@article {pmid39006742,
year = {2024},
author = {Obregon-Perko, V and Mannino, A and Ladner, JT and Hodara, V and Ebrahimi, D and Parodi, L and Callery, J and Palacios, G and Giavedoni, LD},
title = {Adaptation of SIVmac to baboon primary cells results in complete absence of in vivo baboon infectivity.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1408245},
pmid = {39006742},
issn = {2235-2988},
mesh = {Animals ; *Simian Immunodeficiency Virus/genetics/physiology ; *Virus Replication ; *Simian Acquired Immunodeficiency Syndrome/virology/immunology ; *Papio ; Leukocytes, Mononuclear/virology/immunology ; Receptors, CCR5/metabolism/genetics ; CD4-Positive T-Lymphocytes/virology/immunology ; Cells, Cultured ; Serial Passage ; },
abstract = {While simian immunodeficiency virus (SIV) infection is non-pathogenic in naturally infected African nonhuman primate hosts, experimental or accidental infection in rhesus macaques often leads to AIDS. Baboons, widely distributed throughout Africa, do not naturally harbor SIV, and experimental infection of baboons with SIVmac results in transient low-level viral replication. Elucidation of mechanisms of natural immunity in baboons could uncover new targets of antiviral intervention. We tested the hypothesis that an SIVmac adapted to replicate in baboon primary cells will gain the capacity to establish chronic infections in vivo. Here, we generated SIVmac variants in baboon cells through serial passage in PBMC from different donors (SIVbn-PBMC s1), in PBMC from the same donors (SIVbn-PBMC s2), or in isolated CD4 cells from the same donors used for series 2 (SIVbn-CD4). While SIVbn-PBMC s1 and SIVbn-CD4 demonstrated increased replication capacity, SIVbn-PBMC s2 did not. Pharmacological blockade of CCR5 revealed SIVbn-PBMC s1 could more efficiently use available CCR5 than SIVmac, a trait we hypothesize arose to circumvent receptor occupation by chemokines. Sequencing analysis showed that all three viruses accumulated different types of mutations, and that more non-synonymous mutations became fixed in SIVbn-PBMC s1 than SIVbn-PBMC s2 and SIVbn-CD4, supporting the notion of stronger fitness pressure in PBMC from different genetic backgrounds. Testing the individual contribution of several newly fixed SIV mutations suggested that is the additive effect of these mutations in SIVbn-PBMC s1 that contributed to its enhanced fitness, as recombinant single mutant viruses showed no difference in replication capacity over the parental SIVmac239 strain. The replicative capacity of SIVbn-PBMC passage 4 (P4) s1 was tested in vivo by infecting baboons intravenously with SIVbn-PBMC P4 s1 or SIVmac251. While animals infected with SIVmac251 showed the known pattern of transient low-level viremia, animals infected with SIVbn-PBMC P4 s1 had undetectable viremia or viral DNA in lymphoid tissue. These studies suggest that adaptation of SIV to grow in baboon primary cells results in mutations that confer increased replicative capacity in the artificial environment of cell culture but make the virus unable to avoid the restrictive factors generated by a complex multicellular organism.},
}

Animals
*Simian Immunodeficiency Virus/genetics/physiology
*Virus Replication
*Simian Acquired Immunodeficiency Syndrome/virology/immunology
*Papio
Leukocytes, Mononuclear/virology/immunology
Receptors, CCR5/metabolism/genetics
CD4-Positive T-Lymphocytes/virology/immunology
Cells, Cultured
Serial Passage

@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 {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 {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 447/18-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FA 330/12-3//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; KE 447/10-2//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; KE 447/21-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; KO 2251/13-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; /WT_/Wellcome Trust/United Kingdom ; },
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 de Farias, ST},
title = {Major evolutionary transitions before cells: A journey from molecules to organisms.},
journal = {Progress in biophysics and molecular biology},
volume = {191},
number = {},
pages = {11-24},
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 = {41},
number = {2},
pages = {135-155},
doi = {10.1093/imammb/dqae005},
pmid = {38970827},
issn = {1477-8602},
mesh = {*Neoplasms/pathology/physiopathology ; Humans ; *Phenotype ; Animals ; *Models, Biological ; Cell Differentiation/physiology ; Mathematical Concepts ; Cell Communication/physiology ; Biological Evolution ; },
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.},
}

*Neoplasms/pathology/physiopathology
Humans
*Phenotype
Animals
*Models, Biological
Cell Differentiation/physiology
Mathematical Concepts
Cell Communication/physiology
Biological Evolution

@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 = {102-103},
number = {},
pages = {17-24},
doi = {10.1016/j.semcancer.2024.06.003},
pmid = {38969311},
issn = {1096-3650},
mesh = {Humans ; *Neoplasms/pathology/genetics/metabolism ; Animals ; *Neoplasm Metastasis ; *Carcinogenesis/genetics/pathology ; Hypoxia-Inducible Factor 1/metabolism/genetics ; Neovascularization, Pathologic/genetics/pathology/metabolism ; Epithelial-Mesenchymal Transition/genetics ; Tumor Microenvironment/genetics ; Epigenesis, Genetic ; Gene Expression Regulation, Neoplastic ; },
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 tumor 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 tumor 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 tumor 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 tumor promoting microenvironment. Thus, hypoxia in the primary tumor 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 tumors.},
}

Humans
*Neoplasms/pathology/genetics/metabolism
Animals
*Neoplasm Metastasis
*Carcinogenesis/genetics/pathology
Hypoxia-Inducible Factor 1/metabolism/genetics
Neovascularization, Pathologic/genetics/pathology/metabolism
Epithelial-Mesenchymal Transition/genetics
Tumor Microenvironment/genetics
Epigenesis, Genetic
Gene Expression Regulation, Neoplastic

@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 {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 = {66},
number = {5},
pages = {329-337},
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)/ ; },
mesh = {Animals ; *Macrophages/cytology ; Mice ; *Brain/embryology/cytology ; Microglia/cytology/metabolism ; Cerebral Ventricles/embryology/cytology ; },
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.},
}

Animals
*Macrophages/cytology
Mice
*Brain/embryology/cytology
Microglia/cytology/metabolism
Cerebral Ventricles/embryology/cytology

@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 {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},
pmid = {38848676},
issn = {1097-4172},
support = {R01 LM013522/LM/NLM NIH HHS/United States ; R21 CA264361/CA/NCI NIH HHS/United States ; U01 CA260432/CA/NCI NIH HHS/United States ; U54 CA263001/CA/NCI NIH HHS/United States ; },
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 {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 = {34},
number = {6},
pages = {863-876},
doi = {10.1101/gr.278392.123},
pmid = {38839375},
issn = {1549-5469},
mesh = {Animals ; *Ants/genetics ; *Recombination, Genetic ; Chromosome Mapping ; Haplotypes ; Genetic Variation ; Genome, Insect ; Selection, Genetic ; Evolution, Molecular ; },
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 that are enriched with TEs, that have strong haplotype divergence, or that show 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.},
}

Animals
*Ants/genetics
*Recombination, Genetic
Chromosome Mapping
Haplotypes
Genetic Variation
Genome, Insect
Selection, Genetic
Evolution, Molecular

@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 = {16},
number = {6},
pages = {},
pmid = {38813885},
issn = {1759-6653},
support = {NSF-1347116//National Science Foundation/ ; GT15982/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {*Symbiosis ; *Biological Evolution ; Animals ; Bacteria/genetics ; Biodiversity ; Evolution, Molecular ; },
abstract = {Life on Earth comprises prokaryotes and a broad assemblage of endosymbioses. The pages of Molecular Biology and Evolution and Genome Biology and Evolution have provided an essential window into how these endosymbiotic interactions have evolved and shaped biological diversity. Here, we provide a current perspective on this knowledge by drawing on decades of revelatory research published in Molecular Biology and Evolution and Genome Biology and Evolution, and insights from the field at large. The accumulated work 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 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.},
}

*Symbiosis
*Biological Evolution
Animals
Bacteria/genetics
Biodiversity
Evolution, Molecular

@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 {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 = {},
pmid = {38798503},
issn = {2692-8205},
support = {R24 GM137782/GM/NIGMS NIH HHS/United States ; T32 GM139786/GM/NIGMS NIH HHS/United States ; },
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 {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 = {43},
number = {13},
pages = {2530-2551},
pmid = {38773319},
issn = {1460-2075},
support = {R01 CA239645/CA/NCI NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R21 AI156236/AI/NIAID NIH HHS/United States ; W81XWH2210327//DOD | USA | MEDCOM | CDMRP | DOD Peer Reviewed Cancer Research Program (PRCRP)/ ; P30 DK052574/DK/NIDDK NIH HHS/United States ; K08 DK132496/DK/NIDDK NIH HHS/United States ; R01 DK105129/DK/NIDDK NIH HHS/United States ; R01DK105129//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; R01 DK134531/DK/NIDDK NIH HHS/United States ; W81XWH-20-1-0630//DOD | USA | MEDCOM | CDMRP | DOD Peer Reviewed Cancer Research Program (PRCRP)/ ; R01DK134531//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; },
mesh = {Humans ; Animals ; *Neoplasms/pathology/genetics ; *Cell Differentiation ; Tumor Suppressor Protein p53/metabolism/genetics ; Cell Transformation, Neoplastic/genetics/pathology ; Stem Cells ; Carcinogenesis/pathology ; },
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.},
}

Humans
Animals
*Neoplasms/pathology/genetics
*Cell Differentiation
Tumor Suppressor Protein p53/metabolism/genetics
Cell Transformation, Neoplastic/genetics/pathology
Stem Cells
Carcinogenesis/pathology

@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 {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 = {1870},
number = {5},
pages = {167226},
doi = {10.1016/j.bbadis.2024.167226},
pmid = {38734320},
issn = {1879-260X},
mesh = {Humans ; *Neoplasms/genetics/pathology/therapy/metabolism ; *Carcinogenesis/genetics/pathology ; Genetic Heterogeneity ; Oncogenes/genetics ; Animals ; Cell Transformation, Neoplastic/genetics/metabolism ; Genes, Tumor Suppressor ; Gene Expression Regulation, Neoplastic ; },
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.},
}

Humans
*Neoplasms/genetics/pathology/therapy/metabolism
*Carcinogenesis/genetics/pathology
Genetic Heterogeneity
Oncogenes/genetics
Animals
Cell Transformation, Neoplastic/genetics/metabolism
Genes, Tumor Suppressor
Gene Expression Regulation, Neoplastic

@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 = {629},
number = {8014},
pages = {1174-1181},
pmid = {38720073},
issn = {1476-4687},
support = {P01 CA117969/CA/NCI NIH HHS/United States ; P01 CA120964/CA/NCI NIH HHS/United States ; R35 ES028374/ES/NIEHS NIH HHS/United States ; R01 GM104047/GM/NIGMS NIH HHS/United States ; R01 GM135331/GM/NIGMS NIH HHS/United States ; R35 CA197588/CA/NCI NIH HHS/United States ; R01 CA226898/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Humans ; Amino Acid Motifs ; Evolution, Molecular ; Mass Spectrometry ; Phosphoproteins/chemistry/metabolism ; Phosphorylation ; *Phosphotyrosine/metabolism ; *Protein-Tyrosine Kinases/drug effects/metabolism ; Proteome/chemistry/metabolism ; Proteomics ; Signal Transduction ; src Homology Domains ; *Substrate Specificity ; *Tyrosine/metabolism/chemistry ; },
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.},
}

Animals
Humans
Amino Acid Motifs
Evolution, Molecular
Mass Spectrometry
Phosphoproteins/chemistry/metabolism
Phosphorylation
*Phosphotyrosine/metabolism
*Protein-Tyrosine Kinases/drug effects/metabolism
Proteome/chemistry/metabolism
Proteomics
Signal Transduction
src Homology Domains
*Substrate Specificity
*Tyrosine/metabolism/chemistry

@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},
pmid = {38713735},
issn = {1553-7358},
mesh = {*Models, Biological ; *Biological Evolution ; Computational Biology ; Ecosystem ; Animals ; Predatory Behavior/physiology ; Selection, Genetic ; Computer Simulation ; },
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.},
}

*Models, Biological
*Biological Evolution
Computational Biology
Ecosystem
Animals
Predatory Behavior/physiology
Selection, Genetic
Computer Simulation

@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 = {23},
number = {6},
pages = {100782},
pmid = {38705386},
issn = {1535-9484},
mesh = {*Pericytes/metabolism ; Humans ; *Spheroids, Cellular/metabolism ; *Coculture Techniques ; *Cell Hypoxia ; Secretome/metabolism ; Endothelial Cells/metabolism ; Astrocytes/metabolism ; Proteomics/methods ; Cell Communication ; Blood-Brain Barrier/metabolism ; Cells, Cultured ; Brain/metabolism ; Mass Spectrometry ; Signal Transduction ; },
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 cocultures with human endothelial cells and astrocytes. This approach allowed us to characterize the pericyte secretome within a more physiologically relevant multicellular setting encompassing the constituents of the blood-brain barrier. 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 intercellular communication with other blood-brain barrier-residing cells. Moreover, we identified substantial differences in the secretory profiles between hypoxic and normoxic pericytes. Mass spectrometry analysis showed that hypoxic pericytes in coculture increase their release of signals related to protein secretion, mTOR signaling, 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 multicellular 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 signaling in brain pathologies associated with hypoxia.},
}

*Pericytes/metabolism
Humans
*Spheroids, Cellular/metabolism
*Coculture Techniques
*Cell Hypoxia
Secretome/metabolism
Endothelial Cells/metabolism
Astrocytes/metabolism
Proteomics/methods
Cell Communication
Blood-Brain Barrier/metabolism
Cells, Cultured
Brain/metabolism
Mass Spectrometry
Signal Transduction

@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 = {921},
number = {},
pages = {148520},
doi = {10.1016/j.gene.2024.148520},
pmid = {38702020},
issn = {1879-0038},
mesh = {*Phylogeny ; Animals ; *Evolution, Molecular ; Fungi/genetics/metabolism ; HMGB Proteins/genetics/metabolism ; SOX Transcription Factors/genetics/metabolism ; Transcription Factors/genetics/metabolism ; Fungal Proteins/genetics/metabolism ; Wnt Signaling Pathway ; },
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.},
}

*Phylogeny
Animals
*Evolution, Molecular
Fungi/genetics/metabolism
HMGB Proteins/genetics/metabolism
SOX Transcription Factors/genetics/metabolism
Transcription Factors/genetics/metabolism
Fungal Proteins/genetics/metabolism
Wnt Signaling Pathway

@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 = {56},
number = {5},
pages = {1018-1031},
pmid = {38693345},
issn = {1546-1718},
support = {R01GM140370//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; RE 1697/16-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; RE 1697/18-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 1933521//National Science Foundation (NSF)/ ; R21AI171952//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; 852725//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; R01 GM140370/GM/NIGMS NIH HHS/United States ; R21 AI171952/AI/NIAID NIH HHS/United States ; P34181-B//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; 58-8042-9-089//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; ANR-10-LABX-41//LABoratoires d'EXcellence ARCANE (Labex ARCANE)/ ; 410739858//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; TH417/12-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 440231723//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; OPP1172165//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 101001675//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 440540015//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Signal Transduction/genetics ; *Embryophyta/genetics ; *Evolution, Molecular ; *Phylogeny ; Gene Regulatory Networks ; Genome/genetics ; Genome, Plant ; },
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.},
}

*Signal Transduction/genetics
*Embryophyta/genetics
*Evolution, Molecular
*Phylogeny
Gene Regulatory Networks
Genome/genetics
Genome, Plant

@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},
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 {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 {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},
pmid = {38662765},
issn = {1553-7358},
mesh = {Drosophila melanogaster/genetics ; *Intrinsically Disordered Proteins/chemistry/genetics/metabolism ; *Drosophila Proteins/chemistry/genetics/metabolism ; Evolution, Molecular ; Sequence Homology ; Amino Acid Sequence ; },
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.},
}

Drosophila melanogaster/genetics
*Intrinsically Disordered Proteins/chemistry/genetics/metabolism
*Drosophila Proteins/chemistry/genetics/metabolism
Evolution, Molecular
Sequence Homology
Amino Acid Sequence

@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 = {},
pmid = {38659912},
issn = {2692-8205},
support = {R35 GM138030/GM/NIGMS NIH HHS/United States ; },
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 = {189},
number = {},
pages = {114679},
doi = {10.1016/j.fct.2024.114679},
pmid = {38657942},
issn = {1873-6351},
mesh = {Female ; Animals ; Pregnancy ; Mice ; *Acetaminophen/toxicity ; *Ovary/drug effects/metabolism ; Dose-Response Relationship, Drug ; Oocytes/drug effects ; Prenatal Exposure Delayed Effects/chemically induced ; Bone Morphogenetic Protein 15/genetics ; Growth Differentiation Factor 9/genetics/metabolism ; Cell Proliferation/drug effects ; },
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.},
}

Female
Animals
Pregnancy
Mice
*Acetaminophen/toxicity
*Ovary/drug effects/metabolism
Dose-Response Relationship, Drug
Oocytes/drug effects
Prenatal Exposure Delayed Effects/chemically induced
Bone Morphogenetic Protein 15/genetics
Growth Differentiation Factor 9/genetics/metabolism
Cell Proliferation/drug effects

@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 = {10},
number = {5},
pages = {2995-3005},
doi = {10.1021/acsbiomaterials.3c01875},
pmid = {38654432},
issn = {2373-9878},
mesh = {*Calcium/metabolism ; *Cell Survival ; *Reactive Oxygen Species/metabolism ; *TRPV Cation Channels/metabolism ; Humans ; *Hyperthermia, Induced/methods ; *Magnetic Fields ; Temperature ; Ferritins/metabolism ; Hyperthermia/metabolism ; },
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.},
}

*Calcium/metabolism
*Cell Survival
*Reactive Oxygen Species/metabolism
*TRPV Cation Channels/metabolism
Humans
*Hyperthermia, Induced/methods
*Magnetic Fields
Temperature
Ferritins/metabolism
Hyperthermia/metabolism

@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},
mesh = {Animals ; *Neoplasms/genetics/pathology ; Humans ; *Biological Evolution ; Disease Resistance/genetics/physiology ; Selection, Genetic ; Mole Rats/physiology/genetics ; Elephants/genetics ; },
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.},
}

Animals
*Neoplasms/genetics/pathology
Humans
*Biological Evolution
Disease Resistance/genetics/physiology
Selection, Genetic
Mole Rats/physiology/genetics
Elephants/genetics

@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 = {19},
number = {5},
pages = {1151-1160},
doi = {10.1021/acschembio.4c00090},
pmid = {38648729},
issn = {1554-8937},
mesh = {*TRPV Cation Channels/metabolism ; Humans ; *Reactive Oxygen Species/metabolism ; HEK293 Cells ; *Ferritins/metabolism/chemistry ; *Magnetic Fields ; Iron/metabolism ; Calcium/metabolism ; },
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.},
}

*TRPV Cation Channels/metabolism
Humans
*Reactive Oxygen Species/metabolism
HEK293 Cells
*Ferritins/metabolism/chemistry
*Magnetic Fields
Iron/metabolism
Calcium/metabolism

@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 = {46},
number = {6},
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/ ; },
mesh = {*Neoplasms/genetics/pathology ; Humans ; Animals ; Biological Evolution ; Mutation ; Cell Proliferation/genetics ; },
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.},
}

*Neoplasms/genetics/pathology
Humans
Animals
Biological Evolution
Mutation
Cell Proliferation/genetics

@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 = {124},
number = {8},
pages = {4679-4733},
doi = {10.1021/acs.chemrev.3c00420},
pmid = {38621413},
issn = {1520-6890},
mesh = {Animals ; Humans ; Apoptosis/drug effects ; *Ionic Liquids/chemistry/pharmacology ; Oxidative Stress/drug effects ; },
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.},
}

Animals
Humans
Apoptosis/drug effects
*Ionic Liquids/chemistry/pharmacology
Oxidative Stress/drug effects

@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},
pmid = {38604731},
issn = {1549-5469},
support = {/WT_/Wellcome Trust/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/T016019/1/MRC_/Medical Research Council/United Kingdom ; 224501/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; },
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 {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 {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},
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 {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 {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 = {5},
number = {4},
pages = {101489},
pmid = {38554705},
issn = {2666-3791},
mesh = {Humans ; *Lung Neoplasms/genetics ; *Adenocarcinoma/genetics/pathology ; CD8-Positive T-Lymphocytes/pathology ; Ecotype ; Retrospective Studies ; *Adenocarcinoma of Lung ; },
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.},
}

Humans
*Lung Neoplasms/genetics
*Adenocarcinoma/genetics/pathology
CD8-Positive T-Lymphocytes/pathology
Ecotype
Retrospective Studies
*Adenocarcinoma of Lung

@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/CA/NCI NIH HHS/United States ; U2C CA233254/CA/NCI NIH HHS/United States ; U54 CA217376/GF/NIH HHS/United States ; R01 CA140657/CA/NCI NIH HHS/United States ; R21 CA257980/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Child, Preschool ; *Biological Evolution ; *Neoplasms ; },
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.},
}

Humans
Child, Preschool
*Biological Evolution
*Neoplasms

@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 = {16},
number = {4},
pages = {},
pmid = {38547507},
issn = {1759-6653},
support = {//Swedish Research Council/ ; 2017.0322//Knut and Alice Wallenberg Foundation/ ; },
mesh = {*Protein Serine-Threonine Kinases/genetics/metabolism ; Phylogeny ; *Planctomycetes ; Proteome/genetics ; Bacteria/genetics/metabolism ; Threonine/genetics ; Serine/genetics ; },
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 with Pkinase domains. In total, we predicted 525 functional Serine/Threonine kinases in "Ca. Uabimicrobium amorphum", which represent 8% of the proteome and is the highest fraction of Serine/Threonine kinases in a bacterial proteome. The majority of Serine/Threonine kinases 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 Serine/Threonine kinases of other species in the Planctomycetota, although in much lower abundances. A phylogenetic analysis of the Serine/Threonine kinases in the Planctomycetota inferred from the Pkinase domain alone provided support for lineage-specific expansions of the Serine/Threonine kinases 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.},
}

*Protein Serine-Threonine Kinases/genetics/metabolism
Phylogeny
*Planctomycetes
Proteome/genetics
Bacteria/genetics/metabolism
Threonine/genetics
Serine/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 {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 {pmid38519635,
year = {2024},
author = {},
title = {Multicellularity drives ecological diversity in a long-term evolution experiment.},
journal = {Nature ecology & evolution},
volume = {8},
number = {5},
pages = {856-857},
pmid = {38519635},
issn = {2397-334X},
support = {R35 GM138030/GM/NIGMS NIH HHS/United States ; },
mesh = {*Biological Evolution ; *Biodiversity ; Animals ; },
}

*Biological Evolution
*Biodiversity
Animals

@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 = {R01 EY015708/EY/NEI NIH HHS/United States ; EY015708/EY/NEI NIH HHS/United States ; },
mesh = {Animals ; *Signal Transduction/genetics ; *Protein Serine-Threonine Kinases/genetics/metabolism ; Hippo Signaling Pathway ; Biological Evolution ; Cell Proliferation ; },
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.},
}

Animals
*Signal Transduction/genetics
*Protein Serine-Threonine Kinases/genetics/metabolism
Hippo Signaling Pathway
Biological Evolution
Cell Proliferation

@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 {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 = {},
pmid = {38513719},
issn = {1943-2631},
support = {R35GM150720/GM/NIGMS NIH HHS/United States ; R35 GM128804/GM/NIGMS NIH HHS/United States ; T32-GM122740/GF/NIH HHS/United States ; R35 GM150720/GM/NIGMS NIH HHS/United States ; T32 GM122740/GM/NIGMS 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 {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},
mesh = {Animals ; Biological Evolution ; *Phaeophyceae/genetics ; *Sex Chromosomes/genetics ; *Sex Determination Processes/genetics ; Y Chromosome ; *HMGB Proteins/genetics ; Chromosomes, Plant/genetics ; HMG-Box Domains ; *Edible Seaweeds/genetics ; *Laminaria/genetics ; Pollen/genetics ; },
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.},
}

Animals
Biological Evolution
*Phaeophyceae/genetics
*Sex Chromosomes/genetics
*Sex Determination Processes/genetics
Y Chromosome
*HMGB Proteins/genetics
Chromosomes, Plant/genetics
HMG-Box Domains
*Edible Seaweeds/genetics
*Laminaria/genetics
Pollen/genetics

@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},
pmid = {38498818},
issn = {1557-8070},
support = {R35 GM138030/GM/NIGMS NIH HHS/United States ; },
mesh = {Phylogeny ; *Biological Evolution ; *Earth, Planet ; Oxygen ; Photosynthesis ; },
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.},
}

Phylogeny
*Biological Evolution
*Earth, Planet
Oxygen
Photosynthesis

@article {pmid38497809,
year = {2024},
author = {Hörandl, E},
title = {Apomixis and the paradox of sex in plants.},
journal = {Annals of botany},
volume = {134},
number = {1},
pages = {1-18},
pmid = {38497809},
issn = {1095-8290},
support = {HO 4395/10-2//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Apomixis/genetics/physiology ; *Magnoliopsida/genetics/physiology ; Reproduction, Asexual ; Biological Evolution ; Ferns/genetics/physiology ; Reproduction/physiology ; Phylogeny ; Meiosis ; Plants/genetics ; },
abstract = {BACKGROUND: The predominance of sex in eukaryotes, despite the high costs of meiosis and mating, remains an evolutionary enigma. Many theories have been proposed, none of them being conclusive on its own, and they are, in part, not well applicable to land plants. Sexual reproduction is obligate in embryophytes for the great majority of species.

SCOPE: This review compares 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 in comparison to asexuality are 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 for 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 not well understood. In plants in general, the costs of mating are 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.},
}

*Apomixis/genetics/physiology
*Magnoliopsida/genetics/physiology
Reproduction, Asexual
Biological Evolution
Ferns/genetics/physiology
Reproduction/physiology
Phylogeny
Meiosis
Plants/genetics

@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 = {41},
number = {5},
pages = {1371-1385},
pmid = {38492155},
issn = {1573-7330},
support = {81660806//National Natural Science Foundation of China/ ; 82260947//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Female ; *Exosomes/genetics/metabolism/ultrastructure ; *Granulosa Cells/metabolism ; *MicroRNAs/genetics ; *Cell Proliferation/genetics ; Gene Expression Profiling ; Cell Line ; },
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.},
}

Humans
Female
*Exosomes/genetics/metabolism/ultrastructure
*Granulosa Cells/metabolism
*MicroRNAs/genetics
*Cell Proliferation/genetics
Gene Expression Profiling
Cell Line

@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 = {8},
number = {5},
pages = {1010-1020},
pmid = {38486107},
issn = {2397-334X},
support = {R35 GM138030/GM/NIGMS NIH HHS/United States ; R35 GM138354/GM/NIGMS NIH HHS/United States ; },
mesh = {*Biological Evolution ; Saccharomyces cerevisiae/genetics/physiology ; Ecosystem ; },
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.},
}

*Biological Evolution
Saccharomyces cerevisiae/genetics/physiology
Ecosystem

@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 {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 = {},
pmid = {38474088},
issn = {1422-0067},
support = {781282//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; },
mesh = {*Plant Proteins/genetics ; Phloem/metabolism ; Plants/metabolism ; Biological Transport ; *Viridiplantae/metabolism ; },
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.},
}

*Plant Proteins/genetics
Phloem/metabolism
Plants/metabolism
Biological Transport
*Viridiplantae/metabolism

@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 {pmid38465473,
year = {2024},
author = {Borland, G and Wilkie, SE and Thomson, J and Wang, Z and Tullet, JMA and Alic, N and Selman, C},
title = {Polr3b heterozygosity in mice induces both beneficial and deleterious effects on health during ageing with no effect on lifespan.},
journal = {Aging cell},
volume = {23},
number = {5},
pages = {e14141},
pmid = {38465473},
issn = {1474-9726},
support = {BB/S014357/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/N013166/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; Mice ; *Longevity/genetics ; *Aging/genetics ; *RNA Polymerase III/genetics/metabolism ; Female ; Male ; *Heterozygote ; *Mice, Inbred C57BL ; },
abstract = {The genetic pathways that modulate ageing in multicellular organisms are typically highly conserved across wide evolutionary distances. Recently RNA polymerase III (Pol III) was shown to promote ageing in yeast, C. elegans and D. melanogaster. In this study we investigated the role of Pol III in mammalian ageing using C57BL/6N mice heterozygous for Pol III (Polr3b[+/-]). We identified sexually dimorphic, organ-specific beneficial as well as detrimental effects of the Polr3b[+/-] mutation on health. Female Polr3b[+/-] mice displayed improved bone health during ageing, but their ability to maintain an effective gut barrier function was compromised and they were susceptible to idiopathic dermatitis (ID). In contrast, male Polr3b[+/-] mice were lighter than wild-type (WT) males and had a significantly improved gut barrier function in old age. Several metabolic parameters were affected by both age and sex, but no genotype differences were detected. Neither male nor female Polr3b[+/-] mice were long-lived compared to WT controls. Overall, we find no evidence that a reduced Pol III activity extends mouse lifespan but we do find some potential organ- and sex-specific benefits for old-age health.},
}

Animals
Mice
*Longevity/genetics
*Aging/genetics
*RNA Polymerase III/genetics/metabolism
Female
Male
*Heterozygote
*Mice, Inbred C57BL

@article {pmid38462458,
year = {2023},
author = {Libertini, G},
title = {Phenoptosis and the Various Types of Natural Selection.},
journal = {Biochemistry. Biokhimiia},
volume = {88},
number = {12},
pages = {2007-2022},
doi = {10.1134/S0006297923120052},
pmid = {38462458},
issn = {1608-3040},
mesh = {Animals ; Bees ; *Aging/genetics ; Ecosystem ; Selection, Genetic ; *Ants ; Reproduction ; Biological Evolution ; },
abstract = {In the first description of evolution, the fundamental mechanism is the natural selection favoring the individuals best suited for survival and reproduction (selection at the individual level or classical Darwinian selection). However, this is a very reductive description of natural selection that does not consider or explain a long series of known phenomena, including those in which an individual sacrifices or jeopardizes his life on the basis of genetically determined mechanisms (i.e., phenoptosis). In fact, in addition to (i) selection at the individual level, it is essential to consider other types of natural selection such as those concerning: (ii) kin selection and some related forms of group selection; (iii) the interactions between the innumerable species that constitute a holobiont; (iv) the origin of the eukaryotic cell from prokaryotic organisms; (v) the origin of multicellular eukaryotic organisms from unicellular organisms; (vi) eusociality (e.g., in many species of ants, bees, termites); (vii) selection at the level of single genes, or groups of genes; (viii) the interactions between individuals (or more precisely their holobionts) of the innumerable species that make up an ecosystem. These forms of natural selection, which are all effects and not violations of the classical Darwinian selection, also show how concepts as life, species, individual, and phenoptosis are somewhat not entirely defined and somehow arbitrary. Furthermore, the idea of organisms selected on the basis of their survival and reproduction capabilities is intertwined with that of organisms also selected on the basis of their ability to cooperate and interact, even by losing their lives or their distinct identities.},
}

Animals
Bees
*Aging/genetics
Ecosystem
Selection, Genetic
*Ants
Reproduction
Biological Evolution

@article {pmid38459017,
year = {2024},
author = {Stanojković, A and Skoupý, S and Johannesson, H and Dvořák, P},
title = {The global speciation continuum of the cyanobacterium Microcoleus.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {2122},
pmid = {38459017},
issn = {2041-1723},
support = {19-12994Y//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; 23-06507S//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; },
mesh = {*Genetic Speciation ; *Genetic Drift ; Gene Flow ; Genome ; Phylogeny ; },
abstract = {Speciation is a continuous process driven by genetic, geographic, and ecological barriers to gene flow. It is widely investigated in multicellular eukaryotes, yet we are only beginning to comprehend the relative importance of mechanisms driving the emergence of barriers to gene flow in microbial populations. Here, we explored the diversification of the nearly ubiquitous soil cyanobacterium Microcoleus. Our dataset consisted of 291 genomes, of which 202 strains and eight herbarium specimens were sequenced for this study. We found that Microcoleus represents a global speciation continuum of at least 12 lineages, which radiated during Eocene/Oligocene aridification and exhibit varying degrees of divergence and gene flow. The lineage divergence has been driven by selection, geographical distance, and the environment. Evidence of genetic divergence and selection was widespread across the genome, but we identified regions of exceptional differentiation containing candidate genes associated with stress response and biosynthesis of secondary metabolites.},
}

*Genetic Speciation
*Genetic Drift
Gene Flow
Genome
Phylogeny

@article {pmid38447933,
year = {2024},
author = {Park, S and Cho, SW},
title = {Bioengineering toolkits for potentiating organoid therapeutics.},
journal = {Advanced drug delivery reviews},
volume = {208},
number = {},
pages = {115238},
doi = {10.1016/j.addr.2024.115238},
pmid = {38447933},
issn = {1872-8294},
mesh = {Animals ; Mice ; *Organoids ; Tissue Engineering/methods ; Regenerative Medicine ; Bioengineering ; *Neoplasms ; },
abstract = {Organoids are three-dimensional, multicellular constructs that recapitulate the structural and functional features of specific organs. Because of these characteristics, organoids have been widely applied in biomedical research in recent decades. Remarkable advancements in organoid technology have positioned them as promising candidates for regenerative medicine. However, current organoids still have limitations, such as the absence of internal vasculature, limited functionality, and a small size that is not commensurate with that of actual organs. These limitations hinder their survival and regenerative effects after transplantation. Another significant concern is the reliance on mouse tumor-derived matrix in organoid culture, which is unsuitable for clinical translation due to its tumor origin and safety issues. Therefore, our aim is to describe engineering strategies and alternative biocompatible materials that can facilitate the practical applications of organoids in regenerative medicine. Furthermore, we highlight meaningful progress in organoid transplantation, with a particular emphasis on the functional restoration of various organs.},
}

Animals
Mice
*Organoids
Tissue Engineering/methods
Regenerative Medicine
Bioengineering
*Neoplasms

@article {pmid38436556,
year = {2024},
author = {Matsumoto, H and Ueda, M},
title = {Polarity establishment in the plant zygote at a glance.},
journal = {Journal of cell science},
volume = {137},
number = {5},
pages = {},
doi = {10.1242/jcs.261809},
pmid = {38436556},
issn = {1477-9137},
support = {//Japan Advanced Plant Science Network/ ; JP21K20650//Japan Society for the Promotion of Science/ ; JPMJCR2121//Japan Science and Technology Agency/ ; //Suntory Rising Stars Encouragement Program in Life Sciences/ ; 20-6102//Toray Science Foundation/ ; },
mesh = {*Zygote ; Seeds ; *Arabidopsis/genetics ; Meristem ; Transcriptional Activation ; },
abstract = {The complex structures of multicellular organisms originate from a unicellular zygote. In most angiosperms, including Arabidopsis thaliana, the zygote is distinctly polar and divides asymmetrically to produce an apical cell, which generates the aboveground part of the plant body, and a basal cell, which generates the root tip and extraembryonic suspensor. Thus, zygote polarity is pivotal for establishing the apical-basal axis running from the shoot apex to the root tip of the plant body. The molecular mechanisms and spatiotemporal dynamics behind zygote polarization remain elusive. However, advances in live-cell imaging of plant zygotes have recently made significant insights possible. In this Cell Science at a Glance article and the accompanying poster, we summarize our understanding of the early steps in apical-basal axis formation in Arabidopsis, with a focus on de novo transcriptional activation after fertilization and the intracellular dynamics leading to the first asymmetric division of the zygote.},
}

*Zygote
Seeds
*Arabidopsis/genetics
Meristem
Transcriptional Activation

@article {pmid38424063,
year = {2024},
author = {Bayer, EM and Benitez-Alfonso, Y},
title = {Plasmodesmata: Channels Under Pressure.},
journal = {Annual review of plant biology},
volume = {75},
number = {1},
pages = {291-317},
doi = {10.1146/annurev-arplant-070623-093110},
pmid = {38424063},
issn = {1545-2123},
support = {MR/T04263X/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Plasmodesmata/metabolism/physiology ; *Cell Communication ; Plant Development/physiology ; Plants/metabolism ; Plant Physiological Phenomena ; },
abstract = {Multicellularity has emerged multiple times in evolution, enabling groups of cells to share a living space and reducing the burden of solitary tasks. While unicellular organisms exhibit individuality and independence, cooperation among cells in multicellular organisms brings specialization and flexibility. However, multicellularity also necessitates intercellular dependence and relies on intercellular communication. In plants, this communication is facilitated by plasmodesmata: intercellular bridges that allow the direct (cytoplasm-to-cytoplasm) transfer of information between cells. Plasmodesmata transport essential molecules that regulate plant growth, development, and stress responses. They are embedded in the extracellular matrix but exhibit flexibility, adapting intercellular flux to meet the plant's needs.In this review, we delve into the formation and functionality of plasmodesmata and examine the capacity of the plant communication network to respond to developmental and environmental cues. We illustrate how environmental pressure shapes cellular interactions and aids the plant in adapting its growth.},
}

*Plasmodesmata/metabolism/physiology
*Cell Communication
Plant Development/physiology
Plants/metabolism
Plant Physiological Phenomena

@article {pmid38400751,
year = {2024},
author = {Woudenberg, S and Hadid, F and Weijers, D and Borassi, C},
title = {The maternal embrace: the protection of plant embryos.},
journal = {Journal of experimental botany},
volume = {75},
number = {14},
pages = {4210-4218},
pmid = {38400751},
issn = {1460-2431},
support = {//Graduate School Experimental Plant Sciences/ ; /ERC_/European Research Council/International ; ENW-KLEIN2//Netherlands Organization for Scientific Research/ ; },
mesh = {*Seeds/growth & development ; Embryophyta/growth & development ; Biological Evolution ; },
abstract = {All land plants-the embryophytes-produce multicellular embryos, as do other multicellular organisms, such as brown algae and animals. A unique characteristic of plant embryos is their immobile and confined nature. Their embedding in maternal tissues may offer protection from the environment, but also physically constrains development. Across the different land plants, a huge discrepancy is present between their reproductive structures whilst leading to similarly complex embryos. Therefore, we review the roles that maternal tissues play in the control of embryogenesis across land plants. These nurturing, constraining, and protective roles include both direct and indirect effects. In this review, we explore how the maternal surroundings affect embryogenesis and which chemical and mechanical barriers are in place. We regard these questions through the lens of evolution, and identify key questions for future research.},
}

*Seeds/growth & development
Embryophyta/growth & development
Biological Evolution

@article {pmid38388648,
year = {2024},
author = {Ratajczak, MZ and Ratajczak, J},
title = {Leukemogenesis occurs in a microenvironment enriched by extracellular microvesicles/exosomes: recent discoveries and questions to be answered.},
journal = {Leukemia},
volume = {38},
number = {4},
pages = {692-698},
pmid = {38388648},
issn = {1476-5551},
support = {R01 DK074720/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Exosomes/metabolism ; *Cell-Derived Microparticles ; Cell Communication ; Signal Transduction ; Proteins/metabolism ; *Extracellular Vesicles/metabolism ; },
abstract = {In single-cell organisms, extracellular microvesicles (ExMVs) were one of the first cell-cell communication platforms that emerged very early during evolution. Multicellular organisms subsequently adapted this mechanism. Evidence indicates that all types of cells secrete these small circular structures surrounded by a lipid membrane that may be encrusted by ligands and receptors interacting with target cells and harboring inside a cargo comprising RNA species, proteins, bioactive lipids, signaling nucleotides, and even entire organelles "hijacked" from the cells of origin. ExMVs are secreted by normal cells and at higher levels by malignant cells, and there are some differences in their cargo. On the one hand, ExMVs secreted from malignant cells interact with cells in the microenvironment, and in return, they are exposed by a "two-way mechanism" to ExMVs secreted by non-leukemic cells. Therefore, leukemogenesis occurs and progresses in ExMVs enriched microenvironments, and this biological fact has pathologic, diagnostic, and therapeutic implications. We are still trying to decipher this intriguing cell-cell communication language better. We will present a current point of view on this topic and review some selected most recent discoveries and papers.},
}

Humans
*Exosomes/metabolism
*Cell-Derived Microparticles
Cell Communication
Signal Transduction
Proteins/metabolism
*Extracellular Vesicles/metabolism

@article {pmid38386708,
year = {2024},
author = {Ilker, E and Hinczewski, M},
title = {Bioenergetic costs and the evolution of noise regulation by microRNAs.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {9},
pages = {e2308796121},
pmid = {38386708},
issn = {1091-6490},
mesh = {*Eukaryota ; *MicroRNAs/genetics ; Mutant Proteins ; RNA, Messenger ; Energy Metabolism/genetics ; },
abstract = {Noise control, together with other regulatory functions facilitated by microRNAs (miRNAs), is believed to have played important roles in the evolution of multicellular eukaryotic organisms. miRNAs can dampen protein fluctuations via enhanced degradation of messenger RNA (mRNA), but this requires compensation by increased mRNA transcription to maintain the same expression levels. The overall mechanism is metabolically expensive, leading to questions about how it might have evolved in the first place. We develop a stochastic model of miRNA noise regulation, coupled with a detailed analysis of the associated metabolic costs. Additionally, we calculate binding free energies for a range of miRNA seeds, the short sequences which govern target recognition. We argue that natural selection may have fine-tuned the Michaelis-Menten constant [Formula: see text] describing miRNA-mRNA affinity and show supporting evidence from analysis of experimental data. [Formula: see text] is constrained by seed length, and optimal noise control (minimum protein variance at a given energy cost) is achievable for seeds of 6 to 7 nucleotides in length, the most commonly observed types. Moreover, at optimality, the degree of noise reduction approaches the theoretical bound set by the Wiener-Kolmogorov linear filter. The results illustrate how selective pressure toward energy efficiency has potentially shaped a crucial regulatory pathway in eukaryotes.},
}

*Eukaryota
*MicroRNAs/genetics
Mutant Proteins
RNA, Messenger
Energy Metabolism/genetics

@article {pmid38385784,
year = {2024},
author = {Hesse, E and O'Brien, S},
title = {Ecological dependencies and the illusion of cooperation in microbial communities.},
journal = {Microbiology (Reading, England)},
volume = {170},
number = {2},
pages = {},
pmid = {38385784},
issn = {1465-2080},
mesh = {Humans ; *Illusions ; *Microbiota ; Amino Acids ; Biological Evolution ; Nitrogen ; },
abstract = {Ecological dependencies - where organisms rely on other organisms for survival - are a ubiquitous feature of life on earth. Multicellular hosts rely on symbionts to provide essential vitamins and amino acids. Legume plants similarly rely on nitrogen-fixing rhizobia to convert atmospheric nitrogen to ammonia. In some cases, dependencies can arise via loss-of-function mutations that allow one partner to benefit from the actions of another. It is common in microbiology to label ecological dependencies between species as cooperation - making it necessary to invoke cooperation-specific frameworks to explain the phenomenon. However, in many cases, such traits are not (at least initially) cooperative, because they are not selected for because of the benefits they confer on a partner species. In contrast, dependencies in microbial communities may originate from fitness benefits gained from genomic-streamlining (i.e. Black Queen Dynamics). Here, we outline how the Black Queen Hypothesis predicts the formation of metabolic dependencies via loss-of-function mutations in microbial communities, without needing to invoke any cooperation-specific explanations. Furthermore we outline how the Black Queen Hypothesis can act as a blueprint for true cooperation as well as discuss key outstanding questions in the field. The nature of interactions in microbial communities can predict the ability of natural communities to withstand and recover from disturbances. Hence, it is vital to gain a deeper understanding of the factors driving these dynamic interactions over evolutionary time.},
}

Humans
*Illusions
*Microbiota
Amino Acids
Biological Evolution
Nitrogen

@article {pmid38382824,
year = {2024},
author = {Mikhailovsky, GE},
title = {Life, its definition, origin, evolution, and four-dimensional hierarchical structure.},
journal = {Bio Systems},
volume = {237},
number = {},
pages = {105158},
doi = {10.1016/j.biosystems.2024.105158},
pmid = {38382824},
issn = {1872-8324},
mesh = {*Biological Evolution ; Thermodynamics ; *Eukaryota ; Prokaryotic Cells ; },
abstract = {The main unique features of biological systems are reviewed, and four necessary and sufficient attributes of life are formulated, based on the ideas of Ervin Bauer. The possibility of the occurrence of each of these attributes during the origin of life is analyzed. As a result, different scenarios for the origin of life are presented, with their pros and cons. Next, the mainstream of biological evolution is discussed, considering it as a special case of general complexification, and structuredness is defined as a quantitative measure of structural complexity. By introducing the concepts of post-dissipative structure and ratcheting process based on "frozen" patterns, their role in the generation of biological structures underlying biological evolution is demonstrated. Furthermore, it is proposed that all living things can be divided into micro- (unicellular) and macro- (multicellular) creatures, which differ from each other even more radically than the difference between prokaryotes and unicellular eukaryotes. Then the fifth, sufficient, but not necessary attribute of life, hierarchicality, is formulated, which is fully applicable only to macrolife. It is also shown that living organisms are primarily chemodynamic rather than thermodynamic systems, and three basic laws of biochemodynamics are formulated. Finally, fifteen basic features of living beings, grouped into four basic blocks, are summarized.},
}

*Biological Evolution
Thermodynamics
*Eukaryota
Prokaryotic Cells

@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 {pmid38377113,
year = {2024},
author = {Nino Barreat, JG and Katzourakis, A},
title = {Ecological and evolutionary dynamics of cell-virus-virophage systems.},
journal = {PLoS computational biology},
volume = {20},
number = {2},
pages = {e1010925},
pmid = {38377113},
issn = {1553-7358},
mesh = {Humans ; *Virophages ; Apoptosis ; Biological Evolution ; *Coinfection ; Antiviral Agents ; },
abstract = {Microbial eukaryotes, giant viruses and virophages form a unique hyperparasitic system. Virophages are parasites of the virus transcription machinery and can interfere with virus replication, resulting in a benefit to the eukaryotic host population. Surprisingly, virophages can integrate into the genomes of their cell or virus hosts, and have been shown to reactivate during coinfection. This raises questions about the role of integration in the dynamics of cell-virus-virophage systems. We use mathematical models and computational simulations to understand the effect of virophage integration on populations of cells and viruses. We also investigate multicellularity and programmed cell-death (PCD) as potential antiviral defence strategies used by cells. We found that virophages which enter the cell independently of the host virus, such as Mavirus, are expected to integrate commonly into the genomes of their cell hosts. Our models suggest that integrations from virophages without an independent mode of entry like Sputnik, are less likely to become fixed in the cell host population. Alternatively, we found that Sputnik virophages can stably persist integrated in the virus population, as long as they do not completely inhibit virus replication. We also show that increasing virophage inhibition can stabilise oscillatory dynamics, which may explain the long-term persistence of viruses and virophages in the environment. Our results demonstrate that inhibition by virophages and multicellularity are effective antiviral strategies that may act in synergy against viral infection in microbial species.},
}

Humans
*Virophages
Apoptosis
Biological Evolution
*Coinfection
Antiviral Agents

@article {pmid38375870,
year = {2024},
author = {Edelbroek, B and Kjellin, J and Biryukova, I and Liao, Z and Lundberg, T and Noegel, AA and Eichinger, L and Friedländer, MR and Söderbom, F},
title = {Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity.},
journal = {Nucleic acids research},
volume = {52},
number = {6},
pages = {3121-3136},
pmid = {38375870},
issn = {1362-4962},
support = {2021-05793//Swedish Research Council/ ; //Uppsala University/ ; },
mesh = {*Amoebozoa/classification/genetics ; Dictyostelium/genetics ; *MicroRNAs/genetics ; Phylogeny ; *Evolution, Molecular ; *RNA, Protozoan/genetics ; Conserved Sequence/genetics ; RNA Interference ; },
abstract = {MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in both plants and animals. They are thought to have evolved convergently in these lineages and hypothesized to have played a role in the evolution of multicellularity. In line with this hypothesis, miRNAs have so far only been described in few unicellular eukaryotes. Here, we investigate the presence and evolution of miRNAs in Amoebozoa, focusing on species belonging to Acanthamoeba, Physarum and dictyostelid taxonomic groups, representing a range of unicellular and multicellular lifestyles. miRNAs that adhere to both the stringent plant and animal miRNA criteria were identified in all examined amoebae, expanding the total number of protists harbouring miRNAs from 7 to 15. We found conserved miRNAs between closely related species, but the majority of species feature only unique miRNAs. This shows rapid gain and/or loss of miRNAs in Amoebozoa, further illustrated by a detailed comparison between two evolutionary closely related dictyostelids. Additionally, loss of miRNAs in the Dictyostelium discoideum drnB mutant did not seem to affect multicellular development and, hence, demonstrates that the presence of miRNAs does not appear to be a strict requirement for the transition from uni- to multicellular life.},
}

*Amoebozoa/classification/genetics
Dictyostelium/genetics
*MicroRNAs/genetics
Phylogeny
*Evolution, Molecular
*RNA, Protozoan/genetics
Conserved Sequence/genetics
RNA Interference

@article {pmid38352462,
year = {2024},
author = {Kidner, RQ and Goldstone, EB and Laidemitt, MR and Sanchez, MC and Gerdt, C and Brokaw, LP and Ros-Rocher, N and Morris, J and Davidson, WS and Gerdt, JP},
title = {Host lipids regulate multicellular behavior of a predator of a human pathogen.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38352462},
issn = {2692-8205},
support = {R37 AI101438/AI/NIAID NIH HHS/United States ; R01 HL062542/HL/NHLBI NIH HHS/United States ; T32 GM131994/GM/NIGMS NIH HHS/United States ; S10 OD024988/OD/NIH HHS/United States ; P30 GM110907/GM/NIGMS NIH HHS/United States ; R35 GM138376/GM/NIGMS NIH HHS/United States ; HHSN272201700014C/AI/NIAID NIH HHS/United States ; },
abstract = {As symbionts of animals, microbial eukaryotes benefit and harm their hosts in myriad ways. A model microeukaryote (Capsaspora owczarzaki) is a symbiont of Biomphalaria glabrata snails and may prevent transmission of parasitic schistosomes from snails to humans. However, it is unclear which host factors determine Capsaspora's ability to colonize snails. Here, we discovered that Capsaspora forms multicellular aggregates when exposed to snail hemolymph. We identified a molecular cue for aggregation: a hemolymph-derived phosphatidylcholine, which becomes elevated in schistosome-infected snails. Therefore, Capsaspora aggregation may be a response to the physiological state of its host, and it may determine its ability to colonize snails and exclude parasitic schistosomes. Furthermore, Capsaspora is an evolutionary model organism whose aggregation may be ancestral to animals. This discovery, that a prevalent lipid induces Capsaspora multicellularity, suggests that this aggregation phenotype may be ancient. Additionally, the specific lipid will be a useful tool for further aggregation studies.},
}

@article {pmid38351630,
year = {2024},
author = {Iwaï, H and Beyer, HM and Johansson, JEM and Li, M and Wlodawer, A},
title = {The three-dimensional structure of the Vint domain from Tetrahymena thermophila suggests a ligand-regulated cleavage mechanism by the HINT fold.},
journal = {FEBS letters},
volume = {598},
number = {8},
pages = {864-874},
doi = {10.1002/1873-3468.14817},
pmid = {38351630},
issn = {1873-3468},
support = {75N91019D00024/CA/NCI NIH HHS/United States ; 75N91019D00024/CA/NCI NIH HHS/United States ; },
mesh = {*Tetrahymena thermophila/metabolism/genetics ; *Protozoan Proteins/chemistry/metabolism/genetics ; *Protein Domains ; Ligands ; Models, Molecular ; Hedgehog Proteins/metabolism/chemistry/genetics ; Amino Acid Sequence ; Protein Folding ; },
abstract = {Vint proteins have been identified in unicellular metazoans as a novel hedgehog-related gene family, merging the von Willebrand factor type A domain and the Hedgehog/INTein (HINT) domains. We present the first three-dimensional structure of the Vint domain from Tetrahymena thermophila corresponding to the auto-processing domain of hedgehog proteins, shedding light on the unique features, including an adduct recognition region (ARR). Our results suggest a potential binding between the ARR and sulfated glycosaminoglycans like heparin sulfate. Moreover, we uncover a possible regulatory role of the ARR in the auto-processing by Vint domains, expanding our understanding of the HINT domain evolution and their use in biotechnological applications. Vint domains might have played a crucial role in the transition from unicellular to multicellular organisms.},
}

*Tetrahymena thermophila/metabolism/genetics
*Protozoan Proteins/chemistry/metabolism/genetics
*Protein Domains
Ligands
Models, Molecular
Hedgehog Proteins/metabolism/chemistry/genetics
Amino Acid Sequence
Protein Folding

@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 {pmid38334408,
year = {2024},
author = {Wang, R and Meng, Q and Wang, X and Xiao, Y and Sun, R and Zhang, Z and Fu, Y and Di Giuseppe, G and Liang, A},
title = {Comparative genomic analysis of symbiotic and free-living Fluviibacter phosphoraccumulans strains provides insights into the evolutionary origins of obligate Euplotes-bacterial endosymbioses.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {3},
pages = {e0190023},
pmid = {38334408},
issn = {1098-5336},
support = {32270447//MOST | National Natural Science Foundation of China (NSFC)/ ; 31372199//MOST | National Natural Science Foundation of China (NSFC)/ ; 20220302121320//Fundamental Research Program of Shanxi Province/ ; },
mesh = {Phylogeny ; Symbiosis/genetics ; *Euplotes/genetics/microbiology ; *Betaproteobacteria/genetics ; Bacteria/genetics ; Genome, Bacterial ; Genomics ; },
abstract = {UNLABELLED: Endosymbiosis is a widespread and important phenomenon requiring diverse model systems. Ciliates are a widespread group of protists that often form symbioses with diverse microorganisms. Endosymbioses between the ciliate Euplotes and heritable bacterial symbionts are common in nature, and four essential symbionts were described: Polynucleobacter necessarius, "Candidatus Protistobacter heckmanni," "Ca. Devosia symbiotica," and "Ca. Devosia euplotis." Among them, only the genus Polynucleobacter comprises very close free-living and symbiotic representatives, which makes it an excellent model for investigating symbiont replacements and recent symbioses. In this article, we characterized a novel endosymbiont inhabiting the cytoplasm of Euplotes octocarinatus and found that it is a close relative of the free-living bacterium Fluviibacter phosphoraccumulans (Betaproteobacteria and Rhodocyclales). We present the complete genome sequence and annotation of the symbiotic Fluviibacter. Comparative analyses indicate that the genome of symbiotic Fluviibacter is small in size and rich in pseudogenes when compared with free-living strains, which seems to fit the prediction for recently established endosymbionts undergoing genome erosion. Further comparative analysis revealed reduced metabolic capacities in symbiotic Fluviibacter, which implies that the symbiont relies on the host Euplotes for carbon sources, organic nitrogen and sulfur, and some cofactors. We also estimated substitution rates between symbiotic and free-living Fluviibacter pairs for 233 genes; the results showed that symbiotic Fluviibacter displays higher dN/dS mean value than free-living relatives, which suggested that genetic drift is the main driving force behind molecular evolution in endosymbionts.

IMPORTANCE: In the long history of symbiosis research, most studies focused mainly on organelles or bacteria within multicellular hosts. The single-celled protists receive little attention despite harboring an immense diversity of symbiotic associations with bacteria and archaea. One subgroup of the ciliate Euplotes species is strictly dependent on essential symbionts for survival and has emerged as a valuable model for understanding symbiont replacements and recent symbioses. However, almost all of our knowledge about the evolution and functions of Euplotes symbioses comes from the Euplotes-Polynucleobacter system. In this article, we report a novel essential symbiont, which also has very close free-living relatives. Genome analysis indicated that it is a recently established endosymbiont undergoing genome erosion and relies on the Euplotes host for many essential molecules. Our results provide support for the notion that essential symbionts of the ciliate Euplotes evolve from free-living progenitors in the natural water environment.},
}

Phylogeny
Symbiosis/genetics
*Euplotes/genetics/microbiology
*Betaproteobacteria/genetics
Bacteria/genetics
Genome, Bacterial
Genomics

@article {pmid38333966,
year = {2024},
author = {Bowles, AMC and Williamson, CJ and Williams, TA and Donoghue, PCJ},
title = {Cryogenian Origins of Multicellularity in Archaeplastida.},
journal = {Genome biology and evolution},
volume = {16},
number = {2},
pages = {},
pmid = {38333966},
issn = {1759-6653},
support = {RPG-2020-199//Leverhulme Trust/ ; NE/P013678/1//Natural Environment Research Council/ ; //Biosphere Evolution, Transitions and Resilience/ ; //Natural Science Foundation of China/ ; 62220//John Templeton Foundation/ ; GBMF9741//Gordon and Betty Moore Foundation/ ; URF\R\201024//University Research Fellowship to T.W/ ; },
mesh = {Phylogeny ; Biological Evolution ; Plants ; *Embryophyta ; *Chlorophyta ; Fossils ; Evolution, Molecular ; },
abstract = {Earth was impacted by global glaciations during the Cryogenian (720 to 635 million years ago; Ma), events invoked to explain both the origins of multicellularity in Archaeplastida and radiation of the first land plants. However, the temporal relationship between these environmental and biological events is poorly established, due to a paucity of molecular and fossil data, precluding resolution of the phylogeny and timescale of archaeplastid evolution. We infer a time-calibrated phylogeny of early archaeplastid evolution based on a revised molecular dataset and reappraisal of the fossil record. Phylogenetic topology testing resolves deep archaeplastid relationships, identifying two clades of Viridiplantae and placing Bryopsidales as sister to the Chlorophyceae. Our molecular clock analysis infers an origin of Archaeplastida in the late-Paleoproterozoic to early-Mesoproterozoic (1712 to 1387 Ma). Ancestral state reconstruction of cytomorphological traits on this time-calibrated tree reveals many of the independent origins of multicellularity span the Cryogenian, consistent with the Cryogenian multicellularity hypothesis. Multicellular rhodophytes emerged 902 to 655 Ma while crown-Anydrophyta (Zygnematophyceae and Embryophyta) originated 796 to 671 Ma, broadly compatible with the Cryogenian plant terrestrialization hypothesis. Our analyses resolve the timetree of Archaeplastida with age estimates for ancestral multicellular archaeplastids coinciding with the Cryogenian, compatible with hypotheses that propose a role of Snowball Earth in plant evolution.},
}

Phylogeny
Biological Evolution
Plants
*Embryophyta
*Chlorophyta
Fossils
Evolution, Molecular

@article {pmid38327154,
year = {2024},
author = {Gupta, P and Bermejo-Rodriguez, C and Kocher, H and Pérez-Mancera, PA and Velliou, EG},
title = {Chemotherapy Assessment in Advanced Multicellular 3D Models of Pancreatic Cancer: Unravelling the Importance of Spatiotemporal Mimicry of the Tumor Microenvironment.},
journal = {Advanced biology},
volume = {8},
number = {7},
pages = {e2300580},
doi = {10.1002/adbi.202300580},
pmid = {38327154},
issn = {2701-0198},
support = {MR/V028553/1/MRC_/Medical Research Council/United Kingdom ; MR/R025762/1//3D bioNet UKRI/ ; NC/V001167/1//National Centre for the Replacement Refinement and Reduction of Animals in Research/ ; },
mesh = {*Tumor Microenvironment/drug effects ; Humans ; *Pancreatic Neoplasms/drug therapy/pathology/genetics ; *Carcinoma, Pancreatic Ductal/drug therapy/pathology ; Deoxycytidine/analogs & derivatives/pharmacology/therapeutic use ; Cell Line, Tumor ; Gemcitabine ; Drug Resistance, Neoplasm ; Tissue Scaffolds ; },
abstract = {Pancreatic ductal adenocarcinoma (PDAC) is a challenge for global health with very low survival rate and high therapeutic resistance. Hence, advanced preclinical models for treatment screening are of paramount importance. Herein, chemotherapeutic (gemcitabine) assessment on novel (polyurethane) scaffold-based spatially advanced 3D multicellular PDAC models is carried out. Through comprehensive image-based analysis at the protein level, and expression analysis at the mRNA level, the importance of stromal cells is confirmed, primarily activated stellate cells in the chemoresistance of PDAC cells within the models. Furthermore, it is demonstrated that, in addition to the presence of activated stellate cells, the spatial architecture of the scaffolds, i.e., segregation/compartmentalization of the cancer and stromal zones, affect the cellular evolution and is necessary for the development of chemoresistance. These results highlight that, further to multicellularity, mapping the tumor structure/architecture and zonal complexity in 3D cancer models is important for better mimicry of the in vivo therapeutic response.},
}

*Tumor Microenvironment/drug effects
Humans
*Pancreatic Neoplasms/drug therapy/pathology/genetics
*Carcinoma, Pancreatic Ductal/drug therapy/pathology
Deoxycytidine/analogs & derivatives/pharmacology/therapeutic use
Cell Line, Tumor
Gemcitabine
Drug Resistance, Neoplasm
Tissue Scaffolds

@article {pmid38320478,
year = {2024},
author = {Donoghue, PCJ and Clark, JW},
title = {Plant evolution: Streptophyte multicellularity, ecology, and the acclimatisation of plants to life on land.},
journal = {Current biology : CB},
volume = {34},
number = {3},
pages = {R86-R89},
doi = {10.1016/j.cub.2023.12.036},
pmid = {38320478},
issn = {1879-0445},
support = {BB/T012773/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Plants ; Biological Evolution ; Phylogeny ; *Embryophyta ; Acclimatization ; },
abstract = {Land plants are celebrated as one of the three great instances of complex multicellularity, but new phylogenomic and phenotypic analyses are revealing deep evolutionary roots of multicellularity among algal relatives, prompting questions about the causal basis of this major evolutionary transition.},
}

*Plants
Biological Evolution
Phylogeny
*Embryophyta
Acclimatization

@article {pmid38315855,
year = {2024},
author = {Bingham, EP and Ratcliff, WC},
title = {A nonadaptive explanation for macroevolutionary patterns in the evolution of complex multicellularity.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {7},
pages = {e2319840121},
pmid = {38315855},
issn = {1091-6490},
support = {R35 GM138030/GM/NIGMS NIH HHS/United States ; T32 GM142616/GM/NIGMS NIH HHS/United States ; },
mesh = {*Biological Evolution ; *Genetic Drift ; Eukaryota/genetics ; Genome ; Gene Expression Regulation ; },
abstract = {"Complex multicellularity," conventionally defined as large organisms with many specialized cell types, has evolved five times independently in eukaryotes, but never within prokaryotes. A number of hypotheses have been proposed to explain this phenomenon, most of which posit that eukaryotes evolved key traits (e.g., dynamic cytoskeletons, alternative mechanisms of gene regulation, or subcellular compartments) which were a necessary prerequisite for the evolution of complex multicellularity. Here, we propose an alternative, nonadaptive hypothesis for this broad macroevolutionary pattern. By binning cells into groups with finite genetic bottlenecks between generations, the evolution of multicellularity greatly reduces the effective population size (Ne) of cellular populations, increasing the role of genetic drift in evolutionary change. While both prokaryotes and eukaryotes experience this phenomenon, they have opposite responses to drift: eukaryotes tend to undergo genomic expansion, providing additional raw genetic material for subsequent multicellular innovation, while prokaryotes generally face genomic erosion. Taken together, we hypothesize that these idiosyncratic lineage-specific evolutionary dynamics play a fundamental role in the long-term divergent evolution of complex multicellularity across the tree of life.},
}

*Biological Evolution
*Genetic Drift
Eukaryota/genetics
Genome
Gene Expression Regulation

@article {pmid38306281,
year = {2024},
author = {Siljestam, M and Martinossi-Allibert, I},
title = {Anisogamy Does Not Always Promote the Evolution of Mating Competition Traits in Males.},
journal = {The American naturalist},
volume = {203},
number = {2},
pages = {230-253},
doi = {10.1086/727968},
pmid = {38306281},
issn = {1537-5323},
mesh = {Male ; Female ; Humans ; *Models, Biological ; *Biological Evolution ; Semen ; Reproduction ; Fertilization ; },
abstract = {AbstractAnisogamy has evolved in most sexually reproducing multicellular organisms allowing the definition of male and female sexes, producing small and large gametes. Anisogamy, as the initial sexual dimorphism, is a good starting point to understand the evolution of further sexual dimorphisms. For instance, it is generally accepted that anisogamy sets the stage for more intense mating competition in males than in females. We argue that this idea stems from a restrictive assumption on the conditions under which anisogamy evolved in the first place: the absence of sperm limitation (assuming that all female gametes are fertilized). Here, we relax this assumption and present a model that considers the coevolution of gamete size with a mating competition trait, starting in a population without dimorphism. We vary gamete density to produce different scenarios of gamete limitation. We show that while at high gamete density the evolution of anisogamy always results in male investment in competition, gamete limitation at intermediate gamete densities allows for either females or males to invest more into mating competition. Our results thus suggest that anisogamy does not always promote mating competition among males. The conditions under which anisogamy evolves matter, as does the competition trait.},
}

Male
Female
Humans
*Models, Biological
*Biological Evolution
Semen
Reproduction
Fertilization

@article {pmid38301272,
year = {2024},
author = {Mihalič, F and Arcila, D and Pettersson, ME and Farkhondehkish, P and Andersson, E and Andersson, L and Betancur-R, R and Jemth, P},
title = {Conservation of Affinity Rather Than Sequence Underlies a Dynamic Evolution of the Motif-Mediated p53/MDM2 Interaction in Ray-Finned Fishes.},
journal = {Molecular biology and evolution},
volume = {41},
number = {2},
pages = {},
pmid = {38301272},
issn = {1537-1719},
mesh = {Animals ; Humans ; *Tumor Suppressor Protein p53/genetics/chemistry/metabolism ; *Zebrafish ; Phylogeny ; Protein Structure, Tertiary ; Protein Binding ; Proto-Oncogene Proteins c-mdm2/genetics/chemistry/metabolism ; },
abstract = {The transcription factor and cell cycle regulator p53 is marked for degradation by the ubiquitin ligase MDM2. The interaction between these 2 proteins is mediated by a conserved binding motif in the disordered p53 transactivation domain (p53TAD) and the folded SWIB domain in MDM2. The conserved motif in p53TAD from zebrafish displays a 20-fold weaker interaction with MDM2, compared to the interaction in human and chicken. To investigate this apparent difference, we tracked the molecular evolution of the p53TAD/MDM2 interaction among ray-finned fishes (Actinopterygii), the largest vertebrate clade. Intriguingly, phylogenetic analyses, ancestral sequence reconstructions, and binding experiments showed that different loss-of-affinity changes in the canonical binding motif within p53TAD have occurred repeatedly and convergently in different fish lineages, resulting in relatively low extant affinities (KD = 0.5 to 5 μM). However, for 11 different fish p53TAD/MDM2 interactions, nonconserved regions flanking the canonical motif increased the affinity 4- to 73-fold to be on par with the human interaction. Our findings suggest that compensating changes at conserved and nonconserved positions within the motif, as well as in flanking regions of low conservation, underlie a stabilizing selection of "functional affinity" in the p53TAD/MDM2 interaction. Such interplay complicates bioinformatic prediction of binding and calls for experimental validation. Motif-mediated protein-protein interactions involving short binding motifs and folded interaction domains are very common across multicellular life. It is likely that the evolution of affinity in motif-mediated interactions often involves an interplay between specific interactions made by conserved motif residues and nonspecific interactions by nonconserved disordered regions.},
}

Animals
Humans
*Tumor Suppressor Protein p53/genetics/chemistry/metabolism
*Zebrafish
Phylogeny
Protein Structure, Tertiary
Protein Binding
Proto-Oncogene Proteins c-mdm2/genetics/chemistry/metabolism

@article {pmid38277698,
year = {2024},
author = {Krämer, U},
title = {Metal Homeostasis in Land Plants: A Perpetual Balancing Act Beyond the Fulfilment of Metalloproteome Cofactor Demands.},
journal = {Annual review of plant biology},
volume = {75},
number = {1},
pages = {27-65},
doi = {10.1146/annurev-arplant-070623-105324},
pmid = {38277698},
issn = {1545-2123},
mesh = {*Homeostasis ; *Metals/metabolism ; *Embryophyta/metabolism/physiology ; *Metalloproteins/metabolism ; Plant Proteins/metabolism ; },
abstract = {One of life's decisive innovations was to harness the catalytic power of metals for cellular chemistry. With life's expansion, global atmospheric and biogeochemical cycles underwent dramatic changes. Although initially harmful, they permitted the evolution of multicellularity and the colonization of land. In land plants as primary producers, metal homeostasis faces heightened demands, in part because soil is a challenging environment for nutrient balancing. To avoid both nutrient metal limitation and metal toxicity, plants must maintain the homeostasis of metals within tighter limits than the homeostasis of other minerals. This review describes the present model of protein metalation and sketches its transfer from unicellular organisms to land plants as complex multicellular organisms. The inseparable connection between metal and redox homeostasis increasingly draws our attention to more general regulatory roles of metals. Mineral co-option, the use of nutrient or other metals for functions other than nutrition, is an emerging concept beyond that of nutritional immunity.},
}

*Homeostasis
*Metals/metabolism
*Embryophyta/metabolism/physiology
*Metalloproteins/metabolism
Plant Proteins/metabolism

@article {pmid38271513,
year = {2024},
author = {Pennisi, E},
title = {Tiny fossils upend timeline of multicellular life.},
journal = {Science (New York, N.Y.)},
volume = {383},
number = {6681},
pages = {352-353},
doi = {10.1126/science.ado2396},
pmid = {38271513},
issn = {1095-9203},
mesh = {*Biological Evolution ; *Eukaryota ; *Fossils ; },
abstract = {Eukaryotes organized into multicellular forms 1.6 billion years ago.},
}

*Biological Evolution
*Eukaryota
*Fossils

@article {pmid38267842,
year = {2024},
author = {Chapman, H and Hsiung, KC and Rawlinson, I and Galimov, ER and Gems, D},
title = {Colony level fitness analysis identifies a trade-off between population growth rate and dauer yield in Caenorhabditis elegans.},
journal = {BMC ecology and evolution},
volume = {24},
number = {1},
pages = {13},
pmid = {38267842},
issn = {2730-7182},
mesh = {Animals ; *Caenorhabditis elegans ; *Population Growth ; Apoptosis ; Benchmarking ; Biological Assay ; },
abstract = {BACKGROUND: In the evolution from unicellular to multicellular life forms, natural selection favored reduced cell proliferation and even programmed cell death if this increased organismal fitness. Could reduced individual fertility or even programmed organismal death similarly increase the fitness of colonies of closely-related metazoan organisms? This possibility is at least consistent with evolutionary theory, and has been supported by computer modelling. Caenorhabditis elegans has a boom and bust life history, where populations of nematodes that are sometimes near clonal subsist on and consume food patches, and then generate dauer larva dispersal propagules. A recent study of an in silico model of C. elegans predicted that one determinant of colony fitness (measured as dauer yield) is minimization of futile food consumption (i.e. that which does not contribute to dauer yield). One way to achieve this is to optimize colony population structure by adjustment of individual fertility.

RESULTS: Here we describe development of a C. elegans colony fitness assay, and its use to investigate the effect of altering population structure on colony fitness after population bust. Fitness metrics measured were speed of dauer production, and dauer yield, an indirect measure of efficiency of resource utilization (i.e. conversion of food into dauers). We find that with increasing founder number, speed of dauer production increases (due to earlier bust) but dauer yield rises and falls. In addition, some dauer recovery was detected soon after the post-colony bust peak of dauer yield, suggesting possible bet hedging among dauers.

CONCLUSIONS: These results suggest the presence of a fitness trade-off at colony level between speed and efficiency of resource utilization in C. elegans. They also provide indirect evidence that population structure is a determinant of colony level fitness, potentially by affecting level of futile food consumption.},
}

Animals
*Caenorhabditis elegans
*Population Growth
Apoptosis
Benchmarking
Biological Assay

@article {pmid38262417,
year = {2024},
author = {Choi, SW and Graf, L and Choi, JW and Jo, J and Boo, GH and Kawai, H and Choi, CG and Xiao, S and Knoll, AH and Andersen, RA and Yoon, HS},
title = {Ordovician origin and subsequent diversification of the brown algae.},
journal = {Current biology : CB},
volume = {34},
number = {4},
pages = {740-754.e4},
doi = {10.1016/j.cub.2023.12.069},
pmid = {38262417},
issn = {1879-0445},
mesh = {Phylogeny ; Eukaryota/genetics ; Plants ; *Rhodophyta/genetics ; Plastids/genetics ; *Phaeophyceae/genetics ; Evolution, Molecular ; },
abstract = {Brown algae are the only group of heterokont protists exhibiting complex multicellularity. Since their origin, brown algae have adapted to various marine habitats, evolving diverse thallus morphologies and gamete types. However, the evolutionary processes behind these transitions remain unclear due to a lack of a robust phylogenetic framework and problems with time estimation. To address these issues, we employed plastid genome data from 138 species, including heterokont algae, red algae, and other red-derived algae. Based on a robust phylogeny and new interpretations of algal fossils, we estimated the geological times for brown algal origin and diversification. The results reveal that brown algae first evolved true multicellularity, with plasmodesmata and reproductive cell differentiation, during the late Ordovician Period (ca. 450 Ma), coinciding with a major diversification of marine fauna (the Great Ordovician Biodiversification Event) and a proliferation of multicellular green algae. Despite its early Paleozoic origin, the diversification of major orders within this brown algal clade accelerated only during the Mesozoic Era, coincident with both Pangea rifting and the diversification of other heterokont algae (e.g., diatoms), coccolithophores, and dinoflagellates, with their red algal-derived plastids. The transition from ancestral isogamy to oogamy was followed by three simultaneous reappearances of isogamy during the Cretaceous Period. These are concordant with a positive character correlation between parthenogenesis and isogamy. Our new brown algal timeline, combined with a knowledge of past environmental conditions, shed new light on brown algal diversification and the intertwined evolution of multicellularity and sexual reproduction.},
}

Phylogeny
Eukaryota/genetics
Plants
*Rhodophyta/genetics
Plastids/genetics
*Phaeophyceae/genetics
Evolution, Molecular

@article {pmid38255007,
year = {2024},
author = {Gazzellone, A and Sangiorgi, E},
title = {From Churchill to Elephants: The Role of Protective Genes against Cancer.},
journal = {Genes},
volume = {15},
number = {1},
pages = {},
pmid = {38255007},
issn = {2073-4425},
mesh = {Humans ; Animals ; Mice ; *Elephants/genetics ; Alleles ; *Neoplastic Syndromes, Hereditary ; *Medicine ; Cetacea ; },
abstract = {Richard Peto's paradox, first described in 1975 from an epidemiological perspective, established an inverse correlation between the probability of developing cancer in multicellular organisms and the number of cells. Larger animals exhibit fewer tumors compared to smaller ones, though exceptions exist. Mice are more susceptible to cancer than humans, while elephants and whales demonstrate significantly lower cancer prevalence rates than humans. How nature and evolution have addressed the issue of cancer in the animal kingdom remains largely unexplored. In the field of medicine, much attention has been devoted to cancer-predisposing genes, as they offer avenues for intervention, including blocking, downregulating, early diagnosis, and targeted treatment. Predisposing genes also tend to manifest clinically earlier and more aggressively, making them easier to identify. However, despite significant strides in modern medicine, the role of protective genes lags behind. Identifying genes with a mild predisposing effect poses a significant challenge. Consequently, comprehending the protective function conferred by genes becomes even more elusive, and their very existence is subject to questioning. While the role of variable expressivity and penetrance defects of the same variant in a family is well-documented for many hereditary cancer syndromes, attempts to delineate the function of protective/modifier alleles have been restricted to a few instances. In this review, we endeavor to elucidate the role of protective genes observed in the animal kingdom, within certain genetic syndromes that appear to act as cancer-resistant/repressor alleles. Additionally, we explore the role of protective alleles in conditions predisposing to cancer. The ultimate goal is to discern why individuals, like Winston Churchill, managed to live up to 91 years of age, despite engaging in minimal physical activity, consuming large quantities of alcohol daily, and not abstaining from smoking.},
}

Humans
Animals
Mice
*Elephants/genetics
Alleles
*Neoplastic Syndromes, Hereditary
*Medicine
Cetacea

@article {pmid38244543,
year = {2024},
author = {Bierenbroodspot, MJ and Darienko, T and de Vries, S and Fürst-Jansen, JMR and Buschmann, H and Pröschold, T and Irisarri, I and de Vries, J},
title = {Phylogenomic insights into the first multicellular streptophyte.},
journal = {Current biology : CB},
volume = {34},
number = {3},
pages = {670-681.e7},
pmid = {38244543},
issn = {1879-0445},
mesh = {Phylogeny ; Biological Evolution ; Plants/genetics ; *Embryophyta/genetics ; *Streptophyta ; },
abstract = {Streptophytes are best known as the clade containing the teeming diversity of embryophytes (land plants).[1][,][2][,][3][,][4] Next to embryophytes are however a range of freshwater and terrestrial algae that bear important information on the emergence of key traits of land plants. Among these, the Klebsormidiophyceae stand out. Thriving in diverse environments-from mundane (ubiquitous occurrence on tree barks and rocks) to extreme (from the Atacama Desert to the Antarctic)-Klebsormidiophyceae can exhibit filamentous body plans and display remarkable resilience as colonizers of terrestrial habitats.[5][,][6] Currently, the lack of a robust phylogenetic framework for the Klebsormidiophyceae hampers our understanding of the evolutionary history of these key traits. Here, we conducted a phylogenomic analysis utilizing advanced models that can counteract systematic biases. We sequenced 24 new transcriptomes of Klebsormidiophyceae and combined them with 14 previously published genomic and transcriptomic datasets. Using an analysis built on 845 loci and sophisticated mixture models, we establish a phylogenomic framework, dividing the six distinct genera of Klebsormidiophyceae in a novel three-order system, with a deep divergence more than 830 million years ago. Our reconstructions of ancestral states suggest (1) an evolutionary history of multiple transitions between terrestrial-aquatic habitats, with stem Klebsormidiales having conquered land earlier than embryophytes, and (2) that the body plan of the last common ancestor of Klebsormidiophyceae was multicellular, with a high probability that it was filamentous whereas the sarcinoids and unicells in Klebsormidiophyceae are likely derived states. We provide evidence that the first multicellular streptophytes likely lived about a billion years ago.},
}

Phylogeny
Biological Evolution
Plants/genetics
*Embryophyta/genetics
*Streptophyta

@article {pmid38230926,
year = {2024},
author = {Corrales, J and Ramos-Alonso, L and González-Sabín, J and Ríos-Lombardía, N and Trevijano-Contador, N and Engen Berg, H and Sved Skottvoll, F and Moris, F and Zaragoza, O and Chymkowitch, P and Garcia, I and Enserink, JM},
title = {Characterization of a selective, iron-chelating antifungal compound that disrupts fungal metabolism and synergizes with fluconazole.},
journal = {Microbiology spectrum},
volume = {12},
number = {2},
pages = {e0259423},
pmid = {38230926},
issn = {2165-0497},
support = {182524, 208012//Kreftforeningen (NCS)/ ; 2017064, 2018012, 2019096//Ministry of Health and Care Services | Helse Sør-Øst RHF (sorost)/ ; 2017072//Ministry of Health and Care Services | Helse Sør-Øst RHF (sorost)/ ; 261936, 301268, 262652//Norges Forskningsråd (Forskningsrådet)/ ; PID2020-114546RB//Ministerio de Ciencia e Innovación (MCIN)/ ; },
mesh = {Animals ; Humans ; Antifungal Agents/pharmacology ; Fluconazole/pharmacology ; Iron ; Candida ; *Mycoses/microbiology ; Candida albicans ; *Anti-Infective Agents/pharmacology ; Azoles/pharmacology ; Candida glabrata ; Iron Chelating Agents/pharmacology ; Drug Resistance, Fungal ; Microbial Sensitivity Tests ; Mammals ; },
abstract = {Fungal infections are a growing global health concern due to the limited number of available antifungal therapies as well as the emergence of fungi that are resistant to first-line antimicrobials, particularly azoles and echinocandins. Development of novel, selective antifungal therapies is challenging due to similarities between fungal and mammalian cells. An attractive source of potential antifungal treatments is provided by ecological niches co-inhabited by bacteria, fungi, and multicellular organisms, where complex relationships between multiple organisms have resulted in evolution of a wide variety of selective antimicrobials. Here, we characterized several analogs of one such natural compound, collismycin A. We show that NR-6226C has antifungal activity against several pathogenic Candida species, including C. albicans and C. glabrata, whereas it only has little toxicity against mammalian cells. Mechanistically, NR-6226C selectively chelates iron, which is a limiting factor for pathogenic fungi during infection. As a result, NR-6226C treatment causes severe mitochondrial dysfunction, leading to formation of reactive oxygen species, metabolic reprogramming, and a severe reduction in ATP levels. Using an in vivo model for fungal infections, we show that NR-6226C significantly increases survival of Candida-infected Galleria mellonella larvae. Finally, our data indicate that NR-6226C synergizes strongly with fluconazole in inhibition of C. albicans. Taken together, NR-6226C is a promising antifungal compound that acts by chelating iron and disrupting mitochondrial functions.IMPORTANCEDrug-resistant fungal infections are an emerging global threat, and pan-resistance to current antifungal therapies is an increasing problem. Clearly, there is a need for new antifungal drugs. In this study, we characterized a novel antifungal agent, the collismycin analog NR-6226C. NR-6226C has a favorable toxicity profile for human cells, which is essential for further clinical development. We unraveled the mechanism of action of NR-6226C and found that it disrupts iron homeostasis and thereby depletes fungal cells of energy. Importantly, NR-6226C strongly potentiates the antifungal activity of fluconazole, thereby providing inroads for combination therapy that may reduce or prevent azole resistance. Thus, NR-6226C is a promising compound for further development into antifungal treatment.},
}

Animals
Humans
Antifungal Agents/pharmacology
Fluconazole/pharmacology
Iron
Candida
*Mycoses/microbiology
Candida albicans
*Anti-Infective Agents/pharmacology
Azoles/pharmacology
Candida glabrata
Iron Chelating Agents/pharmacology
Drug Resistance, Fungal
Microbial Sensitivity Tests
Mammals

@article {pmid38196363,
year = {2024},
author = {Howe, J and Cornwallis, CK and Griffin, AS},
title = {Conflict-reducing innovations in development enable increased multicellular complexity.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2014},
pages = {20232466},
pmid = {38196363},
issn = {1471-2954},
mesh = {Animals ; Phylogeny ; *Cognition ; Cell Division ; *Stem Cells ; },
abstract = {Obligately multicellular organisms, where cells can only reproduce as part of the group, have evolved multiple times across the tree of life. Obligate multicellularity has only evolved when clonal groups form by cell division, rather than by cells aggregating, as clonality prevents internal conflict. Yet obligately multicellular organisms still vary greatly in 'multicellular complexity' (the number of cells and cell types): some comprise a few cells and cell types, while others have billions of cells and thousands of types. Here, we test whether variation in multicellular complexity is explained by two conflict-suppressing mechanisms, namely a single-cell bottleneck at the start of development, and a strict separation of germline and somatic cells. Examining the life cycles of 129 lineages of plants, animals, fungi and algae, we show using phylogenetic comparative analyses that an early segregation of the germline stem-cell lineage is key to the evolution of more cell types, driven by a strong correlation in the Metazoa. By contrast, the presence of a strict single-cell bottleneck was not related to either the number of cells or the number of cell types, but was associated with early germline segregation. Our results suggest that segregating the germline earlier in development enabled greater evolutionary innovation, although whether this is a consequence of conflict reduction or other non-conflict effects, such as developmental flexibility, is unclear.},
}

Animals
Phylogeny
*Cognition
Cell Division
*Stem Cells

@article {pmid38196360,
year = {2024},
author = {Pequeno, PACL},
title = {Resource adaptation drives the size-complexity rule in termites.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2014},
pages = {20232363},
pmid = {38196360},
issn = {1471-2954},
mesh = {Animals ; *Isoptera ; Food ; *Infertility ; Phenotype ; Phylogeny ; },
abstract = {The size-complexity rule posits that the evolution of larger cooperative groups should favour more division of labour. Examples include more cell types in larger multicellular organisms, and more polymorphic castes in larger eusocial colonies. However, a correlation between division of labour and group size may reflect a shared response of both traits to resource availability and/or profitability. Here, this possibility was addressed by investigating the evolution of sterile caste number (worker and soldier morphotypes) in termites, a major clade of eusocial insects in which the drivers of caste polymorphism are poorly understood. A novel dataset on 90 termite species was compiled from the published literature. The analysis showed that sterile caste number did increase markedly with colony size. However, after controlling for resource adaptations and phylogeny, there was no evidence for this relationship. Rather, sterile caste number increased with increasing nest-food separation and decreased with soil-feeding, through changes in worker (but not soldier) morphotype number. Further, colony size increased with nest-food separation, thus driving the false correlation between sterile caste number and colony size. These findings support adaptation to higher energy acquisition as key to the rise of complex insect societies, with larger size being a by-product.},
}

Animals
*Isoptera
Food
*Infertility
Phenotype
Phylogeny