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

@article {pmid40086443,
year = {2025},
author = {Weiss, B and Rohkin Shalom, S and Dolgova, A and Teh, LS and Kaltenpoth, M and Dale, C and Chiel, E},
title = {Maternal symbiont transmission via envenomation in the parasitoid wasp Spalangia cameroni.},
journal = {Current biology : CB},
volume = {35},
number = {8},
pages = {1693-1705.e4},
doi = {10.1016/j.cub.2025.02.035},
pmid = {40086443},
issn = {1879-0445},
mesh = {Animals ; *Wasps/microbiology/physiology ; *Symbiosis ; Female ; Male ; Larva/microbiology/physiology ; *Wasp Venoms/metabolism ; *Enterobacteriaceae/physiology ; },
abstract = {Microbial symbionts of multicellular hosts originate from free-living ancestors and often persist through vertical transmission, but their mechanisms of establishment are not well understood. Here, we studied acquisition and transmission routes in a nascent symbiosis involving the bacterium Sodalis praecaptivus subsp. spalangiae (Sodalis SC) and the parasitoid wasp Spalangia cameroni. Using fluorescence in situ hybridization, transmission electron microscopy, and experimental infections, we found that oocytes are devoid of Sodalis SC, but the female venom gland is densely colonized. Sodalis SC is injected with the venom into the fly host, subsequently acquired by larval progeny during feeding, invades through the larval gut epithelium into multiple host organs, and eventually localizes in the venom gland. Adult wasps can also acquire Sodalis SC by artificial feeding, but, in this case, the bacterium is not transmitted vertically. Additionally, Sodalis SC is localized in the testes of some males, transmitted paternally at low frequency, and females that inherit Sodalis SC paternally can subsequently transmit it via the venom. To assess the specificity of the symbiosis, we performed experiments with the closely related free-living species Sodalis praecaptivus subsp. praecaptivus (Sodalis PP), known to initiate symbiosis with other insects. Sodalis PP is readily acquired when supplied artificially to wasp larvae but not transmitted to wasp progeny, because it fails to proliferate in the parasitized host. Our results indicate that non-ovarian transmission routes of intracellular symbionts may be more common than currently appreciated and provide a scenario for the early steps in establishing persistent symbiotic associations in insects.},
}

Animals
*Wasps/microbiology/physiology
*Symbiosis
Female
Male
Larva/microbiology/physiology
*Wasp Venoms/metabolism
*Enterobacteriaceae/physiology

@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 = {60},
number = {8},
pages = {1142-1152.e6},
doi = {10.1016/j.devcel.2024.12.022},
pmid = {39793585},
issn = {1878-1551},
mesh = {*Sex Chromosomes/genetics ; Male ; Female ; *Sex Differentiation/genetics ; *Kelp/genetics/growth & development ; Animals ; Transcriptome/genetics ; Sex Determination Processes/genetics ; Gene Expression Regulation, Developmental ; },
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.},
}

*Sex Chromosomes/genetics
Male
Female
*Sex Differentiation/genetics
*Kelp/genetics/growth & development
Animals
Transcriptome/genetics
Sex Determination Processes/genetics
Gene Expression Regulation, Developmental

@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 = {47},
number = {5},
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/ ; },
mesh = {*RNA Editing/genetics ; Animals ; *Fungi/genetics ; *Adenosine/genetics/metabolism ; *Inosine/genetics/metabolism ; *Evolution, Molecular ; *Biological Evolution ; Adaptation, Physiological/genetics ; },
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.},
}

*RNA Editing/genetics
Animals
*Fungi/genetics
*Adenosine/genetics/metabolism
*Inosine/genetics/metabolism
*Evolution, Molecular
*Biological Evolution
Adaptation, Physiological/genetics

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

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

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

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

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

@article {pmid39603922,
year = {2025},
author = {Ryu, J and Kim, Y and Ju, YS},
title = {A more elaborate genetic clock for clonal species.},
journal = {Trends in genetics : TIG},
volume = {41},
number = {4},
pages = {268-270},
doi = {10.1016/j.tig.2024.11.002},
pmid = {39603922},
issn = {0168-9525},
mesh = {*Evolution, Molecular ; *Reproduction, Asexual/genetics ; Animals ; },
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.},
}

*Evolution, Molecular
*Reproduction, Asexual/genetics
Animals

@article {pmid39999802,
year = {2025},
author = {Saier, MH},
title = {Cooperation and Competition Were Primary Driving Forces for Biological Evolution.},
journal = {Microbial physiology},
volume = {35},
number = {1},
pages = {13-29},
doi = {10.1159/000544890},
pmid = {39999802},
issn = {2673-1673},
mesh = {*Biological Evolution ; Humans ; Symbiosis ; Animals ; Cooperative Behavior ; },
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 of 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).},
}

*Biological Evolution
Humans
Symbiosis
Animals
Cooperative Behavior

@article {pmid40181506,
year = {2025},
author = {Lewis, EM and Becker, O and Symons, AN and LaCoss, C and Baclig, AJ and Guzman, A and Sanders, C and Gonzalez, L and Warner, LR and Lewis, K},
title = {The LARP6 La module from Tetrabaena socialis reveals structural and functional differences from plant and animal LARP6 homologues.},
journal = {RNA biology},
volume = {},
number = {},
pages = {},
doi = {10.1080/15476286.2025.2489303},
pmid = {40181506},
issn = {1555-8584},
abstract = {This study identified the LARP6 La Module from Tetrabaena socialis (T. socialis), a four-celled green algae, in an effort to better understand the evolution of LARP6 structure and RNA binding activity in multicellular eukaryotes. Using a combination of sequence alignments, domain boundary screens, and structural modelling, we recombinantly expressed and isolated the TsLARP6 La Module to > 98% purity for in vitro biochemical characterization. The La Module is stably folded and exerts minimal RNA binding activity against single-stranded homopolymeric RNAs. Surprisingly, it exhibits low micromolar binding affinity for the vertebrate LARP6 cognate ligand, a bulged-stem loop found in the 5'UTR of collagen type I mRNA, but does not bind double-stranded RNAs of similar size. These result suggests that the TsLARP6 La Module may prefer structured RNA ligands. In contrast, however, the TsLARP6 La Module does not exhibit the RNA chaperone activity that is observed in vertebrate homologs. Therefore, we conclude that protist LARP6 May have both distinct RNA ligands and binding mechanisms from the previously characterized LARP6 proteins of animals and vascular plants, thus establishing a distinct third class of the LARP6 protein family.},
}

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

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

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

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

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

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

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

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

@article {pmid38951023,
year = {2025},
author = {Brückner, DB and Hannezo, E},
title = {Tissue Active Matter: Integrating Mechanics and Signaling into Dynamical Models.},
journal = {Cold Spring Harbor perspectives in biology},
volume = {17},
number = {4},
pages = {},
pmid = {38951023},
issn = {1943-0264},
mesh = {*Models, Biological ; *Signal Transduction ; *Morphogenesis ; Animals ; Biomechanical Phenomena ; Humans ; Cell Movement ; },
abstract = {The importance of physical forces in the morphogenesis, homeostatic function, and pathological dysfunction of multicellular tissues is being increasingly characterized, both theoretically and experimentally. Analogies between biological systems and inert materials such as foams, gels, and liquid crystals have provided striking insights into the core design principles underlying multicellular organization. However, these connections can seem surprising given that a key feature of multicellular systems is their ability to constantly consume energy, providing an active origin for the forces that they produce. Key emerging questions are, therefore, to understand whether and how this activity grants tissues novel properties that do not have counterparts in classical materials, as well as their consequences for biological function. Here, we review recent discoveries at the intersection of active matter and tissue biology, with an emphasis on how modeling and experiments can be combined to understand the dynamics of multicellular systems. These approaches suggest that a number of key biological tissue-scale phenomena, such as morphogenetic shape changes, collective migration, or fate decisions, share unifying design principles that can be described by physical models of tissue active matter.},
}

*Models, Biological
*Signal Transduction
*Morphogenesis
Animals
Biomechanical Phenomena
Humans
Cell Movement

@article {pmid40112176,
year = {2025},
author = {Matthews, S and Nikoonejad Fard, V and Tollis, M and Seoighe, C},
title = {Variable Gene Copy Number in Cancer-Related Pathways Is Associated With Cancer Prevalence Across Mammals.},
journal = {Molecular biology and evolution},
volume = {42},
number = {3},
pages = {},
pmid = {40112176},
issn = {1537-1719},
support = {U54 CA217376/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; *Neoplasms/genetics ; *Mammals/genetics ; Gene Dosage ; Longevity/genetics ; DNA Copy Number Variations ; Body Size/genetics ; Phylogeny ; Prevalence ; },
abstract = {Cancer is a disease of multicellularity, observed across the tree of life. In principle, animals with larger body sizes and longer lifespans should be at increased risk of developing cancer. However, there is no strong relationship between these traits and cancer across mammals. Previous studies have proposed that increased copy number of cancer-related genes may enhance the robustness of cancer suppression pathways in long-lived mammals, but these studies have not extended beyond known cancer-related genes. In this study, we conducted a phylogenetic generalized least squares analysis to test for associations between copy number of all protein-coding genes and longevity, body size, and cancer prevalence across 94 species of mammals. In addition to investigating the copy number of individual genes, we tested sets of related genes for a relationship between the aggregated gene copy number of the set and these traits. We did not find strong evidence to support the hypothesis that adaptive changes in gene copy number contribute to the lack of correlation between cancer prevalence and body size or lifespan. However, we found several biological processes where aggregate copy number was associated with malignancy rate. The strongest association was for the gene set relating to transforming growth factor beta, a cytokine that plays a role in cancer progression. Overall, this study provides a comprehensive evaluation of the role of gene copy number in adaptation to body size and lifespan and sheds light on the contribution of gene copy number to variation in cancer prevalence across mammals.},
}

Animals
*Neoplasms/genetics
*Mammals/genetics
Gene Dosage
Longevity/genetics
DNA Copy Number Variations
Body Size/genetics
Phylogeny
Prevalence

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

@article {pmid39998200,
year = {2025},
author = {Hu, P},
title = {mSphere of Influence: Rapid evolution of pathogenesis and drug resistance in human pathogenic fungi.},
journal = {mSphere},
volume = {10},
number = {3},
pages = {e0057024},
pmid = {39998200},
issn = {2379-5042},
mesh = {Humans ; *Drug Resistance, Fungal/genetics ; Virulence ; Antifungal Agents/pharmacology ; Cryptococcus/genetics/pathogenicity/drug effects ; Fungi/genetics/pathogenicity/drug effects ; Candida/genetics/drug effects/pathogenicity ; Evolution, Molecular ; DNA Transposable Elements/genetics ; Mycoses/microbiology ; },
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.},
}

Humans
*Drug Resistance, Fungal/genetics
Virulence
Antifungal Agents/pharmacology
Cryptococcus/genetics/pathogenicity/drug effects
Fungi/genetics/pathogenicity/drug effects
Candida/genetics/drug effects/pathogenicity
Evolution, Molecular
DNA Transposable Elements/genetics
Mycoses/microbiology

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

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

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

*Isoptera/physiology
Animals
*Social Behavior
Reproduction/physiology

@article {pmid40052705,
year = {2025},
author = {Kataki, AD and Gupta, PG and Cheema, U and Nisbet, A and Wang, Y and Kocher, HM and Pérez-Mancera, PA and Velliou, EG},
title = {Mapping Tumor-Stroma-ECM Interactions in Spatially Advanced 3D Models of Pancreatic Cancer.},
journal = {ACS applied materials & interfaces},
volume = {17},
number = {11},
pages = {16708-16724},
doi = {10.1021/acsami.5c02296},
pmid = {40052705},
issn = {1944-8252},
mesh = {Humans ; *Pancreatic Neoplasms/pathology/metabolism ; *Extracellular Matrix/metabolism ; *Tumor Microenvironment ; *Stromal Cells/pathology/metabolism ; *Tissue Scaffolds/chemistry ; Cell Line, Tumor ; Carcinoma, Pancreatic Ductal/pathology/metabolism ; Polyurethanes/chemistry ; Extracellular Matrix Proteins/metabolism ; },
abstract = {Bioengineering-based in vitro tumor models are increasingly important as tools for studying disease progression and therapy response for many cancers, including the deadly pancreatic ductal adenocarcinoma (PDAC) that exhibits a tumor/tissue microenvironment of high cellular/biochemical complexity. Therefore, it is crucial for in vitro models to capture that complexity and to enable investigation of the interplay between cancer cells and factors such as extracellular matrix (ECM) proteins or stroma cells. Using polyurethane (PU) scaffolds, we performed a systematic study on how different ECM protein scaffold coatings impact the long-term cell evolution in scaffolds containing only cancer or only stroma cells (activated stellate and endothelial cells). To investigate potential further changes in those biomarkers due to cancer-stroma interactions, we mapped their expression in dual/zonal scaffolds consisting of a cancer core and a stroma periphery, spatially mimicking the fibrotic/desmoplastic reaction in PDAC. In our single scaffolds, we observed that the protein coating affected the cancer cell spatial aggregation, matrix deposition, and biomarker upregulation in a cell-line-dependent manner. In single stroma scaffolds, different levels of fibrosis/desmoplasia in terms of ECM composition/quantity were generated depending on the ECM coating. When studying the evolution of cancer and stroma cells in our dual/zonal model, biomarkers linked to cell aggressiveness/invasiveness were further upregulated by both cancer and stroma cells as compared to single scaffold models. Collectively, our study advances the understanding of how different ECM proteins impact the long-term cell evolution in PU scaffolds. Our findings show that within our bioengineered models, we can stimulate the cells of the PDAC microenvironment to develop different levels of aggressiveness/invasiveness, as well as different levels of fibrosis. Furthermore, we highlight the importance of considering spatial complexity to map cell invasion. Our work contributes to the design of in vitro models with variable, yet biomimetic, tissue-like properties for studying the tumor microenvironment's role in cancer progression.},
}

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

@article {pmid40106424,
year = {2025},
author = {Wright, BA and Osigus, HJ and Schmidt, MJ and Ratcliffe, J and Kamm, K and Martinez-Ortiz, GC and Rehn, M and Kvansakul, M and Schierwater, B and Humbert, PO},
title = {Tolerance of Placozoa for temperate climates: Evidence for known and new placozoan clades in the southern waters of Australia.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0317878},
doi = {10.1371/journal.pone.0317878},
pmid = {40106424},
issn = {1932-6203},
mesh = {Animals ; *Placozoa/genetics/classification ; Haplotypes ; Phylogeny ; Australia ; Climate ; Genetic Variation ; },
abstract = {Placozoans are small multicellular sea-dwelling animals that are typically found in shallow, warm ocean waters and have been reported in various marine environments worldwide. Their unique morphology makes them a powerful new model organism to study the evolutionary cell biology in early metazoans. Yet, knowledge on their biodiversity and ecological distribution is severely limited. Here, we report the isolation of placozoans in the temperate waters of Victoria, Australia, their most southern location known to date. Using light, electron, and confocal microscopy, we describe their morphology and behaviour. In addition to the known haplotypes H2 and H17, we have identified a new haplotype, here designated as H20, which defines a new placozoan clade. This study provides novel insights into the distribution, ecological niche separation and genetic diversity of placozoans, and reports the first morphological and ultrastructural characterisation of placozoan clades isolated from the southern waters of Victoria, Australia.},
}

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

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

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

@article {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 = {26},
number = {3},
pages = {1860-1872},
doi = {10.1021/acs.biomac.4c01627},
pmid = {39898884},
issn = {1526-4602},
mesh = {*Hydrogels/chemistry/pharmacology ; *Organoids/cytology ; *Spheroids, Cellular/cytology ; Humans ; Extracellular Matrix/chemistry ; Intestines/cytology ; Cell Proliferation/drug effects ; Animals ; Oxazoles/chemistry ; Cell Culture Techniques, Three Dimensional/methods ; Cell Culture Techniques/methods ; },
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.},
}

*Hydrogels/chemistry/pharmacology
*Organoids/cytology
*Spheroids, Cellular/cytology
Humans
Extracellular Matrix/chemistry
Intestines/cytology
Cell Proliferation/drug effects
Animals
Oxazoles/chemistry
Cell Culture Techniques, Three Dimensional/methods
Cell Culture Techniques/methods

@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 {pmid39617193,
year = {2025},
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},
mesh = {*Glycerol/pharmacology ; *Cryopreservation/methods ; *Cryoprotective Agents/pharmacology ; *Choanoflagellata/drug effects ; *Dimethyl Sulfoxide/pharmacology ; Cell Survival/drug effects ; },
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.},
}

*Glycerol/pharmacology
*Cryopreservation/methods
*Cryoprotective Agents/pharmacology
*Choanoflagellata/drug effects
*Dimethyl Sulfoxide/pharmacology
Cell Survival/drug effects

@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 {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},
mesh = {Animals ; *Gene Expression Regulation/genetics ; *Promoter Regions, Genetic ; Drosophila/genetics ; Genome/genetics ; Humans ; Transcription, Genetic ; Mammals/genetics ; Evolution, Molecular ; },
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.},
}

Animals
*Gene Expression Regulation/genetics
*Promoter Regions, Genetic
Drosophila/genetics
Genome/genetics
Humans
Transcription, Genetic
Mammals/genetics
Evolution, Molecular

@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 {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 {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 {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},
mesh = {Humans ; *Lab-On-A-Chip Devices ; Drug Discovery ; Animals ; Microphysiological Systems ; },
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.},
}

Humans
*Lab-On-A-Chip Devices
Drug Discovery
Animals
Microphysiological Systems

@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 {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 = {152},
number = {3},
pages = {},
doi = {10.1242/dev.204411},
pmid = {39817858},
issn = {1477-9129},
support = {IOS 1931114//National Science Foundation/ ; NSF DMS 1764421//Northwestern University/ ; SFARI 597491-RWC//Simons Foundation/ ; R01GM157611/GM/NIGMS NIH HHS/United States ; },
mesh = {*Meristem/cytology/metabolism/growth & development ; Pteridaceae/metabolism/genetics ; Cell Lineage ; Germ Cells, Plant/cytology/metabolism/growth & development ; Cell Division ; },
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, although 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 suggested 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 that 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.},
}

*Meristem/cytology/metabolism/growth & development
Pteridaceae/metabolism/genetics
Cell Lineage
Germ Cells, Plant/cytology/metabolism/growth & development
Cell Division

@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 {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 {pmid39737561,
year = {2025},
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 = {245},
number = {5},
pages = {2004-2015},
doi = {10.1111/nph.20372},
pmid = {39737561},
issn = {1469-8137},
mesh = {*Cell Division/genetics ; *Cell Lineage/genetics ; *Gene Expression Regulation, Plant ; *Plant Proteins/genetics/metabolism ; *Germ Cells, Plant/growth & development/cytology ; *Bryopsida/genetics/growth & development/cytology ; *Genes, Plant ; Transcription Factors/genetics/metabolism ; Ovule/genetics/growth & development/cytology ; Mutation/genetics ; Pollen/genetics/cytology/growth & development ; },
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.},
}

*Cell Division/genetics
*Cell Lineage/genetics
*Gene Expression Regulation, Plant
*Plant Proteins/genetics/metabolism
*Germ Cells, Plant/growth & development/cytology
*Bryopsida/genetics/growth & development/cytology
*Genes, Plant
Transcription Factors/genetics/metabolism
Ovule/genetics/growth & development/cytology
Mutation/genetics
Pollen/genetics/cytology/growth & development

@article {pmid39653763,
year = {2025},
author = {Forrester, JV and McMenamin, PG},
title = {Evolution of the ocular immune system.},
journal = {Eye (London, England)},
volume = {39},
number = {3},
pages = {468-477},
pmid = {39653763},
issn = {1476-5454},
mesh = {Humans ; Animals ; *Biological Evolution ; *Eye/immunology ; *Immune System/physiology/immunology ; *Immunity, Innate/physiology ; Adaptive Immunity ; },
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).},
}

Humans
Animals
*Biological Evolution
*Eye/immunology
*Immune System/physiology/immunology
*Immunity, Innate/physiology
Adaptive Immunity

@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 {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 {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 {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 {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 {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 {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 {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},
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 {pmid39445720,
year = {2025},
author = {Compton, ZT and Mellon, W and Harris, VK and Rupp, S and Mallo, D and Kapsetaki, SE and Wilmot, M and Kennington, R and Noble, K and Baciu, C and Ramirez, LN and Peraza, A and Martins, B and Sudhakar, S and Aksoy, S and Furukawa, G and Vincze, O and Giraudeau, M and Duke, EG and Spiro, S and Flach, E and Davidson, H and Li, CI and Zehnder, A and Graham, TA and Troan, BV and Harrison, TM and Tollis, M and Schiffman, JD and Aktipis, CA and Abegglen, LM and Maley, CC and Boddy, AM},
title = {Cancer Prevalence across Vertebrates.},
journal = {Cancer discovery},
volume = {15},
number = {1},
pages = {227-244},
doi = {10.1158/2159-8290.CD-24-0573},
pmid = {39445720},
issn = {2159-8290},
support = {P01 CA091955/CA/NCI NIH HHS/United States ; OTKA K143421//Agence Nationale de la Recherche (ANR)/ ; U54 CA217376/CA/NCI NIH HHS/United States ; ADHS18-198847//Arizona Biomedical Research Commission (ABRC)/ ; U2C CA233254/CA/NCI NIH HHS/United States ; //Hyundai Hope On Wheels (Hope On Wheels)/ ; BC132057//Congressionally Directed Medical Research Programs (CDMRP)/ ; R01 CA140657/CA/NCI NIH HHS/United States ; R21 CA257980/CA/NCI NIH HHS/United States ; T32 CA272303/CA/NCI NIH HHS/United States ; COVER ANR-23-CE02-0019//Agence Nationale de la Recherche (ANR)/ ; U54 CA217376/CA/NCI NIH HHS/United States ; T32 CA272303/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; *Neoplasms/epidemiology/genetics ; Prevalence ; *Vertebrates ; Humans ; },
abstract = {Cancer is pervasive across multicellular species, but what explains the differences in cancer prevalence across species? Using 16,049 necropsy records for 292 species spanning three clades of tetrapods (amphibians, sauropsids, and mammals), we found that neoplasia and malignancy prevalence increases with adult mass (contrary to Peto's paradox) and somatic mutation rate but decreases with gestation time. The relationship between adult mass and malignancy prevalence was only apparent when we controlled for gestation time. Evolution of cancer susceptibility appears to have undergone sudden shifts followed by stabilizing selection. Outliers for neoplasia prevalence include the common porpoise (<1.3%), the Rodrigues fruit bat (<1.6%), the black-footed penguin (<0.4%), ferrets (63%), and opossums (35%). Discovering why some species have particularly high or low levels of cancer may lead to a better understanding of cancer syndromes and novel strategies for the management and prevention of cancer. Significance: Evolution has discovered mechanisms for suppressing cancer in a wide variety of species. By analyzing veterinary necropsy records, we can identify species with exceptionally high or low cancer prevalence. Discovering the mechanisms of cancer susceptibility and resistance may help improve cancer prevention and explain cancer syndromes. See related commentary by Metzger, p. 14.},
}

Animals
*Neoplasms/epidemiology/genetics
Prevalence
*Vertebrates
Humans

@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 {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},
doi = {10.1126/sciadv.adr7434},
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 {pmid39242229,
year = {2025},
author = {Araujo, G and Montoya, JM and Thomas, T and Webster, NS and Lurgi, M},
title = {A mechanistic framework for complex microbe-host symbioses.},
journal = {Trends in microbiology},
volume = {33},
number = {1},
pages = {96-111},
doi = {10.1016/j.tim.2024.08.002},
pmid = {39242229},
issn = {1878-4380},
mesh = {*Symbiosis ; *Microbiota/physiology ; *Host Microbial Interactions/physiology ; *Biological Evolution ; Animals ; Humans ; Bacteria/genetics/classification ; Biodiversity ; Models, Biological ; },
abstract = {Virtually all multicellular organisms on Earth live in symbiotic associations with complex microbial communities: the microbiome. This ancient relationship is of fundamental importance for both the host and the microbiome. Recently, the analyses of numerous microbiomes have revealed an incredible diversity and complexity of symbionts, with different mechanisms identified as potential drivers of this diversity. However, the interplay of ecological and evolutionary forces generating these complex associations is still poorly understood. Here we explore and summarise the suite of ecological and evolutionary mechanisms identified as relevant to different aspects of microbiome complexity and diversity. We argue that microbiome assembly is a dynamic product of ecology and evolution at various spatio-temporal scales. We propose a theoretical framework to classify mechanisms and build mechanistic host-microbiome models to link them to empirical patterns. We develop a cohesive foundation for the theoretical understanding of the combined effects of ecology and evolution on the assembly of complex symbioses.},
}

*Symbiosis
*Microbiota/physiology
*Host Microbial Interactions/physiology
*Biological Evolution
Animals
Humans
Bacteria/genetics/classification
Biodiversity
Models, Biological

@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 = {},
doi = {10.1101/2024.12.22.629997},
pmid = {39763889},
issn = {2692-8205},
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 {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 = {Humans ; *Adaptation, Physiological/genetics ; *Biological Evolution ; Mitochondria/genetics/metabolism ; Selection, Genetic/genetics ; Animals ; Evolution, Molecular ; },
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.},
}

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

@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

@article {pmid39486632,
year = {2025},
author = {Barlow, LA},
title = {Development of ectodermal and endodermal taste buds.},
journal = {Developmental biology},
volume = {518},
number = {},
pages = {20-27},
pmid = {39486632},
issn = {1095-564X},
mesh = {Animals ; *Taste Buds/embryology ; *Ectoderm/embryology/metabolism ; *Endoderm/embryology ; Tongue/embryology ; Humans ; Gene Expression Regulation, Developmental ; },
abstract = {The sense of taste is mediated primarily by taste buds on the tongue. These multicellular sensory organs are induced, patterned and become innervated during embryogenesis such that a functional taste system is present at birth when animals begin to feed. While taste buds have been considered ectodermal appendages, this is only partly accurate as only fungiform taste buds in the anterior tongue arise from the ectoderm. Taste buds found in the posterior tongue actually derive from endoderm. Nonetheless, both anterior and posterior buds are functionally similar, despite their disparate embryonic origins. In this review, I compare the development of ectodermal vs endodermal taste buds, highlighting the many differences in the cellular and molecular genetic mechanisms governing their formation.},
}

Animals
*Taste Buds/embryology
*Ectoderm/embryology/metabolism
*Endoderm/embryology
Tongue/embryology
Humans
Gene Expression Regulation, Developmental

@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 = {*Synthetic Biology/methods ; Humans ; Models, Biological ; Bioengineering/methods ; Biological Evolution ; Animals ; 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.},
}

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

@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 {pmid39414948,
year = {2025},
author = {Laisné, M and Lupien, M and Vallot, C},
title = {Epigenomic heterogeneity as a source of tumour evolution.},
journal = {Nature reviews. Cancer},
volume = {25},
number = {1},
pages = {7-26},
pmid = {39414948},
issn = {1474-1768},
mesh = {Humans ; *Neoplasms/genetics/pathology ; *Epigenesis, Genetic ; *Epigenomics ; *Genetic Heterogeneity ; Animals ; },
abstract = {In the past decade, remarkable progress in cancer medicine has been achieved by the development of treatments that target DNA sequence variants. However, a purely genetic approach to treatment selection is hampered by the fact that diverse cell states can emerge from the same genotype. In multicellular organisms, cell-state heterogeneity is driven by epigenetic processes that regulate DNA-based functions such as transcription; disruption of these processes is a hallmark of cancer that enables the emergence of defective cell states. Advances in single-cell technologies have unlocked our ability to quantify the epigenomic heterogeneity of tumours and understand its mechanisms, thereby transforming our appreciation of how epigenomic changes drive cancer evolution. This Review explores the idea that epigenomic heterogeneity and plasticity act as a reservoir of cell states and therefore as a source of tumour evolution. Best practices to quantify epigenomic heterogeneity and explore its various causes and consequences are discussed, including epigenomic reprogramming, stochastic changes and lasting memory. The design of new therapeutic approaches to restrict epigenomic heterogeneity, with the long-term objective of limiting cancer development and progression, is also addressed.},
}

Humans
*Neoplasms/genetics/pathology
*Epigenesis, Genetic
*Epigenomics
*Genetic Heterogeneity
Animals

@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 {pmid39460541,
year = {2024},
author = {Symonds, K and Wali, U and Duff, L and Snedden, WA},
title = {Characterization of the Calmodulin-Like Protein Family in Chara braunii and their Conserved Interaction with the Calmodulin-Binding Transcription Activator Family.},
journal = {Plant & cell physiology},
volume = {65},
number = {12},
pages = {2040-2053},
doi = {10.1093/pcp/pcae127},
pmid = {39460541},
issn = {1471-9053},
support = {RGPIN-2018-04928, RGPIN-2017-04551//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {*Calmodulin/metabolism/genetics ; *Plant Proteins/metabolism/genetics ; *Calcium/metabolism ; *Chara/metabolism/genetics ; Phylogeny ; Amino Acid Sequence ; Protein Binding ; Calmodulin-Binding Proteins/metabolism/genetics ; Protein Isoforms/metabolism/genetics ; },
abstract = {Calcium sensor proteins play important roles by detecting changes in intracellular calcium and relaying that information onto downstream targets through protein-protein interaction. Very little is known about calcium sensors from plant species that predate land colonization and the evolution of embryophytes. Here, we examined the genome of the multicellular algae, Chara braunii, for orthologs to the evolutionarily conserved calcium sensor calmodulin (CaM) and for CaM-like (CML) proteins. We identified one CaM and eight CML isoforms that range in size from 16.4 to 21.3 kDa and are predicted to have between two to four calcium-binding (EF-hand) domains. Using recombinant protein, we tested whether CbCaM and CbCML1-CbCML7 possess biochemical properties of typical calcium sensors. CbCaM and the CbCMLs all displayed high-affinity calcium binding with estimated global KD,app values in the physiological µM range. In response to calcium binding, CbCaM and the CbCMLs exhibited varying degrees of increase in exposed hydrophobicity, suggesting that different calcium-induced conformational changes occur among isoforms. We found many examples of putative CaM targets encoded in the C. braunii genome and explored the ability of CbCaM and CbCMLs to interact in planta with a representative putative target, a C. braunii CaM-binding transcription factor (CbCAMTA1). CbCaM, CbCML2 and CbCML4 each associated with the C-terminal region of CbCAMTA1. Collectively, our data support the hypothesis that complex calcium signaling and sensing networks involving CaM and CMLs evolved early in the green lineage. Similarly, it seems likely that calcium-mediated regulation of transcription occurs in C. braunii via CAMTAs and is an ancient trait predating embryophytic emergence.},
}

*Calmodulin/metabolism/genetics
*Plant Proteins/metabolism/genetics
*Calcium/metabolism
*Chara/metabolism/genetics
Phylogeny
Amino Acid Sequence
Protein Binding
Calmodulin-Binding Proteins/metabolism/genetics
Protein Isoforms/metabolism/genetics

@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 ; *Embryonic Development/genetics ; Biomechanical Phenomena ; Body Patterning ; Morphogenesis ; Embryo, Nonmammalian ; },
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
*Embryonic Development/genetics
Biomechanical Phenomena
Body Patterning
Morphogenesis
Embryo, Nonmammalian

@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 {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 {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 = {},
doi = {10.7554/eLife.93168},
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 {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},
doi = {10.1002/ece3.70661},
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 = {2024},
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 = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.10.075},
pmid = {39642877},
issn = {1879-0445},
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.},
}

@article {pmid39288541,
year = {2024},
author = {Wen, T and Cheong, KH},
title = {Parrondo's paradox reveals counterintuitive wins in biology and decision making in society.},
journal = {Physics of life reviews},
volume = {51},
number = {},
pages = {33-59},
doi = {10.1016/j.plrev.2024.08.002},
pmid = {39288541},
issn = {1873-1457},
mesh = {Humans ; Animals ; *Decision Making ; Biological Evolution ; Ecosystem ; Biology ; },
abstract = {Parrondo's paradox refers to the paradoxical phenomenon of combining two losing strategies in a certain manner to obtain a winning outcome. It has been applied to uncover unexpected outcomes across various disciplines, particularly at different spatiotemporal scales within ecosystems. In this article, we provide a comprehensive review of recent developments in Parrondo's paradox within the interdisciplinary realm of the physics of life, focusing on its significant applications across biology and the broader life sciences. Specifically, we examine its relevance from genetic pathways and phenotypic regulation, to intercellular interaction within multicellular organisms, and finally to the competition between populations and species in ecosystems. This phenomenon, spanning multiple biological domains and scales, enhances our understanding of the unified characteristics of life and reveals that adaptability in a drastically changing environment, rather than the inherent excellence of a trait, underpins survival in the process of evolution. We conclude by summarizing our findings and discussing future research directions that hold promise for advancing the field.},
}

Humans
Animals
*Decision Making
Biological Evolution
Ecosystem
Biology

@article {pmid39628612,
year = {2022},
author = {Durairaj, P and Li, S},
title = {Functional expression and regulation of eukaryotic cytochrome P450 enzymes in surrogate microbial cell factories.},
journal = {Engineering microbiology},
volume = {2},
number = {1},
pages = {100011},
pmid = {39628612},
issn = {2667-3703},
abstract = {Cytochrome P450 (CYP) enzymes play crucial roles during the evolution and diversification of ancestral monocellular eukaryotes into multicellular eukaryotic organisms due to their essential functionalities including catalysis of housekeeping biochemical reactions, synthesis of diverse metabolites, detoxification of xenobiotics, and contribution to environmental adaptation. Eukaryotic CYPs with versatile functionalities are undeniably regarded as promising biocatalysts with great potential for biotechnological, pharmaceutical and chemical industry applications. Nevertheless, the modes of action and the challenges associated with these membrane-bound proteins have hampered the effective utilization of eukaryotic CYPs in a broader range. This review is focused on comprehensive and consolidated approaches to address the core challenges in heterologous expression of membrane-bound eukaryotic CYPs in different surrogate microbial cell factories, aiming to provide key insights for better studies and applications of diverse eukaryotic CYPs in the future. We also highlight the functional significance of the previously underrated cytochrome P450 reductases (CPRs) and provide a rational justification on the progression of CPR from auxiliary redox partner to function modulator in CYP catalysis.},
}

@article {pmid39454678,
year = {2024},
author = {Wu, J and Gupta, G and Buerki-Thurnherr, T and Nowack, B and Wick, P},
title = {Bridging the gap: Innovative human-based in vitro approaches for nanomaterials hazard assessment and their role in safe and sustainable by design, risk assessment, and life cycle assessment.},
journal = {NanoImpact},
volume = {36},
number = {},
pages = {100533},
doi = {10.1016/j.impact.2024.100533},
pmid = {39454678},
issn = {2452-0748},
mesh = {Humans ; *Nanostructures/toxicity/adverse effects ; Risk Assessment ; Toxicity Tests/methods ; },
abstract = {The application of nanomaterials in industry and consumer products is growing exponentially, which has pressed the development and use of predictive human in vitro models in pre-clinical analysis to closely extrapolate potential toxic effects in vivo. The conventional cytotoxicity investigation of nanomaterials using cell lines from cancer origin and culturing them two-dimensionally in a monolayer without mimicking the proper pathophysiological microenvironment may affect a precise prediction of in vitro effects at in vivo level. In recent years, complex in vitro models (also belonging to the new approach methodologies, NAMs) have been established in unicellular to multicellular cultures either by using cell lines, primary cells or induced pluripotent stem cells (iPSCs), and reconstituted into relevant biological dimensions mimicking in vivo conditions. These advanced in vitro models retain physiologically reliant exposure scenarios particularly appropriate for oral, dermal, respiratory, and intravenous administration of nanomaterials, which have the potential to improve the in vivo predictability and lead to reliable outcomes. In this perspective, we discuss recent developments and breakthroughs in using advanced human in vitro models for hazard assessment of nanomaterials. We identified fit-for-purpose requirements and remaining challenges for the successful implementation of in vitro data into nanomaterials Safe and Sustainable by Design (SSbD), Risk Assessment (RA), and Life Cycle Assessment (LCA). By addressing the gap between in vitro data generation and the utility of in vitro data for nanomaterial safety assessments, a prerequisite for SSbD approaches, we outlined potential key areas for future development.},
}

Humans
*Nanostructures/toxicity/adverse effects
Risk Assessment
Toxicity Tests/methods

@article {pmid39427812,
year = {2024},
author = {Dvořáček, J and Kodrík, D},
title = {Brain and cognition: The need for a broader biological perspective to overcome old biases.},
journal = {Neuroscience and biobehavioral reviews},
volume = {167},
number = {},
pages = {105928},
doi = {10.1016/j.neubiorev.2024.105928},
pmid = {39427812},
issn = {1873-7528},
mesh = {*Cognition/physiology ; *Brain/physiology ; Animals ; Humans ; *Biological Evolution ; Neurons/physiology ; Intelligence/physiology ; },
abstract = {Even with accumulating knowledge, no consensus regarding the understanding of intelligence or cognition exists, and the universal brain bases for these functions remain unclear. Traditionally, our understanding of cognition is based on self-evident principles that appear indisputable when looking only at our species; however, this can distance us from understanding its essence (anthropocentrism, corticocentrism, intellectocentrism, neurocentrism, and idea of orthogenesis of brain evolution). Herein, we use several examples from biology to demonstrate the usefulness of comparative ways of thinking in relativizing these biases. We discuss the relationship between the number of neurons and cognition and draw attention to the highly developed cognitive performance of animals with small brains, to some "tricks" of evolution, to how animals cope with small hardware, to some animals with high-quality brains with an alternative architecture to vertebrates, and to surprising basal cognitive skills in aneural, unicellular organisms. Cognition can be supplemented by the idea of a multicellular organism as a continuum, with many levels of cognitive function, including the possible basal learning in single cells.},
}

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

@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 {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 {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 = {},
number = {},
pages = {},
pmid = {39604729},
issn = {1476-4687},
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.},
}

@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 = {},
doi = {10.1093/gbe/evae244},
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 {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 = {},
doi = {10.3390/genes15111472},
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 = {},
doi = {10.3390/genes15111452},
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 = {},
doi = {10.3390/biom14111435},
pmid = {39595611},
issn = {2218-273X},
mesh = {*Sterols/metabolism/biosynthesis ; Animals ; *Plants/metabolism/parasitology ; *Nematoda/metabolism ; *Insecta/metabolism ; Pest Control ; Oomycetes/metabolism ; Plant Diseases/parasitology/microbiology ; },
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.},
}

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

@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 {pmid39265037,
year = {2024},
author = {Aravind, L and Nicastro, GG and Iyer, LM and Burroughs, AM},
title = {The Prokaryotic Roots of Eukaryotic Immune Systems.},
journal = {Annual review of genetics},
volume = {58},
number = {1},
pages = {365-389},
doi = {10.1146/annurev-genet-111523-102448},
pmid = {39265037},
issn = {1545-2948},
mesh = {Animals ; *Prokaryotic Cells/immunology/metabolism ; *Eukaryota/genetics/immunology ; Humans ; *Immunity, Innate/genetics ; Immune System/immunology/metabolism ; Bacteria/genetics/immunology/metabolism ; Evolution, Molecular ; Phylogeny ; Biological Evolution ; },
abstract = {Over the past two decades, studies have revealed profound evolutionary connections between prokaryotic and eukaryotic immune systems, challenging the notion of their unrelatedness. Immune systems across the tree of life share an operational framework, shaping their biochemical logic and evolutionary trajectories. The diversification of immune genes in the prokaryotic superkingdoms, followed by lateral transfer to eukaryotes, was central to the emergence of innate immunity in the latter. These include protein domains related to nucleotide second messenger-dependent systems, NAD+/nucleotide degradation, and P-loop NTPase domains of the STAND and GTPase clades playing pivotal roles in eukaryotic immunity and inflammation. Moreover, several domains orchestrating programmed cell death, ultimately of prokaryotic provenance, suggest an intimate link between immunity and the emergence of multicellularity in eukaryotes such as animals. While eukaryotes directly adopted some proteins from bacterial immune systems, they repurposed others for new immune functions from bacterial interorganismal conflict systems. These emerging immune components hold substantial biotechnological potential.},
}

Animals
*Prokaryotic Cells/immunology/metabolism
*Eukaryota/genetics/immunology
Humans
*Immunity, Innate/genetics
Immune System/immunology/metabolism
Bacteria/genetics/immunology/metabolism
Evolution, Molecular
Phylogeny
Biological Evolution

@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},
doi = {10.1371/journal.pone.0313428},
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 {pmid39447574,
year = {2024},
author = {Dierschke, T and Levins, J and Lampugnani, ER and Ebert, B and Zachgo, S and Bowman, JL},
title = {Control of sporophyte secondary cell wall development in Marchantia by a Class II KNOX gene.},
journal = {Current biology : CB},
volume = {34},
number = {22},
pages = {5213-5222.e5},
doi = {10.1016/j.cub.2024.09.061},
pmid = {39447574},
issn = {1879-0445},
mesh = {*Cell Wall/metabolism/genetics ; *Marchantia/genetics/growth & development ; *Plant Proteins/genetics/metabolism ; Gene Expression Regulation, Plant ; Germ Cells, Plant/growth & development/metabolism ; },
abstract = {Land plants evolved from an ancestral alga around 470 mya, evolving complex multicellularity in both haploid gametophyte and diploid sporophyte generations. The evolution of water-conducting tissues in the sporophyte generation was crucial for the success of land plants, paving the way for the colonization of a variety of terrestrial habitats. Class II KNOX (KNOX2) genes are major regulators of secondary cell wall formation and seed mucilage (pectin) deposition in flowering plants. Here, we show that, in the liverwort Marchantia polymorpha, loss-of-function alleles of the KNOX2 ortholog, MpKNOX2, or its dimerization partner, MpBELL1, have defects in capsule wall secondary cell wall and spore pectin biosynthesis. Both genes are expressed in the gametophytic calyptra surrounding the sporophyte and exert maternal effects, suggesting intergenerational regulation from the maternal gametophyte to the sporophytic embryo. These findings also suggest the presence of a secondary wall genetic program in the non-vascular liverwort capsule wall, with attributes of secondary walls in vascular tissues.},
}

*Cell Wall/metabolism/genetics
*Marchantia/genetics/growth & development
*Plant Proteins/genetics/metabolism
Gene Expression Regulation, Plant
Germ Cells, Plant/growth & development/metabolism

@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 {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},
doi = {10.1073/pnas.2416656121},
pmid = {39536081},
issn = {1091-6490},
support = {AI039115-27//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI050113-20//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI133654-07//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI133654-07//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
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 {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},
doi = {10.1073/pnas.2414742121},
pmid = {39508768},
issn = {1091-6490},
support = {BSR 83-06072//NSF | BIO | Division of Environmental Biology (DEB)/ ; BSR 89-11038//NSF | BIO | Division of Environmental Biology (DEB)/ ; DBI-2119963//NSF | BIO | Division of Environmental Biology (DEB)/ ; IOS-1922914//NSF | BIO | Division of Integrative Organismal Systems (IOS)/ ; 2R35GM122566//HHS | National Institutes of Health (NIH)/ ; 735927//Gordon and Betty Moore Foundation (GBMF)/ ; },
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 {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 = {*Single-Cell Analysis ; Eukaryota/cytology/genetics ; Animals ; Transcriptome ; Gene Expression Profiling ; Biological Evolution ; Embryonic Development ; },
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.},
}

*Single-Cell Analysis
Eukaryota/cytology/genetics
Animals
Transcriptome
Gene Expression Profiling
Biological Evolution
Embryonic Development

@article {pmid39441990,
year = {2024},
author = {Uppal, S and Waterworth, SC and Nick, A and Vogel, H and Flórez, LV and Kaltenpoth, M and Kwan, JC},
title = {Repeated horizontal acquisition of lagriamide-producing symbionts in Lagriinae beetles.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {39441990},
issn = {1751-7370},
support = {ERC CoG 819585//European Research Council through an ERC Consolidator/ ; 1845890//National Science Foundation/ ; },
mesh = {Animals ; *Symbiosis ; *Coleoptera/microbiology ; *Burkholderia/genetics/metabolism/classification/physiology ; Phylogeny ; Metagenomics ; Genome, Bacterial ; Gene Transfer, Horizontal ; },
abstract = {Microbial symbionts associate with multicellular organisms on a continuum from facultative associations to mutual codependency. In the oldest intracellular symbioses there is exclusive vertical symbiont transmission, and co-diversification of symbiotic partners over millions of years. Such symbionts often undergo genome reduction due to low effective population sizes, frequent population bottlenecks, and reduced purifying selection. Here, we describe multiple independent acquisition events of closely related defensive symbionts followed by genome erosion in a group of Lagriinae beetles. Previous work in Lagria villosa revealed the dominant genome-eroded symbiont of the genus Burkholderia produces the antifungal compound lagriamide, protecting the beetle's eggs and larvae from antagonistic fungi. Here, we use metagenomics to assemble 11 additional genomes of lagriamide-producing symbionts from 7 different host species within Lagriinae from 5 countries, to unravel the evolutionary history of this symbiotic relationship. In each host, we detected one dominant genome-eroded Burkholderia symbiont encoding the lagriamide biosynthetic gene cluster. However, we did not find evidence for host-symbiont co-diversification or for monophyly of the lagriamide-producing symbionts. Instead, our analyses support a single ancestral acquisition of the gene cluster followed by at least four independent symbiont acquisitions and subsequent genome erosion in each lineage. By contrast, a clade of plant-associated relatives retained large genomes but secondarily lost the lagriamide gene cluster. Our results, therefore, reveal a dynamic evolutionary history with multiple independent symbiont acquisitions characterized by a high degree of specificity and highlight the importance of the specialized metabolite lagriamide for the establishment and maintenance of this defensive symbiosis.},
}

Animals
*Symbiosis
*Coleoptera/microbiology
*Burkholderia/genetics/metabolism/classification/physiology
Phylogeny
Metagenomics
Genome, Bacterial
Gene Transfer, Horizontal

@article {pmid39228078,
year = {2024},
author = {Evans, SD and Hughes, IV and Hughes, EB and Dzaugis, PW and Dzaugis, MP and Gehling, JG and García-Bellido, DC and Droser, ML},
title = {A new motile animal with implications for the evolution of axial polarity from the Ediacaran of South Australia.},
journal = {Evolution & development},
volume = {26},
number = {6},
pages = {e12491},
doi = {10.1111/ede.12491},
pmid = {39228078},
issn = {1525-142X},
support = {//Australian Research Council/ ; //Agouron Institute/ ; /NASA/NASA/United States ; 80NSSC19K0472//NASA Exobiology/ ; DP22010277//Agouron Geobiology Fellowship/ ; DP22010277//Australian Research Council Discovery Project/ ; /NASA/NASA/United States ; },
mesh = {Animals ; *Fossils/anatomy & histology ; South Australia ; *Biological Evolution ; Body Patterning ; Phylogeny ; },
abstract = {Fossils of the Ediacara Biota preserve the oldest evidence for complex, macroscopic animals. Most are difficult to constrain phylogenetically, however, the presence of rare, derived groups suggests that many more fossils from this period represent extant groups than are currently appreciated. One approach to recognize such early animals is to instead focus on characteristics widespread in animals today, for example multicellularity, motility, and axial polarity. Here, we describe a new taxon, Quaestio simpsonorum gen. et sp. nov. from the Ediacaran of South Australia. Quaestio is reconstructed with a thin external membrane connecting more resilient tissues with anterior-posterior polarity, left-right asymmetry and tentative evidence for dorsoventral differentiation. Associated trace fossils indicate an epibenthic and motile lifestyle. Our results suggest that Quaestio was a motile eumetazoan with a body plan not previously recognized in the Ediacaran, including definitive evidence of chirality. This organization, combined with previous evidence for axial patterning in a variety of other Ediacara taxa, demonstrates that metazoan body plans were well established in the Precambrian.},
}

Animals
*Fossils/anatomy & histology
South Australia
*Biological Evolution
Body Patterning
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},
doi = {10.1080/15476286.2024.2417152},
pmid = {39508203},
issn = {1555-8584},
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 {pmid39496747,
year = {2024},
author = {Yao, M and Su, Y and Xiong, R and Zhang, X and Zhu, X and Chen, YC and Ao, P},
title = {Deciphering the topological landscape of glioma using a network theory framework.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {26724},
pmid = {39496747},
issn = {2045-2322},
support = {16Z103060007//National Natural Science Foundation of China/ ; 16Z103060007//National Natural Science Foundation of China/ ; 16Z103060007//National Natural Science Foundation of China/ ; 16Z103060007//National Natural Science Foundation of China/ ; 16Z103060007//National Natural Science Foundation of China/ ; 16Z103060007//National Natural Science Foundation of China/ ; 16Z103060007//National Natural Science Foundation of China/ ; },
mesh = {*Glioma/pathology/genetics/metabolism ; Humans ; *Gene Regulatory Networks ; *Neoplastic Stem Cells/metabolism/pathology ; *Brain Neoplasms/pathology/metabolism ; Gene Expression Regulation, Neoplastic ; Astrocytes/metabolism ; },
abstract = {Glioma stem cells have been recognized as key players in glioma recurrence and therapeutic resistance, presenting a promising target for novel treatments. However, the limited understanding of the role glioma stem cells play in the glioma hierarchy has drawn controversy and hindered research translation into therapies. Despite significant advances in our understanding of gene regulatory networks, the dynamics of these networks and their implications for glioma remain elusive. This study employs a systemic theoretical perspective to integrate experimental knowledge into a core endogenous network model for glioma, thereby elucidating its energy landscape through network dynamics computation. The model identifies two stable states corresponding to astrocytic-like and oligodendrocytic-like tumor cells, connected by a transition state with the feature of high stemness, which serves as one of the energy barriers between astrocytic-like and oligodendrocytic-like states, indicating the instability of glioma stem cells in vivo. We also obtained various stable states further supporting glioma's multicellular origins and uncovered a group of transition states that could potentially induce tumor heterogeneity and therapeutic resistance. This research proposes that the transition states linking both glioma stable states are central to glioma heterogeneity and therapy resistance. Our approach may contribute to the advancement of glioma therapy by offering a novel perspective on the complex landscape of glioma biology.},
}

*Glioma/pathology/genetics/metabolism
Humans
*Gene Regulatory Networks
*Neoplastic Stem Cells/metabolism/pathology
*Brain Neoplasms/pathology/metabolism
Gene Expression Regulation, Neoplastic
Astrocytes/metabolism

@article {pmid39480878,
year = {2024},
author = {Petit, C and Kojak, E and Webster, S and Marra, M and Sweeney, B and Chaikin, C and Jemc, JC and Kanzok, SM},
title = {The evolutionarily conserved PhLP3 is essential for sperm development in Drosophila melanogaster.},
journal = {PloS one},
volume = {19},
number = {10},
pages = {e0306676},
doi = {10.1371/journal.pone.0306676},
pmid = {39480878},
issn = {1932-6203},
mesh = {Animals ; *Drosophila melanogaster/genetics/metabolism/growth & development ; Male ; *Drosophila Proteins/genetics/metabolism ; *Spermatogenesis/genetics ; *Spermatozoa/metabolism ; Evolution, Molecular ; Testis/metabolism ; Conserved Sequence ; },
abstract = {Phosducin-like proteins (PhLP) are thioredoxin domain-containing proteins that are highly conserved across unicellular and multicellular organisms. PhLP family proteins are hypothesized to function as co-chaperones in the folding of cytoskeletal proteins. Here, we present the initial molecular, biochemical, and functional characterization of CG4511 as Drosophila melanogaster PhLP3. We cloned the gene into a bacterial expression vector and produced enzymatically active recombinant PhLP3, which showed similar kinetics to previously characterized orthologues. A fly strain homozygous for a P-element insertion in the 5' UTR of the PhLP3 gene exhibited significant downregulation of PhLP3 expression. We found these male flies to be sterile. Microscopic analysis revealed altered testes morphology and impairment of spermiogenesis, leading to a lack of mature sperm. Among the most significant observations was the lack of actin cones during sperm maturation. Excision of the P-element insertion in PhLP3 restored male fertility, spermiogenesis, and seminal vesicle size. Given the high level of conservation of PhLP3, our data suggests PhLP3 may be an important regulator of sperm development across species.},
}

Animals
*Drosophila melanogaster/genetics/metabolism/growth & development
Male
*Drosophila Proteins/genetics/metabolism
*Spermatogenesis/genetics
*Spermatozoa/metabolism
Evolution, Molecular
Testis/metabolism
Conserved Sequence