@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},
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},
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.},
}

@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},
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.},
}

@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 {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 = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.05.052},
pmid = {40532703},
issn = {1879-0445},
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.},
}

@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},
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.},
}

@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 = {},
number = {},
pages = {e0007125},
doi = {10.1128/jb.00071-25},
pmid = {40525847},
issn = {1098-5530},
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.},
}

@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 = {},
doi = {10.1242/dmm.052313},
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-Muinos, FX},
title = {Unconventional role of ATG16L1 in the control of ATP compartmentalization during apoptosis.},
journal = {Autophagy},
volume = {},
number = {},
pages = {},
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 Farias, ST},
title = {Major Transitions in the Physiological Machinery of Cognition.},
journal = {Bio Systems},
volume = {},
number = {},
pages = {105517},
doi = {10.1016/j.biosystems.2025.105517},
pmid = {40499887},
issn = {1872-8324},
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.},
}

@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 = {},
doi = {10.1016/j.neuron.2025.05.019},
pmid = {40499536},
issn = {1097-4199},
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 {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 = {},
number = {},
pages = {e0036325},
doi = {10.1128/jvi.00363-25},
pmid = {40488621},
issn = {1098-5514},
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.},
}

@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 = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00036},
pmid = {40476774},
issn = {2161-5063},
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.},
}

@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 = {},
doi = {10.1101/2025.05.14.654023},
pmid = {40462939},
issn = {2692-8205},
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 = {},
number = {},
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 {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 {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},
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.},
}

@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},
doi = {10.1073/pnas.2423311122},
pmid = {40392851},
issn = {1091-6490},
support = {R35GM133428//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; T32 AG066574/AG/NIA NIH HHS/United States ; Pew Scholarship//Pew Charitable Trusts (PEW)/ ; Career Award at the Scientific Interface//Burroughs Wellcome Fund (BWF)/ ; Discovery Center for Cell Lineage Tracing//Allen Foundation (The Allen Foundation)/ ; },
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, IK and Khatri, S and Herron, MD and Rosenzweig, F},
title = {Genetic predisposition towards multicellularity in Chlamydomonas reinhardtii.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf090},
pmid = {40380887},
issn = {1759-6653},
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 four 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 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.},
}

@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},
doi = {10.1128/aem.02502-24},
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 {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},
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.},
}

@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 = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.04.044},
pmid = {40345196},
issn = {1879-0445},
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.},
}

@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 = {},
number = {},
pages = {e2503557},
doi = {10.1002/advs.202503557},
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/ ; },
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.},
}

@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},
doi = {10.1126/sciadv.adr8298},
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},
doi = {10.3724/SP.J.1123.2024.05003},
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 = {},
number = {},
pages = {105477},
doi = {10.1016/j.biosystems.2025.105477},
pmid = {40324712},
issn = {1872-8324},
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.},
}

@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},
doi = {10.1073/pnas.2414059122},
pmid = {40324073},
issn = {1091-6490},
support = {EAR-0417422//NSF (NSF)/ ; },
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.},
}

@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)/ ; },
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.},
}

@article {pmid40320202,
year = {2025},
author = {Gordon, R},
title = {A Call for Research on the Basis for Polygonal Pleomorphism in Archaea.},
journal = {Bio Systems},
volume = {},
number = {},
pages = {105478},
doi = {10.1016/j.biosystems.2025.105478},
pmid = {40320202},
issn = {1872-8324},
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.},
}

@article {pmid40081461,
year = {2025},
author = {Marijuán, PC and Navarro, J},
title = {Human cognitive limitations and emotions: The emergence of social complexity.},
journal = {Bio Systems},
volume = {251},
number = {},
pages = {105454},
doi = {10.1016/j.biosystems.2025.105454},
pmid = {40081461},
issn = {1872-8324},
mesh = {Humans ; *Cognition/physiology ; *Emotions/physiology ; *Biological Evolution ; Animals ; *Social Behavior ; Brain/physiology ; *Social Evolution ; },
abstract = {An evolutionary approach to human cognition and social complexity, acknowledging the essential role of social emotions, is attempted. From the start, every kind of cognition, either artificial or natural, is limited. In living beings, it is the life cycle, life course, or life history what determines the extension, intensity, and limitations of the cognitive tools evolved to adapt to the own niche: from bacteria to multicellulars, animals, mammals, anthropoids, etc. Herein we will briefly survey some of those instances. In the human case, the essential niche becomes an extended social group with a rich diversity of cognitive links or 'bonds' in continuous interaction. Evolutionarily, the adaptation process to this social niche has involved a series of brain size increases, allowing, above all, the cognitive wonders inherent in language. But it has also involved a restructuring of the cognitive 'shortcuts' - essentially, emotions - that help individuals to navigate their own life in the natural environment and, especially, within the highly complex social milieu. Ultimately, this social adaptation process made possible the emergence of human 'ultrasociality' -the crux of Anthropogenesis-- and the most conspicuous behavioral traits still observable in contemporary societies, the effects of which also reverberate in the practice of science itself.},
}

Humans
*Cognition/physiology
*Emotions/physiology
*Biological Evolution
Animals
*Social Behavior
Brain/physiology
*Social Evolution

@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},
doi = {10.1098/rspb.2024.1195},
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/ ; },
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.},
}

@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 = {},
doi = {10.3390/e27040449},
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 = {62212//John Templeton Foundation (JTF)/ ; },
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.},
}

@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 = {},
number = {},
pages = {115468},
doi = {10.1016/j.fct.2025.115468},
pmid = {40262731},
issn = {1873-6351},
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.},
}

@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},
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.},
}

@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 = {},
number = {},
pages = {},
doi = {10.1021/acsami.5c02422},
pmid = {40231984},
issn = {1944-8252},
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.},
}

@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 = {},
number = {},
pages = {169153},
doi = {10.1016/j.jmb.2025.169153},
pmid = {40228789},
issn = {1089-8638},
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 have not been identified in unicellular eukaryotes. 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.},
}

@article {pmid40226989,
year = {2025},
author = {Lv, CL and Li, B},
title = {Interface morphodynamics in living tissues.},
journal = {Soft matter},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5sm00145e},
pmid = {40226989},
issn = {1744-6848},
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.},
}

@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 = {},
number = {},
pages = {108496},
doi = {10.1016/j.jbc.2025.108496},
pmid = {40220996},
issn = {1083-351X},
abstract = {Collagen IV is a major component of basement membranes, a specialized form of extracellular matrix that enabled the assembly of multicellular epithelial tissues. In mammals, collagen IV assembles from a family of six α-chains (α1 to 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.},
}

@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 {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},
doi = {10.1371/journal.pcbi.1012418},
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 {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 = {DMR-2046683//National Science Foundation (NSF)/ ; PHY-2019745//National Science Foundation (NSF)/ ; RGP0007/2022//Human Frontier Science Program (HFSP)/ ; },
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, K},
title = {The LARP6 La module from Tetrabaena socialis reveals structural and functional differences from plant and animal LARP6 homologues.},
journal = {RNA biology},
volume = {},
number = {},
pages = {},
doi = {10.1080/15476286.2025.2489303},
pmid = {40181506},
issn = {1555-8584},
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.},
}

@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 = {*Archaea/physiology/cytology ; },
abstract = {A microbe from the Dead Sea switches to a tissue-like form when compressed.},
}

*Archaea/physiology/cytology

@article {pmid40179183,
year = {2025},
author = {Rados, T and Leland, OS and Escudeiro, P and Mallon, J and Andre, K and Caspy, I and von Kügelgen, A and Stolovicki, E and Nguyen, S and Patop, IL and Rangel, LT and Kadener, S and Renner, LD and Thiel, V and Soen, Y and Bharat, TAM and Alva, V and Bisson, A},
title = {Tissue-like multicellular development triggered by mechanical compression in archaea.},
journal = {Science (New York, N.Y.)},
volume = {388},
number = {6742},
pages = {109-115},
doi = {10.1126/science.adu0047},
pmid = {40179183},
issn = {1095-9203},
mesh = {Actins/metabolism ; Archaeal Proteins/metabolism ; Glycosylation ; Elasticity ; Biological Evolution ; Biomechanical Phenomena ; Stress, Mechanical ; },
abstract = {The advent of clonal multicellularity is a critical evolutionary milestone, seen often in eukaryotes, rarely in bacteria, and only once in archaea. We show that uniaxial compression induces clonal multicellularity in haloarchaea, forming tissue-like structures. These archaeal tissues are mechanically and molecularly distinct from their unicellular lifestyle, mimicking several eukaryotic features. Archaeal tissues undergo a multinucleate stage followed by tubulin-independent cellularization, orchestrated by active membrane tension at a critical cell size. After cellularization, tissue junction elasticity becomes akin to that of animal tissues, giving rise to two cell types-peripheral (Per) and central scutoid (Scu) cells-with distinct actin and protein glycosylation polarity patterns. Our findings highlight the potential convergent evolution of a biophysical mechanism in the emergence of multicellular systems across domains of life.},
}

Actins/metabolism
Archaeal Proteins/metabolism
Glycosylation
Elasticity
Biological Evolution
Biomechanical Phenomena
Stress, Mechanical

@article {pmid39508584,
year = {2024},
author = {Thomas, F and Asselin, K and MacDonald, N and Brazier, L and Meliani, J and Ujvari, B and Dujon, AM},
title = {Oncogenic processes: a neglected parameter in the evolutionary ecology of animals.},
journal = {Comptes rendus biologies},
volume = {347},
number = {},
pages = {137-157},
doi = {10.5802/crbiol.159},
pmid = {39508584},
issn = {1768-3238},
abstract = {Cancer is a biological process that emerged at the end of the Precambrian era with the rise of multicellular organisms. Traditionally, cancer has been viewed primarily as a disease relevant to human and domesticated animal health, attracting attention mainly from oncologists. In recent years, however, the community of ecologists and evolutionary biologists has recognized the pivotal role of cancer-related issues in the evolutionary paths of various species, influencing multiple facets of their biology. It has become evident that overlooking these issues is untenable for a comprehensive understanding of species evolution and ecosystem functioning. In this article, we highlight some significant advancements in this field, also underscoring the pressing need to consider reciprocal interactions not only between cancer cells and their hosts but also with all entities comprising the holobiont. This reflection gains particular relevance as ecosystems face increasing pollution from mutagenic substances, resulting in a resurgence of cancer cases in wildlife.},
}

@article {pmid39345214,
year = {2024},
author = {Mathieu, J and Huynh, JR},
title = {Incomplete divisions between sister germline cells require Usp8 function.},
journal = {Comptes rendus biologies},
volume = {347},
number = {},
pages = {109-117},
doi = {10.5802/crbiol.161},
pmid = {39345214},
issn = {1768-3238},
mesh = {*Germ Cells ; Animals ; Cell Division ; Endosomal Sorting Complexes Required for Transport/genetics ; Humans ; Ubiquitin Thiolesterase/genetics/metabolism ; },
abstract = {Cytokinetic abscission is the final step of cell division, resulting in two separate daughter cells. While abscission is typically complete across most cell types, germline cells, which produce sexual gametes, do not finish cytokinesis, maintaining connections between sister cells. These connections are essential for sharing cytoplasm as they differentiate into oocyte and sperm. First, we outline the molecular events of cytokinesis during both complete and delayed abscission, highlighting the role of the ESCRT-III proteins. We then focus on recent discoveries that reveal the molecular mechanisms blocking abscission in Drosophila germline cells. The enzyme Usp8 was identified as vital for ensuring incomplete cytokinesis through the regulation of ESCRT-III ubiquitination and localization. Finally, we explore how the processes of incomplete cytokinesis could hold evolutionary importance, suggesting additional studies into choanoflagellates to comprehend the origins of multicellularity.},
}

*Germ Cells
Animals
Cell Division
Endosomal Sorting Complexes Required for Transport/genetics
Humans
Ubiquitin Thiolesterase/genetics/metabolism

@article {pmid40174588,
year = {2025},
author = {Wang, K and Lu, Z and Yao, Z and He, X and Hu, Z and Zhou, D},
title = {Single-cell phylodynamic inference of stem cell differentiation and tumor evolution.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101244},
doi = {10.1016/j.cels.2025.101244},
pmid = {40174588},
issn = {2405-4720},
abstract = {Phylodynamic inference (PI) quantifies population dynamics and evolutionary trajectories using phylogenetic trees. Single-cell lineage tracing enables phylogenetic tree reconstruction for thousands of cells in multicellular organisms, facilitating PI at the cellular level. However, cell differentiation and somatic evolution challenge the direct application of existing PI frameworks to somatic tissues. We introduce scPhyloX, a computational framework modeling structured cell populations by leveraging single-cell phylogenetic trees to infer tissue development and tumor evolution dynamics. A key advancement is its ability to infer time-varying parameters, capturing dynamic biological processes. Simulations demonstrate scPhyloX's accuracy in scenarios including tissue development, disease treatment, and tumor growth. Application to three real datasets reveals insights into somatic dynamics: cycling stem cell overshoot in fly organ development, clonal expansion of multipotent hematopoietic progenitors during human aging, and pronounced subclonal selection in early colorectal tumorigenesis. scPhyloX thus provides a computational approach for investigating somatic tissue development and evolution.},
}

@article {pmid40168695,
year = {2025},
author = {Wang, Q and Chen, C and Zhao, H and Jiao, Y and Chen, H and Wang, P and Song, T},
title = {Magnetotactic bacteria-mediated integrated magnetic targeted hyperthermia for in-situ deep-seated tumor.},
journal = {Colloids and surfaces. B, Biointerfaces},
volume = {252},
number = {},
pages = {114658},
doi = {10.1016/j.colsurfb.2025.114658},
pmid = {40168695},
issn = {1873-4367},
abstract = {Unlike hyperthermia after intratumoral injection, the method of integrated magnetic targeted hyperthermia (iMTH) guides magnetic medium to the target site and then directly performs in-situ heating, showing great potential for effective treatment of deep-seated tumors in the body. Magnetotactic bacteria (MTB), having chain-like arranged magnetic nanoparticles within its body and active movement along an external magnetic field, are considered as a very fitted material for iMTH. However, the amount of MTB concentrated on the deep-seated tumor posed a significant challenge for the successful implementation of iMTH. Herein, we aim to validate the strategy of integrating magnetic targeting and hyperthermia. An in-situ liver tumor model in mouse was developed as deep-seated tumors. After administering the polar MTB MO-1 intravenously via the tail vein, a focusing magnetic field navigated these bacteria to effectively accumulate at the deep-seated tumor site. Immediately afterwards, this targeted aggregation of MO-1 cells triggered a localized magnetic hyperthermia directly at the cancer site under an applied alternating magnetic field. Our findings demonstrated that this hyperthermia induced by the bacteria led to the death of liver cancer cells, thereby effectively curbing the progression and growth of the cancer. These promising results suggested that an iMTH approach was developed, harnessing the power of MTB. This method stands as an exciting and potential therapeutic strategy for the treatment of deep-seated tumors, offering new hope in the fight against cancer.},
}

@article {pmid38562769,
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, A 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 = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.03.17.585428},
pmid = {38562769},
issn = {2692-8205},
abstract = {UNLABELLED: 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.

STATEMENT OF SIGNIFICANCE: This study identifies distinct tumor microenvironment (TME) profiles in Black and White American TNBC patients, providing new insights into the biological mechanisms driving outcome disparities. Our findings highlight the role of the tumor-endothelial-macrophage niche in these disparities, offering a potential therapeutic target for race-inclusive strategies aimed at improving clinical outcomes. By revealing racial differences in treatment response profiles, this work underscores the necessity for tailored therapies in TNBC. These insights lay the groundwork for the development of inclusive, precision-driven treatment approaches that may help mitigate racial disparities and enhance patient outcomes.},
}

@article {pmid40156877,
year = {2025},
author = {Momoi, Y and Kumagai, S and Nishikawa, H},
title = {Immunogenomic precision medicine: a personalized approach based on immunogenomic cancer evolution.},
journal = {International immunology},
volume = {},
number = {},
pages = {},
doi = {10.1093/intimm/dxaf020},
pmid = {40156877},
issn = {1460-2377},
abstract = {Cancer progression can be understood as a process of diversification and selection (the evolutionary theory of cancer). The immune system also plays a critical role in this process of diversification and selection. The cancer immunoediting hypothesis provides a partial explanation of this evolutionary process; immune-evading cancer clones with genomic and/or epigenomic alterations are selected under the pressure of immune surveillance and can become equipped with multiple immunosuppressive mechanisms, leading to the development of clinically apparent cancers. Indeed, inflammatory cancers equip immunosuppressive mechanisms in response to the pressure of the immune system. However, recent studies focusing on human cancers have revealed that certain non-inflammatory cancers, which often harbor a single driver oncogenic mutation, are equipped with immunosuppressive machinery sufficient to evade immune surveillance at the time of malignant transformation. The sequential model of the cancer immunoediting hypothesis is inadequate to explain the development of these non-inflammatory cancers, highlighting the need for a novel concept that can explain their co-evolutionary processes. Moreover, inhibition of oncogenic signaling by specific driver oncogenes has been shown not only to kill cancer cells but also to augment antitumor immunity, suggesting the potential for the advent of molecularly targeted reagents with a variety of immunomodulatory functions from the perspective of personalized therapies. Here, we discuss the processes by which cancer cells and the immune system co-evolve to establish clinically apparent cancers, thereby introducing a new concept of 'immunogenomic cancer evolution', that provides a rationale for the potential of personalized 'immunogenomic cancer precision medicine'.},
}

@article {pmid40153489,
year = {2025},
author = {Kumagai, S and Momoi, Y and Nishikawa, H},
title = {Immunogenomic cancer evolution: A framework to understand cancer immunosuppression.},
journal = {Science immunology},
volume = {10},
number = {105},
pages = {eabo5570},
doi = {10.1126/sciimmunol.abo5570},
pmid = {40153489},
issn = {2470-9468},
mesh = {Humans ; *Neoplasms/immunology/genetics/therapy ; *Tumor Microenvironment/immunology/genetics ; Animals ; Immunotherapy/methods ; Immune Tolerance/immunology/genetics ; Precision Medicine ; Tumor Escape/immunology/genetics ; Genomics ; },
abstract = {The process of tumor development involves tumor cells eluding detection and suppression of immune responses, which can cause decreased tumor cell antigenicity, expression of immunosuppressive molecules, and immunosuppressive cell recruitment to the tumor microenvironment (TME). Immunologically and genomically integrated analysis (immunogenomic analysis) of patient specimens has revealed that oncogenic aberrant signaling is involved in both carcinogenesis and immune evasion. In noninflamed cancers such as epidermal growth factor receptor (EGFR)-mutated lung cancers, genetic abnormalities in cancer cells contribute to the formation of an immunosuppressive TME by recruiting immunosuppressive cells, which cannot be fully explained by the cancer immunoediting hypothesis. This review summarizes the latest findings regarding the links between cancer genetic abnormalities and immunosuppression causing clinical resistance to immunotherapy. We propose the concepts of immunogenomic cancer evolution, in which cancer cell genomic evolution shapes the immunosuppressive TME, and immunogenomic precision medicine, in which cancer immunotherapy can be combined with molecularly targeted reagents that modulate the immunosuppressive TME.},
}

Humans
*Neoplasms/immunology/genetics/therapy
*Tumor Microenvironment/immunology/genetics
Animals
Immunotherapy/methods
Immune Tolerance/immunology/genetics
Precision Medicine
Tumor Escape/immunology/genetics
Genomics

@article {pmid40147421,
year = {2025},
author = {Goswami, P and Ji, R and Shen, J and Roberts, AP and Lin, W},
title = {Genomic and metabolic characterisation of a novel species Magnetominusculus dajiuhuensis DJH-1[Ts] sp. nov. from an acidic peatland.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {3},
pages = {126605},
doi = {10.1016/j.syapm.2025.126605},
pmid = {40147421},
issn = {1618-0984},
abstract = {Magnetotactic bacteria (MTB) are recognised widely for their ability to synthesise intracellular magnetite (Fe3O4) and/or greigite (Fe3S4) nanocrystals and align with Earth's magnetic field. They are crucial for understanding prokaryotic organelle biogenesis. MTB members of the Nitrospirota phylum (previously known as the Nitrospirae phylum) are of interest due to their important ecological roles in the biogeochemical cycling of iron and sulphur. Here, we introduce Magnetominusculus dajiuhuensis DJH-1[Ts], a newly discovered Nitrospirota MTB species that thrives in the acidic Dajiuhu Peatland of central China. By combining electron microscopy, 16S rRNA gene-based analysis and genome-resolved metagenomics, we elucidate its distinctive morphology, genomic features, and metabolic functions. The metagenome-assembled genome, assigned to the genus Magnetominusculus, family Magnetobacteriaceae, order Thermodesulfovibrionales, class Thermodesulfovibrionia according to the GTDB taxonomy, reveals an obligate anaerobe that lives in central China's largest wetland. We propose the formal name Magnetominusculus dajiuhuensis DJH-1[Ts] sp. nov., following the SeqCode system. Genomic and metabolic characterisation of this novel species suggests its potential role in nitrogen, sulphur, and carbon metabolism in aquatic biogeochemistry, particularly in peatlands. The genome of this novel strain indicates that it harnesses the Wood-Ljungdahl pathway for carbon fixation and acetate metabolism in anaerobic conditions, while its potential role in nitrogen cycling is characterised by denitrification and nitrogen fixation. It also participates in reduction of sulphate to sulphide, indicating a role in sulphur cycling in its ecological niche. Taken together, the discovery and characterisation of Magnetominusculus dajiuhuensis DJH-1[Ts] provide new insights into MTB diversity and ecological functions, particularly in peatland biogeochemistry.},
}

@article {pmid40146859,
year = {2025},
author = {Muro, EM and Ballesteros, FJ and Luque, B and Bascompte, J},
title = {The emergence of eukaryotes as an evolutionary algorithmic phase transition.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {13},
pages = {e2422968122},
doi = {10.1073/pnas.2422968122},
pmid = {40146859},
issn = {1091-6490},
support = {310030_197201/SNSF_/Swiss National Science Foundation/Switzerland ; PID2019-109592GBI00//Ministerio de Ciencia, Innovación y Universidades (MICIU)/ ; Excellence Prometeo/2020/085//Conselleria d'Educacio, Universitats i Ocupacio de la Generalitat Valenciana/ ; ASFAE/2022/025//European Union NextGenerationEU 922 and Generalitat Valenciana/ ; PID2020-113737GB-I00//Ministerio de Ciencia, Innovación y Universidades (MICIU)/ ; },
mesh = {*Algorithms ; *Eukaryota/genetics/metabolism ; Evolution, Molecular ; Biological Evolution ; Eukaryotic Cells/metabolism ; Proteins/genetics/metabolism ; Phylogeny ; Models, Genetic ; },
abstract = {The origin of eukaryotes represents one of the most significant events in evolution since it allowed the posterior emergence of multicellular organisms. Yet, it remains unclear how existing regulatory mechanisms of gene activity were transformed to allow this increase in complexity. Here, we address this question by analyzing the length distribution of proteins and their corresponding genes for 6,519 species across the tree of life. We find a scale-invariant relationship between gene mean length and variance maintained across the entire evolutionary history. Using a simple model, we show that this scale-invariant relationship naturally originates through a simple multiplicative process of gene growth. During the first phase of this process, corresponding to prokaryotes, protein length follows gene growth. At the onset of the eukaryotic cell, however, mean protein length stabilizes around 500 amino acids. While genes continued growing at the same rate as before, this growth primarily involved noncoding sequences that complemented proteins in regulating gene activity. Our analysis indicates that this shift at the origin of the eukaryotic cell was due to an algorithmic phase transition equivalent to that of certain search algorithms triggered by the constraints in finding increasingly larger proteins.},
}

*Algorithms
*Eukaryota/genetics/metabolism
Evolution, Molecular
Biological Evolution
Eukaryotic Cells/metabolism
Proteins/genetics/metabolism
Phylogeny
Models, Genetic

@article {pmid40127687,
year = {2025},
author = {Petroll, R and Papareddy, RK and Krela, R and Laigle, A and Riviere, Q and Bišová, K and Mozgová, I and Borg, M},
title = {The expansion and diversification of epigenetic regulatory networks underpins major transitions in the evolution of land plants.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf064},
pmid = {40127687},
issn = {1537-1719},
abstract = {Epigenetic silencing is essential for regulating gene expression and cellular diversity in eukaryotes. While DNA and H3K9 methylation silence transposable elements (TEs), H3K27me3 marks deposited by the Polycomb repressive complex 2 (PRC2) silence varying proportions of TEs and genes across different lineages. Despite the major development role epigenetic silencing plays in multicellular eukaryotes, little is known about how epigenetic regulatory networks were shaped over evolutionary time. Here, we analyse epigenomes from diverse species across the green lineage to infer the chronological epigenetic recruitment of genes during land plant evolution. We first reveal the nature of plant heterochromatin in the unicellular chlorophyte microalga Chlorella sorokiniana and identify several genes marked with H3K27me3, highlighting the deep origin of PRC2-regulated genes in the green lineage. By incorporating genomic phylostratigraphy, we show how genes of differing evolutionary age occupy distinct epigenetic states in plants. While young genes tend to be silenced by H3K9 methylation, genes that emerged in land plants are preferentially marked with H3K27me3, some of which form part of a common network of PRC2-repressed genes across distantly-related species. Finally, we analyse the potential recruitment of PRC2 to plant H3K27me3 domains and identify conserved DNA-binding sites of ancient transcription factor (TF) families known to interact with PRC2. Our findings shed light on the conservation and potential origin of epigenetic regulatory networks in the green lineage, while also providing insight into the evolutionary dynamics and molecular triggers that underlie the adaptation and elaboration of epigenetic regulation, laying the groundwork for its future consideration in other eukaryotic lineages.},
}

@article {pmid40121259,
year = {2025},
author = {Chow, PCK and Bentley, PJ},
title = {Development necessitates evolutionarily conserved factors.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {9910},
pmid = {40121259},
issn = {2045-2322},
mesh = {*Biological Evolution ; Animals ; Transcription Factors/metabolism/genetics ; Morphogenesis/genetics ; Models, Biological ; Evolution, Molecular ; },
abstract = {Early-stage generalised transcription factors in biological development are often evolutionarily conserved across species. Here, we find for the first time that similar factors functionally emerge in an alternative medium of development. Through comprehensively analysing a Neural Cellular Automata (NCA) model of morphogenesis, we find multiple properties of the hidden units that are functionally analogous to early factors in biological development. We test the generalisation abilities of our model through transfer learning of other morphologies and find that developmental strategies learnt by the model are reused to grow new body forms by conserving its early generalised factors. Our paper therefore provides evidence that nature did not become locked into one arbitrary method of developing multicellular organisms: the use of early generalised factors as fundamental control mechanisms and the resulting necessity for evolutionary conservation of those factors may be fundamental to development, regardless of the details of how development is implemented.},
}

*Biological Evolution
Animals
Transcription Factors/metabolism/genetics
Morphogenesis/genetics
Models, Biological
Evolution, Molecular

@article {pmid40112176,
year = {2025},
author = {Matthews, S and Nikoonejad Fard, V and Tollis, M and Seoighe, C},
title = {Variable gene copy number in cancer-related pathways is associated with cancer prevalence across mammals.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf056},
pmid = {40112176},
issn = {1537-1719},
abstract = {Cancer is a disease of multicellularity, observed across the tree of life. In principle, animals with larger body sizes and longer lifespans should be at increased risk of developing cancer. However, there is no strong relationship between these traits and cancer across mammals. Previous studies have proposed that increased copy number of cancer-related genes may enhance the robustness of cancer suppression pathways in long-lived mammals, but these studies have not extended beyond known cancer-related genes. In this study, we conducted a phylogenetic generalised least squares (PGLS) analysis to test for associations between copy number of all protein-coding genes and longevity, body size, and cancer prevalence across 94 species of mammals. In addition to investigating the copy number of individual genes, we tested sets of related genes for a relationship between the aggregated gene copy number of the set and these traits. We did not find strong evidence to support the hypothesis that adaptive changes in gene copy number contribute to the lack of correlation between cancer prevalence and body size or lifespan. However, we found several biological processes where aggregate copy number was associated with malignancy rate. The strongest association was for the gene set relating to transforming growth factor-beta (TGF-β), a cytokine that plays a role in cancer progression. Overall, this study provides a comprehensive evaluation of the role of gene copy number in adaptation to body size and lifespan and sheds light on the contribution of gene copy number to variation in cancer prevalence across mammals.},
}

@article {pmid40109106,
year = {2025},
author = {Korb, J},
title = {Changes of division of labour along the eusociality spectrum in termites, with comparisons to multicellularity.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {380},
number = {1922},
pages = {20230268},
pmid = {40109106},
issn = {1471-2970},
mesh = {*Isoptera/physiology ; Animals ; *Social Behavior ; Reproduction/physiology ; },
abstract = {Eusocial insects are characterized by reproductive division of labour, with one (or a few) individuals specialized in reproduction (queen and in termites, also a king) and the other individuals performing all other tasks (workers). Among workers, further division of labour can occur. Termites have three main castes: reproductives, comprising a queen and king; morphologically differentiated sterile soldiers; and workers. Task division among workers varies greatly depending on lifestyle and degree of workers' reproductive potential, which varies from totipotency to reproduce up to sterility. In wood-dwelling species, which do not forage outside the nest, all tasks are performed by totipotent workers, comprising multiple-instars with less further division of labour. Foraging species with pluripotent workers also have a multi-instar worker caste, but some division of labour between brood care versus foraging and defence exists. The first task seems mainly to be done by smaller-and potentially younger-instars, while the latter two tasks are performed by larger-and potentially older-workers. The highest degree of division of labour occurs in foraging species with sterile workers. Here, morphological worker castes with defined tasks and age polyethism occur. Comparisons with Metazoa reveal striking similarities with termites concerning gradients in germline/soma differentiation and cell totipotency.This article is part of the theme issue 'Division of labour as key driver of social evolution'.},
}

*Isoptera/physiology
Animals
*Social Behavior
Reproduction/physiology

@article {pmid40106424,
year = {2025},
author = {Wright, BA and Osigus, HJ and Schmidt, MJ and Ratcliffe, J and Kamm, K and Martinez-Ortiz, GC and Rehn, M and Kvansakul, M and Schierwater, B and Humbert, PO},
title = {Tolerance of Placozoa for temperate climates: Evidence for known and new placozoan clades in the southern waters of Australia.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0317878},
pmid = {40106424},
issn = {1932-6203},
mesh = {Animals ; *Placozoa/genetics/classification ; Haplotypes ; Phylogeny ; Australia ; Climate ; Genetic Variation ; },
abstract = {Placozoans are small multicellular sea-dwelling animals that are typically found in shallow, warm ocean waters and have been reported in various marine environments worldwide. Their unique morphology makes them a powerful new model organism to study the evolutionary cell biology in early metazoans. Yet, knowledge on their biodiversity and ecological distribution is severely limited. Here, we report the isolation of placozoans in the temperate waters of Victoria, Australia, their most southern location known to date. Using light, electron, and confocal microscopy, we describe their morphology and behaviour. In addition to the known haplotypes H2 and H17, we have identified a new haplotype, here designated as H20, which defines a new placozoan clade. This study provides novel insights into the distribution, ecological niche separation and genetic diversity of placozoans, and reports the first morphological and ultrastructural characterisation of placozoan clades isolated from the southern waters of Victoria, Australia.},
}

Animals
*Placozoa/genetics/classification
Haplotypes
Phylogeny
Australia
Climate
Genetic Variation

@article {pmid40103550,
year = {2025},
author = {Davison, DR and Nedelcu, AM and Eneji, OA and Michod, RE},
title = {Plasticity and the evolution of group-level regulation of cellular differentiation in the volvocine algae.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2043},
pages = {20242477},
pmid = {40103550},
issn = {1471-2954},
support = {/NASA/NASA/United States ; //Division of Molecular and Cellular Biosciences/ ; NSF Postdoctoral Research Fellowships in Biology Program under Grant No. 2209373//Division of Biological Infrastructure/ ; 2029999//Division of Environmental Biology/ ; },
mesh = {*Cell Differentiation ; *Biological Evolution ; },
abstract = {During the evolution of multicellularity, the unit of selection transitions from single cells to integrated multicellular cell groups, necessitating the evolution of group-level traits such as somatic differentiation. However, the processes involved in this change in units of selection are poorly understood. We propose that the evolution of soma in the volvocine algae included an intermediate step involving the plastic development of somatic-like cells. We show that Eudorina elegans, a multicellular volvocine algae species previously thought to be undifferentiated, can develop somatic-like cells following environmental stress (i.e. cold shock). These cells resemble obligate soma in closely related species. We find that somatic-like cells can differentiate directly from cold-shocked cells. This differentiation is a cell-level trait, and the differentiated colony phenotype is a cross-level by-product of cell-level processes. The offspring of cold-shocked colonies also develop somatic-like cells. Since these cells were not directly exposed to the stressor, their differentiation was regulated during group development. Consequently, they are a true group-level trait and not a by-product of cell-level traits. We argue that group-level traits, such as obligate somatic differentiation, can originate through plasticity and that cross-level by-products may be an intermediate step in the evolution of group-level traits.},
}

*Cell Differentiation
*Biological Evolution

@article {pmid40103259,
year = {2025},
author = {Fonseca, A and Ishoey, T and Espinoza, C and Marshall, IPG and Nielsen, LP and Gallardo, VA},
title = {Large Filamentous Bacteria Isolated From Sulphidic Sediments Reveal Novel Species and Distinct Energy and Defence Mechanisms for Survival.},
journal = {Environmental microbiology},
volume = {27},
number = {3},
pages = {e70083},
pmid = {40103259},
issn = {1462-2920},
support = {//the Program "Doctorado en el extranjero Becas Chile" from ANID (former CONICYT)/ ; 1070552//Agencia Nacional de Investigación y Desarrollo/ ; //J. Craig Venter Institute/ ; },
mesh = {*Geologic Sediments/microbiology ; Chile ; *Phylogeny ; Bacteria/genetics/classification/metabolism/isolation & purification ; Genome, Bacterial ; RNA, Ribosomal, 16S/genetics ; Deltaproteobacteria/genetics/classification/isolation & purification/metabolism ; Sulfides/metabolism ; },
abstract = {Various morphotypes of large filamentous bacteria were isolated through micromanipulation from sulphidic sediment mats in the Bay of Concepción, central Chile. This study employed DNA amplification, whole-genome sequencing and bioinformatics analyses to unveil the taxonomic and genomic features of previously unidentified bacteria. The results revealed several novel genera, families and species, including three specimens belonging to Beggiatoales (Beggiatoaceae family), five to Desulfobacterales (Desulfobacteraceae family), two to the Chloroflexi phylum and one to the phylum Firmicutes. Metabolically, Beggiatoaceae bacteria exhibit a flexible and versatile genomic repertoire, enabling them to adapt to variable conditions at the sediment-water interface. All the bacteria demonstrated a mixotrophic mode, gaining energy from both inorganic and organic carbon sources. Except for the Firmicutes bacterium, all others displayed the ability to grow chemolithoautotrophically using H2 and CO2. Remarkably, the reverse tricarboxylic acid (rTCA) and Calvin-Benson-Bassham (CBB) pathways coexisted in one Beggiatoaceae bacterium. Additionally, various defence systems, such as CRISPR-Cas, along with evidence of viral interactions, have been identified. These defence mechanisms suggest that large filamentous bacteria inhabiting sulphidic sediments frequently encounter bacteriophages. Thus, robust defence mechanisms coupled with multicellularity may determine the survival or death of these large bacteria.},
}

*Geologic Sediments/microbiology
Chile
*Phylogeny
Bacteria/genetics/classification/metabolism/isolation & purification
Genome, Bacterial
RNA, Ribosomal, 16S/genetics
Deltaproteobacteria/genetics/classification/isolation & purification/metabolism
Sulfides/metabolism

@article {pmid40086443,
year = {2025},
author = {Weiss, B and Rohkin Shalom, S and Dolgova, A and Teh, LS and Kaltenpoth, M and Dale, C and Chiel, E},
title = {Maternal symbiont transmission via envenomation in the parasitoid wasp Spalangia cameroni.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.02.035},
pmid = {40086443},
issn = {1879-0445},
abstract = {Microbial symbionts of multicellular hosts originate from free-living ancestors and often persist through vertical transmission, but their mechanisms of establishment are not well understood. Here, we studied acquisition and transmission routes in a nascent symbiosis involving the bacterium Sodalis praecaptivus subsp. spalangiae (Sodalis SC) and the parasitoid wasp Spalangia cameroni. Using fluorescence in situ hybridization, transmission electron microscopy, and experimental infections, we found that oocytes are devoid of Sodalis SC, but the female venom gland is densely colonized. Sodalis SC is injected with the venom into the fly host, subsequently acquired by larval progeny during feeding, invades through the larval gut epithelium into multiple host organs, and eventually localizes in the venom gland. Adult wasps can also acquire Sodalis SC by artificial feeding, but, in this case, the bacterium is not transmitted vertically. Additionally, Sodalis SC is localized in the testes of some males, transmitted paternally at low frequency, and females that inherit Sodalis SC paternally can subsequently transmit it via the venom. To assess the specificity of the symbiosis, we performed experiments with the closely related free-living species Sodalis praecaptivus subsp. praecaptivus (Sodalis PP), known to initiate symbiosis with other insects. Sodalis PP is readily acquired when supplied artificially to wasp larvae but not transmitted to wasp progeny, because it fails to proliferate in the parasitized host. Our results indicate that non-ovarian transmission routes of intracellular symbionts may be more common than currently appreciated and provide a scenario for the early steps in establishing persistent symbiotic associations in insects.},
}

@article {pmid40070872,
year = {2025},
author = {Dong, Y and Qian, S and Wang, X and Zhang, W and Lu, W and Qu, J and Cui, M and Chen, L and Zhao, Y and Gao, Y and Giomo, M and Urciuolo, A and Feng, J and Zheng, Y and Jiang, B and Shen, R and Zhu, X and Elvassore, N},
title = {In situ tailored confining microenvironment for lung cancer spheroids.},
journal = {Materials today. Bio},
volume = {31},
number = {},
pages = {101602},
pmid = {40070872},
issn = {2590-0064},
abstract = {The mechanical properties and physical confinement of the extracellular matrix (ECM) are crucial roles in regulating tumor growth and progression. Extensive efforts have been dedicated to replicating the physical characteristics of tumor tissue by developing two-dimensional (2D) and three-dimensional (3D) in vitro models. However, it remains a significant challenge to modulate the local microenvironment around the specific cells according to the culture progress. In this study, we develop a 3D culture platform for multicellular lung cancer spheroids using a gelatin-based hydrogel with adjustable density and stiffness. Then, by utilizing a two-photon mediated bioprinting technique, we construct 3D confining microstructures with micrometer accuracy to enclose the selected spheroids within the hydrogel matrix. Diverse transcriptional profilings of cells are observed in response to the increased ECM density and stiffness compared to the additional confining stress. In addition, changed confining stress can regulate the tumor cells with contrary impacts on the cell cycle-related pathways. Our model not only allows for modifications to the mechanical microenvironment of the overall matrix but also facilitates localized adjustments throughout the culture evolution. This approach serves as a valuable tool for investigating tumor progression and understanding cell-ECM interactions.},
}

@article {pmid40067883,
year = {2025},
author = {Gray, C and Chitnavis, S and Buja, T and Duffy, CDP},
title = {Predicting the diversity of photosynthetic light-harvesting using thermodynamics and machine learning.},
journal = {PLoS computational biology},
volume = {21},
number = {3},
pages = {e1012845},
pmid = {40067883},
issn = {1553-7358},
mesh = {*Photosynthesis/physiology ; *Machine Learning ; *Thermodynamics ; *Light-Harvesting Protein Complexes/metabolism/chemistry ; Computational Biology ; Algorithms ; Models, Biological ; Biological Evolution ; Light ; },
abstract = {Oxygenic photosynthesis is responsible for nearly all biomass production on Earth, and may have been a prerequisite for establishing a complex biosphere rich in multicellular life. Life on Earth has evolved to perform photosynthesis in a wide range of light environments, but with a common basic architecture of a light-harvesting antenna system coupled to a photochemical reaction centre. Using a generalized thermodynamic model of light-harvesting, coupled with an evolutionary algorithm, we predict the type of light-harvesting structures that might evolve in light of different intensities and spectral profiles. We reproduce qualitatively the pigment composition, linear absorption profile and structural topology of the antenna systems of multiple types of oxygenic photoautotrophs, suggesting that the same physical principles underlie the development of distinct antenna structures in various light environments. Finally we apply our model to representative light environments that would exist on Earth-like exoplanets, predicting that both oxygenic and anoxygenic photosynthesis could evolve around low mass stars, though the latter would seem to work better around the coolest M-dwarfs. We see this as an interesting first step toward a general evolutionary model of basic biological processes and proof that it is meaningful to hypothesize on the nature of biology beyond Earth.},
}

*Photosynthesis/physiology
*Machine Learning
*Thermodynamics
*Light-Harvesting Protein Complexes/metabolism/chemistry
Computational Biology
Algorithms
Models, Biological
Biological Evolution
Light

@article {pmid40060608,
year = {2025},
author = {Theriault, HS and Kimmel, HRC and Nunes, AC and Paxhia, A and Hashim, S and Clancy, KBH and Underhill, GH and Harley, BAC},
title = {Matrix tropism influences endometriotic cell attachment patterns.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.22.639314},
pmid = {40060608},
issn = {2692-8205},
abstract = {Due to the extended period for clinical diagnosis, the etiology of endometriotic lesion initiation is not well understood or characterized. Endometriotic lesions are most often found on pelvic tissues and organs, especially the ovaries. To investigate the role of tissue tropism on ovarian endometrioma initiation, we adapted a well-characterized polyacrylamide microarray system to investigate the role of tissue-specific extracellular matrix and adhesion motifs on endometriotic cell attachment, morphology, and size. We report the influence of cell origin (endometriotic vs. non-endometriotic), substrate stiffness mimicking aging and fibrosis, and the role of multicellular (epithelial-stromal) cohorts on cell attachment patterns. We identify multiple ovarian-specific attachment motifs that significantly increase endometriotic (vs. non-endometriotic) cell cohort attachment that could be implicated in early disease etiology.},
}

@article {pmid40059518,
year = {2025},
author = {Tice, AK and Regis, K and Shutt, TE and Spiegel, FW and Brown, MW and Silberman, JD},
title = {Validating the Genus Pocheina (Acrasidae, Heterolobosea, Discoba) Leads to the Recognition of Three Major Lineages Within Acrasidae.},
journal = {The Journal of eukaryotic microbiology},
volume = {72},
number = {2},
pages = {e70004},
doi = {10.1111/jeu.70004},
pmid = {40059518},
issn = {1550-7408},
support = {DEB2100888//National Science Foundation/ ; DEB0329102//National Science Foundation/ ; DEB0316284//National Science Foundation/ ; //Arkansas Biosciences Institute/ ; },
mesh = {*Phylogeny ; *DNA, Protozoan/genetics ; Amoebozoa/classification/genetics ; DNA, Ribosomal Spacer/genetics ; Sequence Analysis, DNA ; DNA, Ribosomal/genetics ; RNA, Ribosomal, 18S/genetics ; },
abstract = {Pocheina and Acrasis are two genera of heterolobosean sorocarpic amoebae within Acrasidae that have historically been considered close relatives. The two genera were differentiated based on their differing fruiting body morphologies. The validity of this taxonomic distinction was challenged when a SSU rRNA phylogenetic study placed an isolate morphologically identified as "Pocheina" rosea within a clade of Acrasis rosea isolates. The authors speculated that pocheinoid fruiting body morphology might be the result of aberrant Ac. rosea fruiting body development, which, if true, would nullify this taxonomic distinction between genera. To clarify Acrasidae systematics, we analyzed SSU rRNA and ITS region sequences from multiple isolates of Pocheina, Acrasis, and Allovahlkampfia generated by Polymerase Chain Reaction (PCR) and transcriptomics. We demonstrate that the initial SSU sequence attributed to "P. rosea" originated from an Ac. rosea DNA contamination in its amplification reaction. Our analyses, based on morphology, SSU and 5.8S rRNA gene phylogenies, as well as comparative analyses of ITS1 and ITS2 sequences, resolve Acrasidae into three major lineages: Allovahlkampfia and the strongly supported clades comprising Pocheina and Acrasis. We confirm that the latter two genera can be identified by their fruiting body morphologies.},
}

*Phylogeny
*DNA, Protozoan/genetics
Amoebozoa/classification/genetics
DNA, Ribosomal Spacer/genetics
Sequence Analysis, DNA
DNA, Ribosomal/genetics
RNA, Ribosomal, 18S/genetics

@article {pmid40056574,
year = {2025},
author = {Klompstra, TM and Yoon, KJ and Koo, BK},
title = {Evolution of organoid genetics.},
journal = {European journal of cell biology},
volume = {104},
number = {2},
pages = {151481},
doi = {10.1016/j.ejcb.2025.151481},
pmid = {40056574},
issn = {1618-1298},
abstract = {Organoids have revolutionized in vitro research by offering three-dimensional, multicellular systems that recapitulate the structure, function, and genetics of human tissues. Initially developed from both pluripotent stem cells (PSCs) and adult stem cells (AdSCs), organoids have expanded to model nearly every major human organ, significantly advancing developmental biology, disease modeling, and therapeutic screening. This review highlights the progression of organoid technologies, emphasizing the integration of genetic tools, including CRISPR-Cas9, prime editing, and lineage tracing. These advancements have facilitated precise modeling of human-specific pathologies and drug responses, often surpassing traditional 2D cultures and animal models in accuracy. Emerging technologies, such as organoid fusion, xenografting, and optogenetics, are expected to further enhance our understanding of cellular interactions and microenvironmental dynamics. As organoid complexity and genetic engineering methods continue to evolve, they will become increasingly indispensable for personalized medicine and translational research, bridging gaps between in vitro and in vivo systems.},
}

@article {pmid40052705,
year = {2025},
author = {Kataki, AD and Gupta, PG and Cheema, U and Nisbet, A and Wang, Y and Kocher, HM and Pérez-Mancera, PA and Velliou, EG},
title = {Mapping Tumor-Stroma-ECM Interactions in Spatially Advanced 3D Models of Pancreatic Cancer.},
journal = {ACS applied materials & interfaces},
volume = {17},
number = {11},
pages = {16708-16724},
pmid = {40052705},
issn = {1944-8252},
mesh = {Humans ; *Pancreatic Neoplasms/pathology/metabolism ; *Extracellular Matrix/metabolism ; *Tumor Microenvironment ; *Stromal Cells/pathology/metabolism ; *Tissue Scaffolds/chemistry ; Cell Line, Tumor ; Carcinoma, Pancreatic Ductal/pathology/metabolism ; Polyurethanes/chemistry ; Extracellular Matrix Proteins/metabolism ; },
abstract = {Bioengineering-based in vitro tumor models are increasingly important as tools for studying disease progression and therapy response for many cancers, including the deadly pancreatic ductal adenocarcinoma (PDAC) that exhibits a tumor/tissue microenvironment of high cellular/biochemical complexity. Therefore, it is crucial for in vitro models to capture that complexity and to enable investigation of the interplay between cancer cells and factors such as extracellular matrix (ECM) proteins or stroma cells. Using polyurethane (PU) scaffolds, we performed a systematic study on how different ECM protein scaffold coatings impact the long-term cell evolution in scaffolds containing only cancer or only stroma cells (activated stellate and endothelial cells). To investigate potential further changes in those biomarkers due to cancer-stroma interactions, we mapped their expression in dual/zonal scaffolds consisting of a cancer core and a stroma periphery, spatially mimicking the fibrotic/desmoplastic reaction in PDAC. In our single scaffolds, we observed that the protein coating affected the cancer cell spatial aggregation, matrix deposition, and biomarker upregulation in a cell-line-dependent manner. In single stroma scaffolds, different levels of fibrosis/desmoplasia in terms of ECM composition/quantity were generated depending on the ECM coating. When studying the evolution of cancer and stroma cells in our dual/zonal model, biomarkers linked to cell aggressiveness/invasiveness were further upregulated by both cancer and stroma cells as compared to single scaffold models. Collectively, our study advances the understanding of how different ECM proteins impact the long-term cell evolution in PU scaffolds. Our findings show that within our bioengineered models, we can stimulate the cells of the PDAC microenvironment to develop different levels of aggressiveness/invasiveness, as well as different levels of fibrosis. Furthermore, we highlight the importance of considering spatial complexity to map cell invasion. Our work contributes to the design of in vitro models with variable, yet biomimetic, tissue-like properties for studying the tumor microenvironment's role in cancer progression.},
}

Humans
*Pancreatic Neoplasms/pathology/metabolism
*Extracellular Matrix/metabolism
*Tumor Microenvironment
*Stromal Cells/pathology/metabolism
*Tissue Scaffolds/chemistry
Cell Line, Tumor
Carcinoma, Pancreatic Ductal/pathology/metabolism
Polyurethanes/chemistry
Extracellular Matrix Proteins/metabolism

@article {pmid40044858,
year = {2025},
author = {Tong, K and Datta, S and Cheng, V and Haas, DJ and Gourisetti, S and Yopp, HL and Day, TC and Lac, DT and Khalil, AS and Conlin, PL and Bozdag, GO and Ratcliff, WC},
title = {Genome duplication in a long-term multicellularity evolution experiment.},
journal = {Nature},
volume = {639},
number = {8055},
pages = {691-699},
pmid = {40044858},
issn = {1476-4687},
mesh = {*Saccharomyces cerevisiae/genetics/cytology ; *Diploidy ; *Gene Duplication ; *Evolution, Molecular ; *Genome, Fungal/genetics ; *Aneuploidy ; Tetraploidy ; Genetic Fitness ; Selection, Genetic ; Time Factors ; Models, Genetic ; Cell Size ; Biological Evolution ; Genomic Instability/genetics ; },
abstract = {Whole-genome duplication (WGD) is widespread across eukaryotes and can promote adaptive evolution[1-4]. However, given the instability of newly formed polyploid genomes[5-7], understanding how WGDs arise in a population, persist, and underpin adaptations remains a challenge. Here, using our ongoing Multicellularity Long Term Evolution Experiment (MuLTEE)[8], we show that diploid snowflake yeast (Saccharomyces cerevisiae) under selection for larger multicellular size rapidly evolve to be tetraploid. From their origin within the first 50 days of the experiment, tetraploids persisted for the next 950 days (nearly 5,000 generations, the current leading edge of our experiment) in 10 replicate populations, despite being genomically unstable. Using synthetic reconstruction, biophysical modelling and counter-selection, we found that tetraploidy evolved because it confers immediate fitness benefits under this selection, by producing larger, longer cells that yield larger clusters. The same selective benefit also maintained tetraploidy over long evolutionary timescales, inhibiting the reversion to diploidy that is typically seen in laboratory evolution experiments. Once established, tetraploidy facilitated novel genetic routes for adaptation, having a key role in the evolution of macroscopic multicellular size via the origin of evolutionarily conserved aneuploidy. These results provide unique empirical insights into the evolutionary dynamics and impacts of WGD, showing how it can initially arise due to its immediate adaptive benefits, be maintained by selection and fuel long-term innovations by creating additional dimensions of heritable genetic variation.},
}

*Saccharomyces cerevisiae/genetics/cytology
*Diploidy
*Gene Duplication
*Evolution, Molecular
*Genome, Fungal/genetics
*Aneuploidy
Tetraploidy
Genetic Fitness
Selection, Genetic
Time Factors
Models, Genetic
Cell Size
Biological Evolution
Genomic Instability/genetics

@article {pmid40044726,
year = {2025},
author = {Gao, Y and Pichugin, Y and Traulsen, A and Zapién-Campos, R},
title = {Evolution of irreversible differentiation under stage-dependent cell differentiation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {7786},
pmid = {40044726},
issn = {2045-2322},
support = {12401644//National Natural Science Foundation of China/ ; 2024JC-YBQN-0005//Natural Science Basic Research Program of Shaanxi Province/ ; },
mesh = {*Cell Differentiation ; *Biological Evolution ; Germ Cells/cytology ; Models, Biological ; Animals ; Cell Division ; Selection, Genetic ; },
abstract = {The specialization of cells is a hallmark of complex multicellularity. Cell differentiation enables the emergence of specialized cell types that carry out separate functions previously executed by a multifunctional ancestor cell. One view about the origin of cell differentiation is that it first occurred randomly in genetically identical cells exposed to the same life history environment. Under these conditions, differentiation trajectories producing more offspring could be favored by natural selection; yet, how dynamic variation in differentiation probabilities can affect the evolution of differentiation patterns is unclear. We develop a theoretical model to investigate the effect of dynamic-stage-dependent-cell differentiation on the evolution of optimal differentiation patterns. Concretely, we model trajectories in which cells can randomly differentiate into germ or soma cell types at each cell division. After comparing many of these trajectories, we found that irreversible differentiation, where cells gradually lose their ability to produce the other cell type, is more favored in small organisms under dynamic than under constant (stage-independent) cell differentiation. Furthermore, we found that the irreversible differentiation of germ cells, where germ cells gradually lose their ability to produce soma cells, is prominent among irreversible patterns. Only large variations in the differentiation probabilities prohibit irreversible trajectories from being the optimal pattern.},
}

*Cell Differentiation
*Biological Evolution
Germ Cells/cytology
Models, Biological
Animals
Cell Division
Selection, Genetic

@article {pmid40042639,
year = {2025},
author = {Zhu, T and Ning, P and Liu, Y and Liu, M and Yang, J and Wang, Z and Li, M},
title = {Knowledge of microalgal Rubiscos helps to improve photosynthetic efficiency of crops.},
journal = {Planta},
volume = {261},
number = {4},
pages = {78},
pmid = {40042639},
issn = {1432-2048},
support = {6651121004//"First class grass land science discipline" program in Shandong Province, the Talents of High Level Scientific Research Foundation of Qingdao Agricultural University/ ; 6651120032//"First class grass land science discipline" program in Shandong Province, the Talents of High Level Scientific Research Foundation of Qingdao Agricultural University/ ; 22278233//National Natural Science Foundation of China/ ; ZR2022QB143//Natural Science Foundation of Shandong Province/ ; ZR2020QC069//Natural Science Foundation of Shandong Province/ ; M2023-05//State Key Laboratory of Microbial Resources, Chinese Academy of Sciences/ ; M2022-07//State Key Laboratory of Microbial Technology Open Projects Fund/ ; },
mesh = {*Microalgae/physiology/metabolism ; *Crops, Agricultural/metabolism/physiology ; *Photosynthesis/physiology ; *Ribulose-Bisphosphate Carboxylase/metabolism ; },
abstract = {A comprehensive understanding of microalgal Rubiscos offers opportunities to enhance photosynthetic efficiency of crops. As food production fails to meet the needs of the expanding population, there is increasing concern about Ribulose-1, 5-diphosphate (RuBP) carboxylase/oxygenase (Rubisco), the enzyme that catalyzes CO2 fixation in photosynthesis. There have been many attempts to optimize Rubisco in crops, but the complex multicellular structure of higher plants makes optimization more difficult. Microalgae have the characteristics of rapid growth, simple structure and easy molecular modification, and the function and properties of their Rubiscos are basically the same as those of higher plants. Research on microalgal Rubiscos helps to broaden the understanding of Rubiscos of higher plants. Also, transferring all or part of better microalgal Rubiscos into crop cells or giving crop Rubiscos the advantages of microalgal Rubiscos can help improve the photosynthesis of crops. In this review, the distribution, origin, evolution, molecular structure, folding, assembly, activation and kinetic properties of microalgal Rubiscos are summarized. Moreover, the development of some effective methods to improve the properties and application of Rubiscos in microalgae are also described.},
}

*Microalgae/physiology/metabolism
*Crops, Agricultural/metabolism/physiology
*Photosynthesis/physiology
*Ribulose-Bisphosphate Carboxylase/metabolism

@article {pmid40027827,
year = {2025},
author = {Price, KL and Tharakan, DM and Salvenmoser, W and Ayers, K and Mah, J and Dunn, C and Hobmayer, B and Cooley, L},
title = {Examination of germline and somatic intercellular bridges in Hydra vulgaris reveals insights into the evolutionarily conserved mechanism of intercellular bridge formation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40027827},
issn = {2692-8205},
support = {F32 GM136029/GM/NIGMS NIH HHS/United States ; R35 GM141961/GM/NIGMS NIH HHS/United States ; },
abstract = {Incomplete cytokinesis results in the formation of stable intercellular bridges that have been extensively studied in bilaterians, where they play essential roles in cell-cell communication and coordination of differentiation. However, little is known about their structure and molecular composition in non-bilaterian animals. This study characterizes germline and somatic intercellular bridges in the cnidarian Hydra vulgaris, providing insights into their evolutionary origins and functional significance. We identified key conserved components, including KIF23, F-actin, and phosphotyrosine. Notably, we observed microtubule localization within Hydra ring canals, suggesting previously unrecognized functions for this cytoskeletal component in intercellular bridge formation. Bioinformatic analyses confirmed the conserved expression of Kif23 and suggested its role as a molecular marker for identifying ring canal-associated components. EdU incorporation during DNA replication demonstrated that cells connected by ring canals exhibit synchronized cell cycles, which may be critical for the coordination of division and differentiation. Our findings reveal that the molecular and structural features of intercellular bridges in Hydra are conserved across evolutionary lineages, highlighting their ancient origins and functional significance in cellular connectivity. The presence of synchronized cell cycles in ring canal-connected cells underscores their role in promoting coordinated cellular behaviors, processes fundamental to multicellular organization. This study provides new perspectives on the evolution of incomplete cytokinesis and establishes a framework for comparative investigations into the diversity and conservation of intercellular bridge mechanisms across metazoans.},
}

@article {pmid40027720,
year = {2025},
author = {Zheng, H and Sarkar, H and Raphael, BJ},
title = {Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40027720},
issn = {2692-8205},
support = {U24 CA248453/CA/NCI NIH HHS/United States ; U24 CA264027/CA/NCI NIH HHS/United States ; },
abstract = {Spatially resolved transcriptomics (SRT) technologies measure gene expression across thousands of spatial locations within a tissue slice. Multiple SRT technologies are currently available and others are in active development with each technology having varying spatial resolution (subcellular, single-cell, or multicellular regions), gene coverage (targeted vs. whole-transcriptome), and sequencing depth per location. For example, the widely used 10x Genomics Visium platform measures whole transcriptomes from multiple-cell-sized spots, while the 10x Genomics Xenium platform measures a few hundred genes at subcellular resolution. A number of studies apply multiple SRT technologies to slices that originate from the same biological tissue. Integration of data from different SRT technologies can overcome limitations of the individual technologies enabling the imputation of expression from unmeasured genes in targeted technologies and/or the deconvolution of ad-mixed expression from technologies with lower spatial resolution. We introduce Spatial Integration for Imputation and Deconvolution (SIID), an algorithm to reconstruct a latent spatial gene expression matrix from a pair of observations from different SRT technologies. SIID leverages a spatial alignment and uses a joint non-negative factorization model to accurately impute missing gene expression and infer gene expression signatures of cell types from ad-mixed SRT data. In simulations involving paired SRT datasets from different technologies (e.g., Xenium and Visium), SIID shows superior performance in reconstructing spot-to-cell-type assignments, recovering cell-type-specific gene expression, and imputing missing data compared to contemporary tools. When applied to real-world 10x Xenium-Visium pairs from human breast and colon cancer tissues, SIID achieves highest performance in imputing holdout gene expression. A PyTorch implementation of SIID is available at https://github.com/raphael-group/siid.},
}

@article {pmid40027677,
year = {2025},
author = {Stoy, KS and MacGillivray, KA and Burnetti, AJ and Barrett, C and Ratcliff, WC},
title = {Multiple pathways to the evolution of positive assortment in aggregative multicellularity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40027677},
issn = {2692-8205},
support = {T32 GM142616/GM/NIGMS NIH HHS/United States ; },
abstract = {The evolutionary transition to multicellularity requires shifting the primary unit of selection from cells to multicellular collectives. How this occurs in aggregative organisms remains poorly understood. Clonal development provides a direct path to multicellular adaptation through genetic identity between cells, but aggregative organisms face a constraint: selection on collective-level traits cannot drive adaptation without positive genetic assortment. We leveraged experimental evolution of flocculating Saccharomyces cerevisiae to examine the evolution and role of genetic assortment in multicellular adaptation. After 840 generations of selection for rapid settling, 13 of 19 lineages evolved increased positive assortment relative to their ancestor. However, assortment provided no competitive advantage during settling selection, suggesting it arose as an indirect effect of selection on cell-level traits rather than through direct selection on collective-level properties. Genetic reconstruction experiments and protein structure modeling revealed two distinct pathways to assortment: kin recognition mediated by mutations in the FLO1 adhesion gene and generally enhanced cellular adhesion that improved flocculation efficiency independent of partner genotype. The evolution of assortment without immediate adaptive benefit suggests that key innovations enabling multicellular adaptation may arise indirectly through cell-level selection. Our results demonstrate fundamental constraints on aggregative multicellularity and help explain why aggregative lineages have remained simple.},
}

@article {pmid40027608,
year = {2025},
author = {Rossine, F and Sanchez, C and Eaton, D and Paulsson, J and Baym, M},
title = {Intracellular competition shapes plasmid population dynamics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40027608},
issn = {2692-8205},
support = {R35 GM133700/GM/NIGMS NIH HHS/United States ; },
abstract = {Conflicts between levels of biological organization are central to evolution, from populations of multicellular organisms to selfish genetic elements in microbes. Plasmids are extrachromosomal, self-replicating genetic elements that underlie much of the evolutionary flexibility of bacteria. Evolving plasmids face selective pressures on their hosts, but also compete within the cell for replication, making them an ideal system for studying the joint dynamics of multilevel selection. While theory indicates that within-cell selection should matter for plasmid evolution, experimental measurement of within-cell plasmid fitness and its consequences has remained elusive. Here we measure the within-cell fitness of competing plasmids and characterize drift and selective dynamics. We achieve this by the controlled splitting of synthetic plasmid dimers to create balanced competition experiments. We find that incompatible plasmids co-occur for longer than expected due to methylation-based plasmid eclipsing. During this period of co-occurrence, less transcriptionally active plasmids display a within-cell selective advantage over their competing plasmids, leading to preferential fixation of silent plasmids. When the transcribed gene is beneficial to the cell, for example an antibiotic resistance gene, there is a cell-plasmid fitness tradeoff mediated by the dominance of the beneficial trait. Surprisingly, more dominant plasmid-encoded traits are less likely to fix but more likely to initially invade than less dominant traits. Taken together, our results show that plasmid evolution is driven by dynamics at two levels, with a transient, but critical, contribution of within-cell fitness.},
}

@article {pmid40008892,
year = {2025},
author = {Leon, F and Espinoza-Esparza, JM and Deng, V and Coyle, MC and Espinoza, S and Booth, DS},
title = {Cell differentiation controls iron assimilation in the choanoflagellate Salpingoeca rosetta.},
journal = {mSphere},
volume = {10},
number = {3},
pages = {e0091724},
doi = {10.1128/msphere.00917-24},
pmid = {40008892},
issn = {2379-5042},
support = {R35GM147404//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; //David and Lucile Packard Foundation (PF)/ ; //NSF | National Science Foundation Graduate Research Fellowship Program (GRFP)/ ; T32GM139786//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {*Choanoflagellata/genetics/metabolism ; *Iron/metabolism ; *Cell Differentiation ; FMN Reductase/metabolism/genetics ; Protozoan Proteins/metabolism/genetics ; },
abstract = {UNLABELLED: Marine microeukaryotes have evolved diverse cellular features that link their life histories to surrounding environments. How those dynamic life histories intersect with the ecological functions of microeukaryotes remains a frontier to understanding their roles in critical biogeochemical cycles. Choanoflagellates, phagotrophs that cycle nutrients through filter feeding, provide models to explore this intersection, for many choanoflagellate species transition between life history stages by differentiating into distinct cell types. Here, we report that cell differentiation in the marine choanoflagellate Salpingoeca rosetta endows one of its cell types with the ability to utilize insoluble ferric colloids. These colloids are a predominant form of iron in marine environments and are largely inaccessible to cell-walled microbes. Therefore, choanoflagellates and other phagotrophic eukaryotes may serve critical ecological roles by cycling this essential nutrient through iron utilization pathways. We found that S. rosetta can utilize these ferric colloids via the expression of a cytochrome b561 iron reductase (cytb561a). This gene and its mammalian ortholog, the duodenal cytochrome b561 (DCYTB) that reduces ferric cations for uptake in gut epithelia, belong to a subgroup of cytochrome b561 proteins with distinct biochemical features that contribute to iron reduction activity. Overall, our findings provide insight into the ecological roles choanoflagellates perform and inform reconstructions of early animal evolution where functionally distinct cell types became an integrated whole at the origin of animal multicellularity.

IMPORTANCE: This study examines how cell differentiation in a choanoflagellate enables the uptake of iron, an essential nutrient. Choanoflagellates are widespread, aquatic microeukaryotes that are the closest living relatives of animals. Similar to their animal relatives, we found that the model choanoflagellate, S. rosetta, divides metabolic functions between distinct cell types. One cell type uses an iron reductase to acquire ferric colloids, a key source of iron in the ocean. We also observed that S. rosetta has three variants of this reductase, each with distinct biochemical properties that likely lead to differences in how they reduce iron. These reductases are variably distributed across ocean regions, suggesting a role for choanoflagellates in cycling iron in marine environments.},
}

*Choanoflagellata/genetics/metabolism
*Iron/metabolism
*Cell Differentiation
FMN Reductase/metabolism/genetics
Protozoan Proteins/metabolism/genetics

@article {pmid40001581,
year = {2025},
author = {Liu, Z and Fan, X and Wu, Y and Zhang, W and Zhang, X and Xu, D and Wang, Y and Sun, K and Wang, W and Ye, N},
title = {Comparative Genomics of Bryopsis hypnoides: Structural Conservation and Gene Transfer Between Chloroplast and Mitochondrial Genomes.},
journal = {Biomolecules},
volume = {15},
number = {2},
pages = {},
pmid = {40001581},
issn = {2218-273X},
mesh = {*Genome, Mitochondrial/genetics ; *Genome, Chloroplast/genetics ; *Phylogeny ; *Genomics/methods ; Codon Usage ; Evolution, Molecular ; Gene Transfer, Horizontal ; RNA, Transfer/genetics ; },
abstract = {Bryopsis hypnoides, a unicellular multinucleate green alga in the genus Bryopsis, plays vital ecological roles and represents a key evolutionary link between unicellular and multicellular algae. However, its weak genetic baseline data have constrained the progress of evolutionary research. In this study, we successfully assembled and annotated the complete circular chloroplast and mitochondrial genomes of B. hypnoides. The chloroplast genome has a total length of 139,745 bp and contains 59 protein-coding genes, 2 rRNA genes, and 11 tRNA genes, with 31 genes associated with photosynthesis. The mitochondrial genome has a total length of 408,555 bp and contains 41 protein-coding genes, 3 rRNA genes, and 18 tRNA genes, with 18 genes involved in oxidative phosphorylation. Based on the data, we conducted a genetic comparison involving repeat sequences, phylogenetic relationships, codon usage preferences, and gene transfer between the two organellar genomes. The major results highlighted that (1) the chloroplast genome favors A/T repeats, whereas the mitochondrial genome prefers C/G repeats; (2) codon usage preference analysis indicated that both organellar genomes prefer codons ending in A/T, with a stronger bias observed in the chloroplast genome; and (3) sixteen fragments with high sequence identity were identified between the two organellar genomes, indicating potential gene transfer. These findings provide critical insights into the organellar genome characteristics and evolution of B. hypnoides.},
}

*Genome, Mitochondrial/genetics
*Genome, Chloroplast/genetics
*Phylogeny
*Genomics/methods
Codon Usage
Evolution, Molecular
Gene Transfer, Horizontal
RNA, Transfer/genetics