@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 = {},
number = {},
pages = {},
doi = {10.1021/acsami.5c02296},
pmid = {40052705},
issn = {1944-8252},
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.},
}

@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 = {},
number = {},
pages = {},
pmid = {40044858},
issn = {1476-4687},
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.},
}

@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 = {},
doi = {10.1101/2025.02.19.639158},
pmid = {40027827},
issn = {2692-8205},
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 = {},
doi = {10.1101/2025.02.17.638195},
pmid = {40027720},
issn = {2692-8205},
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 = {},
doi = {10.1101/2025.02.17.638078},
pmid = {40027677},
issn = {2692-8205},
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 = {},
doi = {10.1101/2025.02.19.639193},
pmid = {40027608},
issn = {2692-8205},
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 = {},
number = {},
pages = {e0091724},
doi = {10.1128/msphere.00917-24},
pmid = {40008892},
issn = {2379-5042},
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.},
}

@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 = {},
doi = {10.3390/biom15020278},
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

@article {pmid39999802,
year = {2025},
author = {Saier, MH},
title = {Cooperation and competition were primary driving forces for biological evolution.},
journal = {Microbial physiology},
volume = {},
number = {},
pages = {1-25},
doi = {10.1159/000544890},
pmid = {39999802},
issn = {2673-1673},
abstract = {BACKGROUND: For many years, scientists have accepted Darwin's conclusion that "Survival of the Fittest" involves successful competition with other organisms for life-endowing molecules and conditions.

SUMMARY: Newly discovered "partial" organisms with minimal genomes that require symbiotic or parasitic relationships for growth and reproduction suggest that cooperation in addition to competition was and still is a primary driving force for survival. These two phenomena are not mutually exclusive, and both can confer a competitive advantage for survival. In fact, cooperation may have been more important in the early evolution for life on Earth before autonomous organisms developed, becoming large genome organisms.

KEY MESSAGES: This suggestion has tremendous consequences with respect to our conception of the early evolution of life on Earth as well as the appearance of intercellular interactions, multicellularity and the nature of interactions between humans and their societies (e.g., Social Darwinism).},
}

@article {pmid39999174,
year = {2025},
author = {Matte, A and LeBoeuf, AC},
title = {Innovation in ant larval feeding facilitated queen-worker divergence and social complexity.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {9},
pages = {e2413742122},
doi = {10.1073/pnas.2413742122},
pmid = {39999174},
issn = {1091-6490},
support = {PR00P3_179776//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; },
mesh = {Animals ; *Ants/physiology ; *Larva/physiology/growth & development ; *Feeding Behavior/physiology ; *Social Behavior ; Phylogeny ; Biological Evolution ; Female ; Reproduction/physiology ; Behavior, Animal/physiology ; },
abstract = {Building differences between genetically equivalent units is a fundamental challenge for all multicellular organisms and superorganisms. In ants, reproductive or worker fate is typically determined during the larval stage, through feeding regimes managed by adult caretakers. However, the feeding care provided to larvae varies significantly across ants, as does phenotypic divergence between queen and worker castes. Here, we employed comparative phylogenetic methods and causal inference to investigate the relationships between larval feeding care, caste size dimorphism, and social complexity across ant diversity. We digitized the life's work of George and Jeanette Wheeler, cataloging the larval morphology of over 700 species, and we compiled data on species diets and larval feeding behaviors from the literature and our own observations. We measured queen-worker size dimorphism in 392 species and gathered data for colony size, worker polymorphism, and worker reproduction. Our analyses revealed that ancestral active-feeding larvae evolved passive morphologies when adults began feeding them individually, typically with processed material and often following a shift to nonpredatory diets. Greater queen-worker size dimorphism coevolved with larval passiveness, alongside traits indicative of increased social complexity, including larger colony sizes, worker subcastes, and a reduction in workers' reproductive potential. Likelihood comparisons of causal phylogenetic models support that extended alloparental care facilitated stronger caste dimorphism, which, in turn and along with increased colony sizes, promoted higher social complexity. Our results suggest that enhanced adult control over larval development enabled greater phenotypic specialization within colonies, with profound implications for social evolution.},
}

Animals
*Ants/physiology
*Larva/physiology/growth & development
*Feeding Behavior/physiology
*Social Behavior
Phylogeny
Biological Evolution
Female
Reproduction/physiology
Behavior, Animal/physiology

@article {pmid39998200,
year = {2025},
author = {Hu, P},
title = {mSphere of Influence: Rapid evolution of pathogenesis and drug resistance in human pathogenic fungi.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0057024},
doi = {10.1128/msphere.00570-24},
pmid = {39998200},
issn = {2379-5042},
abstract = {Pengjie Hu works in the field of fungal pathogenesis, drug resistance, and evolution. In this mSphere of Influence article, he reflects on how three works, "Transposon mobilization in the human fungal pathogen Cryptococcus is mutagenic during infection and promotes drug resistance in vitro" and "Genome-wide analysis of heat stress-stimulated transposon mobility in the human fungal pathogen Cryptococcus deneoformans" by Gusa et al. and "Rapid evolution of an adaptive multicellular morphology of Candida auris during systemic infection" by Bing et al. have impacted his work on the evolution of virulence, resistance, and adaptation in human fungal pathogens.},
}

@article {pmid39884276,
year = {2025},
author = {Van Goor, J and Turdiev, A and Speir, SJ and Manning, J and Haag, ES},
title = {Male secreted short glycoproteins link sperm competition to the reproductive isolation of species.},
journal = {Current biology : CB},
volume = {35},
number = {4},
pages = {911-917.e5},
doi = {10.1016/j.cub.2024.12.040},
pmid = {39884276},
issn = {1879-0445},
mesh = {Animals ; Male ; *Spermatozoa/physiology/metabolism ; *Reproductive Isolation ; Glycoproteins/metabolism/genetics ; Female ; Caenorhabditis elegans/physiology/genetics/metabolism ; },
abstract = {Sperm competition is found across multicellular organisms[1][,][2][,][3][,][4] using both external and internal fertilization.[5][,][6] Sperm competition and post-copulatory cryptic female choice can promote incompatibility between species due to the antagonistic coevolution of the sexes within a species.[7][,][8][,][9][,][10][,][11] This between-species incompatibility is accelerated and markedly asymmetrical when sexual mode differs, producing the "weak inbreeder, strong outcrosser" (WISO) pattern.[12] Here, we show that male secreted short (MSS) sperm glycoproteins of nematodes constitute a gametic effector of WISO. In obligately outcrossing Caenorhabditis, MSS is dispensable for baseline fertility but required for intraspecific sperm competitiveness.[13] MSS is lost in self-fertile lineages, likely as a response to selection for a hermaphrodite-biased sex ratio.[14] Selfing hermaphrodites that mate with males of closely related outcrossing species are rapidly sterilized due to ovarian sperm invasion.[11] The simplification of the male proteome in selfing species suggests that many factors could contribute to invasivity.[13][,][15][,][16] However, restoration of just MSS to the self-fertile C. briggsae is sufficient to induce mild invasivity. Further, MSS+ sperm appear to derive their competitive advantage from this behavior, directly linking interspecies incompatibility with intraspecific competition. MSS-related proteins (MSRPs) remaining in the C. briggsae genome are similar in structure, expression, and localization to MSS but are not necessary for normal sperm competitiveness. Further, overexpression of the MSRP most similar to MSS, Cbr-MSRP-3, is insufficient to enhance competitiveness. We conclude that outcrossing species retain sperm competition factors that contribute to their reproductive isolation from selfing relatives that lost them.},
}

Animals
Male
*Spermatozoa/physiology/metabolism
*Reproductive Isolation
Glycoproteins/metabolism/genetics
Female
Caenorhabditis elegans/physiology/genetics/metabolism

@article {pmid39983731,
year = {2025},
author = {Saha, S and Kalathera, J and Sumi, TS and Mane, V and Zimmermann, S and Waschina, S and Pande, S},
title = {Mass lysis of predatory bacteria drives the enrichment of antibiotic resistance in soil microbial communities.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.01.068},
pmid = {39983731},
issn = {1879-0445},
abstract = {Numerous studies have investigated the effects of antibiotics on the evolution and maintenance of antimicrobial resistance (AMR). However, the impact of microbial interactions in antibiotic-free environments on resistance within complex communities remains unclear. We investigated whether the predatory bacterium M. xanthus, which can produce antimicrobials and employ various contact-dependent and -independent prey-killing mechanisms, influences the abundance of antibiotic-resistant bacteria in its local environment simply through its presence, regardless of active predation. We observed an association between the presence of M. xanthus in soil and the frequency of antibiotic-resistant bacteria. Additionally, culture-based and metagenomic analysis showed that coculturing M. xanthus with soil-derived communities in liquid cultures enriched AMR among non-myxobacterial isolates. This is because the lysis of M. xanthus, triggered during the starvation phase of the coculture experiments, releases diffusible growth-inhibitory compounds that enrich pre-existing resistant bacteria. Furthermore, our results show that death during multicellular fruiting body formation-a starvation-induced stress response in M. xanthus that results in over 90% cell death-also releases growth-inhibitory molecules that enrich resistant bacteria. Hence, the higher abundance of resistant bacteria in soil communities, where M. xanthus can be detected, was because of the diffusible growth-inhibitory substances that were released due to the death of M. xanthus cells during fruiting body formation. Together, our findings demonstrate how the death of M. xanthus, an important aspect of its life cycle, can impact antibiotic resistomes in natural soil communities without the anthropogenic influx of antibiotics.},
}

@article {pmid39981820,
year = {2025},
author = {Du, Y and Wang, C and Zhang, Y and Liu, H},
title = {Evolutionary Origins and Adaptive Significance of A-to-I RNA Editing in Animals and Fungi.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e202400220},
doi = {10.1002/bies.202400220},
pmid = {39981820},
issn = {1521-1878},
support = {32170200//National Natural Science Foundation of China/ ; 31872918//National Natural Science Foundation of China/ ; },
abstract = {Adenosine-to-inosine (A-to-I) RNA editing, capable of protein recoding, has evolved independently in animals and fungi. This study proposes adaptive hypotheses regarding its origins and phenotypic significance, suggesting that A-to-I editing enhances adaptability by alleviating genetic trade-offs. In metazoans, its emergence may have been driven by a development-defense trade-off associated with transposable element activation during the evolution of multicellularity. Late Devonian cooling and End-Permian warming are hypothesized to have driven the emergence of extensive A-to-I recoding in coleoid nervous systems and Sordariomycete sexual fruiting bodies, respectively. These adaptations may have influenced key evolutionary innovations, including the evolution of metazoan nervous systems, coleoid intelligence, and shell loss, and fungal sexual reproductive structures. Additionally, extensive A-to-I recoding is proposed to facilitate accelerated development and specific life-history strategies in both animals and fungi. This paper provides new perspectives on the evolutionary forces shaping A-to-I RNA editing and its role in phenotypic diversity across taxa.},
}

@article {pmid39981724,
year = {2025},
author = {Siemons, C and Jonkers, S and Vlieg, RC and Corral-Martínez, P and van Noort, J and Boutilier, K},
title = {Establishment and maintenance of embryogenic cell fate during microspore embryogenesis.},
journal = {The Plant journal : for cell and molecular biology},
volume = {121},
number = {4},
pages = {e17243},
doi = {10.1111/tpj.17243},
pmid = {39981724},
issn = {1365-313X},
support = {656579//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; 435005024/ZONMW_/ZonMw/Netherlands ; 737.016.013//NWO Building Blocks of Life/ ; },
mesh = {*Pollen/genetics/cytology/embryology ; *Brassica napus/genetics/embryology/cytology ; Seeds/genetics/cytology/growth & development ; Gene Expression Regulation, Plant ; Plant Proteins/metabolism/genetics ; Indoleacetic Acids/metabolism ; Cell Differentiation ; Time-Lapse Imaging ; Plants, Genetically Modified ; },
abstract = {Microspore embryogenesis is a type of in vitro totipotency in which the immature male gametophyte (pollen) develops into a haploid embryo after an abiotic stress treatment. In Brassica napus, heat-stress treatment of male gametophytes induces the development of different types of multicellular embryogenic structures, each with different cellular characteristics and the capacity to form a differentiated embryo. The origin and early development of these different embryogenic structures have not been determined. We used two-photon excitation fluorescence microscopy and time-lapse imaging of cells expressing either a LEAFY COTYLEDON1 (LEC1) embryo identity reporter or a DR5v2 auxin response reporter to follow the development of embryogenic structures starting at the single- to few-cell stage. We show for the first time that the developmental fate of embryogenic structures is defined by the symmetry of the first embryogenic division and that the division plane also predicts the timing of subsequent pollen wall (exine) rupture: suspensorless embryos develop after a symmetric division and undergo late exine rupture, while suspensor-bearing embryos and embryogenic callus develop after an asymmetric division and undergo early exine rupture. Live imaging also captured previously unknown dynamic LEC1 and DR5v2 expression patterns that are associated with changes in exine integrity. This study highlights the developmental plasticity of cultured pollen and uncovers new roles for the first embryogenic cell division plane and the exine in defining and maintaining cell fate during microspore embryogenesis.},
}

*Pollen/genetics/cytology/embryology
*Brassica napus/genetics/embryology/cytology
Seeds/genetics/cytology/growth & development
Gene Expression Regulation, Plant
Plant Proteins/metabolism/genetics
Indoleacetic Acids/metabolism
Cell Differentiation
Time-Lapse Imaging
Plants, Genetically Modified

@article {pmid39979449,
year = {2025},
author = {Thibault, B and Thole, A and D'Angelo, R and Basset, C and Guillermet-Guibert, J},
title = {PI3Kα-specific inhibitor BYL-719 synergizes with cisplatin in vitro in PIK3CA-mutated ovarian cancer cells.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {6265},
pmid = {39979449},
issn = {2045-2322},
support = {ARCPGA2022120005630_6362//Foundation for Cancer Research (ARC)/ ; TOUCAN//ANR/ ; },
mesh = {Humans ; *Cisplatin/pharmacology ; Female ; *Class I Phosphatidylinositol 3-Kinases/antagonists & inhibitors/genetics/metabolism ; *Ovarian Neoplasms/drug therapy/genetics/pathology/metabolism ; Cell Line, Tumor ; *Drug Synergism ; *Mutation ; *Thiazoles/pharmacology ; Phosphoinositide-3 Kinase Inhibitors/pharmacology ; Proto-Oncogene Proteins c-akt/metabolism/antagonists & inhibitors ; Signal Transduction/drug effects ; Antineoplastic Agents/pharmacology ; Drug Resistance, Neoplasm/drug effects/genetics ; },
abstract = {Peritoneal carcinomatosis in ovarian cancer is often associated with ascites where cancer cells grow as aggregates. Given the emerging evidence that multicellular growth enhances resistance to conventional therapies, and that patients frequently develop resistance to platinum salts, we investigated the efficiency of PI3K/Akt signalling pathway targeting in multicellular growth and its importance as a potential therapeutic target in cells resistant to platinum salts. Due to its importance in many cancers and to the frequent mutations of its encoding gene PIK3CA, we focused on targeting PI3Kα using BYL-719 (Alpelisib), an isoform-specific inhibitor already used in clinics. We used a panel of 3 ovarian cancer cell lines, SKOV-3, EFO-21 and OVCAR-3, which come from different histological origins and bear different mutations. PI3K targeting drugs inhibit the activity of the PI3K/Akt pathway in all tested ovarian cancer cell lines with a drastic reduction of the phosphorylation of Akt on the serine 473, regardless the histology or the mutational profile. We showed that when cultured in 3D aggregates, ovarian cancer cells are more resistant to the PI3Kα-specific inhibitor BYL-719 and cisplatin compared to 2D monolayers. BYL-719 synergizes with cisplatin in 3D cultures only in PIK3CA-mutated SKOV-3 cells. This drug combination leads to a major cytotoxicity in 3D aggregates of this cell line. Finally, BYL-719 in combination with cisplatin remains active in 3D aggregates of SKOV-3 cells co-cultured with mesenchymal stem cells. We have identified a signalling pathway of interest for the treatment of advanced ovarian cancer in vitro, which could limit the progression of this disease. These data pave the road to investigate whether PI3Kα-specific inhibitor BYL-719 should be proposed in combination with cisplatin, in priority in patients bearing a PIK3CA mutation.},
}

Humans
*Cisplatin/pharmacology
Female
*Class I Phosphatidylinositol 3-Kinases/antagonists & inhibitors/genetics/metabolism
*Ovarian Neoplasms/drug therapy/genetics/pathology/metabolism
Cell Line, Tumor
*Drug Synergism
*Mutation
*Thiazoles/pharmacology
Phosphoinositide-3 Kinase Inhibitors/pharmacology
Proto-Oncogene Proteins c-akt/metabolism/antagonists & inhibitors
Signal Transduction/drug effects
Antineoplastic Agents/pharmacology
Drug Resistance, Neoplasm/drug effects/genetics

@article {pmid39972731,
year = {2025},
author = {Hoffmann, LA and Giomi, L},
title = {Homochirality in the Vicsek model: Fluctuations and potential implications for cellular flocks.},
journal = {Physical review. E},
volume = {111},
number = {1-2},
pages = {015427},
doi = {10.1103/PhysRevE.111.015427},
pmid = {39972731},
issn = {2470-0053},
mesh = {*Models, Biological ; Animals ; },
abstract = {Chirality is a feature of many biological systems, and much research has been focused on understanding the origin and implications of this property. Famously, sugars and amino acids found in nature are homochiral, i.e., chiral symmetry is broken and only one of the two possible chiral states is ever observed. Certain types of cells show chiral behavior, too. Understanding the origin of cellular chirality and its effect on tissues and cellular dynamics is still an open problem and subject to much (recent) research, e.g., in the context of drosophila morphogenesis. Here, we develop a simple model to describe the possible origin of homochirality in cells. Combining the Vicsek model for collective behavior with the model of Jafarpour et al. [Phys. Rev. Lett. 115, 158101 (2015)0031-900710.1103/PhysRevLett.115.158101], developed to describe the emergence of molecular homochirality, we investigate how a homochiral state might have evolved in cells from an initially symmetric state without any mechanisms that explicitly break chiral symmetry. We investigate the transition to homochirality and show how the "openness" of the system as well as noise determine if and when a globally homochiral state is reached. While hypothetical and explorative in nature, our analysis may serve as a starting point for more realistic models of chirality in flocking multicellular systems.},
}

*Models, Biological
Animals

@article {pmid39970295,
year = {2025},
author = {Raynal, F and Sengupta, K and Plewczynski, D and Aliaga, B and Pancaldi, V},
title = {Global chromatin reorganization and regulation of genes with specific evolutionary ages during differentiation and cancer.},
journal = {Nucleic acids research},
volume = {53},
number = {4},
pages = {},
doi = {10.1093/nar/gkaf084},
pmid = {39970295},
issn = {1362-4962},
support = {//Fondation Toulouse Cancer Santé/ ; //Pierre Fabre Foundation for Research/ ; ANR-23-CE12-0023//Agence Nationale de la Recherche/ ; //Warsaw University of Technology/ ; 2020/37/B/NZ2/03757//National Science Centre/ ; },
mesh = {Humans ; *Cell Differentiation/genetics ; *Chromatin/metabolism/genetics ; *Evolution, Molecular ; Gene Expression Regulation, Neoplastic ; Chromatin Assembly and Disassembly/genetics ; RNA Polymerase II/metabolism/genetics ; Embryonic Stem Cells/metabolism ; Polycomb-Group Proteins/genetics/metabolism ; Leukemia, Lymphocytic, Chronic, B-Cell/genetics/pathology ; Colorectal Neoplasms/genetics/pathology ; Epigenesis, Genetic ; Neoplasms/genetics/pathology ; },
abstract = {Cancer cells are highly plastic, favoring adaptation to changing conditions. Genes related to basic cellular processes evolved in ancient species, while more specialized genes appeared later with multicellularity (metazoan genes) or even after mammals evolved. Transcriptomic analyses have shown that ancient genes are up-regulated in cancer, while metazoan-origin genes are inactivated. Despite the importance of these observations, the underlying mechanisms remain unexplored. Here, we study local and global epigenomic mechanisms that may regulate genes from specific evolutionary periods. Using evolutionary gene age data, we characterize the epigenomic landscape, gene expression regulation, and chromatin organization in several cell types: human embryonic stem cells, normal primary B-cells, primary chronic lymphocytic leukemia malignant B-cells, and primary colorectal cancer samples. We identify topological changes in chromatin organization during differentiation observing patterns in Polycomb repression and RNA polymerase II pausing, which are reversed during oncogenesis. Beyond the non-random organization of genes and chromatin features in the 3D epigenome, we suggest that these patterns lead to preferential interactions among ancient, intermediate, and recent genes, mediated by RNA polymerase II, Polycomb, and the lamina, respectively. Our findings shed light on gene regulation according to evolutionary age and suggest this organization changes across differentiation and oncogenesis.},
}

Humans
*Cell Differentiation/genetics
*Chromatin/metabolism/genetics
*Evolution, Molecular
Gene Expression Regulation, Neoplastic
Chromatin Assembly and Disassembly/genetics
RNA Polymerase II/metabolism/genetics
Embryonic Stem Cells/metabolism
Polycomb-Group Proteins/genetics/metabolism
Leukemia, Lymphocytic, Chronic, B-Cell/genetics/pathology
Colorectal Neoplasms/genetics/pathology
Epigenesis, Genetic
Neoplasms/genetics/pathology

@article {pmid39970120,
year = {2024},
author = {Finoshin, AD and Kravchuk, OI and Mikhailov, KV and Ziganshin, RH and Adameyko, KI and Mikhailov, VS and Lyupina, YV},
title = {[Structure and Function of the Transglutaminase Cluster in the Basal Metazoan Halisarca dujardinii (Sponge)].},
journal = {Molekuliarnaia biologiia},
volume = {58},
number = {5},
pages = {797-810},
pmid = {39970120},
issn = {0026-8984},
mesh = {Animals ; *Transglutaminases/genetics/metabolism ; *Porifera/enzymology/genetics ; Multigene Family ; Reactive Oxygen Species/metabolism ; Cystamine ; Gene Expression Regulation, Enzymologic ; },
abstract = {Transglutaminases are enzymes that carry out post-translational modifications of proteins and participate in the regulation of their activities. Here, we show for the first time that the transglutaminase genes in the basal metazoan, the sea sponge Halisarca dujardinii, are organized in a cluster, similarly to mammalian transglutaminases. The regulatory regions of six transglutaminase genes and their differential expression in the course of the life cycle of H. dujardinii suggest independent regulation of these genes. The decrease in transglutaminase activities by cystamine facilitates restoration of the multicellular structures of this sponge after its mechanical dissociation. For the first time we observed that this decrease in transglutaminase activities was accompanied by generation of the reactive oxygen species in the cells of a basal metazoan. The study of transglutaminases in the basal metazoans and other sea-dwelling organisms might provide better understanding of the evolution and specific functions of these enzymes in higher animals.},
}

Animals
*Transglutaminases/genetics/metabolism
*Porifera/enzymology/genetics
Multigene Family
Reactive Oxygen Species/metabolism
Cystamine
Gene Expression Regulation, Enzymologic

@article {pmid39964480,
year = {2025},
author = {Raynal, F and Sengupta, K and Plewczynski, D and Aliaga, B and Pancaldi, V},
title = {Global chromatin reorganization and regulation of genes with specific evolutionary ages during differentiation and cancer.},
journal = {Nucleic acids research},
volume = {53},
number = {4},
pages = {},
doi = {10.1093/nar/gkaf084},
pmid = {39964480},
issn = {1362-4962},
support = {//Fondation Toulouse Cancer Santé/ ; //Pierre Fabre Foundation for Research/ ; ANR-23-CE12-0023//Agence Nationale de la Recherche/ ; //Warsaw University of Technology/ ; 2020/37/B/NZ2/03757//National Science Centre/ ; },
mesh = {Humans ; *Cell Differentiation/genetics ; *Chromatin/metabolism/genetics ; *Evolution, Molecular ; Gene Expression Regulation, Neoplastic ; Chromatin Assembly and Disassembly/genetics ; RNA Polymerase II/metabolism/genetics ; Embryonic Stem Cells/metabolism ; Polycomb-Group Proteins/genetics/metabolism ; Leukemia, Lymphocytic, Chronic, B-Cell/genetics/pathology ; Colorectal Neoplasms/genetics/pathology ; Epigenesis, Genetic ; Neoplasms/genetics/pathology ; },
abstract = {Cancer cells are highly plastic, favoring adaptation to changing conditions. Genes related to basic cellular processes evolved in ancient species, while more specialized genes appeared later with multicellularity (metazoan genes) or even after mammals evolved. Transcriptomic analyses have shown that ancient genes are up-regulated in cancer, while metazoan-origin genes are inactivated. Despite the importance of these observations, the underlying mechanisms remain unexplored. Here, we study local and global epigenomic mechanisms that may regulate genes from specific evolutionary periods. Using evolutionary gene age data, we characterize the epigenomic landscape, gene expression regulation, and chromatin organization in several cell types: human embryonic stem cells, normal primary B-cells, primary chronic lymphocytic leukemia malignant B-cells, and primary colorectal cancer samples. We identify topological changes in chromatin organization during differentiation observing patterns in Polycomb repression and RNA polymerase II pausing, which are reversed during oncogenesis. Beyond the non-random organization of genes and chromatin features in the 3D epigenome, we suggest that these patterns lead to preferential interactions among ancient, intermediate, and recent genes, mediated by RNA polymerase II, Polycomb, and the lamina, respectively. Our findings shed light on gene regulation according to evolutionary age and suggest this organization changes across differentiation and oncogenesis.},
}

Humans
*Cell Differentiation/genetics
*Chromatin/metabolism/genetics
*Evolution, Molecular
Gene Expression Regulation, Neoplastic
Chromatin Assembly and Disassembly/genetics
RNA Polymerase II/metabolism/genetics
Embryonic Stem Cells/metabolism
Polycomb-Group Proteins/genetics/metabolism
Leukemia, Lymphocytic, Chronic, B-Cell/genetics/pathology
Colorectal Neoplasms/genetics/pathology
Epigenesis, Genetic
Neoplasms/genetics/pathology

@article {pmid39957902,
year = {2025},
author = {Liao, W and Wang, J and Li, Y},
title = {Natural products based on Correa's cascade for the treatment of gastric cancer trilogy: Current status and future perspective.},
journal = {Journal of pharmaceutical analysis},
volume = {15},
number = {2},
pages = {101075},
pmid = {39957902},
issn = {2214-0883},
abstract = {Gastric carcinoma (GC) is a malignancy with multifactorial involvement, multicellular regulation, and multistage evolution. The classic Correa's cascade of intestinal GC specifies a trilogy of malignant transformation of the gastric mucosa, in which normal gastric mucosa gradually progresses from inactive or chronic active gastritis (Phase I) to gastric precancerous lesions (Phase II) and finally to GC (Phase III). Correa's cascade highlights the evolutionary pattern of GC and the importance of early intervention to prevent malignant transformation of the gastric mucosa. Intervening in early gastric mucosal lesions, i.e., Phase I and II, will be the key strategy to prevent and treat GC. Natural products (NPs) have been an important source for drug development due to abundant sources, tremendous safety, and multiple pharmacodynamic mechanisms. This review is the first to investigate and summarize the multi-step effects and regulatory mechanisms of NPs on the Correa's cascade in gastric carcinogenesis. In phase I, NPs modulate Helicobacter pylori urease activity, motility, adhesion, virulence factors, and drug resistance, thereby inhibiting H. pylori-induced gastric mucosal inflammation and oxidative stress, and facilitating ulcer healing. In Phase II, NPs modulate multiple pathways and mediators regulating gastric mucosal cell cycle, apoptosis, autophagy, and angiogenesis to reverse gastric precancerous lesions. In Phase III, NPs suppress cell proliferation, migration, invasion, angiogenesis, and cancer stem cells, induce apoptosis and autophagy, and enhance chemotherapeutic drug sensitivity for the treatment of GC. In contrast to existing work, we hope to uncover NPs with sequential therapeutic effects on multiple phases of GC development, providing new ideas for gastric cancer prevention, treatment, and drug development.},
}

@article {pmid39957727,
year = {2024},
author = {Pineau, RM and Kahn, PC and Lac, DT and Belpaire, TER and Denning, MG and Wong, W and Ratcliff, WC and Bozdag, GO},
title = {Experimental evolution of multicellularity via cuboidal cell packing in fission yeast.},
journal = {Evolution letters},
volume = {8},
number = {5},
pages = {695-704},
pmid = {39957727},
issn = {2056-3744},
abstract = {The evolution of multicellularity represents a major transition in life's history, enabling the rise of complex organisms. Multicellular groups can evolve through multiple developmental modes, but a common step is the formation of permanent cell-cell attachments after division. The characteristics of the multicellular morphology that emerges have profound consequences for the subsequent evolution of a nascent multicellular lineage, but little prior work has investigated these dynamics directly. Here, we examine a widespread yet understudied emergent multicellular morphology: cuboidal packing. Extinct and extant multicellular organisms across the tree of life have evolved to form groups in which spherical cells divide but remain attached, forming approximately cubic subunits. To experimentally investigate the evolution of cuboidal cell packing, we used settling selection to favor the evolution of simple multicellularity in unicellular, spherical Schizosaccharomyces pombe yeast. Multicellular clusters with cuboidal organization rapidly evolved, displacing the unicellular ancestor. These clusters displayed key hallmarks of an evolutionary transition in individuality: groups possess an emergent life cycle driven by physical fracture, group size is heritable, and they respond to group-level selection via multicellular adaptation. In 2 out of 5 lineages, group formation was driven by mutations in the ace2 gene, preventing daughter cell separation after division. Remarkably, ace2 mutations also underlie the transition to multicellularity in Saccharomyces cerevisiae and Candida glabrata, lineages that last shared a common ancestor > 300 million years ago. Our results provide insight into the evolution of cuboidal cell packing, an understudied multicellular morphology, and highlight the deeply convergent potential for a transition to multicellular individuality within fungi.},
}

@article {pmid39711056,
year = {2025},
author = {Schaal, KA and Manhes, P and Velicer, GJ},
title = {Ecological histories govern social exploitation by microorganisms.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrae255},
pmid = {39711056},
issn = {1751-7370},
support = {GM079690//U.S. National Institutes of Health/ ; 31003A_160005/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {*Myxococcus xanthus/genetics/growth & development/physiology ; *Microbial Interactions ; Spores, Bacterial/growth & development ; Genotype ; Phenotype ; Genetic Fitness ; },
abstract = {Exploitation is a common feature of social interactions, which can be modified by ecological context. Here, we investigate effects of ecological history on exploitation phenotypes in bacteria. In experiments with the bacterium Myxococcus xanthus, prior resource levels of different genotypes interacting during cooperative multicellular development were found to regulate social fitness, including whether cheating occurs. Responses of developmental spore production to manipulation of resource-level histories differed between interacting cooperators and cheaters, and relative-fitness advantages gained by cheating after high-resource growth were generally reduced or absent if one or both parties experienced low-resource growth. Low-resource growth also eliminated exploitation in some pairwise mixes of cooperative natural isolates that occurs when both strains have grown under resource abundance. Our results contrast with previous experiments in which cooperator fitness correlated positively with concurrent resource level and suggest that resource-level variation may be important in regulating whether exploitation of cooperators occurs in a natural context.},
}

*Myxococcus xanthus/genetics/growth & development/physiology
*Microbial Interactions
Spores, Bacterial/growth & development
Genotype
Phenotype
Genetic Fitness

@article {pmid39954315,
year = {2025},
author = {Chen, H and Chen, C and Zhao, H and Wei, Y and Wang, P and Wu, LF and Song, T},
title = {Synergistic mechanism of magneto-optical sensing mediated by magnetic response protein Amb0994 and LOV-like protein Amb2291 in Magnetospirillum magneticum AMB-1.},
journal = {Journal of photochemistry and photobiology. B, Biology},
volume = {265},
number = {},
pages = {113124},
doi = {10.1016/j.jphotobiol.2025.113124},
pmid = {39954315},
issn = {1873-2682},
abstract = {Magnetotactic bacteria (MTB), known for their precision in navigating along magnetic fields, also exhibit light-sensitive behaviors. In Magnetospirillum magneticum AMB-1, the photoreceptor Amb2291 is involved in phototaxis regulation and magnetosome synthesis, particularly under oxidative stress. The magnetoreceptor Amb0994 modulates flagellar activity in response to magnetic field changes. Our study used a magneto-optical system to analyze the U-turn motility of north-seeking AMB-1 wild type (WT), amb2291 and amb0994 mutants under reversed magnetic fields and controlled light conditions. The results showed that WT strains consistently executed U-turns in response to magnetic fields, regardless of light variations. The diameters of U-turn of amb0994 mutant were smaller than those of the WT control. When illuminated with blue light in a direction opposite to the magnetic field, Δamb0994 exhibited slower U-turns with diameters similar to WT. In contrast, the Δamb2291 strain exhibited exaggerated U-turn movements under blue light, characterized by larger movement diameters and times compared to the WT, particularly whatever the light propagation direction is the same or opposite to the magnetic field in the initial state of motility. Gene expression analysis revealed that long-term exposure to blue light and magnetic fields led to a significant upregulation of amb2291 in Δamb0994 mutant strains and amb0994 in Δamb2291 mutant strains. These indicate a potential cooperative role of amb2291 and amb0994 in modulating bacterial motility under blue light. This research enhances our understanding of photoreception in MTB and its impact on magnetotaxis, shedding light on how environmental factors interact with microorganisms.},
}

@article {pmid39947017,
year = {2025},
author = {Zunjarrao, S and Gambetta, MC},
title = {Principles of long-range gene regulation.},
journal = {Current opinion in genetics & development},
volume = {91},
number = {},
pages = {102323},
doi = {10.1016/j.gde.2025.102323},
pmid = {39947017},
issn = {1879-0380},
abstract = {Transcription from gene promoters occurs in specific spatiotemporal patterns in multicellular organisms, controlled by genomic regulatory elements. The communication between a regulatory element and a promoter requires a certain degree of physical proximity between them; hence, most gene regulation occurs locally in the genome. However, recent discoveries have revealed long-range gene regulation strategies that enhance interactions between regulatory elements and promoters by overcoming the distances between them in the linear genome. These new findings challenge the traditional view of how gene expression patterns are controlled. This review examines long-range gene regulation strategies recently reported in Drosophila and mammals, offering insights into their mechanisms and evolution.},
}

@article {pmid39944812,
year = {2024},
author = {Klimontov, VV and Shishin, KS and Ivanov, RA and Ponomarenko, MP and Zolotareva, KA and Lashin, SA},
title = {GlucoGenes®, a database of genes and proteins associated with glucose metabolism disorders, its description and applications in bioinformatics research.},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {28},
number = {8},
pages = {1008-1017},
doi = {10.18699/vjgb-24-107},
pmid = {39944812},
issn = {2500-0462},
abstract = {Data on the genetics and molecular biology of diabetes are accumulating rapidly. This poses the challenge of creating research tools for a rapid search for, structuring and analysis of information in this field. We have developed a web resource, GlucoGenes®, which includes a database and an Internet portal of genes and proteins associated with high glucose (hyperglycemia), low glucose (hypoglycemia), and both metabolic disorders. The data were collected using text mining of the publications indexed in PubMed and PubMed Central and analysis of gene networks associated with hyperglycemia, hypoglycemia and glucose variability performed with ANDSystems, a bioinformatics tool. GlucoGenes® is freely available at: https://glucogenes.sysbio.ru/genes/main. GlucoGenes® enables users to access and download information about genes and proteins associated with the risk of hyperglycemia and hypoglycemia, molecular regulators with hyperglycemic and antihyperglycemic activity, genes up-regulated by high glucose and/or low glucose, genes down-regulated by high glucose and/or low glucose, and molecules otherwise associated with the glucose metabolism disorders. With GlucoGenes®, an evolutionary analysis of genes associated with glucose metabolism disorders was performed. The results of the analysis revealed a significant increase (up to 40 %) in the proportion of genes with phylostratigraphic age index (PAI) values corresponding to the time of origin of multicellular organisms. Analysis of sequence conservation using the divergence index (DI) showed that most of the corresponding genes are highly conserved (DI < 0.6) or conservative (DI < 1). When analyzing single nucleotide polymorphism (SNP) in the proximal regions of promoters affecting the affinity of the TATA-binding protein, 181 SNP markers were found in the GlucoGenes® database, which can reduce (45 SNP markers) or increase (136 SNP markers) the expression of 52 genes. We believe that this resource will be a useful tool for further research in the field of molecular biology of diabetes.},
}

@article {pmid39939306,
year = {2025},
author = {Bijonowski, BM and Park, J and Bergert, M and Teubert, C and Diz-Muñoz, A and Galic, M and Wegner, SV},
title = {Intercellular adhesion boots collective cell migration through elevated membrane tension.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1588},
pmid = {39939306},
issn = {2041-1723},
support = {757593//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; GA2268/4-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 386797833//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Cell Movement ; *Cell Adhesion/physiology ; *Cell Membrane/metabolism ; *Phospholipase D/metabolism ; Humans ; Animals ; Cytoskeleton/metabolism ; TOR Serine-Threonine Kinases/metabolism ; Phosphatidic Acids/metabolism ; Signal Transduction ; },
abstract = {In multicellular systems, the migration pattern of individual cells critically relies on the interactions with neighboring cells. Depending on the strength of these interactions, cells either move as a collective, as observed during morphogenesis and wound healing, or migrate individually, as it is the case for immune cells and fibroblasts. Mediators of cell-cell adhesions, such as cadherins coordinate collective dynamics by linking the cytoskeleton of neighboring cells. However, whether intercellular binding alone triggers signals that originate from within the plasma membrane itself, remains unclear. Here, we address this question through artificial photoswitchable cell-cell adhesions that selectively connect adjacent plasma membranes without linking directly to cytoskeletal elements. We find that these intercellular adhesions are sufficient to achieve collective cell migration. Linking adjacent cells increases membrane tension, which activates the enzyme phospholipase D2. The resulting increase in phosphatidic acid, in turn, stimulates the mammalian target of rapamycin, a known actuator of collective cell migration. Collectively, these findings introduce a membrane-based signaling axis as promotor of collective cell dynamics, which is independent of the direct coupling of cell-cell adhesions to the cytoskeleton.},
}

*Cell Movement
*Cell Adhesion/physiology
*Cell Membrane/metabolism
*Phospholipase D/metabolism
Humans
Animals
Cytoskeleton/metabolism
TOR Serine-Threonine Kinases/metabolism
Phosphatidic Acids/metabolism
Signal Transduction

@article {pmid39935786,
year = {2024},
author = {Paredes-Espinosa, MB and Paluh, JL},
title = {Synthetic embryology of the human heart.},
journal = {Frontiers in cell and developmental biology},
volume = {12},
number = {},
pages = {1478549},
pmid = {39935786},
issn = {2296-634X},
abstract = {The evolution of stem cell-based heart models from cells and tissues to organoids and assembloids and recently synthetic embryology gastruloids, is poised to revolutionize our understanding of cardiac development, congenital to adult diseases, and patient customized therapies. Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) have already been integrated into transplantable patches and are in preclinical efforts to reverse fibrotic scarring from myocardial infarctions. To inform on the complexity of heart diseases, multi-tissue morphogenic heart models are needed that replicate fundamental components of heart function to heart organogenesis in vitro and which require a deep understanding of heart development. Organoid and assembloid models capture selected multicellular cardiac processes, such as chamber formation and priming events for vascularization. Gastruloid heart models offer deeper insights as synthetic embryology to mimic multi-staged developmental events of in vivo heart organogenesis including established heart fields, crescent formation and heart tube development along with vascular systemic foundation and even further steps. The human Elongating Multi-Lineage Organized Cardiac (EMLOC) gastruloid model captures these stages and additional events including chamber genesis, patterned vascularization, and extrinsic central and intrinsic cardiac nervous system (CNS-ICNS) integration guided by spatiotemporal and morphogenic processes with neural crest cells. Gastruloid synthetic embryology heart models offer new insights into previously hidden processes of development and provide powerful platforms for addressing heart disease that extends beyond cardiomyocytes, such as arrhythmogenic diseases, congenital defects, and systemic injury interactions, as in spinal cord injuries. The holistic view that is emerging will reveal heart development and disease in unprecedented detail to drive transformative state-of-the-art innovative applications for heart health.},
}

@article {pmid39932998,
year = {2025},
author = {Loiodice, M and Drula, E and McIver, Z and Antonyuk, S and Baslé, A and Lima, M and Yates, EA and Byrne, DP and Coughlan, J and Leech, A and Mesdaghi, S and Rigden, DJ and Drouillard, S and Helbert, W and Henrissat, B and Terrapon, N and Wright, GSA and Couturier, M and Cartmell, A},
title = {Bacterial polysaccharide lyase family 33: Specificity from an evolutionarily conserved binding tunnel.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {7},
pages = {e2421623122},
doi = {10.1073/pnas.2421623122},
pmid = {39932998},
issn = {1091-6490},
mesh = {*Polysaccharide-Lyases/metabolism/genetics/chemistry ; Substrate Specificity ; Bacterial Proteins/metabolism/genetics/chemistry ; Bacteria/enzymology/genetics ; Evolution, Molecular ; Models, Molecular ; Amino Acid Sequence ; Binding Sites ; Protein Binding ; Polysaccharides/metabolism ; Glycosaminoglycans/metabolism ; },
abstract = {Acidic glycans are essential for the biology of multicellular eukaryotes. To utilize them, microbial life including symbionts and pathogens has evolved polysaccharide lyases (PL) that cleave their 1,4 glycosidic linkages via a β-elimination mechanism. PL family 33 (PL33) enzymes have the unusual ability to target a diverse range of glycosaminoglycans (GAGs), as well as the bacterial polymer, gellan gum. In order to gain more detailed insight into PL33 activities we recombinantly expressed 10 PL33 members derived from all major environments and further elucidated the detailed biochemical and biophysical properties of five, showing that their substrate specificity is conferred by variations in tunnel length and topography. The key amino acids involved in catalysis and substrate interactions were identified, and employing a combination of complementary biochemical, structural, and modeling approaches, we show that the tunnel topography is induced by substrate binding to the glycan. Structural and bioinformatic analyses revealed that these features are conserved across several lyase families as well as in mammalian GAG epimerases.},
}

*Polysaccharide-Lyases/metabolism/genetics/chemistry
Substrate Specificity
Bacterial Proteins/metabolism/genetics/chemistry
Bacteria/enzymology/genetics
Evolution, Molecular
Models, Molecular
Amino Acid Sequence
Binding Sites
Protein Binding
Polysaccharides/metabolism
Glycosaminoglycans/metabolism

@article {pmid39926383,
year = {2024},
author = {King, MR},
title = {Simulation of Somatic Evolution Through the Introduction of Random Mutation to the Rules of Conway's Game of Life.},
journal = {Cellular and molecular bioengineering},
volume = {17},
number = {6},
pages = {563-571},
pmid = {39926383},
issn = {1865-5025},
abstract = {INTRODUCTION: Conway's Game of Life (GOL), and related cellular automata (CA) models, have served as interesting simulations of complex behaviors resulting from simple rules of interactions between neighboring cells, that sometime resemble the growth and reproduction of living things. Thus, CA has been applied towards understanding the interaction and reproduction of single-cell organisms, and the growth of larger, disorganized tissues such as tumors. Surprisingly, however, there have been few attempts to adapt simple CA models to recreate the evolution of either new species, or subclones within a multicellular, tumor-like tissue.

METHODS: In this article, I present a modified form of the classic Conway's GOL simulation, in which the three integer thresholds that define GOL (number of neighboring cells, below which a cell will "die of loneliness"; number of neighboring cells, above which a cell will die of overcrowding; and number of neighboring cells that will result in spontaneous birth of a new cell within an empty lattice location) are occasionally altered with a randomized mutation of fractional magnitude during new "cell birth" events. Newly born cells "inherit" the current mutation state of a neighboring parent cell, and over the course of 10,000 generations these mutations tend to accumulate until they impact the behaviors of individual cells, causing them to transition from the sparse, small patterns of live cells characteristic of GOL into a more dense, unregulated growth resembling a connected tumor tissue.

RESULTS: The mutation rate and mutation magnitude were systematically varied in repeated randomized simulation runs, and it was determined that the most important mutated rule for the transition to unregulated, tumor-like growth was the overcrowding threshold, with the spontaneous birth and loneliness thresholds being of secondary importance. Spatial maps of the different "subclones" of cells that spontaneously develop during a typical simulation trial reveal that cells with greater fitness will overgrow the lattice and proliferate while the less fit, "wildtype" GOL cells die out and are replaced with mutant cells.

CONCLUSIONS: This simple modeling approach can be easily modified to add complexity and more realistic biological details, and may yield new understanding of cancer and somatic evolution.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12195-024-00828-9.},
}

@article {pmid39898884,
year = {2025},
author = {Vanhoeijen, R and Okkelman, IA and Rogier, N and Sedlačík, T and Stöbener, DD and Devriendt, B and Dmitriev, RI and Hoogenboom, R},
title = {Poly(2-alkyl-2-oxazoline) Hydrogels as Synthetic Matrices for Multicellular Spheroid and Intestinal Organoid Cultures.},
journal = {Biomacromolecules},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.biomac.4c01627},
pmid = {39898884},
issn = {1526-4602},
abstract = {The extracellular matrix (ECM) plays a crucial role in organoid cultures by supporting cell proliferation and differentiation. A key feature of the ECM is its mechanical influence on the surrounding cells, directly affecting their behavior. Matrigel, the most commonly used ECM, is limited by its animal-derived origin, batch variability, and uncontrollable mechanical properties, restricting its use in 3D cell-model-based mechanobiological studies. Poly(2-alkyl-2-oxazoline) (PAOx) synthetic hydrogels represent an appealing alternative because of their reproducibility and versatile chemistry, enabling tuning of hydrogel stiffness and functionalization. Here, we studied PAOx hydrogels with differing compressive moduli for their potential to support 3D cell growth. PAOx hydrogels support spheroid and organoid growth over several days without the addition of ECM components. Furthermore, we discovered intestinal organoid epithelial polarity reversion in PAOx hydrogels and demonstrate how the tunable mechanical properties of PAOx can be used to study effects on the morphology and oxygenation of live multicellular spheroids.},
}

@article {pmid39896451,
year = {2025},
author = {Scherer, J and Hinczewski, M and Nelms, B},
title = {Ultra-deep sequencing of somatic mutations induced by a maize transposon.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.22.634239},
pmid = {39896451},
issn = {2692-8205},
abstract = {Cells accumulate mutations throughout development, contributing to cancer, aging, and evolution. Quantitative data on the abundance of de novo mutations within plants or animals are limited, as new mutations are often rare within a tissue and fall below the limits of current sequencing depths and error rates. Here, we show that mutations induced by the maize Mutator (Mu) transposon can be reliably quantified down to a detection limit of 1 part in 12,000. We measured the abundance of millions of de novo Mu insertions across four tissue types. Within a tissue, the distribution of de novo Mu allele frequencies was highly reproducible between plants, showing that, despite the stochastic nature of mutation, repeated statistical patterns of mutation abundance emerge. In contrast, there were significant differences in the allele frequency distribution between tissues. At the extremes, root was dominated by a small number of highly abundant de novo insertions, while endosperm was characterized by thousands of insertions at low allele frequencies. Finally, we used the measured pollen allele frequencies to reinterpret a classic genetic experiment, showing that evidence for late Mu activity in pollen are better explained by cell division statistics. These results provide insight into the complexity of mutation accumulation in multicellular organisms and a system to interrogate the factors that shape mutation abundance.},
}

@article {pmid39894974,
year = {2025},
author = {Voronkina, A and Cárdenas, P and Adam, J and Meissner, H and Nowacki, K and Joseph, Y and Tabachnick, KR and Ehrlich, H},
title = {Biosilica 3D Micromorphology of Geodiidae Sponge Spicules Is Patterned by F-Actin.},
journal = {Microscopy research and technique},
volume = {},
number = {},
pages = {},
doi = {10.1002/jemt.24798},
pmid = {39894974},
issn = {1097-0029},
support = {2020/38/A/ST5/00151//National Science Centre/ ; },
abstract = {Demosponges (phylum Porifera) are among the first multicellular organisms on the planet and represent a unique archive of biosilica-based skeletal structures with species-specific microstructures called spicules. With more than 80 morphotypes, this class of sponges is recognized as a unique source of amorphous silica with superficial ornamentation patterned by organic phases. In this study, we investigated spicules of selected representatives of the family Geodiidae (order Tetractinellida), to identify F-actin-containing axial filaments within these 3D skeletal microconstructs defined as oxyspherasters and sterrasters. Their desilicification using 10% HF leads to isolation of multifilamentous, radially oriented organic matrices, which resemble the shape and size of the original spicules. Our data show that highly specific indicators of F-actin such as iFluorTM 594-Phalloidin, iFluorTM 488-Phalloidin, as well as iFluorTM 350-Phalloidin unambiguously confirm its localization within demineralized oxyspherasters and sterrasters of 11 diverse demosponges species belonging to the subfamily Geodiinae (genera Geodia, Rhabdastrella) and the subfamily Erylinae (genera Caminella, Caminus, Erylus, Pachymatisma). Well-defined periodicity in Geodia cydonium sterrasters actin filaments has been observed using atomic force microscopy (AFM) for the first time. The findings of F-actin as a possible pattern driver in spicules of geodiids brings additional light to our knowledge of spiculogenesis in this group. However, no specific actin structures were found between the geodiid subfamilies or genera thereby suggesting a common actin process, present already at the emergence of the family (~170 million years ago).},
}

@article {pmid39890889,
year = {2025},
author = {Paul, CD and Yankaskas, C and Shahi Thakuri, P and Balhouse, B and Salen, S and Bullock, A and Beam, S and Chatman, A and Djikeng, S and Yang, XJ and Wong, G and Dey, I and Holmes, S and Dockey, A and Bailey-Steinitz, L and Zheng, L and Li, W and Chandra, V and Nguyen, J and Sharp, J and Willems, E and Kennedy, M and Dallas, MR and Kuninger, D},
title = {Long-term maintenance of patient-specific characteristics in tumoroids from six cancer indications.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {3933},
pmid = {39890889},
issn = {2045-2322},
mesh = {Humans ; *Neoplasms/pathology/genetics ; *Organoids/pathology/metabolism ; Cell Line, Tumor ; Female ; Cell Culture Techniques/methods ; Tumor Cells, Cultured ; },
abstract = {Tumoroids, sometimes referred to as cancer organoids, are patient-derived cancer cells grown as 3D, self-organized multicellular structures that maintain key characteristics (e.g., genotype, gene expression levels) of the tumor from which they originated. These models have emerged as valuable tools for studying tumor biology, cytotoxicity, and response of patient-derived cells to cancer therapies. However, the establishment and maintenance of tumoroids has historically been challenging, labor intensive, and highly variable from lab to lab, hindering their widespread use. Here, we characterize the establishment and/or expansion of colorectal, lung, head and neck, breast, pancreas, and endometrial tumoroids using the standardized, serum-free Gibco OncoPro Tumoroid Culture Medium. Newly derived tumoroid lines (n = 20) were analyzed by targeted genomic profiling and RNA sequencing and were representative of tumor tissue samples. Tumoroid lines were stable for over 250 days in culture and freeze-thaw competent. Previously established tumoroid lines were also transitioned to OncoPro medium and exhibited, on average, similar growth rates and conserved donor-specific characteristics when compared to original media systems. Additionally, OncoPro medium was compatible with both embedded culture in extracellular matrix and growth in a suspension format for facile culture and scale up. An example application of these models for assessing the cytotoxicity of a natural killer cell line and primary natural killer cells over time and at various doses demonstrated the compatibility of these models with assays used in compound and cell therapy development. We anticipate that the standardization and versatility of this approach will have important benefits for basic cancer research, drug discovery, and personalized medicine and help make tumoroid models more accessible to the cancer research community.},
}

Humans
*Neoplasms/pathology/genetics
*Organoids/pathology/metabolism
Cell Line, Tumor
Female
Cell Culture Techniques/methods
Tumor Cells, Cultured

@article {pmid39883703,
year = {2025},
author = {Wong, W and Bravo, P and Yunker, PJ and Ratcliff, WC and Burnetti, AJ},
title = {Oxygen-binding proteins aid oxygen diffusion to enhance fitness of a yeast model of multicellularity.},
journal = {PLoS biology},
volume = {23},
number = {1},
pages = {e3002975},
doi = {10.1371/journal.pbio.3002975},
pmid = {39883703},
issn = {1545-7885},
mesh = {*Oxygen/metabolism ; *Saccharomyces cerevisiae/metabolism/genetics ; Diffusion ; Myoglobin/metabolism/genetics ; Hemerythrin/metabolism/genetics ; Models, Biological ; Genetic Fitness ; Oxygen Consumption ; },
abstract = {Oxygen availability is a key factor in the evolution of multicellularity, as larger and more sophisticated organisms often require mechanisms allowing efficient oxygen delivery to their tissues. One such mechanism is the presence of oxygen-binding proteins, such as globins and hemerythrins, which arose in the ancestor of bilaterian animals. Despite their importance, the precise mechanisms by which oxygen-binding proteins influenced the early stages of multicellular evolution under varying environmental oxygen levels are not yet clear. We address this knowledge gap by heterologously expressing the oxygen-binding proteins myoglobin and myohemerythrin in snowflake yeast, a model system of simple, undifferentiated multicellularity. These proteins increased the depth and rate of oxygen diffusion, increasing the fitness of snowflake yeast growing aerobically. Experiments show that, paradoxically, oxygen-binding proteins confer a greater fitness benefit for larger organisms when O2 is least limiting. We show via biophysical modeling that this is because facilitated diffusion is more efficient when oxygen is abundant, transporting a greater quantity of O2 which can be used for metabolism. By alleviating anatomical diffusion limitations to oxygen consumption, the evolution of oxygen-binding proteins in the oxygen-rich Neoproterozoic may have been a key breakthrough enabling the evolution of increasingly large, complex multicellular metazoan lineages.},
}

*Oxygen/metabolism
*Saccharomyces cerevisiae/metabolism/genetics
Diffusion
Myoglobin/metabolism/genetics
Hemerythrin/metabolism/genetics
Models, Biological
Genetic Fitness
Oxygen Consumption

@article {pmid39883596,
year = {2025},
author = {Pullen, RM and Decker, SR and Subramanian, V and Adler, MJ and Tobias, AV and Perisin, M and Sund, CJ and Servinsky, MD and Kozlowski, MT},
title = {Considerations for Domestication of Novel Strains of Filamentous Fungi.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.4c00672},
pmid = {39883596},
issn = {2161-5063},
abstract = {Fungi, especially filamentous fungi, are a relatively understudied, biotechnologically useful resource with incredible potential for commercial applications. These multicellular eukaryotic organisms have long been exploited for their natural production of useful commodity chemicals and proteins such as enzymes used in starch processing, detergents, food and feed production, pulping and paper making and biofuels production. The ability of filamentous fungi to use a wide range of feedstocks is another key advantage. As chassis organisms, filamentous fungi can express cellular machinery, and metabolic and signal transduction pathways from both prokaryotic and eukaryotic origins. Their genomes abound with novel genetic elements and metabolic processes that can be harnessed for biotechnology applications. Synthetic biology tools are becoming inexpensive, modular, and expansive while systems biology is beginning to provide the level of understanding required to design increasingly complex synthetic systems. This review covers the challenges of working in filamentous fungi and offers a perspective on the approaches needed to exploit fungi as microbial cell factories.},
}

@article {pmid39838006,
year = {2025},
author = {McCaig, CD},
title = {Multicellularity and Electrical Forces.},
journal = {Reviews of physiology, biochemistry and pharmacology},
volume = {187},
number = {},
pages = {39-46},
pmid = {39838006},
issn = {0303-4240},
mesh = {*Electricity ; *Electrophysiological Phenomena ; *Biological Evolution ; },
abstract = {Multiple single-celled life forms existed for millennia before some individual cells found ways of gathering together to form multicellular organisms. Several of the key elements that drove this step-change in life on Earth involved electrical forces.},
}

*Electricity
*Electrophysiological Phenomena
*Biological Evolution

@article {pmid39877976,
year = {2025},
author = {Pereira Lobo, F and da Costa, DB and da Silva, TTM and de Oliveira, MD},
title = {Molecular and functional convergences associated with complex multicellularity in Eukarya.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf013},
pmid = {39877976},
issn = {1537-1719},
abstract = {A key trait of Eukarya is the independent evolution of complex multicellular (CM) in animals, plants, fungi, brown algae and red algae. This phenotype is characterized by the initial exaptation of cell-cell adhesion genes followed by the emergence of mechanisms for cell-cell communication, together with the expansion of transcription factor gene families responsible for cell and tissue identity. The number of cell types (NCT) is commonly used as a quantitative proxy for biological complexity in comparative genomics studies. While expansions of individual gene families have been associated with NCT variation within individual CM lineages, the molecular and functional roles responsible for the independent evolution of CM across Eukarya remain poorly understood. We employed a phylogeny-aware strategy to conduct a genomic-scale search for associations between NCT and the abundance of genomic components across a phylogenetically diverse set of 81 eukaryotic species, including species from all CM lineages. Our annotation schemas represent two complimentary aspects of genomic information: homology - represented by conserved sequences - and function - represented by Gene Ontology (GO) terms. We found many gene families sharing common biological themes that define CM to be independently expanded in two or more CM lineages, such as components of the extracellular matrix, cell-cell communication mechanisms, and developmental pathways. Additionally, we describe many previously unknown associations of biological themes and biological complexity, such as mechanisms for wound response, immunity, cell migration, regulatory processes, and response to natural rhythms. Together, our findings unveil a set of functional and molecular convergences independently expanded in CM lineages likely due to the common selective pressures in their lifestyles.},
}

@article {pmid39872364,
year = {2025},
author = {Russo, A and Moy, J and Khin, M and Dorsey, TR and Lopez Carrero, A and Burdette, JE},
title = {Loss of phosphatase and tensin homolog (PTEN) increases Lysyl oxidase-like 2 (LOXL2) expression enhancing the growth of fallopian tube epithelial cells as three-dimensional spheroids.},
journal = {Cancer pathogenesis and therapy},
volume = {3},
number = {1},
pages = {68-75},
pmid = {39872364},
issn = {2949-7132},
abstract = {BACKGROUND: High-grade serous ovarian cancer (HGSOC) accounts for 70-80% of all ovarian cancer-related deaths. Multiple studies have suggested that the fallopian tube epithelium (FTE) serves as the cell of origin of HGSOC. Phosphatase and tensin homolog (PTEN) is a tumor suppressor and its loss is sufficient to induce numerous tumorigenic changes in FTE, including increased migration, formation of multicellular tumor spheroids (MTSs), and ovarian colonization. In murine oviductal epithelial (MOE) cells (the equivalent of human FTE) loss of PTEN results in the upregulation of transcripts associated with the extracellular matrix, with a specific focus on the elevation of lysyl oxidase-like 2 (LOXL2). Although LOXL2 is known to drive transformation and invasion in solid tumors and is associated with a poor prognosis in ovarian cancer, its specific role in the tumorigenesis of ovarian cancer originating from FTE remains unclear. Therefore, we aim to investigate whether LOXL2 mediates tumorigenesis from the fallopian tube epithelium.

METHODS: In this study, we utilized clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (CAS9) technology to delete LOXL2 in PTEN-deficient MOE cells to understand its role in mediating the oncogenic effects of PTEN loss. In addition, CRISPR-CAS9 was used to delete LOXL2 in OVCAR8 ovarian cancer cells. We monitored the changes in tumorigenic properties, such as migration, invasion, and growth of three-dimensional (3D) spheroids, to assess whether the loss of LOXL2 resulted in any changes.

RESULTS: We found that a reduction in LOXL2 expression did not significantly change the migration or invasive capabilities of PTEN-depleted MOE or human ovarian cancer cells. However, we found that a reduction in LOXL2 expression resulted in a significant reduction in 3D MTS formation and survival in both lines.

CONCLUSIONS: These results reveal for the first time that PTEN loss in FTE cells increases LOXL2 expression through downregulation of Pax2, and LOXL2 deletion blocks 3D spheroid formation.},
}

@article {pmid39869795,
year = {2025},
author = {Pérez Gallego, R and von Meijenfeldt, FAB and Bale, NJ and Sinninghe Damsté, JS and Villanueva, L},
title = {Emergence and evolution of heterocyte glycolipid biosynthesis enabled specialized nitrogen fixation in cyanobacteria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {5},
pages = {e2413972122},
doi = {10.1073/pnas.2413972122},
pmid = {39869795},
issn = {1091-6490},
support = {694569-MICROLIPIDS//EC | H2020 | PRIORITY 'Excellent science' | H2020 European Research Council (ERC)/ ; Spinoza Award//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; 024.002.002//Ministerie van Onderwijs, Cultuur en Wetenschap (OCW)/ ; },
mesh = {*Nitrogen Fixation/genetics ; *Cyanobacteria/metabolism/genetics ; *Glycolipids/biosynthesis/metabolism ; Phylogeny ; Multigene Family ; Evolution, Molecular ; Biological Evolution ; },
abstract = {Heterocytes, specialized cells for nitrogen fixation in cyanobacteria, are surrounded by heterocyte glycolipids (HGs), which contribute to protection of the nitrogenase enzyme from oxygen. Diverse HGs preserve in the sediment and have been widely used as evidence of past nitrogen fixation, and structural variation has been suggested to preserve taxonomic information and reflect paleoenvironmental conditions. Here, by comprehensive HG identification and screening of HG biosynthetic gene clusters throughout cyanobacteria, we reconstruct the convergent evolutionary history of HG structure, in which different clades produce the same HGs. We find that rudimentary HG biosynthetic machinery was already present in cyanobacteria before the emergence of heterocytes for functions unrelated to nitrogen fixation and identify HG analogs produced by specific and distantly related nonheterocytous cyanobacteria. These structurally less complex molecules represent precursors of HGs, suggesting that HGs arose after a genomic reorganization and expansion of ancestral biosynthetic machinery, enabling the rise of cyanobacterial heterocytes in an increasingly oxygenated atmosphere. Our results open a chapter in the potential use of diagenetic products of HGs and HG analogs as fossils for reconstructing the evolution of multicellularity and division of labor in cyanobacteria.},
}

*Nitrogen Fixation/genetics
*Cyanobacteria/metabolism/genetics
*Glycolipids/biosynthesis/metabolism
Phylogeny
Multigene Family
Evolution, Molecular
Biological Evolution

@article {pmid39868713,
year = {2024},
author = {Montagné, N},
title = {[The role of volatile organic compounds in plant-insect communication].},
journal = {Biologie aujourd'hui},
volume = {218},
number = {3-4},
pages = {141-144},
doi = {10.1051/jbio/2024016},
pmid = {39868713},
issn = {2105-0686},
mesh = {Animals ; *Volatile Organic Compounds/metabolism ; *Insecta/physiology ; *Plants/chemistry/metabolism/parasitology ; Herbivory/physiology ; Animal Communication ; Pollination/physiology ; },
abstract = {Insects and flowering plants are the most abundant and diverse multicellular organisms on Earth, accounting for 75% of known species. Their evolution has been largely interdependent since the so-called Angiosperm Terrestrial Revolution (100-50 Mya), when the explosion of plant diversity stimulated the evolution of pollinating and herbivorous insects. Plant-insect interactions rely heavily on chemical communication via volatile organic compounds (VOCs). These molecules are synthesised by the secondary metabolism of plants through various pathways and include terpenes, benzenoids and aliphatic compounds. As of today, more than 1,700 of these VOCs have notably been identified in flowers. Plants use these molecules to attract pollinators or repel herbivorous insects. VOCs also act as chemical signals for insects, helping them to find food or egg-laying sites. Chemical communication has thus played an important role in the evolutionary history of insects and flowering plants. Tritrophic interactions are a fascinating example of VOC-driven communication. When plants are attacked by herbivores, they emit herbivore-induced volatiles, such as green leaf volatiles and specific terpenes. These signals attract predators or parasitoids of the herbivores, acting as a chemical distress call. For example, parasitoid wasps can identify plants that have been attacked by their host herbivores, even in the absence of the herbivores themselves, thanks to the plant's odour profile. But herbivore-induced volatiles also affect the herbivores themselves. Female moths, for example, use these olfactory cues to avoid laying eggs on plants that have already been attacked. Insects detect VOCs using highly sensitive odorant receptors on their antennae. Herbivorous insects, such as the model moth species S. littoralis, have receptors specific for floral VOCs and herbivore-induced volatiles. Current research aims to understand how the evolution of these receptors has contributed to the adaptation of insects to plant volatiles. In moths, receptors for benzenoids appear to be more ancient and conserved, whereas receptors for terpenes and aliphatic molecules show more recent diversification in response to plant evolution. Research into plant-insect communication also opens up avenues for sustainable agriculture, as VOCs can be used to attract natural pest predators or deter herbivores, reducing the need for chemical pesticides.},
}

Animals
*Volatile Organic Compounds/metabolism
*Insecta/physiology
*Plants/chemistry/metabolism/parasitology
Herbivory/physiology
Animal Communication
Pollination/physiology

@article {pmid39863161,
year = {2025},
author = {Dubey, A and Muthu, G and Narain Seshasayee, AS},
title = {Evolution of transcription factor-containing superfamilies in Eukaryotes.},
journal = {Journal of molecular biology},
volume = {},
number = {},
pages = {168959},
doi = {10.1016/j.jmb.2025.168959},
pmid = {39863161},
issn = {1089-8638},
abstract = {Regulation of gene expression helps determine various phenotypes in most cellular life forms. It is orchestrated at different levels and at the point of transcription initiation by transcription factors (TFs). TFs bind to DNA through domains that are evolutionarily related, by shared membership of the same superfamilies (TF-SFs), to those found in other nucleic acid binding and protein-binding functions (nTFs for non-TFs). Here we ask how TF DNA binding sequence families in eukaryotes have evolved in relation to their nTF relatives. TF numbers scale by power law with the total number of protein-coding genes differently in different clades, with fungi usually showing sub-linear powers whereas chordates show super-linear scaling. The LECA probably encoded a complex regulatory machinery with both TFs and nTFs, but with an excess of nTFs when compared to the relative distribution of TFs and nTFs in extant organisms. Losses drive the evolution of TFs and nTFs, with the possible exception of TFs in animals for some tree topologies. TFs are highly dynamic in evolution, showing higher gain and loss rates than nTFs though both are conserved to similar extents. Gains of TFs and nTFs are driven by the appearance of a large number of new sequence clusters in a small number of nodes, which determine the presence of as many as a third of extant TFs and nTFs as well as the relative presence of TFs and nTFs. Whereas nodes showing explosion of TF numbers belong to multicellular clades, those for nTFs lie among the fungi and the protists.},
}

@article {pmid39853129,
year = {2025},
author = {Espinoza Miranda, SS and Abbaszade, G and Hess, WR and Drescher, K and Saliba, A-E and Zaburdaev, V and Chai, L and Dreisewerd, K and Grünberger, A and Westendorf, C and Müller, S and Mascher, T},
title = {Resolving spatiotemporal dynamics in bacterial multicellular populations: approaches and challenges.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {},
number = {},
pages = {e0013824},
doi = {10.1128/mmbr.00138-24},
pmid = {39853129},
issn = {1098-5557},
abstract = {SUMMARYThe development of multicellularity represents a key evolutionary transition that is crucial for the emergence of complex life forms. Although multicellularity has traditionally been studied in eukaryotes, it originates in prokaryotes. Coordinated aggregation of individual cells within the confines of a colony results in emerging, higher-level functions that benefit the population as a whole. During colony differentiation, an almost infinite number of ecological and physiological population-forming forces are at work, creating complex, intricate colony structures with divergent functions. Understanding the assembly and dynamics of such populations requires resolving individual cells or cell groups within such macroscopic structures. Addressing how each cell contributes to the collective action requires pushing the resolution boundaries of key technologies that will be presented in this review. In particular, single-cell techniques provide powerful tools for studying bacterial multicellularity with unprecedented spatial and temporal resolution. These advancements include novel microscopic techniques, mass spectrometry imaging, flow cytometry, spatial transcriptomics, single-bacteria RNA sequencing, and the integration of spatiotemporal transcriptomics with microscopy, alongside advanced microfluidic cultivation systems. This review encourages exploring the synergistic potential of the new technologies in the study of bacterial multicellularity, with a particular focus on individuals in differentiated bacterial biofilms (colonies). It highlights how resolving population structures at the single-cell level and understanding their respective functions can elucidate the overarching functions of bacterial multicellular populations.},
}

@article {pmid39849824,
year = {2025},
author = {Ndinyanka, TF and Buczak, K and Schmidt, A and Pieters, J},
title = {T cell population size control by coronin 1 uncovered: from a spot identified by two-dimensional gel electrophoresis to quantitative proteomics.},
journal = {Expert review of proteomics},
volume = {},
number = {},
pages = {},
doi = {10.1080/14789450.2025.2450812},
pmid = {39849824},
issn = {1744-8387},
abstract = {INTRODUCTION: Recent work identified members of the evolutionarily conserved coronin protein family as key regulators of cell population size. This work originated ~25 years ago through the identification, by two-dimensional gel electrophoresis, of coronin 1 as a host protein involved in the virulence of Mycobacterium tuberculosis. We here describe the journey from a spot on a 2D gel to the recent realization that coronin proteins represent key controllers of eukaryotic cell population sizes, using ever more sophisticated proteomic techniques.

AREAS COVERED: We discuss the value of 'old school' proteomics using relatively simple and cost-effective technologies that allowed to gain insights into subcellular proteomes and describe how label-free quantitative (phospho)proteomics using mass spectrometry allowed to disentangle the role for coronin 1 in eukaryotic cell population size control. Finally, we mention potential implications of coronin-mediated cell population size control for health and disease.

EXPERT OPINION: Proteome analysis has been revolutionized by the advent of modern-day mass spectrometers and is indispensable for a better understanding of biology. Here, we discuss how careful dissection of physio-pathological processes by a combination of proteomics, genomics, biochemistry and cell biology may allow to zoom in on the unexplored, thereby possibly tackling hitherto unasked questions and defining novel mechanisms.},
}

@article {pmid39841150,
year = {2025},
author = {Isaksson, H and Lind, P and Libby, E},
title = {Adaptive evolutionary trajectories in complexity: Transitions between unicellularity and facultative differentiated multicellularity.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {4},
pages = {e2411692122},
doi = {10.1073/pnas.2411692122},
pmid = {39841150},
issn = {1091-6490},
support = {2018-03630//Vetenskapsrådet (VR)/ ; },
mesh = {*Biological Evolution ; Mutation ; Cell Differentiation ; Adaptation, Physiological ; Models, Biological ; Genetic Fitness ; Stress, Physiological ; },
abstract = {Multicellularity spans a wide gamut in terms of complexity, from simple clonal clusters of cells to large-scale organisms composed of differentiated cells and tissues. While recent experiments have demonstrated that simple forms of multicellularity can readily evolve in response to different selective pressures, it is unknown if continued exposure to those same selective pressures will result in the evolution of increased multicellular complexity. We use mathematical models to consider the adaptive trajectories of unicellular organisms exposed to periodic bouts of abiotic stress, such as drought or antibiotics. Populations can improve survival in response to the stress by evolving multicellularity or cell differentiation-or both; however, these responses have associated costs when the stress is absent. We define a parameter space of fitness-relevant traits and identify where multicellularity, differentiation, or their combination is fittest. We then study the effects of adaptation by allowing populations to fix mutations that improve their fitness. We find that while the same mutation can be beneficial to populations of different complexity, e.g., strict unicellularity or life cycles with stages of differentiated multicellularity, the magnitudes of their effects can differ and alter which is fittest. As a result, we observe adaptive trajectories that gain and lose complexity. We also show that the order of mutations, historical contingency, can cause some transitions to be permanent in the absence of neutral evolution. Ultimately, we find that continued exposure to a selective driver for multicellularity can either lead to increasing complexity or a return to unicellularity.},
}

*Biological Evolution
Mutation
Cell Differentiation
Adaptation, Physiological
Models, Biological
Genetic Fitness
Stress, Physiological

@article {pmid39838007,
year = {2025},
author = {McCaig, CD},
title = {Epithelia Are Scaffolds for Electricity-Dependent Molecular Interactions.},
journal = {Reviews of physiology, biochemistry and pharmacology},
volume = {187},
number = {},
pages = {47-52},
pmid = {39838007},
issn = {0303-4240},
mesh = {Animals ; Epithelium/physiology/metabolism ; Humans ; *Basement Membrane/metabolism/physiology ; Electricity ; Epithelial Cells/metabolism ; Electrophysiological Phenomena ; },
abstract = {Once multicellularity was thriving, a key development involved the emergence of epithelial layers that separated "inside" from "outside". Most epithelia then generate their own transepithelial electrical signals. So electrical forces were instrumental in the development of epithelial tissues, which themselves generate further electrical signals. Epithelia also developed extracellular basement membranes which act as spatially diverse scaffolds to organize multiple molecular interactions, dependent on electrical forces.Epithelia and basement membranes were constructed using electrical forces and their evolution had electrophysiological consequences.},
}

Animals
Epithelium/physiology/metabolism
Humans
*Basement Membrane/metabolism/physiology
Electricity
Epithelial Cells/metabolism
Electrophysiological Phenomena

@article {pmid39833858,
year = {2025},
author = {Hure, V and Piron-Prunier, F and Yehouessi, T and Vitte, C and Kornienko, AE and Adam, G and Nordborg, M and Déléris, A},
title = {Alternative silencing states of transposable elements in Arabidopsis associated with H3K27me3.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {11},
pmid = {39833858},
issn = {1474-760X},
mesh = {*Arabidopsis/genetics ; *DNA Transposable Elements ; *Histones/metabolism ; *Gene Silencing ; *DNA Methylation ; Gene Expression Regulation, Plant ; Arabidopsis Proteins/genetics/metabolism ; Epigenesis, Genetic ; Polycomb-Group Proteins/metabolism/genetics ; },
abstract = {BACKGROUND: The DNA/H3K9 methylation and Polycomb-group proteins (PcG)-H3K27me3 silencing pathways have long been considered mutually exclusive and specific to transposable elements (TEs) and genes, respectively in mammals, plants, and fungi. However, H3K27me3 can be recruited to many TEs in the absence of DNA/H3K9 methylation machinery and sometimes also co-occur with DNA methylation.

RESULTS: In this study, we show that TEs can also be solely targeted and silenced by H3K27me3 in wild-type Arabidopsis plants. These H3K27me3-marked TEs not only comprise degenerate relics but also seemingly intact copies that display the epigenetic features of responsive PcG target genes as well as an active H3K27me3 regulation. We also show that H3K27me3 can be deposited on newly inserted transgenic TE sequences in a TE-specific manner indicating that silencing is determined in cis. Finally, a comparison of Arabidopsis natural accessions reveals the existence of a category of TEs-which we refer to as "bifrons"-that are marked by DNA methylation or H3K27me3 depending on the accession. This variation can be linked to intrinsic TE features and to trans-acting factors and reveals a change in epigenetic status across the TE lifespan.

CONCLUSIONS: Our study sheds light on an alternative mode of TE silencing associated with H3K27me3 instead of DNA methylation in flowering plants. It also suggests dynamic switching between the two epigenetic marks at the species level, a new paradigm that might extend to other multicellular eukaryotes.},
}

*Arabidopsis/genetics
*DNA Transposable Elements
*Histones/metabolism
*Gene Silencing
*DNA Methylation
Gene Expression Regulation, Plant
Arabidopsis Proteins/genetics/metabolism
Epigenesis, Genetic
Polycomb-Group Proteins/metabolism/genetics

@article {pmid39826309,
year = {2025},
author = {Mendes, M and Morais, AS and Carlos, A and Sousa, JJ and Pais, AC and Mihăilă, SM and Vitorino, C},
title = {Organ-on-a-chip: Quo vademus? Applications and regulatory status.},
journal = {Colloids and surfaces. B, Biointerfaces},
volume = {249},
number = {},
pages = {114507},
doi = {10.1016/j.colsurfb.2025.114507},
pmid = {39826309},
issn = {1873-4367},
abstract = {Organ-on-a-chip systems, also referred to as microphysiological systems (MPS), represent an advance in bioengineering microsystems designed to mimic key aspects of human organ physiology and function. Drawing inspiration from the intricate and hierarchical architecture of the human body, these innovative platforms have emerged as invaluable in vitro tools with wide-ranging applications in drug discovery and development, as well as in enhancing our understanding of disease physiology. The facility to replicate human tissues within physiologically relevant three-dimensional multicellular environments empowers organ-on-a-chip systems with versatility throughout different stages of the drug development process. Moreover, these systems can be tailored to mimic specific disease states, facilitating the investigation of disease progression, drug responses, and potential therapeutic interventions. In particular, they can demonstrate, in early-phase pre-clinical studies, the safety and toxicity profiles of potential therapeutic compounds. Furthermore, they play a pivotal role in the in vitro evaluation of drug efficacy and the modeling of human diseases. One of the most promising prospects of organ-on-a-chip technology is to simulate the pathophysiology of specific subpopulations and even individual patients, thereby being used in personalized medicine. By mimicking the physiological responses of diverse patient groups, these systems hold the promise of revolutionizing therapeutic strategies, guiding them towards tailored intervention to the unique needs of each patient. This review presents the development status and evolution of microfluidic platforms that have facilitated the transition from cells to organs recreated on chips and some of the opportunities and applications offered by organ-on-a-chip technology. Additionally, the current potential and future perspectives of these microphysiological systems and the challenges this technology still faces are discussed.},
}

@article {pmid39817858,
year = {2025},
author = {Yang, X and Yan, A and Liu, X and Volkening, A and Zhou, Y},
title = {Single cell derived multicellular meristem: insights into male-to-hermaphrodite conversion and de novo meristem formation in ceratopteris.},
journal = {Development (Cambridge, England)},
volume = {},
number = {},
pages = {},
doi = {10.1242/dev.204411},
pmid = {39817858},
issn = {1477-9129},
support = {IOS 1931114//National Science Foundation/ ; },
abstract = {Land plants alternate between asexual sporophytes and sexual gametophytes. Unlike seed plants, ferns develop free-living gametophytes. Gametophytes of the model fern Ceratopteris exhibit two sex types: hermaphrodites with pluripotent meristems and males lacking meristems. In the absence of the pheromone antheridiogen, males convert to hermaphrodites by forming de novo meristems, though the mechanisms remain unclear. Using long-term time-lapse imaging and computational analyses, we captured male-to-hermaphrodite conversion at single-cell resolution and reconstructed the lineage and division atlas of newly formed meristems. Lineage tracing revealed that the de novo-formed meristem originates from a single non-antheridium cell, the meristem progenitor cell (MPC). During conversion, the MPC lineage showed increased mitotic activity, with marginal cells proliferating faster than inner cells. A mathematical model suggests that stochastic variation in cell division, combined with strong inhibitory signals from dividing marginal cells, is sufficient to explain gametophyte dynamics. Experimental disruption of division timing agreed with the model, showing precise cell cycle progression is essential for MPC establishment and sex-type conversion. These findings reveal cellular mechanisms governing sex conversion and de novo meristem formation in land plants.},
}

@article {pmid39803458,
year = {2025},
author = {Yoffe, L and Bhinder, B and Kang, SW and Zhang, H and Singh, A and Ravichandran, H and Markowitz, G and Martin, M and Kim, J and Zhang, C and Elemento, O and Tansey, W and Bates, S and McGraw, TE and Borczuk, A and Lee, HS and Altorki, NK and Mittal, V},
title = {Acquisition of discrete immune suppressive barriers contributes to the initiation and progression of preinvasive to invasive human lung cancer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39803458},
issn = {2692-8205},
support = {R21 AI159379/AI/NIAID NIH HHS/United States ; UH3 CA244697/CA/NCI NIH HHS/United States ; },
abstract = {Computerized chest tomography (CT)-guided screening in populations at risk for lung cancer has increased the detection of preinvasive subsolid nodules, which progress to solid invasive adenocarcinoma. Despite the clinical significance, there is a lack of effective therapies for intercepting the progression of preinvasive to invasive adenocarcinoma. To uncover determinants of early disease emergence and progression, we used integrated single-cell approaches, including scRNA-seq, multiplexed imaging mass cytometry and spatial transcriptomics, to construct the first high-resolution map of the composition, lineage/functional states, developmental trajectories and multicellular crosstalk networks from microdissected non-solid (preinvasive) and solid compartments (invasive) of individual part-solid nodules. We found that early disease initiation and subsequent progression are associated with the evolution of immune-suppressive cellular phenotypes characterized by decreased cytotoxic CD8 T and NK cells, increased T cell exhaustion and accumulation of immunosuppressive regulatory T cells (Tregs) and M2-like macrophages expressing TREM2. Within Tregs, we identified a unique population of 4-1BB+ Treg subset enriched for the IL2-STAT5 suppressive pathway with transcription profiles supporting discrete metabolic alterations. Spatial analysis showed increased density of suppressive immune cells around tumor cells, increased exhaustion phenotype of both CD4 and CD8 T cells expressing chemokine CXCL13, and spatial microcomplex of endothelial and lymphocyte interactions within tertiary lymphoid structures. The single-cell architecture identifies determinants of early disease emergence and progression, which may be developed not only as diagnostic/prognostic biomarkers but also as targets for disease interception. Additionally, our dataset constitutes a valuable resource for the preinvasive lung cancer research community.},
}

@article {pmid39801500,
year = {2025},
author = {Putra, VDL and Kilian, KA and Knothe Tate, ML},
title = {Stem cell mechanoadaptation. I. Effect of microtubule stabilization and volume changing stresses on cytoskeletal remodeling.},
journal = {APL bioengineering},
volume = {9},
number = {1},
pages = {016102},
pmid = {39801500},
issn = {2473-2877},
abstract = {Here, we report on the first part of a two-part experimental series to elucidate spatiotemporal cytoskeletal remodeling, which underpins the evolution of stem cell shape and fate, and the emergence of tissue structure and function. In Part I of these studies, we first develop protocols to stabilize microtubules exogenously using paclitaxel (PAX) in a standardized model murine embryonic stem cell line (C3H/10T1/2) to maximize comparability with previously published studies. We then probe native and microtubule-stabilized stem cells' capacity to adapt to volume changing stresses effected by seeding at increasing cell densities, which emulates local compression and tissue template formation during development. Within the concentration range of 1-100 nM, microtubule-stabilized stem cells maintain viability and reduce proliferation. PAX stabilization of microtubules is associated with increased cell volume as well as flattening of the cell and nucleus. Compared to control cells, microtubule-stabilized cells exhibit thick, bundled microtubules and highly aligned, thicker and longer F-actin fibers, corresponding to an increase in the Young's modulus of the cell. Both F-actin and microtubule concentration increase with increasing PAX concentration, whereby the increase in F-actin is more prominent in the basal region of the cell. The corresponding increase in microtubule is observed more globally across the apical and basal region of the cell. Seeding at increasing target densities induces local compression on cells. This increase in local compression modulates cell volume and concomitant increases in F-actin and microtubule concentration to a greater degree than microtubule stabilization via PAX. Cells seeded at high density exhibit higher bulk modulus than corresponding cells seeded at low density. These data demonstrate the capacity of stem cells to adapt to an interplay of mechanical and chemical cues, i.e., respective compression and exogenous microtubule stabilization; the resulting cytoskeletal remodeling manifests as evolution of mechanical properties relevant to development of multicellular tissue constructs.},
}

@article {pmid39793585,
year = {2025},
author = {Liesner, D and Cossard, GG and Zheng, M and Godfroy, O and Barrera-Redondo, J and Haas, FB and Coelho, SM},
title = {Developmental pathways underlying sexual differentiation in the U/V sex chromosome system of giant kelp.},
journal = {Developmental cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.devcel.2024.12.022},
pmid = {39793585},
issn = {1878-1551},
abstract = {In many multicellular organisms, sexual development is not determined by XX/XY or ZW/ZZ systems but by U/V sex chromosomes. In U/V systems, sex determination occurs in the haploid phase, with U chromosomes in females and V chromosomes in males. Here, we explore several male, female, and partially sex-reversed male lines of giant kelp to decipher how U/V sex chromosomes and autosomes initiate male versus female development. We identify a key set of genes on the sex chromosomes involved in triggering sexual development and characterize autosomal effector genes underlying sexual differentiation. We show that male, but not female, development involves large-scale transcriptome reorganization with pervasive enrichment in regulatory genes, faster evolutionary rates, and high species-specificity of male-biased genes. Our observations imply that a female-like phenotype is the "ground state", which is complemented by the presence of a U-chromosome but overridden by a dominant male developmental program triggered by the V-chromosome.},
}

@article {pmid39772683,
year = {2025},
author = {Colgren, J and Burkhardt, P},
title = {Electrical signaling and coordinated behavior in the closest relative of animals.},
journal = {Science advances},
volume = {11},
number = {2},
pages = {eadr7434},
pmid = {39772683},
issn = {2375-2548},
mesh = {*Choanoflagellata/physiology ; Animals ; Calcium/metabolism ; Cilia/physiology/metabolism ; Signal Transduction ; },
abstract = {The transition from simple to complex multicellularity involves division of labor and specialization of cell types. In animals, complex sensory-motor systems are primarily built around specialized cells of muscles and neurons, though the evolutionary origins of these and their integration remain unclear. Here, to investigate sensory-behavior coupling in the closest relatives of animals, we established a line of the choanoflagellate, Salpingoeca rosetta, which stably expresses the calcium indicator RGECO1. Using this, we identify a previously unknown cellular behavior associated with electrical signaling, in which ciliary arrest is coupled with apical-basal contraction of the cell. This behavior and the associated calcium transients are synchronized in the multicellular state and result in coordinated ciliary arrest and colony-wide contraction, suggesting that information is spread among the cells. Our work reveals fundamental insights into how choanoflagellates sense and respond to their environment and enhances our understanding of the integration of cellular and organism-wide behavior in the closest protistan relatives of animals.},
}

*Choanoflagellata/physiology
Animals
Calcium/metabolism
Cilia/physiology/metabolism
Signal Transduction

@article {pmid39768330,
year = {2024},
author = {Rehnke, RD},
title = {The "Culture" of Organs: A Holistic Theory on the Origins of the Cancer Tissue Environment.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
pmid = {39768330},
issn = {2075-1729},
abstract = {For over a century, the somatic gene mutation theory of cancer has been a scientific orthodoxy. The recent failures of causal explanations using this theory and the lack of significant progress in addressing the cancer problem medically have led to a new competition of ideas about just what cancer is. This essay presents an alternative view of cancer as a developmental process gone wrong. More specifically, cancer is a breakdown in the autopoietic process of organ maintenance and the multicellular coordination of tissues. Breast cancer is viewed through a systems science perspective as an example of the importance of framing one's theoretical assumptions before making empirical judgments. Finally, a new understanding of the histoarchitecture of the interstitium is presented as a first principle of cancer: a process of cells coming from cells, invading the space between cells.},
}

@article {pmid39763889,
year = {2024},
author = {Park, J and Prokopchuk, G and Popchock, AR and Hao, J and Liao, TW and Yan, S and Hedman, DJ and Larson, JD and Walther, BK and Becker, NA and Basu, A and Maher, LJ and Wheeler, RJ and Asbury, CL and Biggins, S and Lukeš, J and Ha, T},
title = {Probing mechanical selection in diverse eukaryotic genomes through accurate prediction of 3D DNA mechanics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39763889},
issn = {2692-8205},
support = {R35 GM143949/GM/NIGMS NIH HHS/United States ; R35 GM149357/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R35 GM122569/GM/NIGMS NIH HHS/United States ; R35 GM134842/GM/NIGMS NIH HHS/United States ; },
abstract = {Connections between the mechanical properties of DNA and biological functions have been speculative due to the lack of methods to measure or predict DNA mechanics at scale. Recently, a proxy for DNA mechanics, cyclizability, was measured by loop-seq and enabled genome-scale investigation of DNA mechanics. Here, we use this dataset to build a computational model predicting bias-corrected intrinsic cyclizability, with near-perfect accuracy, solely based on DNA sequence. Further, the model predicts intrinsic bending direction in 3D space. Using this tool, we aimed to probe mechanical selection - that is, the evolutionary selection of DNA sequence based on its mechanical properties - in diverse circumstances. First, we found that the intrinsic bend direction of DNA sequences correlated with the observed bending in known protein-DNA complex structures, suggesting that many proteins co-evolved with their DNA partners to capture DNA in its intrinsically preferred bent conformation. We then applied our model to large-scale yeast population genetics data and showed that centromere DNA element II, whose consensus sequence is unknown, leaving its sequence-specific role unclear, is under mechanical selection to increase the stability of inner-kinetochore structure and to facilitate centromeric histone recruitment. Finally, in silico evolution under strong mechanical selection discovered hallucinated sequences with cyclizability values so extreme that they required experimental validation, yet, found in nature in the densely packed mitochondrial(mt) DNA of Namystynia karyoxenos, an ocean-dwelling protist with extreme mitochondrial gene fragmentation. The need to transmit an extraordinarily large amount of mtDNA, estimated to be > 600 Mb, in combination with the absence of mtDNA compaction proteins may have pushed mechanical selection to the extreme. Similarly extreme DNA mechanics are observed in bird microchromosomes, although the functional consequence is not yet clear. The discovery of eccentric DNA mechanics in unrelated unicellular and multicellular eukaryotes suggests that we can predict extreme natural biology which can arise through strong selection. Our methods offer a way to study the biological functions of DNA mechanics in any genome and to engineer DNA sequences with desired mechanical properties.},
}

@article {pmid39763787,
year = {2024},
author = {Week, B and Ralph, PL and Tavalire, HF and Cresko, WA and Bohannan, BJM},
title = {Quantitative Genetics of Microbiome Mediated Traits.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.12.16.628599},
pmid = {39763787},
issn = {2692-8205},
abstract = {Multicellular organisms host a rich assemblage of associated microorganisms, collectively known as their "microbiomes". Microbiomes have the capacity to influence their hosts' fitnesses, but the conditions under which such influences contribute to evolution are not clear. This is due in part to a lack of a comprehensive theoretical framework for describing the combined effects of host and associated microbes on phenotypic variation. Here we begin to address this gap by extending the foundations of quantitative genetic theory to include host-associated microbes, as well as alleles of hosts, as factors that explain quantitative host trait variation. We introduce a way to partition host-associated microbiomes into componenents relevant for predicting a microbiome-mediated response to selection. We then apply our general framework to a simulation model of microbiome inheritance to illustrate principles for predicting host trait dynamics, and to generalize classical narrow and broad sense heritabilities to account for microbial effects. We demonstrate that microbiome-mediated responses to host selection can arise from various transmission modes, not solely vertical, with the contribution of non-vertical modes depending on host life history. Our work lays a foundation for integrating microbiome-mediated host variation and adaptation into our understanding of natural variation.},
}

@article {pmid39752622,
year = {2025},
author = {Bandyadka, S and Lebo, DPV and Mondragon, AA and Serizier, SB and Kwan, J and Peterson, JS and Chasse, AY and Jenkins, VK and Calikyan, A and Ortega, AJ and Campbell, JD and Emili, A and McCall, K},
title = {Multi-modal comparison of molecular programs driving nurse cell death and clearance in Drosophila melanogaster oogenesis.},
journal = {PLoS genetics},
volume = {21},
number = {1},
pages = {e1011220},
pmid = {39752622},
issn = {1553-7404},
support = {F31 GM115177/GM/NIGMS NIH HHS/United States ; R01 LM013154/LM/NLM NIH HHS/United States ; R35 GM127338/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Drosophila melanogaster/genetics ; *Oogenesis/genetics ; Female ; *Apoptosis/genetics ; *Drosophila Proteins/genetics/metabolism ; Oocytes/metabolism ; Ovarian Follicle/metabolism/cytology ; Cell Death/genetics ; Phagocytosis/genetics ; },
abstract = {The death and clearance of nurse cells is a consequential milestone in Drosophila melanogaster oogenesis. In preparation for oviposition, the germline-derived nurse cells bequeath to the developing oocyte all their cytoplasmic contents and undergo programmed cell death. The death of the nurse cells is controlled non-autonomously and is precipitated by epithelial follicle cells of somatic origin acquiring a squamous morphology and acidifying the nurse cells externally. Alternatively, stressors such as starvation can induce the death of nurse cells earlier in mid-oogenesis, manifesting apoptosis signatures, followed by their engulfment by epithelial follicle cells. To identify and contrast the molecular pathways underlying these morphologically and genetically distinct cell death paradigms, both mediated by follicle cells, we compared their genome-wide transcriptional, translational, and secretion profiles before and after differentiating to acquire a phagocytic capability, as well as during well-fed and nutrient-deprived conditions. By coupling the GAL4-UAS system to Translating Ribosome Affinity Purification (TRAP-seq) and proximity labeling (HRP-KDEL) followed by Liquid Chromatography tandem mass-spectrometry, we performed high-throughput screens to identify pathways selectively activated or repressed by follicle cells to employ nurse cell-clearance routines. We also integrated two publicly available single-cell RNAseq atlases of the Drosophila ovary to define the transcriptomic profiles of follicle cells. In this report, we describe the genes and major pathways identified in the screens and the striking consequences to Drosophila melanogaster oogenesis caused by RNAi perturbation of prioritized candidates. To our knowledge, our study is the first of its kind to comprehensively characterize two distinct apoptotic and non-apoptotic cell death paradigms in the same multi-cellular system. Beyond molecular differences in cell death, our investigation may also provide insights into how key systemic trade-offs are made between survival and reproduction when faced with physiological stress.},
}

Animals
*Drosophila melanogaster/genetics
*Oogenesis/genetics
Female
*Apoptosis/genetics
*Drosophila Proteins/genetics/metabolism
Oocytes/metabolism
Ovarian Follicle/metabolism/cytology
Cell Death/genetics
Phagocytosis/genetics

@article {pmid39741147,
year = {2024},
author = {Solé, R and Conde-Pueyo, N and Pla-Mauri, J and Garcia-Ojalvo, J and Montserrat, N and Levin, M},
title = {Open problems in synthetic multicellularity.},
journal = {NPJ systems biology and applications},
volume = {10},
number = {1},
pages = {151},
pmid = {39741147},
issn = {2056-7189},
support = {ERCCoG-2020 101002478 ENGINORG//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; Grant 62212//John Templeton Foundation (JTF)/ ; },
mesh = {Animals ; Humans ; Bioengineering/methods ; Biological Evolution ; Models, Biological ; *Synthetic Biology/methods ; Systems Biology/methods ; },
abstract = {Multicellularity is one of the major evolutionary transitions, and its rise provided the ingredients for the emergence of a biosphere inhabited by complex organisms. Over the last decades, the potential for bioengineering multicellular systems has been instrumental in interrogating nature and exploring novel paths to regeneration, disease, cognition, and behaviour. Here, we provide a list of open problems that encapsulate many of the ongoing and future challenges in the field and suggest conceptual approaches that may facilitate progress.},
}

Animals
Humans
Bioengineering/methods
Biological Evolution
Models, Biological
*Synthetic Biology/methods
Systems Biology/methods

@article {pmid39737561,
year = {2024},
author = {Horiuchi, Y and Umakawa, N and Otani, R and Tamada, Y and Kosetsu, K and Hiwatashi, Y and Wakisaka, R and Yoshida, S and Murata, T and Hasebe, M and Ishikawa, M and Kofuji, R},
title = {Physcomitrium LATERAL SUPPRESSOR genes promote formative cell divisions to produce germ cell lineages in both male and female gametangia.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.20372},
pmid = {39737561},
issn = {1469-8137},
abstract = {The evolution of green plants from aquatic to terrestrial environments is thought to have been facilitated by the acquisition of gametangia, specialized multicellular organs housing gametes. Antheridia and archegonia, responsible for producing and protecting sperm and egg cells, undergo formative cell divisions to produce a cell to differentiate into germ cell lineages and the other cell to give rise to surrounding structures. However, the genes governing this process remain unidentified. We isolated genes expressed during gametangia development from previously established gene-trap lines of Physcomitrium patens and characterized their function during gametangia formation. We identified P. patens LATERAL SUPPRESSOR 1 (PpLAS1) from the gene-trap library, encoding a GRAS transcription factor. The double-deletion mutant with its paralog PpLAS2 failed to form inner cells in both gametangia. PpLASs are expressed in cells undergoing formative cell division, and introducing PpLAS1 into the double-deletion mutant successfully rescued the phenotype. These findings underscore the pivotal role of PpLASs in regulating formative cell divisions, ensuring the separation of reproductive cell lineages from surrounding cells in antheridia and archegonia. Furthermore, they suggest a link between PpLASs and the evolutionary origin of male and female gametangia in the common ancestor of land plants.},
}

@article {pmid39732540,
year = {2025},
author = {Golomb, R and Dahan, O and Dahary, D and Pilpel, Y},
title = {Cell-autonomous adaptation: an overlooked avenue of adaptation in human evolution.},
journal = {Trends in genetics : TIG},
volume = {41},
number = {1},
pages = {12-22},
doi = {10.1016/j.tig.2024.10.009},
pmid = {39732540},
issn = {0168-9525},
mesh = {Animals ; Humans ; *Adaptation, Physiological/genetics ; *Biological Evolution ; Evolution, Molecular ; Mitochondria/genetics/metabolism ; Selection, Genetic/genetics ; },
abstract = {Adaptation to environmental conditions occurs over diverse evolutionary timescales. In multi-cellular organisms, adaptive traits are often studied in tissues/organs relevant to the environmental challenge. We argue for the importance of an underappreciated layer of evolutionary adaptation manifesting at the cellular level. Cell-autonomous adaptations (CAAs) are inherited traits that boost organismal fitness by enhancing individual cell function. For instance, the cell-autonomous enhancement of mitochondrial oxygen utilization in hypoxic environments differs from an optimized erythropoiesis response, which involves multiple tissues. We explore the breadth of CAAs across challenges and highlight their counterparts in unicellular organisms. Applying these insights, we mine selection signals in Andean highlanders, revealing novel candidate CAAs. The conservation of CAAs across species may reveal valuable insights into multi-cellular evolution.},
}

Animals
Humans
*Adaptation, Physiological/genetics
*Biological Evolution
Evolution, Molecular
Mitochondria/genetics/metabolism
Selection, Genetic/genetics

@article {pmid39715844,
year = {2024},
author = {Doctrove, Q and Park, Y and Calame, DG and Kitzman, J and Lenk, GM and Meisler, MH},
title = {Protein family FAM241 in human and mouse.},
journal = {Mammalian genome : official journal of the International Mammalian Genome Society},
volume = {},
number = {},
pages = {},
pmid = {39715844},
issn = {1432-1777},
support = {R01 GM24872/NH/NIH HHS/United States ; 873841//Muscular Dystrophy Association/ ; K12NS098482/NS/NINDS NIH HHS/United States ; },
abstract = {FAM241B was isolated in a genome-wide inactivation screen for generation of enlarged lysosomes. FAM241B and FAM241A comprise protein family FAM241 encoding proteins of 121 and 132 amino acid residues, respectively. The proteins exhibit 25% amino acid sequence identity and contain a domain of unknown function (DUF4605; pfam15378) that is conserved from primitive multicellular eukaryotes through vertebrates. Phylogenetic comparison indicates that duplication of the ancestral FAM241B gene occurred prior to the origin of fish. FAM241B has been deleted from the avian lineage. Fam241a and Fam241b are widely expressed in mouse tissues. Experimental knockout of mouse Fam241a, Fam241b, and the double knockout, did not generate a visible phenotype. Knockout of Fam241A and Fam241B did not exacerbate the phenotype of FIG4 null mice. RNAseq of brain RNA from double knockout mice detected reduced expression of several genes including Arke1e1 and RnaseL. The human variant p.Val115Gly in FAM241B was identified in a patient with developmental delay. Lysosome morphology in patient-derived fibroblasts was normal. In previous studies, FAM241A and FAM241B appeared to co-localize with proteins of the endoplasmic reticulum. The molecular function of this ancient protein family remains to be determined.},
}

@article {pmid39707854,
year = {2024},
author = {Ustyantsev, IG and Borodulina, OR and Kramerov, DA},
title = {[Participation of Proteins of the CPSF Complex in Polyadenylation of Transcripts Read by RNA Polymerase III from SINEs].},
journal = {Molekuliarnaia biologiia},
volume = {58},
number = {3},
pages = {437-447},
pmid = {39707854},
issn = {0026-8984},
mesh = {Humans ; *Polyadenylation ; HeLa Cells ; *Cleavage And Polyadenylation Specificity Factor/metabolism/genetics ; *RNA Polymerase III/metabolism/genetics ; *RNA, Messenger/genetics/metabolism ; mRNA Cleavage and Polyadenylation Factors/metabolism/genetics ; Alu Elements/genetics ; Gene Knockdown Techniques ; Nuclear Proteins ; },
abstract = {SINEs are mobile genetic elements of multicellular eukaryotes that arose during evolution from various tRNAs, as well as from 5S rRNA and 7SL RNA. Like the genes of these RNAs, SINEs are transcribed by RNA polymerase III. The transcripts of some mammalian SINEs have the capability of AAUAAA-dependent polyadenylation, which is unique for transcript generated by RNA polymerase III. Despite a certain similarity with canonical polyadenylation of mRNAs (transcripts of RNA polymerase II), these processes apparently differ significantly. The purpose of this work is to evaluate how important for polyadenylation of SINE transcripts are proteins of the CPSF complex formed by mPSF and mCF subcomplexes which direct mRNA polyadenylation. In HeLa cells, siRNA knockdowns of the CPSF components were carried out, after which the cells were transfected with plasmid constructs containing SINEs. A decrease in polyadenylation of the SINE transcripts as a result of the knockdown of the proteins was evaluated by Northern-hybridization. It turned out that the CPSF components, such as Wdr33 and CPSF30, contributed to the polyadenylation of SINE transcriptions, while the knockdown of CPSF100, CPSF73, and symplekin did not reduce the polyadenylation of these transcripts. Wdr33 and CPSF30, along with the CPSF160 and Fip1 previously studied, are components of the subcomplex mPSF responsible for mRNA polyadenylation. Thus, the available data suggest the importance of all mPSF proteins for polyadenylation of SINE transcripts. At the same time, CPSF100, CPSF73, and symplekin, forming the subcomplex mCF, are responsible for the cleavage of pre-mRNA; therefore, their non-participation in the polyadenylation of SINE transcriptions seems quite natural.},
}

Humans
*Polyadenylation
HeLa Cells
*Cleavage And Polyadenylation Specificity Factor/metabolism/genetics
*RNA Polymerase III/metabolism/genetics
*RNA, Messenger/genetics/metabolism
mRNA Cleavage and Polyadenylation Factors/metabolism/genetics
Alu Elements/genetics
Gene Knockdown Techniques
Nuclear Proteins

@article {pmid39702750,
year = {2024},
author = {Nguyen, NM and Farge, E},
title = {Mechanical induction in metazoan development and evolution: from earliest multi-cellular organisms to modern animal embryos.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {10695},
pmid = {39702750},
issn = {2041-1723},
mesh = {Animals ; *Biological Evolution ; Biomechanical Phenomena ; Body Patterning/physiology ; Embryo, Nonmammalian ; *Embryonic Development/physiology ; Morphogenesis ; },
abstract = {The development and origin of animal body forms have long been intensely explored, from the analysis of morphological traits during antiquity to Newtonian mechanical conceptions of morphogenesis. Advent of molecular biology then focused most interests on the biochemical patterning and genetic regulation of embryonic development. Today, a view is arising of development of multicellular living forms as a phenomenon emerging from non-hierarchical, reciprocal mechanical and mechanotransductive interactions between biochemical patterning and biomechanical morphogenesis. Here we discuss the nature of these processes and put forward findings on how early biochemical and biomechanical patterning of metazoans may have emerged from a primitive behavioural mechanotransducive feeding response to marine environment which might have initiated the development of first animal multicellular organisms.},
}

Animals
*Biological Evolution
Biomechanical Phenomena
Body Patterning/physiology
Embryo, Nonmammalian
*Embryonic Development/physiology
Morphogenesis

@article {pmid39675229,
year = {2025},
author = {Hirashima, T and W P, S and Noda, T},
title = {Collective sperm movement in mammalian reproductive tracts.},
journal = {Seminars in cell & developmental biology},
volume = {166},
number = {},
pages = {13-21},
doi = {10.1016/j.semcdb.2024.12.002},
pmid = {39675229},
issn = {1096-3634},
mesh = {*Sperm Motility/physiology ; Animals ; Male ; Humans ; *Spermatozoa/physiology/metabolism ; Mammals ; Female ; },
abstract = {Mammalian sperm cells travel from their origin in the male reproductive tract to fertilization in the female tract through a complex process driven by coordinated mechanical and biochemical mechanisms. Recent experimental and theoretical advances have illuminated the collective behaviors of sperm both in vivo and in vitro. However, our understanding of the underlying mechano-chemical processes remains incomplete. This review integrates current insights into sperm group movement, examining both immotile and motile states, which are essential for passive transport and active swimming through the reproductive tracts. We provide an overview of the current understanding of collective sperm movement, focusing on the experimental and theoretical mechanisms behind these behaviors. We also explore how sperm motility is regulated through the coordination of mechanical and chemical processes. Emerging evidence highlights the mechanosensitive properties of a sperm flagellum, suggesting that mechanical stimuli regulate flagellar beating at both individual and collective levels. This self-regulatory, mechano-chemical system reflects a broader principle observed in multicellular systems, offering a system-level insight into the regulation of motility and collective dynamics in biological systems.},
}

*Sperm Motility/physiology
Animals
Male
Humans
*Spermatozoa/physiology/metabolism
Mammals
Female

@article {pmid39671305,
year = {2024},
author = {Sun, Y and Chen, Z and Jin, M and Xie, H and Zhao, C},
title = {Ciliary length regulation by intraflagellar transport in zebrafish.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {39671305},
issn = {2050-084X},
support = {32125015//National Natural Science Foundation of China/ ; 31991194//National Natural Science Foundation of China/ ; 32100661//National Natural Science Foundation of China/ ; 2023M733344//China Postdoctoral Science Foundation/ ; },
mesh = {*Zebrafish/embryology ; Animals ; *Cilia/metabolism ; *Animals, Genetically Modified ; Biological Transport ; Zebrafish Proteins/metabolism/genetics ; Flagella/metabolism ; },
abstract = {How cells regulate the size of their organelles remains a fundamental question in cell biology. Cilia, with their simple structure and surface localization, provide an ideal model for investigating organelle size control. However, most studies on cilia length regulation are primarily performed on several single-celled organisms. In contrast, the mechanism of length regulation in cilia across diverse cell types within multicellular organisms remains a mystery. Similar to humans, zebrafish contain diverse types of cilia with variable lengths. Taking advantage of the transparency of zebrafish embryos, we conducted a comprehensive investigation into intraflagellar transport (IFT), an essential process for ciliogenesis. By generating a transgenic line carrying Ift88-GFP transgene, we observed IFT in multiple types of cilia with varying lengths. Remarkably, cilia exhibited variable IFT speeds in different cell types, with longer cilia exhibiting faster IFT speeds. This increased IFT speed in longer cilia is likely not due to changes in common factors that regulate IFT, such as motor selection, BBSome proteins, or tubulin modification. Interestingly, longer cilia in the ear cristae tend to form larger IFT compared to shorter spinal cord cilia. Reducing the size of IFT particles by knocking down Ift88 slowed IFT speed and resulted in the formation of shorter cilia. Our study proposes an intriguing model of cilia length regulation via controlling IFT speed through the modulation of the size of the IFT complex. This discovery may provide further insights into our understanding of how organelle size is regulated in higher vertebrates.},
}

*Zebrafish/embryology
Animals
*Cilia/metabolism
*Animals, Genetically Modified
Biological Transport
Zebrafish Proteins/metabolism/genetics
Flagella/metabolism

@article {pmid39665832,
year = {2024},
author = {Shi, L and Liu, S and Chen, J and Wang, H and Wang, Z},
title = {Microglial polarization pathways and therapeutic drugs targeting activated microglia in traumatic brain injury.},
journal = {Neural regeneration research},
volume = {},
number = {},
pages = {},
doi = {10.4103/NRR.NRR-D-24-00810},
pmid = {39665832},
issn = {1673-5374},
abstract = {Traumatic brain injury can be categorized into primary and secondary injuries. Secondary injuries are the main cause of disability following traumatic brain injury, which involves a complex multicellular cascade. Microglia play an important role in secondary injury and can be activated in response to traumatic brain injury. In this article, we review the origin and classification of microglia as well as the dynamic changes of microglia in traumatic brain injury. We also clarify the microglial polarization pathways and the therapeutic drugs targeting activated microglia. We found that regulating the signaling pathways involved in pro-inflammatory and anti-inflammatory microglia, such as the Toll-like receptor 4 / nuclear factor-kappa B, mitogen-activated protein kinase, Janus kinase/signal transducer and activator of transcription, phosphoinositide 3-kinase/protein kinase B, Notch, and high mobility group box 1 pathways, can alleviate the inflammatory response triggered by microglia in traumatic brain injury, thereby exerting neuroprotective effects. We also reviewed the strategies developed on the basis of these pathways, such as drug and cell replacement therapies. Drugs that modulate inflammatory factors, such as rosuvastatin, have been shown to promote the polarization of anti-inflammatory microglia and reduce the inflammatory response caused by traumatic brain injury. Mesenchymal stem cells possess anti-inflammatory properties, and clinical studies have confirmed their significant efficacy and safety in patients with traumatic brain injury. Additionally, advancements in mesenchymal stem cell-delivery methods-such as combinations of novel biomaterials, genetic engineering, and mesenchymal stem cell exosome therapy-have greatly enhanced the efficiency and therapeutic effects of mesenchymal stem cells in animal models. However, numerous challenges in the application of drug and mesenchymal stem cell treatment strategies remain to be addressed. In the future, new technologies, such as single-cell RNA sequencing and transcriptome analysis, can facilitate further experimental studies. Moreover, research involving non-human primates can help translate these treatment strategies to clinical practice.},
}

@article {pmid39653763,
year = {2024},
author = {Forrester, JV and McMenamin, PG},
title = {Evolution of the ocular immune system.},
journal = {Eye (London, England)},
volume = {},
number = {},
pages = {},
pmid = {39653763},
issn = {1476-5454},
abstract = {The evolution of the ocular immune system should be viewed within the context of the evolution of the immune system, and indeed organisms, as a whole. Since the earliest time, the most primitive responses of single cell organisms involved molecules such as anti-microbial peptides and behaviours such as phagocytosis. Innate immunity took shape ~2.5 billion years ago while adaptive immunity and antigen specificity appeared with vertebrate evolution ~ 500 million years ago. The invention of the microscope and the germ theory of disease precipitated debate on cellular versus humoral immunity, resolved by the discovery of B and T cells. Most recently, our understanding of the microbiome and consideration of the host existing symbiotically with trillions of microbial genes (the holobiont), suggests that the immune system is a sensor of homoeostasis rather than simply a responder to pathogens. Each tissue type in multicellular organisms, such as vertebrates, has a customised response to immune challenge, with powerful reactions most evident in barrier tissues such as the skin and gut mucosa, while the eye and brain occupy the opposite extreme where responses are attenuated. The experimental background which historically led to the concept of immune privilege is discussed in this review; however, we propose that the ocular immune response should not be viewed as unique but simply an example of how the tissues variably respond in nature, more or less to the same challenge (or danger).},
}

@article {pmid39650545,
year = {2024},
author = {Bourrat, P and Takacs, P and Doulcier, G and Nitschke, MC and Black, AJ and Hammerschmidt, K and Rainey, PB},
title = {Individuality Through Ecology: Rethinking the Evolution of Complex Life From an Externalist Perspective.},
journal = {Ecology and evolution},
volume = {14},
number = {12},
pages = {e70661},
pmid = {39650545},
issn = {2045-7758},
abstract = {The evolution of complex life forms, exemplified by multicellular organisms, can be traced through a series of evolutionary transitions in individuality, beginning with the origin of life, followed by the emergence of the eukaryotic cell, and, among other transitions, culminating in the shift from unicellularity to multicellularity. Several attempts have been made to explain the origins of such transitions, many of which have been internalist (i.e., based largely on internal properties of ancestral entities). Here, we show how externalist perspectives can shed new light on questions pertaining to evolutionary transitions in individuality. We do this by presenting the ecological scaffolding framework in which properties of complex life forms arise from an external scaffold. Ultimately, we anticipate that progress will come from recognition of the importance of both the internalist and externalist modes of explanation. We illustrate this by considering an extension of the ecological scaffolding model in which cells modify the environment that later becomes the scaffold giving rise to multicellular individuality.},
}

@article {pmid39642877,
year = {2025},
author = {Torruella, G and Galindo, LJ and Moreira, D and López-García, P},
title = {Phylogenomics of neglected flagellated protists supports a revised eukaryotic tree of life.},
journal = {Current biology : CB},
volume = {35},
number = {1},
pages = {198-207.e4},
doi = {10.1016/j.cub.2024.10.075},
pmid = {39642877},
issn = {1879-0445},
mesh = {*Phylogeny ; *Eukaryota/genetics/classification ; Biological Evolution ; },
abstract = {Eukaryotes evolved from prokaryotic predecessors in the early Proterozoic[1][,][2] and radiated from their already complex last common ancestor,[3] diversifying into several supergroups with unresolved deep evolutionary connections.[4] They evolved extremely diverse lifestyles, playing crucial roles in the carbon cycle.[5][,][6] Heterotrophic flagellates are arguably the most diverse eukaryotes[4][,][7][,][8][,][9] and often occupy basal positions in phylogenetic trees. However, many of them remain undersampled[4][,][10] and/or incertae sedis.[4][,][11][,][12][,][13][,][14][,][15][,][16][,][17][,][18] Progressive improvement of phylogenomic methods and a wider protist sampling have reshaped and consolidated major clades in the eukaryotic tree.[13][,][14][,][15][,][16][,][17][,][18][,][19] This is illustrated by the Opimoda,[14] one of the largest eukaryotic supergroups (Amoebozoa, Ancyromonadida, Apusomonadida, Breviatea, CRuMs [Collodictyon-Rigifila-Mantamonas], Malawimonadida, and Opisthokonta-including animals and fungi).[4][,][14][,][19][,][20][,][21][,][22] However, their deepest evolutionary relationships still remain uncertain. Here, we sequenced transcriptomes of poorly studied flagellates[23][,][24] (14 apusomonads,[25][,][26] 7 ancyromonads,[27] and 1 cultured Mediterranean strain of Meteora sporadica[17]) and conducted comprehensive phylogenomics analyses with an expanded taxon sampling of early-branching protists. Our findings support the monophyly of Opimoda, with CRuMs being sister to the Amorphea (amoebozoans, breviates, apusomonads, and opisthokonts) and ancyromonads and malawimonads forming a moderately supported clade. By mapping key complex phenotypic traits onto this phylogenetic framework, we infer an opimodan biflagellate ancestor with an excavate-like feeding groove, which ancyromonads subsequently lost. Although breviates and apusomonads retained the ancestral biflagellate state, some early-diverging Amorphea lost one or both flagella, facilitating the evolution of amoeboid morphologies, novel feeding modes, and palintomic cell division resulting in multinucleated cells. These innovations likely facilitated the subsequent evolution of fungal and metazoan multicellularity.},
}

*Phylogeny
*Eukaryota/genetics/classification
Biological Evolution

@article {pmid39629215,
year = {2024},
author = {Ley, P and Geelhoed, JS and Vasquez-Cardenas, D and Meysman, FJR},
title = {On the diversity, phylogeny and biogeography of cable bacteria.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1485281},
pmid = {39629215},
issn = {1664-302X},
abstract = {Cable bacteria have acquired a unique metabolism, which induces long-distance electron transport along their centimeter-long multicellular filaments. At present, cable bacteria are thought to form a monophyletic clade with two described genera. However, their diversity has not been systematically investigated. To investigate the phylogenetic relationships within the cable bacteria clade, 16S rRNA gene sequences were compiled from literature and public databases (SILVA 138 SSU and NCBI GenBank). These were complemented with novel sequences obtained from natural sediment enrichments across a wide range of salinities (2-34). To enable taxonomic resolution at the species level, we designed a procedure to attain full-length 16S rRNA gene sequences from individual cable bacterium filaments using an optimized nested PCR protocol and Sanger sequencing. The final database contained 1,876 long 16S rRNA gene sequences (≥800 bp) originating from 92 aquatic locations, ranging from polar to tropical regions and from intertidal to deep sea sediments. The resulting phylogenetic tree reveals 90 potential species-level clades (based on a delineation value of 98.7% 16S rRNA gene sequence identity) that reside within six genus-level clusters. Hence, the diversity of cable bacteria appears to be substantially larger than the two genera and 13 species that have been officially named up to now. Particularly brackish environments with strong salinity fluctuations, as well as sediments with low free sulfide concentrations and deep sea sediments harbor a large pool of novel and undescribed cable bacteria taxa.},
}

@article {pmid39623209,
year = {2025},
author = {Manzano, C and Morimoto, KW and Shaar-Moshe, L and Mason, GA and Cantó-Pastor, A and Gouran, M and De Bellis, D and Ursache, R and Kajala, K and Sinha, N and Bailey-Serres, J and Geldner, N and Del Pozo, JC and Brady, SM},
title = {Regulation and function of a polarly localized lignin barrier in the exodermis.},
journal = {Nature plants},
volume = {11},
number = {1},
pages = {118-130},
pmid = {39623209},
issn = {2055-0278},
support = {HHMI 55108506//Howard Hughes Medical Institute (HHMI)/ ; 55108506//Howard Hughes Medical Institute (HHMI)/ ; NSF 2118017//National Science Foundation (NSF)/ ; PGRP IOS-211980//National Science Foundation (NSF)/ ; PGRP IOS-1856749//National Science Foundation (NSF)/ ; PRFB IOS-1907008//National Science Foundation (NSF)/ ; 655406//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 700057//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; FI-570-2018//United States - Israel Binational Agricultural Research and Development Fund (BARD)/ ; RGP0067/2021//Human Frontier Science Program (HFSP)/ ; Long-term Fellowship ALTF 1046-2015//European Molecular Biology Organization (EMBO)/ ; },
mesh = {*Lignin/metabolism ; *Solanum lycopersicum/genetics/metabolism/growth & development/physiology ; *Gene Expression Regulation, Plant ; *Plant Roots/metabolism/growth & development/genetics ; Plant Proteins/metabolism/genetics ; Transcription Factors/metabolism/genetics ; },
abstract = {Multicellular organisms control environmental interactions through specialized barriers in specific cell types. A conserved barrier in plant roots is the endodermal Casparian strip (CS), a ring-like structure made of polymerized lignin that seals the endodermal apoplastic space. Most angiosperms have another root cell type, the exodermis, that is reported to form a barrier. Our understanding of exodermal developmental and molecular regulation and function is limited as this cell type is absent from Arabidopsis thaliana. We demonstrate that in tomato (Solanum lycopersicum), the exodermis does not form a CS. Instead, it forms a polar lignin cap (PLC) with equivalent barrier function to the endodermal CS but distinct genetic control. Repression of the exodermal PLC in inner cortical layers is conferred by the SlSCZ and SlEXO1 transcription factors, and these two factors genetically interact to control its polar deposition. Several target genes that act downstream of SlSCZ and SlEXO1 in the exodermis are identified. Although the exodermis and endodermis produce barriers that restrict mineral ion uptake, the exodermal PLC is unable to fully compensate for the lack of a CS. The presence of distinct lignin structures acting as apoplastic barriers has exciting implications for a root's response to abiotic and biotic stimuli.},
}

*Lignin/metabolism
*Solanum lycopersicum/genetics/metabolism/growth & development/physiology
*Gene Expression Regulation, Plant
*Plant Roots/metabolism/growth & development/genetics
Plant Proteins/metabolism/genetics
Transcription Factors/metabolism/genetics

@article {pmid39618799,
year = {2024},
author = {Kaneko, K},
title = {Dimensional reduction and adaptation-development-evolution relation in evolved biological systems.},
journal = {Biophysical reviews},
volume = {16},
number = {5},
pages = {639-649},
pmid = {39618799},
issn = {1867-2450},
abstract = {Living systems are complex and hierarchical, with diverse components at different scales, yet they sustain themselves, grow, and evolve over time. How can a theory of such complex biological states be developed? Here we note that for a hierarchical biological system to be robust, it must achieve consistency between micro-scale (e.g., molecular) and macro-scale (e.g., cellular) phenomena. This allows for a universal theory of adaptive change in cells based on biological robustness and consistency between cellular growth and molecular replication. Here, we show how adaptive changes in high-dimensional phenotypes (biological states) are constrained to low-dimensional space, leading to the derivation of a macroscopic law for cellular states. The theory is then extended to evolution, leading to proportionality between evolutionary and environmental responses, as well as proportionality between phenotypic variances due to noise and due to genetic changes. The universality of the results across several models and experiments is demonstrated. Then, by further extending the theory of evolutionary dimensional reduction to multicellular systems, the relationship between multicellular development and evolution, in particular, the developmental hourglass, is demonstrated. Finally, the possibility of collapse of dimensional reduction under nutrient limitation is discussed.},
}

@article {pmid39617193,
year = {2024},
author = {Chandra, S and Rutaganira, FU},
title = {Glycerol improves the viability of a cryopreserved choanoflagellate.},
journal = {Cryobiology},
volume = {118},
number = {},
pages = {105183},
doi = {10.1016/j.cryobiol.2024.105183},
pmid = {39617193},
issn = {1090-2392},
abstract = {The colonial choanoflagellate Salpingoeca rosetta is a tractable model system for studying the origins of multicellularity, but long-term storage strategies for this species have not been tested. In this study, we probed each stage of cryopreservation (cooling, long-term storage, recovery) to identify the optimal protocol for recovery of S. rosetta and co-cultured bacterial cells. Dimethyl sulfoxide (Me2SO; commonly referred to as DMSO), the current cryoprotective agent (CPA) standard, proved to be worse than glycerol at comparable concentrations. Samples treated with either CPA at 5 % showed the poorest recovery. Our results identified 15 % glycerol as the most effective CPA for both S. rosetta and Echinicola pacifica. We also determined that ultra-low temperature freezers can be sufficient for short-term storage. We propose 15 % glycerol and liquid phase nitrogen as the standard cryopreservation protocol for S. rosetta cultures and as a starting point for testing long-term storage strategies for other choanoflagellates and heterotrophic protists.},
}

@article {pmid39614268,
year = {2024},
author = {He, R and Liu, Y and Fu, W and He, X and Liu, S and Xiao, D and Tao, Y},
title = {Mechanisms and cross-talk of regulated cell death and their epigenetic modifications in tumor progression.},
journal = {Molecular cancer},
volume = {23},
number = {1},
pages = {267},
pmid = {39614268},
issn = {1476-4598},
mesh = {Humans ; *Neoplasms/genetics/pathology/metabolism ; *Epigenesis, Genetic ; Animals ; *Disease Progression ; *Regulated Cell Death/genetics ; Gene Expression Regulation, Neoplastic ; Signal Transduction ; },
abstract = {Cell death is a fundamental part of life for metazoans. To maintain the balance between cell proliferation and metabolism of human bodies, a certain number of cells need to be removed regularly. Hence, the mechanisms of cell death have been preserved during the evolution of multicellular organisms. Tumorigenesis is closely related with exceptional inhibition of cell death. Mutations or defects in cell death-related genes block the elimination of abnormal cells and enhance the resistance of malignant cells to chemotherapy. Therefore, the investigation of cell death mechanisms enables the development of drugs that directly induce tumor cell death. In the guidelines updated by the Cell Death Nomenclature Committee (NCCD) in 2018, cell death was classified into 12 types according to morphological, biochemical and functional classification, including intrinsic apoptosis, extrinsic apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, PARP-1 parthanatos, entotic cell death, NETotic cell death, lysosome-dependent cell death, autophagy-dependent cell death, immunogenic cell death, cellular senescence and mitotic catastrophe. The mechanistic relationships between epigenetic controls and cell death in cancer progression were previously unclear. In this review, we will summarize the mechanisms of cell death pathways and corresponding epigenetic regulations. Also, we will explore the extensive interactions between these pathways and discuss the mechanisms of cell death in epigenetics which bring benefits to tumor therapy.},
}

Humans
*Neoplasms/genetics/pathology/metabolism
*Epigenesis, Genetic
Animals
*Disease Progression
*Regulated Cell Death/genetics
Gene Expression Regulation, Neoplastic
Signal Transduction

@article {pmid39609399,
year = {2024},
author = {Maione, AS and Iengo, L and Sala, L and Massaiu, I and Chiesa, M and Lippi, M and Ghilardi, S and Florindi, C and Lodola, F and Zaza, A and Tondo, C and Schiavone, M and Banfi, C and Pompilio, G and Poggio, P and Sommariva, E},
title = {Cardiomyocyte and stromal cell cross-talk influences the pathogenesis of arrhythmogenic cardiomyopathy: a multi-level analysis uncovers DLK1-NOTCH pathway role in fibro-adipose remodelling.},
journal = {Cell death discovery},
volume = {10},
number = {1},
pages = {484},
pmid = {39609399},
issn = {2058-7716},
abstract = {Arrhythmogenic Cardiomyopathy (ACM) is a life-threatening, genetically determined disease primarily caused by mutations in desmosomal genes, such as PKP2. Currently, there is no etiological therapy for ACM due to its complex and not fully elucidated pathogenesis. Various cardiac cell types affected by the genetic mutation, such as cardiomyocytes (CM) and cardiac mesenchymal stromal cells (cMSC), individually contribute to the ACM phenotype, driving functional abnormalities and fibro-fatty substitution, respectively. However, the relative importance of the CM and cMSC alterations, as well as their reciprocal influence in disease progression remain poorly understood. We hypothesised that ACM-dependent phenotypes are driven not only by alterations in individual cell types but also by the reciprocal interactions between CM and cMSC, which may further impact disease pathogenesis. We utilized a patient-specific, multicellular cardiac system composed of either control or PKP2-mutated CM and cMSC to assess the mutation's role in fibro-fatty phenotype by immunofluorescence, and contractile behaviour of co-cultures using cell motion detection software. Additionally, we investigated reciprocal interactions both in silico and via multi-targeted proteomics. We demonstrated that ACM CM can promote fibro-adipose differentiation of cMSC. Conversely, ACM cMSC contribute to increasing the rate of abnormal contractile events with likely arrhythmic significance. Furthermore, we showed that an ACM-causative mutation alters the CM-cMSC interaction pattern. We identified the CM-sourced DLK1 as a novel regulator of fibro-adipose remodelling in ACM. Our study challenges the paradigm of exclusive cell-specific mechanisms in ACM. A deeper understanding of the cell-cell influence is crucial for identifying novel therapeutic targets for ACM, and this concept is exploitable for other cardiomyopathies.},
}

@article {pmid39604729,
year = {2024},
author = {Yang, R and Hunker, O and Wise, M and Bleichert, F},
title = {Multiple mechanisms for licensing human replication origins.},
journal = {Nature},
volume = {636},
number = {8042},
pages = {488-498},
pmid = {39604729},
issn = {1476-4687},
mesh = {Humans ; *Origin Recognition Complex/metabolism/chemistry ; *Replication Origin ; *DNA Replication ; *Minichromosome Maintenance Proteins/metabolism/chemistry ; Protein Multimerization ; Models, Molecular ; DNA/metabolism/chemistry ; Microscopy, Electron ; },
abstract = {Loading of replicative helicases is obligatory for the assembly of DNA replication machineries. The eukaryotic MCM2-7 replicative helicase motor is deposited onto DNA by the origin recognition complex (ORC) and co-loader proteins as a head-to-head double hexamer to license replication origins. Although extensively studied in budding yeast[1-4], the mechanisms of origin licensing in multicellular eukaryotes remain poorly defined. Here we use biochemical reconstitution and electron microscopy to reconstruct the human MCM loading pathway. We find that unlike in yeast, the ORC6 subunit of the ORC is not essential for-but enhances-human MCM loading. Electron microscopy analyses identify several intermediates en route to MCM double hexamer formation in the presence and absence of ORC6, including a DNA-loaded, closed-ring MCM single hexamer intermediate that can mature into a head-to-head double hexamer through multiple mechanisms. ORC6 and ORC3 facilitate the recruitment of the ORC to the dimerization interface of the first hexamer into MCM-ORC (MO) complexes that are distinct from the yeast MO complex[5,6] and may orient the ORC for second MCM hexamer loading. Additionally, MCM double hexamer formation can proceed through dimerization of independently loaded MCM single hexamers, promoted by a propensity of human MCM2-7 hexamers to self-dimerize. This flexibility in human MCM loading may provide resilience against cellular replication stress, and the reconstitution system will enable studies addressing outstanding questions regarding DNA replication initiation and replication-coupled events in the future.},
}

Humans
*Origin Recognition Complex/metabolism/chemistry
*Replication Origin
*DNA Replication
*Minichromosome Maintenance Proteins/metabolism/chemistry
Protein Multimerization
Models, Molecular
DNA/metabolism/chemistry
Microscopy, Electron

@article {pmid39603922,
year = {2024},
author = {Ryu, J and Kim, Y and Ju, YS},
title = {A more elaborate genetic clock for clonal species.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2024.11.002},
pmid = {39603922},
issn = {0168-9525},
abstract = {The genetic clock is a well-established tool used in evolutionary biology for estimating divergence times between species, individuals, or cells based on DNA sequence changes. Yu et al. have revisited the clock to make it applicable to clonal multicellular organisms that expand through asexual reproduction mechanisms, enabling more comprehensive evolutionary tracking.},
}

@article {pmid39602309,
year = {2024},
author = {Wan, J and Ji, R and Liu, J and Ma, K and Pan, Y and Lin, W},
title = {Biomineralization in magnetotactic bacteria: From diversity to molecular discovery-based applications.},
journal = {Cell reports},
volume = {43},
number = {12},
pages = {114995},
doi = {10.1016/j.celrep.2024.114995},
pmid = {39602309},
issn = {2211-1247},
mesh = {*Magnetosomes/metabolism ; *Biomineralization ; Magnetospirillum/metabolism/genetics ; Bacteria/metabolism/genetics ; },
abstract = {The synthesis of magnetic nanoparticles (Fe3O4 or Fe3S4) within the membrane-bound organelles known as magnetosomes in magnetotactic bacteria (MTB) is a remarkable example of microbial-controlled biomineralization. Studying MTB biomineralization is crucial not only for understanding the origin and evolution of magnetoreception and bacterial organelles but also for advancing biotechnological and biomedical applications of MTB cells and magnetosomes. After decades of research, MTB have revealed unexpected diversity and complexity. The mechanisms underlying magnetosome biomineralization in MTB have been continuously documented using a few model MTB strains. In this review, we provide an overview of recent findings related to MTB diversity and focus primarily on the current understanding of magnetosome biosynthesis. Additionally, we summarize the growing biotechnological and biomedical applications derived from molecular studies of MTB and their magnetosomes.},
}

*Magnetosomes/metabolism
*Biomineralization
Magnetospirillum/metabolism/genetics
Bacteria/metabolism/genetics

@article {pmid39596672,
year = {2024},
author = {Madhani, H and Nejad Kourki, A},
title = {The Evolution of Complex Multicellularity in Land Plants.},
journal = {Genes},
volume = {15},
number = {11},
pages = {},
pmid = {39596672},
issn = {2073-4425},
mesh = {*Embryophyta/genetics/growth & development ; *Biological Evolution ; },
abstract = {The evolution of complex multicellularity in land plants represents a pivotal event in the history of life on Earth, characterized by significant increases in biological complexity. This transition, classified as a Major Evolutionary Transition (MET), is best understood through the framework of Evolutionary Transitions in Individuality (ETIs), which focuses on formerly independent entities forming higher-level units that lose their reproductive autonomy. While much of the ETI literature has concentrated on the early stages of multicellularity, such as the formation and maintenance stages, this paper seeks to address the less explored transformation stage. To do so, we apply an approach that we call Transitions in Structural Complexity (TSCs), which focuses on the emergence of new units of organization via the three key evolutionary processes of modularization, subfunctionalization, and integration to the evolution of land plants. To lay the groundwork, we first explore the relationships between sex, individuality, and units of selection to highlight a sexual life cycle-based perspective on ETIs by examining the early stages of the transition to multicellularity (formation) in the sexual life cycle of the unicellular common ancestor of land plants, emphasizing the differences between the transition to multicellularity in eumetazoans and land plants. We then directly apply the TSC approach in this group, identifying key evolutionary events such as the distinct evolutionary innovations like shoot, root, vascular systems, and specialized reproductive structures, arguing that bringing these under the broader rubric of TSCs affords a degree of explanatory unification. By examining these evolutionary processes, this paper provides a new perspective on the evolution of multicellularity in land plants, highlighting both parallels and distinctions with the animal kingdom.},
}

*Embryophyta/genetics/growth & development
*Biological Evolution

@article {pmid39596652,
year = {2024},
author = {Stein, WD},
title = {An Orthologics Study of the Notch Signaling Pathway.},
journal = {Genes},
volume = {15},
number = {11},
pages = {},
pmid = {39596652},
issn = {2073-4425},
mesh = {*Signal Transduction ; *Receptors, Notch/metabolism/genetics ; Animals ; Humans ; Evolution, Molecular ; Membrane Proteins/genetics/metabolism ; Phylogeny ; },
abstract = {The Notch signaling pathway plays a major role in embryological development and in the ongoing life processes of many animals. Its role is to provide cell-to-cell communication in which a Sender cell, bearing membrane-embedded ligands, instructs a Receiver cell, bearing membrane-embedded receptors, to adopt one of two available fates. Elucidating the evolution of this pathway is the topic of this paper, which uses an orthologs approach, providing a comprehensive basis for the study. Using BLAST searches, orthologs were identified for all the 49 components of the Notch signaling pathway. The historical time course of integration of these proteins, as the animals evolved, was elucidated. Insofar as cell-to-cell communication is of relevance only in multicellular animals, it is not surprising that the Notch system became functional only with the evolutionary appearance of Metazoa, the first multicellular animals. Porifera contributed a quarter of the Notch pathway proteins, the Cnidaria brought the total to one-half, but the system reached completion only when humans appeared. A literature search elucidated the roles of the Notch system's components in modern descendants of the ortholog-contributing ancestors. A single protein, the protein tyrosine kinase (PTK) of the protozoan Ministeria vibrans, was identified as a possible pre-Metazoan ancestor of all three of the Notch pathway proteins, DLL, JAG, and NOTCH. A scenario for the evolution of the Notch signaling pathway is presented and described as the co-option of its components, clade by clade, in a repurposing of genes already present in ancestral unicellular organisms.},
}

*Signal Transduction
*Receptors, Notch/metabolism/genetics
Animals
Humans
Evolution, Molecular
Membrane Proteins/genetics/metabolism
Phylogeny

@article {pmid39595611,
year = {2024},
author = {Dahlin, P and Ruthes, AC},
title = {Loss of Sterol Biosynthesis in Economically Important Plant Pests and Pathogens: A Review of a Potential Target for Pest Control.},
journal = {Biomolecules},
volume = {14},
number = {11},
pages = {},
pmid = {39595611},
issn = {2218-273X},
mesh = {Animals ; Insecta/metabolism ; Nematoda/metabolism ; Oomycetes/metabolism ; *Pest Control ; Plant Diseases/parasitology/microbiology ; *Plants/metabolism/parasitology ; *Sterols/metabolism/biosynthesis ; },
abstract = {Sterol biosynthesis is a crucial metabolic pathway in plants and various plant pathogens. Their vital physiological role in multicellular organisms and their effects on growth and reproduction underline their importance as membrane compounds, hormone precursors, and signaling molecules. Insects, nematodes, and oomycetes of the Peronosporales group, which harbor important agricultural pests and pathogens, have lost the ability to synthesize their own sterols. These organisms rely on the acquisition of sterols from their host and are dependent on the sterol composition of the host. It is thought that sterol-synthesizing enzymes were lost during co-evolution with the hosts, which provided the organisms with sufficient amounts of the required sterols. To meet the essential requirements of these organisms, some sterol auxotrophs retained a few remaining sterol-modifying enzymes. Several molecular and biochemical investigations have suggested promising avenues for pest and pathogen control by targeting host sterol composition, sterol uptake, or sterol modification in organisms that have lost the ability to biosynthesize sterol de novo. This review examines the loss of sterol biosynthesis de novo in insects, nematodes, and oomycetes with the aim of investigating the sterol metabolic constraints and sterol acquisition of these organisms. This will shed light on its potential as a control target for the management of sterol-dependent organisms in a comprehensive agronomic approach.},
}

Animals
Insecta/metabolism
Nematoda/metabolism
Oomycetes/metabolism
*Pest Control
Plant Diseases/parasitology/microbiology
*Plants/metabolism/parasitology
*Sterols/metabolism/biosynthesis

@article {pmid39591964,
year = {2025},
author = {Lu, X and Zhang, Q and Wang, Z and Cheng, X and Yan, H and Cai, S and Zhang, H and Liu, Q},
title = {Development of an inducible DNA barcoding system to understand lineage changes in Arabidopsis regeneration.},
journal = {Developmental cell},
volume = {60},
number = {2},
pages = {305-319.e5},
doi = {10.1016/j.devcel.2024.10.023},
pmid = {39591964},
issn = {1878-1551},
mesh = {*Arabidopsis/genetics ; *Regeneration/genetics/physiology ; *DNA Barcoding, Taxonomic/methods ; *Cell Lineage/genetics ; },
abstract = {Plants demonstrate a high degree of developmental plasticity, capable of regenerating entire individuals from detached somatic tissues-a regenerative phenomenon rarely observed in metazoa. Consequently, elucidating the lineage relationship between somatic founder cells and descendant cells in regenerated plant organs has long been a pursuit. In this study, we developed and optimized both DNA barcode- and multi-fluorescence-based cell-lineage tracing toolsets, employing an inducible method to mark individual cells in Arabidopsis donor somatic tissues at the onset of regeneration. Utilizing these complementary methods, we scrutinized cell identities at the single-cell level and presented compelling evidence that all cells in the regenerated Arabidopsis plants, irrespective of their organ types, originated from a single progenitor cell in the donor somatic tissue. Our discovery suggests a single-cell passage directing the transition from multicellular donor tissue to regenerated plants, thereby creating opportunities for cell-cell competition during plant regeneration-a strategy for maximizing survival.},
}

*Arabidopsis/genetics
*Regeneration/genetics/physiology
*DNA Barcoding, Taxonomic/methods
*Cell Lineage/genetics

@article {pmid39589477,
year = {2024},
author = {Krueger, KE},
title = {Survey for Activating Oncogenic Mutation Variants in Metazoan Germline Genes.},
journal = {Journal of molecular evolution},
volume = {92},
number = {6},
pages = {930-943},
pmid = {39589477},
issn = {1432-1432},
mesh = {Animals ; *Germ-Line Mutation/genetics ; Humans ; Neoplasms/genetics ; Oncogenes/genetics ; Mutation, Missense/genetics ; Germ Cells/metabolism ; },
abstract = {Most cancers present with mutations or amplifications in distinctive tumor promoter genes that activate principal cell-signaling cascades promoting cell proliferation, dedifferentiation, cell survival, and replicative immortality. Somatic mutations found in this these driver proto-oncogenes invariably result in constitutive activation of the encoded protein. A salient feature of the activating mutations observed throughout many thousands of clinical tumor specimens reveals these driver missense mutations are recurrent and restricted to just one or very few codons of the entire gene, suggesting they have been positively selected during the course of tumor development. The purpose of this study is to investigate whether these characteristic oncogenic driver mutations are observed in the germline genes of any metazoan species. Six well-known tumor promoter genes were chosen for this survey including BRAF, KRAS, JAK2, PIK3CA, EGFR, and IDH1/2. The sites of all driver mutations were found to occur in highly conserved regions of each gene comparing protein sequences throughout diverse phyla of metazoan species. None of the oncogenic missense mutations were found in germlines of any species of current genome and protein databases. Despite many tumors readily selecting these somatic mutations, the conclusion drawn from this study is that these variants are negatively rejected if encountered as a germline mutation. While cancer expansion ensues from dysregulated growth elicited by these mutations, this effect is likely detrimental to embryonic development and/or survival of multicellular organisms. Although all oncogenic mutations considered here are gain-of-function where five of the six increase activity of the encoded proteins, clonal advancement promotes tumor growth by these genomic changes without conferring selection advantages benefiting the organism or species.},
}

Animals
*Germ-Line Mutation/genetics
Humans
Neoplasms/genetics
Oncogenes/genetics
Mutation, Missense/genetics
Germ Cells/metabolism

@article {pmid39587099,
year = {2024},
author = {Sheikh, S and Fu, CJ and Brown, MW and Baldauf, SL},
title = {The Acrasis kona genome and developmental transcriptomes reveal deep origins of eukaryotic multicellular pathways.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {10197},
pmid = {39587099},
issn = {2041-1723},
support = {VR 2017-04351//Vetenskapsrådet (Swedish Research Council)/ ; 2100888//National Science Foundation (NSF)/ ; },
mesh = {*Transcriptome ; *Dictyostelium/genetics/growth & development ; Genome, Protozoan ; Amoeba/genetics ; Phylogeny ; Gene Transfer, Horizontal ; Protozoan Proteins/genetics/metabolism ; Proteome/metabolism/genetics ; Genome ; },
abstract = {Acrasids are amoebae with the capacity to form multicellular fruiting bodies in a process known as aggregative multicellularity (AGM). This makes acrasids the only known example of multicellularity among the earliest branches of eukaryotes (the former Excavata). Here, we report the Acrasis kona genome sequence plus transcriptomes from pre-, mid- and post-developmental stages. The genome is rich in novelty and genes with strong signatures of horizontal transfer, and multigene families encode nearly half of the amoeba's predicted proteome. Development in A. kona appears molecularly simple relative to the AGM model, Dictyostelium discoideum. However, the acrasid also differs from the dictyostelid in that it does not appear to be starving during development. Instead, developing A. kona appears to be very metabolically active, does not induce autophagy and does not up-regulate its proteasomal genes. Together, these observations strongly suggest that starvation is not essential for AGM development. Nonetheless, development in the two amoebae appears to employ remarkably similar pathways for signaling, motility and, potentially, construction of an extracellular matrix surrounding the developing cell mass. Much of this similarity is also shared with animal development, suggesting that much of the basic tool kit for multicellular development arose early in eukaryote evolution.},
}

*Transcriptome
*Dictyostelium/genetics/growth & development
Genome, Protozoan
Amoeba/genetics
Phylogeny
Gene Transfer, Horizontal
Protozoan Proteins/genetics/metabolism
Proteome/metabolism/genetics
Genome

@article {pmid39574678,
year = {2024},
author = {Zhu, L and Beichman, A and Harris, K},
title = {Population size interacts with reproductive longevity to shape the germline mutation rate.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39574678},
issn = {2692-8205},
support = {R35 GM133428/GM/NIGMS NIH HHS/United States ; T32 AG066574/AG/NIA NIH HHS/United States ; },
abstract = {Mutation rates vary across the tree of life by many orders of magnitude, with lower mutation rates in species that reproduce quickly and maintain large effective population sizes. A compelling explanation for this trend is that large effective population sizes facilitate selection against weakly deleterious "mutator alleles" such as variants that interfere with the molecular efficacy of DNA repair. However, in multicellular organisms, the relationship of the mutation rate to DNA repair efficacy is complicated by variation in reproductive age. Long generation times leave more time for mutations to accrue each generation, and late reproduction likely amplifies the fitness consequences of any DNA repair defect that creates extra mutations in the sperm or eggs. Here, we present theoretical and empirical evidence that a long generation time amplifies the strength of selection for low mutation rates in the spermatocytes and 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 DNA proofreading and repair in their germ cells. In contrast, species with different generation times accumulate similar mutation loads during embryonic development. 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.},
}

@article {pmid39574581,
year = {2024},
author = {Bonefas, KM and Venkatachalam, I and Iwase, S},
title = {KDM5C is a sex-biased brake against germline gene expression programs in somatic lineages.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39574581},
issn = {2692-8205},
support = {R01 NS116008/NS/NINDS NIH HHS/United States ; R01 NS089896/NS/NINDS NIH HHS/United States ; T32 NS076401/NS/NINDS NIH HHS/United States ; T32 GM007544/GM/NIGMS NIH HHS/United States ; T32 GM149391/GM/NIGMS NIH HHS/United States ; R21 MH135290/MH/NIMH NIH HHS/United States ; T32 HD079342/HD/NICHD NIH HHS/United States ; R21 NS104774/NS/NINDS NIH HHS/United States ; },
abstract = {The division of labor among cellular lineages is a pivotal step in the evolution of multicellularity. In mammals, the soma-germline boundary is formed during early embryogenesis, when genes that drive germline identity are repressed in somatic lineages through DNA and histone modifications at promoter CpG islands (CGIs). Somatic misexpression of germline genes is a signature of cancer and observed in select neurodevelopmental disorders. However, it is currently unclear if all germline genes use the same repressive mechanisms and if factors like development and sex influence their dysregulation. Here, we examine how cellular context influences the formation of somatic tissue identity in mice lacking lysine demethylase 5c (KDM5C), an X chromosome eraser of histone 3 lysine 4 di and tri-methylation (H3K4me2/3). We found male Kdm5c knockout (-KO) mice aberrantly express many tissue-specific genes within the brain, the majority of which are unique to the germline. By developing a comprehensive list of mouse germline-enriched genes, we observed Kdm5c-KO cells aberrantly express key drivers of germline fate during early embryogenesis but late-stage spermatogenesis genes within the mature brain. KDM5C binds CGIs within germline gene promoters to facilitate DNA CpG methylation as embryonic stem cells differentiate into epiblast-like cells (EpiLCs). However, the majority of late-stage spermatogenesis genes expressed within the Kdm5c-KO brain did not harbor promoter CGIs. These CGI-free germline genes were not bound by KDM5C and instead expressed through ectopic activation by RFX transcription factors. Furthermore, germline gene repression is sexually dimorphic, as female EpiLCs require a higher dose of KDM5C to maintain germline silencing. Altogether, these data revealed distinct regulatory classes of germline genes and sex-biased silencing mechanisms in somatic cells.},
}

@article {pmid39571576,
year = {2024},
author = {Denoeud, F and Godfroy, O and Cruaud, C and Heesch, S and Nehr, Z and Tadrent, N and Couloux, A and Brillet-Guéguen, L and Delage, L and Mckeown, D and Motomura, T and Sussfeld, D and Fan, X and Mazéas, L and Terrapon, N and Barrera-Redondo, J and Petroll, R and Reynes, L and Choi, SW and Jo, J and Uthanumallian, K and Bogaert, K and Duc, C and Ratchinski, P and Lipinska, A and Noel, B and Murphy, EA and Lohr, M and Khatei, A and Hamon-Giraud, P and Vieira, C and Avia, K and Akerfors, SS and Akita, S and Badis, Y and Barbeyron, T and Belcour, A and Berrabah, W and Blanquart, S and Bouguerba-Collin, A and Bringloe, T and Cattolico, RA and Cormier, A and Cruz de Carvalho, H and Dallet, R and De Clerck, O and Debit, A and Denis, E and Destombe, C and Dinatale, E and Dittami, S and Drula, E and Faugeron, S and Got, J and Graf, L and Groisillier, A and Guillemin, ML and Harms, L and Hatchett, WJ and Henrissat, B and Hoarau, G and Jollivet, C and Jueterbock, A and Kayal, E and Knoll, AH and Kogame, K and Le Bars, A and Leblanc, C and Le Gall, L and Ley, R and Liu, X and LoDuca, ST and Lopez, PJ and Lopez, P and Manirakiza, E and Massau, K and Mauger, S and Mest, L and Michel, G and Monteiro, C and Nagasato, C and Nègre, D and Pelletier, E and Phillips, N and Potin, P and Rensing, SA and Rousselot, E and Rousvoal, S and Schroeder, D and Scornet, D and Siegel, A and Tirichine, L and Tonon, T and Valentin, K and Verbruggen, H and Weinberger, F and Wheeler, G and Kawai, H and Peters, AF and Yoon, HS and Hervé, C and Ye, N and Bapteste, E and Valero, M and Markov, GV and Corre, E and Coelho, SM and Wincker, P and Aury, JM and Cock, JM},
title = {Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems.},
journal = {Cell},
volume = {187},
number = {24},
pages = {6943-6965.e39},
doi = {10.1016/j.cell.2024.10.049},
pmid = {39571576},
issn = {1097-4172},
mesh = {*Phaeophyceae/genetics ; *Ecosystem ; *Phylogeny ; *Genomics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome/genetics ; },
abstract = {Brown seaweeds are keystone species of coastal ecosystems, often forming extensive underwater forests, and are under considerable threat from climate change. In this study, analysis of multiple genomes has provided insights across the entire evolutionary history of this lineage, from initial emergence, through later diversification of the brown algal orders, down to microevolutionary events at the genus level. Emergence of the brown algal lineage was associated with a marked gain of new orthologous gene families, enhanced protein domain rearrangement, increased horizontal gene transfer events, and the acquisition of novel signaling molecules and key metabolic pathways, the latter notably related to biosynthesis of the alginate-based extracellular matrix, and halogen and phlorotannin biosynthesis. We show that brown algal genome diversification is tightly linked to phenotypic divergence, including changes in life cycle strategy and zoid flagellar structure. The study also showed that integration of large viral genomes has had a significant impact on brown algal genome content throughout the emergence of the lineage.},
}

*Phaeophyceae/genetics
*Ecosystem
*Phylogeny
*Genomics
*Evolution, Molecular
Gene Transfer, Horizontal
Genome/genetics

@article {pmid39570883,
year = {2024},
author = {Petersen, M and Reyes-Vigil, F and Campo, M and Brusés, JL},
title = {Classical cadherins evolutionary constraints in primates is associated with their expression in the central nervous system.},
journal = {PloS one},
volume = {19},
number = {11},
pages = {e0313428},
pmid = {39570883},
issn = {1932-6203},
mesh = {Animals ; *Cadherins/genetics/metabolism ; *Primates/genetics ; *Evolution, Molecular ; Mice ; *Central Nervous System/metabolism ; Humans ; Phylogeny ; Selection, Genetic ; },
abstract = {Classical cadherins (CDH) comprise a family of single-pass transmembrane glycoproteins that contribute to tissue morphogenesis by regulating cell-cell adhesion, cytoskeletal dynamics, and cell signaling. CDH are grouped into type I (CDH 1, 2, 3, 4 and 15) and type II (CDH 5, 6, 7, 8, 9, 10, 11, 12, 18, 20, 22 and 24), based on the folding of the cadherin binding domain involved in trans-dimer formation. CDH are exclusively found in metazoans, and the origin and expansion of the gene family coincide with the emergence of multicellularity and vertebrates respectively. This study examined the evolutionary changes of CDH orthologs in primates and the factors that influence selective pressure to investigate the varying constraints exerted among CDH. Pairwise comparisons of the number of amino acid substitutions and of the ratio of non-synonymous substitutions per non-synonymous sites (dN) over synonymous substitutions per synonymous sites (dS), show that CDH2, CDH4, and most type II CDH have been under significantly higher negative selective pressure as compared to CDH1, CDH3, CDH5 and CDH19. Evaluation of gene essentiality as determined by the effect of germline deletion on animal viability, morphogenic phenotype, and reproductive fitness, show no correlation with the with extent of negative selection observed on CDH. Spearman's correlation analysis shows a positive correlation between CDH expression levels (E) in mouse and human tissues and their rate of evolution (R), as observed in most proteins expressed on the cell surface. However, CDH expression in the CNS show a significant E-R negative correlation, indicating that the strong negative selection exerted on CDH2, CDH4, and most type II CDH is associated with their expression in the CNS. CDH participate in a variety of cellular processes in the CNS including neuronal migration and functional assembly of neural circuits, which could profoundly influence animal fitness. Therefore, our findings suggest that the unusually high negative selective pressure exerted on CDH2, CDH4 and most type II CDH is due to their role in CNS formation and function and may have contributed to shape the evolution of the CNS in primates.},
}

Animals
*Cadherins/genetics/metabolism
*Primates/genetics
*Evolution, Molecular
Mice
*Central Nervous System/metabolism
Humans
Phylogeny
Selection, Genetic

@article {pmid39564455,
year = {2024},
author = {Schaap, P},
title = {NOVEL INVENTION OF SPORE INDUCTION IN A SISTER SPECIES TO GROUP 4 DICTYOSTELIA.},
journal = {Open research Europe},
volume = {4},
number = {},
pages = {239},
pmid = {39564455},
issn = {2732-5121},
abstract = {BACKGROUND: Dictyostelia are soil amoebas that aggregate to form fruiting bodies with spores and stalk cells in response to starvation. Where known, species across the dictyostelid phylogeny use secreted cAMP, detected by cAMP receptors (cARs) to induce the differentiation of spores and to organize fruiting body construction. However, recent deletion of the single cAR of Polyspondylium violaceum (Pvio) left both its fruiting bodies and spores intact.

METHODS: To investigate whether Pvio sporulation can occur in the absence of secreted cAMP and to explore alternative inducers in a bioassay , three prespore genes were identified and gene fusions of their promoters with the LacZ reporter gene were transformed into Pvio cells. After assessing the spatial expression pattern of the genes and the stage at which prespore gene expression initiated, the effect of cAMP and other Dictyostelium discoideum (Ddis) signal molecules were tested on prespore gene expression in vitro.

RESULTS: Pvio genes g4562 (psp1), g2696 (psp2) and g2380 (psp3) were identified as homologs of Ddis spore coat genes. They were first expressed around 4 h of starvation in aggregation centres and later in the posterior 4/5 [th] of emerging sorogens and the spore head of early fruiting bodies. Cells from dissociated 4 h aggregates and shaken in suspension for 6 h increased prespore- LacZ reporter activity 4-fold for psp1 and 6-fold for psp2, but this increase was at least 5-fold higher when cells were plated on solid substratum for 6 h to develop normally. cAMP had no effect on prespore gene induction and neither had the Pvio chemoattractant glorin nor the Ddis chemoattractants and differentiation inducers folate, c-di-GMP, DIF-1, GABA, cGMP and 8Br-cAMP.

CONCLUSIONS: The Pvio lineage uniquely evolved a novel genetic network for synthesis, detection and processing of the signal that triggers its main survival strategy.},
}

@article {pmid39543096,
year = {2024},
author = {Gao, Y and Tan, DS and Girbig, M and Hu, H and Zhou, X and Xie, Q and Yeung, SW and Lee, KS and Ho, SY and Cojocaru, V and Yan, J and Hochberg, GKA and de Mendoza, A and Jauch, R},
title = {The emergence of Sox and POU transcription factors predates the origins of animal stem cells.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9868},
pmid = {39543096},
issn = {2041-1723},
support = {C7064-22G//Research Grants Council, University Grants Committee (RGC, UGC)/ ; },
mesh = {Animals ; Mice ; *SOX Transcription Factors/metabolism/genetics ; *Induced Pluripotent Stem Cells/metabolism/cytology ; *SOXB1 Transcription Factors/metabolism/genetics ; POU Domain Factors/metabolism/genetics ; Octamer Transcription Factor-3/metabolism/genetics ; Humans ; Evolution, Molecular ; Phylogeny ; Stem Cells/metabolism/cytology ; Cellular Reprogramming/genetics ; },
abstract = {Stem cells are a hallmark of animal multicellularity. Sox and POU transcription factors are associated with stemness and were believed to be animal innovations, reported absent in their unicellular relatives. Here we describe unicellular Sox and POU factors. Choanoflagellate and filasterean Sox proteins have DNA-binding specificity similar to mammalian Sox2. Choanoflagellate-but not filasterean-Sox can replace Sox2 to reprogram mouse somatic cells into induced pluripotent stem cells (iPSCs) through interacting with the mouse POU member Oct4. In contrast, choanoflagellate POU has a distinct DNA-binding profile and cannot generate iPSCs. Ancestrally reconstructed Sox proteins indicate that iPSC formation capacity is pervasive among resurrected sequences, thus loss of Sox2-like properties fostered Sox family subfunctionalization. Our findings imply that the evolution of animal stem cells might have involved the exaptation of a pre-existing set of transcription factors, where pre-animal Sox was biochemically similar to extant Sox, whilst POU factors required evolutionary innovations.},
}

Animals
Mice
*SOX Transcription Factors/metabolism/genetics
*Induced Pluripotent Stem Cells/metabolism/cytology
*SOXB1 Transcription Factors/metabolism/genetics
POU Domain Factors/metabolism/genetics
Octamer Transcription Factor-3/metabolism/genetics
Humans
Evolution, Molecular
Phylogeny
Stem Cells/metabolism/cytology
Cellular Reprogramming/genetics

@article {pmid39539009,
year = {2024},
author = {Kosztyo, BS and Richards, EJ},
title = {Structural Diversity and Distribution of Nuclear Matrix Constituent Protein Class Nuclear Lamina Proteins in Streptophytic Algae.},
journal = {Genome biology and evolution},
volume = {16},
number = {11},
pages = {},
pmid = {39539009},
issn = {1759-6653},
support = {URoL-2022048//National Science Foundation/ ; },
mesh = {*Streptophyta/metabolism/genetics ; Plant Proteins/genetics/metabolism/chemistry ; Nuclear Lamina/metabolism ; Nuclear Matrix/metabolism ; Algal Proteins/metabolism/chemistry/genetics ; Phylogeny ; Nuclear Proteins/metabolism/genetics/chemistry ; Amino Acid Sequence ; Evolution, Molecular ; Proteome ; },
abstract = {Nuclear matrix constituent proteins in plants function like animal lamins, providing the structural foundation of the nuclear lamina and regulating nuclear organization and morphology. Although they are well characterized in angiosperms, the presence and structure of nuclear matrix constituent proteins in more distantly related species, such as streptophytic algae, are relatively unknown. The rapid evolution of nuclear matrix constituent proteins throughout the plant lineage has caused a divergence in protein sequence that makes similarity-based searches less effective. Structural features are more likely to be conserved compared to primary amino acid sequence; therefore, we developed a filtration protocol to search for diverged nuclear matrix constituent proteins based on four physical characteristics: intrinsically disordered content, isoelectric point, number of amino acids, and the presence of a central coiled-coil domain. By setting parameters to recognize the properties of bona fide nuclear matrix constituent protein proteins in angiosperms, we filtered eight complete proteomes from streptophytic algae species and identified strong nuclear matrix constituent protein candidates in six taxa in the Classes Zygnematophyceae, Charophyceae, and Klebsormidiophyceae. Through analysis of these proteins, we observed structural variance in domain size between nuclear matrix constituent proteins in algae and land plants, as well as a single block of amino acid conservation. Our analysis indicates that nuclear matrix constituent proteins are absent in the Mesostigmatophyceae. The presence versus absence of nuclear matrix constituent protein proteins does not correlate with the distribution of different forms of mitosis (e.g. closed/semi-closed/open) but does correspond to the transition from unicellularity to multicellularity in the streptophytic algae, suggesting that a nuclear matrix constituent protein-based nucleoskeleton plays important roles in supporting cell-to-cell interactions.},
}

*Streptophyta/metabolism/genetics
Plant Proteins/genetics/metabolism/chemistry
Nuclear Lamina/metabolism
Nuclear Matrix/metabolism
Algal Proteins/metabolism/chemistry/genetics
Phylogeny
Nuclear Proteins/metabolism/genetics/chemistry
Amino Acid Sequence
Evolution, Molecular
Proteome

@article {pmid39536081,
year = {2024},
author = {Huang, J and Larmore, CJ and Priest, SJ and Xu, Z and Dietrich, FS and Yadav, V and Magwene, PM and Sun, S and Heitman, J},
title = {Distinct evolutionary trajectories following loss of RNA interference in Cryptococcus neoformans.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {47},
pages = {e2416656121},
pmid = {39536081},
issn = {1091-6490},
support = {R37 AI039115/AI/NIAID NIH HHS/United States ; AI050113-20//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01 AI039115/AI/NIAID NIH HHS/United States ; AI039115-27//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01 AI100272/AI/NIAID NIH HHS/United States ; AI133654-07//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01 AI133654/AI/NIAID NIH HHS/United States ; R01 AI050113/AI/NIAID NIH HHS/United States ; },
mesh = {*Cryptococcus neoformans/genetics ; *RNA Interference ; Evolution, Molecular ; DNA Transposable Elements/genetics ; Retroelements/genetics ; Fungal Proteins/genetics/metabolism ; Loss of Function Mutation ; Mutation ; Drug Resistance, Fungal/genetics ; },
abstract = {While increased mutation rates typically have negative consequences in multicellular organisms, hypermutation can be advantageous for microbes adapting to the environment. Previously, we identified two hypermutator Cryptococcus neoformans clinical isolates that rapidly develop drug resistance due to transposition of a retrotransposon, Cnl1. Cnl1-mediated hypermutation is caused by a nonsense mutation in a gene encoding an RNA interference (RNAi) component, ZNF3, combined with a tremendous transposon burden. To elucidate adaptive mechanisms following RNAi loss, two bioinformatic pipelines were developed to identify RNAi loss-of-function (LOF) mutations in a collection of 387 sequenced C. neoformans isolates. Remarkably, several RNAi-loss isolates were identified that are not hypermutators and have not accumulated transposons. To test whether these RNAi LOF mutations can cause hypermutation, the mutations were introduced into a nonhypermutator strain with a high transposon burden, which resulted in a hypermutator phenotype. To further investigate whether RNAi-loss isolates can become hypermutators, in vitro passaging was performed. Although no hypermutators were found in two C. neoformans RNAi-loss strains after short-term passage, hypermutation was observed in a passaged Cryptococcus deneoformans strain with an increased transposon burden. Consistent with a two-step evolution, when an RNAi-loss isolate was crossed with an isolate containing a high Cnl1 burden, F1 hypermutator progeny inheriting a high transposon burden were identified. In addition to Cnl1 transpositions, insertions of a gigantic DNA transposon KDZ1 (~11 kb) contributed to hypermutation in the progeny. Our results suggest that RNAi loss is relatively common (7/387, ~1.8%) and enables distinct evolutionary trajectories: hypermutation following transposon accumulation or survival without hypermutation.},
}

*Cryptococcus neoformans/genetics
*RNA Interference
Evolution, Molecular
DNA Transposable Elements/genetics
Retroelements/genetics
Fungal Proteins/genetics/metabolism
Loss of Function Mutation
Mutation
Drug Resistance, Fungal/genetics

@article {pmid39515324,
year = {2024},
author = {Smith, ML and Marting, PR and Bailey, CS and Chuttong, B and Maul, ER and Molinari, R and Prathibha, P and Rowe, EB and Spott, MR and Koger, B},
title = {Form, function, and evolutionary origins of architectural symmetry in honey bee nests.},
journal = {Current biology : CB},
volume = {34},
number = {24},
pages = {5813-5821.e5},
doi = {10.1016/j.cub.2024.10.022},
pmid = {39515324},
issn = {1879-0445},
mesh = {Animals ; Bees/physiology/anatomy & histology ; *Nesting Behavior ; *Biological Evolution ; },
abstract = {Symmetry is pervasive across the tree of life,[1][,][2][,][3][,][4][,][5] and organisms (including humans) build symmetrical structures for reproduction, locomotion, or aesthetics.[6][,][7][,][8][,][9] Symmetry, however, does not necessarily span across levels of biological organization (e.g., symmetrical body plans often have asymmetric organs).[10] If and how symmetry exists in structures built by social insect collectives, where there is no blueprint or central organizer, remains an open question.[11] Here, we show that honey bees actively organize nest contents symmetrically on either side of their double-sided comb; 79% ± 7% of cell contents match their backside counterpart, creating a mirror image inside the nest. Experimentally restricting colonies to opposite sides of comb, we find that independent colonies will symmetrically mimic each other's nest organization. We then examine the mechanism by which independent colonies can indirectly coordinate nest symmetry, showing that 100% of colonies (n = 6) perfectly co-localize their brood nest with a randomly positioned heat source, indicating that heat drives nest site initiation and early brood production. Nest symmetry also has adaptive benefits: two-sided nests grow more quickly, rear more brood, and have a more stable thermal environment than one-sided nests do. Finally, examining the evolutionary origins, we show that symmetry persists in three-dimensional (3D) nests of Apis mellifera and across multiple Apis species, coinciding with the onset of double-sided combs, which made it possible to symmetrically stockpile nest contents. This work shows that, similar to molecular mechanisms that create symmetry in multicellular organisms, there are behavioral processes that create functional symmetry in the collective organization of animal architecture.},
}

Animals
Bees/physiology/anatomy & histology
*Nesting Behavior
*Biological Evolution

@article {pmid39508768,
year = {2024},
author = {Lynch, M},
title = {The bioenergetic cost of building a metazoan.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {46},
pages = {e2414742121},
pmid = {39508768},
issn = {1091-6490},
support = {2R35GM122566//HHS | National Institutes of Health (NIH)/ ; R35 GM122566/GM/NIGMS NIH HHS/United States ; IOS-1922914//NSF | BIO | Division of Integrative Organismal Systems (IOS)/ ; BSR 83-06072//NSF | BIO | Division of Environmental Biology (DEB)/ ; 735927//Gordon and Betty Moore Foundation (GBMF)/ ; BSR 89-11038//NSF | BIO | Division of Environmental Biology (DEB)/ ; DBI-2119963//NSF | BIO | Division of Environmental Biology (DEB)/ ; },
mesh = {Animals ; *Energy Metabolism ; *Adenosine Triphosphate/metabolism ; *Biomass ; Daphnia/growth & development/metabolism/physiology ; Phylogeny ; },
abstract = {All life forms depend on the conversion of energy into biomass used in growth and reproduction. For unicellular heterotrophs, the energetic cost associated with building a cell scales slightly sublinearly with cell weight. However, observations on multiple Daphnia species and numerous other metazoans suggest that although a similar size-specific scaling is retained in multicellular heterotrophs, there is a quantum leap in the energy required to build a replacement soma, presumably owing to the added investment in nonproductive features such as cell adhesion, support tissue, and intercellular communication and transport. Thus, any context-dependent ecological advantages that accompany the evolution of multicellularity come at a high baseline bioenergetic cost. At the phylogenetic level, for both unicellular and multicellular eukaryotes, the energetic expense per unit biomass produced declines with increasing adult size of a species, but there is a countergradient scaling within the developmental trajectories of individual metazoan species, with the cost of biomass production increasing with size. Translation of the results into the universal currency of adenosine triphosphate (ATP) hydrolyses provides insight into the demands on the electron-transport/ATP-synthase machinery per organism and on the minimum doubling times for biomass production imposed by the costs of duplicating the energy-producing infrastructure.},
}

Animals
*Energy Metabolism
*Adenosine Triphosphate/metabolism
*Biomass
Daphnia/growth & development/metabolism/physiology
Phylogeny

@article {pmid39508203,
year = {2024},
author = {Neumann, SA and Gaspin, C and Sáez-Vásquez, J},
title = {Plant ribosomes as a score to fathom the melody of 2'-O-methylation across evolution.},
journal = {RNA biology},
volume = {21},
number = {1},
pages = {70-81},
pmid = {39508203},
issn = {1555-8584},
support = {ANR-20-CE12-0024-01//ANR (Agence Nationale de la Recherche) MetRibo/ ; ANR-10-LABX-41//“Laboratoires d’Excellence (LABEX) TULIP/ ; },
mesh = {Methylation ; *Ribosomes/metabolism ; *RNA, Ribosomal/metabolism/genetics/chemistry ; *Plants/metabolism/genetics ; Humans ; Evolution, Molecular ; Methyltransferases/metabolism/genetics/chemistry ; RNA, Plant/metabolism/genetics/chemistry ; Archaea/genetics/metabolism ; RNA, Transfer/metabolism/genetics/chemistry ; },
abstract = {2'-O-ribose methylation (2'-O-Me) is one of the most common RNA modifications detected in ribosomal RNAs (rRNA) from bacteria to eukaryotic cells. 2'-O-Me favours a specific RNA conformation and protects RNA from hydrolysis. Moreover, rRNA 2'-O-Me might stabilize its interactions with messenger RNA (mRNA), transfer RNA (tRNA) or proteins. The extent of rRNA 2'-O-Me fluctuates between species from 3-4 sites in bacteria to tens of sites in archaea, yeast, algae, plants and human. Depending on the organism as well as the rRNA targeting site and position, the 2'-O-Me reaction can be carried out by several site-specific RNA methyltransferases (RMTase) or by a single RMTase associated to specific RNA guides. Here, we review current progresses in rRNA 2'-O-Me (sites/Nm and RMTases) in plants and compare the results with molecular clues from unicellular (bacteria, archaea, algae and yeast) as well as multicellular (human and plants) organisms.},
}

Methylation
*Ribosomes/metabolism
*RNA, Ribosomal/metabolism/genetics/chemistry
*Plants/metabolism/genetics
Humans
Evolution, Molecular
Methyltransferases/metabolism/genetics/chemistry
RNA, Plant/metabolism/genetics/chemistry
Archaea/genetics/metabolism
RNA, Transfer/metabolism/genetics/chemistry

@article {pmid39506108,
year = {2024},
author = {Olivetta, M and Bhickta, C and Chiaruttini, N and Burns, J and Dudin, O},
title = {A multicellular developmental program in a close animal relative.},
journal = {Nature},
volume = {635},
number = {8038},
pages = {382-389},
pmid = {39506108},
issn = {1476-4687},
mesh = {Animals ; Biological Evolution ; *Embryonic Development ; *Eukaryota/classification/cytology/genetics/growth & development ; Gene Expression Profiling ; Single-Cell Analysis ; Transcriptome ; Zygote/cytology/growth & development/metabolism ; *Phylogeny ; Time Factors ; },
abstract = {All animals develop from a single-celled zygote into a complex multicellular organism through a series of precisely orchestrated processes[1,2]. Despite the remarkable conservation of early embryogenesis across animals, the evolutionary origins of how and when this process first emerged remain elusive. Here, by combining time-resolved imaging and transcriptomic profiling, we show that single cells of the ichthyosporean Chromosphaera perkinsii-a close relative that diverged from animals about 1 billion years ago[3,4]-undergo symmetry breaking and develop through cleavage divisions to produce a prolonged multicellular colony with distinct co-existing cell types. Our findings about the autonomous and palintomic developmental program of C. perkinsii hint that such multicellular development either is much older than previously thought or evolved convergently in ichthyosporeans.},
}

Animals
Biological Evolution
*Embryonic Development
*Eukaryota/classification/cytology/genetics/growth & development
Gene Expression Profiling
Single-Cell Analysis
Transcriptome
Zygote/cytology/growth & development/metabolism
*Phylogeny
Time Factors

@article {pmid39499080,
year = {2024},
author = {Smith, OER and Bharat, TAM},
title = {Architectural dissection of adhesive bacterial cell surface appendages from a "molecular machines" viewpoint.},
journal = {Journal of bacteriology},
volume = {206},
number = {12},
pages = {e0029024},
pmid = {39499080},
issn = {1098-5530},
support = {/WT_/Wellcome Trust/United Kingdom ; 223788/WT_/Wellcome Trust/United Kingdom ; MC_UP_1201/31/MRC_/Medical Research Council/United Kingdom ; MC_UP_1201/31//UKRI | Medical Research Council (MRC)/ ; 225317/Z/22/Z//Wellcome Trust (WT)/ ; EP/V026623/1//UK Research and Innovation (UKRI)/ ; Lister Prize//Lister Institute of Preventive Medicine (Lister Institute)/ ; Philip Leverhulme Prize//Leverhulme Trust/ ; EMBO YIP//European Molecular Biology Organization (EMBO)/ ; },
mesh = {*Bacterial Adhesion/physiology ; *Bacteria/metabolism/genetics ; Adhesins, Bacterial/metabolism/genetics ; Biofilms/growth & development ; Bacterial Proteins/metabolism/genetics ; Bacterial Physiological Phenomena ; },
abstract = {The ability of bacteria to interact with and respond to their environment is crucial to their lifestyle and survival. Bacterial cells routinely need to engage with extracellular target molecules, in locations spatially separated from their cell surface. Engagement with distant targets allows bacteria to adhere to abiotic surfaces and host cells, sense harmful or friendly molecules in their vicinity, as well as establish symbiotic interactions with neighboring cells in multicellular communities such as biofilms. Binding to extracellular molecules also facilitates transmission of information back to the originating cell, allowing the cell to respond appropriately to external stimuli, which is critical throughout the bacterial life cycle. This requirement of bacteria to bind to spatially separated targets is fulfilled by a myriad of specialized cell surface molecules, which often have an extended, filamentous arrangement. In this review, we compare and contrast such molecules from diverse bacteria, which fulfil a range of binding functions critical for the cell. Our comparison shows that even though these extended molecules have vastly different sequence, biochemical and functional characteristics, they share common architectural principles that underpin bacterial adhesion in a variety of contexts. In this light, we can consider different bacterial adhesins under one umbrella, specifically from the point of view of a modular molecular machine, with each part fulfilling a distinct architectural role. Such a treatise provides an opportunity to discover fundamental molecular principles governing surface sensing, bacterial adhesion, and biofilm formation.},
}

*Bacterial Adhesion/physiology
*Bacteria/metabolism/genetics
Adhesins, Bacterial/metabolism/genetics
Biofilms/growth & development
Bacterial Proteins/metabolism/genetics
Bacterial Physiological Phenomena

@article {pmid39498496,
year = {2024},
author = {Hojo, H and Tani, S and Ohba, S},
title = {Modeling of skeletal development and diseases using human pluripotent stem cells.},
journal = {Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research},
volume = {40},
number = {1},
pages = {5-19},
pmid = {39498496},
issn = {1523-4681},
support = {20H03885//Japan Society for the Promotion of Science/ ; //Rising Star Award from American Society for Bone and Mineral Research/ ; JP21bm0704071//Japan Agency for Medical Research and Development/ ; JPMJFR225N//Japan Science and Technology Agency/ ; JPMJER2401//JST ERATO program/ ; },
mesh = {Humans ; *Pluripotent Stem Cells/metabolism/cytology ; *Models, Biological ; *Bone Development ; Bone Diseases/pathology ; Bone and Bones/metabolism/embryology ; Animals ; },
abstract = {Human skeletal elements are formed from distinct origins at distinct positions of the embryo. For example, the neural crest produces the facial bones, the paraxial mesoderm produces the axial skeleton, and the lateral plate mesoderm produces the appendicular skeleton. During skeletal development, different combinations of signaling pathways are coordinated from distinct origins during the sequential developmental stages. Models for human skeletal development have been established using human pluripotent stem cells (hPSCs) and by exploiting our understanding of skeletal development. Stepwise protocols for generating skeletal cells from different origins have been designed to mimic developmental trails. Recently, organoid methods have allowed the multicellular organization of skeletal cell types to recapitulate complicated skeletal development and metabolism. Similarly, several genetic diseases of the skeleton have been modeled using patient-derived induced pluripotent stem cells and genome-editing technologies. Model-based drug screening is a powerful tool for identifying drug candidates. This review briefly summarizes our current understanding of the embryonic development of skeletal tissues and introduces the current state-of-the-art hPSC methods for recapitulating skeletal development, metabolism, and diseases. We also discuss the current limitations and future perspectives for applications of the hPSC-based modeling system in precision medicine in this research field.},
}

Humans
*Pluripotent Stem Cells/metabolism/cytology
*Models, Biological
*Bone Development
Bone Diseases/pathology
Bone and Bones/metabolism/embryology
Animals