@article {pmid38991084,
year = {2024},
author = {Landis, JB and Guercio, AM and Brown, KE and Fiscus, CJ and Morrell, PL and Koenig, D},
title = {Natural selection drives emergent genetic homogeneity in a century-scale experiment with barley.},
journal = {Science (New York, N.Y.)},
volume = {385},
number = {6705},
pages = {eadl0038},
doi = {10.1126/science.adl0038},
pmid = {38991084},
issn = {1095-9203},
mesh = {*Hordeum/genetics ; *Selection, Genetic ; *Genetic Variation ; *Alleles ; Genotype ; Crosses, Genetic ; Genome, Plant ; },
abstract = {Direct observation is central to our understanding of adaptation, but evolution is rarely documented in a large, multicellular organism for more than a few generations. In this study, we observed evolution across a century-scale competition experiment, barley composite cross II (CCII). CCII was founded in 1929 in Davis, California, with thousands of genotypes, but we found that natural selection has massively reduced genetic diversity, leading to a single lineage constituting most of the population by generation 50. Selection favored alleles originating from climates similar to that of Davis and targeted loci contributing to reproductive development, including the barley diversification loci Vrs1, HvCEN, Ppd-H1, and Vrn-H2. Our findings point to selection as the predominant force shaping genomic variation in one of the world's oldest biological experiments.},
}

*Hordeum/genetics
*Selection, Genetic
*Genetic Variation
*Alleles
Genotype
Crosses, Genetic
Genome, Plant

@article {pmid38990940,
year = {2024},
author = {Zomer, A and Ingham, CJ and von Meijenfeldt, FAB and Escobar Doncel, Á and van de Kerkhof, GT and Hamidjaja, R and Schouten, S and Schertel, L and Müller, KH and Catón, L and Hahnke, RL and Bolhuis, H and Vignolini, S and Dutilh, BE},
title = {Structural color in the bacterial domain: The ecogenomics of a 2-dimensional optical phenotype.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {29},
pages = {e2309757121},
doi = {10.1073/pnas.2309757121},
pmid = {38990940},
issn = {1091-6490},
support = {40-43500-98-4102/435004516//ZonMw (Netherlands Organisation for Health Research and Development)/ ; 860125//EC | HORIZON EUROPE Framework Programme (Horizon Europe)/ ; 2110570//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 722842//EC | HORIZON EUROPE Framework Programme (Horizon Europe)/ ; P2ZHP2_183998/SNSF_/Swiss National Science Foundation/Switzerland ; SNSF3//Isaac Newton Trust/ ; SNSF 40B1-0_198708/SNSF_/Swiss National Science Foundation/Switzerland ; 865694//EC | European Research Council (ERC)/ ; 101001637//EC | European Research Council (ERC)/ ; BB/V00364X/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 390713860//Deutsche Forschungsgemeinschaft (DFG)/ ; },
mesh = {*Genome, Bacterial ; Phenotype ; Color ; Bacteria/genetics/metabolism ; Proteobacteria/genetics/metabolism ; Phylogeny ; Metagenome ; Genome-Wide Association Study ; Bacteroidetes/genetics/metabolism ; },
abstract = {Structural color is an optical phenomenon resulting from light interacting with nanostructured materials. Although structural color (SC) is widespread in the tree of life, the underlying genetics and genomics are not well understood. Here, we collected and sequenced a set of 87 structurally colored bacterial isolates and 30 related strains lacking SC. Optical analysis of colonies indicated that diverse bacteria from at least two different phyla (Bacteroidetes and Proteobacteria) can create two-dimensional packing of cells capable of producing SC. A pan-genome-wide association approach was used to identify genes associated with SC. The biosynthesis of uroporphyrin and pterins, as well as carbohydrate utilization and metabolism, was found to be involved. Using this information, we constructed a classifier to predict SC directly from bacterial genome sequences and validated it by cultivating and scoring 100 strains that were not part of the training set. We predicted that SCr is widely distributed within gram-negative bacteria. Analysis of over 13,000 assembled metagenomes suggested that SC is nearly absent from most habitats associated with multicellular organisms except macroalgae and is abundant in marine waters and surface/air interfaces. This work provides a large-scale ecogenomics view of SC in bacteria and identifies microbial pathways and evolutionary relationships that underlie this optical phenomenon.},
}

*Genome, Bacterial
Phenotype
Color
Bacteria/genetics/metabolism
Proteobacteria/genetics/metabolism
Phylogeny
Metagenome
Genome-Wide Association Study
Bacteroidetes/genetics/metabolism

@article {pmid38990824,
year = {2024},
author = {Schaible, GA and Jay, ZJ and Cliff, J and Schulz, F and Gauvin, C and Goudeau, D and Malmstrom, RR and Ruff, SE and Edgcomb, V and Hatzenpichler, R},
title = {Multicellular magnetotactic bacteria are genetically heterogeneous consortia with metabolically differentiated cells.},
journal = {PLoS biology},
volume = {22},
number = {7},
pages = {e3002638},
pmid = {38990824},
issn = {1545-7885},
mesh = {*In Situ Hybridization, Fluorescence ; Metagenome ; Microbial Consortia/genetics ; Genome, Bacterial ; Bacteria/genetics/metabolism ; Genetic Variation ; Phylogeny ; },
abstract = {Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single-cell resolution. We separately sequenced the metagenomes of 22 individual MMB consortia, representing 8 new species, and quantified the genetic diversity within each MMB consortium. This revealed that, counter to conventional views, cells within MMB consortia are not clonal. Single consortia metagenomes were then used to reconstruct the species-specific metabolic potential and infer the physiological capabilities of MMB. To validate genomic predictions, we performed stable isotope probing (SIP) experiments and interrogated MMB consortia using fluorescence in situ hybridization (FISH) combined with nanoscale secondary ion mass spectrometry (NanoSIMS). By coupling FISH with bioorthogonal noncanonical amino acid tagging (BONCAT), we explored their in situ activity as well as variation of protein synthesis within cells. We demonstrate that MMB consortia are mixotrophic sulfate reducers and that they exhibit metabolic differentiation between individual cells, suggesting that MMB consortia are more complex than previously thought. These findings expand our understanding of MMB diversity, ecology, genomics, and physiology, as well as offer insights into the mechanisms underpinning the multicellular nature of their unique lifestyle.},
}

*In Situ Hybridization, Fluorescence
Metagenome
Microbial Consortia/genetics
Genome, Bacterial
Bacteria/genetics/metabolism
Genetic Variation
Phylogeny

@article {pmid38990205,
year = {2024},
author = {Sims, NA},
title = {Osteoclast-derived coupling factors: origins and state-of-play Louis V Avioli Lecture, ASBMR 2023.},
journal = {Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research},
volume = {},
number = {},
pages = {},
doi = {10.1093/jbmr/zjae110},
pmid = {38990205},
issn = {1523-4681},
abstract = {Coupling, the mechanism that controls the sequence of events in bone remodelling, is a fundamental theory for understanding the way the skeleton changes throughout life. This review is an adapted version of the Louis V Avioli lecture, delivered at the Annual Scientific Meeting of the American Society of Bone and Mineral Research. It outlines the history of the coupling concept and details how coupling occurs within trabecular and cortical bone and describes its multiple contexts and the many mechanisms suggested to couple bone forming osteoblasts to the prior action of osteoclasts on the same bone surface. These mechanisms include signals produced at each stage of the remodelling sequence (resorption, reversal, and formation), such as factors released by osteoclasts through their resorptive action and through protein synthesis, molecules deposited in the cement line during the reversal phase, and potentially signals from osteocytes within the local bone environment. The review highlights two examples of coupling factors (Cardiotrophin 1 and EphrinB2:EphB4) to illustrate the limited data available, and the need to integrate both the many functions of these factors within the basic multicellular unit (BMU), and the multiple origins of these factors, including other cell types present during the remodelling sequence (such as osteocytes, macrophages, endothelial cells, and T-cells).},
}

@article {pmid38985841,
year = {2024},
author = {Valencia-Montoya, WA and Pierce, NE and Bellono, NW},
title = {Evolution of Sensory Receptors.},
journal = {Annual review of cell and developmental biology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-cellbio-120123-112853},
pmid = {38985841},
issn = {1530-8995},
abstract = {Sensory receptors are at the interface between an organism and its environment and thus represent key sites for biological innovation. Here, we survey major sensory receptor families to uncover emerging evolutionary patterns. Receptors for touch, temperature, and light constitute part of the ancestral sensory toolkit of animals, often predating the evolution of multicellularity and the nervous system. In contrast, chemoreceptors exhibit a dynamic history of lineage-specific expansions and contractions correlated with the disparate complexity of chemical environments. A recurring theme includes independent transitions from neurotransmitter receptors to sensory receptors of diverse stimuli from the outside world. We then provide an overview of the evolutionary mechanisms underlying sensory receptor diversification and highlight examples where signatures of natural selection are used to identify novel sensory adaptations. Finally, we discuss sensory receptors as evolutionary hotspots driving reproductive isolation and speciation, thereby contributing to the stunning diversity of animals.},
}

@article {pmid38981695,
year = {2024},
author = {Kulakova, MA and Maslakov, GP and Poliushkevich, LO},
title = {Irreducible Complexity of Hox Gene: Path to the Canonical Function of the Hox Cluster.},
journal = {Biochemistry. Biokhimiia},
volume = {89},
number = {6},
pages = {987-1001},
doi = {10.1134/S0006297924060014},
pmid = {38981695},
issn = {1608-3040},
mesh = {Animals ; *Genes, Homeobox ; Homeodomain Proteins/genetics/metabolism ; Multigene Family ; Humans ; Evolution, Molecular ; Gene Expression Regulation, Developmental ; },
abstract = {The evolution of major taxa is often associated with the emergence of new gene families. In all multicellular animals except sponges and comb jellies, the genomes contain Hox genes, which are crucial regulators of development. The canonical function of Hox genes involves colinear patterning of body parts in bilateral animals. This general function is implemented through complex, precisely coordinated mechanisms, not all of which are evolutionarily conserved and fully understood. We suggest that the emergence of this regulatory complexity was preceded by a stage of cooperation between more ancient morphogenetic programs or their individual elements. Footprints of these programs may be present in modern animals to execute non-canonical Hox functions. Non-canonical functions of Hox genes are involved in maintaining terminal nerve cell specificity, autophagy, oogenesis, pre-gastrulation embryogenesis, vertical signaling, and a number of general biological processes. These functions are realized by the basic properties of homeodomain protein and could have triggered the evolution of ParaHoxozoa and Nephrozoa subsequently. Some of these non-canonical Hox functions are discussed in our review.},
}

Animals
*Genes, Homeobox
Homeodomain Proteins/genetics/metabolism
Multigene Family
Humans
Evolution, Molecular
Gene Expression Regulation, Developmental

@article {pmid38979061,
year = {2024},
author = {Balasenthilkumaran, NV and Whitesell, JC and Pyle, L and Friedman, RS and Kravets, V},
title = {Network approach reveals preferential T-cell and macrophage association with α-linked β-cells in early stage of insulitis in NOD mice.},
journal = {Frontiers in network physiology},
volume = {4},
number = {},
pages = {1393397},
pmid = {38979061},
issn = {2674-0109},
support = {R01 DK111733/DK/NIDDK NIH HHS/United States ; },
abstract = {One of the challenges in studying islet inflammation-insulitis-is that it is a transient phenomenon. Traditional reporting of the insulitis progression is based on cumulative, donor-averaged values of leucocyte density in the vicinity of pancreatic islets, that hinder intra- and inter-islet heterogeneity of disease progression. Here, we aimed to understand why insulitis is non-uniform, often with peri-insulitis lesions formed on one side of an islet. To achieve this, we demonstrated the applicability of network theory in detangling intra-islet multi-cellular interactions during insulitis. Specifically, we asked the question "What is unique about regions of the islet that interact with immune cells first". This study utilized the non-obese diabetic mouse model of type one diabetes and examined the interplay among α-, β-, T-cells, myeloid cells, and macrophages in pancreatic islets during the progression of insulitis. Disease evolution was tracked based on the T/β cell ratio in individual islets. In the early stage, we found that immune cells are preferentially interacting with α-cell-rich regions of an islet. At the islet periphery α-linked β-cells were found to be targeted significantly more compared to those without α-cell neighbors. Additionally, network analysis revealed increased T-myeloid, and T-macrophage interactions with all β-cells.},
}

@article {pmid38977899,
year = {2024},
author = {Kollmar, M and Welz, T and Ravi, A and Kaufmann, T and Alzahofi, N and Hatje, K and Alghamdi, A and Kim, J and Briggs, DA and Samol-Wolf, A and Pylypenko, O and Hume, AN and Burkhardt, P and Faix, J and Kerkhoff, E},
title = {Actomyosin organelle functions of SPIRE actin nucleators precede animal evolution.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {832},
pmid = {38977899},
issn = {2399-3642},
support = {KE 447/10-2//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; KE 447/18-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; KE 447/21-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; KO 2251/13-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FA 330/12-3//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Animals ; *Organelles/metabolism ; *Actomyosin/metabolism ; Microfilament Proteins/metabolism/genetics ; Myosin Type V/metabolism/genetics ; Actins/metabolism ; Humans ; Choanoflagellata/metabolism ; Actin Cytoskeleton/metabolism ; Biological Evolution ; Evolution, Molecular ; Formins/metabolism ; rab GTP-Binding Proteins/metabolism ; Phylogeny ; Nuclear Proteins ; },
abstract = {An important question in cell biology is how cytoskeletal proteins evolved and drove the development of novel structures and functions. Here we address the origin of SPIRE actin nucleators. Mammalian SPIREs work with RAB GTPases, formin (FMN)-subgroup actin assembly proteins and class-5 myosin (MYO5) motors to transport organelles along actin filaments towards the cell membrane. However, the origin and extent of functional conservation of SPIRE among species is unknown. Our sequence searches show that SPIRE exist throughout holozoans (animals and their closest single-celled relatives), but not other eukaryotes. SPIRE from unicellular holozoans (choanoflagellate), interacts with RAB, FMN and MYO5 proteins, nucleates actin filaments and complements mammalian SPIRE function in organelle transport. Meanwhile SPIRE and MYO5 proteins colocalise to organelles in Salpingoeca rosetta choanoflagellates. Based on these observations we propose that SPIRE originated in unicellular ancestors of animals providing an actin-myosin driven exocytic transport mechanism that may have contributed to the evolution of complex multicellular animals.},
}

Animals
*Organelles/metabolism
*Actomyosin/metabolism
Microfilament Proteins/metabolism/genetics
Myosin Type V/metabolism/genetics
Actins/metabolism
Humans
Choanoflagellata/metabolism
Actin Cytoskeleton/metabolism
Biological Evolution
Evolution, Molecular
Formins/metabolism
rab GTP-Binding Proteins/metabolism
Phylogeny
Nuclear Proteins

@article {pmid38975338,
year = {2024},
author = {Amanya, SB and Oyewole-Said, D and Ernste, KJ and Bisht, N and Murthy, A and Vazquez-Perez, J and Konduri, V and Decker, WK},
title = {The mARS complex: a critical mediator of immune regulation and homeostasis.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1423510},
pmid = {38975338},
issn = {1664-3224},
support = {R01 AI127387/AI/NIAID NIH HHS/United States ; R01 AI153326/AI/NIAID NIH HHS/United States ; },
mesh = {*Homeostasis/immunology ; Animals ; Humans ; *Amino Acyl-tRNA Synthetases/immunology/metabolism ; Immunomodulation ; },
abstract = {Over the course of evolution, many proteins have undergone adaptive structural changes to meet the increasing homeostatic regulatory demands of multicellularity. Aminoacyl tRNA synthetases (aaRS), enzymes that catalyze the attachment of each amino acid to its cognate tRNA, are such proteins that have acquired new domains and motifs that enable non-canonical functions. Through these new domains and motifs, aaRS can assemble into large, multi-subunit complexes that enhance the efficiency of many biological functions. Moreover, because the complexity of multi-aminoacyl tRNA synthetase (mARS) complexes increases with the corresponding complexity of higher eukaryotes, a contribution to regulation of homeostatic functions in multicellular organisms is hypothesized. While mARS complexes in lower eukaryotes may enhance efficiency of aminoacylation, little evidence exists to support a similar role in chordates or other higher eukaryotes. Rather, mARS complexes are reported to regulate multiple and variegated cellular processes that include angiogenesis, apoptosis, inflammation, anaphylaxis, and metabolism. Because all such processes are critical components of immune homeostasis, it is important to understand the role of mARS complexes in immune regulation. Here we provide a conceptual analysis of the current understanding of mARS complex dynamics and emerging mARS complex roles in immune regulation, the increased understanding of which should reveal therapeutic targets in immunity and immune-mediated disease.},
}

*Homeostasis/immunology
Animals
Humans
*Amino Acyl-tRNA Synthetases/immunology/metabolism
Immunomodulation

@article {pmid38971878,
year = {2024},
author = {Wang, P and Driscoll, WW and Travisano, M},
title = {Genomic sequencing reveals convergent adaptation during experimental evolution in two budding yeast species.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {825},
pmid = {38971878},
issn = {2399-3642},
support = {1724011//Center for Hierarchical Manufacturing, National Science Foundation (Center for Hierarchical Manufacturing)/ ; 16-IDEAS16-0002//National Aeronautics and Space Administration (NASA)/ ; },
mesh = {*Kluyveromyces/genetics/physiology ; Saccharomyces cerevisiae/genetics ; Genome, Fungal ; Mutation ; Evolution, Molecular ; Adaptation, Physiological/genetics ; Selection, Genetic ; Biological Evolution ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Genomics/methods ; },
abstract = {Convergent evolution is central in the origins of multicellularity. Identifying the basis for convergent multicellular evolution is challenging because of the diverse evolutionary origins and environments involved. Haploid Kluyveromyces lactis populations evolve multicellularity during selection for increased settling in liquid media. Strong genomic and phenotypic convergence is observed between K. lactis and previously selected S. cerevisiae populations under similar selection, despite their >100-million-year divergence. We find K. lactis multicellularity is conferred by mutations in genes ACE2 or AIM44, with ACE2 being predominant. They are a subset of the six genes involved in the S. cerevisiae multicellularity. Both ACE2 and AIM44 regulate cell division, indicating that the genetic convergence is likely due to conserved cellular replication mechanisms. Complex population dynamics involving multiple ACE2/AIM44 genotypes are found in most K. lactis lineages. The results show common ancestry and natural selection shape convergence while chance and contingency determine the degree of divergence.},
}

*Kluyveromyces/genetics/physiology
Saccharomyces cerevisiae/genetics
Genome, Fungal
Mutation
Evolution, Molecular
Adaptation, Physiological/genetics
Selection, Genetic
Biological Evolution
Saccharomyces cerevisiae Proteins/genetics/metabolism
Genomics/methods

@article {pmid38971326,
year = {2024},
author = {Prosdocimi, F and Farias, ST},
title = {Major evolutionary transitions before cells: a journey from molecules to organisms.},
journal = {Progress in biophysics and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pbiomolbio.2024.07.002},
pmid = {38971326},
issn = {1873-1732},
abstract = {Basing on logical assumptions and necessary steps of complexification along biological evolution, we propose here an evolutionary path from molecules to cells presenting four ages and three major transitions. At the first age, the basic biomolecules were formed and become abundant. The first transition happened with the event of a chemical symbiosis between nucleic acids and peptides worlds, which marked the emergence of both life and the process of organic encoding. FUCA, the first living process, was composed of self-replicating RNAs linked to amino acids and capable to catalyze their binding. The second transition, from the age of FUCA to the age of progenotes, involved the duplication and recombination of proto-genomes, leading to specialization in protein production and the exploration of protein to metabolite interactions in the prebiotic soup. Enzymes and metabolic pathways were incorporated into biology from protobiotic reactions that occurred without chemical catalysts, step by step. Then, the fourth age brought origin of organisms and lineages, occurring when specific proteins capable to stackle together facilitated the formation of peptidic capsids. LUCA was constituted as a progenote capable to operate the basic metabolic functions of a cell, but still unable to interact with lipid molecules. We present evidence that the evolution of lipid interaction pathways occurred at least twice, with the development of bacterial-like and archaeal-like membranes. Also, data in literature suggest at least two paths for the emergence of DNA biosynthesis, allowing the stabilization of early life strategies in viruses, archaeas and bacterias. Two billion years later, the eukaryotes arouse, and after 1,5 billion years of evolution, they finally learn how to evolve multicellularity via tissue specialization.},
}

@article {pmid38970827,
year = {2024},
author = {Ernesto Alvarez, F and Clairambault, J},
title = {Phenotype divergence and cooperation in isogenic multicellularity and in cancer.},
journal = {Mathematical medicine and biology : a journal of the IMA},
volume = {},
number = {},
pages = {},
doi = {10.1093/imammb/dqae005},
pmid = {38970827},
issn = {1477-8602},
abstract = {We discuss the mathematical modelling of two of the main mechanisms that pushed forward the emergence of multicellularity: phenotype divergence in cell differentiation and between-cell cooperation. In line with the atavistic theory of cancer, this disease being specific of multicellular animals, we set special emphasis on how both mechanisms appear to be reversed, however not totally impaired, rather hijacked, in tumour cell populations. Two settings are considered: the completely innovating, tinkering, situation of the emergence of multicellularity in the evolution of species, which we assume to be constrained by external pressure on the cell populations, and the completely planned-in the body plan-situation of the physiological construction of a developing multicellular animal from the zygote, or of bet hedging in tumours, assumed to be of clonal formation, although the body plan is largely-but not completely-lost in its constituting cells. We show how cancer impacts these two settings and we sketch mathematical models for them. We present here our contribution to the question at stake with a background from biology, from mathematics and from philosophy of science.},
}

@article {pmid38969311,
year = {2024},
author = {Bhattacharya, R and Brown, JS and Gatenby, RA and Ibrahim-Hashim, A},
title = {A gene for all seasons: The evolutionary consequences of HIF-1 in carcinogenesis, tumor growth and metastasis.},
journal = {Seminars in cancer biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.semcancer.2024.06.003},
pmid = {38969311},
issn = {1096-3650},
abstract = {Oxygen played a pivotal role in the evolution of multicellularity during the Cambrian Explosion. Not surprisingly, responses to fluctuating oxygen concentrations are integral to the evolution of cancer-a disease characterized by the breakdown of multicellularity. Poorly organized tumour vasculature results in chaotic patterns of blood flow characterized by large spatial and temporal variations in intra-tumoral oxygen concentrations. Hypoxia-inducible growth factor (HIF-1) plays a pivotal role in enabling cells to adapt, metabolize, and proliferate in low oxygen conditions. HIF-1 is often constitutively activated in cancers, underscoring its importance in cancer progression. Here, we argue that the phenotypic changes mediated by HIF-1, in addition to adapting the cancer cells to their local environment, also "pre-adapt" them for proliferation at distant, metastatic sites. HIF-1-mediated adaptations include a metabolic shift towards anaerobic respiration or glycolysis, activation of cell survival mechanisms like phenotypic plasticity and epigenetic reprogramming, and formation of tumour vasculature through angiogenesis. Hypoxia induced epigenetic reprogramming can trigger epithelial to mesenchymal transition in cancer cells-the first step in the metastatic cascade. Highly glycolytic cells facilitate local invasion by acidifying the tumour microenvironment. New blood vessels, formed due to angiogenesis, provide cancer cells a conduit to the circulatory system. Moreover, survival mechanisms acquired by cancer cells in the primary site allow them to remodel tissue at the metastatic site generating tumour promoting microenvironment. Thus, hypoxia in the primary tumour promoted adaptations conducive to all stages of the metastatic cascade from the initial escape entry into a blood vessel, intravascular survival, extravasation into distant tissues, and establishment of secondary tumours.},
}

@article {pmid38960448,
year = {2024},
author = {Parker, J},
title = {Organ Evolution: Emergence of Multicellular Function.},
journal = {Annual review of cell and developmental biology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-cellbio-111822-121620},
pmid = {38960448},
issn = {1530-8995},
abstract = {Instances of multicellularity across the tree of life have fostered the evolution of complex organs composed of distinct cell types that cooperate, producing emergent biological functions. How organs originate is a fundamental evolutionary problem that has eluded deep mechanistic and conceptual understanding. Here I propose a cell- to organ-level transitions framework, whereby cooperative division of labor originates and becomes entrenched between cell types through a process of functional niche creation, cell type subfunctionalization, and irreversible ratcheting of cell interdependencies. Comprehending this transition hinges on explaining how these processes unfold molecularly in evolving populations. Recent single-cell transcriptomic studies and analyses of terminal fate specification indicate that cellular functions are conferred by modular gene expression programs. These discrete components of functional variation may be deployed or combined within cells to introduce new properties into multicellular niches, or partitioned across cells to establish division of labor. Tracing gene expression program evolution at the level of single cells in populations may reveal transitions toward organ complexity.},
}

@article {pmid38951023,
year = {2024},
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 = {},
number = {},
pages = {},
doi = {10.1101/cshperspect.a041653},
pmid = {38951023},
issn = {1943-0264},
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.},
}

@article {pmid38948761,
year = {2024},
author = {Narayanasamy, N and Bingham, E and Fadero, T and Ozan Bozdag, G and Ratcliff, WC and Yunker, P and Thutupalli, S},
title = {Metabolically-driven flows enable exponential growth in macroscopic multicellular yeast.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38948761},
issn = {2692-8205},
support = {R35 GM138030/GM/NIGMS NIH HHS/United States ; R35 GM138354/GM/NIGMS NIH HHS/United States ; T32 GM142616/GM/NIGMS NIH HHS/United States ; },
abstract = {The ecological and evolutionary success of multicellular lineages is due in no small part to their increased size relative to unicellular ancestors. However, large size also poses biophysical challenges, especially regarding the transport of nutrients to all cells; these constraints are typically overcome through multicellular innovations (e.g., a circulatory system). Here we show that an emergent biophysical mechanism - spontaneous fluid flows arising from metabolically-generated density gradients - can alleviate constraints on nutrient transport, enabling exponential growth in nascent multicellular clusters of yeast lacking any multicellular adaptations for nutrient transport or fluid flow. Surprisingly, beyond a threshold size, the metabolic activity of experimentally-evolved snowflake yeast clusters drives large-scale fluid flows that transport nutrients throughout the cluster at speeds comparable to those generated by the cilia of extant multicellular organisms. These flows support exponential growth at macroscopic sizes that theory predicts should be diffusion limited. This work demonstrates how simple physical mechanisms can act as a 'biophysical scaffold' to support the evolution of multicellularity by opening up phenotypic possibilities prior to genetically-encoded innovations. More broadly, our findings highlight how co-option of conserved physical processes is a crucial but underappreciated facet of evolutionary innovation across scales.},
}

@article {pmid38939413,
year = {2024},
author = {Tassinari, S and D'Angelo, E and Caicci, F and Grange, C and Burrello, J and Fassan, M and Brossa, A and Bao, RQ and Spolverato, G and Agostini, M and Collino, F and Bussolati, B},
title = {Profile of matrix-entrapped extracellular vesicles of microenvironmental and infiltrating cell origin in decellularized colorectal cancer and adjacent mucosa.},
journal = {Journal of extracellular biology},
volume = {3},
number = {3},
pages = {e144},
pmid = {38939413},
issn = {2768-2811},
abstract = {Cellular elements that infiltrate and surround tumours and pre-metastatic tissues have a prominent role in tumour invasion and growth. The extracellular vesicles specifically entrapped and stored within the extracellular matrix (ECM-EVs) may reflect the different populations of the tumour microenvironment and their change during tumour progression. However, their profile is at present unknown. To elucidate this aspect, we isolated and characterized EVs from decellularized surgical specimens of colorectal cancer and adjacent colon mucosa and analyzed their surface marker profile. ECM-EVs in tumours and surrounding mucosa mainly expressed markers of lymphocytes, natural killer cells, antigen-presenting cells, and platelets, as well as epithelial cells, representing a multicellular microenvironment. No difference in surface marker expression was observed between tumour and mucosa ECM-EVs in stage II-III tumours. At variance, in the colon mucosa adjacent to stage IV carcinomas, ECM-EV profile showed a significantly increased level of immune, epithelial and platelet markers in comparison to the matrix of the corresponding tumour. The increase of EVs from immune cells and platelets was not observed in the mucosa adjacent to low-stage tumours. In addition, CD25, a T-lymphocyte marker, resulted specifically overexpressed by ECM-EVs from stage IV carcinomas, possibly correlated with the pro-tolerogenic environment found in the corresponding tumour tissue. These results outline the tissue microenvironmental profile of EVs in colorectal carcinoma-derived ECM and unveil a profound change in the healthy mucosa adjacent to high-stage tumours.},
}

@article {pmid38924758,
year = {2024},
author = {Crockett, WW and Shaw, JO and Simpson, C and Kempes, CP},
title = {Physical constraints during Snowball Earth drive the evolution of multicellularity.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2025},
pages = {20232767},
doi = {10.1098/rspb.2023.2767},
pmid = {38924758},
issn = {1471-2954},
mesh = {*Biological Evolution ; Ice Cover ; Eukaryota/physiology ; Earth, Planet ; Fossils ; Temperature ; },
abstract = {Molecular and fossil evidence suggests that complex eukaryotic multicellularity evolved during the late Neoproterozoic era, coincident with Snowball Earth glaciations, where ice sheets covered most of the globe. During this period, environmental conditions-such as seawater temperature and the availability of photosynthetically active light in the oceans-likely changed dramatically. Such changes would have had significant effects on both resource availability and optimal phenotypes. Here, we construct and apply mechanistic models to explore (i) how environmental changes during Snowball Earth and biophysical constraints generated selective pressures, and (ii) how these pressures may have had differential effects on organisms with different forms of biological organization. By testing a series of alternative-and commonly debated-hypotheses, we demonstrate how multicellularity was likely acquired differently in eukaryotes and prokaryotes owing to selective differences on their size due to the biophysical and metabolic regimes they inhabit: decreasing temperatures and resource availability instigated by the onset of glaciations generated selective pressures towards smaller sizes in organisms in the diffusive regime and towards larger sizes in motile heterotrophs. These results suggest that changing environmental conditions during Snowball Earth glaciations gave multicellular eukaryotes an evolutionary advantage, paving the way for the complex multicellular lineages that followed.},
}

*Biological Evolution
Ice Cover
Eukaryota/physiology
Earth, Planet
Fossils
Temperature

@article {pmid38923935,
year = {2024},
author = {Ghosh, S and Mellado Sanchez, M and Sue-Ob, K and Roy, D and Jones, A and Blazquez, MA and Sadanandom, A},
title = {Charting the evolutionary path of the SUMO modification system in plants reveals molecular hardwiring of development to stress adaptation.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koae192},
pmid = {38923935},
issn = {1532-298X},
abstract = {SUMO modification is part of the spectrum of Ubiquitin-like (UBL) systems that give rise to proteoform complexity through post-translational modifications (PTMs). Proteoforms are essential modifiers of cell signaling for plant adaptation to changing environments. Exploration of the evolutionary emergence of Ubiquitin-like (UBL) systems unveils their origin from prokaryotes where it is linked to the mechanisms that enable sulfur uptake into biomolecules. We explore the emergence of the SUMO machinery across the plant lineage from single-cell to land plants. We reveal the evolutionary point at which plants acquired the ability to form SUMO chains through the emergence of SUMO E4 ligases hinting at its role in facilitating multicellularity. Additionally, we explore the possible mechanism for the neofunctionalization of SUMO proteases through the fusion of conserved catalytic domains with divergent sequences. We highlight the pivotal role of SUMO proteases in plant development and adaptation, offering new insights into target specificity mechanisms of SUMO modification during plant evolution. Correlating the emergence of adaptive traits in the plant lineage with established experimental evidence for SUMO in developmental processes we propose that SUMO modification has evolved to link developmental processes to adaptive functions in land plants.},
}

@article {pmid38908045,
year = {2024},
author = {Mascarenhas, DP and Zamboni, DS},
title = {Innate immune responses and monocyte-derived phagocyte recruitment in protective immunity to pathogenic bacteria: insights from Legionella pneumophila.},
journal = {Current opinion in microbiology},
volume = {80},
number = {},
pages = {102495},
doi = {10.1016/j.mib.2024.102495},
pmid = {38908045},
issn = {1879-0364},
abstract = {Legionella species are Gram-negative intracellular bacteria that evolved in soil and freshwater environments, where they infect and replicate within various unicellular protozoa. The primary virulence factor of Legionella is the expression of a type IV secretion system (T4SS), which contributes to the translocation of effector proteins that subvert biological processes of the host cells. Because of its evolution in unicellular organisms, T4SS effector proteins are not adapted to subvert specific mammalian signaling pathways and immunity. Consequently, Legionella pneumophila has emerged as an interesting infection model for investigating immune responses against pathogenic bacteria in multicellular organisms. This review highlights recent advances in our understanding of mammalian innate immunity derived from studies involving L. pneumophila. This includes recent insights into inflammasome-mediated mechanisms restricting bacterial replication in macrophages, mechanisms inducing cell death in response to infection, induction of effector-triggered immunity, activation of specific pulmonary cell types in mammalian lungs, and the protective role of recruiting monocyte-derived cells to infected lungs.},
}

@article {pmid38907301,
year = {2024},
author = {Martinez, P and Bailly, X and Sprecher, SG and Hartenstein, V},
title = {The Acoel nervous system: morphology and development.},
journal = {Neural development},
volume = {19},
number = {1},
pages = {9},
pmid = {38907301},
issn = {1749-8104},
support = {PID2021-124415NB-I00//Spanish "Ministerio de Ciencia, Innovación y Universidades"/ ; 310030_219348/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {Animals ; *Nervous System/growth & development/embryology ; *Neurogenesis/physiology ; Platyhelminths/growth & development/physiology ; Biological Evolution ; Neurons/cytology/physiology ; },
abstract = {Acoel flatworms have played a relevant role in classical (and current) discussions on the evolutionary origin of bilaterian animals. This is mostly derived from the apparent simplicity of their body architectures. This tenet has been challenged over the last couple of decades, mostly because detailed studies of their morphology and the introduction of multiple genomic technologies have unveiled a complexity of cell types, tissular arrangements and patterning mechanisms that were hidden below this 'superficial' simplicity. One tissue that has received a particular attention has been the nervous system (NS). The combination of ultrastructural and single cell methodologies has revealed unique cellular diversity and developmental trajectories for most of their neurons and associated sensory systems. Moreover, the great diversity in NS architectures shown by different acoels offers us with a unique group of animals where to study key aspects of neurogenesis and diversification od neural systems over evolutionary time.In this review we revisit some recent developments in the characterization of the acoel nervous system structure and the regulatory mechanisms that contribute to their embryological development. We end up by suggesting some promising avenues to better understand how this tissue is organized in its finest cellular details and how to achieve a deeper knowledge of the functional roles that genes and gene networks play in its construction.},
}

Animals
*Nervous System/growth & development/embryology
*Neurogenesis/physiology
Platyhelminths/growth & development/physiology
Biological Evolution
Neurons/cytology/physiology

@article {pmid38894655,
year = {2024},
author = {Murayama, F and Asai, H and Patra, AK and Wake, H and Miyata, T and Hattori, Y},
title = {A novel preparation for histological analyses of intraventricular macrophages in the embryonic brain.},
journal = {Development, growth & differentiation},
volume = {},
number = {},
pages = {},
doi = {10.1111/dgd.12935},
pmid = {38894655},
issn = {1440-169X},
support = {JPMJCR22P6//Core Research for Evolutional Science and Technology/ ; JPMJFR214C//Fusion Oriented REsearch for disruptive Science and Technology/ ; JP20H05899//Japan Society for the Promotion of Science/ ; JP21H02656//Japan Society for the Promotion of Science/ ; JP23H02658//Japan Society for the Promotion of Science/ ; JP23H04161//Japan Society for the Promotion of Science/ ; //The Uehara Memorial Foundation/ ; //Takeda Science Foundation/ ; //The Sumitomo Foundation/ ; //The Nakajima Foundation/ ; //Tokai Pathways to Global Excellence (T-GEx)/ ; },
abstract = {Microglia colonize the brain starting on embryonic day (E) 9.5 in mice, and their population increases with development. We have previously demonstrated that some microglia are derived from intraventricular macrophages, which frequently infiltrate the pallium at E12.5. To address how the infiltration of intraventricular macrophages is spatiotemporally regulated, histological analyses detecting how these cells associate with the surrounding cells at the site of infiltration into the pallial surface are essential. Using two-photon microscopy-based in vivo imaging, we demonstrated that most intraventricular macrophages adhere to the ventricular surface. This is a useful tool for imaging intraventricular macrophages maintaining their original position, but this method cannot be used for observing deeper brain regions. Meanwhile, we found that conventional cryosection-based and naked pallial slice-based observation resulted in unexpected detachment from the ventricular surface of intraventricular macrophages and their mislocation, suggesting that previous histological analyses might have failed to determine their physiological number and location in the ventricular space. To address this, we sought to establish a methodological preparation that enables us to delineate the structure and cellular interactions when intraventricular macrophages infiltrate the pallium. Here, we report that brain slices pretreated with agarose-embedding maintained adequate density and proper positioning of intraventricular macrophages on the ventricular surface. This method also enabled us to perform the immunostaining. We believe that this is helpful for conducting histological analyses to elucidate the mechanisms underlying intraventricular macrophage infiltration into the pallium and their cellular properties, leading to further understanding of the process of microglial colonization into the developing brain.},
}

@article {pmid38883608,
year = {2024},
author = {Puginier, E and Leal-Fischer, K and Gaitan, J and Lallouet, M and Scotti, PA and Raoux, M and Lang, J},
title = {Extracellular electrophysiology on clonal human β-cell spheroids.},
journal = {Frontiers in endocrinology},
volume = {15},
number = {},
pages = {1402880},
pmid = {38883608},
issn = {1664-2392},
mesh = {Humans ; *Insulin-Secreting Cells/physiology/metabolism/cytology ; *Spheroids, Cellular ; Electrophysiological Phenomena ; Insulin Secretion/physiology ; Glucose/metabolism/pharmacology ; Insulin/metabolism ; Action Potentials/physiology ; Animals ; },
abstract = {BACKGROUND: Pancreatic islets are important in nutrient homeostasis and improved cellular models of clonal origin may very useful especially in view of relatively scarce primary material. Close 3D contact and coupling between β-cells are a hallmark of physiological function improving signal/noise ratios. Extracellular electrophysiology using micro-electrode arrays (MEA) is technically far more accessible than single cell patch clamp, enables dynamic monitoring of electrical activity in 3D organoids and recorded multicellular slow potentials (SP) provide unbiased insight in cell-cell coupling.

OBJECTIVE: We have therefore asked whether 3D spheroids enhance clonal β-cell function such as electrical activity and hormone secretion using human EndoC-βH1, EndoC-βH5 and rodent INS-1 832/13 cells.

METHODS: Spheroids were formed either by hanging drop or proprietary devices. Extracellular electrophysiology was conducted using multi-electrode arrays with appropriate signal extraction and hormone secretion measured by ELISA.

RESULTS: EndoC-βH1 spheroids exhibited increased signals in terms of SP frequency and especially amplitude as compared to monolayers and even single cell action potentials (AP) were quantifiable. Enhanced electrical signature in spheroids was accompanied by an increase in the glucose stimulated insulin secretion index. EndoC-βH5 monolayers and spheroids gave electrophysiological profiles similar to EndoC-βH1, except for a higher electrical activity at 3 mM glucose, and exhibited moreover a biphasic profile. Again, physiological concentrations of GLP-1 increased AP frequency. Spheroids also exhibited a higher secretion index. INS-1 cells did not form stable spheroids, but overexpression of connexin 36, required for cell-cell coupling, increased glucose responsiveness, dampened basal activity and consequently augmented the stimulation index.

CONCLUSION: In conclusion, spheroid formation enhances physiological function of the human clonal β-cell lines and these models may provide surrogates for primary islets in extracellular electrophysiology.},
}

Humans
*Insulin-Secreting Cells/physiology/metabolism/cytology
*Spheroids, Cellular
Electrophysiological Phenomena
Insulin Secretion/physiology
Glucose/metabolism/pharmacology
Insulin/metabolism
Action Potentials/physiology
Animals

@article {pmid38858515,
year = {2024},
author = {Yu, L and Renton, J and Burian, A and Khachaturyan, M and Bayer, T and Kotta, J and Stachowicz, JJ and DuBois, K and Baums, IB and Werner, B and Reusch, TBH},
title = {A somatic genetic clock for clonal species.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {38858515},
issn = {2397-334X},
support = {RGP0042_2020//Human Frontier Science Program (HFSP)/ ; RGP0042_2020//Human Frontier Science Program (HFSP)/ ; RGP0042_2020//Human Frontier Science Program (HFSP)/ ; RGP0042_2020//Human Frontier Science Program (HFSP)/ ; RGP0042_2020//Human Frontier Science Program (HFSP)/ ; },
abstract = {Age and longevity are key parameters for demography and life-history evolution of organisms. In clonal species, a widespread life history among animals, plants, macroalgae and fungi, the sexually produced offspring (genet) grows indeterminately by producing iterative modules, or ramets, and so obscure their age. Here we present a novel molecular clock based on the accumulation of fixed somatic genetic variation that segregates among ramets. Using a stochastic model, we demonstrate that the accumulation of fixed somatic genetic variation will approach linearity after a lag phase, and is determined by the mitotic mutation rate, without direct dependence on asexual generation time. The lag phase decreased with lower stem cell population size, number of founder cells for the formation of new modules, and the ratio of symmetric versus asymmetric cell divisions. We calibrated the somatic genetic clock on cultivated eelgrass Zostera marina genets (4 and 17 years respectively). In a global data set of 20 eelgrass populations, genet ages were up to 1,403 years. The somatic genetic clock is applicable to any multicellular clonal species where the number of founder cells is small, opening novel research avenues to study longevity and, hence, demography and population dynamics of clonal species.},
}

@article {pmid38854040,
year = {2024},
author = {Gahan, JM and Helfrich, LW and Wetzel, LA and Bhanu, NV and Yuan, ZF and Garcia, BA and Klose, R and Booth, DS},
title = {Chromatin profiling identifies putative dual roles for H3K27me3 in regulating transposons and cell type-specific genes in choanoflagellates.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38854040},
support = {/WT_/Wellcome Trust/United Kingdom ; R35 GM147404/GM/NIGMS NIH HHS/United States ; },
abstract = {Gene expression is tightly controlled during animal development to allow the formation of specialized cell types. Our understanding of how animals evolved this exquisite regulatory control remains elusive, but evidence suggests that changes in chromatin-based mechanisms may have contributed. To investigate this possibility, here we examine chromatin-based gene regulatory features in the closest relatives of animals, choanoflagellates. Using Salpingoeca rosetta as a model system, we examined chromatin accessibility and histone modifications at the genome scale and compared these features to gene expression. We first observed that accessible regions of chromatin are primarily associated with gene promoters and found no evidence of distal gene regulatory elements resembling the enhancers that animals deploy to regulate developmental gene expression. Remarkably, a histone modification deposited by polycomb repressive complex 2, histone H3 lysine 27 trimethylation (H3K27me3), appeared to function similarly in S. rosetta to its role in animals, because this modification decorated genes with cell type-specific expression. Additionally, H3K27me3 marked transposons, retaining what appears to be an ancestral role in regulating these elements. We further uncovered a putative new bivalent chromatin state at cell type-specific genes that consists of H3K27me3 and histone H3 lysine 4 mono-methylation (H3K4me1). Together, our discoveries support the scenario that gene-associated histone modification states that underpin development emerged before the evolution of animal multicellularity.},
}

@article {pmid38747603,
year = {2024},
author = {Hu, W-f and Yang, J-y and Wang, J-j and Yuan, S-f and Yue, X-j and Zhang, Z and Zhang, Y-q and Meng, J-y and Li, Y-z},
title = {Characteristics and immune functions of the endogenous CRISPR-Cas systems in myxobacteria.},
journal = {mSystems},
volume = {9},
number = {6},
pages = {e0121023},
doi = {10.1128/msystems.01210-23},
pmid = {38747603},
issn = {2379-5077},
support = {2018YFA0900400//MOST | National Key Research and Development Program of China (NKPs)/ ; 2018YFA0901704//MOST | National Key Research and Development Program of China (NKPs)/ ; 2021YFC2101000//MOST | National Key Research and Development Program of China (NKPs)/ ; 32070030//MOST | National Natural Science Foundation of China (NSFC)/ ; ZR2019BC041//| Natural Science Foundation of Shandong Province ()/ ; },
mesh = {*CRISPR-Cas Systems/genetics ; *Genome, Bacterial/genetics ; *Myxococcales/genetics ; Phylogeny ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; },
abstract = {UNLABELLED: The clustered regularly interspaced short palindromic repeats and their associated proteins (CRISPR-Cas) system widely occurs in prokaryotic organisms to recognize and destruct genetic invaders. Systematic collation and characterization of endogenous CRISPR-Cas systems are conducive to our understanding and potential utilization of this natural genetic machinery. In this study, we screened 39 complete and 692 incomplete genomes of myxobacteria using a combined strategy to dispose of the abridged genome information and revealed at least 19 CRISPR-Cas subtypes, which were distributed with a taxonomic difference and often lost stochastically in intraspecies strains. The cas genes in each subtype were evolutionarily clustered but deeply separated, while most of the CRISPRs were divided into four types based on the motif characteristics of repeat sequences. The spacers recorded in myxobacterial CRISPRs were in high G+C content, matching lots of phages, tiny amounts of plasmids, and, surprisingly, massive organismic genomes. We experimentally demonstrated the immune and self-target immune activities of three endogenous systems in Myxococcus xanthus DK1622 against artificial genetic invaders and revealed the microhomology-mediated end-joining mechanism for the immunity-induced DNA repair but not homology-directed repair. The panoramic view and immune activities imply potential omnipotent immune functions and applications of the endogenous CRISPR-Cas machinery.

IMPORTANCE: Serving as an adaptive immune system, clustered regularly interspaced short palindromic repeats and their associated proteins (CRISPR-Cas) empower prokaryotes to fend off the intrusion of external genetic materials. Myxobacteria are a collective of swarming Gram-stain-negative predatory bacteria distinguished by intricate multicellular social behavior. An in-depth analysis of their intrinsic CRISPR-Cas systems is beneficial for our understanding of the survival strategies employed by host cells within their environmental niches. Moreover, the experimental findings presented in this study not only suggest the robust immune functions of CRISPR-Cas in myxobacteria but also their potential applications.},
}

*CRISPR-Cas Systems/genetics
*Genome, Bacterial/genetics
*Myxococcales/genetics
Phylogeny
Clustered Regularly Interspaced Short Palindromic Repeats/genetics

@article {pmid38848676,
year = {2024},
author = {Patel, AS and Yanai, I},
title = {A developmental constraint model of cancer cell states and tumor heterogeneity.},
journal = {Cell},
volume = {187},
number = {12},
pages = {2907-2918},
doi = {10.1016/j.cell.2024.04.032},
pmid = {38848676},
issn = {1097-4172},
mesh = {Animals ; Humans ; Carcinogenesis/pathology/genetics ; *Models, Biological ; *Neoplasms/pathology/genetics/metabolism ; Single-Cell Analysis ; Transcriptome/genetics ; Neoplastic Stem Cells/pathology ; },
abstract = {Cancer is a disease that stems from a fundamental liability inherent to multicellular life forms in which an individual cell is capable of reneging on the interests of the collective organism. Although cancer is commonly described as an evolutionary process, a less appreciated aspect of tumorigenesis may be the constraints imposed by the organism's developmental programs. Recent work from single-cell transcriptomic analyses across a range of cancer types has revealed the recurrence, plasticity, and co-option of distinct cellular states among cancer cell populations. Here, we note that across diverse cancer types, the observed cell states are proximate within the developmental hierarchy of the cell of origin. We thus posit a model by which cancer cell states are directly constrained by the organism's "developmental map." According to this model, a population of cancer cells traverses the developmental map, thereby generating a heterogeneous set of states whose interactions underpin emergent tumor behavior.},
}

Animals
Humans
Carcinogenesis/pathology/genetics
*Models, Biological
*Neoplasms/pathology/genetics/metabolism
Single-Cell Analysis
Transcriptome/genetics
Neoplastic Stem Cells/pathology

@article {pmid38678594,
year = {2024},
author = {Tsuchikane, Y and Watanabe, M and Kawaguchi, YW and Uehara, K and Nishiyama, T and Sekimoto, H and Tsuchimatsu, T},
title = {Diversity of genome size and chromosome number in homothallic and heterothallic strains of the Closterium peracerosum-strigosum-littorale complex (Desmidiales, Zygnematophyceae, Streptophyta).},
journal = {Journal of phycology},
volume = {60},
number = {3},
pages = {654-667},
doi = {10.1111/jpy.13457},
pmid = {38678594},
issn = {1529-8817},
support = {25304012//Japan Society for the Promotion of Science/ ; 26650147//Japan Society for the Promotion of Science/ ; 18K06367//Japan Society for the Promotion of Science/ ; 19K22446//Japan Society for the Promotion of Science/ ; 19K22448//Japan Society for the Promotion of Science/ ; 15H05237//Japan Society for the Promotion of Science/ ; 16H04836//Japan Society for the Promotion of Science/ ; 16K02518//Japan Society for the Promotion of Science/ ; 18K19365//Japan Society for the Promotion of Science/ ; 20K21451//Japan Society for the Promotion of Science/ ; 21H02549//Japan Society for the Promotion of Science/ ; 22H05177//Japan Society for the Promotion of Science/ ; 19K06827//Japan Society for the Promotion of Science/ ; 24K09588//Japan Society for the Promotion of Science/ ; 15K18583//Japan Society for the Promotion of Science/ ; 17K15165//Japan Society for the Promotion of Science/ ; 22K21352//Japan Society for the Promotion of Science/ ; },
mesh = {*Genome Size ; *Phylogeny ; Closterium/genetics ; },
abstract = {The evolutionary transitions of mating systems between outcrossing and self-fertilization are often suggested to associate with the cytological and genomic changes, but the empirical reports are limited in multicellular organisms. Here we used the unicellular zygnematophycean algae, the Closterium peracerosum-strigosum-littorale (C. psl.) complex, to address whether genomic properties such as genome sizes and chromosome numbers are associated with mating system transitions between homothallism (self-fertility) and heterothallism (self-sterility). Phylogenetic analysis revealed the polyphyly of homothallic strains, suggesting multiple transitions between homothallism and heterothallism in the C. psl. complex. Flow cytometry analysis identified a more than 2-fold genome size variation, ranging from 0.53 to 1.42 Gbp, which was positively correlated with chromosome number variation between strains. Although we did not find consistent trends in genome size change and mating system transitions, the mean chromosome sizes tend to be smaller in homothallic strains than in their relative heterothallic strains. This result suggests that homothallic strains possibly have more fragmented chromosomes, which is consistent with the argument that self-fertilizing populations may tolerate more chromosomal rearrangements.},
}

*Genome Size
*Phylogeny
Closterium/genetics

@article {pmid38844845,
year = {2024},
author = {Almeida, LV and Reis-Cunha, JL and Bartholomeu, DC},
title = {dgfr: an R package to assess sequence diversity of gene families.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {207},
pmid = {38844845},
issn = {1471-2105},
support = {MR/T016019/1//MRC New Investigator Research Grant/ ; APQ-01822-18//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; 310531/2023-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {*Multigene Family ; *Software ; *Genetic Variation/genetics ; Sequence Alignment/methods ; },
abstract = {BACKGROUND: Gene families are groups of homologous genes that often have similar biological functions. These families are formed by gene duplication events throughout evolution, resulting in multiple copies of an ancestral gene. Over time, these copies can acquire mutations and structural variations, resulting in members that may vary in size, motif ordering and sequence. Multigene families have been described in a broad range of organisms, from single-celled bacteria to complex multicellular organisms, and have been linked to an array of phenomena, such as host-pathogen interactions, immune evasion and embryonic development. Despite the importance of gene families, few approaches have been developed for estimating and graphically visualizing their diversity patterns and expression profiles in genome-wide studies.

RESULTS: Here, we introduce an R package named dgfr, which estimates and enables the visualization of sequence divergence within gene families, as well as the visualization of secondary data such as gene expression. The package takes as input a multi-fasta file containing the coding sequences (CDS) or amino acid sequences from a multigene family, performs a pairwise alignment among all sequences, and estimates their distance, which is subjected to dimension reduction, optimal cluster determination, and gene assignment to each cluster. The result is a dataset that allows for the visualization of sequence divergence and expression within the gene family, an approximation of the number of clusters present in the family.

CONCLUSIONS: dgfr provides a way to estimate and study the diversity of gene families, as well as visualize the dispersion and secondary profile of the sequences. The dgfr package is available at https://github.com/lailaviana/dgfr under the GPL-3 license.},
}

*Multigene Family
*Software
*Genetic Variation/genetics
Sequence Alignment/methods

@article {pmid38844553,
year = {2024},
author = {Liao, H and Choi, J and Shendure, J},
title = {Molecular recording using DNA Typewriter.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {38844553},
issn = {1750-2799},
abstract = {Recording molecular information to genomic DNA is a powerful means of investigating topics ranging from multicellular development to cancer evolution. With molecular recording based on genome editing, events such as cell divisions and signaling pathway activity drive specific alterations in a cell's DNA, marking the genome with information about a cell's history that can be read out after the fact. Although genome editing has been used for molecular recording, capturing the temporal relationships among recorded events in mammalian cells remains challenging. The DNA Typewriter system overcomes this limitation by leveraging prime editing to facilitate sequential insertions to an engineered genomic region. DNA Typewriter includes three distinct components: DNA Tape as the 'substrate' to which edits accrue in an ordered manner, the prime editor enzyme, and prime editing guide RNAs, which program insertional edits to DNA Tape. In this protocol, we describe general design considerations for DNA Typewriter, step-by-step instructions on how to perform recording experiments by using DNA Typewriter in HEK293T cells, and example scripts for analyzing DNA Typewriter data (https://doi.org/10.6084/m9.figshare.22728758). This protocol covers two main applications of DNA Typewriter: recording sequential transfection events with programmed barcode insertions by using prime editing and recording lineage information during the expansion of a single cell to many. Compared with other methods that are compatible with mammalian cells, DNA Typewriter enables the recording of temporal information with higher recording capacities and can be completed within 4-6 weeks with basic expertise in molecular cloning, mammalian cell culturing and DNA sequencing data analysis.},
}

@article {pmid38839375,
year = {2024},
author = {Errbii, M and Gadau, J and Becker, K and Schrader, L and Oettler, J},
title = {Causes and consequences of a complex recombinational landscape in the ant Cardiocondyla obscurior.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.278392.123},
pmid = {38839375},
issn = {1549-5469},
abstract = {Eusocial Hymenoptera have the highest recombination rates among all multicellular animals studied so far, but it is unclear why this is and how this affects the biology of individual species. A high-resolution linkage map for the ant Cardiocondyla obscurior corroborates genome-wide high recombination rates reported for ants (8.1 cM/Mb). However, recombination is locally suppressed in regions either enriched with TEs, with strong haplotype divergence, or showing signatures of epistatic selection in C. obscurior The results do not support the hypotheses that high recombination rates are linked to phenotypic plasticity or to modulating selection efficiency. Instead, genetic diversity and the frequency of structural variants correlate positively with local recombination rates, potentially compensating for the low levels of genetic variation expected in haplodiploid social Hymenoptera with low effective population size. Ultimately, the data show that recombination contributes to within-population polymorphism and to the divergence of the lineages within C. obscurior.},
}

@article {pmid38832756,
year = {2024},
author = {Bierenbroodspot, M and Pröschold, T and Fürst-Jansen, JMR and de Vries, S and Irisarri, I and Darienko, T and de Vries, J},
title = {Phylogeny and evolution of streptophyte algae.},
journal = {Annals of botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/aob/mcae091},
pmid = {38832756},
issn = {1095-8290},
abstract = {The Streptophyta emerged about a billion years ago. Nowadays, this branch of the green lineage is most famous for one of its clades, the land plants (Embryophyta). While Embryophyta make up the major share of species numbers in Streptophyta, there is a diversity of likely more than 5000 species of streptophyte algae that form a paraphyletic grade next to land plants. Here, we focus on the deep divergences that gave rise to the diversity of streptophytes-and thus, particularly on the streptophyte algae. Phylogenomic efforts have not only clarified the position of streptophyte algae to land plants but recent efforts have also begun to unravel the relationships and major radiations within streptophyte algal diversity. We illustrate how new phylogenomic perspectives have changed our view on the evolutionary emergence of key traits such as intricate signaling networks that are intertwined with multicellular growth and the chemodiverse hotbed from which they emerged. These traits are key for the biology of land plants-but were bequeathed from their algal progenitors.},
}

@article {pmid38831923,
year = {2023},
author = {Jackson, JA and Romeo, N and Mietke, A and Burns, KJ and Totz, JF and Martin, AC and Dunkel, J and Alsous, JI},
title = {Scaling behaviour and control of nuclear wrinkling.},
journal = {Nature physics},
volume = {19},
number = {12},
pages = {1927-1935},
pmid = {38831923},
issn = {1745-2473},
support = {R35 GM144115/GM/NIGMS NIH HHS/United States ; },
abstract = {The cell nucleus is enveloped by a complex membrane, whose wrinkling has been implicated in disease and cellular aging. The biophysical dynamics and spectral evolution of nuclear wrinkling during multicellular development remain poorly understood due to a lack of direct quantitative measurements. Here, we characterize the onset and dynamics of nuclear wrinkling during egg development in the fruit fly when nurse cell nuclei increase in size and display stereotypical wrinkling behavior. A spectral analysis of three-dimensional high-resolution live imaging data from several hundred nuclei reveals a robust asymptotic power-law scaling of angular fluctuations consistent with renormalization and scaling predictions from a nonlinear elastic shell model. We further demonstrate that nuclear wrinkling can be reversed through osmotic shock and suppressed by microtubule disruption, providing tuneable physical and biological control parameters for probing mechanical properties of the nuclear envelope. Our findings advance the biophysical understanding of nuclear membrane fluctuations during early multicellular development.},
}

@article {pmid38820160,
year = {2024},
author = {Stillinovic, M and Sarangdhar, MA and Andina, N and Tardivel, A and Greub, F and Bombaci, G and Ansermet, C and Zatti, M and Saha, D and Xiong, J and Sagae, T and Yokogawa, M and Osawa, M and Heller, M and Keogh, A and Keller, I and Angelillo-Scherrer, A and Allam, R},
title = {Ribonuclease inhibitor and angiogenin system regulates cell type-specific global translation.},
journal = {Science advances},
volume = {10},
number = {22},
pages = {eadl0320},
pmid = {38820160},
issn = {2375-2548},
mesh = {*Ribonuclease, Pancreatic/metabolism/genetics ; Humans ; *Protein Biosynthesis ; Animals ; Mice ; *Ribosomes/metabolism ; RNA, Messenger/genetics/metabolism ; Gene Expression Regulation ; Cell Line ; Organ Specificity ; Carrier Proteins ; },
abstract = {Translation of mRNAs is a fundamental process that occurs in all cell types of multicellular organisms. Conventionally, it has been considered a default step in gene expression, lacking specific regulation. However, recent studies have documented that certain mRNAs exhibit cell type-specific translation. Despite this, it remains unclear whether global translation is controlled in a cell type-specific manner. By using human cell lines and mouse models, we found that deletion of the ribosome-associated protein ribonuclease inhibitor 1 (RNH1) decreases global translation selectively in hematopoietic-origin cells but not in the non-hematopoietic-origin cells. RNH1-mediated cell type-specific translation is mechanistically linked to angiogenin-induced ribosomal biogenesis. Collectively, this study unravels the existence of cell type-specific global translation regulators and highlights the complex translation regulation in vertebrates.},
}

*Ribonuclease, Pancreatic/metabolism/genetics
Humans
*Protein Biosynthesis
Animals
Mice
*Ribosomes/metabolism
RNA, Messenger/genetics/metabolism
Gene Expression Regulation
Cell Line
Organ Specificity
Carrier Proteins

@article {pmid38813885,
year = {2024},
author = {Bennett, GM and Kwak, Y and Maynard, R},
title = {Endosymbioses have shaped the evolution of biological diversity and complexity time and time again.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae112},
pmid = {38813885},
issn = {1759-6653},
abstract = {Life on Earth comprises prokaryotes and a broad assemblage of endosymbioses. The pages of Molecular Biology and Evolution (MBE) and Genome Biology and Evolution (GBE) have provided an essential window into how endosymbioses have evolved and shaped biological diversity. Here, we provide a current perspective on this knowledge by drawing on decades of revelatory research published in MBE and GBE, and insights from the field at large. The accumulated work clearly illustrates how endosymbioses provide hosts with novel phenotypes that allow them to transition between adaptive landscapes to access environmental resources. Such endosymbiotic relationships have shaped and reshaped life on Earth. The early serial establishment of mitochondria and chloroplasts through endosymbioses permitted massive upscaling of cellular energetics, multicellularity, and terrestrial planetary greening. These endosymbioses are also the foundation upon which all later ones are built, including everything from land-plant endosymbioses with fungi and bacteria to the nutritional endosymbioses found in invertebrate animals. Common evolutionary mechanisms have shaped this broad range of interactions. Endosymbionts generally experience adaptive and stochastic genome streamlining, the extent of which depends on several key factors (e.g., mode of transmission). Hosts, in contrast, adapt complex mechanisms of resource exchange, cellular integration and regulation, and genetic support mechanisms to prop up degraded symbionts. However, there are significant differences between endosymbiotic interactions not only in how partners have evolved with each other, but also in the scope of their influence on biological diversity. These differences are important considerations for predicting how endosymbioses will persist and adapt to a changing planet.},
}

@article {pmid38811562,
year = {2024},
author = {Li, XC and Gandara, L and Ekelöf, M and Richter, K and Alexandrov, T and Crocker, J},
title = {Rapid response of fly populations to gene dosage across development and generations.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {4551},
pmid = {38811562},
issn = {2041-1723},
mesh = {Animals ; *Drosophila Proteins/genetics/metabolism ; *Gene Expression Regulation, Developmental ; *Gene Regulatory Networks ; Female ; *Drosophila melanogaster/genetics/growth & development/embryology ; *Gene Dosage ; Homeodomain Proteins/genetics/metabolism ; Phenotype ; Male ; Embryo, Nonmammalian/metabolism ; Drosophila/genetics/embryology/metabolism ; Mutagenesis ; Trans-Activators ; },
abstract = {Although the effects of genetic and environmental perturbations on multicellular organisms are rarely restricted to single phenotypic layers, our current understanding of how developmental programs react to these challenges remains limited. Here, we have examined the phenotypic consequences of disturbing the bicoid regulatory network in early Drosophila embryos. We generated flies with two extra copies of bicoid, which causes a posterior shift of the network's regulatory outputs and a decrease in fitness. We subjected these flies to EMS mutagenesis, followed by experimental evolution. After only 8-15 generations, experimental populations have normalized patterns of gene expression and increased survival. Using a phenomics approach, we find that populations were normalized through rapid increases in embryo size driven by maternal changes in metabolism and ovariole development. We extend our results to additional populations of flies, demonstrating predictability. Together, our results necessitate a broader view of regulatory network evolution at the systems level.},
}

Animals
*Drosophila Proteins/genetics/metabolism
*Gene Expression Regulation, Developmental
*Gene Regulatory Networks
Female
*Drosophila melanogaster/genetics/growth & development/embryology
*Gene Dosage
Homeodomain Proteins/genetics/metabolism
Phenotype
Male
Embryo, Nonmammalian/metabolism
Drosophila/genetics/embryology/metabolism
Mutagenesis
Trans-Activators

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

@article {pmid38798503,
year = {2024},
author = {Perotti, O and Esparza, GV and Booth, DS},
title = {A red algal polysaccharide influences the multicellular development of the choanoflagellate Salpingoeca rosetta.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.05.14.594265},
pmid = {38798503},
abstract = {We uncovered an interaction between a choanoflagellate and alga, in which porphyran, a polysaccharide produced by the red alga Porphyra umbilicalis , induces multicellular development in the choanoflagellate Salpingoeca rosetta . We first noticed this possible interaction when we tested the growth of S. rosetta in media that was steeped with P. umbilicalis as a nutritional source. Under those conditions, S. rosetta formed multicellular rosette colonies even in the absence of any bacterial species that can induce rosette development. In biochemical purifications, we identified porphyran, a extracellular polysaccharide produced by red algae, as the rosette inducing factor The response of S. rosetta to porphyran provides a biochemical insight for associations between choanoflagellates and algae that have been observed since the earliest descriptions of choanoflagellates. Moreover, this work provides complementary evidence to ecological and geochemical studies that show the profound impact algae have exerted on eukaryotes and their evolution, including a rise in algal productivity that coincided with the origin of animals, the closest living relatives of choanoflagellates.},
}

@article {pmid38798415,
year = {2024},
author = {Kidner, RQ and Goldstone, EB and Rodefeld, HJ and Brokaw, LP and Gonzalez, AM and Ros-Rocher, N and Gerdt, JP},
title = {Exogenous lipid vesicles induce endocytosis-mediated cellular aggregation in a close unicellular relative of animals.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.05.14.593945},
pmid = {38798415},
abstract = {Capsaspora owczarzaki is a protozoan that may both reveal aspects of animal evolution and also curtail the spread of schistosomiasis, a neglected tropical disease. Capsaspora exhibits a chemically regulated aggregative behavior that resembles cellular aggregation in some animals. This behavior may have played a key role in the evolution of animal multicellularity. Additionally, this aggregative behavior may be important for Capsaspora 's ability to colonize the intermediate host of parasitic schistosomes and potentially prevent the spread of schistosomiasis. Both applications demand elucidation of the molecular mechanism of Capsaspora aggregation. Toward this goal, we first determined the necessary chemical properties of lipid cues that activate aggregation. We found that a wide range of abundant zwitterionic lipids induced aggregation, revealing that the aggregative behavior could be activated by diverse lipid-rich conditions. Furthermore, we demonstrated that aggregation in Capsaspora requires clathrin-mediated endocytosis, highlighting the potential significance of endocytosis-linked cellular signaling in recent animal ancestors. Finally, we found that aggregation was initiated by post-translational activation of cell-cell adhesion-not transcriptional regulation of cellular adhesion machinery. Our findings illuminate the chemical, molecular and cellular mechanisms that regulate Capsaspora aggregative behavior-with implications for the evolution of animal multicellularity and the transmission of parasites.},
}

@article {pmid38791309,
year = {2024},
author = {Bibo-Verdugo, B and Salvesen, G},
title = {Evolution of Caspases and the Invention of Pyroptosis.},
journal = {International journal of molecular sciences},
volume = {25},
number = {10},
pages = {},
pmid = {38791309},
issn = {1422-0067},
mesh = {*Pyroptosis ; Humans ; *Caspases/metabolism ; Animals ; *Immunity, Innate ; Evolution, Molecular ; Apoptosis ; },
abstract = {The protein scaffold that includes the caspases is ancient and found in all domains of life. However, the stringent specificity that defines the caspase biologic function is relatively recent and found only in multicellular animals. During the radiation of the Chordata, members of the caspase family adopted roles in immunity, events coinciding with the development of substrates that define the modern innate immune response. This review focuses on the switch from the non-inflammatory cellular demise of apoptosis to the highly inflammatory innate response driven by distinct members of the caspase family, and the interplay between these two regulated cell death pathways.},
}

*Pyroptosis
Humans
*Caspases/metabolism
Animals
*Immunity, Innate
Evolution, Molecular
Apoptosis

@article {pmid38790063,
year = {2024},
author = {Zhang, B and Xiao, L and Lyu, L and Zhao, F and Miao, M},
title = {Exploring the landscape of symbiotic diversity and distribution in unicellular ciliated protists.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {96},
pmid = {38790063},
issn = {2049-2618},
mesh = {*Symbiosis ; *Ciliophora/genetics/classification/physiology ; *Bacteria/genetics/classification ; Archaea/genetics/classification ; Phylogeny ; Metagenome ; Biodiversity ; },
abstract = {BACKGROUND: The eukaryotic-bacterial symbiotic system plays an important role in various physiological, developmental, and evolutionary processes. However, our current understanding is largely limited to multicellular eukaryotes without adequate consideration of diverse unicellular protists, including ciliates.

RESULTS: To investigate the bacterial profiles associated with unicellular organisms, we collected 246 ciliate samples spanning the entire Ciliophora phylum and conducted single-cell based metagenome sequencing. This effort has yielded the most extensive collection of bacteria linked to unicellular protists to date. From this dataset, we identified 883 bacterial species capable of cohabiting with ciliates, unveiling the genomes of 116 novel bacterial cohabitants along with 7 novel archaeal cohabitants. Highlighting the intimate relationship between ciliates and their cohabitants, our study unveiled that over 90% of ciliates coexist with bacteria, with individual hosts fostering symbiotic relationships with multiple bacteria concurrently, resulting in the observation of seven distinct symbiotic patterns among bacteria. Our exploration of symbiotic mechanisms revealed the impact of host digestion on the intracellular diversity of cohabitants. Additionally, we identified the presence of eukaryotic-like proteins in bacteria as a potential contributing factor to their resistance against host digestion, thereby expanding their potential host range.

CONCLUSIONS: As the first large-scale analysis of prokaryotic associations with ciliate protists, this study provides a valuable resource for future research on eukaryotic-bacterial symbioses. Video Abstract.},
}

*Symbiosis
*Ciliophora/genetics/classification/physiology
*Bacteria/genetics/classification
Archaea/genetics/classification
Phylogeny
Metagenome
Biodiversity

@article {pmid38778808,
year = {2023},
author = {Ondracka, A and Dudin, O and Bråte, J},
title = {Time-resolved small RNA transcriptomics of the ichthyosporean Sphaeroforma arctica.},
journal = {F1000Research},
volume = {12},
number = {},
pages = {542},
pmid = {38778808},
issn = {2046-1402},
mesh = {*Transcriptome ; Mesomycetozoea/genetics ; MicroRNAs/genetics ; Gene Expression Profiling ; },
abstract = {Ichthyosporea, a clade of holozoans, represent a clade closely related to animals, and thus hold a key phylogenetic position for understanding the origin of animals. We have previously discovered that an ichthyosporean, Sphaeroforma arctica, contains microRNAs (miRNAs) as well as the miRNA processing machinery. This was the first discovery of miRNAs among the closest single-celled relatives of animals and raised intriguing questions about the roles of regulatory small RNAs in cell development and differentiation in unicellular eukaryotes. Like many ichthyosporeans, S. arctica also undergoes a transient multicellular developmental life cycle. As miRNAs are, among other roles, key regulators of gene expression during development in animals, we wanted to investigate the dynamics of miRNAs during the developmental cycle in S. arctica. Here we have therefore collected a comprehensive time-resolved small RNA transcriptome linked to specific life stages with a substantially higher sequencing depth than before, which can enable further discovery of functionally relevant small RNAs. The data consists of Illumina-sequenced small RNA libraries from two independent biological replicates of the entire life cycle of S. arctica with high temporal resolution. The dataset is directly linked and comes from the same samples as a previously published mRNA-seq dataset, thus enabling direct cross-functional analyses.},
}

*Transcriptome
Mesomycetozoea/genetics
MicroRNAs/genetics
Gene Expression Profiling

@article {pmid38773319,
year = {2024},
author = {Cho, CJ and Brown, JW and Mills, JC},
title = {Origins of cancer: ain't it just mature cells misbehaving?.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {},
pmid = {38773319},
issn = {1460-2075},
support = {K08 DK132496/DK/NIDDK NIH HHS/United States ; R21 AI156236/AI/NIAID NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; R01DK105129//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; R01DK134531//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; P30 DK056338/DK/NIDDK NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; W81XWH-20-1-0630//DOD | USA | MEDCOM | CDMRP | DOD Peer Reviewed Cancer Research Program (PRCRP)/ ; W81XWH2210327//DOD | USA | MEDCOM | CDMRP | DOD Peer Reviewed Cancer Research Program (PRCRP)/ ; R01 CA239645/CA/NCI NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; },
abstract = {A pervasive view is that undifferentiated stem cells are alone responsible for generating all other cells and are the origins of cancer. However, emerging evidence demonstrates fully differentiated cells are plastic, can be coaxed to proliferate, and also play essential roles in tissue maintenance, regeneration, and tumorigenesis. Here, we review the mechanisms governing how differentiated cells become cancer cells. First, we examine the unique characteristics of differentiated cell division, focusing on why differentiated cells are more susceptible than stem cells to accumulating mutations. Next, we investigate why the evolution of multicellularity in animals likely required plastic differentiated cells that maintain the capacity to return to the cell cycle and required the tumor suppressor p53. Finally, we examine an example of an evolutionarily conserved program for the plasticity of differentiated cells, paligenosis, which helps explain the origins of cancers that arise in adults. Altogether, we highlight new perspectives for understanding the development of cancer and new strategies for preventing carcinogenic cellular transformations from occurring.},
}

@article {pmid38773187,
year = {2024},
author = {MacDonald, N and Raven, N and Diep, W and Evans, S and Pannipitiya, S and Bramwell, G and Vanbeek, C and Thomas, F and Russell, T and Dujon, AM and Telonis-Scott, M and Ujvari, B},
title = {The molecular evolution of cancer associated genes in mammals.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {11650},
pmid = {38773187},
issn = {2045-2322},
mesh = {Animals ; *Evolution, Molecular ; *Mammals/genetics ; *Neoplasms/genetics ; *Phylogeny ; Humans ; Selection, Genetic ; Oncogenes/genetics ; Genes, Tumor Suppressor ; Genetic Predisposition to Disease ; },
abstract = {Cancer is a disease that many multicellular organisms have faced for millions of years, and species have evolved various tumour suppression mechanisms to control oncogenesis. Although cancer occurs across the tree of life, cancer related mortality risks vary across mammalian orders, with Carnivorans particularly affected. Evolutionary theory predicts different selection pressures on genes associated with cancer progression and suppression, including oncogenes, tumour suppressor genes and immune genes. Therefore, we investigated the evolutionary history of cancer associated gene sequences across 384 mammalian taxa, to detect signatures of selection across categories of oncogenes (GRB2, FGL2 and CDC42), tumour suppressors (LITAF, Casp8 and BRCA2) and immune genes (IL2, CD274 and B2M). This approach allowed us to conduct a fine scale analysis of gene wide and site-specific signatures of selection across mammalian lineages under the lens of cancer susceptibility. Phylogenetic analyses revealed that for most species the evolution of cancer associated genes follows the species' evolution. The gene wide selection analyses revealed oncogenes being the most conserved, tumour suppressor and immune genes having similar amounts of episodic diversifying selection. Despite BRCA2's status as a key caretaker gene, episodic diversifying selection was detected across mammals. The site-specific selection analyses revealed that the two apoptosis associated domains of the Casp8 gene of bats (Chiroptera) are under opposing forces of selection (positive and negative respectively), highlighting the importance of site-specific selection analyses to understand the evolution of highly complex gene families. Our results highlighted the need to critically assess different types of selection pressure on cancer associated genes when investigating evolutionary adaptations to cancer across the tree of life. This study provides an extensive assessment of cancer associated genes in mammals with highly representative, and substantially large sample size for a comparative genomic analysis in the field and identifies various avenues for future research into the mechanisms of cancer resistance and susceptibility in mammals.},
}

Animals
*Evolution, Molecular
*Mammals/genetics
*Neoplasms/genetics
*Phylogeny
Humans
Selection, Genetic
Oncogenes/genetics
Genes, Tumor Suppressor
Genetic Predisposition to Disease

@article {pmid38770108,
year = {2024},
author = {Luu, N and Zhang, S and Lam, RHW and Chen, W},
title = {Mechanical Constraints in Tumor Guide Emergent Spatial Patterns of Glioblastoma Cancer Stem Cells.},
journal = {Mechanobiology in medicine},
volume = {2},
number = {1},
pages = {},
pmid = {38770108},
issn = {2949-9070},
abstract = {The mechanical constraints in the overcrowding glioblastoma (GBM) microenvironment have been implicated in the regulation of tumor heterogeneity and disease progression. Especially, such mechanical cues can alter cellular DNA transcription and give rise to a subpopulation of tumor cells called cancer stem cells (CSCs). These CSCs with stem-like properties are critical drivers of tumorigenesis, metastasis, and treatment resistance. Yet, the biophysical and molecular machinery underlying the emergence of CSCs in tumor remained unexplored. This work employed a two-dimensional micropatterned multicellular model to examine the impact of mechanical constraints arisen from geometric confinement on the emergence and spatial patterning of CSCs in GBM tumor. Our study identified distinct spatial distributions of GBM CSCs in different geometric patterns, where CSCs mostly emerged in the peripheral regions. The spatial pattern of CSCs was found to correspond to the gradients of mechanical stresses resulted from the interplay between the cell-ECM and cell-cell interactions within the confined environment. Further mechanistic study highlighted a Piezo1-RhoA-focal adhesion signaling axis in regulating GBM cell mechanosensing and the subsequent CSC phenotypic transformation. These findings provide new insights into the biophysical origin of the unique spatial pattern of CSCs in GBM tumor and offer potential avenues for targeted therapeutic interventions.},
}

@article {pmid38766090,
year = {2024},
author = {Balasenthilkumaran, NV and Whitesell, JC and Pyle, L and Friedman, R and Kravets, V},
title = {Network approach reveals preferential T-cell and macrophage association with α-linked β-cells in early stage of insulitis in NOD mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.05.06.592831},
pmid = {38766090},
abstract = {One of the challenges in studying islet inflammation - insulitis - is that it is a transient phenomenon. Traditional reporting of the insulitis progression is based on cumulative, donor-averaged values of leucocyte density in the vicinity of pancreatic islets, that hinders intra- and inter-islet heterogeneity of disease progression. Here, we aimed to understand why insulitis is non-uniform, often with peri-insulitis lesions formed on one side of an islet. To achieve this, we demonstrated applicability of network theory in detangling intra-islet multi-cellular interactions during insulitis. Specifically, we asked the question "what is unique about regions of the islet which interact with immune cells first". This study utilized the non-obese diabetic mouse model of type one diabetes and examined the interplay among α-, β-, T-cells, myeloid cells, and macrophages in pancreatic islets during the progression of insulitis. Disease evolution was tracked based on T/β cell ratio in individual islets. In the early stage, we found that immune cells are preferentially interacting with α-cell-rich regions of an islet. At the islet periphery α-linked β-cells were found to be targeted significantly more compared to those without α-cell neighbors. Additionally, network analysis revealed increased T-myeloid, and T-macrophage interactions with all β-cells.},
}

@article {pmid38755817,
year = {2024},
author = {Derényi, I and Demeter, MC and Pérez-Jiménez, M and Grajzel, D and Szöllősi, GJ},
title = {How mutation accumulation depends on the structure of the cell lineage tree.},
journal = {Physical review. E},
volume = {109},
number = {4-1},
pages = {044407},
doi = {10.1103/PhysRevE.109.044407},
pmid = {38755817},
issn = {2470-0053},
mesh = {*Cell Lineage ; *Models, Genetic ; Mutation Accumulation ; Mutation ; },
abstract = {All the cells of a multicellular organism are the product of cell divisions that trace out a single binary tree, the so-called cell lineage tree. Because cell divisions are accompanied by replication errors, the shape of the cell lineage tree is a key determinant of how somatic evolution, which can potentially lead to cancer, proceeds. Carcinogenesis requires the accumulation of a certain number of driver mutations. By mapping the accumulation of mutations into a graph theoretical problem, we present an exact numerical method to calculate the probability of collecting a given number of mutations and show that for low mutation rates it can be approximated with a simple analytical formula, which depends only on the distribution of the lineage lengths, and is dominated by the longest lineages. Our results are crucial in understanding how natural selection can shape the cell lineage trees of multicellular organisms and curtail somatic evolution.},
}

*Cell Lineage
*Models, Genetic
Mutation Accumulation
Mutation

@article {pmid38735988,
year = {2024},
author = {Aprile, D and Patrone, D and Peluso, G and Galderisi, U},
title = {Multipotent/pluripotent stem cell populations in stromal tissues and peripheral blood: exploring diversity, potential, and therapeutic applications.},
journal = {Stem cell research & therapy},
volume = {15},
number = {1},
pages = {139},
pmid = {38735988},
issn = {1757-6512},
support = {PE0000006 MNESYS//European Commission/ ; },
mesh = {Humans ; *Pluripotent Stem Cells/cytology/metabolism ; *Multipotent Stem Cells/cytology/metabolism ; Cell Differentiation ; Stromal Cells/cytology/metabolism ; Animals ; },
abstract = {The concept of "stemness" incorporates the molecular mechanisms that regulate the unlimited self-regenerative potential typical of undifferentiated primitive cells. These cells possess the unique ability to navigate the cell cycle, transitioning in and out of the quiescent G0 phase, and hold the capacity to generate diverse cell phenotypes. Stem cells, as undifferentiated precursors endow with extraordinary regenerative capabilities, exhibit a heterogeneous and tissue-specific distribution throughout the human body. The identification and characterization of distinct stem cell populations across various tissues have revolutionized our understanding of tissue homeostasis and regeneration. From the hematopoietic to the nervous and musculoskeletal systems, the presence of tissue-specific stem cells underlines the complex adaptability of multicellular organisms. Recent investigations have revealed a diverse cohort of non-hematopoietic stem cells (non-HSC), primarily within bone marrow and other stromal tissue, alongside established hematopoietic stem cells (HSC). Among these non-HSC, a rare subset exhibits pluripotent characteristics. In vitro and in vivo studies have demonstrated the remarkable differentiation potential of these putative stem cells, known by various names including multipotent adult progenitor cells (MAPC), marrow-isolated adult multilineage inducible cells (MIAMI), small blood stem cells (SBSC), very small embryonic-like stem cells (VSELs), and multilineage differentiating stress enduring cells (MUSE). The diverse nomenclatures assigned to these primitive stem cell populations may arise from different origins or varied experimental methodologies. This review aims to present a comprehensive comparison of various subpopulations of multipotent/pluripotent stem cells derived from stromal tissues. By analysing isolation techniques and surface marker expression associated with these populations, we aim to delineate the similarities and distinctions among stromal tissue-derived stem cells. Understanding the nuances of these tissue-specific stem cells is critical for unlocking their therapeutic potential and advancing regenerative medicine. The future of stem cells research should prioritize the standardization of methodologies and collaborative investigations in shared laboratory environments. This approach could mitigate variability in research outcomes and foster scientific partnerships to fully exploit the therapeutic potential of pluripotent stem cells.},
}

Humans
*Pluripotent Stem Cells/cytology/metabolism
*Multipotent Stem Cells/cytology/metabolism
Cell Differentiation
Stromal Cells/cytology/metabolism
Animals

@article {pmid38734320,
year = {2024},
author = {Lenz, G},
title = {Heterogeneity generating capacity in tumorigenesis and cancer therapeutics.},
journal = {Biochimica et biophysica acta. Molecular basis of disease},
volume = {},
number = {},
pages = {167226},
doi = {10.1016/j.bbadis.2024.167226},
pmid = {38734320},
issn = {1879-260X},
abstract = {Cells of multicellular organisms generate heterogeneity in a controlled and transient fashion during embryogenesis, which can be reactivated in pathologies such as cancer. Although genomic heterogeneity is an important part of tumorigenesis, continuous generation of phenotypic heterogeneity is central for the adaptation of cancer cells to the challenges of tumorigenesis and response to therapy. Here I discuss the capacity of generating heterogeneity, hereafter called cell hetness, in cancer cells both as the activation of hetness oncogenes and inactivation of hetness tumor suppressor genes, which increase the generation of heterogeneity, ultimately producing an increase in adaptability and cell fitness. Transcriptomic high hetness states in therapy-tolerant cell states denote its importance in cancer resistance to therapy. The definition of the concept of hetness will allow the understanding of its origins, its control during embryogenesis, its loss of control in tumorigenesis and cancer therapeutics and its active targeting.},
}

@article {pmid38720073,
year = {2024},
author = {Yaron-Barir, TM and Joughin, BA and Huntsman, EM and Kerelsky, A and Cizin, DM and Cohen, BM and Regev, A and Song, J and Vasan, N and Lin, TY and Orozco, JM and Schoenherr, C and Sagum, C and Bedford, MT and Wynn, RM and Tso, SC and Chuang, DT and Li, L and Li, SS and Creixell, P and Krismer, K and Takegami, M and Lee, H and Zhang, B and Lu, J and Cossentino, I and Landry, SD and Uduman, M and Blenis, J and Elemento, O and Frame, MC and Hornbeck, PV and Cantley, LC and Turk, BE and Yaffe, MB and Johnson, JL},
title = {The intrinsic substrate specificity of the human tyrosine kinome.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {38720073},
issn = {1476-4687},
abstract = {Phosphorylation of proteins on tyrosine (Tyr) residues evolved in metazoan organisms as a mechanism of coordinating tissue growth[1]. Multicellular eukaryotes typically have more than 50 distinct protein Tyr kinases that catalyse the phosphorylation of thousands of Tyr residues throughout the proteome[1-3]. How a given Tyr kinase can phosphorylate a specific subset of proteins at unique Tyr sites is only partially understood[4-7]. Here we used combinatorial peptide arrays to profile the substrate sequence specificity of all human Tyr kinases. Globally, the Tyr kinases demonstrate considerable diversity in optimal patterns of residues surrounding the site of phosphorylation, revealing the functional organization of the human Tyr kinome by substrate motif preference. Using this information, Tyr kinases that are most compatible with phosphorylating any Tyr site can be identified. Analysis of mass spectrometry phosphoproteomic datasets using this compendium of kinase specificities accurately identifies specific Tyr kinases that are dysregulated in cells after stimulation with growth factors, treatment with anti-cancer drugs or expression of oncogenic variants. Furthermore, the topology of known Tyr signalling networks naturally emerged from a comparison of the sequence specificities of the Tyr kinases and the SH2 phosphotyrosine (pTyr)-binding domains. Finally we show that the intrinsic substrate specificity of Tyr kinases has remained fundamentally unchanged from worms to humans, suggesting that the fidelity between Tyr kinases and their protein substrate sequences has been maintained across hundreds of millions of years of evolution.},
}

@article {pmid38598600,
year = {2024},
author = {Wang, H and Marucci, G and Munke, A and Hassan, MM and Lalle, M and Okamoto, K},
title = {High-resolution comparative atomic structures of two Giardiavirus prototypes infecting G. duodenalis parasite.},
journal = {PLoS pathogens},
volume = {20},
number = {4},
pages = {e1012140},
doi = {10.1371/journal.ppat.1012140},
pmid = {38598600},
issn = {1553-7374},
mesh = {*Giardia lamblia/ultrastructure/pathogenicity ; *Giardiavirus/genetics ; Cryoelectron Microscopy ; Animals ; Capsid/ultrastructure/metabolism ; Humans ; Phylogeny ; },
abstract = {The Giardia lamblia virus (GLV) is a non-enveloped icosahedral dsRNA and endosymbiont virus that infects the zoonotic protozoan parasite Giardia duodenalis (syn. G. lamblia, G. intestinalis), which is a pathogen of mammals, including humans. Elucidating the transmission mechanism of GLV is crucial for gaining an in-depth understanding of the virulence of the virus in G. duodenalis. GLV belongs to the family Totiviridae, which infects yeast and protozoa intracellularly; however, it also transmits extracellularly, similar to the phylogenetically, distantly related toti-like viruses that infect multicellular hosts. The GLV capsid structure is extensively involved in the longstanding discussion concerning extracellular transmission in Totiviridae and toti-like viruses. Hence, this study constructed the first high-resolution comparative atomic models of two GLV strains, namely GLV-HP and GLV-CAT, which showed different intracellular localization and virulence phenotypes, using cryogenic electron microscopy single-particle analysis. The atomic models of the GLV capsids presented swapped C-terminal extensions, extra surface loops, and a lack of cap-snatching pockets, similar to those of toti-like viruses. However, their open pores and absence of the extra crown protein resemble those of other yeast and protozoan Totiviridae viruses, demonstrating the essential structures for extracellular cell-to-cell transmission. The structural comparison between GLV-HP and GLV-CAT indicates the first evidence of critical structural motifs for the transmission and virulence of GLV in G. duodenalis.},
}

*Giardia lamblia/ultrastructure/pathogenicity
*Giardiavirus/genetics
Cryoelectron Microscopy
Animals
Capsid/ultrastructure/metabolism
Humans
Phylogeny

@article {pmid38713735,
year = {2024},
author = {Oszoli, I and Zachar, I},
title = {Group-selection via aggregative propagule-formation enables cooperative multicellularity in an individual based, spatial model.},
journal = {PLoS computational biology},
volume = {20},
number = {5},
pages = {e1012107},
doi = {10.1371/journal.pcbi.1012107},
pmid = {38713735},
issn = {1553-7358},
abstract = {The emergence of multicellularity is one of the major transitions in evolution that happened multiple times independently. During aggregative multicellularity, genetically potentially unrelated lineages cooperate to form transient multicellular groups. Unlike clonal multicellularity, aggregative multicellular organisms do not rely on kin selection instead other mechanisms maintain cooperation against cheater phenotypes that benefit from cooperators but do not contribute to groups. Spatiality with limited diffusion can facilitate group selection, as interactions among individuals are restricted to local neighbourhoods only. Selection for larger size (e.g. avoiding predation) may facilitate the emergence of aggregation, though it is unknown, whether and how much role such selection played during the evolution of aggregative multicellularity. We have investigated the effect of spatiality and the necessity of predation on the stability of aggregative multicellularity via individual-based modelling on the ecological timescale. We have examined whether aggregation facilitates the survival of cooperators in a temporally heterogeneous environment against cheaters, where only a subset of the population is allowed to periodically colonize a new, resource-rich habitat. Cooperators constitutively produce adhesive molecules to promote aggregation and propagule-formation while cheaters spare this expense to grow faster but cannot aggregate on their own, hence depending on cooperators for long-term survival. We have compared different population-level reproduction modes with and without individual selection (predation) to evaluate the different hypotheses. In a temporally homogeneous environment without propagule-based colonization, cheaters always win. Predation can benefit cooperators, but it is not enough to maintain the necessary cooperator amount in successive dispersals, either randomly or by fragmentation. Aggregation-based propagation however can ensure the adequate ratio of cooperators-to-cheaters in the propagule and is sufficient to do so even without predation. Spatiality combined with temporal heterogeneity helps cooperators via group selection, thus facilitating aggregative multicellularity. External stress selecting for larger size (e.g. predation) may facilitate aggregation, however, according to our results, it is neither necessary nor sufficient for aggregative multicellularity to be maintained when there is effective group-selection.},
}

@article {pmid38705386,
year = {2024},
author = {Enström, A and Carlsson, R and Buizza, C and Lewi, M and Paul, G},
title = {Pericyte-Specific Secretome Profiling in Hypoxia Using TurboID in a Multicellular In Vitro Spheroid-Model.},
journal = {Molecular & cellular proteomics : MCP},
volume = {},
number = {},
pages = {100782},
doi = {10.1016/j.mcpro.2024.100782},
pmid = {38705386},
issn = {1535-9484},
abstract = {Cellular communication within the brain is imperative for maintaining homeostasis and mounting effective responses to pathological triggers like hypoxia. However, a comprehensive understanding of the precise composition and dynamic release of secreted molecules has remained elusive, confined primarily to investigations using isolated monocultures. To overcome these limitations, we utilized the potential of TurboID, a non-toxic biotin ligation enzyme, to capture and enrich secreted proteins specifically originating from human brain pericytes in spheroid co-cultures with human endothelial cells and astrocytes. This approach allowed us to characterize the pericyte secretome within a more physiologically relevant multi-cellular setting encompassing the constituents of the blood-brain barrier (BBB). Through a combination of mass spectrometry and multiplex immunoassays, we identified a wide spectrum of different secreted proteins by pericytes. Our findings demonstrate that the pericytes secretome is profoundly shaped by their inter-cellular communication with other BBB-residing cells. Moreover, we identified substantial differences in the secretory profiles between hypoxic and normoxic pericytes. Mass spectrometry analysis showed that hypoxic pericytes in co-culture increase their release of signals related to protein secretion, mTOR signalling and the complement system, while hypoxic pericytes in monocultures showed an upregulation in proliferative pathways including G2M checkpoints, E2F- and Myc-targets. In addition, hypoxic pericytes show an upregulation of proangiogenic proteins such as VEGFA but display downregulation of canonical proinflammatory cytokines such as CXCL1, MCP-1, and CXCL6. Understanding the specific composition of secreted proteins in the multi-cellular brain microvasculature is crucial for advancing our knowledge of brain homeostasis and the mechanisms underlying pathology. This study has implications for the identification of targeted therapeutic strategies aimed at modulating microvascular signalling in brain pathologies associated with hypoxia.},
}

@article {pmid38513719,
year = {2024},
author = {Brown, AL and Meiborg, AB and Franz-Wachtel, M and Macek, B and Gordon, S and Rog, O and Weadick, CJ and Werner, MS},
title = {Characterization of the Pristionchus pacificus "epigenetic toolkit" reveals the evolutionary loss of the histone methyltransferase complex PRC2.},
journal = {Genetics},
volume = {227},
number = {1},
pages = {},
doi = {10.1093/genetics/iyae041},
pmid = {38513719},
issn = {1943-2631},
support = {R35 GM128804/GM/NIGMS NIH HHS/United States ; R35 GM150720/GM/NIGMS NIH HHS/United States ; R35GM150720/GM/NIGMS NIH HHS/United States ; T32-GM122740/GF/NIH HHS/United States ; },
mesh = {Animals ; *Epigenesis, Genetic ; *Evolution, Molecular ; *Caenorhabditis elegans/genetics ; Polycomb Repressive Complex 2/genetics/metabolism ; Histone Methyltransferases/metabolism/genetics ; Nematoda/genetics ; Helminth Proteins/genetics/metabolism ; },
abstract = {Comparative approaches have revealed both divergent and convergent paths to achieving shared developmental outcomes. Thus, only through assembling multiple case studies can we understand biological principles. Yet, despite appreciating the conservation-or lack thereof-of developmental networks, the conservation of epigenetic mechanisms regulating these networks is poorly understood. The nematode Pristionchus pacificus has emerged as a model system of plasticity and epigenetic regulation as it exhibits a bacterivorous or omnivorous morph depending on its environment. Here, we determined the "epigenetic toolkit" available to P. pacificus as a resource for future functional work on plasticity, and as a comparison with Caenorhabditis elegans to investigate the conservation of epigenetic mechanisms. Broadly, we observed a similar cast of genes with putative epigenetic function between C. elegans and P. pacificus. However, we also found striking differences. Most notably, the histone methyltransferase complex PRC2 appears to be missing in P. pacificus. We described the deletion/pseudogenization of the PRC2 genes mes-2 and mes-6 and concluded that both were lost in the last common ancestor of P. pacificus and a related species P. arcanus. Interestingly, we observed the enzymatic product of PRC2 (H3K27me3) by mass spectrometry and immunofluorescence, suggesting that a currently unknown methyltransferase has been co-opted for heterochromatin silencing. Altogether, we have provided an inventory of epigenetic genes in P. pacificus to compare with C. elegans. This inventory will enable reverse-genetic experiments related to plasticity and has revealed the first loss of PRC2 in a multicellular organism.},
}

Animals
*Epigenesis, Genetic
*Evolution, Molecular
*Caenorhabditis elegans/genetics
Polycomb Repressive Complex 2/genetics/metabolism
Histone Methyltransferases/metabolism/genetics
Nematoda/genetics
Helminth Proteins/genetics/metabolism

@article {pmid38702020,
year = {2024},
author = {Pozdnyakov, IR and Selyuk, AO and Kalashnikova, VA and Karpov, SA},
title = {HMG-B transcription factors of unicellular opisthokonts and their relatedness to the Sox-Tcf/Lef-Mata proteins of Metazoa and fungi.},
journal = {Gene},
volume = {},
number = {},
pages = {148520},
doi = {10.1016/j.gene.2024.148520},
pmid = {38702020},
issn = {1879-0038},
abstract = {A phylogenetic analysis of transcription factors of the Sox-Tcf/Lef-Mata (STM) family of the HMG-B superfamily was carried out in order to clarify the evolutionary roots of the Wnt signaling pathway in unicellular organisms. The data set for analysis included protein sequences of metazoans, fungi, unicellular opisthokonts, apusomonads and amoebozoans. The topology of the phylogenetic tree suggests that STM-related proteins arose in the common ancestor of Opisthokonta and Amoebozoa, two of amoebozoan STM proteins are sister-related to opisthokont ones and the three known lineages of STM transcription factors (STM family in narrow sence) are found in Opisthokonta only. Of these, the holozoan Sox protein branch is the result of either the first or second branching, that originated in the common ancestor of Opisthokonta. The lineage containing Tcf/Lef proteins (holozoan) and the lineage containing Mata proteins (holomycotan) are sister. They derived either at the time of the Holozoa and Holomycota divergence or originate from two paralogs of the common ancestor of Opisthokonta, which arose after the separation of the Sox lineage. Interaction with Armadillo-like proteins may be an original feature of the STM protein family and existed in the unicellular ancestors of multicellular animals; a connection is possible between the presence of Mata-related proteins in Aphelidium protococcorum and specific genome feature of this species.},
}

@article {pmid38700417,
year = {2024},
author = {Maloney, KM and Halverson, GP and Lechte, M and Gibson, TM and Bui, TH and Schiffbauer, JD and Laflamme, M},
title = {The paleoredox context of early eukaryotic evolution: insights from the Tonian Mackenzie Mountains Supergroup, Canada.},
journal = {Geobiology},
volume = {22},
number = {3},
pages = {e12598},
doi = {10.1111/gbi.12598},
pmid = {38700417},
issn = {1472-4669},
support = {//National Science Foundation/ ; //Polar Continental Shelf Program/ ; //Queen Elizabeth II Graduate Scholarship in Science & Technology (QEII-GSST)/ ; //Agouron Institute/ ; //Geological Society of America Graduate Research Grant/ ; GH RGPIN2017-04025//National Science and Engineering Research Council of Canada (NSERC)/ ; ML RGPIN435402//National Science and Engineering Research Council of Canada (NSERC)/ ; NSF IF 1636643//Northern Scientific Training Program/ ; },
mesh = {*Oxidation-Reduction ; *Fossils ; *Biological Evolution ; Geologic Sediments/chemistry/analysis ; Eukaryota ; Canada ; Ecosystem ; Chlorophyta ; },
abstract = {Tonian (ca. 1000-720 Ma) marine environments are hypothesised to have experienced major redox changes coinciding with the evolution and diversification of multicellular eukaryotes. In particular, the earliest Tonian stratigraphic record features the colonisation of benthic habitats by multicellular macroscopic algae, which would have been powerful ecosystem engineers that contributed to the oxygenation of the oceans and the reorganisation of biogeochemical cycles. However, the paleoredox context of this expansion of macroalgal habitats in Tonian nearshore marine environments remains uncertain due to limited well-preserved fossils and stratigraphy. As such, the interdependent relationship between early complex life and ocean redox state is unclear. An assemblage of macrofossils including the chlorophyte macroalga Archaeochaeta guncho was recently discovered in the lower Mackenzie Mountains Supergroup in Yukon (Canada), which archives marine sedimentation from ca. 950-775 Ma, permitting investigation into environmental evolution coincident with eukaryotic ecosystem evolution and expansion. Here we present multi-proxy geochemical data from the lower Mackenzie Mountains Supergroup to constrain the paleoredox environment within which these large benthic macroalgae thrived. Two transects show evidence for basin-wide anoxic (ferruginous) oceanic conditions (i.e., high FeHR/FeT, low Fepy/FeHR), with muted redox-sensitive trace metal enrichments and possible seasonal variability. However, the weathering of sulfide minerals in the studied samples may obscure geochemical signatures of euxinic conditions. These results suggest that macroalgae colonized shallow environments in an ocean that remained dominantly anoxic with limited evidence for oxygenation until ca. 850 Ma. Collectively, these geochemical results provide novel insights into the environmental conditions surrounding the evolution and expansion of benthic macroalgae and the eventual dominance of oxygenated oceanic conditions required for the later emergence of animals.},
}

*Oxidation-Reduction
*Fossils
*Biological Evolution
Geologic Sediments/chemistry/analysis
Eukaryota
Canada
Ecosystem
Chlorophyta

@article {pmid38693345,
year = {2024},
author = {Feng, X and Zheng, J and Irisarri, I and Yu, H and Zheng, B and Ali, Z and de Vries, S and Keller, J and Fürst-Jansen, JMR and Dadras, A and Zegers, JMS and Rieseberg, TP and Dhabalia Ashok, A and Darienko, T and Bierenbroodspot, MJ and Gramzow, L and Petroll, R and Haas, FB and Fernandez-Pozo, N and Nousias, O and Li, T and Fitzek, E and Grayburn, WS and Rittmeier, N and Permann, C and Rümpler, F and Archibald, JM and Theißen, G and Mower, JP and Lorenz, M and Buschmann, H and von Schwartzenberg, K and Boston, L and Hayes, RD and Daum, C and Barry, K and Grigoriev, IV and Wang, X and Li, FW and Rensing, SA and Ben Ari, J and Keren, N and Mosquna, A and Holzinger, A and Delaux, PM and Zhang, C and Huang, J and Mutwil, M and de Vries, J and Yin, Y},
title = {Genomes of multicellular algal sisters to land plants illuminate signaling network evolution.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {38693345},
issn = {1546-1718},
support = {852725//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 101001675//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 440231723//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; TH417/12-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 440540015//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 410739858//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; RE 1697/16-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; RE 1697/18-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; P34181-B//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; OPP1172165//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; ANR-10-LABX-41//LABoratoires d'EXcellence ARCANE (Labex ARCANE)/ ; 1933521//National Science Foundation (NSF)/ ; 58-8042-9-089//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; R21AI171952//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; R01GM140370//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; },
abstract = {Zygnematophyceae are the algal sisters of land plants. Here we sequenced four genomes of filamentous Zygnematophyceae, including chromosome-scale assemblies for three strains of Zygnema circumcarinatum. We inferred traits in the ancestor of Zygnematophyceae and land plants that might have ushered in the conquest of land by plants: expanded genes for signaling cascades, environmental response, and multicellular growth. Zygnematophyceae and land plants share all the major enzymes for cell wall synthesis and remodifications, and gene gains shaped this toolkit. Co-expression network analyses uncover gene cohorts that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution.},
}

@article {pmid38691595,
year = {2024},
author = {Yu, P and Li, Y and Fang, W and Feng, XQ and Li, B},
title = {Mechanochemical dynamics of collective cells and hierarchical topological defects in multicellular lumens.},
journal = {Science advances},
volume = {10},
number = {18},
pages = {eadn0172},
doi = {10.1126/sciadv.adn0172},
pmid = {38691595},
issn = {2375-2548},
mesh = {*Mechanotransduction, Cellular ; *Models, Biological ; *Morphogenesis ; Biomechanical Phenomena ; Animals ; },
abstract = {Collective cell dynamics is essential for tissue morphogenesis and various biological functions. However, it remains incompletely understood how mechanical forces and chemical signaling are integrated to direct collective cell behaviors underlying tissue morphogenesis. Here, we propose a three-dimensional (3D) mechanochemical theory accounting for biochemical reaction-diffusion and cellular mechanotransduction to investigate the dynamics of multicellular lumens. We show that the interplay between biochemical signaling and mechanics can trigger either pitchfork or Hopf bifurcation to induce diverse static mechanochemical patterns or generate oscillations with multiple modes both involving marked mechanical deformations in lumens. We uncover the crucial role of mechanochemical feedback in emerging morphodynamics and identify the evolution and morphogenetic functions of hierarchical topological defects including cell-level hexatic defects and tissue-level orientational defects. Our theory captures the common mechanochemical traits of collective dynamics observed in experiments and could provide a mechanistic context for understanding morphological symmetry breaking in 3D lumen-like tissues.},
}

*Mechanotransduction, Cellular
*Models, Biological
*Morphogenesis
Biomechanical Phenomena
Animals

@article {pmid38690760,
year = {2024},
author = {},
title = {Transitions in development - an interview with Thibaut Brunet.},
journal = {Development (Cambridge, England)},
volume = {151},
number = {9},
pages = {},
doi = {10.1242/dev.202942},
pmid = {38690760},
issn = {1477-9129},
mesh = {Animals ; *Biological Evolution ; *Developmental Biology/history ; *Choanoflagellata ; History, 21st Century ; Morphogenesis ; History, 20th Century ; },
abstract = {Thibaut Brunet is a group leader at the Institut Pasteur in Paris, France, where he works on choanoflagellates (known as 'choanos' for short). These unicellular organisms are close relatives of animals that have the potential to form multicellular assemblies under certain conditions, and Thibaut's lab are leveraging them to gain insights into how animal morphogenesis evolved. We met with Thibaut over Zoom to discuss his career path so far, and learnt how an early interest in dinosaurs contributed to his life-long fascination with evolutionary biology.},
}

Animals
*Biological Evolution
*Developmental Biology/history
*Choanoflagellata
History, 21st Century
Morphogenesis
History, 20th Century

@article {pmid38685127,
year = {2024},
author = {Trigos, AS and Bongiovanni, F and Zhang, Y and Zethoven, M and Tothill, R and Pearson, R and Papenfuss, AT and Goode, DL},
title = {Disruption of metazoan gene regulatory networks in cancer alters the balance of co-expression between genes of unicellular and multicellular origins.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {110},
pmid = {38685127},
issn = {1474-760X},
support = {MCRF17005//Victorian Cancer Agency/ ; 2003115//National Health and Medical Research Council/ ; 2003887//National Health and Medical Research Council/ ; },
mesh = {*Gene Regulatory Networks ; *Neoplasms/genetics ; Humans ; Animals ; Gene Expression Regulation, Neoplastic ; Evolution, Molecular ; },
abstract = {BACKGROUND: Metazoans inherited genes from unicellular ancestors that perform essential biological processes such as cell division, metabolism, and protein translation. Multicellularity requires careful control and coordination of these unicellular genes to maintain tissue integrity and homeostasis. Gene regulatory networks (GRNs) that arose during metazoan evolution are frequently altered in cancer, resulting in over-expression of unicellular genes. We propose that an imbalance in co-expression of unicellular (UC) and multicellular (MC) genes is a driving force in cancer.

RESULTS: We combine gene co-expression analysis to infer changes to GRNs in cancer with protein sequence conservation data to distinguish genes with UC and MC origins. Co-expression networks created using RNA sequencing data from 31 tumor types and normal tissue samples are divided into modules enriched for UC genes, MC genes, or mixed UC-MC modules. The greatest differences between tumor and normal tissue co-expression networks occur within mixed UC-MC modules. MC and UC genes not commonly co-expressed in normal tissues form distinct co-expression modules seen only in tumors. The degree of rewiring of genes within mixed UC-MC modules increases with tumor grade and stage. Mixed UC-MC modules are enriched for somatic mutations in cancer genes, particularly amplifications, suggesting an important driver of the rewiring observed in tumors is copy number changes.

CONCLUSIONS: Our study shows the greatest changes to gene co-expression patterns during tumor progression occur between genes of MC and UC origins, implicating the breakdown and rewiring of metazoan gene regulatory networks in cancer development and progression.},
}

*Gene Regulatory Networks
*Neoplasms/genetics
Humans
Animals
Gene Expression Regulation, Neoplastic
Evolution, Molecular

@article {pmid38662765,
year = {2024},
author = {Singleton, MD and Eisen, MB},
title = {Evolutionary analyses of intrinsically disordered regions reveal widespread signals of conservation.},
journal = {PLoS computational biology},
volume = {20},
number = {4},
pages = {e1012028},
doi = {10.1371/journal.pcbi.1012028},
pmid = {38662765},
issn = {1553-7358},
abstract = {Intrinsically disordered regions (IDRs) are segments of proteins without stable three-dimensional structures. As this flexibility allows them to interact with diverse binding partners, IDRs play key roles in cell signaling and gene expression. Despite the prevalence and importance of IDRs in eukaryotic proteomes and various biological processes, associating them with specific molecular functions remains a significant challenge due to their high rates of sequence evolution. However, by comparing the observed values of various IDR-associated properties against those generated under a simulated model of evolution, a recent study found most IDRs across the entire yeast proteome contain conserved features. Furthermore, it showed clusters of IDRs with common "evolutionary signatures," i.e. patterns of conserved features, were associated with specific biological functions. To determine if similar patterns of conservation are found in the IDRs of other systems, in this work we applied a series of phylogenetic models to over 7,500 orthologous IDRs identified in the Drosophila genome to dissect the forces driving their evolution. By comparing models of constrained and unconstrained continuous trait evolution using the Brownian motion and Ornstein-Uhlenbeck models, respectively, we identified signals of widespread constraint, indicating conservation of distributed features is mechanism of IDR evolution common to multiple biological systems. In contrast to the previous study in yeast, however, we observed limited evidence of IDR clusters with specific biological functions, which suggests a more complex relationship between evolutionary constraints and function in the IDRs of multicellular organisms.},
}

@article {pmid38659912,
year = {2024},
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 Conlin, PL and Bozdag, GO and Ratcliff, WC},
title = {Whole-genome duplication in the Multicellularity Long Term Evolution Experiment.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.18.588554},
pmid = {38659912},
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. 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 undergo spontaneous WGD. From its origin within the first 50 days of the experiment, tetraploids persist for the next 950 days (nearly 5,000 generations, the current leading edge of our experiment) in ten replicate populations, despite being genomically unstable. Using synthetic reconstruction, biophysical modeling, and counter-selection experiments, we found that tetraploidy evolved because it confers immediate fitness benefits in this environment, 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, playing 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 {pmid38657942,
year = {2024},
author = {Wu, T and Huang, J and Li, Y and Guo, Y and Wang, H and Zhang, Y},
title = {Prenatal acetaminophen exposure and the developing ovary: time, dose, and course consequences for fetal mice.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {},
number = {},
pages = {114679},
doi = {10.1016/j.fct.2024.114679},
pmid = {38657942},
issn = {1873-6351},
abstract = {Acetaminophen is an emerging endocrine disrupting chemical and has been detected in various natural matrices. Numerous studies have documented developmental toxicity associated with prenatal acetaminophen exposure (PAcE). In this study, we established a PAcE Kunming mouse model at different time (middle pregnancy and third trimester), doses (low, middle, high) and courses (single or multi-) to systematically investigate their effects on fetal ovarian development. The findings indicated PAcE affected ovarian development, reduced fetal ovarian oocyte number and inhibited cell proliferation. A reduction in mRNA expression was observed for genes associated with oocyte markers (NOBOX and Figlα), follicular development markers (BMP15 and GDF9), and pre-granulosa cell steroid synthase (SF1 and StAR). Notably, exposure in middle pregnancy, high dose, multi-course resulted in the most pronounced inhibition of oocyte development; exposure in third trimester, high dose and multi-course led to the most pronounced inhibition of follicular development; and in third trimester, low dose and single course, the inhibition of pre-granulosa cell function was most pronounced. Mechanistic investigations revealed that PAcE had the most pronounced suppression of the ovarian Notch signaling pathway. Overall, PAcE caused fetal ovarian multicellular toxicity and inhibited follicular development with time, dose and course differences.},
}

@article {pmid38604731,
year = {2024},
author = {Reis-Cunha, JL and Pimenta-Carvalho, SA and Almeida, LV and Coqueiro-Dos-Santos, A and Marques, CA and Black, JA and Damasceno, J and McCulloch, R and Bartholomeu, DC and Jeffares, DC},
title = {Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites.},
journal = {Genome research},
volume = {34},
number = {3},
pages = {441-453},
doi = {10.1101/gr.278550.123},
pmid = {38604731},
issn = {1549-5469},
mesh = {*Aneuploidy ; *Chromosome Duplication ; *Gene Expression Regulation ; *Genome, Protozoan ; Evolution, Molecular ; Trypanosomatina/genetics ; Phylogeny ; },
abstract = {Aneuploidy is widely observed in both unicellular and multicellular eukaryotes, usually associated with adaptation to stress conditions. Chromosomal duplication stability is a tradeoff between the fitness cost of having unbalanced gene copies and the potential fitness gained from increased dosage of specific advantageous genes. Trypanosomatids, a family of protozoans that include species that cause neglected tropical diseases, are a relevant group to study aneuploidies. Their life cycle has several stressors that could select for different patterns of chromosomal duplications and/or losses, and their nearly universal use of polycistronic transcription increases their reliance on gene expansion/contraction, as well as post-transcriptional control as mechanisms for gene expression regulation. By evaluating the data from 866 isolates covering seven trypanosomatid genera, we have revealed that aneuploidy tolerance is an ancestral characteristic of trypanosomatids but has a reduced occurrence in a specific monophyletic clade that has undergone large genomic reorganization and chromosomal fusions. We have also identified an ancient chromosomal duplication that was maintained across these parasite's speciation, named collectively as the trypanosomatid ancestral supernumerary chromosome (TASC). TASC has most genes in the same coding strand, is expressed as a disomic chromosome (even having four copies), and has increased potential for functional variation, but it purges highly deleterious mutations more efficiently than other chromosomes. The evidence of stringent control over gene expression in this chromosome suggests that these parasites have adapted to mitigate the fitness cost associated with this ancient chromosomal duplication.},
}

*Aneuploidy
*Chromosome Duplication
*Gene Expression Regulation
*Genome, Protozoan
Evolution, Molecular
Trypanosomatina/genetics
Phylogeny

@article {pmid38654432,
year = {2024},
author = {Chen, C and Chen, H and Wang, P and Wang, X and Wang, X and Chen, C},
title = {Ca[2+] Overload Decreased Cellular Viability in Magnetic Hyperthermia without a Macroscopic Temperature Rise.},
journal = {ACS biomaterials science & engineering},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsbiomaterials.3c01875},
pmid = {38654432},
issn = {2373-9878},
abstract = {Magnetic hyperthermia is a crucial medical engineering technique for treating diseases, which usually uses alternating magnetic fields (AMF) to interplay with magnetic substances to generate heat. Recently, it has been found that in some cases, there is no detectable temperature increment after applying an AMF, which caused corresponding effects surprisingly. The mechanisms involved in this phenomenon are not yet fully understood. In this study, we aimed to explore the role of Ca[2+] overload in the magnetic hyperthermia effect without a perceptible temperature rise. A cellular system expressing the fusion proteins TRPV1 and ferritin was prepared. The application of an AMF (518 kHz, 16 kA/m) could induce the fusion protein to release a large amount of iron ions, which then participates in the production of massive reactive oxygen radicals (ROS). Both ROS and its induced lipid oxidation enticed the opening of ion channels, causing intracellular Ca[2+] overload, which further led to decreased cellular viability. Taken together, Ca[2+] overload triggered by elevated ROS and the induced oxidation of lipids contributes to the magnetic hyperthermia effect without a perceptible temperature rise. These findings would be beneficial for expanding the application of temperature-free magnetic hyperthermia, such as in cellular and neural regulation, design of new cancer treatment methods.},
}

@article {pmid38652695,
year = {2024},
author = {Xin, H and Wang, Y and Zhang, W and Yu, B and Neumann, P and Ning, Y and Zhang, T and Wu, Y and Jiang, N and Jiang, J and Xi, M},
title = {Celine, a long interspersed nuclear element retrotransposon, colonizes in the centromeres of poplar chromosomes.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiae214},
pmid = {38652695},
issn = {1532-2548},
abstract = {Centromeres in most multicellular eukaryotes are composed of long arrays of repetitive DNA sequences. Interestingly, several transposable elements, including the well-known long terminal repeat (LTR) retrotransposon CRM (centromeric retrotransposon of maize), were found to be enriched in functional centromeres marked by the centromeric histone H3 (CENH3). Here we report a centromeric long interspersed nuclear element (LINE), Celine, in Populus species. Celine has colonized preferentially in the CENH3-associated chromatin of every poplar chromosome, with 84% of the Celine elements localized in the CENH3-binding domains. By contrast, only 51% of the CRM elements were bound to CENH3 domains in Populus trichocarpa. These results suggest different centromere targeting mechanisms employed by Celine and CRM elements. Nevertheless, the high target specificity seems to be detrimental to further amplification of the Celine elements, leading to a shorter life span and patchy distribution among plant species compared to the CRM elements. Using a phylogenetically guided approach we were able to identify Celine-like LINE elements in tea plant (Camellia sinensis) and green ash tree (Fraxinus pennsylvanica). The centromeric localization of these Celine-like LINEs was confirmed in both species. We demonstrate that the centromere targeting property of Celine-like LINEs is of primitive origin and has been conserved among distantly related plant species.},
}

@article {pmid38651959,
year = {2024},
author = {Thomas, F and Ujvari, B and Dujon, AM},
title = {[Evolution of cancer resistance in the animal kingdom].},
journal = {Medecine sciences : M/S},
volume = {40},
number = {4},
pages = {343-350},
doi = {10.1051/medsci/2024038},
pmid = {38651959},
issn = {1958-5381},
abstract = {Cancer is an inevitable collateral problem inherent in the evolution of multicellular organisms, which appeared at the end of the Precambrian. Faced to this constraint, a range of diverse anticancer defenses has evolved across the animal kingdom. Today, investigating how animal organisms, especially those of large size and long lifespan, manage cancer-related issues has both fundamental and applied outcomes, as it could inspire strategies for preventing or treating human cancers. In this article, we begin by presenting the conceptual framework for understanding evolutionary theories regarding the development of anti-cancer defenses. We then present a number of examples that have been extensively studied in recent years, including naked mole rats, elephants, whales, placozoa, xenarthras (such as sloths, armadillos and anteaters) and bats. The contributions of comparative genomics to understanding evolutionary convergences are also discussed. Finally, we emphasize that natural selection has also favored anti-cancer adaptations aimed at avoiding mutagenic environments, for example by maximizing immediate reproductive efforts in the event of cancer. Exploring these adaptive solutions holds promise for identifying novel approaches to improve human health.},
}

@article {pmid38648729,
year = {2024},
author = {Chen, C and Chen, H and Wang, P and Wang, X and Wang, X and Chen, C and Pan, W},
title = {Reactive Oxygen Species Activate a Ferritin-Linked TRPV4 Channel under a Static Magnetic Field.},
journal = {ACS chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschembio.4c00090},
pmid = {38648729},
issn = {1554-8937},
abstract = {Magnetogenetics has shown great potential for cell function and neuromodulation using heat or force effects under different magnetic fields; however, there is still a contradiction between experimental effects and underlying mechanisms by theoretical computation. In this study, we aimed to investigate the role of reactive oxygen species (ROS) in mechanical force-dependent regulation from a physicochemical perspective. The transient receptor potential vanilloid 4 (TRPV4) cation channels fused to ferritin (T4F) were overexpressed in HEK293T cells and exposed to static magnetic fields (sMF, 1.4-5.0 mT; gradient: 1.62 mT/cm). An elevation of ROS levels was found under sMF in T4F-overexpressing cells, which could lead to lipid oxidation. Compared with the overexpression of TRPV4, ferritin in T4F promoted the generation of ROS under the stimulation of sMF, probably related to the release of iron ions from ferritin. Then, the resulting ROS regulated the opening of the TRPV4 channel, which was attenuated by the direct addition of ROS inhibitors or an iron ion chelator, highlighting a close relationship among iron release, ROS production, and TRPV4 channel activation. Taken together, these findings indicate that the produced ROS under sMF act on the TRPV4 channel, regulating the influx of calcium ions. The study would provide a scientific basis for the application of magnetic regulation in cellular or neural regulation and disease treatment and contribute to the development of the more sensitive regulatory technology.},
}

@article {pmid38646013,
year = {2024},
author = {Baron, V and Sommer, ST and Fiegle, DJ and Pfeuffer, AM and Peyronnet, R and Volk, T and Seidel, T},
title = {Effects of electro-mechanical uncouplers, hormonal stimulation and pacing rate on the stability and function of cultured rabbit myocardial slices.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {12},
number = {},
pages = {1363538},
pmid = {38646013},
issn = {2296-4185},
abstract = {Introduction: Recent advances have enabled organotypic culture of beating human myocardial slices that are stable for weeks. However, human myocardial samples are rare, exhibit high variability and frequently originate from diseased hearts. Thus, there is a need to adapt long-term slice culture for animal myocardium. When applied to animal cardiac slices, studies in healthy or genetically modified myocardium will be possible. We present the culture of slices from rabbit hearts, which resemble the human heart in microstructure, electrophysiology and excitation-contraction coupling. Methods: Left ventricular myocardium from New Zealand White rabbits was cut using a vibratome and cultured in biomimetic chambers for up to 7 days (d). Electro-mechanical uncoupling agents 2,3-butanedione monoxime (BDM) and cytochalasin D (CytoD) were added during initiation of culture and effects on myocyte survival were quantified. We investigated pacing rates (0.5 Hz, 1 Hz, and 2 Hz) and hormonal supplements (cortisol, T3, catecholamines) at physiological plasma concentrations. T3 was buffered using BSA. Contractile force was recorded continuously. Glucose consumption and lactate production were measured. Whole-slice Ca[2+] transients and action potentials were recorded. Effects of culture on microstructure were investigated with confocal microscopy and image analysis. Results: Protocols for human myocardial culture resulted in sustained contracture and myocyte death in rabbit slices within 24 h, which could be prevented by transient application of a combination of BDM and CytoD. Cortisol stabilized contraction amplitude and kinetics in culture. T3 and catecholaminergic stimulation did not further improve stability. T3 and higher pacing rates increased metabolic rate and lactate production. T3 stabilized the response to β-adrenergic stimulation over 7 d. Pacing rates above 1 Hz resulted in progredient decline in contraction force. Image analysis revealed no changes in volume fractions of cardiomyocytes or measures of fibrosis over 7 d. Ca[2+] transient amplitudes and responsiveness to isoprenaline were comparable after 1 d and 7 d, while Ca[2+] transient duration was prolonged after 7 d in culture. Conclusions: A workflow for rabbit myocardial culture has been established, preserving function for up to 7 d. This research underscores the importance of glucocorticoid signaling in maintaining tissue function and extending culture duration. Furthermore, BDM and CytoD appear to protect from tissue damage during the initiation phase of tissue culture.},
}

@article {pmid38644621,
year = {2024},
author = {Daignan-Fornier, B and Pradeu, T},
title = {Critically assessing atavism, an evolution-centered and deterministic hypothesis on cancer.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e2300221},
doi = {10.1002/bies.202300221},
pmid = {38644621},
issn = {1521-1878},
support = {//NewMoon research program of the University of Bordeaux/ ; GBMF9021//Gordon and Betty Moore Foundation/ ; },
abstract = {Cancer is most commonly viewed as resulting from somatic mutations enhancing proliferation and invasion. Some hypotheses further propose that these new capacities reveal a breakdown of multicellularity allowing cancer cells to escape proliferation and cooperation control mechanisms that were implemented during evolution of multicellularity. Here we critically review one such hypothesis, named "atavism," which puts forward the idea that cancer results from the re-expression of normally repressed genes forming a program, or toolbox, inherited from unicellular or simple multicellular ancestors. This hypothesis places cancer in an interesting evolutionary perspective that has not been widely explored and deserves attention. Thinking about cancer within an evolutionary framework, especially the major transitions to multicellularity, offers particularly promising perspectives. It is therefore of the utmost important to analyze why one approach that tries to achieve this aim, the atavism hypothesis, has not so far emerged as a major theory on cancer. We outline the features of the atavism hypothesis that, would benefit from clarification and, if possible, unification.},
}

@article {pmid38621413,
year = {2024},
author = {Egorova, KS and Kibardin, AV and Posvyatenko, AV and Ananikov, VP},
title = {Mechanisms of Biological Effects of Ionic Liquids: From Single Cells to Multicellular Organisms.},
journal = {Chemical reviews},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.chemrev.3c00420},
pmid = {38621413},
issn = {1520-6890},
abstract = {The review presents a detailed discussion of the evolving field studying interactions between ionic liquids (ILs) and biological systems. Originating from molten salt electrolytes to present multiapplication substances, ILs have found usage across various fields due to their exceptional physicochemical properties, including excellent tunability. However, their interactions with biological systems and potential influence on living organisms remain largely unexplored. This review examines the cytotoxic effects of ILs on cell cultures, biomolecules, and vertebrate and invertebrate organisms. Our understanding of IL toxicity, while growing in recent years, is yet nascent. The established findings include correlations between harmful effects of ILs and their ability to disturb cellular membranes, their potential to trigger oxidative stress in cells, and their ability to cause cell death via apoptosis. Future research directions proposed in the review include studying the distribution of various ILs within cellular compartments and organelles, investigating metabolic transformations of ILs in cells and organisms, detailed analysis of IL effects on proteins involved in oxidative stress and apoptosis, correlation studies between IL doses, exposure times and resulting adverse effects, and examination of effects of subtoxic concentrations of ILs on various biological objects. This review aims to serve as a critical analysis of the current body of knowledge on IL-related toxicity mechanisms. Furthermore, it can guide researchers toward the design of less toxic ILs and the informed use of ILs in drug development and medicine.},
}

@article {pmid38614077,
year = {2024},
author = {Nelson, DR and Mystikou, A and Jaiswal, A and Rad-Menendez, C and Preston, MJ and De Boever, F and El Assal, DC and Daakour, S and Lomas, MW and Twizere, JC and Green, DH and Ratcliff, WC and Salehi-Ashtiani, K},
title = {Macroalgal deep genomics illuminate multiple paths to aquatic, photosynthetic multicellularity.},
journal = {Molecular plant},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molp.2024.03.011},
pmid = {38614077},
issn = {1752-9867},
support = {R35 GM138030/GM/NIGMS NIH HHS/United States ; },
abstract = {Macroalgae are multicellular, aquatic autotrophs that play vital roles in global climate maintenance and have diverse applications in biotechnology and eco-engineering, which are directly linked to their multicellularity phenotypes. However, their genomic diversity and the evolutionary mechanisms underlying multicellularity in these organisms remain uncharacterized. In this study, we sequenced 110 macroalgal genomes from diverse climates and phyla, and identified key genomic features that distinguish them from their microalgal relatives. Genes for cell adhesion, extracellular matrix formation, cell polarity, transport, and cell differentiation distinguish macroalgae from microalgae across all three major phyla, constituting conserved and unique gene sets supporting multicellular processes. Adhesome genes show phylum- and climate-specific expansions that may facilitate niche adaptation. Collectively, our study reveals genetic determinants of convergent and divergent evolutionary trajectories that have shaped morphological diversity in macroalgae and provides genome-wide frameworks to understand photosynthetic multicellular evolution in aquatic environments.},
}

@article {pmid38379073,
year = {2024},
author = {Deng, S and Gong, H and Zhang, D and Zhang, M and He, X},
title = {A statistical method for quantifying progenitor cells reveals incipient cell fate commitments.},
journal = {Nature methods},
volume = {21},
number = {4},
pages = {597-608},
pmid = {38379073},
issn = {1548-7105},
support = {32293190//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32200492//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Mice ; Phylogeny ; Cell Differentiation/genetics ; *Stem Cells ; *Embryonic Development ; Cell Division ; },
abstract = {Quantifying the number of progenitor cells that found an organ, tissue or cell population is of fundamental importance for understanding the development and homeostasis of a multicellular organism. Previous efforts rely on marker genes that are specifically expressed in progenitors. This strategy is, however, often hindered by the lack of ideal markers. Here we propose a general statistical method to quantify the progenitors of any tissues or cell populations in an organism, even in the absence of progenitor-specific markers, by exploring the cell phylogenetic tree that records the cell division history during development. The method, termed targeting coalescent analysis (TarCA), computes the probability that two randomly sampled cells of a tissue coalesce within the tissue-specific monophyletic clades. The inverse of this probability then serves as a measure of the progenitor number of the tissue. Both mathematic modeling and computer simulations demonstrated the high accuracy of TarCA, which was then validated using real data from nematode, fruit fly and mouse, all with related cell phylogenetic trees. We further showed that TarCA can be used to identify lineage-specific upregulated genes during embryogenesis, revealing incipient cell fate commitments in mouse embryos.},
}

Animals
Mice
Phylogeny
Cell Differentiation/genetics
*Stem Cells
*Embryonic Development
Cell Division

@article {pmid38600528,
year = {2024},
author = {Lindsey, CR and Knoll, AH and Herron, MD and Rosenzweig, F},
title = {Fossil-calibrated molecular clock data enable reconstruction of steps leading to differentiated multicellularity and anisogamy in the Volvocine algae.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {79},
pmid = {38600528},
issn = {1741-7007},
support = {80NSSC20K0621//Ames Research Center/ ; 80NSSC23K1357//Ames Research Center/ ; OAC-1828187//National Science Foundation/ ; },
mesh = {Phylogeny ; Biological Evolution ; *Volvox/genetics ; Fossils ; Plants ; *Chlorophyceae ; Cell Differentiation ; },
abstract = {BACKGROUND: Throughout its nearly four-billion-year history, life has undergone evolutionary transitions in which simpler subunits have become integrated to form a more complex whole. Many of these transitions opened the door to innovations that resulted in increased biodiversity and/or organismal efficiency. The evolution of multicellularity from unicellular forms represents one such transition, one that paved the way for cellular differentiation, including differentiation of male and female gametes. A useful model for studying the evolution of multicellularity and cellular differentiation is the volvocine algae, a clade of freshwater green algae whose members range from unicellular to colonial, from undifferentiated to completely differentiated, and whose gamete types can be isogamous, anisogamous, or oogamous. To better understand how multicellularity, differentiation, and gametes evolved in this group, we used comparative genomics and fossil data to establish a geologically calibrated roadmap of when these innovations occurred.

RESULTS: Our ancestral-state reconstructions, show that multicellularity arose independently twice in the volvocine algae. Our chronograms indicate multicellularity evolved during the Carboniferous-Triassic periods in Goniaceae + Volvocaceae, and possibly as early as the Cretaceous in Tetrabaenaceae. Using divergence time estimates we inferred when, and in what order, specific developmental changes occurred that led to differentiated multicellularity and oogamy. We find that in the volvocine algae the temporal sequence of developmental changes leading to differentiated multicellularity is much as proposed by David Kirk, and that multicellularity is correlated with the acquisition of anisogamy and oogamy. Lastly, morphological, molecular, and divergence time data suggest the possibility of cryptic species in Tetrabaenaceae.

CONCLUSIONS: Large molecular datasets and robust phylogenetic methods are bringing the evolutionary history of the volvocine algae more sharply into focus. Mounting evidence suggests that extant species in this group are the result of two independent origins of multicellularity and multiple independent origins of cell differentiation. Also, the origin of the Tetrabaenaceae-Goniaceae-Volvocaceae clade may be much older than previously thought. Finally, the possibility of cryptic species in the Tetrabaenaceae provides an exciting opportunity to study the recent divergence of lineages adapted to live in very different thermal environments.},
}

Phylogeny
Biological Evolution
*Volvox/genetics
Fossils
Plants
*Chlorophyceae
Cell Differentiation

@article {pmid38582791,
year = {2024},
author = {Wang, H and Guan, Z and Zheng, L},
title = {Single-cell RNA sequencing explores the evolution of the ecosystem from leukoplakia to head and neck squamous cell carcinoma.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {8097},
pmid = {38582791},
issn = {2045-2322},
support = {SBGJ202102175//the Henan Provincial Medical Science and Technology Research Plan/ ; },
mesh = {Humans ; Squamous Cell Carcinoma of Head and Neck/genetics ; *Ecosystem ; Leukoplakia ; *Head and Neck Neoplasms/genetics ; Sequence Analysis, RNA ; Prognosis ; Tumor Microenvironment/genetics ; },
abstract = {It has been found that progression from leukoplakia to head and neck squamous cell carcinoma (HNSCC) is a long-term process that may involve changes in the multicellular ecosystem. We acquired scRNA-seq samples information from gene expression omnibus and UCSC Xena database. The BEAM function was used to construct the pseudotime trajectory and analyze the differentially expressed genes in different branches. We used the ssGSEA method to explore the correlation between each cell subgroup and survival time, and obtained the cell subgroup related to prognosis. During the progression from leukoplakia to HNSCC, we found several prognostic cell subgroups, such as AURKB + epithelial cells, SFRP1 + fibroblasts, SLC7A8 + macrophages, FCER1A + CD1C + dendritic cells, and TRGC2 + NK/T cells. All cell subgroups had two different fates, one tending to cell proliferation, migration, and enhancement of angiogenesis capacity, and the other tending to inflammatory immune response, leukocyte chemotaxis, and T cell activation. Tumor-promoting genes such as CD163 and CD209 were highly expressed in the myeloid cells, and depletion marker genes such as TIGIT, LAG3 were highly expressed in NK/T cells. Our study may provide a reference for the molecular mechanism of HNSCC and theoretical basis for the development of new therapeutic strategies.},
}

Humans
Squamous Cell Carcinoma of Head and Neck/genetics
*Ecosystem
Leukoplakia
*Head and Neck Neoplasms/genetics
Sequence Analysis, RNA
Prognosis
Tumor Microenvironment/genetics

@article {pmid38537926,
year = {2024},
author = {Shao, S and Liu, K and Du, J and Yin, C and Wang, M and Wang, Y},
title = {Functional characterization of serine proteinase inhibitor Kazal-Type in the red claw crayfish Cherax quadricarinatus.},
journal = {Fish & shellfish immunology},
volume = {148},
number = {},
pages = {109525},
doi = {10.1016/j.fsi.2024.109525},
pmid = {38537926},
issn = {1095-9947},
mesh = {Humans ; Animals ; *Serine Proteinase Inhibitors/genetics/chemistry ; *Astacoidea ; Phylogeny ; Escherichia coli ; Recombinant Proteins/genetics ; Bacteria/metabolism ; },
abstract = {Serine protease inhibitors Kazal type (SPINKs) function in physiological and immunological processes across multicellular organisms. In the present study, we identified a SPINK gene, designated as CqSPINK, in the red claw crayfish Cherax quadricarinatus, which is the ortholog of human SPINK5. The deduced CqSPINK contains two Kazal domains consisting of 45 amino acid residues with a typical signature motif C-X3-C-X5-PVCG-X5-Y-X3-C-X6-C-X12-14-C. Each Kazal domain contains six conserved cysteine residues forming three pairs of disulfide bonds, segmenting the structure into three rings. Phylogenetic analysis revealed CqSPINK as a homolog of human SPINK5. CqSPINK expression was detected exclusively in hepatopancreas and epithelium, with rapid up-regulation in hepatopancreas upon Vibrio parahaemolyticus E1 challenge. Recombinant CqSPINK protein (rCqSPINK) was heterologously expressed in Escherichia coli and purified for further study. Proteinase inhibition assays demonstrated that rCqSPINK could potently inhibit proteinase K and subtilisin A, weakly inhibit α-chymotrypsin and elastase, but extremely weak inhibit trypsin. Furthermore, CqSPINK inhibited bacterial secretory proteinase activity from Bacillus subtilis, E. coli, and Staphylococcus aureus, and inhibited B. subtilis growth. These findings suggest CqSPINK's involvement in antibacterial immunity through direct inhibition of bacterial proteases, contributing to resistance against pathogen invasion.},
}

Humans
Animals
*Serine Proteinase Inhibitors/genetics/chemistry
*Astacoidea
Phylogeny
Escherichia coli
Recombinant Proteins/genetics
Bacteria/metabolism

@article {pmid38554705,
year = {2024},
author = {Deng, Y and Xia, L and Zhang, J and Deng, S and Wang, M and Wei, S and Li, K and Lai, H and Yang, Y and Bai, Y and Liu, Y and Luo, L and Yang, Z and Chen, Y and Kang, R and Gan, F and Pu, Q and Mei, J and Ma, L and Lin, F and Guo, C and Liao, H and Zhu, Y and Liu, Z and Liu, C and Hu, Y and Yuan, Y and Zha, Z and Yuan, G and Zhang, G and Chen, L and Cheng, Q and Shen, S and Liu, L},
title = {Multicellular ecotypes shape progression of lung adenocarcinoma from ground-glass opacity toward advanced stages.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {101489},
doi = {10.1016/j.xcrm.2024.101489},
pmid = {38554705},
issn = {2666-3791},
abstract = {Lung adenocarcinoma is a type of cancer that exhibits a wide range of clinical radiological manifestations, from ground-glass opacity (GGO) to pure solid nodules, which vary greatly in terms of their biological characteristics. Our current understanding of this heterogeneity is limited. To address this gap, we analyze 58 lung adenocarcinoma patients via machine learning, single-cell RNA sequencing (scRNA-seq), and whole-exome sequencing, and we identify six lung multicellular ecotypes (LMEs) correlating with distinct radiological patterns and cancer cell states. Notably, GGO-associated neoantigens in early-stage cancers are recognized by CD8[+] T cells, indicating an immune-active environment, while solid nodules feature an immune-suppressive LME with exhausted CD8[+] T cells, driven by specific stromal cells such as CTHCR1[+] fibroblasts. This study also highlights EGFR(L858R) neoantigens in GGO samples, suggesting potential CD8[+] T cell activation. Our findings offer valuable insights into lung adenocarcinoma heterogeneity, suggesting avenues for targeted therapies in early-stage disease.},
}

@article {pmid38553457,
year = {2024},
author = {Kapsetaki, SE and Cisneros, LH and Maley, CC},
title = {Cell-in-cell phenomena across the tree of life.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {7535},
pmid = {38553457},
issn = {2045-2322},
support = {U54 CA217376/GF/NIH HHS/United States ; },
abstract = {Cells in obligately multicellular organisms by definition have aligned fitness interests, minimum conflict, and cannot reproduce independently. However, some cells eat other cells within the same body, sometimes called cell cannibalism. Such cell-in-cell events have not been thoroughly discussed in the framework of major transitions to multicellularity. We performed a systematic screening of 508 articles, from which we chose 115 relevant articles in a search for cell-in-cell events across the tree of life, the age of cell-in-cell-related genes, and whether cell-in-cell events are associated with normal multicellular development or cancer. Cell-in-cell events are found across the tree of life, from some unicellular to many multicellular organisms, including non-neoplastic and neoplastic tissue. Additionally, out of the 38 cell-in-cell-related genes found in the literature, 14 genes were over 2.2 billion years old, i.e., older than the common ancestor of some facultatively multicellular taxa. All of this suggests that cell-in-cell events may have originated before the origins of obligate multicellularity. Thus, our results show that cell-in-cell events exist in obligate multicellular organisms, but are not a defining feature of them. The idea of eradicating cell-in-cell events from obligate multicellular organisms as a way of treating cancer, without considering that cell-in-cell events are also part of normal development, should be abandoned.},
}

@article {pmid38547507,
year = {2024},
author = {Odelgard, A and Hägglund, E and Guy, L and Andersson, SGE},
title = {Phylogeny and Expansion of Serine/Threonine Kinases in Phagocytotic Bacteria in the Phylum Planctomycetota.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae068},
pmid = {38547507},
issn = {1759-6653},
abstract = {The recently isolated bacterium "Candidatus Uabimicrobium amorphum" is the only known prokaryote that can engulf other bacterial cells. Its proteome contains a high fraction of proteins involved in signal transduction systems, which is a feature normally associated with multicellularity in eukaryotes. Here, we present a protein-based phylogeny which shows that "Ca. Uabimicrobium amorphum" represents an early diverging lineage that clusters with the Saltatorellus clade within the phylum Planctomycetota. A gene flux analysis indicated a gain of 126 protein families for signal transduction functions in "Ca. Uabimicrobium amorphum", of which 66 families contained eukaryotic-like Serine/Threonine kinases (STKs) with Pkinase domains. In total, we predicted 525 functional STKs in "Ca. Uabimicrobium amorphum", which represent 8% of the proteome and is the highest fraction of STKs in a bacterial proteome. The majority of STKs in this species are membrane proteins and 30% contain long, tandem arrays of WD40 or TPR domains. The pKinase domain was predicted to be located in the cytoplasm, while the WD40 and TPR domains were predicted to be located in the periplasm. Such domain combinations were also identified in the STKs of other species in the Planctomycetota, although in much lower abundances. A phylogenetic analysis of the STKs in the Planctomycetota inferred from the Pkinase domain alone provided support for lineage-specific expansions of the STKs in "Ca. Uabimicrobium amorphum". The results imply that expansions of eukaryotic-like signal transduction systems are not restricted to multicellular organisms, but have occurred in parallel in prokaryotes with predatory lifestyles and phagocytotic-like behaviors.},
}

@article {pmid38531970,
year = {2024},
author = {Domazet-Lošo, M and Široki, T and Šimičević, K and Domazet-Lošo, T},
title = {Macroevolutionary dynamics of gene family gain and loss along multicellular eukaryotic lineages.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {2663},
pmid = {38531970},
issn = {2041-1723},
support = {IP-2016-06-5924//Hrvatska Zaklada za Znanost (Croatian Science Foundation)/ ; KK.01.1.1.01.0009 DATACROSS//EC | European Regional Development Fund (Europski Fond za Regionalni Razvoj)/ ; },
mesh = {*Biological Evolution ; *Genome ; Phylogeny ; Evolution, Molecular ; },
abstract = {The gain and loss of genes fluctuate over evolutionary time in major eukaryotic clades. However, the full profile of these macroevolutionary trajectories is still missing. To give a more inclusive view on the changes in genome complexity across the tree of life, here we recovered the evolutionary dynamics of gene family gain and loss ranging from the ancestor of cellular organisms to 352 eukaryotic species. We show that in all considered lineages the gene family content follows a common evolutionary pattern, where the number of gene families reaches the highest value at a major evolutionary and ecological transition, and then gradually decreases towards extant organisms. This supports theoretical predictions and suggests that the genome complexity is often decoupled from commonly perceived organismal complexity. We conclude that simplification by gene family loss is a dominant force in Phanerozoic genomes of various lineages, probably underpinned by intense ecological specializations and functional outsourcing.},
}

*Biological Evolution
*Genome
Phylogeny
Evolution, Molecular

@article {pmid38527900,
year = {2024},
author = {Li, R and Chen, X and Yang, X},
title = {Navigating the landscapes of spatial transcriptomics: How computational methods guide the way.},
journal = {Wiley interdisciplinary reviews. RNA},
volume = {15},
number = {2},
pages = {e1839},
doi = {10.1002/wrna.1839},
pmid = {38527900},
issn = {1757-7012},
support = {20221080084//Tsinghua University/ ; 31671381//National Natural Science Foundation of China/ ; 32330022//National Natural Science Foundation of China/ ; 81972912//National Natural Science Foundation of China/ ; 2023YFC3043300//Ministry of Science and Technology of the People's Republic of China/ ; },
mesh = {*Gene Expression Profiling ; Transcriptome ; Algorithms ; *Biomedical Research ; RNA ; },
abstract = {Spatially resolved transcriptomics has been dramatically transforming biological and medical research in various fields. It enables transcriptome profiling at single-cell, multi-cellular, or sub-cellular resolution, while retaining the information of geometric localizations of cells in complex tissues. The coupling of cell spatial information and its molecular characteristics generates a novel multi-modal high-throughput data source, which poses new challenges for the development of analytical methods for data-mining. Spatial transcriptomic data are often highly complex, noisy, and biased, presenting a series of difficulties, many unresolved, for data analysis and generation of biological insights. In addition, to keep pace with the ever-evolving spatial transcriptomic experimental technologies, the existing analytical theories and tools need to be updated and reformed accordingly. In this review, we provide an overview and discussion of the current computational approaches for mining of spatial transcriptomics data. Future directions and perspectives of methodology design are proposed to stimulate further discussions and advances in new analytical models and algorithms. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Evolution and Genomics > Computational Analyses of RNA RNA Export and Localization > RNA Localization.},
}

*Gene Expression Profiling
Transcriptome
Algorithms
*Biomedical Research
RNA

@article {pmid38526062,
year = {2024},
author = {Wielgoss, S and Van Dyken, JD and Velicer, GJ},
title = {Mutation rate and effective population size of the model cooperative bacterium Myxococcus xanthus.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae066},
pmid = {38526062},
issn = {1759-6653},
abstract = {Intrinsic rates of genetic mutation have diverged greatly across taxa and exhibit statistical associations with several other parameters and features. These include effective population size (Ne), genome size, and gametic multicellularity, with the latter being associated with both increased mutation rates and decreased effective population sizes. However, data sufficient to test for possible relationships between microbial multicellularity and mutation rate (µ) are lacking. Here we report estimates of two key population-genetic parameters, Ne and µ, for Myxococcus xanthus, a bacterial model organism for the study of aggregative multicellular development, predation, and social swarming. To estimate µ, we conducted an ∼400-day mutation-accumulation (MA) experiment with 46 lineages subjected to regular single colony bottlenecks prior to clonal regrowth. Upon conclusion, we sequenced one clonal-isolate genome per lineage. Given collective evolution for 85,323 generations across all lines, we calculate a per base-pair mutation rate of ∼5.5 × 10-10 per site per generation, one of the highest mutation rates among free-living eubacteria. Given our estimate of µ, we derived Ne at ∼107 from neutral diversity at four-fold degenerate sites across two dozen M. xanthus natural isolates. This estimate is below average for eubacteria and strengthens an already clear negative correlation between µ and Ne in prokaryotes. The higher and lower than average mutation rate and Ne for M. xanthus, respectively, amplify the question of whether any features of its multicellular life-cycle - such as group-size reduction during fruiting-body development - or its highly structured spatial distribution have significantly influenced how these parameters have evolved.},
}

@article {pmid38519635,
year = {2024},
author = {},
title = {Multicellularity drives ecological diversity in a long-term evolution experiment.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {38519635},
issn = {2397-334X},
}

@article {pmid38514634,
year = {2024},
author = {Carreira de Paula, J and García Olmedo, P and Gómez-Moracho, T and Buendía-Abad, M and Higes, M and Martín-Hernández, R and Osuna, A and de Pablos, LM},
title = {Promastigote EPS secretion and haptomonad biofilm formation as evolutionary adaptations of trypanosomatid parasites for colonizing honeybee hosts.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {27},
pmid = {38514634},
issn = {2055-5008},
mesh = {Humans ; Bees ; Animals ; *Parasites ; Ecosystem ; *Trypanosomatina/parasitology ; Biological Evolution ; },
abstract = {Bees are major pollinators involved in the maintenance of all terrestrial ecosystems. Biotic and abiotic factors placing these insects at risk is a research priority for ecological and agricultural sustainability. Parasites are one of the key players of this global decline and the study of their mechanisms of action is essential to control honeybee colony losses. Trypanosomatid parasites and particularly the Lotmaria passim are widely spread in honeybees, however their lifestyle is poorly understood. In this work, we show how these parasites are able to differentiate into a new parasitic lifestyle: the trypanosomatid biofilms. Using different microscopic techniques, we demonstrated that the secretion of Extracellular Polymeric Substances by free-swimming unicellular promastigote forms is a prerequisite for the generation and adherence of multicellular biofilms to solid surfaces in vitro and in vivo. Moreover, compared to human-infective trypanosomatid parasites our study shows how trypanosomatid parasites of honeybees increases their resistance and thus resilience to drastic changes in environmental conditions such as ultralow temperatures and hypoosmotic shock, which would explain their success thriving within or outside their hosts. These results set up the basis for the understanding of the success of this group of parasites in nature and to unveil the impact of such pathogens in honeybees, a keystones species in most terrestrial ecosystems.},
}

Humans
Bees
Animals
*Parasites
Ecosystem
*Trypanosomatina/parasitology
Biological Evolution

@article {pmid38517944,
year = {2024},
author = {Phillips, JE and Pan, D},
title = {The Hippo kinase cascade regulates a contractile cell behavior and cell density in a close unicellular relative of animals.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
pmid = {38517944},
issn = {2050-084X},
support = {EY015708/EY/NEI NIH HHS/United States ; },
abstract = {The genomes of close unicellular relatives of animals encode orthologs of many genes that regulate animal development. However, little is known about the function of such genes in unicellular organisms or the evolutionary process by which these genes came to function in multicellular development. The Hippo pathway, which regulates cell proliferation and tissue size in animals, is present in some of the closest unicellular relatives of animals, including the amoeboid organism Capsaspora owczarzaki. We previously showed that the Capsaspora ortholog of the Hippo pathway nuclear effector Yorkie/YAP/TAZ (coYki) regulates actin dynamics and the three-dimensional morphology of Capsaspora cell aggregates, but is dispensable for cell proliferation control (Phillips et al., 2022). However, the function of upstream Hippo pathway components, and whether and how they regulate coYki in Capsaspora, remained unknown. Here, we analyze the function of the upstream Hippo pathway kinases coHpo and coWts in Capsaspora by generating mutant lines for each gene. Loss of either kinase results in increased nuclear localization of coYki, indicating an ancient, premetazoan origin of this Hippo pathway regulatory mechanism. Strikingly, we find that loss of either kinase causes a contractile cell behavior and increased density of cell packing within Capsaspora aggregates. We further show that this increased cell density is not due to differences in proliferation, but rather actomyosin-dependent changes in the multicellular architecture of aggregates. Given its well-established role in cell density-regulated proliferation in animals, the increased density of cell packing in coHpo and coWts mutants suggests a shared and possibly ancient and conserved function of the Hippo pathway in cell density control. Together, these results implicate cytoskeletal regulation but not proliferation as an ancestral function of the Hippo pathway kinase cascade and uncover a novel role for Hippo signaling in regulating cell density in a proliferation-independent manner.},
}

@article {pmid38516913,
year = {2024},
author = {Dsilva, GJ and Galande, S},
title = {From sequence to consequence: Deciphering the complex cisregulatory landscape.},
journal = {Journal of biosciences},
volume = {49},
number = {},
pages = {},
pmid = {38516913},
issn = {0973-7138},
abstract = {Cell type-specific expression of genes plays a pivotal role in the development and evolution of multicellular organisms over millions of years. The majority of regulatory control resides within the non-coding regions of the genome, referred to as 'dark matter', which contains cis-regulatory modules. These cis-regulatory modules function collectively and can impact gene expression even when located far from the target gene, exhibiting context-specific behaviour. Consequently, the cis-regulatory code governing gene expression patterns is intricate, in contrast to the universally understood genetic code. This overview centres on the current knowledge regarding cis-regulatory elements, primarily enhancers and their role in governing the spatiotemporal gene expression patterns, and how they have evolved and adapted across different species.},
}

@article {pmid38513029,
year = {2024},
author = {Luthringer, R and Raphalen, M and Guerra, C and Colin, S and Martinho, C and Zheng, M and Hoshino, M and Badis, Y and Lipinska, AP and Haas, FB and Barrera-Redondo, J and Alva, V and Coelho, SM},
title = {Repeated co-option of HMG-box genes for sex determination in brown algae and animals.},
journal = {Science (New York, N.Y.)},
volume = {383},
number = {6689},
pages = {eadk5466},
doi = {10.1126/science.adk5466},
pmid = {38513029},
issn = {1095-9203},
abstract = {In many eukaryotes, genetic sex determination is not governed by XX/XY or ZW/ZZ systems but by a specialized region on the poorly studied U (female) or V (male) sex chromosomes. Previous studies have hinted at the existence of a dominant male-sex factor on the V chromosome in brown algae, a group of multicellular eukaryotes distantly related to animals and plants. The nature of this factor has remained elusive. Here, we demonstrate that an HMG-box gene acts as the male-determining factor in brown algae, mirroring the role HMG-box genes play in sex determination in animals. Over a billion-year evolutionary timeline, these lineages have independently co-opted the HMG box for male determination, representing a paradigm for evolution's ability to recurrently use the same genetic "toolkit" to accomplish similar tasks.},
}

@article {pmid38500675,
year = {2024},
author = {Narula, K and Sinha, A and Choudhary, P and Ghosh, S and Elagamey, E and Sharma, A and Sengupta, A and Chakraborty, N and Chakraborty, S},
title = {Combining extracellular matrix proteome and phosphoproteome of chickpea and meta-analysis reveal novel proteoforms and evolutionary significance of clade-specific wall-associated events in plant.},
journal = {Plant direct},
volume = {8},
number = {3},
pages = {e572},
pmid = {38500675},
issn = {2475-4455},
abstract = {Extracellular matrix (ECM) plays central roles in cell architecture, innate defense and cell wall integrity (CWI) signaling. During transition to multicellularity, modular domain structures of ECM proteins and proteoforms have evolved due to continuous adaptation across taxonomic clades under different ecological niche. Although this incredible diversity has to some extent been investigated at protein level, extracellular phosphorylation events and molecular evolution of ECM proteoform families remains unexplored. We developed matrisome proteoform atlas in a grain legume, chickpea and performed meta-analyses of 74 plant matrisomes. MS/MS analysis identified 1,424 proteins and 315 phosphoproteins involved in diverse functions. Cross-species ECM protein network identified proteoforms associated with CWI maintenance system. Phylogenetic characterization of eighteen matrix protein families highlighted the role of taxon-specific paralogs and orthologs. Novel information was acquired on gene expansion and loss, co-divergence, sub functionalization and neofunctionalization during evolution. Modular networks of matrix protein families and hub proteins showed higher diversity across taxonomic clades than among organs. Furthermore, protein families differ in nonsynonymous to synonymous substitution rates. Our study pointed towards the matrix proteoform functionality, sequence divergence variation, interactions between wall remodelers and molecular evolution using a phylogenetic framework. This is the first report on comprehensive matrisome proteoform network illustrating presence of CWI signaling proteins in land plants.},
}

@article {pmid38334416,
year = {2024},
author = {Földi, C and Merényi, Z and Balázs, B and Csernetics, Á and Miklovics, N and Wu, H and Hegedüs, B and Virágh, M and Hou, Z and Liu, X-B and Galgóczy, L and Nagy, LG},
title = {Snowball: a novel gene family required for developmental patterning of fruiting bodies of mushroom-forming fungi (Agaricomycetes).},
journal = {mSystems},
volume = {9},
number = {3},
pages = {e0120823},
pmid = {38334416},
issn = {2379-5077},
support = {LP2019-13/2019//Hungarian Academy of Sciences/ ; KDP-17-4/PALY-2021//Ministry of Innovation and Technology (Hungary)/ ; OTKA 142188//National Research Development and Innovation Office (Hungary)/ ; },
mesh = {Fruiting Bodies, Fungal/genetics ; Phylogeny ; Fungal Proteins/genetics ; *Agaricales/genetics ; *Basidiomycota/metabolism ; *Ascomycota/metabolism ; },
abstract = {UNLABELLED: The morphogenesis of sexual fruiting bodies of fungi is a complex process determined by a genetically encoded program. Fruiting bodies reached the highest complexity levels in the Agaricomycetes; yet, the underlying genetics is currently poorly known. In this work, we functionally characterized a highly conserved gene termed snb1, whose expression level increases rapidly during fruiting body initiation. According to phylogenetic analyses, orthologs of snb1 are present in almost all agaricomycetes and may represent a novel conserved gene family that plays a substantial role in fruiting body development. We disrupted snb1 using CRISPR/Cas9 in the agaricomycete model organism Coprinopsis cinerea. snb1 deletion mutants formed unique, snowball-shaped, rudimentary fruiting bodies that could not differentiate caps, stipes, and lamellae. We took advantage of this phenotype to study fruiting body differentiation using RNA-Seq analyses. This revealed differentially regulated genes and gene families that, based on wild-type RNA-Seq data, were upregulated early during development and showed tissue-specific expression, suggesting a potential role in differentiation. Taken together, the novel gene family of snb1 and the differentially expressed genes in the snb1 mutants provide valuable insights into the complex mechanisms underlying developmental patterning in the Agaricomycetes.

IMPORTANCE: Fruiting bodies of mushroom-forming fungi (Agaricomycetes) are complex multicellular structures, with a spatially and temporally integrated developmental program that is, however, currently poorly known. In this study, we present a novel, conserved gene family, Snowball (snb), termed after the unique, differentiation-less fruiting body morphology of snb1 knockout strains in the model mushroom Coprinopsis cinerea. snb is a gene of unknown function that is highly conserved among agaricomycetes and encodes a protein of unknown function. A comparative transcriptomic analysis of the early developmental stages of differentiated wild-type and non-differentiated mutant fruiting bodies revealed conserved differentially expressed genes which may be related to tissue differentiation and developmental patterning fruiting body development.},
}

Fruiting Bodies, Fungal/genetics
Phylogeny
Fungal Proteins/genetics
*Agaricales/genetics
*Basidiomycota/metabolism
*Ascomycota/metabolism

@article {pmid38499447,
year = {2024},
author = {Piccini, C and Martínez de la Escalera, G and Segura, A and Croci, C and Kruk, C},
title = {The Microcystis-microbiome interactions: origins of the colonial lifestyle.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae035},
pmid = {38499447},
issn = {1574-6941},
abstract = {Species of the Microcystis genus are the most common bloom-forming toxic cyanobacteria worldwide. They belong to a clade of unicellular cyanobacteria whose ability to reach high biomasses during blooms is linked to the formation of colonies. Colonial lifestyle provides several advantages under stressing conditions of light intensity, ultraviolet light, toxic substances and grazing. The progression from a single-celled organism to multicellularity in Microcystis has usually been interpreted as individual phenotypic responses of the cyanobacterial cells to the environment. Here, we synthesize current knowledge about Microcystis colonial lifestyle and its role in the organism ecology. We then briefly review the available information on Microcystis microbiome and propose that changes leading from single cells to colonies are the consequence of specific and tightly regulated signals between the cyanobacterium and its microbiome through a biofilm-like mechanism. The resulting colony is a multi-specific community of interdependent microorganisms.},
}

@article {pmid38498818,
year = {2024},
author = {Bozdag, GO and Szeinbaum, N and Conlin, PL and Chen, K and Fos, SM and Garcia, A and Penev, PI and Schaible, GA and Trubl, G},
title = {Chapter 5: Major Biological Innovations in the History of Life on Earth.},
journal = {Astrobiology},
volume = {24},
number = {S1},
pages = {S107-S123},
doi = {10.1089/ast.2021.0119},
pmid = {38498818},
issn = {1557-8070},
abstract = {All organisms living on Earth descended from a single, common ancestral population of cells, known as LUCA-the last universal common ancestor. Since its emergence, the diversity and complexity of life have increased dramatically. This chapter focuses on four key biological innovations throughout Earth's history that had a significant impact on the expansion of phylogenetic diversity, organismal complexity, and ecospace habitation. First is the emergence of the last universal common ancestor, LUCA, which laid the foundation for all life-forms on Earth. Second is the evolution of oxygenic photosynthesis, which resulted in global geochemical and biological transformations. Third is the appearance of a new type of cell-the eukaryotic cell-which led to the origin of a new domain of life and the basis for complex multicellularity. Fourth is the multiple independent origins of multicellularity, resulting in the emergence of a new level of complex individuality. A discussion of these four key events will improve our understanding of the intertwined history of our planet and its inhabitants and better inform the extent to which we can expect life at different degrees of diversity and complexity elsewhere.},
}

@article {pmid38497809,
year = {2024},
author = {Hörandl, E},
title = {Apomixis and the paradox of sex in plants.},
journal = {Annals of botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/aob/mcae044},
pmid = {38497809},
issn = {1095-8290},
abstract = {BACKGROUND: The predominance of sex in eukaryotes, despite the high costs of meiosis and mating, is still an evolutionary enigma. Many theories have been proposed, none of them being conclusive on its own, and they are partly not well applicable to land plants. Sexual reproduction is obligate in embryophytes for the great majority of species.

SCOPE: This review will compare the main forms of sexual and asexual reproduction in ferns and angiosperms, based on the generation cycling of sporophyte and gametophyte (leaving vegetative propagation aside). The benefits of sexual reproduction for maintenance of genomic integrity compared to asexuality will be discussed in the light of developmental, evolutionary, genetic and phylogenetic studies.

CONCLUSIONS: Asexual reproduction represents modifications of the sexual pathway, with various forms of facultative sexuality. For sexual land plants, meiosis provides direct DNA repair mechanisms of oxidative damage in reproductive tissues. The ploidy alternations of meiosis-syngamy cycles, and prolonged, multicellular stages in the haploid phase in the gametophytes provide a high efficiency of purifying selection against recessive deleterious mutations. Asexual lineages might buffer effects of such mutations via polyploidy, and can purge the mutational load via facultative sexuality. The role of organelle-nuclear genome compatibility for maintenance of genome integrity is still not well understood. The costs of mating are in plants in general low because of predominant hermaphroditism. Phylogenetic patterns in the Archaeplastid clade suggest that high frequencies of sexuality in land plants are concomitant with a stepwise increase of intrinsic and extrinsic stress factors. Furthermore, expansion of genome size in land plants would increase the potential mutational load. Sexual reproduction appears to be essential for keeping long term genomic integrity, and only rare combinations of extrinsic and intrinsic factors allow for shifts to asexuality.},
}

@article {pmid38493178,
year = {2024},
author = {Bing, J and Guan, Z and Zheng, T and Ennis, CL and Nobile, CJ and Chen, C and Chu, H and Huang, G},
title = {Rapid evolution of an adaptive multicellular morphology of Candida auris during systemic infection.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {2381},
pmid = {38493178},
issn = {2041-1723},
support = {31930005 and 82272359//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32170193 and 32000018//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32170193 and 32000018//National Natural Science Foundation of China (National Science Foundation of China)/ ; R35GM124594//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {Animals ; Mice ; Candida/genetics ; *Candidiasis/microbiology ; Candida auris ; Saccharomyces cerevisiae ; Phenotype ; *Sepsis ; Antifungal Agents ; Microbial Sensitivity Tests ; Mammals ; },
abstract = {Candida auris has become a serious threat to public health. The mechanisms of how this fungal pathogen adapts to the mammalian host are poorly understood. Here we report the rapid evolution of an adaptive C. auris multicellular aggregative morphology in the murine host during systemic infection. C. auris aggregative cells accumulate in the brain and exhibit obvious advantages over the single-celled yeast-form cells during systemic infection. Genetic mutations, specifically de novo point mutations in genes associated with cell division or budding processes, underlie the rapid evolution of this aggregative phenotype. Most mutated C. auris genes are associated with the regulation of cell wall integrity, cytokinesis, cytoskeletal properties, and cellular polarization. Moreover, the multicellular aggregates are notably more recalcitrant to the host antimicrobial peptides LL-37 and PACAP relative to the single-celled yeast-form cells. Overall, to survive in the host, C. auris can rapidly evolve a multicellular aggregative morphology via genetic mutations.},
}

Animals
Mice
Candida/genetics
*Candidiasis/microbiology
Candida auris
Saccharomyces cerevisiae
Phenotype
*Sepsis
Antifungal Agents
Microbial Sensitivity Tests
Mammals

@article {pmid38492155,
year = {2024},
author = {Li, X and Gao, T and Ma, X and Zhong, J and Qin, L and Nian, Y and Wang, X and Luo, Y},
title = {Extraction and identification of exosomes from three different sources of human ovarian granulosa cells and analysis of their differential miRNA expression profiles.},
journal = {Journal of assisted reproduction and genetics},
volume = {},
number = {},
pages = {},
pmid = {38492155},
issn = {1573-7330},
support = {81660806//National Natural Science Foundation of China/ ; 82260947//National Natural Science Foundation of China/ ; },
abstract = {OBJECTIVE: As important functional cells in the ovary, ovarian granulosa cells are involved in the regulation of oocyte growth and development and play an important role in the study of female fertility preservation. Based on the importance of granulosa cell functionalism, in this study, we analyzed the exosome secretion capacity of human ovarian granulosa cells (SVOG/KGN-cell line, PGC-primary cells) and the differences in their miRNA expression.

METHODS: Cells were identified by hematoxylin-eosin staining (HE) and FSHR immunofluorescence staining; CCK8 and colony-forming assay were performed to compare cell proliferation capacity; exosomes were extracted and identified by ultra-high speed centrifugation, transmission electron microscopy (TEM), nanoparticle tracking analysis (NTA), and western blot analysis (WB), and the expression profile of each cellular exosomal miRNA was analyzed by miRNA high-throughput sequencing.

RESULTS: The proliferative abilities of the three granulosa cells differed, but all had the ability to secrete exosomes. In the exosomes of SVOG, KGN, and PGC cells, 218, 327, and 471 miRNAs were detected, respectively. When compared to the exosomal miRNAs of PGC cells, 111 miRNAs were significantly different in SVOG, and 70 miRNAs were washed two significantly different in KGN cells. These differential miRNA functions were mainly enriched in the cell cycle, cell division/differentiation, multicellular biogenesis, and protein binding.

CONCLUSION: Human ovarian granulosa cells of different origins are capable of secreting exosomes, but there are still some differences in their exosomes and exosomal miRNAs, and experimental subjects should be selected rationally according to the actual situation.},
}

@article {pmid38486107,
year = {2024},
author = {Pineau, RM and Libby, E and Demory, D and Lac, DT and Day, TC and Bravo, P and Yunker, PJ and Weitz, JS and Bozdag, GO and Ratcliff, WC},
title = {Emergence and maintenance of stable coexistence during a long-term multicellular evolution experiment.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {38486107},
issn = {2397-334X},
support = {DEB-1845363//NSF | BIO | Division of Environmental Biology (DEB)/ ; 1845363//NSF | BIO | Division of Environmental Biology (DEB)/ ; 5R35GM138030//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 5R35GM138030//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 1R35GM138354//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 1R35GM138354//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 1R35GM138354//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35GM138030//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
abstract = {The evolution of multicellular life spurred evolutionary radiations, fundamentally changing many of Earth's ecosystems. Yet little is known about how early steps in the evolution of multicellularity affect eco-evolutionary dynamics. Through long-term experimental evolution, we observed niche partitioning and the adaptive divergence of two specialized lineages from a single multicellular ancestor. Over 715 daily transfers, snowflake yeast were subjected to selection for rapid growth, followed by selection favouring larger group size. Small and large cluster-forming lineages evolved from a monomorphic ancestor, coexisting for over ~4,300 generations, specializing on divergent aspects of a trade-off between growth rate and survival. Through modelling and experimentation, we demonstrate that coexistence is maintained by a trade-off between organismal size and competitiveness for dissolved oxygen. Taken together, this work shows how the evolution of a new level of biological individuality can rapidly drive adaptive diversification and the expansion of a nascent multicellular niche, one of the most historically impactful emergent properties of this evolutionary transition.},
}

@article {pmid38481381,
year = {2024},
author = {Wu, Z and Liu, D and Ou, Y and Xu, Z and Heng, G and Liu, W and Fu, N and Wang, J and Jiang, D and Gan, L and Dong, J and Wang, X and Chen, Z and Zhang, L and Zhang, C},
title = {Mechanism and endoscopic-treatment-induced evolution of biliary non-anastomotic stricture after liver transplantation revealed by single-cell RNA sequencing.},
journal = {Clinical and translational medicine},
volume = {14},
number = {3},
pages = {e1622},
pmid = {38481381},
issn = {2001-1326},
support = {2022TIAD-GPX0236//Technical Innovation and Application of Chongqing/ ; 2022TIAD-GPX0238//Technical Innovation and Application of Chongqing/ ; 82270687//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Liver Transplantation/adverse effects ; Constriction, Pathologic/surgery/etiology ; Retrospective Studies ; Endothelial Cells ; Sequence Analysis, RNA ; Bile Acids and Salts ; },
abstract = {BACKGROUND: Biliary complications, especially non-anastomotic stricture (NAS), are the main complications after liver transplantation. Insufficient sampling and no recognized animal models obstruct the investigation. Thus, the mechanisms and alterations that occur during endoscopic treatment (ET) of NAS remain unclear.

METHODS: Samples were obtained with endoscopic forceps from the hilar bile ducts of NAS patients receiving continuous biliary stent implantation after diagnosis. Retrospective analysis of multiple studies indicated that the duration of ET for NAS was approximately 1-2 years. Thus, we divided the patients into short-term treatment (STT) and long-term treatment (LTT) groups based on durations of less or more than 1 year. Samples were subjected to single-cell RNA sequencing. Transcriptomic differences between STT and normal groups were defined as the NAS mechanism. Similarly, alterations from STT to LTT groups were regarded as endoscopic-treatment-induced evolution.

RESULTS: In NAS, inflammation and immune-related pathways were upregulated in different cell types, with nonimmune cells showing hypoxia pathway upregulation and immune cells showing ATP metabolism pathway upregulation, indicating heterogeneity. We confirmed a reduction in bile acid metabolism-related SPP1[+] epithelial cells in NAS. Increases in proinflammatory and profibrotic fibroblast subclusters indicated fibrotic progression in NAS. Furthermore, immune disorders in NAS were exacerbated by an increase in plasma cells and dysfunction of NK and NKT cells. ET downregulated multicellular immune and inflammatory responses and restored epithelial and endothelial cell proportions.

CONCLUSIONS: This study reveals the pathophysiological and genetic mechanisms and evolution of NAS induced by ET, thereby providing preventive and therapeutic insights into NAS.

HIGHLIGHTS: For the first time, single-cell transcriptome sequencing was performed on the bile ducts of patients with biliary complications. scRNA-seq analysis revealed distinct changes in the proportion and phenotype of multiple cell types during Nonanastomotic stricture (NAS) and endoscopic treatment. A reduction in bile acid metabolism-related SPP1+ epithelial cells and VEGFA+ endothelial cells, along with explosive infiltration of plasma cells and dysfunction of T and NK cells in NAS patients. SPP1+ macrophages and BST2+ T cells might serve as a surrogate marker for predicting endoscopic treatment.},
}

Humans
*Liver Transplantation/adverse effects
Constriction, Pathologic/surgery/etiology
Retrospective Studies
Endothelial Cells
Sequence Analysis, RNA
Bile Acids and Salts

@article {pmid38476944,
year = {2024},
author = {von Hoyningen-Huene, AJE and Bang, C and Rausch, P and Rühlemann, M and Fokt, H and He, J and Jensen, N and Knop, M and Petersen, C and Schmittmann, L and Zimmer, T and Baines, JF and Bosch, TCG and Hentschel, U and Reusch, TBH and Roeder, T and Franke, A and Schulenburg, H and Stukenbrock, E and Schmitz, RA},
title = {The archaeome in metaorganism research, with a focus on marine models and their bacteria-archaea interactions.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1347422},
pmid = {38476944},
issn = {1664-302X},
abstract = {Metaorganism research contributes substantially to our understanding of the interaction between microbes and their hosts, as well as their co-evolution. Most research is currently focused on the bacterial community, while archaea often remain at the sidelines of metaorganism-related research. Here, we describe the archaeome of a total of eleven classical and emerging multicellular model organisms across the phylogenetic tree of life. To determine the microbial community composition of each host, we utilized a combination of archaea and bacteria-specific 16S rRNA gene amplicons. Members of the two prokaryotic domains were described regarding their community composition, diversity, and richness in each multicellular host. Moreover, association with specific hosts and possible interaction partners between the bacterial and archaeal communities were determined for the marine models. Our data show that the archaeome in marine hosts predominantly consists of Nitrosopumilaceae and Nanoarchaeota, which represent keystone taxa among the porifera. The presence of an archaeome in the terrestrial hosts varies substantially. With respect to abundant archaeal taxa, they harbor a higher proportion of methanoarchaea over the aquatic environment. We find that the archaeal community is much less diverse than its bacterial counterpart. Archaeal amplicon sequence variants are usually host-specific, suggesting adaptation through co-evolution with the host. While bacterial richness was higher in the aquatic than the terrestrial hosts, a significant difference in diversity and richness between these groups could not be observed in the archaeal dataset. Our data show a large proportion of unclassifiable archaeal taxa, highlighting the need for improved cultivation efforts and expanded databases.},
}

@article {pmid38471558,
year = {2024},
author = {Jung, J and Loschko, T and Reich, S and Rassoul-Agha, M and Werner, MS},
title = {Newly identified nematodes from the Great Salt Lake are associated with microbialites and specially adapted to hypersaline conditions.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2018},
pages = {20232653},
pmid = {38471558},
issn = {1471-2954},
mesh = {Animals ; *Ecosystem ; Lakes/chemistry ; Phylogeny ; *Nematoda ; Bacteria ; },
abstract = {Extreme environments enable the study of simplified food-webs and serve as models for evolutionary bottlenecks and early Earth ecology. We investigated the biodiversity of invertebrate meiofauna in the benthic zone of the Great Salt Lake (GSL), Utah, USA, one of the most hypersaline lake systems in the world. The hypersaline bays within the GSL are currently thought to support only two multicellular animals: brine fly larvae and brine shrimp. Here, we report the presence, habitat, and microbial interactions of novel free-living nematodes. Nematode diversity drops dramatically along a salinity gradient from a freshwater river into the south arm of the lake. In Gilbert Bay, nematodes primarily inhabit reef-like organosedimentary structures built by bacteria called microbialites. These structures likely provide a protective barrier to UV and aridity, and bacterial associations within them may support life in hypersaline environments. Notably, sampling from Owens Lake, another terminal lake in the Great Basin that lacks microbialites, did not recover nematodes from similar salinities. Phylogenetic divergence suggests that GSL nematodes represent previously undescribed members of the family Monhysteridae-one of the dominant fauna of the abyssal zone and deep-sea hydrothermal vents. These findings update our understanding of halophile ecosystems and the habitable limit of animals.},
}

Animals
*Ecosystem
Lakes/chemistry
Phylogeny
*Nematoda
Bacteria

@article {pmid38474088,
year = {2024},
author = {Jiménez-López, D and Xoconostle-Cázares, B and Calderón-Pérez, B and Vargas-Hernández, BY and Núñez-Muñoz, LA and Ramírez-Pool, JA and Ruiz-Medrano, R},
title = {Evolutionary and Structural Analysis of PP16 in Viridiplantae.},
journal = {International journal of molecular sciences},
volume = {25},
number = {5},
pages = {},
doi = {10.3390/ijms25052839},
pmid = {38474088},
issn = {1422-0067},
support = {781282//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; },
abstract = {Members of the phloem protein 16 (PP16) gene family are induced by elicitors in rice and the corresponding proteins from cucurbits, which display RNA binding and intercellular transport activities, are accumulated in phloem sap. These proteins facilitate the movement of protein complexes through the phloem translocation flow and may be involved in the response to water deficit, among other functions. However, there is scant information regarding their function in other plants, including the identification of paralog genes in non-vascular plants and chlorophytes. In the present work, an evolutionary and structural analysis of the PP16 family in green plants (Viridiplantae) was carried out. Data mining in different databases indicated that PP16 likely originated from a larger gene present in an ancestral lineage that gave rise to chlorophytes and multicellular plants. This gene encodes a protein related to synaptotagmin, which is involved in vesicular transport in animal systems, although other members of this family play a role in lipid turnover in endomembranes and organelles. These proteins contain a membrane-binding C2 domain shared with PP16 proteins in vascular plants. In silico analysis of the predicted structure of the PP16 protein family identified several β-sheets, one α-helix, and intrinsically disordered regions. PP16 may have been originally involved in vesicular trafficking and/or membrane maintenance but specialized in long-distance signaling during the emergence of the plant vascular system.},
}

@article {pmid38472019,
year = {2024},
author = {Cui, L and Zhu, K and Li, R and Chang, C and Wu, L and Liu, W and Fu, D and Liu, P and Qiu, H and Tang, G and Li, Q and Gaines, RR and Tao, Y and Wang, Y and Li, J and Zhang, X},
title = {The Cambrian microfossil Qingjiangonema reveals the co-evolution of sulfate-reducing bacteria and the oxygenation of Earth's surface.},
journal = {Science bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2024.03.001},
pmid = {38472019},
issn = {2095-9281},
abstract = {Sulfate reduction is an essential metabolism that maintains biogeochemical cycles in marine and terrestrial ecosystems. Sulfate reducers are exclusively prokaryotic, phylogenetically diverse, and may have evolved early in Earth's history. However, their origin is elusive and unequivocal fossils are lacking. Here we report a new microfossil, Qingjiangonema cambria, from ∼518-million-year-old black shales that yield the Qingjiang biota. Qingjiangonema is a long filamentous form comprising hundreds of cells filled by equimorphic and equidimensional pyrite microcrystals with a light sulfur isotope composition. Multiple lines of evidence indicate Qingjiangonema was a sulfate-reducing bacterium that exhibits similar patterns of cell organization to filamentous forms within the phylum Desulfobacterota, including the sulfate-reducing Desulfonema and sulfide-oxidizing cable bacteria. Phylogenomic analyses confirm separate, independent origins of multicellularity in Desulfonema and in cable bacteria. Molecular clock analyses infer that the Desulfobacterota, which encompass a majority of sulfate-reducing taxa, diverged ∼2.41 billion years ago during the Paleoproterozoic Great Oxygenation Event, while cable bacteria diverged ∼0.56 billion years ago during or immediately after the Neoproterozoic Oxygenation Event. Taken together, we interpret Qingjiangonema as a multicellular sulfate-reducing microfossil and propose that cable bacteria evolved from a multicellular filamentous sulfate-reducing ancestor. We infer that the diversification of the Desulfobacterota and the origin of cable bacteria may have been responses to oxygenation events in Earth's history.},
}