@article {pmid40829782,
year = {2025},
author = {Norte, DM and Avitia-Dominguez, LA and Rozen, DE},
title = {Evolution and Ecology of Streptomyces.},
journal = {Annual review of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-micro-051524-032254},
pmid = {40829782},
issn = {1545-3251},
abstract = {Streptomyces are among the most well-studied and important groups of bacteria, largely owing to their prolific production of biomedically important compounds like antibiotics and antifungals. Research over more than a half-century has elucidated the molecular and mechanistic details of Streptomyces multicellular development and the production of secondary metabolites. In contrast, the evolutionary and ecological mechanisms that underlie these phenotypes are comparatively understudied. Our aim in this review is to examine these aspects of Streptomyces biology, with a focus on the benefits associated with their complex life cycle, their multicellular architecture and development, and their production of antibiotics. In addition to highlighting existing studies, we point to clear knowledge gaps that can serve to motivate further research on these bacteria. A greater understanding of Streptomyces evolution and ecology is needed to improve our ability to exploit these organisms for biomedical and agricultural applications.},
}

@article {pmid40198726,
year = {2025},
author = {Liu, X and Pitchford, JW and Constable, GWA},
title = {Cell size and selection for stress-induced cell fusion in unicellular eukaryotes.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1012418},
pmid = {40198726},
issn = {1553-7358},
mesh = {*Cell Fusion ; *Models, Biological ; *Cell Size ; Biological Evolution ; *Stress, Physiological/physiology ; *Eukaryota/physiology/cytology ; *Eukaryotic Cells/physiology/cytology ; Selection, Genetic ; },
abstract = {In unicellular organisms, sexual reproduction typically begins with the fusion of two cells (plasmogamy) followed by the fusion of their two haploid nuclei (karyogamy) and finally meiosis. Most work on the evolution of sexual reproduction focuses on the benefits of the genetic recombination that takes place during meiosis. However, the selection pressures that may have driven the early evolution of binary cell fusion, which sets the stage for the evolution of karyogamy by bringing nuclei together in the same cell, have seen less attention. In this paper we develop a model for the coevolution of cell size and binary cell fusion rate. The model assumes that larger cells experience a survival advantage from their larger cytoplasmic volume. We find that under favourable environmental conditions, populations can evolve to produce larger cells that undergo obligate binary cell fission. However, under challenging environmental conditions, populations can evolve to subsequently produce smaller cells under binary cell fission that nevertheless retain a survival advantage by fusing with other cells. The model thus parsimoniously recaptures the empirical observation that sexual reproduction is typically triggered by adverse environmental conditions in many unicellular eukaryotes and draws conceptual links to the literature on the evolution of multicellularity.},
}

*Cell Fusion
*Models, Biological
*Cell Size
Biological Evolution
*Stress, Physiological/physiology
*Eukaryota/physiology/cytology
*Eukaryotic Cells/physiology/cytology
Selection, Genetic

@article {pmid39896451,
year = {2025},
author = {Scherer, J and Hinczewski, M and Nelms, B},
title = {Quantitative and sensitive sequencing of somatic mutations induced by a maize transposon.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.22.634239},
pmid = {39896451},
issn = {2692-8205},
support = {R35 GM151237/GM/NIGMS NIH HHS/United States ; },
abstract = {Cells accumulate mutations throughout development, contributing to cancer, aging, and evolution. Quantitative data on the abundance of de novo mutations within plants or animals are limited, as new mutations are often rare within a tissue and fall below the limits of current sequencing depths and error rates. Here, we show that mutations induced by the maize Mutator (Mu) transposon can be reliably quantified down to a detection limit of 1 part in 16,000. We measured the abundance of millions of de novo Mu insertions across four tissue types. Within a tissue, the distribution of de novo Mu allele frequencies was highly reproducible between plants, showing that, despite the stochastic nature of mutation, repeated statistical patterns of mutation abundance emerge. In contrast, there were significant differences in the allele frequency distribution between tissues. At the extremes, root was dominated by a small number of highly abundant de novo insertions, while endosperm was characterized by thousands of insertions at low allele frequencies. Finally, we used the measured pollen allele frequencies to reinterpret a classic genetic experiment, showing that evidence for late Mu activity in pollen are better explained by cell division statistics. These results provide insight into the complexity of mutation accumulation in multicellular organisms and a system to interrogate the factors that shape mutation abundance.},
}

@article {pmid38798687,
year = {2024},
author = {Starr, AL and Nishimura, T and Igarashi, KJ and Funamoto, C and Nakauchi, H and Fraser, HB},
title = {Disentangling cell-intrinsic and extrinsic factors underlying evolution.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38798687},
issn = {2692-8205},
support = {R01 DK121851/DK/NIDDK NIH HHS/United States ; R01 HG012285/HG/NHGRI NIH HHS/United States ; },
abstract = {A key goal of developmental biology is to determine the extent to which cells and organs develop autonomously, as opposed to requiring interactions with other cells or environmental factors. Chimeras have played a foundational role in this by enabling qualitative classification of cell-intrinsically vs. extrinsically driven processes. Here, we extend this framework to precisely decompose evolutionary divergence in any quantitative trait into cell-intrinsic, extrinsic, and intrinsic-extrinsic interaction components. Applying this framework to thousands of gene expression levels in reciprocal rat-mouse chimeras, we found that the majority of their divergence is attributable to cell-intrinsic factors, though extrinsic factors also play an integral role. For example, a rat-like extracellular environment extrinsically up-regulates the expression of a key transcriptional regulator of the endoplasmic reticulum (ER) stress response in some but not all cell types, which in turn strongly predicts extrinsic up-regulation of its target genes and of the ER stress response pathway as a whole. This effect is also seen at the protein level, suggesting propagation through multiple regulatory levels. Applying our framework to a cellular trait, neuronal differentiation, revealed a complex interaction of intrinsic and extrinsic factors. Finally, we show that imprinted genes are dramatically mis-expressed in species-mismatched environments, suggesting that mismatch between rapidly evolving intrinsic and extrinsic mechanisms controlling gene imprinting may contribute to barriers to interspecies chimerism. Overall, our conceptual framework opens new avenues to investigate the mechanistic basis of developmental processes and evolutionary divergence across myriad quantitative traits in any multicellular organism.},
}

@article {pmid25574294,
year = {2014},
author = {Weber, CF},
title = {Hormones and antibiotics in nature: a laboratory module designed to broaden undergraduate perspectives on typically human-centered topics.},
journal = {Journal of microbiology & biology education},
volume = {15},
number = {2},
pages = {277-286},
pmid = {25574294},
issn = {1935-7877},
abstract = {Bringing discovery-based research into undergraduate laboratory courses increases student motivation and learning gains over traditional exercises that merely teach technique or demonstrate well-documented phenomena. Laboratory experiences are further enhanced when they are designed to challenge student perspectives on topics relevant to their lives. To this end, a laboratory module on antibiotics and hormones, which are generally discussed in the context of human health, was developed for students to explore the multifaceted roles of antibiotics and hormones in nature (e.g. interspecies communication) via reading primary scientific literature and performing discovery-based experiments. The main objective of this module was to increase the general biological literacy of students as determined by their ability to connect the Five Core Concepts of Biological Literacy (American Association for the Advancement of Science, Vision and Change in Undergraduate Education: A Call to Action, 2011) to the topics "hormones" and "antibiotics" in pre- and postmodule surveys. After discussing unpublished research findings, cell biology students performed experiments demonstrating that: 1) fungi may promote fern growth via hormone production, 2) novel bacterial isolates in the genus Streptomyces produce antifungal compounds, and 3) subinhibitory antibiotic concentrations may enhance soil bacterial growth. The third finding provided evidence supporting a hypothesis framed in a scientific article that students read and discussed. Student perspectives on premodule surveys focused on roles of hormones and antibiotics in the human body (e.g. development, fighting infection), but their broadened postmodule perspectives encompassed the roles of these molecules in organismal communication and possibly the evolution of multicellularity.},
}

@article {pmid40816379,
year = {2025},
author = {Raza, RZ and Raza, S and Naveed, S and Ali, S},
title = {Evolution in neuropsychiatric cis-regulatory enhancers through human-specific neuronal mutations within transcription factor binding sites.},
journal = {Biochimica et biophysica acta. Proteins and proteomics},
volume = {},
number = {},
pages = {141095},
doi = {10.1016/j.bbapap.2025.141095},
pmid = {40816379},
issn = {1878-1454},
abstract = {cis-Regulatory elements (CREs) in multicellular genomes play a significant role in precise regulation of the genes. Increasing evidence has shown that alterations in CREs have had a drastic effect on the human brain evolution, neuronal cell adaptation and physiology. The human-specific sequence acceleration in CREs has not only changed the overall cognitive function of the human brain, but also seems to have strongly increased the risk of developing psychiatric disorders. Mapping the human-specific neuronal mutations within CREs remains to be a challenge and can largely impact the way DNA binding domain of the transcription factors interact with the CREs. In this study, we have identified human-specific neuronal mutations within transcription factor binding sites in neuropsychiatric enhancers of three major psychiatric disorders i.e. autism spectrum disorder, schizophrenia and bipolar disorder and studied the impact of human-specific neuronal mutations on binding affinities with the respective transcription factors via molecular dynamic simulation. Moreover, we have also identified signals of positive selection in the same set of empirically confirmed neuropsychiatric enhancers and correlated it with the way transcription factors bind with the human-specific and their counterpart ancestral allele harboring transcription factor binding sites.},
}

@article {pmid40816359,
year = {2025},
author = {Uzoigwe, CE},
title = {Negative Membrane Potentials Potentiate Multicellularity.},
journal = {Bio Systems},
volume = {},
number = {},
pages = {105565},
doi = {10.1016/j.biosystems.2025.105565},
pmid = {40816359},
issn = {1872-8324},
abstract = {Why did evolution almost exclusively select negative membrane potentials? Why did natural selection not favour positive membrane potentials? Further, membrane constituents are also negatively charged, in the form phospholipids. Putative cis-charge repulsion represents an obstacle to the emergency of multicellularity. This is compounded by the fact that cells at the centre of nascent multicellular species are deprived of nutrients by diffusion and exposed to the highest levels metabolic detritus. Multicellularity appears ab initio maladaptive. We present the hypothesis here that multicellularity may have been initiated, driven and potentiated by purely physical processes - one classical and one quantum. In water, negatively charged particles in the nano- to macro-molecular size-range, can aggregate, while positively charged repel one another. This counter-intuitive phenomenon has been consistently observed and recently attributed to the orientation of water molecules against the negatively charged surface and their re-orientation as negatively charged particles approach. This classical attraction works at long range, on a macromolecular scale. As two interfaces approximate closer, there is quantum attraction. Quantum nuclear effects of water hydrogen atoms are accentuated at interfacial layers compared to the bulk, due to the contraction of hydrogen bonds. This creates differences between the interfacial water and bulk in quantum free energy, which is only extinguished with the extrusion of intervening water. Quantum and classical attraction cooperate to initiate and stabilise multicellularity, while the whole process is possible because the membrane potential is negative and hydrogen is the dominant isotope rather deuterium or tritium.},
}

@article {pmid40803489,
year = {2025},
author = {Miller, WB and Cárdenas-García, JF and Baluška, F and Reber, AS and Slijepčević, P and Little, JC},
title = {A Biogenic Principle within the Constructal Law: The Flow of Information in Biological Systems.},
journal = {Bio Systems},
volume = {},
number = {},
pages = {105553},
doi = {10.1016/j.biosystems.2025.105553},
pmid = {40803489},
issn = {1872-8324},
abstract = {The Constructal Law states that 'for a finite-size flow system to persist in time (to live) it must evolve such that it provides greater and greater access to the currents that flow through it.' Arising from thermodynamics, this illuminating principle explains the properties and design features of many physical systems. It is now proposed that the definition of 'currents that flow' within the Constructal Law should be recognized to include the flow of information in living systems as a biogenic corollary. As the foundation of our biological system, cells seek to maximize their effective information about their external and internal environment. As their constructs, multicellular organisms reflect this requirement, accounting for living forms and their anatomic features. The cellular senome represents the crucial element of this flow, acting as the bioactive interface between environmental syntactic information and the internally-generated cellular semantic information upon which cellular actions depend. A Biogenic Principle as a corollary of the Constructal Law is presented, stating that for any finite-size living system to persist in time (to live), it must evolve to provide greater and greater access to the flow of information between itself and its environment, balanced against the constraining flow dynamics of natural physical systems. Within this biogenic principle, a Central Axiom of Biological Information can be identified: there is no unilateral flow of information in living systems.},
}

@article {pmid40794838,
year = {2025},
author = {von der Heyde, B and Srinivasan, A and Birwa, SK and von der Heyde, EL and Höhn, SSMH and Goldstein, RE and Hallmann, A},
title = {Spatiotemporal distribution of the glycoprotein pherophorin II reveals stochastic geometry of the growing ECM of Volvox carteri.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {33},
pages = {e2425759122},
doi = {10.1073/pnas.2425759122},
pmid = {40794838},
issn = {1091-6490},
support = {207510/Z/17/Z//Wellcome Trust (WT)/ ; 307079/Z/23/Z//Wellcome Trust (WT)/ ; 62220//John Templeton Foundation (JTF)/ ; },
mesh = {*Volvox/metabolism/growth & development ; *Extracellular Matrix/metabolism ; *Glycoproteins/metabolism ; Stochastic Processes ; *Algal Proteins/metabolism ; Microscopy, Confocal ; },
abstract = {The evolution of multicellularity involved the transformation of a simple cell wall of unicellular ancestors into a complex, multifunctional extracellular matrix (ECM). A suitable model organism to study the formation and expansion of an ECM during ontogenesis is the multicellular green alga Volvox carteri, which, along with the related volvocine algae, produces a complex, self-organized ECM composed of multiple substructures. These self-assembled structures primarily consist of hydroxyproline-rich glycoproteins, a major component of which is pherophorins. To investigate the geometry of the growing ECM, we fused the yfp gene with the gene for pherophorin II (PhII) in V. carteri. Confocal microscopy reveals PhII:YFP localization at key ECM structures, including the boundaries of compartments surrounding each somatic cell and the outer surface of the organism. Image analysis during the life cycle allows the stochastic geometry of growing compartments to be quantified; their areas and aspect ratios exhibit robust gamma distributions and exhibit a structural transition from a tight polygonal to a looser acircular packing geometry with stable eccentricity over time, evoking parallels and distinctions with the behavior of hydrated foams. These results provide quantitative insight into a general, open question in biology: how do cells collectively produce a complex structure external to themselves in a robust and accurate manner?},
}

*Volvox/metabolism/growth & development
*Extracellular Matrix/metabolism
*Glycoproteins/metabolism
Stochastic Processes
*Algal Proteins/metabolism
Microscopy, Confocal

@article {pmid40785347,
year = {2025},
author = {Mulvey, H and Dolan, L},
title = {The evolution of RHO of plant (ROP) proteins and their morphogenetic functions.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70455},
pmid = {40785347},
issn = {1469-8137},
support = {787613/ERC_/European Research Council/International ; ALTF 490-2024//European Molecular Biology Organization/ ; },
abstract = {The ability of a cell to polarise, and direct cell growth or orient cell division, for example, is fundamental for the morphogenesis of multicellular organisms. A key molecular system for signalling cell polarity in diverse eukaryotes involves the RHO family of small GTPases. Since its origin in early eukaryotes, the RHO family has evolved independently in different lineages, and the plant-specific subfamily of RHO - RHO of plants (ROP) - was established in the streptophyte algal ancestors of land plants. Insights from both bryophytes and vascular plants have revealed conserved roles for ROP signalling in land plant morphogenesis. Synthesising our current understanding of how ROP signalling evolved and how it regulates morphogenesis in extant land plants, we propose that this polarity signalling system was co-opted to spatially coordinate morphogenetic mechanisms that evolved in the algal ancestors of land plants.},
}

@article {pmid40776808,
year = {2025},
author = {Suárez, J and Stencel, A and Ronai, I},
title = {Top-Down Coercive Mechanisms and the Major Transitions in Evolution.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e70047},
doi = {10.1002/bies.70047},
pmid = {40776808},
issn = {1521-1878},
support = {2023/51/B/HS1/01021//National Science Centre OPUS 26/ ; LEO23-2-9791-HUM-FIF-22//Fundación BBVA - Beca Leonardo/ ; },
abstract = {We propose that top-down coercive mechanisms have played a role in the origin and maintenance of the Major Transitions in Evolution (MTE). Top-down coercion has potentially been underappreciated due to the lack of a conceptual framework. Therefore, we provide a formalized top-down coercion framework for the MTE. Our conceptualization of top-down biological coercion is a loss of potential due to a constraint from the top-down. We also present three case studies of coercive top-down mechanisms in the evolution of eukaryotic cells, multicellularity and eusocial insect colonies. The MTE project studies the origin and maintenance of new levels of individuality in the biological hierarchy. Previously, the MTE has been conceived as a bottom-up process. Our coercion framework provides new empirical questions regarding the origin of transitions and helps reframe discussions of fitness in the MTE.},
}

@article {pmid40773527,
year = {2025},
author = {Gao, Y and Zhao, X and Li, C},
title = {The evolution of irreversible cell differentiation under cell death effect.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0315255},
pmid = {40773527},
issn = {1932-6203},
mesh = {*Cell Differentiation/physiology ; *Cell Death/physiology ; *Models, Biological ; *Biological Evolution ; Animals ; },
abstract = {Cell differentiation is an important characteristic of multicellular organisms which produce new-typed cells to engage in diverse life functions. Irreversible differentiation, as an important differentiation pattern, describes cells differentiated by determined trajectories to form specialized cell types. It has been found that differentiated cell types often show different death rates. Yet, it is still unclear what role cell death plays in shaping the formation of irreversible cell differentiation. Here, we establish a theoretical model to investigate the impact of cell death on the evolution of irreversible cell differentiation in multicellular organisms. Irreversible differentiation refers to the loss of a cell type's differentiation potential, and it is constructed by the sequences of differentiation probabilities of a cell type across cell divisions. We show that irreversible differentiation is more likely to occur when cell death rates between cell types are linear. Meanwhile, differences in death rates between cell types affect the emergence conditions of irreversible differentiation, whereas no significant impacts on that from equal cell death rates. Additionally, we found that cell death impacts the cell number and cell composition of a mature organism. These findings provide insights into understanding the role of cell death in the formation of cells' irreversible differentiation.},
}

*Cell Differentiation/physiology
*Cell Death/physiology
*Models, Biological
*Biological Evolution
Animals

@article {pmid40770989,
year = {2025},
author = {Javaux, EJ},
title = {A diverse Palaeoproterozoic microbial ecosystem implies early eukaryogenesis.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {380},
number = {1931},
pages = {20240092},
pmid = {40770989},
issn = {1471-2970},
support = {//Fonds De La Recherche Scientifique - FNRS/ ; //Belgian Federal Science Policy Office/ ; },
mesh = {*Fossils ; *Biological Evolution ; *Eukaryota/physiology ; *Microbiota ; *Ecosystem ; Symbiosis ; },
abstract = {Microbial interactions may lead to major events in life and planetary evolution, such as eukaryogenesis, the birth of complex nucleated cells. In synergy with microbiology, cellular palaeobiology may shed some light on this very ancient and debated affair and its circumstances. The 1.78-1.73 Ga McDermott Formation, McArthur Basin (Australia), preserves a microfossil assemblage that provides unique insights into the evolution of early eukaryotes. The fossil cells display a level of morphological complexity, disparity and plasticity requiring a complex cytoskeleton and an endomembrane system, pushing back the minimum age of uncontested eukaryotic fossils by more than 100 million years (Ma). They also document an earlier appearance of reproduction by budding, simple multicellularity and diverse programmed openings of cyst wall implying a life cycle, as well as possible evidence for microbial symbiosis and behaviour, including eukaryovory and ectosymbiosis. This microbial community that also includes cyanobacterial cells preserving thylakoids, microbial mats and other microfossils, thrived in supratidal to intertidal marine environments with heterogeneous but mostly suboxic to anoxic redox conditions. Taken together, these observations imply early eukaryogenesis, including mitochondrial endosymbiosis in micro-/nano-oxic niches, and suggest a >1.75 Ga minimum age for the Last Eukaryotic Common Ancestor (LECA), preceded by a deeper history of the domain Eukarya, consistent with several molecular clocks and the fossil record.This article is part of the discussion meeting issue 'Chance and purpose in the evolution of biospheres'.},
}

*Fossils
*Biological Evolution
*Eukaryota/physiology
*Microbiota
*Ecosystem
Symbiosis

@article {pmid40768352,
year = {2025},
author = {Scherer, J and Hinczewski, M and Nelms, B},
title = {Quantitative and sensitive sequencing of somatic mutations induced by a maize transposon.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {32},
pages = {e2426650122},
doi = {10.1073/pnas.2426650122},
pmid = {40768352},
issn = {1091-6490},
support = {R35GM151237//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*Zea mays/genetics ; *DNA Transposable Elements/genetics ; *Mutation ; Gene Frequency ; Pollen/genetics ; },
abstract = {Cells accumulate mutations throughout development, contributing to cancer, aging, and evolution. Quantitative data on the abundance of de novo mutations within plants or animals are limited, as new mutations are often rare within a tissue and fall below the limits of current sequencing depths and error rates. Here, we show that mutations induced by the maize Mutator (Mu) transposon can be reliably quantified down to a detection limit of 1 part in 16,000. We measured the abundance of millions of de novo Mu insertions across four tissue types. Within a tissue, the distribution of de novo Mu allele frequencies was highly reproducible between plants, showing that, despite the stochastic nature of mutation, repeated statistical patterns of mutation abundance emerge. In contrast, there were significant differences in the allele frequency distribution between tissues. At the extremes, root was dominated by a small number of highly abundant de novo insertions, while endosperm was characterized by thousands of insertions at low allele frequencies. Finally, we used the measured pollen allele frequencies to reinterpret a classic genetic experiment, showing that evidence for late Mu activity in pollen is better explained by cell division statistics. These results provide insight into the complexity of mutation accumulation in multicellular organisms and a system to interrogate the factors that shape mutation abundance.},
}

*Zea mays/genetics
*DNA Transposable Elements/genetics
*Mutation
Gene Frequency
Pollen/genetics

@article {pmid40764636,
year = {2025},
author = {Gross, BJ and Soltwedel, JR and Shelton, E and Gomez, C and Campàs, O},
title = {STRESS, an automated geometrical characterization of deformable particles for in vivo measurements of cell and tissue mechanical stresses.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {28599},
pmid = {40764636},
issn = {2045-2322},
mesh = {Animals ; *Stress, Mechanical ; Software ; *Mechanotransduction, Cellular ; Zebrafish ; Microspheres ; },
abstract = {From cellular mechanotransduction to the formation of embryonic tissues and organs, mechanics has been shown to play an important role in the control of cell behavior and embryonic development. Most of our existing knowledge of how mechanics affects cell behavior comes from in vitro studies, mainly because measuring cell and tissue mechanics in 3D multicellular systems, and especially in vivo, remains challenging. Oil microdroplet sensors, and more recently gel microbeads, use surface deformations to directly quantify mechanical stresses within developing tissues, in vivo and in situ, as well as in 3D in vitro systems like organoids or multicellular spheroids. However, an automated analysis software able to quantify the spatiotemporal evolution of stresses and their characteristics from particle deformations is lacking. Here we develop STRESS (Surface Topography Reconstruction for Evaluation of Spatiotemporal Stresses), an analysis software to quantify the geometry of deformable particles of spherical topology, such as microdroplets or gel microbeads, that enables the automatic quantification of the temporal evolution of stresses in the system and the spatiotemporal features of stress inhomogeneities in the tissue. As a test case, we apply these new code to measure the temporal evolution of mechanical stresses using oil microdroplets in developing zebrafish tissues. Starting from a 3D timelapse of a droplet, the software automatically calculates the statistics of local anisotropic stresses, decouples the deformation modes associated with tissue- and cell-scale stresses, obtains their spatial features on the droplet surface and analyzes their spatiotemporal variations using spatial and temporal stress autocorrelations. We provide fully automated software in Matlab/Python and also in Napari (napari-STRESS), which allows the visualization of mechanical stresses on the droplet surface together with the microscopy images of the biological systems. The automated nature of the analysis will help users obtain quantitative information about mechanical stresses in a wide range of 3D multicellular systems, from developing embryos or tissue explants to organoids.},
}

Animals
*Stress, Mechanical
Software
*Mechanotransduction, Cellular
Zebrafish
Microspheres

@article {pmid40752570,
year = {2025},
author = {Igamberdiev, AU},
title = {The development of code systems during eukaryogenesis and the rise of multicellularity.},
journal = {Bio Systems},
volume = {255},
number = {},
pages = {105546},
doi = {10.1016/j.biosystems.2025.105546},
pmid = {40752570},
issn = {1872-8324},
abstract = {The expansion of the set of biological codes associated with the appearance and complexification of eukaryotic cells (eukaryogenesis) and the evolution of multicellularity is based on the development of higher codes operating over the genetic system. In the course of evolution, the perception-action functional cycles described by Jakob von Uexküll become complemented by the secondary meta-cycles, which perceive the work of the primary cycles, and finally by tertiary cycles of meta-reflexivity, which perceive and evaluate the previous activity of the secondary functional cycles and generate a new field of meanings associated with conscious experience. The development of secondary and tertiary cycles forms the basis of higher-level codes operating over the genetic system and resulting in the evolutionary separation between unikonts and bikonts, in the divergence between protostomes and deuterostomes, in all events of cellular differentiation manifested as differentiation trees, and finally in the appearance of consciousness. The expansion of codes associated with the rise of eukaryotic organelles and with the cytoskeleton rearrangements in the ontogenesis of multicellular organisms determines the course of the evolutionary process toward complexification. The internally controlled recombination process, in particular, in the course of meiotic cell division and ontogenetic differentiation, becomes the driving factor of progressive evolution. It corresponds to the growing role of the epigenome and epigenetic regulation in the complexification of biological organization. It is concluded that the evolutionary process unfolds as a propagating non-deducible construction following the generation of functional redundancy, which is achieved through gene duplication, symbiosis, and cell-cell interactions, and becomes an important precondition for the appearance of new evolutionary acquisitions.},
}

@article {pmid40745143,
year = {2025},
author = {de Los Reyes Corrales, T and Casas-Tintó, S},
title = {Drosophila melanogaster as a Model System for Human Glioblastoma.},
journal = {Advances in experimental medicine and biology},
volume = {1482},
number = {},
pages = {209-227},
doi = {10.1007/978-3-031-97035-1_11},
pmid = {40745143},
issn = {0065-2598},
mesh = {Animals ; *Drosophila melanogaster/genetics ; Humans ; *Glioblastoma/pathology/genetics/metabolism ; *Disease Models, Animal ; *Brain Neoplasms/pathology/genetics/metabolism ; Cell Communication ; Signal Transduction ; },
abstract = {Glioblastoma (GB) is the most common and aggressive malignant primary brain tumor of the central nervous system in humans. It originates from neoplastic glial cells that infiltrate the brain parenchyma, leading to neurological symptoms, including progressive memory loss, speech and language deficits, epileptic seizures, and vomiting as hallmarks of neurodegenerative processes. Conventional therapies have failed to effectively treat GB due to its diffuse nature and high recurrence rates after treatment. To address these challenges, different models have been developed to study the early stages of gliomagenesis and cell-to-cell interactions. These include animal models, cellular lines, coculture assays, organoid models, and bioinformatics approaches. Among those models, nonmammalian models such as Drosophila melanogaster recapitulate the genetic, cellular, and physiological characteristics of GB in patients, reproducing glial proliferation, invasion, and the alteration of signaling pathways involved in tumor growth.As observed in humans, Drosophila GB model reproduces the cell-to-cell communication involving glioma cell-glioma cell and neuron-glioma cell communication as a bidirectional communication system through signals from GB to neuron or neuronal activity and signals that the tumor vampirizes from the neurons. This multicellular network appears to be crucial for GB growth and invasion, presenting promising opportunities to develop novel treatments aimed at overcoming therapy resistance.},
}

Animals
*Drosophila melanogaster/genetics
Humans
*Glioblastoma/pathology/genetics/metabolism
*Disease Models, Animal
*Brain Neoplasms/pathology/genetics/metabolism
Cell Communication
Signal Transduction

@article {pmid40718753,
year = {2025},
author = {Xiao, Y and Li, T and Rodrigo, A},
title = {Models of microbiome evolution incorporating host resource provisioning.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf059},
pmid = {40718753},
issn = {2730-6151},
abstract = {Multicellular hosts and their associated microbial partners (i.e. microbiomes) often interact in mutually beneficial ways. Consequently, hosts may choose to allocate resources to regulate and recruit appropriate microbes. In doing so, hosts may incur an energetic cost and, in turn, these costs can affect host fitness. It remains unclear how hosts have evolved to balance the costs of expending resources to manage their microbiomes against the benefits that might accrue by doing so. To address this question, we extend a previously developed agent-based computational model of host-microbiome evolution by incorporating a resource provisioning process, to determine how hosts have evolved to balance the costs and benefits of expending resources to manage their microbiomes. Our results indicate that resource provisioning will evolve when hosts provide a high percentage of microbes to their offspring and contribute a low percentage of their microbiome to the environment. In contrast, resource provisioning will not evolve when hosts contribute a high percentage of their microbiome to the environment. This is because hosts that do not provide resources to acquire microbes can nonetheless still acquire microbes from the environmental contributions of hosts that do provide such resources. Since resource provisioning incurs a fitness cost to the host, over evolutionary time, resource provisioning will not be favored. Our results also show that hosts are less likely to provide resources to acquire beneficial microbes if hosts can obtain a high proportion of these microbes from the environment.},
}

@article {pmid40713951,
year = {2025},
author = {Johnson, JAI and Bergman, DR and Rocha, HL and Zhou, DL and Cramer, E and Mclean, IC and Dance, YW and Booth, M and Nicholas, Z and Lopez-Vidal, T and Deshpande, A and Heiland, R and Bucher, E and Shojaeian, F and Dunworth, M and Forjaz, A and Getz, M and Godet, I and Kurtoglu, F and Lyman, M and Metzcar, J and Mitchell, JT and Raddatz, A and Solorzano, J and Sundus, A and Wang, Y and DeNardo, DG and Ewald, AJ and Gilkes, DM and Kagohara, LT and Kiemen, AL and Thompson, ED and Wirtz, D and Wood, LD and Wu, PH and Zaidi, N and Zheng, L and Zimmerman, JW and Phillip, JM and Jaffee, EM and Gray, JW and Coussens, LM and Chang, YH and Heiser, LM and Stein-O'Brien, GL and Fertig, EJ and Macklin, P},
title = {Human interpretable grammar encodes multicellular systems biology models to democratize virtual cell laboratories.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.06.048},
pmid = {40713951},
issn = {1097-4172},
abstract = {Cells interact as dynamically evolving ecosystems. While recent single-cell and spatial multi-omics technologies quantify individual cell characteristics, predicting their evolution requires mathematical modeling. We propose a conceptual framework-a cell behavior hypothesis grammar-that uses natural language statements (cell rules) to create mathematical models. This enables systematic integration of biological knowledge and multi-omics data to generate in silico models, enabling virtual "thought experiments" that test and expand our understanding of multicellular systems and generate new testable hypotheses. This paper motivates and describes the grammar, offers a reference implementation, and demonstrates its use in developing both de novo mechanistic models and those informed by multi-omics data. We show its potential through examples in cancer and its broader applicability in simulating brain development. This approach bridges biological, clinical, and systems biology research for mathematical modeling at scale, allowing the community to predict emergent multicellular behavior.},
}

@article {pmid40703446,
year = {2025},
author = {Kershenbaum, S and Ireland, D and Sabry, Z and Rabeler, C and Shetty, V and Aboobaker, A and Collins, ES},
title = {Variation in phenotype, genotype, and somatic diversity among asexual Schmidtea mediterranea planarians.},
journal = {iScience},
volume = {28},
number = {8},
pages = {113035},
pmid = {40703446},
issn = {2589-0042},
abstract = {Most multicellular life reproduces sexually, utilizing a single-celled stage that acts as a genetic bottleneck. This bottleneck limits the evolution of selfish cell adaptations by ensuring all cells descend from a single progenitor. We investigated an obligately asexual strain of Schmidtea mediterranea planarians that reproduces by self-bisection and lacks a single-cell bottleneck. Using 2.5 yearlong data on planarian reproductive behavior combined with genotyping, we revealed two previously undescribed genetically distinct substrains within the CIW4 strain. One substrain showed reduced fitness, which correlated with substantial losses of heterozygosity and increased somatic diversity. By genotyping consecutive head offspring over multiple generations, we found that only ∼9% of potential de novo mutations were transmitted to the next generation via the tail, suggesting that fission acts as a genetic bottleneck. Our study uncovers significant diversity in a fissiparous animal and proposes how somatic diversity can be controlled in the absence of a single-cell bottleneck.},
}

@article {pmid40700772,
year = {2025},
author = {Guyomar, T and De Simone, A},
title = {Gradients, waves and nematics: quantitative perspectives on regeneration.},
journal = {Seminars in cell & developmental biology},
volume = {174},
number = {},
pages = {103632},
doi = {10.1016/j.semcdb.2025.103632},
pmid = {40700772},
issn = {1096-3634},
abstract = {Regeneration restores a damaged body part to its original size, shape and structure. Research over the last decades identified signaling pathways, cell types and cellular processes that are key for regeneration. Moreover, mechanical cues and electric potentials are increasingly implicated in modulating regenerative processes. An intriguing open question regards how these chemical, mechanical and electric signals are dynamically organized to coordinate cell behaviors across large regenerating tissues and long regenerative timescales for proper morphogenesis. In addition, it is less explored how regeneration is stopped once tissues reach their proper final form. These questions and related models cross-talk with physical notions like information, pattern formation, self-organization, and control. An interdisciplinary approach combining methods and concepts of developmental biology and physics is offering new quantitative insights on these questions. In this approach, researchers characterize the spatial organization and temporal dynamics of chemical, mechanical and electric signal inputs and relate them to cell and tissue behaviors. Initial observations inform theory; in turn, theory guides experiments and data analysis, while state-of-the-art perturbations allow testing these models. After illustrating this approach, we provide examples of its application to animal regeneration in vivo. These works are extending the notion of "morphogen", contributing to establishing the emerging field of quantitative regeneration and uncovering principles of multicellular organization.},
}

@article {pmid40695321,
year = {2025},
author = {Ara, PS and Casacuberta, E and Scazzocchio, C and Ruiz-Trillo, I and Najle, SR},
title = {CRISPR-Cas9 genome editing in Corallochytrium limacisporum,a key species for understanding animal origins.},
journal = {Open biology},
volume = {15},
number = {7},
pages = {250066},
doi = {10.1098/rsob.250066},
pmid = {40695321},
issn = {2046-2441},
support = {4973.01//Moore Foundation - MMI Experimental Model Systems/ ; PID2023-153273NB-I00//MICIU/ AEI /10.13039/501100011033/ ; "ERDF A way of making Europe", PID2023-153273NB-I00//MICIU/AEI/10.13039/501100011033/ ; exp. 2021 SGR 00751//Departament de Recerca i Universitats de la Generalitat de Catalunya/ ; },
mesh = {*CRISPR-Cas Systems ; *Gene Editing/methods ; Animals ; Point Mutation ; },
abstract = {Microbial holozoans are the closest unicellular relatives of animals. They share a substantial gene repertoire with animals and exhibit complex life cycles. Studying these organisms is crucial for understanding the evolution of multicellularity, and significant progress has been made in uncovering key aspects of the biology of the four microbial holozoans lineages: choanoflagellates, filastereans, ichthyosporeans and corallochytreans. However, reverse genetic tools are still lacking in corallochytreans, one of the earliest-branching holozoan lineages and the only known group with both coenocytic and binary fission development. Here, we present CRISPR-Cas9-mediated gene inactivation and point mutation methodologies in the corallochytrean Corallochytrium limacisporum. As a proof of concept, we inactivated the fkb12 gene, a component of the mTOR pathway, conferring rapamycin resistance, and introduced a point mutation in sdhB, encoding a subunit of succinate dehydrogenase, conferring carboxin resistance. Our results demonstrate the presence of both non-homologous end-joining and homology-directed repair pathways in C. limacisporum and shows an editing efficiency of approximately 2%. Furthermore, simultaneous gene targeting revealed a co-editing frequency of approximately 20%. Finally, this study establishes unequivocally that C. limacisporum is haploid, making it an ideal model for genetic studies and gene editing applications to unravel the molecular mechanisms involved in animal origins.},
}

*CRISPR-Cas Systems
*Gene Editing/methods
Animals
Point Mutation

@article {pmid40695282,
year = {2025},
author = {Perotti, ON and Viramontes-Esparza, G and Booth, DS},
title = {A red algal polysaccharide influences the multicellular development of the choanoflagellate Salpingoeca rosetta.},
journal = {Current biology : CB},
volume = {35},
number = {15},
pages = {3767-3776.e4},
doi = {10.1016/j.cub.2025.06.059},
pmid = {40695282},
issn = {1879-0445},
mesh = {*Choanoflagellata/growth & development/drug effects/physiology ; *Polysaccharides/metabolism ; *Porphyra/chemistry/metabolism ; *Rhodophyta/chemistry ; },
abstract = {The choanoflagellate Salpingoeca rosetta exemplifies the capacity of marine microeukaryotes to integrate environmental cues into their life histories. Some of the cues that S. rosetta detects are lipids from their bacterial prey that induce the development of multicellular colonies called rosettes.[1][,][2][,][3] In the aquatic environments where S. rosetta would encounter bacterial cues, microbial communities gain refuge[4][,][5][,][6][,][7][,][8][,][9][,][10][,][11] and food[12][,][13][,][14] from algae. For example, microbes in coastal environments benefit from macroalgae that annually release ∼10[14] g of carbon,[15][,][16] primarily in the form of polysaccharides that comprise ∼80% of dissolved organic carbon in surface waters.[17] Despite the ecological impact of algae and historical descriptions of choanoflagellates attached to algae,[18][,][19][,][20] the influence of algae on choanoflagellate life history transitions has remained unexplored. Here, we report that porphyran, a polysaccharide produced by the red macroalga Porphyra umbilicalis, induces multicellular development in S. rosetta. We first noticed this response when S. rosetta formed multicellular rosette colonies while growing in media prepared from P. umbilicalis, even though rosette-inducing bacteria were absent. By biochemically purifying extracts of P. umbilicalis, we identified porphyran as the rosette-inducing factor. This response provides a biochemical insight that indicates algal polysaccharides may serve as cues to mediate associations between choanoflagellates and algae. Moreover, this observation complements evidence from environmental and geochemical studies that show the impact that algae have exerted on the ecology and evolution of eukaryotes,[21] including a rise in algal productivity during the origin of animals,[22] the closest living relatives of choanoflagellates.},
}

*Choanoflagellata/growth & development/drug effects/physiology
*Polysaccharides/metabolism
*Porphyra/chemistry/metabolism
*Rhodophyta/chemistry

@article {pmid40675986,
year = {2025},
author = {Zhu, Q and Balasubramanian, A and Asirvatham, JR and Chatterjee, M and Piyarathna, B and Kaur, J and Mohamed, N and Wu, L and Wang, S and Pourfarrokh, N and Binsol, PD and Bhargava, M and Rasaily, U and Xu, Y and Zheng, J and Jebakumar, D and Rao, A and Gutierrez, C and Omilian, AR and Morrison, C and Das, GM and Ambrosone, C and Seeley, EH and Chen, SH and Li, Y and Chang, E and Li, X and Baker, E and Aneja, R and Zhang, XH and Sreekumar, A},
title = {Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in Black American and White American patients with TNBC.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6584},
pmid = {40675986},
issn = {2041-1723},
support = {P30 CA016056/CA/NCI NIH HHS/United States ; RR220035//Cancer Prevention and Research Institute of Texas (Cancer Prevention Research Institute of Texas)/ ; P20 CA284971/CA/NCI NIH HHS/United States ; P30 CA013148/CA/NCI NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; P20 CA284971-01//U.S. Department of Health & Human Services | NIH | Center for Scientific Review (NIH Center for Scientific Review)/ ; R01 CA227904/CA/NCI NIH HHS/United States ; RO1CA227904//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; P50 CA186784/CA/NCI NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; RR024574//U.S. Department of Health & Human Services | NIH | Center for Scientific Review (NIH Center for Scientific Review)/ ; },
mesh = {Female ; Humans ; *Black or African American/genetics ; Macrophages/immunology ; T-Lymphocytes/immunology ; Transcriptome ; *Triple Negative Breast Neoplasms/genetics/immunology/pathology/ethnology/mortality ; *Tumor Microenvironment/immunology/genetics ; *White/genetics ; },
abstract = {Racial disparities in the clinical outcomes of triple-negative breast cancer (TNBC) have been well-documented, but the underlying biological mechanisms remain poorly understood. To investigate these disparities, we employed a multi-omic approach integrating imaging mass cytometry and spatial transcriptomics to characterize the tumor microenvironment (TME) in self-identified Black American (BA) and White American (WA) TNBC patients. Our analysis revealed that the TME in BA patients is marked by a network of endothelial cells, macrophages, and mesenchymal-like cells, which correlates with reduced patient survival. In contrast, the WA TNBC microenvironment is enriched in T-cells and neutrophils, indicative of T-cell exhaustion and suppressed immune responses. Ligand-receptor and pathway analyses further demonstrated that BA TNBC tumors exhibit a relatively "immune-cold" profile, while WA TNBC tumors display features of an "inflamed" TME, suggesting the evolution of a unique immunosuppressive mechanism. These findings provide insight into racially distinct tumor-promoting and immunosuppressive microenvironments, which may contribute to the observed differences in clinical outcomes among BA and WA TNBC patients.},
}

Female
Humans
*Black or African American/genetics
Macrophages/immunology
T-Lymphocytes/immunology
Transcriptome
*Triple Negative Breast Neoplasms/genetics/immunology/pathology/ethnology/mortality
*Tumor Microenvironment/immunology/genetics
*White/genetics

@article {pmid40673909,
year = {2025},
author = {Souza, FHS and Toma, GA and Vidal, JAD and Garrido-Ramos, MA and Souza, GM and Dos Santos, RZ and Porto-Foresti, F and Liehr, T and Utsunomia, R and Cioffi, MB},
title = {Comparative Satellitomics in Arowanas (Telostei, Osteoglossiformes) Sheds Light on the Evolution of Ancient Satellite DNAs.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.13008},
pmid = {40673909},
issn = {1749-4877},
abstract = {A significant fraction of the genomes of most multicellular eukaryotes includes extensive arrays of tandemly repeated sequences, collectively referred to as satellite DNAs (satDNAs). However, the mechanisms responsible for generating and maintaining varying satDNA abundances across lineages and temporal scales are still unclear. This work focused on arowana fishes (Teleostei, Osteoglossiformes) as a model; their widespread intercontinental distribution and basal phylogenetic position within Teleostei make them a compelling model for evolutionary research, especially in the realm of satDNA molecular evolution. Through the integration of genomic and chromosomal data, we analyzed and compared the catalogs of satDNA families (i.e., satellitomes) of four out of the six extant arowana species, elucidating ancestral evolutionary trends and establishing their temporal history. Arowanas displayed a small number of satDNA families, ranging from 16 to 25 in Osteoglossum bicirrhosum and Scleropages formosus, respectively. Alongside the identification of some shared satDNAs, many considered species-specific, nonetheless possess a limited number of copies in other species. The minimal variation observed both within and across species highlights the long-term conservation of satDNAs during evolution, since specific ones (referred to as long-term conserved satDNAs) may have endured throughout a lengthy evolutionary period. Moreover, fluorescence in situ hybridization (FISH) investigations conducted with the most abundant satDNAs demonstrated unique hybridization patterns for homologous orthologous ones, signifying their dynamic genomic positioning. Besides, the similarities of satDNAs among species align with their phylogenetic relationships, showing the high dynamism of arowanas' satDNAs, with several evolutionary events driving their sequence diversity.},
}

@article {pmid40672161,
year = {2025},
author = {Ho, C and Glykofrydis, F and Godage, G and Poon, K and Kunnan, M and Swedlund, B and Murillo, S and Morsut, L},
title = {Derivation of cardiomyocyte-propelled motile aggregates from stem cells.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.09.663178},
pmid = {40672161},
issn = {2692-8205},
abstract = {Robotics draws inspiration from biology, particularly animal locomotion based on muscle-driven contractions. While traditional engineering assembles components sequentially, locomotive animals are built via self-organized developmental programs. Stem cells, under the right conditions, can mimic these processes in vitro, offering a pathway to develop muscle-propelled biobots in a self-organized building process. Here, we demonstrate that existent cardiogenic gastruloid protocols can produce motile aggregates from mouse embryonic stem cells, although with very limited efficiency. We then identify a novel protocol that yields contractile aggregates with higher frequency and larger contractile areas. In this novel protocol, mesendoderm induction using TGF-beta ligands is followed by cardiogenic induction with FGFs and VEGF. Synthetic organizers further control contraction localization. Aggregates developed via this protocol show enhanced motility, marking a step forward towards building motile cardiobots from self-organized biological material. This strategy opens new possibilities for designing autonomous biobots and studying the evolution of muscle-powered movement of multicellular organisms and cardiovascular development.},
}

@article {pmid40657372,
year = {2025},
author = {Wang, Y and Cao, G and Zeng, H and Zhi, Y and Xu, M and Wang, Y and Liu, M and Ruan, Y and Tse, KY and Zhang, Q and Gao, J and Han, Z and Li, F},
title = {Multi-Omics Analysis Reveals the transforming growth factor-β Signaling-Driven Multicellular Interactions with Prognostic Relevance in Cervical Cancer Progression.},
journal = {Journal of Cancer},
volume = {16},
number = {9},
pages = {2857-2876},
pmid = {40657372},
issn = {1837-9664},
abstract = {While cervical cancer (CC) prognosis depends on tumor staging, the spatiotemporal evolution of tumor microenvironment (TME) heterogeneity during metastatic progression remains poorly characterized at single-cell resolution. We employed an integrative multi-omics approach, combining single-cell RNA sequencing (scRNA-seq; n = 11), spatial transcriptomics (ST), and bulk RNA-seq data from the TCGA-CESC cohort (n = 304), to systematically map TME remodeling across CC progression stages. scRNA-seq was performed on primary lesions from patients with localized (n = 3), regional (n = 4), and metastatic (n = 4) diseases, with in-depth analyses focusing on cellular characteristics, cell type composition alterations, functional changes, differentiation trajectories, and cell-cell interaction networks. These findings were further validated using spatial transcriptomics, bulk RNA-seq data, and multiple immunohistochemistry (mIHC) experiments. ScRNA-seq data revealed that the TME of the metastatic group displayed a distinct immunosuppressive phenotype. Three key subclusters closely linked to TME remodeling in this group were identified. Notably, a novel metastasis-associated epithelial subpopulation (Epi0_AGR2), characterized by both epithelial-mesenchymal transition (EMT) and chemokine secretory phenotypes, was discovered. Gene Set Variation Analysis (GSVA) revealed that transforming growth factor β (TGF-β) signaling activation served as its primary transcriptional driver. Additionally, a neutrophil subset with pro-tumor and immunosuppressive properties, as well as a cancer-associated fibroblasts (CAFs) subset that promoted angiogenesis, were enriched in the metastatic group. Cell-cell interaction analysis and spatial mapping further revealed the formation of coordinated Epi0-neutrophil-CAFs niches, which established TGF-β-CXCL1/2/8-OSM/OSMR feedforward loops. Importantly, a computational model derived from the TME metastatic niche signature demonstrated significant prognostic stratification in the TCGA cohort (HR = 2.5179, p = 0.0144). In all, this study provides the first comprehensive delineation of stage-specific TME dynamics in CC, revealing TGF-β-driven cellular cooperativity as a metastatic switch. The joint framework establishes a potential clinically translatable tool for precision prognosis and therapeutic targeting.},
}

@article {pmid40654998,
year = {2025},
author = {Ye, Z and Swenty, T and Zelhof, AC and Lynch, M},
title = {Evolutionary Analysis of Gene-expression Localization in the Model Crustacean, Daphnia pulex.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.01.651673},
pmid = {40654998},
issn = {2692-8205},
abstract = {Whole-genome sequencing provides lists of genes of putative relevance to organismal biology. However, in all metazoans, a large fraction of inferred genes has no known functions, in some cases with no orthologs in related species, and even orthology at the DNA-sequence level often not providing indisputable evidence of gene function. A first step towards resolving the functional features of gene encyclopedias in multicellular species is to evaluate the tissues in which individual genes are expressed. Here, we report on assays of expression for the full sets of protein-coding and long-noncoding RNA (lncRNA) genes across eight tissues of the microcrustacean Daphnia pulex. We also take advantage of a large database on levels of polymorphism and divergence for each gene to infer various features of selection operating on genes expressed in different tissues, including novel genes restricted to particular Daphnia lineages. In addition to generating a resource for future work on the molecular, cellular, and developmental biology of the model species D. pulex, this study highlights a number of novel findings. These include the identification of sets of genes experiencing unusual forms of positive selection, the discovery of unusual patterns of evolution in the pool of testes-specific genes, rapid turnover and sequence evolution of lncRNA genes, and the pervasive operation of selection on genes thought to be D. pulex-specific.},
}

@article {pmid40654956,
year = {2025},
author = {Schaal, KA and La Fortezza, M and Velicer, GJ},
title = {Predation, evo-devo, and historical contingency: A nematode predator drives evolution of aggregative multicellularity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.04.652091},
pmid = {40654956},
issn = {2692-8205},
abstract = {Research into the evolution of multicellularity often focuses on clonal multicellularity, yet aggregative multicellularity (AM) may respond to different drivers and is also highly interesting evolutionarily, for example in its behavioral, regulatory, morphological, and social complexity and diversity. We investigate the potential for predation to shape AM evolution across different combinations of three species comprising a multi-trophic food web. Together in a three-species community, the fruiting bacterium Myxococcus xanthus is a mesopredator, while the bacterivorous nematode Pristionchus pacificus is apex predator and the bacterium Escherichia coli is a shared basal prey for both predators. The number and morphology of M. xanthus fruiting bodies is found to respond evolutionarily to nematodes, regardless of whether E. coli is present. E. coli alone with M. xanthus tends to reduce both fruiting body formation and spore production, but adding nematodes eliminates those negative effects. M. xanthus lineages with an ancestral antibiotic-resistance mutation evolved less overall, revealing strong historical contingency and suggesting potential tradeoffs between antibiotic-resistance and responsiveness to biotic selection. Our results suggest that predation both of and by mesopredators has played important roles in the evolution of aggregative multicellularity and reveal complex inter-trophic evolutionary interactions in a relatively simple three-species food web.},
}

@article {pmid40654874,
year = {2025},
author = {Quick, SR and Bains, J and Gerdt, C and Walker, B and Goldstone, EB and Jakuszeit, T and Baggaley, AW and Croze, OA and Gerdt, JP},
title = {Chemokinesis by a microbial predator.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.01.651543},
pmid = {40654874},
issn = {2692-8205},
abstract = {Regulated motility is vital for many cells-both for unicellular microbes and for cells within multicellular bodies. Different conditions require different rates and directions of movement. For the microbial predator Capsaspora owczarzaki , its motility is likely essential for predation. This organism has been shown to prey on diverse organisms, including the schistosome parasites that co-reside with it in Biomphalaria glabrata snails. Capsaspora is also an evolutionary model for the unicellular ancestor of animals. This phylogenic placement makes Capsaspora 's motility an attractive target for understanding the evolution of motility in animal cells. Until now, little was known of how Capsaspora regulates it rate and direction of motility. Here we found that it exhibits chemokinesis (increased movement in response to chemical factors) in response to proteins released from prey cells. Chemokinesis also occurs in response to pure proteins-including bovine serum albumin. We found that this chemokinesis behavior is dependent on Capsaspora cell density, which suggests that the regulated motility is a cooperative behavior (possibly to improve cooperative feeding). We developed a mathematical model of Capsaspora motility and found that chemokinesis alone does not benefit Capsaspora predation. However, when coupled with chemotaxis (directional motility along a chemical gradient toward prey), chemokinesis may improve predation. Finally, we quantitatively analyzed Capsaspora 's previously reported chemotaxis behavior. These findings lay a foundation for characterizing the mechanisms of regulated motility in a predator of a human pathogen and a model for the ancestor of animals.},
}

@article {pmid40654712,
year = {2025},
author = {Guo, T and Wall, D},
title = {Experimental evolution of promiscuous kin recognition from a homotypic specific cell surface receptor.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.04.652116},
pmid = {40654712},
issn = {2692-8205},
abstract = {Recognizing the difference between self and nonself is a crucial step in the development of multicellularity. Myxococcus xanthus is a model organism for studying these processes during the transition from single cell to multicellular life. The polymorphic cell surface receptor TraA helps to mediate these transitions by directing cooperative behavior toward kin or clonemates. TraA is a highly specific receptor, capable of recognizing other TraA proteins with identical or nearly identical sequences by homotypic binding, but the molecular basis of recognition is poorly understood. In this study, we designed a targeted TraA library, consisting of thousands of variants, which changed 10 predicted specificity residues. By screening this library, we identified TraA variants with different combinations of substitutions that resulted in altered recognition, often leading to promiscuous TraA-TraA binding. Additionally, we identified key residues that dictate specificity between distant TraA groups and showed that changing these residues altered the recognition specificity. Furthermore, we propose a model to explain how TraA recognition specificity evolved through the generation of intermediate promiscuous variants driven by reward/punishment interactions. Our results highlight the malleable nature of the TraA variable domain involved in specificity, shedding light on the molecular and evolutionary basis of social recognition in M. xanthus .},
}

@article {pmid40634599,
year = {2025},
author = {Coyle, MC and King, N},
title = {The evolutionary foundations of transcriptional regulation in animals.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
pmid = {40634599},
issn = {1471-0064},
abstract = {The development of a single-celled zygote into a complex, multicellular animal is directed by transcription factors and regulatory RNAs that coordinate spatio-temporal gene expression patterns. Given the morphological complexity of animals, some prior work has hypothesized that the origin of animals required the evolution of unique and markedly complex transcriptional regulatory mechanisms. Such postulated animal innovations include the evolution of greater numbers of transcription factors, new transcription factor families, distal enhancers and the emergence of long non-coding RNAs. Here, we revisit these explanations in light of new genomic and functional data from diverse early-branching animals and close relatives of animals, which provide essential phylogenetic context for reconstructing the origin of animals. These experimental models also offer examples of how some animal developmental pathways were built from core mechanisms inherited from their protistan ancestors. These new data provide fresh perspectives on whether animal origins entailed fundamental innovations in transcriptional regulation or whether, alternatively, a gradual accumulation of smaller changes sufficed to generate the complex developmental and cell differentiation mechanisms of early animals.},
}

@article {pmid40600879,
year = {2025},
author = {Johnson, NC and Marín, C},
title = {Functional team selection as a framework for local adaptation in plants and their belowground microbiomes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf137},
pmid = {40600879},
issn = {1751-7370},
abstract = {Multicellular organisms are hosts to diverse communities of smaller organisms known as microbiomes. Plants have distinctive microbiomes that can provide important functions related to nutrition, defense, and stress tolerance. Empirical studies provide convincing evidence that in some -but not all - circumstances, belowground microbiomes help plants adapt to their local environment. The purpose of this review is to develop functional team selection (FTS) as a framework to help predict the conditions necessary for root microbiomes to generate local adaptation for their plant hosts. FTS envisions plants and their microbiomes as complex adaptive systems, and plant adaptations as emergent properties of these systems. If plants have the capacity to recognize and cultivate beneficial microbes and suppress pathogens, then it is possible for plants to evolve the capacity to gain adaptations by curating their microbiome. In resource-limited and stressful environments, the emergent functions of complex microbial systems may contribute to positive feedback linked to plant vigor, and ultimately, local adaptation. The key factors in this process are: 1) selective force, 2) host constitution, 3) microbial diversity, and 4) time. There is increasing interest in harnessing beneficial microbial interactions in agriculture and many microbial growth-promoting products are commercially available, but their use is controversial because a large proportion of these products fail to consistently enhance plant growth. The FTS framework may help direct the development of durable plant-microbiome systems that enhance crop production and diminish pathogens. It may also provide valuable insights for understanding and managing other kinds of host-microbe systems.},
}

@article {pmid40588585,
year = {2025},
author = {Mondo, SJ and Grigoriev, IV},
title = {A genomic perspective on fungal diversity and evolution.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40588585},
issn = {1740-1534},
abstract = {Originating from aquatic unicellular ancestors, over the course of ~1 billion years, the fungi have evolved to occupy nearly all aerobic environments on the planet, diversified into millions of different 'species' and have developed complex multicellular structures. Their relatively small, simple genomes have facilitated massive-scale sequencing and allowed us to explore genome evolution across an ancient eukaryotic kingdom. With thousands of genomes from diverse lineages now available, this Review will discuss insights into fungal biology and evolution gleaned with genomics and other multi-omics approaches. Using published genomes available through GenBank and the Joint Genome Institute's MycoCosm platform, we generated kingdom-wide phylogenies and used them to highlight how fungal genomes have changed over time. With this phylogeny as a guide, we also discuss major evolutionary transitions that occurred across the fungal kingdom. Although progress has been made, these efforts are hampered by biases in genome representation and limited characterization of gene functions. Here, we discuss these challenges and possible future directions to address them, including initiatives to characterize conserved genes of unknown function and scale up sequencing towards 10,000 annotated fungal genomes.},
}

@article {pmid40584024,
year = {2025},
author = {Jiang, SP and Lin, BQ and Zhou, XQ and Li, MH and Feng, ZC and Qin, YY and Lin, SQ and Zhou, ZQ and Peng, Y and Li, L},
title = {Airway Organoid Models as Pivotal Tools for Unraveling Molecular Mechanisms and Therapeutic Targets in Respiratory Diseases: A Literature Review.},
journal = {Therapeutics and clinical risk management},
volume = {21},
number = {},
pages = {975-986},
pmid = {40584024},
issn = {1176-6336},
abstract = {Respiratory inflammatory and infectious diseases continue to impose a substantial global health burden, compounded by persistent gaps in understanding their pathogenic mechanisms and limited therapeutic advancements. To address these challenges, this review systematically analyzed literature from PubMed, Web of Science, and Scopus databases (2005-2025) to evaluate the evolution and applications of airway organoid models in respiratory disease research. Key findings include: (1) the convergence of traditional culture techniques with advanced methodologies - including 3D matrix embedding, bioprinting and organoids-on-chips technologies - has enabled unprecedented recapitulation of human airway architecture and multicellular interactions; (2) these novel models provide unique insights into disease pathogenesis, host-microbe dynamics, and drug response variability; (3) the inherent capacity to maintain native cellular diversity and disease-associated phenotypes positions airway organoids as crucial platforms for personalized medicine approaches. Collectively, these advances establish airway organoids as transformative tools that bridge conventional in vitro models and clinical reality. Looking ahead, coupling organs-on-chips platforms with microgravity culture and single-cell lineage tracing will catalyze fundamental breakthroughs in respiratory disease research.},
}

@article {pmid40568125,
year = {2025},
author = {Katharios-Lanwermeyer, S and Zarrella, TM and Godsil, M and Severin, S and Casiano, AE and Tai, CH and Khare, A},
title = {Stenotrophomonas maltophilia exhibits defensive multicellularity in response to a Pseudomonas aeruginosa quorum sensing molecule.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.02.651457},
pmid = {40568125},
issn = {2692-8205},
abstract = {Microorganisms commonly exist in polymicrobial communities, where they can respond to interspecies secreted molecules by altering behaviors and physiology, however, the underlying mechanisms remain underexplored. Here we investigated interactions between Stenotrophomonas maltophilia and Pseudomonas aeruginosa , co-infecting opportunistic pathogens found in pneumonia and chronic lung infections, including in cystic fibrosis. We found that S. maltophilia forms robust protective multicellular aggregates upon exposure to P. aeruginosa secreted factors. Experimental evolution for lack of aggregation selected for fimbrial mutations and we found that fimbriae are required on both interacting S. maltophilia cells for aggregation. Untargeted metabolomics and targeted validations revealed that the quorum sensing molecule Pseudomonas quinolone signal (PQS) directly induced S. maltophilia aggregation, and co-localized with the aggregates. Further, in co-culture with P. aeruginosa , wild-type S. maltophilia formed aggregates, resulting in up to 75-fold increased survival from P. aeruginosa competition compared to fimbrial mutants. Finally, multiple other bacterial species similarly aggregated upon exposure to P. aeruginosa exoproducts, indicating a more general response. Collectively, our work identifies a novel multispecies interaction where a quorum sensing molecule from a co-infecting pathogen is sensed as a 'danger' signal, thereby inducing a protective multicellular response.},
}

@article {pmid40566225,
year = {2025},
author = {Hale, ZF and Cánez, GA and Michaels, TCT},
title = {Fisher Information and the Dynamics of Multicellular Ageing.},
journal = {Entropy (Basel, Switzerland)},
volume = {27},
number = {6},
pages = {},
pmid = {40566225},
issn = {1099-4300},
support = {SNF 219703/SNSF_/Swiss National Science Foundation/Switzerland ; },
abstract = {Information theory has long been integrated into the study of biological ageing, for example, in examining the roles of genetic and epigenetic fidelity in cellular and organismal longevity. Here, we introduce a theoretical model that interprets ageing in multicellular systems through the lens of Fisher information. Previous theories have suggested that the ageing of multicellular organisms is an inevitable consequence of the inherent tension between individual cell reproduction and the homeostasis of the multicellular system. Utilising concepts from information theory and statistical mechanics, we show that Fisher information parametrises the dynamics of this tension through non-monotonic behaviour, which depends on an optimal balance of competition and cooperation between cells. Moreover, Fisher information suggests that the ability to infer true biological age from a sample evolves through complex dynamics over an organism's lifespan.},
}

@article {pmid40555192,
year = {2025},
author = {Parker, J and Pennell, M},
title = {The cellular substrate of evolutionary novelty.},
journal = {Current biology : CB},
volume = {35},
number = {12},
pages = {R626-R637},
pmid = {40555192},
issn = {1879-0445},
support = {R35 GM151348/GM/NIGMS NIH HHS/United States ; },
mesh = {*Biological Evolution ; Animals ; Phenotype ; *Gene Expression ; },
abstract = {A major challenge in biology is comprehending how complex multicellular novelties evolve. Central to this problem is explaining how qualitatively new phenotypic traits - typically the focus of comparative developmental and macroevolutionary studies above the species level - can become established through population genetic processes. Here, we suggest that a resolution may be found by acknowledging the fundamental entities from which functional organismal phenotypes are constructed. We argue that these are not genes, proteins or cell types, but rather gene expression programs (GEPs): sets of co-expressed transcripts that collectively encode cellular subfunctions. We advance that, because GEPs are the smallest, elemental functional units underlying phenotypes, it follows that they represent the substrate upon which population genetic processes must act to explain the origin of evolutionary novelty at the cellular level and above. Novelty arises through the evolution of novel GEPs, through novel synergisms between GEPs that become co-expressed within the same cell or through interactions between different GEPs juxtaposed in cooperating cells within organs. The revolution in single cell biology offers the chance to trace evolution at the resolution of GEPs in populations and across clades, potentially unifying our view of multicellular phenotypic evolution.},
}

*Biological Evolution
Animals
Phenotype
*Gene Expression

@article {pmid40544609,
year = {2025},
author = {Tsikolia, N and Nguyen, DTL and Tee, YH},
title = {Mechanisms of left-right symmetry breaking across scales.},
journal = {Current opinion in cell biology},
volume = {95},
number = {},
pages = {102564},
doi = {10.1016/j.ceb.2025.102564},
pmid = {40544609},
issn = {1879-0410},
mesh = {Animals ; *Body Patterning ; Humans ; Cilia/metabolism ; Cell Polarity ; },
abstract = {Establishment of left-right (LR) asymmetry relies on a multistep interplay of molecular signaling and physical processes. Initial LR symmetry breaking in several model vertebrates was shown to take place at the LR organizer (LRO) where chiral rotation of monocilia produces a leftward fluid flow. Subsequent bending of sensory cilia triggers Pkd2-channel-mediated calcium transients which in turn are required for induction of asymmetrical signaling upstream of morphological asymmetries, emphasizing the role of mechanosensation in flow detection. Crucially, unidirectional flow and its detection were suggested to require cellular-scale asymmetries including planar cell polarity-mediated posterior position and ultrastructural chirality of motile cilia as well as asymmetric Pkd2 localization within sensory cilia. Alternative mechanisms of LR symmetry breaking operate in models like the chick embryo, where asymmetry of gene expression is preceded by leftward primitive node rotation suggesting mechanisms based on cytoskeletal chirality known from invertebrate models including Caenorhabditis elegans and fruit fly. Investigation of chirality at the cellular level suggests that chirality of components of cytoskeleton, particularly actin filaments, is amplified by distinct modules based i.e. on formin-actin and myosin-actin interactions which drive intracellular swirling and cortical flow, providing a basis for LR asymmetry. Cellular chirality can organize LR asymmetry of multicellular behavior as observed in the chiral alignment of fibroblasts. The integration of molecular, cellular, and tissue-scale chirality highlights conserved and divergent mechanisms underpinning LR symmetry breaking across species. Unraveling these processes may illuminate pathways connecting cytoskeletal dynamics to organismal asymmetry, offering insights into development and evolution.},
}

Animals
*Body Patterning
Humans
Cilia/metabolism
Cell Polarity

@article {pmid40540574,
year = {2025},
author = {Narayanasamy, N and Bingham, E and Fadero, T and Bozdag, GO and Ratcliff, WC and Yunker, P and Thutupalli, S},
title = {Metabolically driven flows enable exponential growth in macroscopic multicellular yeast.},
journal = {Science advances},
volume = {11},
number = {25},
pages = {eadr6399},
pmid = {40540574},
issn = {2375-2548},
support = {R35 GM138030/GM/NIGMS NIH HHS/United States ; R35 GM138354/GM/NIGMS NIH HHS/United States ; T32 GM142616/GM/NIGMS NIH HHS/United States ; },
mesh = {*Saccharomyces cerevisiae/growth & development/metabolism ; Models, Biological ; },
abstract = {The ecological and evolutionary success of multicellular lineages stems substantially from their increased size relative to unicellular ancestors. However, large size poses biophysical challenges, especially regarding nutrient transport: These constraints are typically overcome through multicellular innovations. Here, we show that an emergent biophysical mechanism-spontaneous fluid flows arising from metabolically generated density gradients-can alleviate constraints on nutrient transport, enabling exponential growth in nascent multicellular clusters of yeast lacking any multicellular adaptations for nutrient transport or fluid flow. Beyond a threshold size, the metabolic activity of experimentally evolved snowflake yeast clusters drives large-scale fluid flows that transport nutrients throughout the cluster at speeds comparable to those generated by ciliary actuation in extant multicellular organisms. These flows support exponential growth at macroscopic sizes that theory predicts should be diffusion limited. This demonstrates how simple physical mechanisms can act as a "biophysical scaffold" to support the evolution of multicellularity by opening up phenotypic possibilities before genetically encoded innovations.},
}

*Saccharomyces cerevisiae/growth & development/metabolism
Models, Biological

@article {pmid40540527,
year = {2025},
author = {Bailey, DM and Macefield, VG and Poole, DC},
title = {Physiology of nitrogen: A life or death matter.},
journal = {Experimental physiology},
volume = {},
number = {},
pages = {},
doi = {10.1113/EP092946},
pmid = {40540527},
issn = {1469-445X},
support = {WM170007//Royal Society Wolfson Research Fellowship/ ; //Elizabeth Chapin Burke Chair in Health and Human Sciences/ ; },
abstract = {With each breath, four out of every five molecules we inspire are nitrogen (N2), since this gas constitutes ∼80% of the atmospheric air that surrounds us. Despite its abundance and unlike molecular oxygen, N2 has traditionally held less appeal among physiologists given its lack of reactivity and corresponding inability to support combustion or life, rendering it metabolically nugatory. The controversial application of N2 asphyxiation for the inhumane purposes of human execution of convicted criminals and assisted suicide of a terminally ill patient has thrust this important gas into the scientific and public spotlight, sparking widespread condemnation. In the current review, we take an opportunity to explore the molecular bases and clinical consequences linked to the Janus-faced physiology of N2 to better explain its life-and-death qualities. We highlight the complex history that led to its discovery and the physio-geochemical evolution of Earth's uniquely N2-rich atmosphere, including intimate links with oxygen (O2), another life-and-death homonuclear diatomic gas that preceded aerobic respiration and the emergence of complex multicellular life. Diving deep into N2's quantum state, we expose its unique physiochemical properties to better understand why this gas is metabolically inert and physiologically deadly when in excess and especially to the exclusion of O2. We apply this integrated physiological knowledge to further inform the controversial public debate and directly challenge the misconceived notion that N2 gas asphyxiation offers a quick, indolent and dignified death for the inhumane purposes of human execution and assisted suicide.},
}

@article {pmid40539330,
year = {2025},
author = {Krishnan, H and Muzaffar, S and Sharma, S and Ramya, V and Ghosh, A and Sowdhamini, R and Raghu, P},
title = {Conserved biochemical activity and function of phosphatidylinositol 5-phosphate 4-kinase regulates growth and development.},
journal = {Journal of cell science},
volume = {138},
number = {13},
pages = {},
doi = {10.1242/jcs.263881},
pmid = {40539330},
issn = {1477-9137},
support = {RTI 4006//Department of Atomic Energy, Government of India (DAE)/ ; IA/S/14/2/501540//The Wellcome Trust DBT India Alliance/ ; RTI 4006//Department of Atomic Energy, Government of India/ ; IA/S/14/2/501540//Wellcome-DBT India Alliance/ ; BT/PR40187/BTIS/137/9/2021//Department of Biotechnology/ ; IBAB/MSCB/182/2022//Institute of Bioinformatics and Applied Biotechnology/ ; JBR/2021/000006//Institute of Bioinformatics and Applied Biotechnology/ ; //Science and Engineering Research Board/ ; },
mesh = {Animals ; *Phosphotransferases (Alcohol Group Acceptor)/metabolism/genetics/chemistry ; Humans ; *Porifera/enzymology/genetics ; Drosophila melanogaster/growth & development/enzymology ; Signal Transduction ; Phosphatidylinositol Phosphates/metabolism ; Phylogeny ; },
abstract = {Co-ordination of function between multiple cells, mediated by hormones or growth factors, is a crucial requirement for multicellularity. Phosphoinositides, generated by lipid kinase activity, are second messengers that mediate such signalling. Phosphatidylinositol 5-phosphate 4-kinase (PIP4K) is a lipid kinase that phosphorylates phosphatidylinositol 5-phosphate (PI5P) to generate phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2]. A comprehensive bioinformatics analysis of the tree of life, revealed that PIP4K is a metazoan-specific enzyme, but with homologues in choanoflagellates. We find that PIP4K from the sponge Amphimedon queenslandica (AqPIP4K), regarded as the earliest evolved metazoan, shows biochemical activity highly conserved with human PIP4K. Further, AqPIP4K was able to rescue the reduced cell size, growth and development of a Drosophila PIP4K mutant. These phenotypes are regulated through activity of the insulin receptor, a member of the receptor tyrosine kinase family, that is unique to metazoans. Overall, our work defines PIP4K as part of a signal transduction motif required to regulate receptor tyrosine kinase signalling for intercellular communication in the earliest forms of metazoans.},
}

Animals
*Phosphotransferases (Alcohol Group Acceptor)/metabolism/genetics/chemistry
Humans
*Porifera/enzymology/genetics
Drosophila melanogaster/growth & development/enzymology
Signal Transduction
Phosphatidylinositol Phosphates/metabolism
Phylogeny

@article {pmid40532703,
year = {2025},
author = {Glotzer, M},
title = {A key role for centralspindlin and Ect2 in the development of multicellularity and the emergence of Metazoa.},
journal = {Current biology : CB},
volume = {35},
number = {13},
pages = {3251-3262.e1},
pmid = {40532703},
issn = {1879-0445},
support = {R35 GM127091/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Cytokinesis/physiology ; Phylogeny ; *Biological Evolution ; *Kinesins/genetics/metabolism ; },
abstract = {Obligate multicellularity evolved at least five times in eukaryotes, including at the origin of Metazoa, 650-850 million years ago.[1][,][2][,][3][,][4] While obligate multicellularity could result from cell-cell adhesion, aggregation-based mechanisms for multicellularity are susceptible to mixing with genetically unrelated cells.[5] Alternatively, or in addition, multicellularity can emerge from a series of mitotic divisions followed by incomplete cytokinesis, resulting in a cluster of cells connected by intercellular bridges.[6][,][7][,][8][,][9][,][10] In addition to being multicellular, all five clades of extant Metazoa are diploid organisms that reproduce via eggs and sperm (anisogamy).[7][,][11][,][12][,][13] Thus, by inference, the last common ancestor (LCA) of Metazoa could produce sperm and eggs and could cleave fertilized eggs into smaller cells that self-organize into fertile organisms[14]-processes that directly involve the cytokinetic machinery. Here, I present an integrated analysis into the emergence of three regulators of cytokinesis. Phylogenetic analysis and structural modeling indicate that Kif23, Cyk4, and Ect2 are highly conserved across all metazoans. These proteins cooperate to link the plane of cell division with the position of the spindle during anaphase and subsequently nucleate the assembly of stable intercellular bridges,[15][,][16][,][17][,][18] structures prevalent in metazoan germ lines.[7] The closest relatives of Metazoa, Choanoflagellata, encode orthologs of Kif23 and Ect2. Choanoflagellate species variably encode proteins homologous to Cyk4, a subset of which are predicted to interact with Kif23. These findings, in light of prior knowledge, suggest that the evolutionary refinement of these three cytokinetic regulators was a proximal prerequisite for the evolution of defining features of Metazoa.},
}

Animals
*Cytokinesis/physiology
Phylogeny
*Biological Evolution
*Kinesins/genetics/metabolism

@article {pmid40531620,
year = {2025},
author = {Mathavarajah, S and Chipurupalli, S and Habib, EB and Kim, WD and Aoki, MM and Corkery, DP and Whelan, KIT and Lukacs, J and Erkan, M and Martinez, VD and Smith, KS and Montgomery, SB and Salsman, J and Huber, RJ and Dellaire, G},
title = {The evolutionarily conserved PRP4K-CHMP4B/vps32 splicing circuit regulates autophagy.},
journal = {Cell reports},
volume = {44},
number = {7},
pages = {115870},
doi = {10.1016/j.celrep.2025.115870},
pmid = {40531620},
issn = {2211-1247},
mesh = {*Autophagy/genetics ; Humans ; *Dictyostelium/metabolism/genetics ; *RNA Splicing ; *Endosomal Sorting Complexes Required for Transport/metabolism/genetics ; Lysosomes/metabolism ; Autophagosomes/metabolism ; *Protozoan Proteins/metabolism/genetics ; *Protein Serine-Threonine Kinases/metabolism/genetics ; *Evolution, Molecular ; },
abstract = {The pre-mRNA processing factor 4 kinase (PRP4K) is an essential gene in animal cells, making interrogation of its function challenging. Here, we report characterization of a viable knockout model of PRP4K in the social amoeba Dictyostelium discoideum, revealing a function for PRP4K in splicing events controlling autophagy. When prp4k knockout amoebae undergo multicellular development, we observe defects in differentiation linked to abnormal autophagy and aberrant secretion of stalk cell inducer c-di-GMP. Autophagosome-lysosome fusion is impaired after PRP4K loss in both human cell lines and amoebae. PRP4K loss results in mis-splicing and reduced expression of the ESCRT-III gene CHMP4B in human cells and its ortholog vps32 in Dictyostelium, and re-expression of CHMP4B or Vps32 cDNA (respectively) restores normal autophagosome-lysosome fusion in PRP4K-deficient cells. Thus, our work reveals a PRP4K-CHMP4B/vps32 splicing circuit regulating autophagy that is conserved over at least 600 million years of evolution.},
}

*Autophagy/genetics
Humans
*Dictyostelium/metabolism/genetics
*RNA Splicing
*Endosomal Sorting Complexes Required for Transport/metabolism/genetics
Lysosomes/metabolism
Autophagosomes/metabolism
*Protozoan Proteins/metabolism/genetics
*Protein Serine-Threonine Kinases/metabolism/genetics
*Evolution, Molecular

@article {pmid40530903,
year = {2025},
author = {Fotedar, R and Zalar, P and Al Malaki, A and Al Zeyara, A and Kaul, R and Kolecka, A and Fell, JW and Boekhout, T and Gunde-Cimerman, N},
title = {Euryhaline Black Yeasts From the Arabian Gulf: Descriptions of Salinomyces qatarensis sp. nov. and Hortaea werneckii Genotypic Variations.},
journal = {IUBMB life},
volume = {77},
number = {6},
pages = {e70026},
doi = {10.1002/iub.70026},
pmid = {40530903},
issn = {1521-6551},
support = {NPRP 6-647-1-127//Qatar Foundation/ ; MRIC UL I0-0022//Slovenian Research and Innovation Agency: Infrastructural Centre Mycosmo:/ ; P1-0198,P4-0432//Slovenian Research and Innovation Agency: Infrastructural Centre Mycosmo:/ ; },
mesh = {Phylogeny ; *Ascomycota/genetics/classification/isolation & purification ; Genotype ; Genetic Variation ; Seawater/microbiology ; Salinity ; DNA, Fungal/genetics ; RNA Polymerase II/genetics ; },
abstract = {The Arabian Gulf surrounding Qatar is an oligotrophic marine environment characterized by extreme conditions, such as increased water temperatures and high salinity compared to other semi-enclosed seas, such as the Mediterranean Sea. Thirty-six black yeast-like isolates were obtained from marine waters surrounding Qatar, representing 4% of all isolated yeasts. DNA sequence analysis of the internal transcribed spacers (ITS1, ITS2), the 5.8S rRNA gene, and the D1/D2 domains of the LSU rDNA identified 20 isolates as Hortaea werneckii, and 15 (75%) of them represent previously unknown genotypes with a wide NaCl tolerance at 37°C. In addition, 16 meristematic black yeast-like cultures were isolated that grew as multi-cellular bodies and reproduced by endoconidiation. Phylogenetic analysis based on the D1/D2 domains of LSU rDNA, partial sequences of the second largest subunit of RNA polymerase II (RPB2) and translation elongation factor 1-alpha (TEF) of selected representative strains of Dothideomycetes and of morphologically similar taxa, Pseudotaeniolina globosa and Trimmatostroma salinum, supported the proposal of meristematic black yeast-like cultures as a new species, Salinomyces qatarensis sp. nov., within Teratosphaeriaceae, Mycosphaerellales. The holotype is designated as CBS 150510, with ex-type strains EXF-15246 and QCC/Y38/18, and the species is registered in Mycobank as MB#848869. In addition, based on the above molecular analysis, a new combination was proposed for an euryhaline fungus from Mediterranean salterns, Trimmatostroma salinum, into the genus Verrucocladosporium as V. salinum, MB#856063. This study increases our knowledge of the distribution and genetic diversity of Hortaea werneckii, the etiological agent of tinea nigra. In addition, the description of S. qatarensis and the combination of euryhaline T. salinum to Verrucocladosporium provides support for halotolerance as one of the traits in Dothideomycetes.},
}

Phylogeny
*Ascomycota/genetics/classification/isolation & purification
Genotype
Genetic Variation
Seawater/microbiology
Salinity
DNA, Fungal/genetics
RNA Polymerase II/genetics

@article {pmid40525847,
year = {2025},
author = {Kroos, L and Wall, D and Islam, ST and Whitworth, DE and Muñoz-Dorado, J and Higgs, PI and Singer, M and Mauriello, EM and Treuner-Lange, A and Søgaard-Andersen, L and Kaimer, C and Elías-Arnanz, M and Stojković, EA and Müller, R and Volz, C and Velicer, GJ and Nan, B},
title = {Milestones in the development of Myxococcus xanthus as a model multicellular bacterium.},
journal = {Journal of bacteriology},
volume = {207},
number = {7},
pages = {e0007125},
pmid = {40525847},
issn = {1098-5530},
mesh = {*Myxococcus xanthus/physiology/genetics/growth & development/cytology ; History, 20th Century ; History, 21st Century ; Models, Biological ; },
abstract = {From the humblest of beginnings (i.e. a pile of dry cow dung) over 80 years ago, the Gram-negative bacterium Myxococcus xanthus has emerged as a premier model system for studying diverse fields of bacteriology, including multicellular development, sporulation, motility, cell-envelope biogenesis, spatiotemporal regulation, signaling, photoreception, kin recognition, social evolution, and predation. As the flagship representative of myxobacteria found in varied terrestrial and aquatic environments, M. xanthus research has evolved into a collaborative global effort, as reflected by the contributions to this article. In celebration of the upcoming 50th anniversary of the International Conference on the Biology of Myxobacteria, this review highlights the historical and ongoing contributions of M. xanthus as a multifaceted model bacterium.},
}

*Myxococcus xanthus/physiology/genetics/growth & development/cytology
History, 20th Century
History, 21st Century
Models, Biological

@article {pmid40523936,
year = {2025},
author = {Muthukumar, G and Weissman, JS},
title = {Shaping the composition of the mitochondrial outer membrane.},
journal = {Nature cell biology},
volume = {27},
number = {6},
pages = {890-901},
pmid = {40523936},
issn = {1476-4679},
support = {T32GM007287//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
mesh = {*Mitochondrial Membranes/metabolism/chemistry ; Humans ; Animals ; *Mitochondria/metabolism ; *Mitochondrial Proteins/metabolism/chemistry/genetics ; Endoplasmic Reticulum/metabolism ; },
abstract = {Mitochondria are critical double-membraned organelles that act as biosynthetic and bioenergetic cellular factories, with the outer membrane providing an interface with the rest of the cell. Mitochondrial outer membrane proteins regulate a variety of processes, including metabolism, innate immunity and apoptosis. Although the biophysical and functional diversity of these proteins is highly documented, the mechanisms of their biogenesis and the integration of that into cellular homeostasis are just starting to take shape. Here, focusing on α-helical outer membrane proteins, we review recent insights into the mechanisms of synthesis and cytosolic chaperoning, insertion and assembly in the lipid bilayer, and quality control of unassembled or mislocalized transmembrane domains. We further discuss the role convergent evolution played in this process, comparing key biogenesis players from lower eukaryotes, including yeast and trypanosomes, with multicellular metazoan systems, and draw comparisons with the endoplasmic reticulum biogenesis system, in which membrane proteins face similar challenges.},
}

*Mitochondrial Membranes/metabolism/chemistry
Humans
Animals
*Mitochondria/metabolism
*Mitochondrial Proteins/metabolism/chemistry/genetics
Endoplasmic Reticulum/metabolism

@article {pmid40523311,
year = {2025},
author = {Chen, Z and Zhang, X and Deng, M and Li, C and Nguyen, TT and Liu, M and Dou, K and Ishibashi, T and Wang, J and Yan, Y},
title = {Epigenetic reprogramming induced by key metabolite depletion is an evolutionarily ancient path to tumorigenesis.},
journal = {Disease models & mechanisms},
volume = {18},
number = {6},
pages = {},
pmid = {40523311},
issn = {1754-8411},
support = {GRF16103620//University Grants Committee/ ; T13-602/21N//University Grants Committee/ ; GRF16104324//University Grants Committee/ ; JCYJ20200109140201722//Science, Technology and Innovation Commission of Shenzhen Municipality/ ; Z0428//Hong Kong University of Science and Technology/ ; 32170548//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Carcinogenesis/genetics/pathology/metabolism ; Humans ; *Epigenesis, Genetic ; DNA Methylation/genetics ; *Drosophila melanogaster/genetics/metabolism ; Histones/metabolism ; Methionine/metabolism ; Acetylation ; Acetyl Coenzyme A/metabolism ; Mutation/genetics ; S-Adenosylmethionine/metabolism ; *Cellular Reprogramming/genetics ; Neoplasms/genetics/pathology/metabolism ; *Biological Evolution ; *Evolution, Molecular ; },
abstract = {Tumor growth is a challenge for multicellular life forms. Contrary to human tumors, which take years to form, tumors in short-living species can arise within days without accumulating multiple mutations, raising the question whether the paths to tumorigenesis in diverse species have any commonalities. In a fly tumor model caused by loss of cell polarity genes, we identified two key metabolic changes: first, systemic depletion of acetyl-CoA leading to a reduction in histone acetylation levels and stochastic silencing of actively transcribed genes; and second, defects in the methionine cycle causing systemic depletion of S-adenosyl methionine, which further reduces histone methylation levels and causes stochastic activation of transposons. Perturbation of the methionine metabolic process inhibits tumor growth. To understand the evolutionary origin of tumorigenesis, we performed comparative studies of fly and human tumors and found that human tumors with metabolic signatures similar to those of fly tumors have a lower mutational load, younger patient age and lower DNA methylation levels. This study indicates that depletion of key metabolites is an evolutionarily ancient driving force for tumorigenesis.},
}

Animals
*Carcinogenesis/genetics/pathology/metabolism
Humans
*Epigenesis, Genetic
DNA Methylation/genetics
*Drosophila melanogaster/genetics/metabolism
Histones/metabolism
Methionine/metabolism
Acetylation
Acetyl Coenzyme A/metabolism
Mutation/genetics
S-Adenosylmethionine/metabolism
*Cellular Reprogramming/genetics
Neoplasms/genetics/pathology/metabolism
*Biological Evolution
*Evolution, Molecular

@article {pmid40517085,
year = {2025},
author = {Schoenle, A and Francis, O and Archibald, JM and Burki, F and de Vries, J and Dumack, K and Eme, L and Florent, I and Hehenberger, E and Hoffmeyer, TT and Irisarri, I and Lara, E and Leger, MM and Lukeš, J and Massana, R and Mathur, V and Nitsche, F and Strassert, JFH and Worden, AZ and Yurchenko, V and Del Campo, J and Waldvogel, AM},
title = {Protist genomics: key to understanding eukaryotic evolution.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2025.05.004},
pmid = {40517085},
issn = {0168-9525},
abstract = {All eukaryotes other than animals, plants, and fungi are protists. Protists are highly diverse and found in nearly all environments, with key roles in planetary health and biogeochemical cycles. They represent the majority of eukaryotic diversity, making them essential for understanding eukaryotic evolution. However, these mainly unicellular, microscopic organisms are understudied and the generation of protist genomes lags far behind most multicellular lineages. Current genomic methods, which are primarily designed for animals and plants, are poorly suited for protists. Advancing protist genome research requires reevaluating plant- and animal-centric genomic standards. Future efforts must leverage emerging technologies and bioinformatics tools, ultimately enhancing our understanding of eukaryotic molecular and cell biology, ecology, and evolution.},
}

@article {pmid40509663,
year = {2025},
author = {van Dijk, JR and Geelhoed, JS and Geerlings, N and Choyikutty, JA and Boschker, HTS and Verbruggen, E and Meysman, FJR},
title = {Inactive "Ghost" Cells Do Not Affect Motility and Long-Range Electron Transport in Filamentous Cable Bacteria.},
journal = {Environmental microbiology},
volume = {27},
number = {6},
pages = {e70117},
pmid = {40509663},
issn = {1462-2920},
support = {G038819N//Fonds Wetenschappelijk Onderzoek/ ; S004523N//Fonds Wetenschappelijk Onderzoek/ ; //Universiteit Antwerpen/ ; PRINGLE 101046719//HORIZON EUROPE European Innovation Council/ ; EMBO ALTF 102-2023//European Molecular Biology Organization/ ; },
mesh = {Electron Transport ; *Bacteria/metabolism/cytology ; Oxidation-Reduction ; Sulfur/metabolism ; *Bacterial Physiological Phenomena ; },
abstract = {Cable bacteria are multicellular filamentous microorganisms that perform electrogenic sulphur oxidation over centimetre-long distances. These filaments contain so-called "ghost cells", which display a highly reduced cytoplasmic content and a lack of metabolic activity. However, the origin and abundance of these ghost cells are not well understood, raising questions about their formation and potential impact on the functioning of the entire filaments. Here, we quantified the abundance of ghost cells in cable bacteria via a targeted propidium iodide staining technique and investigated their morphology and possible origin. Microscopy revealed that ghost cells are present in filaments under in situ conditions, and hence, they are not an artefact from filament sampling. Interestingly, filaments containing ghost cells retained gliding motility, as well as the capacity for long-distance electron transport, thus suggesting that the functionality of the filament as a whole remains largely unaffected by the presence of these ghost cells. Noteworthy is the higher frequency of ghost cells near the ends of filaments, and within filament fragments retrieved from oxic environments. Our findings provide new insights into the adaptive strategies of filamentous bacteria, highlighting their ability to maintain functionality at the organism level despite the fact that some individual cells are no longer metabolically active.},
}

Electron Transport
*Bacteria/metabolism/cytology
Oxidation-Reduction
Sulfur/metabolism
*Bacterial Physiological Phenomena

@article {pmid40509562,
year = {2025},
author = {Terraza-Silvestre, E and Bandera-Linero, J and Oña-Sánchez, D and Pimentel-Muiños, FX},
title = {Unconventional role of ATG16L1 in the control of ATP compartmentalization during apoptosis.},
journal = {Autophagy},
volume = {21},
number = {9},
pages = {2085-2087},
doi = {10.1080/15548627.2025.2519051},
pmid = {40509562},
issn = {1554-8635},
abstract = {The autophagy mediator ATG16L1 forms part of a complex that is essential for MAP1LC3/LC3 lipidation and autophagosome formation in the canonical macroautophagic/autophagic pathway. However, ATG16L1 is also involved in unconventional activities where LC3 becomes lipidated in single-membrane structures unrelated to double-membrane autophagosomes. Such atypical activities usually require the C-terminal domain of the molecule that includes 7 WD40-type repetitions (WD40 domain, WDD). The WDD acts as a docking site for upstream inducers that engage the LC3 lipidation ability of ATG16L1 in alternative membrane compartments. Given that this domain is absent in the yeast Atg16 ortholog, an intriguing idea proposes that it was added to the primitive protein during evolution to perform new physiological roles required by the appearance of multicellularity. Identification of such atypical activities and their physiological implications at the organismal level are important issues that remain to be clarified. In a recent report we describe an unconventional autophagic pathway that restrains the immunogenic potential of apoptosis, a key feature of homeostatic and developmentally regulated cell death in multicellular organisms. This signaling route emanates from apoptotic mitochondria and induces the formation of single-membrane, LC3-positive vesicles through a mechanism that requires the WDD of ATG16L1. The induced vesicles sequester ATP to inhibit the amount of ATP released from apoptotic cells and, consequently, prevent the activation of co-cultured phagocytes. Thus, this is a pathway that contributes to maintain the immunosilent nature of apoptotic cell death.},
}

@article {pmid40499887,
year = {2025},
author = {Just, BB and de Farias, ST},
title = {Major transitions in the physiological machinery of cognition.},
journal = {Bio Systems},
volume = {254},
number = {},
pages = {105517},
doi = {10.1016/j.biosystems.2025.105517},
pmid = {40499887},
issn = {1872-8324},
mesh = {Animals ; Humans ; *Biological Evolution ; *Brain/physiology ; *Cognition/physiology ; Neurons/physiology ; },
abstract = {Cognition refers to the processes organisms use to interact with and understand their world, a fundamental biological function present in all cellular life. As with any biological process, cognitive capacity and its underlying mechanisms vary widely across species. Evolution has shaped cognition, leading to increasingly complex forms in certain lineages. The concept of evolutionary transitions, introduced by Maynard-Smith and Szathmary, describes major shifts in biological organization. In 2021, Ginsburg & Jablonka, and in 2023, Barron and collaborators explored cognitive transitions within neural systems, the evolution of cognition in aneural organisms remains understudied. Building on prior frameworks, we analyze cognitive transitions in the aneural realm, focusing on the physiological machinery responsible for cognition. The first transition is the emergence of cognitive machinery in prokaryotic cells (cellular cognition), followed by its complexification in eukaryotes (complex cellular cognition). The third transition marks cognition based on multiple cells (multicellular-based cognition). The fourth is the development of neurons and a diffuse nervous system (decentralized neural cognition), followed by its centralization (brain cognition). The sixth transition involves advanced brain architectures enabling complex cognition (complex brain cognition). The final transition is the emergence of human cognition, supported by symbols and culture (cultural-linguistic cognition). This hierarchical framework captures the increasing complexity of cognitive machinery across evolutionary transitions. By incorporating aneural cognition, we provide a more comprehensive view of the diversity of cognitive systems in nature.},
}

Animals
Humans
*Biological Evolution
*Brain/physiology
*Cognition/physiology
Neurons/physiology

@article {pmid40499536,
year = {2025},
author = {Wu, L and Pandey, V and Casha, VH and Qu, Z and Jami-Alahmadi, Y and Gradinaru, V and Wohlschlegel, JA and Khakh, BS},
title = {The cell-surface shared proteome of astrocytes and neurons and the molecular foundations of their multicellular interactions.},
journal = {Neuron},
volume = {},
number = {},
pages = {},
pmid = {40499536},
issn = {1097-4199},
support = {R01 AG075955/AG/NIA NIH HHS/United States ; R01 DA047444/DA/NIDA NIH HHS/United States ; R01 MH134926/MH/NIMH NIH HHS/United States ; R35 NS111583/NS/NINDS NIH HHS/United States ; },
abstract = {Neurons and astrocytes are predominant brain cells that extensively interact, but the molecular basis of their interactions remains largely unexplored. We identified and mapped striatal astrocytic and neuronal cell-surface proteins (CSPs) and found that many were shared, representing the cell-surface shared proteome of astrocytes and neurons (CS SPAN) bridging striatal astrocyte-neuron interaction sites. CS SPAN was replete with extracellular matrix proteins, cell adhesion molecules, transporters, ion channels, and G protein-coupled receptors. By mapping the cellular origins of astrocytic CSPs, we identified astrocytic interactions with diverse parenchymal cells. Broadly concordant with human data, in a mouse model of Huntington's disease (HD), pathophysiology and its genetic attenuation were accompanied by altered and restored CS SPAN and CSPs, respectively. CS SPAN also included molecules dysregulated in diverse brain disorders. Our study reveals the astrocyte-neuron interface in molecular terms and provides a mechanistic foundation for exploring its physiological roles and contributions to brain diseases.},
}

@article {pmid40494281,
year = {2025},
author = {Dudin, O},
title = {Omaya Dudin.},
journal = {Current biology : CB},
volume = {35},
number = {11},
pages = {R400-R403},
doi = {10.1016/j.cub.2025.04.015},
pmid = {40494281},
issn = {1879-0445},
mesh = {*Biological Evolution ; History, 21st Century ; History, 20th Century ; },
abstract = {Interview with Omaya Dudin, who uses Ichthyosporea as models to study how and why unicellular organisms evolved multicellularity at the University of Geneva.},
}

*Biological Evolution
History, 21st Century
History, 20th Century

@article {pmid40492701,
year = {2025},
author = {Zhang, Z and Jin, J and Sun, Y and Wang, Y and Zhao, J and Guo, S and Zou, Y and Chen, W and Stephenson, SL and Li, Y and Qiu, J and Liu, P},
title = {The overlooked amoebae of an agroecosystem of black soil land in China: five new species of dictyostelids.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {7},
pages = {e0002525},
pmid = {40492701},
issn = {1098-5336},
support = {No. 32370020,No. 32070009//National Natural Science Foundation of China/ ; No. 20220101187JC//Natural Science Foundation of Jilin Province/ ; No. D17014//111 Project/ ; No. 20250205020GH//Science and Technology Development Program of Jilin Province/ ; },
mesh = {China ; Phylogeny ; *Soil/parasitology ; *Soil Microbiology ; Ecosystem ; RNA, Ribosomal, 18S/genetics/analysis ; *Amoeba/classification/genetics/isolation & purification ; },
abstract = {UNLABELLED: China's northeastern black soil region, a global black soil hotspot, is vital for supporting national food security with its fertile and agricultural-friendly soil. The dictyostelids are well-known eukaryotic microorganisms with an unusual multicellular stage in their life cycle, and they inhabit surface soils worldwide. Although numerous species have been isolated from forest ecosystems and their remarkable biological activities have been reported, species of plant-associated dictyostelids of agroecosystems remain surprisingly understudied, especially in the agroecosystems of the black soil region of Jilin Province. In this study, the diversity of this group was evaluated based on corn, cabbage, and soybean soil samples from black soil land, including mollisol and chernozem soil types in Jilin Province of China. Morphological characterization and molecular analyses of the nuclear small subunit (18S) were used for species delineation. A total of 20 strains of dictyostelids were isolated from four localities, and on the basis of morphological examination and molecular phylogenetic analyses, five species of dictyostelids are described as new to science. These are Coremiostelium viridiflava, Raperostelium macrosorus, Dictyostelium torta, Cavenderia densissima, and Polysphondylium sparsiramus. These new species are described in detail, with morphological and molecular distinctions from their closest relatives explicitly discussed. This study not only revealed the diversity of dictyostelids in agroecosystems but also provided more research data for further studies in black soil land microbe protection in China.

IMPORTANCE: Despite the recognition of the presence of dictyostelids in various ecosystems, only limited information is available on their diversity and characteristics, particularly in the agroecosystems of China's northeastern black soil region. These eukaryotic microorganisms are known for their multicellular life cycle stages and widespread occurrence in surface soils. However, the species of dictyostelid in the black soil region of Jilin Province remain largely unexplored. In this study, a total of 20 dictyostelid strains, including five newly described species, were isolated and characterized from soil samples. Morphological examination and molecular phylogenetic analysis were conducted to document these new species. This research not only revealed the diversity of dictyostelid species in this important agroecosystem but also provided valuable data for future studies on microbe protection in China's black soil land. The discovery and detailed analysis of these new species contribute to our understanding of dictyostelid ecology, biology, and potential roles in agroecosystems.},
}

China
Phylogeny
*Soil/parasitology
*Soil Microbiology
Ecosystem
RNA, Ribosomal, 18S/genetics/analysis
*Amoeba/classification/genetics/isolation & purification

@article {pmid40489295,
year = {2025},
author = {Piccinini, G and Valdrè, U and Milani, L},
title = {The Early Evolution of Tudor Genes in Holozoa and How Their Distribution Was Influenced by Life History Traits in Metazoa.},
journal = {Genome biology and evolution},
volume = {17},
number = {6},
pages = {},
pmid = {40489295},
issn = {1759-6653},
support = {//Ricerca Fondamentale Orientata/ ; //University of Bologna/ ; },
mesh = {Animals ; *Evolution, Molecular ; Phylogeny ; *Life History Traits ; Multigene Family ; RNA, Small Interfering/genetics ; },
abstract = {Early metazoan evolution was characterized by the expansion of multiple gene families, such as the Tudor family, involved in novel multicellularity-related functions. In eukaryotes, Tudor genes (i.e. genes including at least one Tudor domain) are numerous, heterogeneous, and mostly associated with gene expression regulation. However, they underwent an animal-specific expansion, with novel elements almost exclusively involved in retrotransposon regulation through Piwi-interacting RNAs, as spatiotemporal regulators of the key-element Piwi, another previously considered animal-specific gene. Here, we used online-available proteomes covering 25 major taxonomic groups to characterize the Tudor gene family at a holozoan-wide level, confirming the apomorphic metazoan expansion of Piwi-interacting RNA-related Tudor genes. However, we also annotated elements of the Piwi-interacting RNA pathway (Tudor and Piwi genes) in Ichthyosporea species, suggesting that elements of the Piwi-interacting RNA pathway were already present in the holozoan common ancestors. We observed an outstanding variability (34-fold) of Tudor gene number between and within metazoan phyla that could be associated with convergent genomic and phenotypic evolutions: expansions were usually sided by whole-genome duplications and/or life history traits such as parthenogenesis; reductions were mostly associated to overall phenotypic and genomic simplifications, like in almost all considered endoparasites. Lastly, we phylogenetically tested, and mostly (but not completely) confirmed, a previously proposed model for the evolution of the Tudor domain secondary structures.},
}

Animals
*Evolution, Molecular
Phylogeny
*Life History Traits
Multigene Family
RNA, Small Interfering/genetics

@article {pmid40488621,
year = {2025},
author = {Foster, CSP and Walker, GJ and Jean, T and Wong, M and Brassil, L and Isaacs, SR and Lyu, Y and Turville, S and Kelleher, A and Rawlinson, WD},
title = {Long-term serial passaging of SARS-CoV-2 reveals signatures of convergent evolution.},
journal = {Journal of virology},
volume = {99},
number = {7},
pages = {e0036325},
pmid = {40488621},
issn = {1098-5514},
mesh = {*SARS-CoV-2/genetics ; Chlorocebus aethiops ; Animals ; Humans ; Vero Cells ; *COVID-19/virology ; Genome, Viral ; *Evolution, Molecular ; Serial Passage ; Mutation ; Whole Genome Sequencing ; Spike Glycoprotein, Coronavirus/genetics ; },
abstract = {Understanding viral evolutionary dynamics is crucial to pandemic responses, prediction of virus adaptation over time, and virus surveillance for public health strategies. Whole-genome sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has enabled fine-grained studies of virus evolution in the human population. Serial passaging in vitro offers a complementary controlled environment to investigate the emergence and persistence of genetic variants that may confer selective advantage. In this study, nine virus lineages, including four "variants of concern" and three former "variants under investigation," were sampled over ≥33 serial passages (range 33-100) in Vero E6 cells. WGS was used to examine virus evolutionary dynamics and identify key mutations with implications for fitness and/or transmissibility. Viruses accumulated mutations regularly during serial passaging. Many low-frequency variants were lost, but others became fixed, suggesting either in vitro benefits or at least a lack of deleterious effect. Mutations arose convergently both across passage lines and when compared with contemporaneous SARS-CoV-2 clinical sequences. These mutations included some that are hypothesized to drive lineage success through host immune evasion (e.g., S:A67V, S:H655Y). The appearance of these mutations in vitro suggested key mutations can arise convergently even in the absence of a multicellular host immune response through mechanisms other than immune-driven mutation. Such mutations may provide other benefits to the viruses in vitro, or arise stochastically. Our quantitative investigation into SARS-CoV-2 evolutionary dynamics spans the greatest number of serial passages to date and will inform measures to reduce the effects of SARS-CoV-2 infection on the human population.IMPORTANCEThe ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a challenge for long-term public health efforts to minimize the effects of coronavirus disease 2019. Whole-genome sequencing of outbreak cases has enabled global contact tracing efforts and the identification of mutations of concern within the virus' genome. However, complementary approaches are necessary to inform our understanding of virus evolution and clinical outcomes. Here, we charted the evolution of the virus within a controlled cell culture environment, focusing on nine different virus lineages. Our approach demonstrates how SARS-CoV-2 continues to evolve readily in vitro, with changes mirroring those seen in outbreak cases globally. Findings of the study are important for (i) investigating the mechanisms of how mutations arise, (ii) predicting the future evolutionary trajectory of SARS-CoV-2, and (iii) informing treatment and prevention design.},
}

*SARS-CoV-2/genetics
Chlorocebus aethiops
Animals
Humans
Vero Cells
*COVID-19/virology
Genome, Viral
*Evolution, Molecular
Serial Passage
Mutation
Whole Genome Sequencing
Spike Glycoprotein, Coronavirus/genetics

@article {pmid40476774,
year = {2025},
author = {Múgica-Galán, P and Miró-Bueno, J and Hueso-Gil, Á and Japón, P and Goñi-Moreno, Á},
title = {Standardized Quorum Sensing Tools for Gram-Negative Bacteria.},
journal = {ACS synthetic biology},
volume = {14},
number = {6},
pages = {2380-2385},
pmid = {40476774},
issn = {2161-5063},
mesh = {*Quorum Sensing/genetics ; *Pseudomonas putida/genetics/physiology/metabolism ; *Synthetic Biology/methods ; Plasmids/genetics ; Escherichia coli/genetics ; *Gram-Negative Bacteria/genetics/physiology ; },
abstract = {Engineering synthetic consortia to perform distributed functions requires robust quorum sensing (QS) systems to facilitate communication between cells. However, the current QS toolbox lacks standardized implementations, which are particularly valuable for use in bacteria beyond the model species Escherichia coli. We developed a set of three QS systems encompassing both sender and receiver modules, constructed using backbones from the SEVA (Standard European Vector Architecture) plasmid collection. This increases versatility, allowing plasmid features like the origin of replication or antibiotic marker to be easily swapped. The systems were characterized using the synthetic biology chassis Pseudomonas putida. We first tested individual modules, then combined sender and receiver modules in the same host, and finally assessed the performance across separate cells to evaluate consortia dynamics. Alongside the QS set, we provide mathematical models and rate parameters to support the design efforts. Together, these tools advance the engineering of robust and predictable multicellular functions.},
}

*Quorum Sensing/genetics
*Pseudomonas putida/genetics/physiology/metabolism
*Synthetic Biology/methods
Plasmids/genetics
Escherichia coli/genetics
*Gram-Negative Bacteria/genetics/physiology

@article {pmid40467258,
year = {2025},
author = {Li, Y and Liu, Y and Zheng, B and Zhang, C and Cai, Y and Cheng, Y and Wang, J},
title = {Multicellular behavior and genomic characterization of Salmonella Typhimurium in animal-derived food chains in Xinjiang, China: Phenotypic resistance, biofilm formation, and sequence types.},
journal = {Food research international (Ottawa, Ont.)},
volume = {214},
number = {},
pages = {116698},
doi = {10.1016/j.foodres.2025.116698},
pmid = {40467258},
issn = {1873-7145},
mesh = {*Biofilms/growth & development ; Animals ; China ; *Salmonella typhimurium/genetics/drug effects/isolation & purification/physiology/classification ; *Food Microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Phenotype ; Anti-Bacterial Agents/pharmacology ; Sheep ; Cattle ; Whole Genome Sequencing ; Genome, Bacterial ; },
abstract = {Salmonella Typhimurium Is a globally significant foodborne pathogen that causes diseases in livestock and poultry, which can lead to human infections and fatalities through contaminated food. In this study, we investigated the prevalence of Salmonella Typhimurium in the animal-derived food chain in Xinjiang, China. Among 5075 samples, the detection rate of Salmonella was 8.26 % (419/5075). Of these isolates, 27.21 % (114/419) were identified as Salmonella Typhimurium. Phenotypic analysis revealed significant antibiotic resistance: 82.46 % (94/114) of the strains exhibited multidrug resistance (MDR), with high resistance rates to amoxicillin / clavulanic acid, ampicillin, and tetracycline. Congo red plate assays demonstrated that 62.28 % (71/114) of the strains exhibited multicellular behavior (RDAR morphotype). Biofilm formation assays indicated that 96.49 % (110/114) of the strains possessed biofilm-forming capabilities, with 18.18 % (20/110) showing strong biofilm formation. Notably, strains displaying multicellular behavior exhibited enhanced biofilm formation, and biofilm capability was positively correlated with antibiotic resistance phenotypes. Whole-genome sequencing of 40 representative strains identified four sequence types (ST19, ST34, ST99, ST128), with ST34 being the most predominant. Distinct host preferences were observed: ST34 strains originated exclusively from cattle and sheep, while ST19, ST99, and ST128 strains were isolated from geese and pigeons. Resistance gene profiling revealed that strains harboring resistance genes exhibited stronger resistance phenotypes, while ST99 and ST128 strains lacked detectable resistance genes. Plasmids R64, R478, and pKPC_CAV1321 were identified in cattle- and sheep-derived strains, whereas pSLT-BT and pSPCV plasmids were predicted in strains from geese and pigeons. Pan-genome analysis and phylogenetic reconstruction demonstrated distinct genetic clustering among ST types, with ST19 and ST128 showing closer evolutionary relationships. This study provides comprehensive insights into the prevalence, phenotypic characteristics, and genomic diversity of Salmonella Typhimurium in the animal-derived food chain in Xinjiang. Our findings contribute to region-specific pathogen control strategies, enhancing public health safety and consumer protection.},
}

*Biofilms/growth & development
Animals
China
*Salmonella typhimurium/genetics/drug effects/isolation & purification/physiology/classification
*Food Microbiology
Drug Resistance, Multiple, Bacterial/genetics
Phenotype
Anti-Bacterial Agents/pharmacology
Sheep
Cattle
Whole Genome Sequencing
Genome, Bacterial

@article {pmid40462939,
year = {2025},
author = {Li, R and Dharamshi, JE and Kwok, K and Ruiz-Trillo, I and Gerdt, JP},
title = {A close unicellular relative reveals aggregative multicellularity was key to the evolution of animals.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40462939},
issn = {2692-8205},
support = {R35 GM138376/GM/NIGMS NIH HHS/United States ; },
abstract = {How animals evolved complex multicellularity from their unicellular ancestors remains unanswered. Unicellular relatives of animals exhibit simple multicellularity through clonal division, formation of multinucleate coenocytes, or aggregation.[1] Therefore, animal multicellularity may have evolved from one (or a combination) of these behaviours. Aggregation has classically been dismissed as a means to complex multicellularity.[2] However, aggregation occurs in many extant animal cells and has also been recently described in three different unicellular relatives of animals (the choanoflagellates Salpingoeca rosetta and Choanoeca flexa, and the filasterean Capsaspora owczarzaki).[3-6] It is unclear whether aggregation in these species is derived or ancestral, and its relevance for animal origins remains unknown. To fill this gap, we investigated whether an additional unicellular relative of animals can undergo aggregation. We discovered that the marine free-living bacterivorous filasterean Ministeria vibrans [7] forms homogeneous aggregates with reproducible kinetics that have long-term stability when cultured with an alphaproteobacterium. We found that many multicellularity genes involved in animal cell adhesion, signaling, and transcriptional regulation were deployed during this process. Our findings suggest that the last unicellular ancestor of animals had the capacity to aggregate using key animal multicellularity genes and that improved feeding and sexual reproduction may be evolutionary drivers of this aggregation.},
}

@article {pmid40446803,
year = {2025},
author = {Starr, AL and Nishimura, T and Igarashi, KJ and Funamoto, C and Nakauchi, H and Fraser, HB},
title = {Disentangling cell-intrinsic and cell-extrinsic factors underlying evolution.},
journal = {Cell genomics},
volume = {5},
number = {8},
pages = {100891},
doi = {10.1016/j.xgen.2025.100891},
pmid = {40446803},
issn = {2666-979X},
abstract = {A long-standing question in biology is the extent to which cells function autonomously as opposed to requiring interactions with other cells or environmental factors. Here, we develop a framework to use interspecies chimeras to precisely decompose evolutionary divergence in any cellular trait into cell-intrinsic and cell-extrinsic components. Applying this framework to thousands of gene expression levels in reciprocal rat-mouse chimeras, we found that most divergence is cell intrinsic, though extrinsic factors also play an integral role. For example, cell-extrinsic regulation of a transcription factor can propagate to its target genes, leading to cell-type-specific extrinsic regulation of both their mRNA and their protein levels. We also show that imprinted genes are dramatically misexpressed in chimeras, suggesting a mismatch between rapidly evolving intrinsic and extrinsic imprinting mechanisms. Overall, our conceptual framework opens up new avenues to investigate the mechanistic basis of the evolution, development, and regulation of myriad cellular traits in any multicellular organism.},
}

@article {pmid40435533,
year = {2025},
author = {Martins, T and Kimata, Y},
title = {Mitotic signalling in progenitor cells: Integrating cell division with cell specification.},
journal = {Current opinion in cell biology},
volume = {95},
number = {},
pages = {102542},
doi = {10.1016/j.ceb.2025.102542},
pmid = {40435533},
issn = {1879-0410},
mesh = {Animals ; Humans ; *Mitosis ; *Stem Cells/cytology/metabolism ; *Signal Transduction ; Cell Differentiation ; Cell Cycle Proteins/metabolism ; },
abstract = {Mitotic signalling mediated by cell cycle regulators (CCRs) is pivotal for coordinating cell division and fate specification across metazoans. CCRs, including cyclin-dependent kinases and ubiquitin ligases, use post-translational modifications for rapid, dynamic regulation of the cell cycle, ensuring its unidirectionality and integration with fate determination. This review explores recent findings that further elucidate CCRs' noncanonical functions, particularly in progenitor cells. Advancements in quantitative in vivo imaging, precise genome editing, and single-cell omics have provided unprecedented spatiotemporal resolution into the mechanisms through which CCRs regulate asymmetric cell division, epigenetic regulation, and cell cycle variations. The evolution of CCRs underscores their crucial role in integrating cellular and developmental signals in multicellular organisms, with implications for disease and therapeutic strategies.},
}

Animals
Humans
*Mitosis
*Stem Cells/cytology/metabolism
*Signal Transduction
Cell Differentiation
Cell Cycle Proteins/metabolism

@article {pmid40412365,
year = {2025},
author = {Zheng, J and Wu, Y and Zhang, L and Yang, L and Jin, J and Li, C and Tong, S and Yu, J},
title = {Overexpression of NtMYB306c reduces the glandular trichomes density in tobacco.},
journal = {Biochemical and biophysical research communications},
volume = {772},
number = {},
pages = {152061},
doi = {10.1016/j.bbrc.2025.152061},
pmid = {40412365},
issn = {1090-2104},
mesh = {*Nicotiana/genetics/metabolism ; *Trichomes/genetics/metabolism ; *Transcription Factors/genetics/metabolism ; *Plant Proteins/genetics/metabolism ; Gene Expression Regulation, Plant ; Plant Leaves/genetics/metabolism ; Plants, Genetically Modified/genetics ; Phylogeny ; },
abstract = {Trichomes, as multicellular structures with diverse functions, play a crucial role in protecting plants against various stresses. Nicotiana tabacum (tobacco) leaves are characterized by numerous glandular trichomes, which are responsible for the production of substantial quantities of secondary metabolites and are critical determinants of tobacco quality. Although their importance is well established, the molecular regulatory mechanisms governing the development of tobacco glandular trichomes remain poorly characterized. Through comparative transcriptome analysis of trichome and trichome-free leaves, we identified NtMYB306c, an R2R3-MYB transcription factor that is phylogenetically distinct from its paralog NtMYB306a (designated as NtMYB306e in this study) and shows highly expressed in trichomes. Functional characterization revealed that overexpression of NtMYB306c significantly suppresses glandular trichome density and markedly alters the expression of three key regulatory genes, NtJAZ3, NtCycB2 and NtHD9 and the key gene LOX1 in JA biosynthesis. Protein-protein interaction screening identified NtMYB308, another member of the R2R3-MYB family. Bioinformatic analysis predicted that its Arabidopsis thaliana homolog interacts with GL3, EGL3, and TTG1, core components of the MBW complex that regulates Arabidopsis glandular trichome development. Yeast two-hybrid (Y2H) and co-immunoprecipitation (Co-IP) assays confirmed the physical interaction between NtMYB306c and NtMYB308, while bioinformatic analysis identified MYB binding sites in the promoter region of NtJAZ3. Collectively, our study demonstrates that NtMYB306c regulates the density of tobacco glandular trichomes via its interaction with NtMYB308.},
}

*Nicotiana/genetics/metabolism
*Trichomes/genetics/metabolism
*Transcription Factors/genetics/metabolism
*Plant Proteins/genetics/metabolism
Gene Expression Regulation, Plant
Plant Leaves/genetics/metabolism
Plants, Genetically Modified/genetics
Phylogeny

@article {pmid40399443,
year = {2025},
author = {Gatenby, RA and Teer, JK and Tsai, KY and Brown, JS},
title = {Parallel and convergent dynamics in the evolution of primary breast and lung adenocarcinomas.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {775},
pmid = {40399443},
issn = {2399-3642},
mesh = {Humans ; *Breast Neoplasms/genetics/pathology ; *Lung Neoplasms/genetics/pathology ; Female ; *Adenocarcinoma of Lung/genetics/pathology ; Mutation ; *Evolution, Molecular ; Gene Expression Regulation, Neoplastic ; },
abstract = {Cancer development requires an evolutionary transformation from mammalian cells fully regulated by and integrated into multicellular tissue to cancer cells that, as single cell protists, are individually subject to Darwinian selection. Through genetic and epigenetic mechanisms of inheritance, the evolving cancer phenotype must acquire independence from host controls, downregulate differentiated functions that benefit the host but not individual cells, and generate phenotypic traits that increase fitness in the context of the selection forces within the local microenvironment. Here, we investigate this evolutionary transition in breast (BRCA) and lung (LUAD, without EGFR, KRAS or BRAF driver mutations) adenocarcinomas using bulk mutation and expression data from the TCGA database. We define evolution selection for genes and molecular pathways based on 1) changes in gene expression compared to normal tissue, and 2) significantly larger or smaller observed mutation rates compared to those expected based on the gene size. We find BRCA and LUAD disable different genes and gene pathways associated with tissue-specific signaling and differentiated functions but promote common molecular pathways associated with cell cycle, cell-cell interactions, cytoskeleton, voltage gated ion channels, and microenvironmental niche construction. Thus, tissue-specific parallel evolution in early cancer development is followed by convergence to a common cancer phenotype.},
}

Humans
*Breast Neoplasms/genetics/pathology
*Lung Neoplasms/genetics/pathology
Female
*Adenocarcinoma of Lung/genetics/pathology
Mutation
*Evolution, Molecular
Gene Expression Regulation, Neoplastic

@article {pmid40392851,
year = {2025},
author = {Zhu, L and Beichman, A and Harris, K},
title = {Population size interacts with reproductive longevity to shape the germline mutation rate.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {21},
pages = {e2423311122},
pmid = {40392851},
issn = {1091-6490},
support = {T32 AG066574/AG/NIA NIH HHS/United States ; R35GM133428//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; Career Award at the Scientific Interface//Burroughs Wellcome Fund (BWF)/ ; Discovery Center for Cell Lineage Tracing//Allen Foundation (The Allen Foundation)/ ; R35 GM133428/GM/NIGMS NIH HHS/United States ; Pew Scholarship//Pew Charitable Trusts (PEW)/ ; },
mesh = {*Mutation Rate ; *Germ-Line Mutation/genetics ; Animals ; Population Density ; Male ; *Reproduction/genetics ; Female ; *Longevity/genetics ; DNA Repair ; Germ Cells ; Spermatogonia ; DNA Damage ; },
abstract = {Mutation rates vary across the tree of life by many orders of magnitude, with fewer mutations occurring each generation in species that reproduce quickly and maintain large effective population sizes. A compelling explanation is that large effective population sizes facilitate selection against weakly deleterious "mutator alleles" such as variants that modulate cell division or interfere with the molecular efficacy of DNA repair. However, while the fidelity of a single cell division largely determines microorganisms' mutation rates, the relationship of the mutation rate to the molecular determinants of DNA damage and repair is more complex in multicellular species with long generation times. Since long generations leave more time for mutations to accrue each generation, we posit that a long generation time likely amplifies the fitness consequences of any damage agent or DNA repair defect that creates extra mutations in the spermatogonia or oocytes. This leads to the counterintuitive prediction that the species with the highest germline mutation rates per generation are also the species with most effective mechanisms for avoiding and repairing mutations in their reproductive cells. Consistent with this, we show that mutation rates in the reproductive cells are inversely correlated with generation time; in contrast, the number of germline mutations that occur during prepuberty development trends weakly upward as generation time increases. Our results parallel recent findings that the longest-lived species have the lowest mutation rates in adult somatic tissues, potentially due to selection to keep the lifetime mutation load below a harmful threshold.},
}

*Mutation Rate
*Germ-Line Mutation/genetics
Animals
Population Density
Male
*Reproduction/genetics
Female
*Longevity/genetics
DNA Repair
Germ Cells
Spermatogonia
DNA Damage

@article {pmid40380887,
year = {2025},
author = {Chen, ICK and Khatri, S and Herron, MD and Rosenzweig, F},
title = {Genetic Predisposition Toward Multicellularity in Chlamydomonas reinhardtii.},
journal = {Genome biology and evolution},
volume = {17},
number = {6},
pages = {},
pmid = {40380887},
issn = {1759-6653},
support = {NNA17BB05A//NASA Astrobiology Institute Award/ ; 80NSSC20K0621//NASA Exobiology/ ; 80NSSC23K1357//NASA ICAR/ ; },
mesh = {*Chlamydomonas reinhardtii/genetics/cytology ; *Biological Evolution ; Selection, Genetic ; Genotype ; Evolution, Molecular ; },
abstract = {The evolution from unicellular to multicellular organisms facilitates further phenotypic innovations, notably cellular differentiation. Multiple research groups have shown that, in the laboratory, simple, obligate multicellularity can evolve from a unicellular ancestor under appropriate selection. However, little is known about the extent to which deterministic factors such as ancestral genotype and environmental context influence the likelihood of this evolutionary transition. To test whether certain genotypes are predisposed to evolve multicellularity in different environments, we carried out a set of 24 evolution experiments, each founded by a population consisting of 10 different strains of the unicellular green alga Chlamydomonas reinhardtii, all in equal proportions. Twelve of the initially identical replicate populations were subjected to predation by the protist Paramecium tetraurelia, while the other 12 were subjected to settling selection by slow centrifugation. Population subsamples were transferred to fresh media on a weekly basis for a total of 40 transfers (∼600 generations). Heritable multicellular structures arose in 4 of 12 predation-selected populations (6 multicellular isolates in total), but never in the settling selection populations. By comparing whole genome sequences of the founder and evolved strains, we discovered that every multicellular isolate arose from one of two founders. Cell cluster size varied not only among evolved strains derived from different ancestors but also among strains derived from the same ancestor. These findings show that both deterministic and stochastic factors influence whether initially unicellular populations can evolve simple multicellular structures.},
}

*Chlamydomonas reinhardtii/genetics/cytology
*Biological Evolution
Selection, Genetic
Genotype
Evolution, Molecular

@article {pmid40369312,
year = {2025},
author = {Gaspard-Boulinc, LC and Gortana, L and Walter, T and Barillot, E and Cavalli, FMG},
title = {Cell-type deconvolution methods for spatial transcriptomics.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
pmid = {40369312},
issn = {1471-0064},
abstract = {Spatial transcriptomics is a powerful method for studying the spatial organization of cells, which is a critical feature in the development, function and evolution of multicellular life. However, sequencing-based spatial transcriptomics has not yet achieved cellular-level resolution, so advanced deconvolution methods are needed to infer cell-type contributions at each location in the data. Recent progress has led to diverse tools for cell-type deconvolution that are helping to describe tissue architectures in health and disease. In this Review, we describe the varied types of cell-type deconvolution methods for spatial transcriptomics, contrast their capabilities and summarize them in a web-based, interactive table to enable more efficient method selection.},
}

@article {pmid40359149,
year = {2025},
author = {Khey, J and Travisano, M},
title = {Historical effects during experimental evolution of multicellularity in Saccharomyces cerevisiae.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/evolut/qpaf101},
pmid = {40359149},
issn = {1558-5646},
abstract = {Natural selection is the basis of adaptive evolution, and any adaptations that arise are contingent upon the genetic background of a population. Because the genetic background is a product of prior evolution, adaptive evolution is also contingent upon the evolutionary history of a population. Here, we show the scope for historically contingent outcomes across several selection experiments involving alternating adaptations for size. Previously, replicate laboratory yeast populations rapidly evolved multicellularity via settling selection and then reverted to unicellularity during selection in a spatially structured environment. In this study, we show that genetic recombination via selfing regenerates multicellularity from some secondarily unicellular genotypes, and those same genotypes give rise to populations that rapidly re-evolved multicellularity under settling selection. We also observe that some secondarily derived multicellular phenotypes had different cellular architectures across populations. Because source lineages in our study varied in their degree of common ancestry, we can identify the depth of historical contingency. Our results show that the earliest adaptive changes in a lineage have substantial, persistent evolutionary consequences, demonstrating historically contingent outcomes even when evolutionary history is only measured in hundreds of generations.},
}

@article {pmid40353769,
year = {2025},
author = {Nakanishi, N and Takahashi, M and Kumano, G},
title = {Diversification of cnidarian mechanosensory neurons across life cycle phases: evidence from Hydrozoa.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icaf027},
pmid = {40353769},
issn = {1557-7023},
abstract = {Over the course of more than half a billion years of independent evolution, cnidarians (e.g., sea anemones, corals and jellyfishes) have evolved diverse, multicellular, mechanosensory structures ranging from tentacles of hydroids to gravity-sensors of moon jellyfish. The ectodermal epithelium of mechanosensory structures houses the mechanosensory neuron-known as the concentric hair cell-characterized by an apical mechanosensory apparatus consisting of a single cilium surrounded by one or multiple rings of microvilli/stereovilli. While distinct concentric hair cell types are known to occur within life-cycle-stage-specific structures such as the sea anemone tentacles, it is unclear whether diverse concentric hair cell types exist across life cycle phases of any cnidarian. Here we report evidence from the hydrozoan Cladonema pacificum that concentric hair cells of sedentary polyps are distinct from those of free-swimming medusae. By carrying out touch assays, we demonstrate that polyps and medusae exhibit distinct mechanosensory behaviors. Moreover, we find that concentric hair cells in the ectodermal epithelium of touch-sensitive regions in polyps differ from those in medusae in the morphology of apical sensory apparatuses. Furthermore, polyp-type concentric hair cells are not retained in the ectoderm of medusa buds, and medusa-type concentric hair cells begin to form de novo during medusa formation. Taken together, these findings suggest that distinct mechanosensitive behaviors of polyps and medusae are mediated by morphologically different sets of mechanosensory neurons that develop via life-cycle-stage-specific mechanisms. We propose that cell type diversification of mechanosensory neurons occurred not only within a given life cycle phase but across life cycle phases in cnidarian evolution.},
}

@article {pmid40347540,
year = {2025},
author = {Irulappan, M and Ramkumar, PS and Rajendhran, J and Munavar, MH and Balasubramaniam, S},
title = {Integrating classical genetics and whole-genome sequencing to reveal the chromosomal basis of hygromycin resistance in Escherichia coli.},
journal = {Mutation research},
volume = {830},
number = {},
pages = {111906},
doi = {10.1016/j.mrfmmm.2025.111906},
pmid = {40347540},
issn = {1873-135X},
mesh = {*Escherichia coli/genetics/drug effects ; *Whole Genome Sequencing/methods ; *Drug Resistance, Bacterial/genetics ; *Hygromycin B/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Genome, Bacterial ; *Chromosomes, Bacterial/genetics ; Escherichia coli Proteins/genetics ; },
abstract = {Hygromycin B (HygB), a broad-spectrum antibiotic, is widely used in molecular biology, agriculture, and veterinary medicine. It inhibits protein synthesis by binding to ribosomes, and its plasmid-borne resistance gene serves as a selectable marker for applications in gene manipulation technologies. The binding site of the P1 phage-borne toxin Doc, which induces bacterial apoptosis, overlaps with the binding site of HygB in helix h44 of 16S rRNA. Hence isolation and characterization of chromosomal HygB resistance would largely serve as gateway to understand the less studied but imperative and emerging modes of drug resistance like bacterial multicellularity and heteroresistance. In this study we have investigated the chromosomal origin of HygB resistance in E. coli through a combination of classical genetics and whole-genome sequencing. Eight HygB-resistant mutants were analyzed, and co-transduction experiments revealed a narrow region (71.8-75.8 min) to have conferred resistance. Whole-genome sequencing confirmed a single base pair change in the fusA gene (A1754 to G1754) as the cause. This is a maiden report on a missense mutation of fusA leading to HygB resistance and these findings provide valuable insights into the mechanisms of HygB resistance.},
}

*Escherichia coli/genetics/drug effects
*Whole Genome Sequencing/methods
*Drug Resistance, Bacterial/genetics
*Hygromycin B/pharmacology
*Anti-Bacterial Agents/pharmacology
Genome, Bacterial
*Chromosomes, Bacterial/genetics
Escherichia coli Proteins/genetics

@article {pmid40345196,
year = {2025},
author = {Petroll, R and West, JA and Ogden, M and McGinley, O and Craig, RJ and Coelho, SM and Borg, M},
title = {The expanded Bostrychia moritziana genome unveils evolution in the most diverse and complex order of red algae.},
journal = {Current biology : CB},
volume = {35},
number = {12},
pages = {2771-2788.e8},
doi = {10.1016/j.cub.2025.04.044},
pmid = {40345196},
issn = {1879-0445},
mesh = {*Rhodophyta/genetics ; *Genome, Plant ; *Evolution, Molecular ; *Biological Evolution ; Genome Size ; Phylogeny ; },
abstract = {Red algae are an ancient eukaryotic lineage that were among the first to evolve multicellularity. Although they share a common origin with modern-day plants and display complex multicellular development, comprehensive genome data from the most highly evolved red algal groups remain scarce. Here, we present a chromosome-level genome assembly of Bostrychia moritziana, a complex red seaweed in the Rhodomelaceae family of the Ceramiales-the largest and most diverse order of red algae. Contrary to the view that red algal genomes are typically small, we report significant genome size expansion in Bostrychia and other Ceramiales, which represents one of at least three independent expansion events in red algal evolution. Our analyses suggest that these expansions do not involve polyploidy or ancient whole-genome duplications, but in Bostrychia rather stem from the proliferation of a single lineage of giant Plavaka DNA transposons. Consistent with its enlarged genome, Bostrychia has an increased gene content shaped by de novo gene emergence and amplified gene families in common with other Ceramiales, providing insight into the genetic adaptations underpinning this successful and species-rich order. Finally, our sex-specific assemblies resolve the UV sex chromosomes in Bostrychia, which feature expanded gene-rich sex-linked regions. Notably, each sex chromosome harbors a three amino acid loop extension homeodomain (TALE-HD) transcription factor orthologous to ancient regulators of haploid-diploid transitions in other multicellular lineages. Together, our findings offer a unique perspective of the genomic adaptations driving red algal diversity and demonstrate how this red seaweed lineage can provide insight into the evolutionary origins and universal principles underpinning complex multicellularity.},
}

*Rhodophyta/genetics
*Genome, Plant
*Evolution, Molecular
*Biological Evolution
Genome Size
Phylogeny

@article {pmid40344646,
year = {2025},
author = {Xu, Y and Luo, H and Wang, J and Liu, H and Chen, L and Ji, H and Deng, Z and Liu, X},
title = {CD103[+] T Cells Eliminate Damaged Alveolar Epithelial Type II Cells Under Oxidative Stress to Prevent Lung Tumorigenesis.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {12},
number = {28},
pages = {e2503557},
pmid = {40344646},
issn = {2198-3844},
support = {2022YFA1103900//National Key R&D Program of China/ ; 2020YFA0509102//National Key R&D Program of China/ ; 2023YFA1800200//National Key R&D Program of China/ ; 2019278//Shanghai Post-doctoral Excellence Program/ ; 32470972//National Natural Science Foundation of China/ ; 31900641//National Natural Science Foundation of China/ ; 32170904//National Natural Science Foundation of China/ ; 2021B0909050003//High-level Innovative Research Institute/ ; },
mesh = {Animals ; *Oxidative Stress/immunology ; *Integrin alpha Chains/metabolism/immunology ; Mice ; *Lung Neoplasms/immunology/pathology/metabolism ; *Alveolar Epithelial Cells/immunology/metabolism/pathology ; *Antigens, CD/metabolism/immunology ; *Carcinogenesis/immunology ; CD8-Positive T-Lymphocytes/immunology ; *T-Lymphocytes/immunology/metabolism ; Mice, Inbred C57BL ; },
abstract = {The nexus between aging-associated immune deteriorations and tumorigenesis of lung cancers remains elusive. In a mouse model with Med23 depletion in T cells (Med23 [-/-]), it is found a strong association between the decline of CD103[+] T cells and spontaneous alveolar epithelial type II cell (AT2 cell)-originated lung adenocarcinomas. The reduction of CD103[+] T cells in the lung results in an accumulation of AT2 cells bearing oxidative damages, which appears to be the major origin of the lung adenocarcinoma. Functional experiments reveal CD103[+] T cells can eradicate oxidative-damage-bearing AT2 cells as well as ROS-dependent, KRAS (G12D)-driven tumorigenesis. In vitro co-cultures prove CD103[+] T cells, especially CD103[+] CD8[+] T cells, exhibit a killing capacity that matches the oxidative stress level in the target cells. In aged animals, it is found the abundance of CD103[+] CD8[+] T cells in the lung declines with age, accompanied by an accumulation of oxidative-damage-bearing AT2 cells. Collectively, the study establishes the vital function of CD103[+] T cells in surveilling epithelial cells under oxidative stress to prevent malignancies, and unravels a potential immuno-dysregulation in the aged lung which contributes to tumorigenesis.},
}

Animals
*Oxidative Stress/immunology
*Integrin alpha Chains/metabolism/immunology
Mice
*Lung Neoplasms/immunology/pathology/metabolism
*Alveolar Epithelial Cells/immunology/metabolism/pathology
*Antigens, CD/metabolism/immunology
*Carcinogenesis/immunology
CD8-Positive T-Lymphocytes/immunology
*T-Lymphocytes/immunology/metabolism
Mice, Inbred C57BL

@article {pmid40333983,
year = {2025},
author = {Jinno, C and Fujisaki, K and Yotsui, I and Ouchi, M and Singh, P and Naramoto, S and Takezawa, D and Sakata, Y and Fujita, T},
title = {Abscisic acid signaling regulates primary plasmodesmata density for plant cell-to-cell communication.},
journal = {Science advances},
volume = {11},
number = {19},
pages = {eadr8298},
pmid = {40333983},
issn = {2375-2548},
mesh = {*Abscisic Acid/metabolism/pharmacology ; *Plasmodesmata/metabolism ; *Cell Communication ; *Signal Transduction ; *Bryopsida/metabolism/genetics ; Gene Expression Regulation, Plant ; *Plant Cells/metabolism ; Plant Proteins/metabolism/genetics ; Plant Growth Regulators/metabolism ; },
abstract = {Cell-to-cell communication is essential for multicellular organisms. Plasmodesmata (PD) are plant-specific nanopore structures pivotal for cell-to-cell communication and plant survival. However, how PD form and their structure, regulation, and evolution remain largely unknown. Here, we demonstrate that the exogenous supply of abscisic acid (ABA), a well-conserved phytohormone in land plants, reduces primary PD density in the moss Physcomitrium patens. This regulation requires all core components of the ABA signaling pathway. Furthermore, we reveal that ABA-INSENSITIVE 5, a well-conserved transcription factor in the ABA signaling pathway of land plants, plays a pivotal role in PD density regulation, whereas ABA-INSENSITIVE 3 does not. Our findings show that the ABA-induced reduction in primary PD density is mediated by these ABA-responsive factors in P. patens. Considering previous reports on ABA-dependent PD regulation in both moss and angiosperms, we propose that the ABA-mediated control of PD biogenesis and permeability represents a conserved mechanism in land plants, with critical implications for cell-to-cell communication and stress adaptation.},
}

*Abscisic Acid/metabolism/pharmacology
*Plasmodesmata/metabolism
*Cell Communication
*Signal Transduction
*Bryopsida/metabolism/genetics
Gene Expression Regulation, Plant
*Plant Cells/metabolism
Plant Proteins/metabolism/genetics
Plant Growth Regulators/metabolism

@article {pmid40333173,
year = {2025},
author = {Twyman, KZ and Gardner, A},
title = {The clonality window: relatedness and the group covariance effect in the evolution of division of labour.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/evolut/qpaf093},
pmid = {40333173},
issn = {1558-5646},
abstract = {Cellular division of labour is closely associated with the emergence of organismality in the evolution of obligate multicellularity. Michod has suggested that a trade-off between viability and fecundity may-through a 'group covariance effect'-lead to a group's fitness being augmented above the average of its constituents' fitnesses, offering a first step towards division of labour and obligate multicellularity. However, it is difficult to see how a group's fitness could be different from the aggregate of its constituents. Here, we investigate the same fitness trade-off and its consequences for division of labour. We recover the covariance effect, revealing that it is a consequence of cells sharing the products of their labours and clarifying that the group's fitness remains equal to the aggregate of the fitnesses of its constituent cells. We show that the covariance effect imparts an inclusive-fitness benefit for cells that share, but that-all else being equal-natural selection favours sharing only when groupmates are genetically identical, yielding a 'clonality window'. Lastly, we find that sharing is a critical determinant as to whether division of labour is favoured by natural selection, such that the 'clonality window' is also a prerequisite for division of labour in Michod's trade-off scenario.},
}

@article {pmid40331617,
year = {2025},
author = {Cheng, XH and Yu, WJ and Wang, DX and Jiang, LY and Hu, LH},
title = {[Enriching plasma exosomes for proteomic analysis using a phosphatidylserine-imprinted polymer].},
journal = {Se pu = Chinese journal of chromatography},
volume = {43},
number = {5},
pages = {539-546},
pmid = {40331617},
issn = {1872-2059},
mesh = {*Exosomes/chemistry ; Humans ; *Phosphatidylserines/chemistry ; *Proteomics/methods ; *Polymers/chemistry ; *Molecular Imprinting/methods ; },
abstract = {Exosomes are 40-160 nm vesicular nano-bodies secreted by most cells that carry large amounts of biologically active substances originating from the parent cell. Proteins in exosomes are protected by phospholipid bilayer membranes that protect them from degradation by enzymes within body fluids. Along with nucleic acid, proteins and metabolites, exosomes are biomolecules that are considered to be among the most important for discovering tumor markers. Plasma is among the most commonly used body fluids in clinical settings; it is highly complex and contains many proteins and metabolites that interfere with exosome isolation. Consequently, the development of methods for effectively isolating exosomes is a key challenge prior to their use in clinical research. In this study, we used a phosphatidylserine molecularly imprinted polymer (PS-MIP) to enrich plasma exosomes. Subsequent immunoblotting analyses for the CD9, TSG101, and CD81 exosome marker proteins showed that signals can be detected using only 5 μL of plasma, thereby demonstrating the efficiency and specificity of the enrichment protocol. Transmission electron microscope (TEM) and nanoparticle tracking analysis (NTA) data revealed that the enriched vesicles are 30-100 nm in size with elliptical or cup-shaped structures, consistent with the morphology and particle-size-distribution characteristics of the exosomes, suggesting that PS-MIP is capable of successfully isolating exosomes. Nanoflow cytometry revealed that 75.4% of the multi-angle laser scattering (MALS) signal is derived from the PS-MIP-enriched exosomes, which indicates that these enriched exosomes are highly pure and free of interference from impurities, such as aggregated protein particles that are similar in size to the exosomes themselves. This method was used to analyze the proteomes and potential exosomal protein markers of clinical plasma samples from three pancreatic-cancer patients and three healthy volunteers. A total of 1052 proteins and 4545 peptides were identified in the plasma exosomes of healthy volunteers, with a total of 972 proteins and 4096 peptides identified in the plasma exosomes of the pancreatic-cancer patients. Further bioinformatics analyses revealed that the Vesiclepedia database covered 84% of the proteins identified in the plasma exosomes isolated using the PS-MIP method; these proteins comprise 77 of the 100 most frequently identified exosomal proteins in the ExoCarta database. The identified proteins from the cellular components were subjected to gene ontology (GO) analysis, which revealed that they are mainly derived from the exosomes, thereby demonstrating the high selectivity of the PS-MIP method for enriching plasma exosomes and providing specificity for subsequent tumor-marker screening. Label-free quantitative analysis showed that 11 proteins were upregulated and 24 proteins were downregulated in the plasma exosomes of patients with pancreatic cancer compared to those of healthy volunteers. The highly expressed and lowly expressed proteins in the plasma exosomes of patients with pancreatic cancer were subjected to GO, which showed that highly expressed proteins related to the positive regulation of metabolic and biological processes were found in the plasma exosomes of patients with pancreatic cancer compared to those of healthy volunteers, whereas the most significantly under-expressed proteins are related immune-system processes, followed by stimulus-responsive, multicellular bioprocesses, bioregulatory, and interspecies-interacting biological-process-related proteins. The top three proteins, which are relatively highly correlated through protein-protein interaction networks (PPI) analysis, were determined to be complement factor D (CFD), complement component 3 (C3), and von Willebrand factor (VWF). Among the upregulated proteins in the exosomes of patients with pancreatic cancer, exostosin-like glycosyltransferase 2 (EXTL2), α-2-macroglobulin like 1 (A2ML1), and Parkinson's disease protein 7 (PARK7) were the most significantly overexpressed. Hence, these proteins are potential biomarkers for the diagnostic and prognostic assessment of pancreatic cancer and may provide support for further clinical studies into pancreatic cancer.},
}

*Exosomes/chemistry
Humans
*Phosphatidylserines/chemistry
*Proteomics/methods
*Polymers/chemistry
*Molecular Imprinting/methods

@article {pmid40324712,
year = {2025},
author = {Jureček, M and Švorcová, J},
title = {Flowing boundaries in autopoietic systems and microniche construction.},
journal = {Bio Systems},
volume = {254},
number = {},
pages = {105477},
doi = {10.1016/j.biosystems.2025.105477},
pmid = {40324712},
issn = {1872-8324},
mesh = {Animals ; Humans ; *Biological Evolution ; *Models, Biological ; },
abstract = {Organismal boundaries might seem like a straightforward and unproblematic organismal feature to study. They serve as fundamental demarcation lines that differentiate life from its environment, define identity, and maintain the functionality of organisms. But do they amount to an actual demarcation of organismal self? In this paper, we examine the philosophical and biological underpinnings of these boundaries, explore the essentialist and non-essentialist perspectives, and categorise organismal boundaries into three types: life-defining, physical, and those based on structural coupling. We shall argue largely against excessive reliance on physical boundaries, point to the inconsistencies and limitations of such thinking with the help of some formal approaches to boundaries (e.g., Markov blankets or theories such as (M, R) systems or the theory of autopoiesis), and try to harmonise the approaches by introducing a concept of boundary based on structural coupling. Autopoietic systems, such as cells, are structurally coupled to their environment, meaning their structures and those of their environment constantly influence each other. Organisms exhibit varying levels of the coupling capacity, of extending beyond their membranes to modify environments on scales ranging from molecular to planetary. Unicellular organisms, colonies, and multicellular entities construct niches that shape their survival and evolution. Building on the niche construction theory, we introduce the concept of microniches to describe various controlled spaces within organisms whose status of 'internal' is not always straightforward from the host perspective (e.g., intercellular spaces, digestive systems, or xylem). In the next step, we explain how these microniches are a direct result of structural coupling and how this concept can explain what is or is not part of a biological entity. We conclude with a discussion of Kantian organic wholes, starting with the cell in its entirety enclosed by a membrane and moving on to higher-order structures such as multicellular organisms or colonies, which differ in how they are established. Organic wholes of various levels are defined by informational boundaries and shared evolutionary norms that enable cohesion, cooperation, and distinction from the external environment across diverse biological and cultural systems. By integrating various philosophical and biological perspectives, we want to deepen our understanding of how life defines and sustains its boundaries and challenge certain established forms of thinking about organismal boundaries, which often rely on the physical or spatial approach.},
}

Animals
Humans
*Biological Evolution
*Models, Biological

@article {pmid40324073,
year = {2025},
author = {Hoffman, PF},
title = {Ecosystem relocation on Snowball Earth: Polar-alpine ancestry of the extant surface biosphere?.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {20},
pages = {e2414059122},
pmid = {40324073},
issn = {1091-6490},
support = {EAR-0417422//NSF (NSF)/ ; },
mesh = {*Ecosystem ; Earth, Planet ; Oceans and Seas ; Ice Cover ; Fossils ; Biological Evolution ; },
abstract = {Geological observations informed by climate dynamics imply that the oceans were 99.9% covered by light-blocking ice shelves during two discrete, self-reversing Snowball Earth epochs spanning a combined 60 to 70 Myr of the Cryogenian Period (720 to 635 Ma). The timescale for initial ice advances across the tropical oceans is ~300 y in an ice-atmosphere-ocean general circulation model in Cryogenian paleogeography. Areas of optically thin oceanic ice are usually invoked to account for fossil marine phototrophs, including macroscopic multicellular eukaryotes, before and after each Snowball, but different taxa. Ecosystem relocation is a scenario that does not require thin marine ice. Assume that long before Cryogenian Snowballs, diverse supra- and periglacial biomes were established in polar-alpine regions. When the Snowball onsets occurred, those biomes migrated in step with their ice margins to the equatorial zone of net sublimation. There, they prospered and evolved, their habitat areas expanded, and the cruelty of winter reduced. Nutrients were supplied by dust (loess) derived from cozonal ablative lands where surface winds were strong. When each Snowball finally ended, those biomes were mostly inundated by the meltwater-dominated and rapidly warming lid of a nutrient-rich but depauperate ocean. Some taxa returned to the mountaintops while others restocked the oceans. This ecosystem relocation scenario makes testable predictions. The lineages required for post-Cryogenian biotic radiations should be present in modern polar-alpine biomes. Legacies of polar-alpine ancestry should be found in the genomes of living organisms. Examples of such tests are highlighted herein.},
}

*Ecosystem
Earth, Planet
Oceans and Seas
Ice Cover
Fossils
Biological Evolution

@article {pmid40320517,
year = {2025},
author = {Khan, I and Guo, J and Karamat, U and Li, G and Fu, M},
title = {Identification and expression profiles of tubby‑like proteins coding genes in Brassica rapa (B. rapa) in response to hormone and drought stress.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {584},
pmid = {40320517},
issn = {1471-2229},
mesh = {*Brassica rapa/genetics/physiology/metabolism/drug effects ; *Droughts ; *Plant Proteins/genetics/metabolism ; *Plant Growth Regulators/metabolism/pharmacology ; Gene Expression Regulation, Plant/drug effects ; Stress, Physiological/genetics ; Abscisic Acid/pharmacology ; Gene Expression Profiling ; Ethylenes/pharmacology/metabolism ; Multigene Family ; Phylogeny ; Genes, Plant ; },
abstract = {BACKGROUND: Tubby-like proteins (TLPs) are a widespread multigene family found in single-celled to multicellular eukaryotes. Despite their significance, no reports of TLPs in B. rapa have been made up to this point.

RESULTS: Herein, we identified 14 TLPs in the B. rapa genome and renamed them BrTUB1-BrTUB14 based on their chromosomal location. The bulk of BrTUB proteins contain two characteristic domains: the F-box and Tubby domains. Subcellular localization prediction confirmed that BrTUBs are localized in the nucleus. Expression profiling showed that many BrTUB reacts to a variety of stressors, including drought stress and hormonal treatments (ABA and ethylene). In particular, the BrTUB1 displayed elevated expression to ABA and the drought stress treatment.

CONCLUSION: This study is the first thorough identification of the BrTUB family, providing critical insights into its function and regulation, and laying the groundwork for future functional analyses, particularly concerning drought tolerance of B. rapa.},
}

*Brassica rapa/genetics/physiology/metabolism/drug effects
*Droughts
*Plant Proteins/genetics/metabolism
*Plant Growth Regulators/metabolism/pharmacology
Gene Expression Regulation, Plant/drug effects
Stress, Physiological/genetics
Abscisic Acid/pharmacology
Gene Expression Profiling
Ethylenes/pharmacology/metabolism
Multigene Family
Phylogeny
Genes, Plant

@article {pmid40320413,
year = {2025},
author = {Liu, J and Costello, JH and Kanso, E},
title = {Flow physics of nutrient transport drives functional design of ciliates.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {4154},
pmid = {40320413},
issn = {2041-1723},
support = {RAISE IOS-2034043//National Science Foundation (NSF)/ ; CBET-210020//National Science Foundation (NSF)/ ; R01-HL153622//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; N00014-19-1-2035//United States Department of Defense | United States Navy | ONR | Office of Naval Research Global (ONR Global)/ ; },
mesh = {*Cilia/physiology/metabolism ; *Ciliophora/physiology/metabolism ; *Nutrients/metabolism ; Biological Transport ; Models, Biological ; Animals ; Phagocytosis/physiology ; },
abstract = {Phagotrophy, the ability of cells to ingest organic particles, marked a pivotal milestone in evolution, enabling the emergence of single-celled eukaryotes that consume other organisms and leading to multicellular life. However, reliance on food particles also created a mechanical challenge-how to coordinate the transfer of particles from the exterior environment to the cell interior? Here, we investigate this important link using mechanistic models of ciliates, a clade of single-celled eukaryotes that either swim or attach and generate feeding currents to capture prey. We demonstrate that ciliates optimize their feeding efficiency by designating a specific portion of the cell surface as a 'mouth,' and optimal cilia coverage varies by life strategy: for sessile ciliates, prey encounter is most efficient when cilia are arranged in bands around oral structures while ciliates that swim display diverse ciliary arrangements that meet the cell's nutritional needs. Importantly, beyond a threshold of doubling nutrient uptake, further increases in feeding flux do not seem to be a dominant selective force in cell design.},
}

*Cilia/physiology/metabolism
*Ciliophora/physiology/metabolism
*Nutrients/metabolism
Biological Transport
Models, Biological
Animals
Phagocytosis/physiology

@article {pmid40320202,
year = {2025},
author = {Gordon, R},
title = {A call for research on the basis for polygonal pleomorphism in archaea.},
journal = {Bio Systems},
volume = {252},
number = {},
pages = {105478},
doi = {10.1016/j.biosystems.2025.105478},
pmid = {40320202},
issn = {1872-8324},
mesh = {*Archaea/physiology/cytology ; Biological Evolution ; *Morphogenesis/physiology ; },
abstract = {Morphogenesis is a major unsolved problem. It is usually tackled in the embryogenesis of multicellular organisms, but rarely leans on studies of single-cell organisms. But the latter often have fascinating, puzzling shapes, whose understanding may be key to multicellular embryogenesis, wound healing, and regeneration. Here, I call for new directions in studying what may have been the first shaped, single-celled organisms, the Domain of Archaea, which might have been LUCA (Last Universal Common Ancestor), the first organisms at the origin of life. While their shaping is usually attributed to the "crystallinity" of the S-layer, this may have the liquidity of a bubble raft.},
}

*Archaea/physiology/cytology
Biological Evolution
*Morphogenesis/physiology

@article {pmid40304066,
year = {2025},
author = {Kahwa, I and Omara, T and Ayesiga, I and Shah, K and Ambe, GNNN and Panwala, ZJ and Mbabazi, R and Iqbal, S and Kyarimpa, C and Nagawa, CB and Chauhan, NS},
title = {Nutraceutical benefits of seaweeds and their phytocompounds: a functional approach to disease prevention and management.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.14287},
pmid = {40304066},
issn = {1097-0010},
abstract = {Seaweeds (SWD), macroalgae or sea vegetables are a diverse group of over 9000 macroscopic and multicellular marine algae taxonomically classified (based on morphology and pigmentation) as green, brown and red algae. With microalgae, SWD represents one of the most researched oceanic resources turned to as treasure troves of bioactive compounds with ethnomedicinal, pharmaceutical, cosmeceutical and dietetic end-uses for millennia. This review compiles the nutraceutical uses of SWD and their bioactive compounds in nutrition and traditional management of diseases, offering future perspectives on using this group of organisms to improve human life. The review reveals that the nutraceutical application of SWD as nutrient-dense marine foods for treating diseases may be correlated with their inherent biosynthesis and possession of minerals, vitamins, dietary fibres and bioactive compounds. Compounds of algal origin have been validated and found to elicit antimicrobial, anti-inflammatory, free radical scavenging (antioxidant), antiproliferative and antidiabetic activities, among others. © 2025 Society of Chemical Industry.},
}

@article {pmid40300626,
year = {2025},
author = {Doulcier, G and Remigi, P and Rexin, D and Rainey, PB},
title = {Evolutionary dynamics of nascent multicellular lineages.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2045},
pages = {20241195},
pmid = {40300626},
issn = {1471-2954},
support = {//Max-Planck-Gesellschaft/ ; //Université de Recherche Paris Sciences et Lettres/ ; //Marsden Fund Council/Royal Society of New Zealand/ ; //John Templeton Foundation/ ; },
mesh = {*Biological Evolution ; },
abstract = {The evolution of multicellular organisms involves the emergence of cellular collectives that eventually become units of selection in their own right. The process can be facilitated by ecological conditions that impose heritable variance in fitness on nascent collectives, with long-term persistence depending on the capacity of competing lineages to transition reliably between soma- and germ-like stages of proto-life cycles. Prior work with experimental bacterial populations showed rapid increases in collective-level fitness, with the capacity to switch between life cycle phases being a particular focus of selection. Here, we report experiments in which the most successful lineage from the earlier study was further propagated for 10 life cycle generations under regimes that required different investments in the soma-like phase. To explore the adaptive significance of switching, a control was included in which reliable transitioning between life cycle phases was abolished. The switch proved central to the maintenance of fitness. Moreover, in a non-switch treatment, where solutions to producing a robust and enduring soma-phase were required, the evolution of mutL-dependent switching emerged de novo. A newly developed computational pipeline (colgen) was used to display the moment-by-moment evolutionary dynamics of lineages, providing rare visual evidence of the roles of chance, history and selection. Colgen, underpinned by a Bayesian model, was further used to propagate hundreds of mutations back through temporal genealogical series, predict lineages and time points corresponding to changes of likely adaptive significance, and in one instance, via a combination of targeted sequencing, genetics and analyses of fitness consequences, the adaptive significance of a single mutation was demonstrated. Overall, our results shed light on the mechanisms by which collectives adapt to new selective challenges and demonstrate the value of genealogy-centred approaches for investigating the dynamics of lineage-level selection.},
}

*Biological Evolution

@article {pmid40282684,
year = {2025},
author = {Sawada, Y and Daigaku, Y and Toma, K},
title = {Maximum Entropy Production Principle of Thermodynamics for the Birth and Evolution of Life.},
journal = {Entropy (Basel, Switzerland)},
volume = {27},
number = {4},
pages = {},
pmid = {40282684},
issn = {1099-4300},
abstract = {Research on the birth and evolution of life are reviewed with reference to the maximum entropy production principle (MEPP). It has been shown that this principle is essential for consistent understanding of the birth and evolution of life. First, a recent work for the birth of a self-replicative system as pre-RNA life is reviewed in relation to the MEPP. A critical condition of polymer concentration in a local system is reported by a dynamical system approach, above which, an exponential increase of entropy production is guaranteed. Secondly, research works of early stage of evolutions are reviewed; experimental research for the numbers of cells necessary for forming a multi-cellular organization, and numerical research of differentiation of a model system and its relation with MEPP. It is suggested by this review article that the late stage of evolution is characterized by formation of society and external entropy production. A hypothesis on the general route of evolution is discussed from the birth to the present life which follows the MEPP. Some examples of life which happened to face poor thermodynamic condition are presented with thermodynamic discussion. It is observed through this review that MEPP is consistently useful for thermodynamic understanding of birth and evolution of life, subject to a thermodynamic condition far from equilibrium.},
}

@article {pmid40276264,
year = {2025},
author = {Compton, ZT and Ågren, JA and Marusyk, A and Nedelcu, AM},
title = {The Elephant and the Spandrel.},
journal = {Evolution, medicine, and public health},
volume = {13},
number = {1},
pages = {92-100},
pmid = {40276264},
issn = {2050-6201},
abstract = {Comparative oncology has made great strides in identifying patterns of cancer prevalence and risk across the tree of life. Such studies have often centered on elucidating the evolution of mechanisms that prevent the development and progression of cancer, especially in large animals such as elephants. Conclusions from this approach, however, may have been exaggerated, given that the deep evolutionary origins of multicellularity suggest that the preeminent functions of the identified mechanisms may be unrelated to cancer. Instead, cancer suppression may have emerged as an evolutionary byproduct, or "spandrel". We propose a novel evolutionary perspective that highlights the importance of somatic maintenance as the underlying axis of natural selection. We argue that by shifting the focus of study from cancer suppression to somatic maintenance, we can gain a deeper understanding of the evolutionary pressures that shaped the mechanisms responsible for the observed variation in cancer prevalence across species.},
}

@article {pmid40263560,
year = {2025},
author = {Mukhopadhyay, J and Ngobeli, R and Ghosh, G and Elburg, MA},
title = {Age of the Western Iron Ore Group, India, and implications for pre-GOE oxygenation of oceans at the twilight of Archean-Proterozoic transition.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {13951},
pmid = {40263560},
issn = {2045-2322},
abstract = {Increasing concentrations of oxygen in the early atmosphere contributed to the development of the Earth's ozone shield and thus ushered in the growth of photoautotrophs. The proliferation of multicellular life is linked with the rise of atmospheric oxygen, known as the Great Oxidation Event (GOE). However, it has become evident that the permanent trend of rising oxygen in the atmosphere was preceded by multiple fluctuations. It is imperative to gather information from immediate pre- and post-GOE successions for constraining this transformation. The greenstone successions from > 3.8 Ga to the Archean-Proterozoic transition are important candidates for deciphering the evolution of the atmosphere and hydrosphere. The Archean Singhbhum craton, eastern India, hosts a well-preserved low-grade greenstone succession, the Western Iron Ore Group (W-IOG), containing banded iron formations (BIF) from pre-GOE stratigraphy. We report here zircon U-Pb LA-ICPMS age of ~ 2500 Ma from felsic tuff below the BIF and detrital zircon age of ~ 2730 Ma from underlying sandstones that constrain the age of the younger cycle of BIF deposition in the W-IOG as Neoarchean grading into the Paleoproterozoic. The newly reported Neoarchean to Paleoproterozoic age of the W-IOG provides potential opportunity for future research on the tempos and events immediately ahead of the GOE in the oceanic realm at the Archean-Proterozoic boundary.},
}

@article {pmid40263484,
year = {2025},
author = {Pai, VP and Pio-Lopez, L and Sperry, MM and Erickson, P and Tayyebi, P and Levin, M},
title = {Basal Xenobot transcriptomics reveals changes and novel control modality in cells freed from organismal influence.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {646},
pmid = {40263484},
issn = {2399-3642},
support = {S10 OD032203/OD/NIH HHS/United States ; 62212//John Templeton Foundation (JTF)/ ; },
mesh = {Animals ; *Transcriptome ; *Xenopus laevis/genetics/embryology ; Embryo, Nonmammalian/metabolism ; *Gene Expression Regulation, Developmental ; Gene Expression Profiling ; Ectoderm/metabolism/cytology ; },
abstract = {Would transcriptomes change if cell collectives acquired a novel morphogenetic and behavioral phenotype in the absence of genomic editing, transgenes, heterologous materials, or drugs? We investigate the effects of morphology and nascent emergent life history on gene expression in the basal (no engineering, no sculpting) form of Xenobots -autonomously motile constructs derived from Xenopus embryo ectodermal cell explants. To investigate gene expression differences between cells in the context of an embryo with those that have been freed from instructive signals and acquired novel lived experiences, we compare transcriptomes of these basal Xenobots with age-matched Xenopus embryos. Basal Xenobots show significantly larger inter-individual gene variability than age-matched embryos, suggesting increased exploration of the transcriptional space. We identify at least 537 (non-epidermal) transcripts uniquely upregulated in these Xenobots. Phylostratigraphy shows a majority of transcriptomic shifts in the basal Xenobots towards evolutionarily ancient transcripts. Pathway analyses indicate transcriptomic shifts in the categories of motility machinery, multicellularity, stress and immune response, metabolism, thanatotranscriptome, and sensory perception of sound and mechanical stimuli. We experimentally confirm that basal Xenobots respond to acoustic stimuli via changes in behavior. Together, these data may have implications for evolution, biomedicine, and synthetic morphoengineering.},
}

Animals
*Transcriptome
*Xenopus laevis/genetics/embryology
Embryo, Nonmammalian/metabolism
*Gene Expression Regulation, Developmental
Gene Expression Profiling
Ectoderm/metabolism/cytology

@article {pmid40262731,
year = {2025},
author = {Kong, Z and Zhu, L and Liu, Y and Liu, Y and Chen, G and Wang, H},
title = {Effects of different stages, dosages and courses of prenatal dexamethasone exposure on testicular development in mice.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {201},
number = {},
pages = {115468},
doi = {10.1016/j.fct.2025.115468},
pmid = {40262731},
issn = {1873-6351},
mesh = {Animals ; *Dexamethasone/administration & dosage/toxicity/adverse effects ; Male ; *Testis/drug effects/growth & development/embryology ; Female ; Pregnancy ; Mice ; *Prenatal Exposure Delayed Effects ; Testosterone/blood ; Dose-Response Relationship, Drug ; Leydig Cells/drug effects ; Apoptosis/drug effects ; Cell Proliferation/drug effects ; Sertoli Cells/drug effects ; },
abstract = {PURPOSE: Observe the effects of prenatal dexamethasone exposure (PDE) at different stages, dosages, and courses on testicular morphology and multicellular function in offspring mice.

METHODS: Pregnant Kunming mice were subjected to subcutaneous injections of dexamethasone at different stages [GD (gestational day) 14-15 and 16-17], dosages (0.2, 0.4, and 0.8 mg/kg·d), and courses (GD 14-15 and 14-17). Pregnant mice were euthanized on GD 18, and fetal serum and testicular samples were collected to assess serum testosterone level, testicular morphology, cellular proliferation/apoptosis function, expression of multicellular marker/functional gene, and the expression of developmental regulatory signalling pathways such as Notch and Wnt.

RESULTS: PDE could lead to widening of the interstitial area and reduction of seminiferous tubules in fetal testicular tissue, accompanied by significant impairment of Sertoli cell function, particularly evident during late gestation, at high doses, and with multiple courses. However, changes in Leydig cells and spermatogonia function of PDE are not significant. Furthermore, we discovered that PDE could activate the Notch signalling pathway in Sertoli cells while inhibiting the Wnt signalling pathway.

CONCLUSION: PDE could affect fetal testicular development, especially for Sertoli cells during late gestation, at high doses and multiple courses. This study confirms the effects of PDE on testicular tissue morphology and multicellular function, providing a comprehensive understanding of the testicular developmental toxicity of dexamethasone and evidence for guiding rational medication during pregnancy.},
}

Animals
*Dexamethasone/administration & dosage/toxicity/adverse effects
Male
*Testis/drug effects/growth & development/embryology
Female
Pregnancy
Mice
*Prenatal Exposure Delayed Effects
Testosterone/blood
Dose-Response Relationship, Drug
Leydig Cells/drug effects
Apoptosis/drug effects
Cell Proliferation/drug effects
Sertoli Cells/drug effects

@article {pmid40261324,
year = {2025},
author = {Hiralal, A and Ley, P and van Dijk, JR and Li, C and Pankratov, D and Alingapoyil Choyikutty, J and Pankratova, G and Geelhoed, JS and Vasquez-Cardenas, D and Reimers, CE and Meysman, FJR},
title = {A novel cable bacteria species with a distinct morphology and genomic potential.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {5},
pages = {e0250224},
pmid = {40261324},
issn = {1098-5336},
support = {N00014-17-1-2599,N00014-21-1-2251//Office of Naval Research/ ; M/A-02R/ECO-59-PD//Oregon State University/ ; 11D7822N,1139224N,S004523N//Research Foundation Flanders/ ; 101081327//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; PRINGLE 101046719//HORIZON EUROPE European Innovation Council/ ; },
mesh = {Phylogeny ; *Genome, Bacterial ; *Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics/analysis ; *Bacteria/genetics/classification ; Genomics ; },
abstract = {Cable bacteria form a group of multicellular prokaryotes that enable electron transfer over centimeter-scale distances within marine and freshwater sediments. To this end, the periplasm of these filamentous bacteria contains specialized conductive fibers, which extend along the full length of each filament and incorporate a novel Ni-containing NiBiD cofactor. Currently, the cable bacteria include two recognized genera, Candidatus Electrothrix and Candidatus Electronema, but the genetic and morphological diversity within the clade remains underexplored. Here, we report the isolation and characterization of a novel cable bacteria species from an intertidal estuarine mudflat within Yaquina Bay (Oregon, USA). A clonal enrichment culture of a single strain (designated YB6) was generated, and filaments were subjected to genomic, morphological, spectroscopic, and electrical characterization. Strain YB6 shares key physiological traits with other cable bacteria, such as long-distance electron conduction and the presence of the nickel bis(dithiolene) cofactor. At the same time, YB6 exhibits distinctive morphological features, including pronounced surface ridges that are up to three times wider than in other cable bacteria. Additionally, filaments are extensively enveloped by extracellular sheaths. Genomic analysis reveals that strain YB6 harbors metabolic pathways and genes found in both the Ca. Electrothrix and Ca. Electronema genera. Phylogenetic and phylogenomic analyses indicate that strain YB6 represents a novel species (average nucleotide identity <95%) that forms an early branch within the Ca. Electrothrix clade. The proposed name is Ca. Electrothrix yaqonensis sp. nov., honoring the Yako'n tribe of Native Americans whose ancestral lands encompassed Yaquina Bay.IMPORTANCEThis study expands our understanding of the genetic and morphological diversity of cable bacteria, a group of prokaryotes with a unique metabolism based on long-range conduction. We present the detailed morphological and genomic characterization of a novel species: Ca. Electrothrix yaqonensis, strain YB6, isolated from an intertidal estuarine mudflat. Importantly, the strain exhibits a distinctive ridge morphology (harboring the conductive fibers) and abundant formation of extracellular sheaths. Genomic analysis reveals that YB6 shares metabolic features with both Ca. Electrothrix and Ca. Electronema genera.},
}

Phylogeny
*Genome, Bacterial
*Geologic Sediments/microbiology
RNA, Ribosomal, 16S/genetics/analysis
*Bacteria/genetics/classification
Genomics

@article {pmid40254399,
year = {2025},
author = {Durymanov, M},
title = {Tumor Spheroids, Tumor Organoids, Tumor Explants, and Tumoroids: What Are the Differences between Them?.},
journal = {Biochemistry. Biokhimiia},
volume = {90},
number = {2},
pages = {200-213},
doi = {10.1134/S0006297924604234},
pmid = {40254399},
issn = {1608-3040},
mesh = {Humans ; *Organoids/pathology/metabolism ; *Spheroids, Cellular/pathology/metabolism ; *Neoplasms/pathology/metabolism ; Tumor Microenvironment ; Animals ; Cell Culture Techniques, Three Dimensional ; },
abstract = {Three-dimensional (3D) cell cultures that mimic tumor microenvironment have become an essential tool in cancer research and drug response analysis, significantly enhancing our understanding of tumor biology and advancing personalized medicine. Currently, the most widely mentioned 3D multicellular culture models include spheroids, organoids, tumor explants, and tumoroids. These 3D structures, exploited for various applications, are generated from cancer and non-cancer cells of different origin using multiple techniques. However, despite extensive research and numerous studies, consistent definitions of these 3D culture models are not clearly established. The manuscript provides a comprehensive overview of these models, detailing brief history of their research, unique biological characteristics, advantages, limitations, and specific applications.},
}

Humans
*Organoids/pathology/metabolism
*Spheroids, Cellular/pathology/metabolism
*Neoplasms/pathology/metabolism
Tumor Microenvironment
Animals
Cell Culture Techniques, Three Dimensional

@article {pmid40245677,
year = {2025},
author = {Tsubota, KI and Horikoshi, S and Hiraiwa, T and Okuda, S},
title = {Strain softening and hysteresis arising from 3D multicellular dynamics during long-term large deformation.},
journal = {Journal of the mechanical behavior of biomedical materials},
volume = {168},
number = {},
pages = {107001},
doi = {10.1016/j.jmbbm.2025.107001},
pmid = {40245677},
issn = {1878-0180},
mesh = {*Stress, Mechanical ; Biomechanical Phenomena ; Viscosity ; Elasticity ; Animals ; Humans ; },
abstract = {Living tissues exhibit complex mechanical properties, including viscoelastic and elastoplastic responses, that are crucial for regulating cell behaviors and tissue deformations. Despite their significance, the intricate properties of three-dimensional (3D) cell constructs are not well understood and are inadequately implemented in biomaterial engineering. To address this gap, we developed a numerical method to analyze the dynamic properties of cell constructs using a 3D vertex model framework. By focusing on 3D tissues composed of confluent homogeneous cells, we characterized their properties in response to various deformation magnitudes and time scales. Stress relaxation tests revealed that large deformations initially induced relaxation in the shapes of individual cells. This process is amplified by subsequent transient cell rearrangements, homogenizing cell shapes and leading to tissue fluidization. Additionally, dynamic viscoelastic analyses showed that tissues exhibited strain softening and hysteresis during large deformations. Interestingly, this strain softening originates from multicellular structures independent of cell rearrangement, while hysteresis arises from cell rearrangement. Moreover, tissues exhibit elastoplastic responses over the long term, which are well represented by the Ramberg-Osgood model. These findings highlight the characteristic properties of cell constructs emerging from their structures and rearrangements, especially during long-term large deformations. The developed method offers a new approach to uncover the dynamic nature of 3D tissue mechanics and could serve as a technical foundation for exploring tissue mechanics and advancing biomaterial engineering.},
}

*Stress, Mechanical
Biomechanical Phenomena
Viscosity
Elasticity
Animals
Humans

@article {pmid40231984,
year = {2025},
author = {Chen, C and Zhao, H and Yuan, W and Chen, H and Wang, P and Wang, Q and Chen, C and Song, T},
title = {Tumoral Nanovesicles-Loaded Magnetotactic Bacteria for Tumor-Targeted Therapy under a Swing Magnetic Field.},
journal = {ACS applied materials & interfaces},
volume = {17},
number = {17},
pages = {25048-25058},
doi = {10.1021/acsami.5c02422},
pmid = {40231984},
issn = {1944-8252},
mesh = {Humans ; Magnetic Fields ; Mice ; Animals ; Reactive Oxygen Species/metabolism ; *Neoplasms/drug therapy/pathology ; Cell Line, Tumor ; *Magnetospirillum/chemistry ; *Antineoplastic Agents/chemistry/pharmacology ; Cell Survival/drug effects ; Mice, Inbred BALB C ; },
abstract = {Tumor heterogeneity poses numerous challenges for targeted drug therapy. Although tumor cell-derived nanovesicles (NVs) have emerged as an intriguing method for tumor targeting, how to exert the antitumor effect after targeting remains a key concern. Magnetotactic bacteria (MTB) synthesize chain-like magnetite (Fe3O4) crystals with inherent magnetic moments, which could generate significant torque under a desired magnetic field and move along the magnetic field using their own flagella. Herein, a composite of MTB AMB-1 and NVs was fabricated via electrostatic adsorption where AMB-1 could transport NVs to the tumor site by a guiding magnetic field, while NVs also assist AMB-1 in binding to tumor cells. Subsequently, under the influence of a swing magnetic field (sMF), MTB exert physical stimuli on the cells, inducing the changes of mitochondrial membrane potential and cellular reactive oxygen species (ROS). Finally, it is revealed that the NVs-loaded AMB-1 induced a decrease in cellular viability and significantly inhibited the growth of tumors in vivo under the sMF. Therefore, by remote control of the guidance and stimuli production, the NVs-loaded AMB-1 was highly promising to advance the development of targeted therapeutic strategies for tumors under the context of tumor heterogeneity.},
}

Humans
Magnetic Fields
Mice
Animals
Reactive Oxygen Species/metabolism
*Neoplasms/drug therapy/pathology
Cell Line, Tumor
*Magnetospirillum/chemistry
*Antineoplastic Agents/chemistry/pharmacology
Cell Survival/drug effects
Mice, Inbred BALB C

@article {pmid40230370,
year = {2025},
author = {Jahan, I and Scott, TJ and Strassmann, JE and Queller, DC},
title = {Testing the coordination hypothesis: incompatibilities in aggregative development of an experimentally evolved social amoeba.},
journal = {Evolution letters},
volume = {9},
number = {2},
pages = {236-248},
pmid = {40230370},
issn = {2056-3744},
abstract = {Multicellular organisms that form by aggregation of cells arguably do not achieve high levels of complexity. Conflict among the cells is a widely accepted explanation for this, but an alternative hypothesis is that mixing cells of different genotypes leads to failures of coordination, which we call the "coordination hypothesis." We empirically tested the coordination hypothesis in the social amoeba Dictyostelium discoideum. We mixed D. discoideum clones that had evolved in isolation for generations and acquired mutations that have not been tested against each other by selection. To quantify the effect of incompatibilities, we measured performance in terms of the developmental traits of slug migration and spore production. Importantly, we mixed lines evolved from the same ancestor under conditions that would not select for the evolution of de novo kin recognition. Our results show no evidence of incompatibilities in four traits related to the coordinated movement of slugs toward light in the social amoeba. Spore production was higher than expected in mixtures, in apparent contradiction to the coordination hypothesis. However, we found support for coordination incompatibilities in an interaction between migration and spore production: in mixtures, fewer cells succeeded at both migrating and becoming spores.},
}

@article {pmid40228789,
year = {2025},
author = {McFarland, A and Fenton, M and Madsen, JJ and Ye, L},
title = {Unraveling a Receptor-Mediated Bioluminescence Signaling Pathway in Red Tide Algae.},
journal = {Journal of molecular biology},
volume = {437},
number = {13},
pages = {169153},
doi = {10.1016/j.jmb.2025.169153},
pmid = {40228789},
issn = {1089-8638},
mesh = {*Receptors, G-Protein-Coupled/metabolism/genetics ; *Signal Transduction ; *Dinoflagellida/metabolism/genetics ; *Harmful Algal Bloom ; Luminescence ; Humans ; },
abstract = {G protein-coupled receptors (GPCRs) are ubiquitous transmembrane proteins in multicellular life. Human vision, taste, and neuron activity are all mediated by GPCRs, and a large percentage of currently approved drugs target GPCRs. However, our understanding of GPCRs in single-celled eukaryotes is incomplete, and many of the components of GPCR signal transduction are underrepresented in protists. Previous works studying bioluminescent dinoflagellates-single-celled algae involved in coral reef endosymbiosis and toxic red tide blooms-implicate GPCRs in a signaling pathway for bioluminescence but have not elucidated the individual components comprising the pathway. Herein, we identified a novel GPCR in dinoflagellates-Bioluminescence-Inducing Receptor 1 (BIR1)-which plays a significant role in the signaling pathway for bioluminescence in red tide blooms in response to wave turbulence. Additionally, we identified a full endogenous G-protein complex and downstream effectors that are integral to known calcium signaling networks. Based on these identifications, we used knockdown and knockout techniques to demonstrate the integral role of BIR1 in bioluminescence and highlight its role in predator response and shear force-elicited GPCR signaling in red tide blooms. This advance opens avenues for red tide control and supports the existence of similar GPCR pathways involved in bloom toxicity dynamics.},
}

*Receptors, G-Protein-Coupled/metabolism/genetics
*Signal Transduction
*Dinoflagellida/metabolism/genetics
*Harmful Algal Bloom
Luminescence
Humans

@article {pmid40226989,
year = {2025},
author = {Lv, CL and Li, B},
title = {Interface morphodynamics in living tissues.},
journal = {Soft matter},
volume = {21},
number = {19},
pages = {3670-3687},
doi = {10.1039/d5sm00145e},
pmid = {40226989},
issn = {1744-6848},
mesh = {Humans ; Extracellular Matrix/metabolism ; Animals ; *Morphogenesis ; Models, Biological ; Cell Adhesion ; },
abstract = {Interfaces between distinct tissues or between tissues and environments are common in multicellular organisms. The evolution and stability of these interfaces are essential for tissue development, and their dysfunction can lead to diseases such as cancer. Mounting efforts, either theoretical or experimental, have been devoted to uncovering the morphodynamics of tissue interfaces. Here, we review the recent progress of studies on interface morphodynamics. The regulatory mechanisms governing interface evolution are dissected, with a focus on adhesion, cortical tension, cell activity, extracellular matrix, and microenvironment. We examine the methodologies used to study morphodynamics, emphasizing the characteristics of experimental techniques and theoretical models. Finally, we explore the broader implications of interface morphodynamics in tissue morphogenesis and diseases, offering a comprehensive perspective on this rapidly developing field.},
}

Humans
Extracellular Matrix/metabolism
Animals
*Morphogenesis
Models, Biological
Cell Adhesion

@article {pmid40220996,
year = {2025},
author = {Page-McCaw, PS and Pokidysheva, EN and Darris, CE and Chetyrkin, S and Fidler, AL and Gallup, J and , and Murawala, P and Hudson, JK and Boudko, SP and Hudson, BG},
title = {Collagen IV of basement membranes: I. Origin and diversification of COL4 genes enabling metazoan multicellularity, evolution, and adaptation.},
journal = {The Journal of biological chemistry},
volume = {301},
number = {5},
pages = {108496},
pmid = {40220996},
issn = {1083-351X},
support = {R01 DK018381/DK/NIDDK NIH HHS/United States ; R01 DK131101/DK/NIDDK NIH HHS/United States ; R25 DK096999/DK/NIDDK NIH HHS/United States ; },
mesh = {*Collagen Type IV/genetics/metabolism/chemistry ; Animals ; Humans ; *Evolution, Molecular ; Phylogeny ; *Basement Membrane/metabolism ; Nephritis, Hereditary/genetics/metabolism ; },
abstract = {Collagen IV (Col-IV) is a major component of basement membranes, a specialized form of extracellular matrix that enabled the assembly of multicellular epithelial tissues. In mammals, Col-IV assembles from a family of six α-chains (α1-α6), forming three supramolecular scaffolds: Col-IV[α121], Col-IV[α345], and Col-IV[α121-α556]. The α-chains are encoded by six genes (COL4A1-6) that occur in pairs in a head-to-head arrangement. In Alport syndrome, variants in COL4A3, 4, or 5 genes, encoding Col-IV[α345] scaffold in glomerular basement membrane (GBM), the kidney ultrafilter, cause progressive renal failure in millions of people worldwide. The molecular mechanisms of how variants cause dysfunction remain obscure. Here, we gained insights into Col-IV[α345] function by determining its evolutionary lineage, as revealed from phylogenetic analyses and tissue expression of COL4 gene pairs. We found that the COL4A⟨1|2⟩ gene pair emerged in basal Ctenophores and Cnidaria phyla and is highly conserved across metazoans. The COL4A⟨1|2⟩ duplicated and arose as the progenitor to the COL4A⟨3|4⟩ gene pair in cyclostomes, coinciding with emergence of kidney GBM, and expressed and conserved in jawed vertebrates, except for amphibians, and a second duplication as the progenitor to the COL4A⟨5|6⟩ gene pair and conserved in jawed vertebrates. These findings revealed that Col-IV[α121] is the progenitor scaffold, expressed ubiquitously in metazoan basement membranes, and which evolved into vertebrate Col-IV[α345] and expressed in GBM. The Col-IV[α345] scaffold, in comparison, has an increased number of cysteine residues, varying in number with osmolarity of the environment. Cysteines mediate disulfide crosslinks between protomers, an adaptation enabling a compact GBM that withstands the high hydrostatic pressure associated with glomerular ultrafiltration.},
}

*Collagen Type IV/genetics/metabolism/chemistry
Animals
Humans
*Evolution, Molecular
Phylogeny
*Basement Membrane/metabolism
Nephritis, Hereditary/genetics/metabolism

@article {pmid40214419,
year = {2025},
author = {Wei, Y and Chen, H and Li, X and Wang, Z and Song, T},
title = {A magneto-optical microscopic control system for analysis of magnetotaxis and phototaxis sensing in magnetotactic bacteria.},
journal = {The Review of scientific instruments},
volume = {96},
number = {4},
pages = {},
doi = {10.1063/5.0254144},
pmid = {40214419},
issn = {1089-7623},
mesh = {*Magnetospirillum/physiology ; Magnetic Fields ; *Phototaxis ; *Microscopy/instrumentation/methods ; Bacterial Proteins/metabolism ; Light ; },
abstract = {A magneto-optical microscopic control system (MO-MCS) was developed for analyzing the magnetotaxis and phototaxis sensing in magnetotactic bacteria (MTB). The system includes a microscopic image acquisition device, a planar magnetic field generator, a multi-wavelength illumination device, and a host computer control system. The MO-MCS can accurately adjust parameters such as the magnetic field intensity, direction, and the duration and intensity of illumination. Using the system, we analyzed the motion characteristics of Magnetospirillum magneticum AMB-1 wild-type and corresponding mutant strains under various illumination conditions when the magnetic field was reversed. The experiments indicated that the photoreceptor protein Amb2291 and the magnetosensitive protein Amb0994 play complementary roles in the motion behavior of bacteria in response to magnetic field changes under blue light. The MO-MCS provides a valuable tool for investigating the response mechanisms of micro-organisms to environmental physical factors.},
}

*Magnetospirillum/physiology
Magnetic Fields
*Phototaxis
*Microscopy/instrumentation/methods
Bacterial Proteins/metabolism
Light

@article {pmid40188154,
year = {2025},
author = {Nguyen, AQ and Huang, J and Bi, D},
title = {Origin of yield stress and mechanical plasticity in model biological tissues.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3260},
pmid = {40188154},
issn = {2041-1723},
support = {R35 GM150494/GM/NIGMS NIH HHS/United States ; PHY-2019745//National Science Foundation (NSF)/ ; RGP0007/2022//Human Frontier Science Program (HFSP)/ ; DMR-2046683//National Science Foundation (NSF)/ ; },
mesh = {*Stress, Mechanical ; *Models, Biological ; Biomechanical Phenomena ; Animals ; Humans ; },
abstract = {During development and under normal physiological conditions, biological tissues are continuously subjected to substantial mechanical stresses. In response to large deformations, cells in a tissue must undergo multicellular rearrangements to maintain integrity and robustness. However, how these events are connected in time and space remains unknown. Here, using theoretical modeling, we study the mechanical plasticity of cell monolayers under large deformations. Our results suggest that the jamming-unjamming (solid-fluid) transition can vary significantly depending on the degree of deformation, implying that tissues are highly unconventional materials. We elucidate the origins of this behavior. We also demonstrate how large deformations are accommodated through a series of cellular rearrangements, similar to avalanches in non-living materials. We find that these 'tissue avalanches' are governed by stress redistribution and the spatial distribution of "soft" or vulnerable spots, which are more prone to undergo rearrangements. Finally, we propose a simple and experimentally accessible framework to infer tissue-level stress and predict avalanches based on static images.},
}

*Stress, Mechanical
*Models, Biological
Biomechanical Phenomena
Animals
Humans

@article {pmid40183649,
year = {2025},
author = {Zielenkiewicz, U and Kaushal, V and Kaczanowski, S},
title = {On the origins and evolution of apoptosis: the predator‒mitochondrial prey hypothesis.},
journal = {Journal of evolutionary biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jeb/voaf039},
pmid = {40183649},
issn = {1420-9101},
abstract = {Different types of programmed cell death have been described both in unicellular and multicellular organisms. The fundamental mode of eukaryotic cell death is programmed cell death initiated by mitochondria, which is frequently referred to as apoptosis (or mitochondrial apoptosis). It is initiated by mitochondria through mitochondrial permeability transition and the release of apoptotic factors. It is widely thought that mitochondrial apoptosis evolved concurrently with mitochondrial domestication. Programmed cell death initiated by mitochondria is observed in various multicellular and unicellular eukaryotes. We discuss key hypotheses-namely, the "pleiotropy", "addiction", "immunological", and our "predator-mitochondrial prey" hypotheses-to explain the mechanisms of mitochondrial domestication that lead to apoptosis. In this perspective paper, we present evidence from various phylogenetic and experimental studies that strongly indicates our hypothesis is the most plausible. For the first time, we also present evidence that challenges the assumptions underlying all other hypotheses.},
}

@article {pmid40181506,
year = {2025},
author = {Lewis, EM and Becker, O and Symons, AN and LaCoss, C and Baclig, AJ and Guzman, A and Sanders, C and Gonzalez, L and Warner, LR and Lewis, KA},
title = {The LARP6 La module from Tetrabaena socialis reveals structural and functional differences from plant and animal LARP6 homologues.},
journal = {RNA biology},
volume = {22},
number = {1},
pages = {1-9},
pmid = {40181506},
issn = {1555-8584},
support = {T34 GM136483/GM/NIGMS NIH HHS/United States ; R15 GM141770/GM/NIGMS NIH HHS/United States ; P20 GM103408/GM/NIGMS NIH HHS/United States ; P20 GM109095/GM/NIGMS NIH HHS/United States ; R15 GM119096/GM/NIGMS NIH HHS/United States ; },
mesh = {*Ribonucleoproteins/chemistry/metabolism/genetics ; Animals ; *Autoantigens/chemistry/metabolism/genetics ; SS-B Antigen ; Models, Molecular ; Protein Binding ; Amino Acid Sequence ; *RNA-Binding Proteins/metabolism/chemistry/genetics ; Nucleic Acid Conformation ; *Chlorophyta/genetics/metabolism ; },
abstract = {This study identified the LARP6 La Module from Tetrabaena socialis (T. socialis), a four-celled green algae, in an effort to better understand the evolution of LARP6 structure and RNA-binding activity in multicellular eukaryotes. Using a combination of sequence alignments, domain boundary screens, and structural modelling, we recombinantly expressed and isolated the TsLARP6 La Module to > 98% purity for in vitro biochemical characterization. The La Module is stably folded and exerts minimal RNA binding activity against single-stranded homopolymeric RNAs. Surprisingly, it exhibits low micromolar binding affinity for the vertebrate LARP6 cognate ligand, a bulged-stem loop found in the 5'UTR of collagen type I mRNA, but does not bind double-stranded RNAs of similar size. These result suggests that the TsLARP6 La Module may prefer structured RNA ligands. In contrast, however, the TsLARP6 La Module does not exhibit the RNA chaperone activity that is observed in vertebrate homologs. Therefore, we conclude that protist LARP6 may have both distinct RNA ligands and binding mechanisms from the previously characterized LARP6 proteins of animals and vascular plants, thus establishing a distinct third class of the LARP6 protein family.},
}

*Ribonucleoproteins/chemistry/metabolism/genetics
Animals
*Autoantigens/chemistry/metabolism/genetics
SS-B Antigen
Models, Molecular
Protein Binding
Amino Acid Sequence
*RNA-Binding Proteins/metabolism/chemistry/genetics
Nucleic Acid Conformation
*Chlorophyta/genetics/metabolism

@article {pmid40179202,
year = {2025},
author = {Pillai, EK and Brunet, T},
title = {Archaea go multicellular under pressure.},
journal = {Science (New York, N.Y.)},
volume = {388},
number = {6742},
pages = {28-29},
doi = {10.1126/science.adw6689},
pmid = {40179202},
issn = {1095-9203},
mesh = {Cell Division ; *Haloferax volcanii/cytology/physiology ; Oceans and Seas ; Pressure ; *Seawater/microbiology ; },
abstract = {A microbe from the Dead Sea switches to a tissue-like form when compressed.},
}

Cell Division
*Haloferax volcanii/cytology/physiology
Oceans and Seas
Pressure
*Seawater/microbiology