inhibiting progress. I illustrate here that seeking and resolving paradoxes can provide a different perspective from that of the dominant canon, opening vistas that address major issues pertinent to world health.
Bioluminescence is the production of visible light by living organisms. It occurs through the oxidation of luciferin substrates catalysed by luciferase enzymes. Auxiliary proteins, such as fluorescent proteins and lucife...Bioluminescence is the production of visible light by living organisms. It occurs through the oxidation of luciferin substrates catalysed by luciferase enzymes. Auxiliary proteins, such as fluorescent proteins and luciferin-binding proteins, can modify the light emitted wavelength or stabilize reactive luciferin molecules, respectively. Additionally, calcium ions are crucial for the luminescence across various species. Despite the large phylogenetic distribution of bioluminescent organisms, only a few systems have been comprehensively studied. Notably, cnidarian species of the genus utilize a coelenterazine-dependent luciferase, a calcium-dependent coelenterazine-binding protein and a green fluorescent protein. We investigated the bioluminescence of three sea pen species: , and (Pennatuloidea, Anthozoa). Their light-emission spectra reveal peaks at 510, 513 and 485 nm, respectively. A coelenterazine-based reaction was demonstrated in all three species. Using transcriptome analyses, we identified transcripts coding for luciferases, green fluorescent proteins and coelenterazine-binding proteins for and . Immunodetection confirmed the expression of luciferase in and . We also expressed recombinant luciferase of , confirming its activity. We highlighted the role of calcium ions in bioluminescence, possibly associated with the mechanism of substrate release at the level of coelenterazine-binding proteins. The study proposes a model for anthozoan bioluminescence, offering new avenues for future ecological and functional research on these luminous organisms.
The Notch pathway is an evolutionarily conserved signalling system that operates to influence an astonishing array of cell fate decisions in different developmental contexts. To identify novel effectors of Notch signalli...The Notch pathway is an evolutionarily conserved signalling system that operates to influence an astonishing array of cell fate decisions in different developmental contexts. To identify novel effectors of Notch signalling, we analysed the whole transcriptome of wing and eye imaginal discs in which an activated form of Notch was overexpressed. A LIM-homeodomain protein, Arrowhead (Awh), was identified as a novel candidate that plays a crucial role in Notch-mediated developmental events. alleles show strong genetic interaction with Notch pathway components. Awh loss-of-function upregulates Notch targets Cut and Wingless. Awh gain-of-function downregulates Notch targets by reducing the expression of the ligand Delta. Consequently, the expression of the Wingless effector molecule Armadillo and its downstream targets, Senseless and Vestigial, also gets downregulated. Awh overexpression leads to ectopic expression of , a segment polarity gene in the anterior region of wing disc, leading to patterning defects. Additionally, Notch gain-of-function-mediated neuronal defects get significantly rescued with Awh overexpression. Activated Notch inhibits Awh activity, suggesting a regulatory loop between Awh and Notch. Additionally, the defects caused by Awh gain-of-function were remarkably rescued by Chip, a LIM interaction domain containing transcriptional co-factor. The present study highlights the novel feedback regulation between Awh and Notch.
Retroposition is a gene duplication mechanism that uses RNA molecules as intermediaries to generate new gene copies. Dinoflagellates are proposed as an ideal model for exploring this process due to the tagging of retroge...Retroposition is a gene duplication mechanism that uses RNA molecules as intermediaries to generate new gene copies. Dinoflagellates are proposed as an ideal model for exploring this process due to the tagging of retrogenes with DNA-encoded remnants of the dinoflagellate-specific splice-leader motif at their 5' end. We conducted a comprehensive search for retrogenes in dinoflagellate transcriptomes to uncover their functional nature and the processes underlying their redundancy. We obtained a high-confidence set of hypothetical functional retrogenes widespread through the dinoflagellate lineage. Through annotations and gene ontology enrichment analysis, we found that the functional diversity of retrogenes reflects the most prevalent and active processes during stress periods, particularly those involving post-translational modifications and cell signalling pathways. Additionally, the significant presence of retrogenes linked to specific biological processes involved in symbiosis and toxin production underscores the role of retrogenes in adaptation. The expression profile and codon composition similar to protein-coding genes confirm the operational status of retrogenes and strengthen the idea that retrogenes recapitulate parental gene expression and function. This study provides new evidence supporting widespread gene retroposition across dinoflagellates and highlights the functional link of retrogenes with the core activity of the cell.
Many examples of self-organized embryonic patterning can be attributed to chemically mediated systems comprising interacting morphogens. However, mechanical patterning also contributes to the emergence of biological form...Many examples of self-organized embryonic patterning can be attributed to chemically mediated systems comprising interacting morphogens. However, mechanical patterning also contributes to the emergence of biological forms. For example, various studies have demonstrated that diverse patterns arise from elastic instabilities associated with the constrained growth of soft materials, which generate wrinkles, creases and folds. Here, we show that between days 12 and 13 of development, transient experimentally increased activity of the sonic hedgehog pathway in the chicken embryo, through a single intravenous injection of smoothened agonist (SAG), abolishes the Turing-like chemical patterning of reticulate scales on the ventral footpad and promotes a transition to mechanical labyrinthine skin folding. Using hybridization, nanoindentation and labelling of proliferating cells, we confirm that skin surface folding is associated with the loss of signalling placode pre-patterning as well as increased epidermal growth and stiffness. Using additional hydrocortisone treatments, we also demonstrate that experimentally induced hyper-keratinization of the skin mechanically restricts SAG-induced folding. Finally, we verify our experimental findings with mechanical growth simulations built from volumetric light sheet fluorescence microscopy data. Overall, we reveal that pharmacological perturbation of the underlying gene regulatory network can abolish chemical skin appendage patterning and replace it with self-organized mechanical folding.
The gut microbiota influences human and animal cognition and behaviour through its effects on the endocrine and immune systems. The microbiome-behaviour relationship may be especially relevant for fish, due to their dive...The gut microbiota influences human and animal cognition and behaviour through its effects on the endocrine and immune systems. The microbiome-behaviour relationship may be especially relevant for fish, due to their diverse evolutionary history and potential implications for farming and conservation. Yet, there is limited research on the interaction between gut microbiome and behaviour in non-model fish. We manipulated the rearing environment and diet of fish from two inbred strains of the self-fertilizing mangrove killifish () and assessed the effects on the gut microbiome and its interactions with anxiety-like behaviours. We found that microbiota composition and alpha diversity were significantly influenced by host genetics (strain), hatching mode (naturally or artificial dechorionation) and diet, but not by environmental enrichment. Fish activity level and inspections of a novel object were strongly associated with microbiota community composition and alpha diversity. The microbial taxa associated with differences in behaviour were dominated by Bacteroidales, potentially related to the production of metabolites affecting neural development. We suggest that the association between microbiome and fish behaviour could be an indirect effect of the modulation of the gut microbiota by host genetics and early rearing conditions, which could be affecting the production of microbial metabolites that interact with the fish physiology.
The allocation of resources in animals is shaped by adaptive trade-offs aimed at maximizing fitness. At the heart of these trade-offs, lies metabolism and the conversion of food resources into energy, a process mostly oc...The allocation of resources in animals is shaped by adaptive trade-offs aimed at maximizing fitness. At the heart of these trade-offs, lies metabolism and the conversion of food resources into energy, a process mostly occurring in mitochondria. Yet, the conversion of nutrients to utilizable energy molecules (adenosine triphosphate) inevitably leads to the by-production of reactive oxygen species (ROS) that may cause damage to important biomolecules such as proteins or lipids. The 'ROS theory of ageing' has thus proposed that the relationship between lifespan and metabolic rate may be mediated by ROS production. However, the relationship is not as straightforward as it may seem: not only are mitochondrial ROS crucial for various cellular functions, but mitochondria are also actually equipped with antioxidant systems, and many extra-mitochondrial sources also produce ROS. In this review, we discuss how viewing the mitochondrion as a regulator of cellular oxidative homeostasis, not merely a ROS producer, may provide new insights into the role of oxidative stress in the reproduction-survival trade-off. We suggest several avenues to test how mitochondrial oxidative buffering capacity might complement current bioenergetic and evolutionary studies.
Ito R, Kamiya M, Takayama K
… +14 more, Mori S, Matsumoto R, Takebayashi M, Ojima H, Fujimura S, Yamamoto H, Ohno M, Ihara M, Okajima T, Yamashita A, Colman F, Lycett GJ, Sattelle DB, Matsuda K
Lumen formation and inflation are crucial for tubular organ morphogenesis and function. However, the key signalling pathways for lumenogenesis regulation were not well identified. Here, we performed tissue-specific trans...Lumen formation and inflation are crucial for tubular organ morphogenesis and function. However, the key signalling pathways for lumenogenesis regulation were not well identified. Here, we performed tissue-specific transcriptomic sequencing for the isolated notochord tissue, in which 10 551 genes in total were identified. To investigate crucial signalling pathways in regulating lumenogenesis, KEGG was performed and the results showed that the Rap1 signalling pathway, vascular endothelial growth factor signalling pathway, mitogen activated protein kinase (MAPK) signalling pathway (plant) and Ras signalling pathway might play important roles in lumenogenesis. Moreover, correlation analysis with proteomic data and comparison analysis of single-cell transcriptomic data were further utilized to identify the potential critical roles of the Rap1 signalling pathway and Ras signalling pathway in lumenogenesis. To verify their functions in lumenogenesis, the Ras/calcium-Rap1-MAPK signalling axis was blocked, and the results showed that the notochord lumenogenesis failed. Meanwhile, we identified that CDC42 was a potential downstream target factor of the Ras-Rap1-MAPK signalling axis, playing crucial functions in notochord lumenogenesis. Overall, we systematically revealed the key regulatory signalling pathways for notochord lumen formation and verified a lumenogenesis-related signalling axis, providing a foundational data resource for exploring the mechanisms of lumenogenesis.
Global climate change is characterized by increased extreme temperatures affecting insects at all trophic levels. Zinc finger proteins (ZFPs) are key regulators of gene expression and cell differentiation in eukaryotes,...Global climate change is characterized by increased extreme temperatures affecting insects at all trophic levels. Zinc finger proteins (ZFPs) are key regulators of gene expression and cell differentiation in eukaryotes, essential for stress resistance in both animals and plants. Using CRISPR/Cas9 for gene deletion, this study predicted and examined the structure of ZFP320 in the diamondback moth () and investigated its function in temperature stress response through a comprehensive age-stage, two-sex life table analysis. We found encodes a 387 amino acid protein (43 kDa) with no transmembrane domains, featuring a ZnF-C2H2 domain. Quantitative fluorescence analysis showed that ZFP320 expression increased under high temperatures. ZFP320 knockout altered antioxidant gene expression, resulting in higher levels of superoxide dismutase and catalase in mutant strains compared with wild-type strain. Life table analysis revealed that the mutant strains had shorter fecundity and oviposition periods under both normal and high temperatures. Additionally, mutant strains exhibited lower parameters (, , ), as well as reduced survival rates and critical thermal maxima. Notably, plays a crucial role in temperature adaptation, paving the way for future investigations on the significance of ZFPs in 's temperature tolerance.