@article {pmid38060007,
year = {2023},
author = {Romei, M and Carpentier, M and Chomilier, J and Lecointre, G},
title = {Origins and Functional Significance of Eukaryotic Protein Folds.},
journal = {Journal of molecular evolution},
volume = {},
number = {},
pages = {},
pmid = {38060007},
issn = {1432-1432},
support = {IPV program of Sorbonne University, PhD grant//Sorbonne Université/ ; },
abstract = {Folds are the architecture and topology of a protein domain. Categories of folds are very few compared to the astronomical number of sequences. Eukaryotes have more protein folds than Archaea and Bacteria. These folds are of two types: shared with Archaea and/or Bacteria on one hand and specific to eukaryotic clades on the other hand. The first kind of folds is inherited from the first endosymbiosis and confirms the mixed origin of eukaryotes. In a dataset of 1073 folds whose presence or absence has been evidenced among 210 species equally distributed in the three super-kingdoms, we have identified 28 eukaryotic folds unambiguously inherited from Bacteria and 40 eukaryotic folds unambiguously inherited from Archaea. Compared to previous studies, the repartition of informational function is higher than expected for folds originated from Bacteria and as high as expected for folds inherited from Archaea. The second type of folds is specifically eukaryotic and associated with an increase of new folds within eukaryotes distributed in particular clades. Reconstructed ancestral states coupled with dating of each node on the tree of life provided fold appearance rates. The rate is on average twice higher within Eukaryota than within Bacteria or Archaea. The highest rates are found in the origins of eukaryotes, holozoans, metazoans, metazoans stricto sensu, and vertebrates: the roots of these clades correspond to bursts of fold evolution. We could correlate the functions of some of the fold synapomorphies within eukaryotes with significant evolutionary events. Among them, we find evidence for the rise of multicellularity, adaptive immune system, or virus folds which could be linked to an ecological shift made by tetrapods.},
}

@article {pmid38053292,
year = {2023},
author = {Shelake, RM and Pramanik, D and Kim, JY},
title = {CRISPR base editor-based targeted random mutagenesis (BE-TRM) toolbox for directed evolution.},
journal = {BMB reports},
volume = {},
number = {},
pages = {},
pmid = {38053292},
issn = {1976-670X},
abstract = {Directed evolution (DE) of desired locus by targeted random mutagenesis (TRM) tools is a powerful approach for generating genetic variations with novel or improved functions, particularly in complex genomes. TRM-based DE involves developing a mutant library of targeted DNA sequences and screening the variants for the desired properties. However, DE methods have for a long time been confined to bacteria and yeasts. Lately, CRISPR/Cas and DNA deaminase-based tools that circumvent enduring barriers such as longer life cycle, small library sizes, and low mutation rates have been developed to facilitate DE in native genetic environments of multicellular organisms. Notably, deaminase-based base editing-TRM (BE-TRM) tools have greatly expanded the scope and efficiency of DE schemes by enabling base substitutions and randomization of targeted DNA sequences. BE-TRM tools provide a robust platform for the continuous molecular evolution of desired proteins, metabolic pathway engineering, creation of a mutant library of desired locus to evolve novel functions, and other applications, such as predicting mutants conferring antibiotic resistance. This review provides timely updates on the recent advances in BE-TRM tools for DE, their applications in biology, and future directions for further improvements.},
}

@article {pmid38039969,
year = {2023},
author = {Mulvey, H and Dolan, L},
title = {RHO of plant signaling was established early in streptophyte evolution.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2023.11.007},
pmid = {38039969},
issn = {1879-0445},
abstract = {The algal ancestors of land plants underwent a transition from a unicellular to a multicellular body plan.[1] This transition likely took place early in streptophyte evolution, sometime after the divergence of the Chlorokybophyceae/Mesostigmatophyceae lineage, but before the divergence of the Klebsormidiophyceae lineage.[2] How this transition was brought about is unknown; however, it was likely facilitated by the evolution of novel mechanisms to spatially regulate morphogenesis. In land plants, RHO of plant (ROP) signaling plays a conserved role in regulating polarized cell growth and cell division orientation to orchestrate morphogenesis.[3][,][4][,][5][,][6][,][7][,][8] ROP constitutes a plant-specific subfamily of the RHO GTPases, which are more widely conserved throughout eukaryotes.[9][,][10] Although the RHO family originated in early eukaryotes,[11][,][12] how and when the ROP subfamily originated had remained elusive. Here, we demonstrate that ROP signaling was established early in the streptophyte lineage, sometime after the divergence of the Chlorokybophyceae/Mesostigmatophyceae lineage, but before the divergence of the Klebsormidiophyceae lineage. This period corresponds to when the unicellular-to-multicellular transition likely took place in the streptophytes. In addition to being critical for the complex morphogenesis of extant land plants, we speculate that ROP signaling contributed to morphological evolution in early streptophytes.},
}

@article {pmid38040554,
year = {2023},
author = {Arnoux-Courseaux, M and Coudert, Y},
title = {Re-examining meristems through the lens of evo-devo.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2023.11.003},
pmid = {38040554},
issn = {1878-4372},
abstract = {The concept of the meristem was introduced in 1858 to characterize multicellular, formative, and proliferative tissues that give rise to the entire plant body, based on observations of vascular plants. Although its original definition did not encompass bryophytes, this concept has been used and continuously refined over the past 165 years to describe the diverse apices of all land plants. Here, we re-examine this matter in light of recent evo-devo research and show that, despite displaying high anatomical diversity, land plant meristems are unified by shared genetic control. We also propose a modular view of meristem function and highlight multiple evolutionary mechanisms that are likely to have contributed to the assembly and diversification of the varied meristems during the course of plant evolution.},
}

@article {pmid38029070,
year = {2023},
author = {Liu, N and Jiang, T and Cui, WP and Qi, XQ and Li, XG and Lu, Y and Wu, LF and Zhang, WJ},
title = {The TorRS two component system regulates expression of TMAO reductase in response to high hydrostatic pressure in Vibrio fluvialis.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1291578},
doi = {10.3389/fmicb.2023.1291578},
pmid = {38029070},
issn = {1664-302X},
abstract = {High hydrostatic pressure (HHP) regulated gene expression is one of the most commonly adopted strategies for microbial adaptation to the deep-sea environments. Previously we showed that the HHP-inducible trimethylamine N-oxide (TMAO) reductase improves the pressure tolerance of deep-sea strain Vibrio fluvialis QY27. Here, we investigated the molecular mechanism of HHP-responsive regulation of TMAO reductase TorA. By constructing torR and torS deletion mutants, we demonstrated that the two-component regulator TorR and sensor TorS are responsible for the HHP-responsive regulation of torA. Unlike known HHP-responsive regulatory system, the abundance of torR and torS was not affected by HHP. Complementation of the ΔtorS mutant with TorS altered at conserved phosphorylation sites revealed that the three sites were indispensable for substrate-induced regulation, but only the histidine located in the alternative transmitter domain was involved in pressure-responsive regulation. Taken together, we demonstrated that the induction of TMAO reductase by HHP is mediated through the TorRS system and proposed a bifurcation of signal transduction in pressure-responsive regulation from the substrate-induction. This work provides novel knowledge of the pressure regulated gene expression and will promote the understanding of the microbial adaptation to the deep-sea HHP environment.},
}

@article {pmid38026691,
year = {2023},
author = {Yoshida, K and Kato, D and Sugio, S and Takeda, I and Wake, H},
title = {Activity-dependent oligodendrocyte calcium dynamics and their changes in Alzheimer's disease.},
journal = {Frontiers in cellular neuroscience},
volume = {17},
number = {},
pages = {1154196},
doi = {10.3389/fncel.2023.1154196},
pmid = {38026691},
issn = {1662-5102},
abstract = {Oligodendrocytes (OCs) form myelin around axons, which is dependent on neuronal activity. This activity-dependent myelination plays a crucial role in training and learning. Previous studies have suggested that neuronal activity regulates proliferation and differentiation of oligodendrocyte precursor cells (OPCs) and myelination. In addition, deficient activity-dependent myelination results in impaired motor learning. However, the functional response of OC responsible for neuronal activity and their pathological changes is not fully elucidated. In this research, we aimed to understand the activity-dependent OC responses and their different properties by observing OCs using in vivo two-photon microscopy. We clarified that the Ca[2+] activity in OCs is neuronal activity dependent and differentially regulated by neurotransmitters such as glutamate or adenosine triphosphate (ATP). Furthermore, in 5-month-old mice models of Alzheimer's disease, a period before the appearance of behavioral abnormalities, the elevated Ca[2+] responses in OCs are ATP dependent, suggesting that OCs receive ATP from damaged tissue. We anticipate that our research will help in determining the correct therapeutic strategy for neurodegenerative diseases beyond the synapse.},
}

@article {pmid38018379,
year = {2023},
author = {Digel, L and Mierzwa, M and Bonné, R and Zieger, S and Pavel, I and Ferapontova, E and Koren, K and Boesen, T and Harnisch, F and Marshall, I and Nielsen, LP and Kuhn, A},
title = {Cable Bacteria Skeletons as Catalytically Active Electrodes.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e202312647},
doi = {10.1002/anie.202312647},
pmid = {38018379},
issn = {1521-3773},
abstract = {Cable bacteria are multicellular, filamentous bacteria that use internal conductive fibers to transport electrons over centimeter distances from donors within anoxic sediment layers to oxygen at the surface. We extracted the fibers and used them as free-standing bio-based electrodes to investigate their electrocatalytic behavior. The fibers catalyzed the reversible interconversion of oxygen and water, and an electric current was running through the fibers even when the potential difference was generated solely by a gradient of oxygen concentration. Oxygen reduction as well as oxygen evolution were confirmed by optical measurements. Within living cable bacteria, oxygen reduction by direct electrocatalysis on the fibers and not by membrane-bound proteins readily explains exceptionally high cell-specific oxygen consumption rates observed in the oxic zone, while electrocatalytic water oxidation may provide oxygen to cells in the anoxic zone.},
}

@article {pmid38015755,
year = {2023},
author = {Zhang, Y and Fu, M and Wang, H and Sun, H},
title = {Advances in the Construction and Application of Thyroid Organoids.},
journal = {Physiological research},
volume = {72},
number = {5},
pages = {557-564},
pmid = {38015755},
issn = {1802-9973},
abstract = {Organoids are complex multicellular structures that stem cells self-organize in three-dimensional (3D) cultures into anatomical structures and functional units similar to those seen in the organs from which they originate. This review describes the construction of thyroid organoids and the research progress that has occurred in models of thyroid-related disease. As a novel tool for modeling in a 3D multicellular environment, organoids help provide some useful references for the study of the pathogenesis of thyroid disease.},
}

@article {pmid38014282,
year = {2023},
author = {Bingham, EP and Ratcliff, WC},
title = {A non-adaptive explanation for macroevolutionary patterns in the evolution of complex multicellularity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.11.11.566713},
pmid = {38014282},
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 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, non-adaptive 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: mutational biases in eukaryotes tend to drive genomic expansion, providing additional raw genetic material for subsequent multicellular innovation, while prokaryotes generally face genomic erosion. These effects become more severe as organisms evolve larger size and more stringent genetic bottlenecks between generations- both of which are hallmarks of complex multicellularity. Taken together, we hypothesize that it is these idiosyncratic lineagespecific mutational biases, rather than cell-biological innovations within eukaryotes, that underpins the long-term divergent evolution of complex multicellularity across the tree of life.},
}

@article {pmid37978256,
year = {2023},
author = {Ongenae, V and Kempff, A and van Neer, V and Shomar, H and Tesson, F and Rozen, D and Briegel, A and Claessen, D},
title = {Genome sequence and characterization of Streptomyces phages Vanseggelen and Verabelle, representing two new species within the genus Camvirus.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {20153},
pmid = {37978256},
issn = {2045-2322},
support = {VI.C.192.002//NWO Vici/ ; },
mesh = {*Bacteriophages ; *Streptomyces/genetics ; Genome, Viral ; DNA, Viral/genetics ; *Siphoviridae/genetics ; Phylogeny ; },
abstract = {Despite the rising interest in bacteriophages, little is known about their infection cycle and lifestyle in a multicellular host. Even in the model system Streptomyces, only a small number of phages have been sequenced and well characterized so far. Here, we report the complete characterization and genome sequences of Streptomyces phages Vanseggelen and Verabelle isolated using Streptomyces coelicolor as a host. A wide range of Streptomyces strains could be infected by both phages, but neither of the two phages was able to infect members of the closely related sister genus Kitasatospora. The phages Vanseggelen and Verabelle have a double-stranded DNA genome with lengths of 48,720 and 48,126 bp, respectively. Both phage genomes contain 72 putative genes, and the presence of an integrase encoding protein indicates a lysogenic lifestyle. Characterization of the phages revealed their stability over a wide range of temperatures (30-45 °C) and pH values (4-10). In conclusion, Streptomyces phage Vanseggelen and Streptomyces phage Verabelle are newly isolated phages that can be classified as new species in the genus Camvirus, within the subfamily Arquattrovirinae.},
}

*Bacteriophages
*Streptomyces/genetics
Genome, Viral
DNA, Viral/genetics
*Siphoviridae/genetics
Phylogeny

@article {pmid37552891,
year = {2023},
author = {Goehring, L and Huang, TT and Smith, DJ},
title = {Transcription-Replication Conflicts as a Source of Genome Instability.},
journal = {Annual review of genetics},
volume = {57},
number = {},
pages = {157-179},
doi = {10.1146/annurev-genet-080320-031523},
pmid = {37552891},
issn = {1545-2948},
support = {R01 ES031658/ES/NIEHS NIH HHS/United States ; R35 GM139610/GM/NIGMS NIH HHS/United States ; },
abstract = {Transcription and replication both require large macromolecular complexes to act on a DNA template, yet these machineries cannot simultaneously act on the same DNA sequence. Conflicts between the replication and transcription machineries (transcription-replication conflicts, or TRCs) are widespread in both prokaryotes and eukaryotes and have the capacity to both cause DNA damage and compromise complete, faithful replication of the genome. This review will highlight recent studies investigating the genomic locations of TRCs and the mechanisms by which they may be prevented, mitigated, or resolved. We address work from both model organisms and mammalian systems but predominantly focus on multicellular eukaryotes owing to the additional complexities inherent in the coordination of replication and transcription in the context of cell type-specific gene expression and higher-order chromatin organization.},
}

@article {pmid38003023,
year = {2023},
author = {Toch, K and Buczek, M and Labocha, MK},
title = {Genetic Interactions in Various Environmental Conditions in Caenorhabditis elegans.},
journal = {Genes},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/genes14112080},
pmid = {38003023},
issn = {2073-4425},
support = {2015/17/B/NZ8/02366//National Science Center/ ; },
abstract = {Although it is well known that epistasis plays an important role in many evolutionary processes (e.g., speciation, evolution of sex), our knowledge on the frequency and prevalent sign of epistatic interactions is mainly limited to unicellular organisms or cell cultures of multicellular organisms. This is even more pronounced in regard to how the environment can influence genetic interactions. To broaden our knowledge in that respect we studied gene-gene interactions in a whole multicellular organism, Caenorhabditis elegans. We screened over one thousand gene interactions, each one in standard laboratory conditions, and under three different stressors: heat shock, oxidative stress, and genotoxic stress. Depending on the condition, between 7% and 22% of gene pairs showed significant genetic interactions and an overall sign of epistasis changed depending on the condition. Sign epistasis was quite common, but reciprocal sign epistasis was extremally rare. One interaction was common to all conditions, whereas 78% of interactions were specific to only one environment. Although epistatic interactions are quite common, their impact on evolutionary processes will strongly depend on environmental factors.},
}

@article {pmid37996670,
year = {2024},
author = {Spradling, AC},
title = {The Ancient Origin and Function of Germline Cysts.},
journal = {Results and problems in cell differentiation},
volume = {71},
number = {},
pages = {3-21},
pmid = {37996670},
issn = {0080-1844},
abstract = {Gamete production in most animal species is initiated within an evolutionarily ancient multicellular germline structure, the germline cyst, whose interconnected premeiotic cells synchronously develop from a single progenitor arising just downstream from a stem cell. Cysts in mice, Drosophila, and many other animals protect developing sperm, while in females, cysts generate nurse cells that guard sister oocytes from transposons (TEs) and help them grow and build a Balbiani body. However, the origin and extreme evolutionary conservation of germline cysts remains a mystery. We suggest that cysts arose in ancestral animals like Hydra and Planaria whose multipotent somatic and germline stem cells (neoblasts) express genes conserved in all animal germ cells and frequently begin differentiation in cysts. A syncytial state is proposed to help multipotent stem cell chromatin transition to an epigenetic state with heterochromatic domains suitable for TE repression and specialized function. Most modern animals now lack neoblasts but have retained stem cells and cysts in their early germlines, which continue to function using this ancient epigenetic strategy.},
}

@article {pmid37990147,
year = {2023},
author = {Jin, H and Zhang, W and Liu, H and Bao, Y},
title = {Genome-wide identification and characteristic analysis of ETS gene family in blood clam Tegillarca granosa.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {700},
pmid = {37990147},
issn = {1471-2164},
support = {LZ20C190001//Key Natural Science Foundation of Zhejiang/ ; 32273123//National Science Foundation of China/ ; 2021C02069-7//Zhejiang Major Program of Science and Technology/ ; LQ23C190007//Science Foundation of Zhejiang/ ; 2021S014//Ningbo Public Benefit Research Key Project/ ; },
mesh = {Humans ; Animals ; Phylogeny ; *Arcidae/genetics/metabolism ; Proto-Oncogene Proteins c-ets/genetics/metabolism ; Genome ; *Bivalvia/genetics ; },
abstract = {BACKGROUND: ETS transcription factors, known as the E26 transformation-specific factors, assume a critical role in the regulation of various vital biological processes in animals, including cell differentiation, the cell cycle, and cell apoptosis. However, their characterization in mollusks is currently lacking.

RESULTS: The current study focused on a comprehensive analysis of the ETS genes in blood clam Tegillarca granosa and other mollusk genomes. Our phylogenetic analysis revealed the absence of the SPI and ETV subfamilies in mollusks compared to humans. Additionally, several ETS genes in mollusks were found to lack the PNT domain, potentially resulting in a diminished ability of ETS proteins to bind target genes. Interestingly, the bivalve ETS1 genes exhibited significantly high expression levels during the multicellular proliferation stage and in gill tissues. Furthermore, qRT-PCR results showed that Tg-ETS-14 (ETS1) is upregulated in the high total hemocyte counts (THC) population of T. granosa, suggesting it plays a significant role in stimulating hemocyte proliferation.

CONCLUSION: Our study significantly contributes to the comprehension of the evolutionary aspects concerning the ETS gene family, while also providing valuable insights into its role in fostering hemocyte proliferation across mollusks.},
}

Humans
Animals
Phylogeny
*Arcidae/genetics/metabolism
Proto-Oncogene Proteins c-ets/genetics/metabolism
Genome
*Bivalvia/genetics

@article {pmid37993452,
year = {2023},
author = {Nicolas, E and Simion, P and Guérineau, M and Terwagne, M and Colinet, M and Virgo, J and Lingurski, M and Boutsen, A and Dieu, M and Hallet, B and Van Doninck, K},
title = {Horizontal acquisition of a DNA ligase improves DNA damage tolerance in eukaryotes.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {7638},
pmid = {37993452},
issn = {2041-1723},
abstract = {Bdelloid rotifers are part of the restricted circle of multicellular animals that can withstand a wide range of genotoxic stresses at any stage of their life cycle. In this study, bdelloid rotifer Adineta vaga is used as a model to decipher the molecular basis of their extreme tolerance. Proteomic analysis shows that a specific DNA ligase, different from those usually involved in DNA repair in eukaryotes, is strongly over-represented upon ionizing radiation. A phylogenetic analysis reveals its orthology to prokaryotic DNA ligase E, and its horizontal acquisition by bdelloid rotifers and plausibly other eukaryotes. The fungus Mortierella verticillata, having a single copy of this DNA Ligase E homolog, also exhibits an increased radiation tolerance with an over-expression of this DNA ligase E following X-ray exposure. We also provide evidence that A. vaga ligase E is a major contributor of DNA breaks ligation activity, which is a common step of all important DNA repair pathways. Consistently, its heterologous expression in human cell lines significantly improves their radio-tolerance. Overall, this study highlights the potential of horizontal gene transfers in eukaryotes, and their contribution to the adaptation to extreme conditions.},
}

@article {pmid37981028,
year = {2023},
author = {Rossi, SA and García-Barbazán, I and Chamorro-Herrero, I and Taborda, CP and Zaragoza, Ó and Zambrano, A},
title = {Use of 2D Minilungs from Human Embryonic Stem Cells to Study the Interaction of Cryptococcus neoformans with the Respiratory Tract.},
journal = {Microbes and infection},
volume = {},
number = {},
pages = {105260},
doi = {10.1016/j.micinf.2023.105260},
pmid = {37981028},
issn = {1769-714X},
abstract = {Organoids can meet the needs between the use of cell culture and in vivo work, bringing together aspects of multicellular tissues, providing a more similar in vitro system for the study of various components, including host-interactions with pathogens and drug response. Organoids are structures that resemble organs in vivo, originating from pluripotent stem cells (PSCs) or adult stem cells (ASCs). There is great interest in deepening the understanding of the use of this technology to produce information about fungal infections and their treatments. This work aims the use 2D human lung organoid derived from human embryonic stem cells (hESCs), to investigate Cryptococcus neoformans-host interactions. C. neoformans is an opportunistic fungus acquired by inhalation that causes systemic mycosis mainly in immunocompromised individuals. Our work highlights the suitability of human minilungs for the study of C. neoformans infection (adhesion, invasion and replication), the interaction with the surfactant and induction of the host's alveolar pro-inflammatory response.},
}

@article {pmid37971931,
year = {2023},
author = {Zou, Y and Sabljić, I and Horbach, N and Dauphinee, AN and Åsman, A and Sancho Temino, L and Minina, EA and Drag, M and Stael, S and Poreba, M and Ståhlberg, J and Bozhkov, PV},
title = {Thermoprotection by a cell membrane-localized metacaspase in a green alga.},
journal = {The Plant cell},
volume = {},
number = {},
pages = {},
doi = {10.1093/plcell/koad289},
pmid = {37971931},
issn = {1532-298X},
abstract = {Caspases are restricted to animals, while other organisms, including plants possess metacaspases (MCAs), a more ancient and broader class of structurally related yet biochemically distinct proteases. Our current understanding of plant MCAs is derived from studies in streptophytes, and mostly in Arabidopsis (Arabidopsis thaliana) with nine MCAs with partially redundant activities. In contrast to streptophytes, most chlorophytes contain only one or two uncharacterized MCAs, providing an excellent platform for MCA research. Here we investigated CrMCA-II, the single type-II MCA from the model chlorophyte Chlamydomonas (Chlamydomonas reinhardtii). Surprisingly, unlike other studied MCAs and similar to caspases, CrMCA-II dimerizes both in vitro and in vivo. Furthermore, activation of CrMCA-II in vivo correlated with its dimerization. Most of CrMCA-II in the cell was present as a proenzyme (zymogen) attached to the plasma membrane (PM). Deletion of CrMCA-II by genome editing compromised thermotolerance, leading to increased cell death under heat stress. Adding back either wild-type or a catalytically dead CrMCA-II restored thermoprotection, suggesting that its proteolytic activity is dispensable for this effect. Finally, we connected the non-proteolytic role of CrMCA-II in thermotolerance to the ability to modulate PM fluidity. Our study reveals an ancient, MCA-dependent thermotolerance mechanism retained by Chlamydomonas and probably lost during the evolution of multicellularity.},
}

@article {pmid37963956,
year = {2023},
author = {Tissot, S and Guimard, L and Meliani, J and Boutry, J and Dujon, AM and Capp, JP and Tökölyi, J and Biro, PA and Beckmann, C and Fontenille, L and Do Khoa, N and Hamede, R and Roche, B and Ujvari, B and Nedelcu, AM and Thomas, F},
title = {The impact of food availability on tumorigenesis is evolutionarily conserved.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {19825},
pmid = {37963956},
issn = {2045-2322},
abstract = {The inability to control cell proliferation results in the formation of tumors in many multicellular lineages. Nonetheless, little is known about the extent of conservation of the biological traits and ecological factors that promote or inhibit tumorigenesis across the metazoan tree. Particularly, changes in food availability have been linked to increased cancer incidence in humans, as an outcome of evolutionary mismatch. Here, we apply evolutionary oncology principles to test whether food availability, regardless of the multicellular lineage considered, has an impact on tumorigenesis. We used two phylogenetically unrelated model systems, the cnidarian Hydra oligactis and the fish Danio rerio, to investigate the impact of resource availability on tumor occurrence and progression. Individuals from healthy and tumor-prone lines were placed on four diets that differed in feeding frequency and quantity. For both models, frequent overfeeding favored tumor emergence, while lean diets appeared more protective. In terms of tumor progression, high food availability promoted it, whereas low resources controlled it, but without having a curative effect. We discuss our results in light of current ideas about the possible conservation of basic processes governing cancer in metazoans (including ancestral life history trade-offs at the cell level) and in the framework of evolutionary medicine.},
}

@article {pmid37961564,
year = {2023},
author = {Mukherjee, A and Huang, Y and Elgeti, J and Oh, S and Neliat, AR and Schüttler, J and Benites, NC and Liu, X and Barboiu, M and Stocker, H and Kirschner, MW and Basan, M},
title = {Membrane potential mediates an ancient mechano-transduction mechanism for multi-cellular homeostasis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.11.02.565386},
pmid = {37961564},
abstract = {Membrane potential is a property of all living cells [1] . However, its physiological role in nonexcitable cells is poorly understood. Resting membrane potential is typically considered fixed for a given cell type and under tight homeostatic control [2] , akin to body temperature in mammals. Contrary to this widely accepted paradigm, we found that membrane potential is a dynamic property that directly reflects tissue density and mechanical forces acting on the cell. Serving as a quasi-instantaneous, global readout of density and mechanical pressure, membrane potential is integrated with signal transduction networks by affecting the conformation and clustering of proteins in the membrane [3,4] , as well as the transmembrane flux of key signaling ions [5,6] . Indeed, we show that important mechano-sensing pathways, YAP, Jnk and p38 [7-121314] , are directly controlled by membrane potential. We further show that mechano-transduction via membrane potential plays a critical role in the homeostasis of epithelial tissues, setting tissue density by controlling proliferation and cell extrusion of cells. Moreover, a wave of depolarization triggered by mechanical stretch enhances the speed of wound healing. Mechano-transduction via membrane potential likely constitutes an ancient homeostatic mechanism in multi-cellular organisms, potentially serving as a steppingstone for the evolution of excitable tissues and neuronal mechano-sensing. The breakdown of membrane potential mediated homeostatic regulation may contribute to tumor growth.},
}

@article {pmid37317487,
year = {2023},
author = {Fulda, FC},
title = {Agential autonomy and biological individuality.},
journal = {Evolution & development},
volume = {25},
number = {6},
pages = {353-370},
doi = {10.1111/ede.12450},
pmid = {37317487},
issn = {1525-142X},
mesh = {Humans ; Animals ; *Biological Evolution ; *Symbiosis ; },
abstract = {What is a biological individual? How are biological individuals individuated? How can we tell how many individuals there are in a given assemblage of biological entities? The individuation and differentiation of biological individuals are central to the scientific understanding of living beings. I propose a novel criterion of biological individuality according to which biological individuals are autonomous agents. First, I articulate an ecological-dynamical account of natural agency according to which, agency is the gross dynamical capacity of a goal-directed system to bias its repertoire to respond to its conditions as affordances. Then, I argue that agents or agential dynamical systems can be agentially dependent on, or agentially autonomous from, other agents and that this agential dependence/autonomy can be symmetrical or asymmetrical, strong or weak. Biological individuals, I propose, are all and only those agential dynamical systems that are strongly agentially autonomous. So, to determine how many individuals there are in a given multiagent aggregate, such as multicellular organism, a colony, symbiosis, or a swarm, we first have to identify how many agential dynamical systems there are, and then what their relations of agential dependence/autonomy are. I argue that this criterion is adequate to the extent that it vindicates the paradigmatic cases, and explains why the paradigmatic cases are paradigmatic, and why the problematic cases are problematic. Finally, I argue for the importance of distinguishing between agential and causal dependence and show the relevance of agential autonomy for understanding the explanatory structure of evolutionary developmental biology.},
}

Humans
Animals
*Biological Evolution
*Symbiosis

@article {pmid37953852,
year = {2023},
author = {Gavrilov-Zimin, IA},
title = {Ancient reproductive modes and criteria of multicellularity.},
journal = {Comparative cytogenetics},
volume = {17},
number = {},
pages = {195-238},
pmid = {37953852},
issn = {1993-0771},
abstract = {It is demonstrated that the initial method of fertilization in animals (Metazoa), embryophyte plants (Embryophyta), most groups of multicellular oogamous algae, oogamous and pseudoogamous multicellular fungi was internal fertilization (in the broad meaning) in/on the body of a maternal organism. Accordingly, during the bisexual process, the initial method of formation of a daughter multicellular organism in animals was viviparity, and in embryophyte plants and most groups of oogamous multicellular algae - the germination of a zygote in/on the body of maternal organism. The reproductive criteria of multicellularity are proposed and discussed. In this regard, the multicellularity is considered to subdivide terminologically into three variants: 1) protonemal, the most simple, characteristic of multicellular prokaryotes, most groups of multicellular algae and gametophytes of some higher plants; 2) siphonoseptal, found among multicellular fungi, some groups of green and yellow-green algae; 3) embryogenic, most complicated, known in all animals (Metazoa), all sporophytes and some gametophytes of higher plants (Embryophyta), charophyte green algae Charophyceae s.s., oogamous species of green and brown algae, some genera of red algae. In addition to the well-known division of reproduction methods into sexual and asexual, it is proposed to divide the reproduction of multicellular organisms into monocytic (the emergence of a new organism from one cell sexually or asexually) and polycytic (fragmentation, longitudinal / transverse division or budding based on many cells of the body of the mother organism), since these two ways have different evolutionary and ontogenetic origins.},
}

@article {pmid37949064,
year = {2023},
author = {Liu, D and Vargas-García, CA and Singh, A and Umen, J},
title = {A cell-based model for size control in the multiple fission alga Chlamydomonas reinhardtii.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2023.10.023},
pmid = {37949064},
issn = {1879-0445},
abstract = {Understanding how population-size homeostasis emerges from stochastic individual cell behaviors remains a challenge in biology.[1][,][2][,][3][,][4][,][5][,][6][,][7] The unicellular green alga Chlamydomonas reinhardtii (Chlamydomonas) proliferates using a multiple fission cell cycle, where a prolonged G1 phase is followed by n rounds of alternating division cycles (S/M) to produce 2[n] daughters. A "Commitment" sizer in mid-G1 phase ensures sufficient cell growth before completing the cell cycle. A mitotic sizer couples mother-cell size to division number (n) such that daughter size distributions are uniform regardless of mother size distributions. Although daughter size distributions were highly robust to altered growth conditions, ∼40% of daughter cells fell outside of the 2-fold range expected from a "perfect" multiple fission sizer.[7][,][8] A simple intuitive power law model with stochastic noise failed to reproduce individual division behaviors of tracked single cells. Through additional iterative modeling, we identified an alternative modified threshold (MT) model, where cells need to cross a threshold greater than 2-fold their median starting size to become division-competent (i.e., Committed), after which their behaviors followed a power law model. The Commitment versus mitotic size threshold uncoupling in the MT model was likely a key pre-adaptation in the evolution of volvocine algal multicellularity. A similar experimental approach was used in size mutants mat3/rbr and dp1 that are, respectively, missing repressor or activator subunits of the retinoblastoma tumor suppressor complex (RBC). Both mutants showed altered relationships between Commitment and mitotic sizer, suggesting that RBC functions to decouple the two sizers.},
}

@article {pmid37947621,
year = {2023},
author = {Wang, X and Xu, X and Wang, Z},
title = {The Post-Translational Role of UFMylation in Physiology and Disease.},
journal = {Cells},
volume = {12},
number = {21},
pages = {},
doi = {10.3390/cells12212543},
pmid = {37947621},
issn = {2073-4409},
support = {32090031, 32000911//NSFC/ ; },
abstract = {Ubiquitin-fold modifier 1 (UFM1) is a newly identified ubiquitin-like protein that has been conserved during the evolution of multicellular organisms. In a similar manner to ubiquitin, UFM1 can become covalently linked to the lysine residue of a substrate via a dedicated enzymatic cascade. Although a limited number of substrates have been identified so far, UFM1 modification (UFMylation) has been demonstrated to play a vital role in a variety of cellular activities, including mammalian development, ribosome biogenesis, the DNA damage response, endoplasmic reticulum stress responses, immune responses, and tumorigenesis. In this review, we summarize what is known about the UFM1 enzymatic cascade and its biological functions, and discuss its recently identified substrates. We also explore the pathological role of UFMylation in human disease and the corresponding potential therapeutic targets and strategies.},
}

@article {pmid37745323,
year = {2023},
author = {Johnson, JAI and Stein-O'Brien, GL and Booth, M and Heiland, R and Kurtoglu, F and Bergman, D and Bucher, E and Deshpande, A and Forjaz, A and Getz, M and Godet, I and Lyman, M and Metzcar, J and Mitchell, J and Raddatz, A and Rocha, HL and Solorzano, J and Sundus, A and Wang, Y and Gilkes, DM and Kagohara, LT and Kiemen, AL and Thompson, ED and Wirtz, D and Wu, PH and Zaidi, N and Zheng, L and Zimmerman, JW and Jaffee, EM and Chang, YH and Coussens, L and Gray, J and Heiser, LM and Fertig, EJ and Macklin, P},
title = {Digitize your Biology! Modeling multicellular systems through interpretable cell behavior.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.09.17.557982},
pmid = {37745323},
support = {R00 NS122085/NS/NINDS NIH HHS/United States ; 75N91019D00024/CA/NCI NIH HHS/United States ; P50 CA062924/CA/NCI NIH HHS/United States ; K08 CA248624/CA/NCI NIH HHS/United States ; P01 CA247886/CA/NCI NIH HHS/United States ; U54 CA268083/CA/NCI NIH HHS/United States ; U54 CA274371/CA/NCI NIH HHS/United States ; U01 CA253403/CA/NCI NIH HHS/United States ; U01 CA212007/CA/NCI NIH HHS/United States ; U01 CA232137/CA/NCI NIH HHS/United States ; },
abstract = {Cells are fundamental units of life, constantly interacting and evolving as dynamical systems. While recent spatial multi-omics can quantitate individual cells' characteristics and regulatory programs, forecasting their evolution ultimately requires mathematical modeling. We develop a conceptual framework--a cell behavior hypothesis grammar--that uses natural language statements (cell rules) to create mathematical models. This allows us to systematically integrate biological knowledge and multi-omics data to make them computable. We can then perform virtual "thought experiments" that challenge and extend our understanding of multicellular systems, and ultimately generate new testable hypotheses. In this paper, we motivate and describe the grammar, provide a reference implementation, and demonstrate its potential through a series of examples in tumor biology and immunotherapy. Altogether, this approach provides a bridge between biological, clinical, and systems biology researchers for mathematical modeling of biological systems at scale, allowing the community to extrapolate from single-cell characterization to emergent multicellular behavior.},
}

@article {pmid37475165,
year = {2023},
author = {Lamża, Ł},
title = {Diversity of 'simple' multicellular eukaryotes: 45 independent cases and six types of multicellularity.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {98},
number = {6},
pages = {2188-2209},
doi = {10.1111/brv.13001},
pmid = {37475165},
issn = {1469-185X},
mesh = {Phylogeny ; *Eukaryota/genetics ; *Fungi ; Biological Evolution ; },
abstract = {Multicellularity evolved multiple times in the history of life, with most reviewers agreeing that it appeared at least 20 times in eukaryotes. However, a specific list of multicellular eukaryotes with clear criteria for inclusion has not yet been published. Herein, an updated critical review of eukaryotic multicellularity is presented, based on current understanding of eukaryotic phylogeny and new discoveries in microbiology, phycology and mycology. As a result, 45 independent multicellular lineages are identified that fall into six distinct types. Functional criteria, as distinct from a purely topological definition of a cell, are introduced to bring uniformity and clarity to the existing definitions of terms such as colony, multicellularity, thallus or plasmodium. The category of clonal multicellularity is expanded to include: (i) septated multinucleated thalli found in Pseudofungi and early-branching Fungi such as Chytridiomycota and Blastocladiomycota; and (ii) multicellular reproductive structures formed by plasmotomy in intracellular parasites such as Phytomyxea. Furthermore, (iii) endogeneous budding, as found in Paramyxida, is described as a form of multicellularity. The best-known case of clonal multicellularity, i.e. (iv) non-separation of cells after cell division, as known from Metazoa and Ochrophyta, is also discussed. The category of aggregative multicellularity is expanded to include not only (v) pseudoplasmodial forms, such a sorocarp-forming Acrasida, but also (vi) meroplasmodial organisms, such as members of Variosea or Filoreta. A common set of topological, geometric, genetic and life-cycle criteria are presented that form a coherent, philosophically sound framework for discussing multicellularity. A possibility of a seventh type of multicellularity is discussed, that of multi-species superorganisms formed by protists with obligatory bacterial symbionts, such as some members of Oxymonada or Parabasalia. Its inclusion is dependent on the philosophical stance taken towards the concepts of individuality and organism in biology. Taxa that merit special attention are identified, such as colonial Centrohelea, and a new speculative form of multicellularity, possibly present in some reticulopodial amoebae, is briefly described. Because of insufficient phylogenetic and morphological data, not all lineages could be unequivocally identified, and the true total number of all multicellular eukaryotic lineages is therefore higher, likely close to a hundred.},
}

Phylogeny
*Eukaryota/genetics
*Fungi
Biological Evolution

@article {pmid37931037,
year = {2023},
author = {Dupouy, G and Cashell, R and Brychkova, G and Tuteja, R and McKeown, PC and Spillane, C},
title = {PICKLE RELATED 2 is a Neofunctionalized Gene Duplicate Under Positive Selection With Antagonistic Effects to the Ancestral PICKLE Gene on the Seed Transcriptome.},
journal = {Genome biology and evolution},
volume = {15},
number = {11},
pages = {},
doi = {10.1093/gbe/evad191},
pmid = {37931037},
issn = {1759-6653},
abstract = {The evolution and diversification of proteins capable of remodeling domains has been critical for transcriptional reprogramming during cell fate determination in multicellular eukaryotes. Chromatin remodeling proteins of the CHD3 family have been shown to have important and antagonistic impacts on seed development in the model plant, Arabidopsis thaliana, yet the basis of this functional divergence remains unknown. In this study, we demonstrate that genes encoding the CHD3 proteins PICKLE (PKL) and PICKLE-RELATED 2 (PKR2) originated from a duplication event during the diversification of crown Brassicaceae, and that these homologs have undergone distinct evolutionary trajectories since this duplication, with PKR2 fast evolving under positive selection, while PKL is subject to purifying selection. We find that the rapid evolution of PKR2 under positive selection reduces the encoded protein's intrinsic disorder, possibly suggesting a tertiary structure configuration which differs from that of PKL. Our whole genome transcriptome analysis in seeds of pkr2 and pkl mutants reveals that they act antagonistically on the expression of specific sets of genes, providing a basis for their differing roles in seed development. Our results provide insights into how gene duplication and neofunctionalization can lead to differing and antagonistic selective pressures on transcriptomes during plant reproduction, as well as on the evolutionary diversification of the CHD3 family within seed plants.},
}

@article {pmid37925718,
year = {2023},
author = {Fung, L and Konkol, A and Ishikawa, T and Larson, BT and Brunet, T and Goldstein, RE},
title = {Swimming, Feeding, and Inversion of Multicellular Choanoflagellate Sheets.},
journal = {Physical review letters},
volume = {131},
number = {16},
pages = {168401},
doi = {10.1103/PhysRevLett.131.168401},
pmid = {37925718},
issn = {1079-7114},
abstract = {The recent discovery of the striking sheetlike multicellular choanoflagellate species Choanoeca flexa that dynamically interconverts between two hemispherical forms of opposite orientation raises fundamental questions in cell and evolutionary biology, as choanoflagellates are the closest living relatives of animals. It similarly motivates questions in fluid and solid mechanics concerning the differential swimming speeds in the two states and the mechanism of curvature inversion triggered by changes in the geometry of microvilli emanating from each cell. Here we develop fluid dynamical and mechanical models to address these observations and show that they capture the main features of the swimming, feeding, and inversion of C. flexa colonies, which can be viewed as active, shape-shifting polymerized membranes.},
}

@article {pmid37921840,
year = {2023},
author = {Dai, J and Li, XG and Zhang, WJ and Wu, LF},
title = {Tepidibacter hydrothermalis sp. nov., a novel anaerobic bacterium isolated from a deep-sea hydrothermal vent.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {73},
number = {11},
pages = {},
doi = {10.1099/ijsem.0.006151},
pmid = {37921840},
issn = {1466-5034},
abstract = {A novel anaerobic heterotrophic bacterium, designated strain SWIR-1[T], was isolated from a deep-sea hydrothermal vent field sample collected from the Southwest Indian Ridge at a depth of 2700 m. Phylogenetic analysis indicated that strain SWIR-1[T] belongs to the genus Tepidibacter, and the most closely related species are Tepidibacter mesophilus B1[T] (99.1 % 16S rRNA gene sequence similarity), Tepidibacter formicigenes DV1184[T] (94.6 %) and Tepidibacter thalassicus SC562[T] (93.9 %). Strain SWIR-1[T] shares 77.3-87.2 % average nucleotide identity and 21.5-35.7 % digital DNA-DNA hybridization values with the three type strains of Tepidibacter species. Cells of strain SWIR-1[T] were Gram-stain-positive, motile, short straight rods. Endospores were observed in stationary-phase cells when grown on Thermococcales rich medium. Strain SWIR-1[T] grew at 15-45 °C (optimum, 30°C), at pH 5.5-8.0 (optimum, pH 7.0) and with 1.0-6.0 % (w/v) NaCl (optimum, 2.0 %). Substrates utilized by strain SWIR-1[T] included complex proteinaceous, chitin, starch, lactose, maltose, fructose, galactose, glucose, rhamnose, arabinose, ribose, alanine, glycine and glycerol. The major fermentation products from glucose were acetate, lactate, H2 and CO2. Elemental sulphur, sulphate, thiosulphate, sulphite, fumarate, nitrate, nitrite and FeCl3 are not used as terminal electron acceptors. The main cellular fatty acids consisted of iso-C15 : 0 (28.4 %), C15 : 1 iso F (15.4 %) and C16 : 0 (9.8 %). The major polar lipids were phospholipids and glycolipids. No respiratory quinones were detected. Genomic comparison revealed a distinctive blended gene cluster comprising hyb-tat-hyp genes, which play a crucial role in the synthesis, maturation, activation and export of NiFe-hydrogenase. Based on the phylogenetic analysis, genomic, physiologic and chemotaxonomic characteristics, strain SWIR-1[T] is considered to represent a novel species within the genus Tepidibacter, for which the name Tepidibacter hydrothermalis sp. nov. is proposed. The type strain is strain SWIR-1[T] (=DSM 113848[T]=MCCC 1K07078[T]).},
}

@article {pmid37916911,
year = {2023},
author = {Ekdahl, LI and Salcedo, JA and Dungan, MM and Mason, DV and Myagmarsuren, D and Murphy, HA},
title = {Selection on plastic adherence leads to hyper-multicellular strains and incidental virulence in the budding yeast.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
doi = {10.7554/eLife.81056},
pmid = {37916911},
issn = {2050-084X},
support = {R15-GM122032/NH/NIH HHS/United States ; },
abstract = {Many disease-causing microbes are not obligate pathogens; rather, they are environmental microbes taking advantage of an ecological opportunity. The existence of microbes whose life cycle does not require a host and are not normally pathogenic, yet are well-suited to host exploitation, is an evolutionary puzzle. One hypothesis posits that selection in the environment may favor traits that incidentally lead to pathogenicity and virulence, or serve as pre-adaptations for survival in a host. An example of such a trait is surface adherence. To experimentally test the idea of 'accidental virulence', replicate populations of Saccharomyces cerevisiae were evolved to attach to a plastic bead for hundreds of generations. Along with plastic adherence, two multicellular phenotypes- biofilm formation and flor formation- increased; another phenotype, pseudohyphal growth, responded to the nutrient limitation. Thus, experimental selection led to the evolution of highly-adherent, hyper-multicellular strains. Wax moth larvae injected with evolved hyper-multicellular strains were significantly more likely to die than those injected with evolved non-multicellular strains. Hence, selection on plastic adherence incidentally led to the evolution of enhanced multicellularity and increased virulence. Our results support the idea that selection for a trait beneficial in the open environment can inadvertently generate opportunistic, 'accidental' pathogens.},
}

@article {pmid37905027,
year = {2023},
author = {Page-McCaw, PS and Pokidysheva, EN and Darris, CE and Chetyrkin, S and Fidler, AL and Murawala, P and Gallup, J and , and Hudson, JK and Hudson, BG},
title = {Collagen IV of basement membranes: I. Origin and diversification of COL4 genes enabling animal evolution.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.10.18.563013},
pmid = {37905027},
abstract = {Collagen IV is a primordial component of basement membranes, a specialized form of extracellular matrix that enabled multi-cellular epithelial tissues. In mammals, collagen IV assembles from a family of six α-chains (α1 to α6), encoded by six genes (COL4A1 to COL4A6), into three distinct scaffolds: the α121, the α345 and a mixed scaffold containing both α121 and α565. The six mammalian COL4A genes occur in pairs that occur in a head-to-head arrangement on three distinct chromosomes. In Alport syndrome, variants in the COL4A3, 4 or 5 genes cause either loss or defective assembly of the collagen IV [α345] scaffold which results in a dysfunctional glomerular basement membrane, proteinuria and progression to renal failure in millions of people worldwide. Here, we determine the evolutionary emergence and diversification of the COL4A genes using comparative genomics and biochemical analyses. Using syntenic relationships to genes closely linked to the COL4A genes, we determine that the COL4A3 and COL4A4 gene pair appeared in cyclostomes (hagfish and lampreys) while the COL4A5 and COL4A6 gene pair emerged in gnathostomes, jawed vertebrates. The more basal chordate species, lancelets and tunicates, do not have discrete kidneys and have a single COL4A gene pair, though often with single isolated COL4 genes similar to those found in C elegans . Remarkably, while the six COL4A genes are conserved in vertebrates, amphibians have lost the COL4A3 and COL4A4 genes. Our findings of the evolutionary emergence of these genes, together with the amphibian double-knockout, opens an experimental window to gain insights into functionality of the Col IV [α345] scaffold.},
}

@article {pmid37904088,
year = {2023},
author = {Balasubramanian, RN and Gao, M and Umen, J},
title = {Identification of cell-type specific alternative transcripts in the multicellular alga Volvox carteri.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {654},
pmid = {37904088},
issn = {1471-2164},
support = {1755430//Division of Integrative Organismal Systems/ ; },
abstract = {BACKGROUND: Cell type specialization is a hallmark of complex multicellular organisms and is usually established through implementation of cell-type-specific gene expression programs. The multicellular green alga Volvox carteri has just two cell types, germ and soma, that have previously been shown to have very different transcriptome compositions which match their specialized roles. Here we interrogated another potential mechanism for differentiation in V. carteri, cell type specific alternative transcript isoforms (CTSAI).

METHODS: We used pre-existing predictions of alternative transcripts and de novo transcript assembly with HISAT2 and Ballgown software to compile a list of loci with two or more transcript isoforms, identified a small subset that were candidates for CTSAI, and manually curated this subset of genes to remove false positives. We experimentally verified three candidates using semi-quantitative RT-PCR to assess relative isoform abundance in each cell type.

RESULTS: Of the 1978 loci with two or more predicted transcript isoforms 67 of these also showed cell type isoform expression biases. After curation 15 strong candidates for CTSAI were identified, three of which were experimentally verified, and their predicted gene product functions were evaluated in light of potential cell type specific roles. A comparison of genes with predicted alternative splicing from Chlamydomonas reinhardtii, a unicellular relative of V. carteri, identified little overlap between ortholog pairs with alternative splicing in both species. Finally, we interrogated cell type expression patterns of 126 V. carteri predicted RNA binding protein (RBP) encoding genes and found 40 that showed either somatic or germ cell expression bias. These RBPs are potential mediators of CTSAI in V. carteri and suggest possible pre-adaptation for cell type specific RNA processing and a potential path for generating CTSAI in the early ancestors of metazoans and plants.

CONCLUSIONS: We predicted numerous instances of alternative transcript isoforms in Volvox, only a small subset of which showed cell type specific isoform expression bias. However, the validated examples of CTSAI supported existing hypotheses about cell type specialization in V. carteri, and also suggested new hypotheses about mechanisms of functional specialization for their gene products. Our data imply that CTSAI operates as a minor but important component of V. carteri cellular differentiation and could be used as a model for how alternative isoforms emerge and co-evolve with cell type specialization.},
}

@article {pmid37894891,
year = {2023},
author = {Wang, K and Li, W and Cui, H and Qin, S},
title = {Phylogenetic Analysis and Characterization of Diguanylate Cyclase and Phosphodiesterase in Planktonic Filamentous Cyanobacterium Arthrospira sp.},
journal = {International journal of molecular sciences},
volume = {24},
number = {20},
pages = {},
pmid = {37894891},
issn = {1422-0067},
mesh = {Phosphoric Diester Hydrolases/genetics/metabolism ; *Spirulina/metabolism ; Phylogeny ; Bacterial Proteins/genetics/metabolism ; Escherichia coli/genetics/metabolism ; *Escherichia coli Proteins/genetics/metabolism ; Phosphorus-Oxygen Lyases/genetics/metabolism ; Cyclic GMP/metabolism ; Gene Expression Regulation, Bacterial ; },
abstract = {Cyclic di-GMP (c-di-GMP) is a second messenger of intracellular communication in bacterial species, which widely modulates diverse cellular processes. However, little is known about the c-di-GMP network in filamentous multicellular cyanobacteria. In this study, we preliminarily investigated the c-di-GMP turnover proteins in Arthrospira based on published protein data. Bioinformatics results indicate the presence of at least 149 potential turnover proteins in five Arthrospira subspecies. Some proteins are highly conserved in all tested Arthrospira, whereas others are specifically found only in certain subspecies. To further validate the protein catalytic activity, we constructed a riboswitch-based c-di-GMP expression assay system in Escherichia coli and confirmed that a GGDEF domain protein, Adc11, exhibits potential diguanylate cyclase activity. Moreover, we also evaluated a protein with a conserved HD-GYP domain, Ahd1, the expression of which significantly improved the swimming ability of E. coli. Enzyme-linked immunosorbent assay also showed that overexpression of Ahd1 reduced the intracellular concentration of c-di-GMP, which is presumed to exhibit phosphodiesterase activity. Notably, meta-analyses of transcriptomes suggest that Adc11 and Ahd1 are invariable. Overall, this work confirms the possible existence of a functional c-di-GMP network in Arthrospira, which will provide support for the revelation of the biological function of the c-di-GMP system in Arthrospira.},
}

Phosphoric Diester Hydrolases/genetics/metabolism
*Spirulina/metabolism
Phylogeny
Bacterial Proteins/genetics/metabolism
Escherichia coli/genetics/metabolism
*Escherichia coli Proteins/genetics/metabolism
Phosphorus-Oxygen Lyases/genetics/metabolism
Cyclic GMP/metabolism
Gene Expression Regulation, Bacterial

@article {pmid37895205,
year = {2023},
author = {Ashouri, A and Zhang, C and Gaiti, F},
title = {Decoding Cancer Evolution: Integrating Genetic and Non-Genetic Insights.},
journal = {Genes},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/genes14101856},
pmid = {37895205},
issn = {2073-4425},
support = {/CAPMC/CIHR/Canada ; },
abstract = {The development of cancer begins with cells transitioning from their multicellular nature to a state akin to unicellular organisms. This shift leads to a breakdown in the crucial regulators inherent to multicellularity, resulting in the emergence of diverse cancer cell subpopulations that have enhanced adaptability. The presence of different cell subpopulations within a tumour, known as intratumoural heterogeneity (ITH), poses challenges for cancer treatment. In this review, we delve into the dynamics of the shift from multicellularity to unicellularity during cancer onset and progression. We highlight the role of genetic and non-genetic factors, as well as tumour microenvironment, in promoting ITH and cancer evolution. Additionally, we shed light on the latest advancements in omics technologies that allow for in-depth analysis of tumours at the single-cell level and their spatial organization within the tissue. Obtaining such detailed information is crucial for deepening our understanding of the diverse evolutionary paths of cancer, allowing for the development of effective therapies targeting the key drivers of cancer evolution.},
}

@article {pmid37894679,
year = {2023},
author = {Wang, X and Zhang, J and Li, Q and Jia, R and Qiao, M and Cui, W},
title = {In Situ Observation of Cellular Structure Changes in and Chain Segregations of Anabaena sp. PCC 7120 on TiO2 Films under a Photocatalytic Device.},
journal = {Molecules (Basel, Switzerland)},
volume = {28},
number = {20},
pages = {},
doi = {10.3390/molecules28207200},
pmid = {37894679},
issn = {1420-3049},
support = {2020GGJS124; YSPTZX202212; 2019xjpy04//Training Plan of Young Backbone Teachers in Universities of Henan Province; the Academician Innovation Center of Hainan Province (Felix Dapare Dakra); Scientific Research Foundation of DeZhou University/ ; },
abstract = {Cyanobacteria outbreaks are serious water pollution events, causing water crises around the world. Photocatalytic disinfection, as an effective approach, has been widely used to inhibit blue algae growth. In this study, a tiny reaction room containing a TiO2 film was designed to fulfill in situ optical observation of the destruction process of a one-dimensional multicellular microorganism, Anabaena sp. PCC 7120, which is also a typical bacterial strain causing water blooms. It was found that the fragment number increased exponentially with the activation time. The fracture mechanics of the algae chains were hypothesized to be the combining functions of increased local tensile stress originated from the cell contracting as well as the oxidative attacks coming from reactive oxygen species (ROSs). It was assumed that the oxidative species were the root cause of cellular structure changes in and chain fractures of Anabaena sp. PCC 7120 in the photocatalytic inactivation activity.},
}

@article {pmid37889142,
year = {2023},
author = {Pentz, JT and MacGillivray, K and DuBose, JG and Conlin, PL and Reinhardt, E and Libby, E and Ratcliff, WC},
title = {Evolutionary consequences of nascent multicellular life cycles.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
doi = {10.7554/eLife.84336},
pmid = {37889142},
issn = {2050-084X},
support = {T32GM142616/NH/NIH HHS/United States ; },
abstract = {A key step in the evolutionary transition to multicellularity is the origin of multicellular groups as biological individuals capable of adaptation. Comparative work, supported by theory, suggests clonal development should facilitate this transition, although this hypothesis has never been tested in a single model system. We evolved 20 replicate populations of otherwise isogenic clonally reproducing 'snowflake' yeast (Δace2/∆ace2) and aggregative 'floc' yeast (GAL1p::FLO1 /GAL1p::FLO1) with daily selection for rapid growth in liquid media, which favors faster cell division, followed by selection for rapid sedimentation, which favors larger multicellular groups. While both genotypes adapted to this regime, growing faster and having higher survival during the group-selection phase, there was a stark difference in evolutionary dynamics. Aggregative floc yeast obtained nearly all their increased fitness from faster growth, not improved group survival; indicating that selection acted primarily at the level of cells. In contrast, clonal snowflake yeast mainly benefited from higher group-dependent fitness, indicating a shift in the level of Darwinian individuality from cells to groups. Through genome sequencing and mathematical modeling, we show that the genetic bottlenecks in a clonal life cycle also drive much higher rates of genetic drift-a result with complex implications for this evolutionary transition. Our results highlight the central role that early multicellular life cycles play in the process of multicellular adaptation.},
}

@article {pmid37888162,
year = {2023},
author = {Choi, J and Lee, EJ and Jang, WB and Kwon, SM},
title = {Development of Biocompatible 3D-Printed Artificial Blood Vessels through Multidimensional Approaches.},
journal = {Journal of functional biomaterials},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/jfb14100497},
pmid = {37888162},
issn = {2079-4983},
support = {21A0101L1//Korean Fund for Regenerative Medicine/ ; },
abstract = {Within the human body, the intricate network of blood vessels plays a pivotal role in transporting nutrients and oxygen and maintaining homeostasis. Bioprinting is an innovative technology with the potential to revolutionize this field by constructing complex multicellular structures. This technique offers the advantage of depositing individual cells, growth factors, and biochemical signals, thereby facilitating the growth of functional blood vessels. Despite the challenges in fabricating vascularized constructs, bioprinting has emerged as an advance in organ engineering. The continuous evolution of bioprinting technology and biomaterial knowledge provides an avenue to overcome the hurdles associated with vascularized tissue fabrication. This article provides an overview of the biofabrication process used to create vascular and vascularized constructs. It delves into the various techniques used in vascular engineering, including extrusion-, droplet-, and laser-based bioprinting methods. Integrating these techniques offers the prospect of crafting artificial blood vessels with remarkable precision and functionality. Therefore, the potential impact of bioprinting in vascular engineering is significant. With technological advances, it holds promise in revolutionizing organ transplantation, tissue engineering, and regenerative medicine. By mimicking the natural complexity of blood vessels, bioprinting brings us one step closer to engineering organs with functional vasculature, ushering in a new era of medical advancement.},
}

@article {pmid37882538,
year = {2023},
author = {Morreale, DP and St Geme Iii, JW and Planet, PJ},
title = {Phylogenomic analysis of the understudied Neisseriaceae species reveals a poly- and paraphyletic Kingella genus.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0312323},
doi = {10.1128/spectrum.03123-23},
pmid = {37882538},
issn = {2165-0497},
abstract = {Taxonomic classification and phylogenetic analysis of the Neisseriaceae family have focused on the pathogens Neisseria meningitidis and Neisseria gonorrhoeae. Less is known about the relationships of commensal Neisseria species and other Neisseriaceae genera, raising the possibility that the phylogeny of this family may not agree with current taxonomy. In this study, we used available nucleotide sequences and a phylogenetic approach to assess the Kingella genus and its relatives. We found that this genus is both paraphyletic and polyphyletic. Kingella potus is more closely related to Neisseria bacilliformis than to other Kingella species. The Alysiella and Simonsiella genera form a distinct clade within the Kingella genus that is closely related to the pathogens K. kingae and K. negevensis. We find a phylogenetic relationship between Conchiformibius, Alysiella, Simonsiella, and Kingella, which we name the CASK clade. Finally, we define the gene sets that differentiate each genus of the CASK clade from one another and from the rest of the Neisseriaceae family. IMPORTANCE Understanding the evolutionary relationships between the species in the Neisseriaceae family has been a persistent challenge in bacterial systematics due to high recombination rates in these species. Previous studies of this family have focused on Neisseria meningitidis and N. gonorrhoeae. However, previously understudied Neisseriaceae species are gaining new attention, with Kingella kingae now recognized as a common human pathogen and with Alysiella and Simonsiella being unique in the bacterial world as multicellular organisms. A better understanding of the genomic evolution of the Neisseriaceae can lead to the identification of specific genes and traits that underlie the remarkable diversity of this family.},
}

@article {pmid37874138,
year = {2023},
author = {Paterlini, A},
title = {A year at the forefront of plasmodesmal biology.},
journal = {Biology open},
volume = {12},
number = {10},
pages = {},
doi = {10.1242/bio.060123},
pmid = {37874138},
issn = {2046-6390},
abstract = {Cell-cell communication is a central feature of multicellular organisms, enabling division of labour and coordinated responses. Plasmodesmata are membrane-lined pores that provide regulated cytoplasmic continuity between plant cells, facilitating signalling and transport across neighboring cells. Plant development and survival profoundly depend on the existence and functioning of these structures, bringing them to the spotlight for both fundamental and applied research. Despite the rich conceptual and translational rewards in sight, however, the study of plasmodesmata poses significant challenges. This Review will mostly focus on research published between May 2022 and May 2023 and intends to provide a short overview of recent discoveries, innovations, community resources and hypotheses.},
}

@article {pmid37849208,
year = {2023},
author = {Arenzon, JJ and Peliti, L},
title = {Emergent cooperative behavior in transient compartments.},
journal = {Physical review. E},
volume = {108},
number = {3-1},
pages = {034409},
doi = {10.1103/PhysRevE.108.034409},
pmid = {37849208},
issn = {2470-0053},
mesh = {Humans ; *Cooperative Behavior ; Population Dynamics ; *Game Theory ; Biological Evolution ; },
abstract = {We introduce a minimal model of multilevel selection on structured populations, considering the interplay between game theory and population dynamics. Through a bottleneck process, finite groups are formed with cooperators and defectors sampled from an infinite pool. After the fragmentation, these transient compartments grow until the maximal number of individuals per compartment is attained. Eventually, all compartments are merged and well mixed, and the whole process is repeated. We show that cooperators, even if interacting only through mean-field intragroup interactions that favor defectors, may perform well because of the intergroup competition and the size diversity among the compartments. These cycles of isolation and coalescence may therefore be important in maintaining diversity among different species or strategies and may help to understand the underlying mechanisms of the scaffolding processes in the transition to multicellularity.},
}

Humans
*Cooperative Behavior
Population Dynamics
*Game Theory
Biological Evolution

@article {pmid37865203,
year = {2023},
author = {Liu, Y and Liu, Y and Chen, S and Liu, Y and Kong, Z and Guo, Y and Wang, H},
title = {Prenatal exposure to acetaminophen at different doses, courses and time causes testicular dysplasia in offspring mice and its mechanism.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {140496},
doi = {10.1016/j.chemosphere.2023.140496},
pmid = {37865203},
issn = {1879-1298},
abstract = {Epidemiological investigation suggested that the use of acetaminophen during pregnancy may cause offspring testicular dysplasia, but no systematic study has been conducted. In this study, Kunming mice were given acetaminophen at different doses (100/200/400 mg/kg.d), courses (single/multiple), time (second/third trimester) during pregnancy. Fetal blood and testes were collected on gestaional day 18 for detection. The results indicated abnormal testicular development in the PAcE (prenatal acetaminophen exposure) groups. The maximum diameter/cross-sectional area decreased, the interstitial space widened, and decreased proliferation/increased apoptosis were observed, especially in the high-dose, multi-course and second-trimester groups. Meanwhile, the serum testosterone level decreased in PAcE groups, and the steroid synthesis function in Leydig cells, Sertoli and spermatogenic cell function were inhibited, it was more significant in high-dose, multi-course and second-trimester groups. Furthermore, Wnt signal pathway was activated but Notch signal pathway was inhibited in the PAcE groups. Finally, in vitro experiment, acetaminophen could inhibit spermatogonial cell proliferation, enhance apoptosis, and change Wnt/Notch signal pathway. In conclusion, this study confirmed that PAcE can change fetal testicular development in a dose, course and time-dependent manner, and found that multicellular function impaired. This study provides theoretical and experimental basis for systematically elucidating the developmental toxicity of acetaminophen in testis.},
}

@article {pmid37863060,
year = {2023},
author = {Mishina, T and Chiu, MC and Hashiguchi, Y and Oishi, S and Sasaki, A and Okada, R and Uchiyama, H and Sasaki, T and Sakura, M and Takeshima, H and Sato, T},
title = {Massive horizontal gene transfer and the evolution of nematomorph-driven behavioral manipulation of mantids.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2023.09.052},
pmid = {37863060},
issn = {1879-0445},
abstract = {To complete their life cycle, a wide range of parasites must manipulate the behavior of their hosts.[1] This manipulation is a well-known example of the "extended phenotype,[2]" where genes in one organism have phenotypic effects on another organism. Recent studies have explored the parasite genes responsible for such manipulation of host behavior, including the potential molecular mechanisms.[3][,][4] However, little is known about how parasites have acquired the genes involved in manipulating phylogenetically distinct hosts.[4] In a fascinating example of the extended phenotype, nematomorph parasites have evolved the ability to induce their terrestrial insect hosts to enter bodies of water, where the parasite then reproduces. Here, we comprehensively analyzed nematomorphs and their mantid hosts, focusing on the transcriptomic changes associated with host manipulations and sequence similarity between host and parasite genes to test molecular mimicry. The nematomorph's transcriptome changed during host manipulation, whereas no distinct changes were found in mantids. We then discovered numerous possible host-derived genes in nematomorphs, and these genes were frequently up-regulated during host manipulation. Our findings suggest a possible general role of horizontal gene transfer (HGT) in the molecular mechanisms of host manipulation, as well as in the genome evolution of manipulative parasites. The evidence of HGT between multicellular eukaryotes remains scarce but is increasing and, therefore, elucidating its mechanisms will advance our understanding of the enduring influence of HGT on the evolution of the web of life.},
}

@article {pmid37862637,
year = {2023},
author = {Yin, S and Mahadevan, L},
title = {Contractility-Induced Phase Separation in Active Solids.},
journal = {Physical review letters},
volume = {131},
number = {14},
pages = {148401},
doi = {10.1103/PhysRevLett.131.148401},
pmid = {37862637},
issn = {1079-7114},
abstract = {Experiments over many decades are suggestive that the combination of cellular contractility and active phase separation in cell-matrix composites can enable spatiotemporal patterning in multicellular tissues across scales. To characterize these phenomena, we provide a general theory that incorporates active cellular contractility into the classical Cahn-Hilliard-Larché model for phase separation in passive viscoelastic solids. Within this framework, we show how a homogeneous cell-matrix mixture can be destabilized by activity via either a pitchfork or Hopf bifurcation, resulting in stable phase separation and/or traveling waves. Numerical simulations of the full equations allow us to track the evolution of the resulting self-organized patterns in periodic and mechanically constrained domains, and in different geometries. Altogether, our study underscores the importance of integrating both cellular activity and mechanical phase separation in understanding patterning in soft, active biosolids in both in vivo and in vitro settings.},
}

@article {pmid36824773,
year = {2023},
author = {Kapsetaki, SE and Compton, Z and Dolan, J and Harris, VK and Rupp, SM and Duke, EG and Harrison, TM and Aksoy, S and Giraudeau, M and Vincze, O and McGraw, KJ and Aktipis, A and Tollis, M and Boddy, AM and Maley, CC},
title = {Life history and cancer in birds: clutch size predicts cancer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {36824773},
abstract = {Cancer is a disease that affects nearly all multicellular life, including birds. However, little is known about what factors explain the variance in cancer prevalence among species. Litter size is positively correlated with cancer prevalence in managed species of mammals, and larger body size, but not incubation or nestling period, is linked to tumor prevalence in wild birds. Also, birds that produce more elaborate sexual traits are expected to have fewer resources for cancer defenses and thus higher cancer prevalence. In this study, we examined whether cancer prevalence is associated with a wide variety of life history traits (clutch size, incubation length, body mass, lifespan, and the extent of sexual dimorphism) across 108 species of managed birds in 25 different zoological facilities, sanctuaries, and veterinary clinics. We found that clutch size was positively correlated with cancer and neoplasia (both benign and malignant) prevalence, even after controlling for body mass. Cancer prevalence was not associated with incubation length, body mass, lifespan, or sexual dimorphism. The positive correlations of clutch size with cancer prevalence and neoplasia prevalence suggest that there may be life-history trade-offs between reproductive investment and somatic maintenance (in the form of cancer prevention mechanisms) in managed birds.},
}

@article {pmid37850657,
year = {2023},
author = {Ma, Q and Li, Q and Zheng, X and Pan, J},
title = {CellCommuNet: an atlas of cell-cell communication networks from single-cell RNA sequencing of human and mouse tissues in normal and disease states.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkad906},
pmid = {37850657},
issn = {1362-4962},
support = {CSTB2023NSCQ-MSX0289//Chongqing Medical University/ ; //Natural Science Foundation of Chongqing/ ; BJRC202214//Chongqing Medical University/ ; CXQT21016//University Innovation Research Group Project of Chongqing/ ; W0056//Chongqing Medical University/ ; },
abstract = {Cell-cell communication, as a basic feature of multicellular organisms, is crucial for maintaining the biological functions and microenvironmental homeostasis of cells, organs, and whole organisms. Alterations in cell-cell communication contribute to many diseases, including cancers. Single-cell RNA sequencing (scRNA-seq) provides a powerful method for studying cell-cell communication by enabling the analysis of ligand-receptor interactions. Here, we introduce CellCommuNet (http://www.inbirg.com/cellcommunet/), a comprehensive data resource for exploring cell-cell communication networks in scRNA-seq data from human and mouse tissues in normal and disease states. CellCommuNet currently includes 376 single datasets from multiple sources, and 118 comparison datasets between disease and normal samples originating from the same study. CellCommuNet provides information on the strength of communication between cells and related signalling pathways and facilitates the exploration of differences in cell-cell communication between healthy and disease states. Users can also search for specific signalling pathways, ligand-receptor pairs, and cell types of interest. CellCommuNet provides interactive graphics illustrating cell-cell communication in different states, enabling differential analysis of communication strength between disease and control samples. This comprehensive database aims to be a valuable resource for biologists studying cell-cell communication networks.},
}

@article {pmid37848052,
year = {2023},
author = {Horinouchi, Y and Togashi, T},
title = {Unicellular and multicellular developmental variations in algal zygotes produce sporophytes.},
journal = {Biology letters},
volume = {19},
number = {10},
pages = {20230313},
doi = {10.1098/rsbl.2023.0313},
pmid = {37848052},
issn = {1744-957X},
abstract = {The emergence of sporophytes, that is, diploid multicellular bodies in plants, facilitated plant diversification and the evolution of complexity. Although sporophytes may have evolved in an ancestral alga exhibiting a haplontic life cycle with a unicellular diploid and multicellular haploid (gametophyte) phase, the mechanism by which this novelty originated remains largely unknown. Ulotrichalean marine green algae (Ulvophyceae) are one of the few extant groups with haplontic-like life cycles. In this study, we show that zygotes of the ulotrichalean alga Monostroma angicava, which usually develop into unicellular cysts, exhibit a developmental variation producing multicellular reproductive sporophytes. Multicellular development likely occurred stochastically in individual zygotes, but its ratio responded plastically to growth conditions. Sporophytes showed identical morphological development to gametophytes, which should reflect the expression of the same genetic programme directing multicellular development. Considering that sporophytes were evolutionarily derived in Ulotrichales, this implies that sporophytes emerged by co-opting the gametophyte developmental programme to the diploid phase. This study suggests a possible mechanism of sporophyte formation in haplontic life cycles, contributing to the understanding of the evolutionary transition from unicellular to multicellular diploid body plans in green plants.},
}

@article {pmid37847422,
year = {2023},
author = {Baluška, F and Miller, WB and Reber, AS},
title = {Sentient cells as basic units of tissues, organs and organismal physiology.},
journal = {The Journal of physiology},
volume = {},
number = {},
pages = {},
doi = {10.1113/JP284419},
pmid = {37847422},
issn = {1469-7793},
abstract = {Cells evolved some 4 billion years ago, and since then the integrity of the structural and functional continuity of cellular life has been maintained via highly conserved and ancient processes of cell reproduction and division. The plasma membrane as well as all the cytoplasmic structures are reproduced and inherited uninterruptedly by each of the two daughter cells resulting from every cell division. Although our understanding of the evolutionary emergence of the very first cells is obscured by the extremely long timeline since that revolutionary event, the generally accepted position is that the de novo formation of cells is not possible; all present cells are products of other prior cells. This essential biological principle was first discovered by Robert Remak and then effectively coined as Omnis Cellula e Cellula (every cell of the cell) by Rudolf Virchow: all currently living cells have direct structural and functional connections to the very first cells. Based on our previous theoretical analysis, all cells are endowed with individual sentient cognition that guides their individual agency, behaviour and evolution. There is a vital consequence of this new sentient and cognitive view of cells: when cells assemble as functional tissue ecologies and organs within multicellular organisms, including plants, animals and humans, these cellular aggregates display derivative versions of aggregate tissue- and organ-specific sentience and consciousness. This innovative view of the evolution and physiology of all currently living organisms supports a singular principle: all organismal physiology is based on cellular physiology that extends from unicellular roots.},
}

@article {pmid37841858,
year = {2023},
author = {Kapsetaki, SE and Cisneros, LH and Maley, CC},
title = {Cell-in-cell phenomena across the tree of life.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-3376588/v1},
pmid = {37841858},
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 review of 508 articles to 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. 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. Therefore, we propose that cell-in-cell events originated before the origins of obligate multicellularity. Cell-in-cell events are found almost everywhere: across some unicellular and many multicellular organisms, mostly in malignant rather than benign tissue, and in non-neoplastic cells. Thus, our results show that cell-in-cell events exist in obligate multicellular organisms, but are not a defining feature of them. The idea of eradicating cell-in-cell events from obligate multicellular organisms as a way of treating cancer, without considering that cell-in-cell events are also part of normal development, should be abandoned.},
}

@article {pmid37834047,
year = {2023},
author = {Borodulina, OR and Ustyantsev, IG and Kramerov, DA},
title = {SINEs as Potential Expression Cassettes: Impact of Deletions and Insertions on Polyadenylation and Lifetime of B2 and Ves SINE Transcripts Generated by RNA Polymerase III.},
journal = {International journal of molecular sciences},
volume = {24},
number = {19},
pages = {},
doi = {10.3390/ijms241914600},
pmid = {37834047},
issn = {1422-0067},
support = {19-14-00327//Russian Scientific Foundation/ ; },
abstract = {Short Interspersed Elements (SINEs) are common in the genomes of most multicellular organisms. They are transcribed by RNA polymerase III from an internal promoter comprising boxes A and B. As transcripts of certain SINEs from mammalian genomes can be polyadenylated, such transcripts should contain the AATAAA sequence as well as those called β- and τ-signals. One of the goals of this work was to evaluate how autonomous and independent other SINE parts are β- and τ-signals. Extended regions outside of β- and τ-signals were deleted from SINEs B2 and Ves and the derived constructs were used to transfect HeLa cells in order to evaluate the relative levels of their transcripts as well as their polyadenylation efficiency. If the deleted regions affected boxes A and B, the 5'-flanking region of the U6 RNA gene with the external promoter was inserted upstream. Such substitution of the internal promoter in B2 completely restored its transcription. Almost all tested deletions/substitutions did not reduce the polyadenylation capacity of the transcripts, indicating a weak dependence of the function of β- and τ-signals on the neighboring sequences. A similar analysis of B2 and Ves constructs containing a 55-bp foreign sequence inserted between β- and τ-signals showed an equal polyadenylation efficiency of their transcripts compared to those of constructs without the insertion. The acquired poly(A)-tails significantly increased the lifetime and thus the cellular level of such transcripts. The data obtained highlight the potential of B2 and Ves SINEs as cassettes for the expression of relatively short sequences for various applications.},
}

@article {pmid37833973,
year = {2023},
author = {Hellman, L},
title = {Phenotypic and Functional Heterogeneity of Monocytes and Macrophages.},
journal = {International journal of molecular sciences},
volume = {24},
number = {19},
pages = {},
doi = {10.3390/ijms241914525},
pmid = {37833973},
issn = {1422-0067},
abstract = {Macrophages are likely to be the first immune cells to have appeared during the evolution of multicellular organisms [...].},
}

@article {pmid37832511,
year = {2023},
author = {Walker, LM and Sherpa, RN and Ivaturi, S and Brock, DA and Larsen, TJ and Walker, JR and Strassmann, JE and Queller, DC},
title = {Parallel evolution of the G protein-coupled receptor GrlG and the loss of fruiting body formation in the social amoeba Dictyostelium discoideum evolved under low relatedness.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkad235},
pmid = {37832511},
issn = {2160-1836},
abstract = {Aggregative multicellularity relies on cooperation among formerly independent cells to form a multicellular body. Previous work with Dictyostelium discoideum showed that experimental evolution under low relatedness profoundly decreased cooperation, as indicated by the loss of fruiting body formation in many clones and an increase of cheaters that contribute proportionally more to spores than to the dead stalk. Using whole-genome sequencing and variant analysis of these lines we identified 38 single nucleotide polymorphisms (SNPs) in 29 genes. Each gene had one variant except for grlG (encoding a G protein-coupled receptor), which had ten unique SNPs and five structural variants. Variants in the 5' half of grlG-the region encoding the signal peptide and the extracellular binding domain-were significantly associated with the loss of fruiting body formation; the association was not significant in the 3' half of the gene. These results suggest that the loss of grlG was adaptive under low relatedness and that at least the 5' half of the gene is important for cooperation and multicellular development. This is surprising given some previous evidence that grlG encodes a folate receptor involved in predation, which occurs only during the single-celled stage. However, non-fruiting mutants showed little increase in a parallel evolution experiment where the multicellular stage was prevented from happening. This shows that non-fruiting mutants are not generally selected by any predation advantage, but rather by something - likely cheating - during the multicellular stage.},
}

@article {pmid37817595,
year = {2023},
author = {Bourke, AFG},
title = {Conflict and conflict resolution in the major transitions.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {2008},
pages = {20231420},
doi = {10.1098/rspb.2023.1420},
pmid = {37817595},
issn = {1471-2954},
abstract = {Conflict and conflict resolution have been argued to be fundamental to the major transitions in evolution. These were key events in life's history in which previously independently living individuals cooperatively formed a higher-level individual, such as a multicellular organism or eusocial colony. Conflict has its central role because, to proceed stably, the evolution of individuality in each major transition required within-individual conflict to be held in check. This review revisits the role of conflict and conflict resolution in the major transitions, addressing recent work arguing for a minor role. Inclusive fitness logic suggests that differences between the kin structures of clones and sexual families support the absence of conflict at the origin of multicellularity but, by contrast, suggest that key conflicts existed at the origin of eusociality. A principal example is conflict over replacing the founding queen (queen replacement). Following the origin of each transition, conflict remained important, because within-individual conflict potentially disrupts the attainment of maximal individuality (organismality) in the system. The conclusion is that conflict remains central to understanding the major transitions, essentially because conflict arises from differences in inclusive fitness optima while conflict resolution can help the system attain a high degree of coincidence of inclusive fitness interests.},
}

@article {pmid37805982,
year = {2023},
author = {Germano, DPJ and Zanca, A and Johnston, ST and Flegg, JA and Osborne, JM},
title = {Free and Interfacial Boundaries in Individual-Based Models of Multicellular Biological systems.},
journal = {Bulletin of mathematical biology},
volume = {85},
number = {11},
pages = {111},
doi = {10.1007/s11538-023-01214-8},
pmid = {37805982},
issn = {1522-9602},
support = {DP200100747//Australian Research Council/ ; FT210100034//Australian Research Council/ ; DE200100998//Australian Research Council/ ; },
abstract = {Coordination of cell behaviour is key to a myriad of biological processes including tissue morphogenesis, wound healing, and tumour growth. As such, individual-based computational models, which explicitly describe inter-cellular interactions, are commonly used to model collective cell dynamics. However, when using individual-based models, it is unclear how descriptions of cell boundaries affect overall population dynamics. In order to investigate this we define three cell boundary descriptions of varying complexities for each of three widely used off-lattice individual-based models: overlapping spheres, Voronoi tessellation, and vertex models. We apply our models to multiple biological scenarios to investigate how cell boundary description can influence tissue-scale behaviour. We find that the Voronoi tessellation model is most sensitive to changes in the cell boundary description with basic models being inappropriate in many cases. The timescale of tissue evolution when using an overlapping spheres model is coupled to the boundary description. The vertex model is demonstrated to be the most stable to changes in boundary description, though still exhibits timescale sensitivity. When using individual-based computational models one should carefully consider how cell boundaries are defined. To inform future work, we provide an exploration of common individual-based models and cell boundary descriptions in frequently studied biological scenarios and discuss their benefits and disadvantages.},
}

@article {pmid37804416,
year = {2023},
author = {Sarabia-Sánchez, MA and Robles-Flores, M},
title = {WNT Signaling in Stem Cells: A Look into the Non-Canonical Pathway.},
journal = {Stem cell reviews and reports},
volume = {},
number = {},
pages = {},
pmid = {37804416},
issn = {2629-3277},
support = {IN229420 and IV200220//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; },
abstract = {Tissue homeostasis is crucial for multicellular organisms, wherein the loss of cells is compensated by generating new cells with the capacity for proliferation and differentiation. At the origin of these populations are the stem cells, which have the potential to give rise to cells with both capabilities, and persevere for a long time through the self-renewal and quiescence. Since the discovery of stem cells, an enormous effort has been focused on learning about their functions and the molecular regulation behind them. Wnt signaling is widely recognized as essential for normal and cancer stem cell. Moreover, β-catenin-dependent Wnt pathway, referred to as canonical, has gained attention, while β-catenin-independent Wnt pathways, known as non-canonical, have remained conspicuously less explored. However, recent evidence about non-canonical Wnt pathways in stem cells begins to lay the foundations of a conceivably vast field, and on which we aim to explain this in the present review. In this regard, we addressed the different aspects in which non-canonical Wnt pathways impact the properties of stem cells, both under normal conditions and also under disease, specifically in cancer.},
}

@article {pmid37799611,
year = {2023},
author = {Buschi, E and Dell'Anno, A and Tangherlini, M and Stefanni, S and Lo Martire, M and Núñez-Pons, L and Avila, C and Corinaldesi, C},
title = {Rhodobacteraceae dominate the core microbiome of the sea star Odontaster validus (Koehler, 1906) in two opposite geographical sectors of the Antarctic Ocean.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1234725},
pmid = {37799611},
issn = {1664-302X},
abstract = {Microbiota plays essential roles in the health, physiology, and in adaptation of marine multi-cellular organisms to their environment. In Antarctica, marine organisms have a wide range of unique physiological functions and adaptive strategies, useful for coping with extremely cold conditions. However, the role of microbiota associated with Antarctic organisms in such adaptive strategies is underexplored. In the present study, we investigated the diversity and putative functions of the microbiome of the sea star Odontaster validus, one of the main keystone species of the Antarctic benthic ecosystems. We compared the whole-body bacterial microbiome of sea stars from different sites of the Antarctic Peninsula and Ross Sea, two areas located in two opposite geographical sectors of the Antarctic continent. The taxonomic composition of O. validus microbiomes changed both between and within the two Antarctic sectors, suggesting that environmental and biological factors acting both at large and local scales may influence microbiome diversity. Despite this, one bacterial family (Rhodobacteraceae) was shared among all sea star individuals from the two geographical sectors, representing up to 95% of the microbial core, and suggesting a key functional role of this taxon in holobiont metabolism and well-being. In addition, the genus Roseobacter belonging to this family was also present in the surrounding sediment, implying a potential horizontal acquisition of dominant bacterial core taxa via host-selection processes from the environment.},
}

@article {pmid37797407,
year = {2023},
author = {Paloschi, V and Pauli, J and Winski, G and Wu, Z and Li, Z and Botti, L and Meucci, S and Conti, P and Rogowitz, F and Glukha, N and Hummel, N and Busch, A and Chernogubova, E and Jin, H and Sachs, N and Eckstein, HH and Dueck, A and Boon, RA and Bausch, AR and Maegdefessel, L},
title = {Utilization of an Artery-on-a-chip to Unravel Novel Regulators and Therapeutic Targets in Vascular Diseases.},
journal = {Advanced healthcare materials},
volume = {},
number = {},
pages = {e2302907},
doi = {10.1002/adhm.202302907},
pmid = {37797407},
issn = {2192-2659},
abstract = {In this study, organ-on-chip technology is used to develop an in vitro model of medium-to-large size arteries, the artery-on-a-chip (AoC), with the objective to recapitulate the structure of the arterial wall and the relevant hemodynamic forces affecting luminal cells. AoCs exposed either to in vivo-like shear stress values or kept in static conditions are assessed to generate a panel of novel genes modulated by shear stress. Considering the crucial role played by shear stress alterations in carotid arteries affected by atherosclerosis (CAD) and abdominal aortic aneurysms (AAA) disease development/progression, a patient cohort of hemodynamically relevant specimens was utilized, consisting of diseased and non-diseased (internal control) vessel regions from the same patient. Genes activated by shear stress followed the same expression pattern in non-diseased segments of human vessels. Single cell RNA sequencing enables us to discriminate the unique cell subpopulations between non-diseased and diseased vessel portions, revealing an enrichment of flow activated genes in structural cells originating from non-diseased specimens. Furthermore, the AoC served as a platform for drug-testing. It reproduced the effects of a therapeutic agent (lenvatinib) previously used in preclinical AAA studies, therefore extending our understanding of its therapeutic effect through a multicellular structure. This article is protected by copyright. All rights reserved.},
}

@article {pmid37783374,
year = {2023},
author = {Igamberdiev, AU and Gordon, R},
title = {Macroevolution, differentiation trees, and the growth of coding systems.},
journal = {Bio Systems},
volume = {},
number = {},
pages = {105044},
doi = {10.1016/j.biosystems.2023.105044},
pmid = {37783374},
issn = {1872-8324},
abstract = {An open process of evolution of multicellular organisms is based on the rearrangement and growth of the program of differentiation that underlies biological morphogenesis. The maintenance of the final (adult) stable non-equilibrium state (stasis) of a developmental system determines the direction of the evolutionary process. This state is achieved via the sequence of differentiation events representable as differentiation trees. A special type of morphogenetic code, acting as a metacode governing gene expression, may include electromechanical signals appearing as differentiation waves. The excessive energy due to the incorporation of mitochondria in eukaryotic cells resulted not only in more active metabolism but also in establishing the differentiation code for interconnecting cells and forming tissues, which fueled the evolutionary process. The "invention" of "continuing differentiation" distinguishes multicellular eukaryotes from multicellular prokaryotes. The Janus-faced control, involving both top-down control by differentiation waves and bottom-up control via the mechanical consequences of cell differentiations, underlies the process of morphogenesis and results in the achievement of functional stable final states. Duplications of branches of the differentiation tree may be the basis for continuing differentiation and macroevolution, analogous to gene duplication permitting divergence of genes. Metamorphoses, if they are proven to be fusions of disparate species, may be classified according to the topology of fusions of two differentiation trees. In the process of unfolding of morphogenetic structures, microevolution can be defined as changes of the differentiation tree that preserve topology of the tree, while macroevolution represents any change that alters the topology of the differentiation tree.},
}

@article {pmid37765506,
year = {2023},
author = {Wegner, L and Porth, ML and Ehlers, K},
title = {Multicellularity and the Need for Communication-A Systematic Overview on (Algal) Plasmodesmata and Other Types of Symplasmic Cell Connections.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {18},
pages = {},
doi = {10.3390/plants12183342},
pmid = {37765506},
issn = {2223-7747},
support = {EH 372/1-1//Deutsche Forschungsgemeinschaft/ ; },
abstract = {In the evolution of eukaryotes, the transition from unicellular to simple multicellular organisms has happened multiple times. For the development of complex multicellularity, characterized by sophisticated body plans and division of labor between specialized cells, symplasmic intercellular communication is supposed to be indispensable. We review the diversity of symplasmic connectivity among the eukaryotes and distinguish between distinct types of non-plasmodesmatal connections, plasmodesmata-like structures, and 'canonical' plasmodesmata on the basis of developmental, structural, and functional criteria. Focusing on the occurrence of plasmodesmata (-like) structures in extant taxa of fungi, brown algae (Phaeophyceae), green algae (Chlorophyta), and streptophyte algae, we present a detailed critical update on the available literature which is adapted to the present classification of these taxa and may serve as a tool for future work. From the data, we conclude that, actually, development of complex multicellularity correlates with symplasmic connectivity in many algal taxa, but there might be alternative routes. Furthermore, we deduce a four-step process towards the evolution of canonical plasmodesmata and demonstrate similarity of plasmodesmata in streptophyte algae and land plants with respect to the occurrence of an ER component. Finally, we discuss the urgent need for functional investigations and molecular work on cell connections in algal organisms.},
}

@article {pmid37748879,
year = {2023},
author = {Kurakin, G},
title = {Lipoxygenase in a Giant Sulfur Bacterium: An Evolutionary Solution for Size and Complexity?.},
journal = {Biochemistry. Biokhimiia},
volume = {88},
number = {6},
pages = {842-845},
doi = {10.1134/S0006297923060111},
pmid = {37748879},
issn = {1608-3040},
mesh = {*Lipoxygenase/genetics ; *Lipoxygenases ; Biological Evolution ; Bacteria ; Sulfur ; },
abstract = {Discovery of Thiomargarita magnifica - an exceptionally large giant sulfur bacterium - urges us to pay additional attention to the giant sulfur bacteria and to revisit our recent bioinformatic finding of lipoxygenases in the representatives of the genus Beggiatoa. These close relatives of Thiomargarita magnifica meet the similar size requirements by forming multicellular structures. We hypothesize that their lipoxygenases are a part of the oxylipin signaling system that provides high level of cell-to-cell signaling complexity which, in turn, enables them to reach large sizes.},
}

*Lipoxygenase/genetics
*Lipoxygenases
Biological Evolution
Bacteria
Sulfur

@article {pmid37747940,
year = {2023},
author = {Murali, R and Yu, H and Speth, DR and Wu, F and Metcalfe, KS and Crémière, A and Laso-Pèrez, R and Malmstrom, RR and Goudeau, D and Woyke, T and Hatzenpichler, R and Chadwick, GL and Connon, SA and Orphan, VJ},
title = {Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea.},
journal = {PLoS biology},
volume = {21},
number = {9},
pages = {e3002292},
doi = {10.1371/journal.pbio.3002292},
pmid = {37747940},
issn = {1545-7885},
abstract = {Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic (ANME) archaea in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we used comparative metagenomics and phylogenetics to investigate the metabolic adaptation among the 4 main syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a, and Seep-SRB1g) and identified features associated with their syntrophic lifestyle that distinguish them from their non-syntrophic evolutionary neighbors in the phylum Desulfobacterota. We show that the protein complexes involved in direct interspecies electron transfer (DIET) from ANME to the SRB outer membrane are conserved between the syntrophic lineages. In contrast, the proteins involved in electron transfer within the SRB inner membrane differ between clades, indicative of convergent evolution in the adaptation to a syntrophic lifestyle. Our analysis suggests that in most cases, this adaptation likely occurred after the acquisition of the DIET complexes in an ancestral clade and involve horizontal gene transfers within pathways for electron transfer (CbcBA) and biofilm formation (Pel). We also provide evidence for unique adaptations within syntrophic SRB clades, which vary depending on the archaeal partner. Among the most widespread syntrophic SRB, Seep-SRB1a, subclades that specifically partner ANME-2a are missing the cobalamin synthesis pathway, suggestive of nutritional dependency on its partner, while closely related Seep-SRB1a partners of ANME-2c lack nutritional auxotrophies. Our work provides insight into the features associated with DIET-based syntrophy and the adaptation of SRB towards it.},
}

@article {pmid37743376,
year = {2023},
author = {Zhang, Z and Huo, W and Wang, X and Ren, Z and Zhao, J and Liu, Y and He, K and Zhang, F and Li, W and Jin, S and Yang, D},
title = {Origin, evolution, and diversification of the wall-associated kinase gene family in plants.},
journal = {Plant cell reports},
volume = {},
number = {},
pages = {},
pmid = {37743376},
issn = {1432-203X},
support = {232300421116//Natural Science Foundation of Henan Province/ ; },
abstract = {The study of the origin, evolution, and diversification of the wall-associated kinase gene family in plants facilitates their functional investigations in the future. Wall-associated kinases (WAKs) make up one subfamily of receptor-like kinases (RLKs), and function directly in plant cell elongation and responses to biotic and abiotic stresses. The biological functions of WAKs have been extensively characterized in angiosperms; however, the origin and evolutionary history of the WAK family in green plants remain unclear. Here, we performed a comprehensive analysis of the WAK family to reveal its origin, evolution, and diversification in green plants. In total, 1061 WAK genes were identified in 37 species from unicellular algae to multicellular plants, and the results showed that WAK genes probably originated before bryophyte differentiation and were widely distributed in land plants, especially angiosperms. The phylogeny indicated that the land plant WAKs gave rise to five clades and underwent lineage-specific expansion after species differentiation. Cis-acting elements and expression patterns analyses of WAK genes in Arabidopsis and rice demonstrated the functional diversity of WAK genes in these two species. Many gene gains and losses have occurred in angiosperms, leading to an increase in the number of gene copies. The evolutionary trajectory of the WAK family during polyploidization was uncovered using Gossypium species. Our results provide insights into the evolution of WAK genes in green plants, facilitating their functional investigations in the future.},
}

@article {pmid37741353,
year = {2023},
author = {Ma, C and Li, X and Xiao, H and Li, B and Gu, H and Guo, Y and Wang, H and Wen, Y and Chen, L},
title = {Course-, dose-, and stage-dependent toxic effects of prenatal acetaminophen exposure on fetal long bone development.},
journal = {Toxicology letters},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.toxlet.2023.09.007},
pmid = {37741353},
issn = {1879-3169},
abstract = {Acetaminophen is a common analgesic and fever reduction medicine for pregnant women. Epidemiological studies suggest that prenatal acetaminophen usage affects offspring health and development. However, the effects of prenatal acetaminophen exposure (PAcE) on fetal long bone development and its potential mechanisms have not been elucidated. Based on clinical dosing characteristics, fetal mouse femurs were obtained for detection after oral gavage of acetaminophen at different doses (0, 100 or 400mg/kg d), courses (single or multiple times) or stages (mid- or late pregnancy) during pregnancy in Kunming mice. The results showed that compared with the control group, PAcE reduced the length of total femur and the primary ossification center (POC), delayed the mineralization of POC and the ossification of epiphyseal region, and down-regulated the mRNA expression of osteogenic function markers (such as Runx2, Bsp, Ocn, Col1a1) in fetal femur, particularly in the high dose, multiple courses, and mid-pregnancy group. Meanwhile, the osteoclast and angiogenic function were also inhibited by PAcE at high dose, multiple courses, and mid-pregnancy, but the inhibition level was less than osteogenic function. Moreover, the alteration of canonical Wnt signalling pathway in PAcE fetal bone were consistent with its osteogenesis function changes. In conclusion, PAcE caused development toxicity and multi-cellular function inhibition in fetal long bone, particularly in the high dose, multiple treatments and mid-pregnancy group, and the alteration of canonical Wnt signalling pathway may be its potential mechanism.},
}

@article {pmid37727796,
year = {2023},
author = {Craig, JM and Kumar, S and Hedges, SB},
title = {The origin of eukaryotes and rise in complexity were synchronous with the rise in oxygen.},
journal = {Frontiers in bioinformatics},
volume = {3},
number = {},
pages = {1233281},
pmid = {37727796},
issn = {2673-7647},
abstract = {The origin of eukaryotes was among the most important events in the history of life, spawning a new evolutionary lineage that led to all complex multicellular organisms. However, the timing of this event, crucial for understanding its environmental context, has been difficult to establish. The fossil and biomarker records are sparse and molecular clocks have thus far not reached a consensus, with dates spanning 2.1-0.91 billion years ago (Ga) for critical nodes. Notably, molecular time estimates for the last common ancestor of eukaryotes are typically hundreds of millions of years younger than the Great Oxidation Event (GOE, 2.43-2.22 Ga), leading researchers to question the presumptive link between eukaryotes and oxygen. We obtained a new time estimate for the origin of eukaryotes using genetic data of both archaeal and bacterial origin, the latter rarely used in past studies. We also avoided potential calibration biases that may have affected earlier studies. We obtained a conservative interval of 2.2-1.5 Ga, with an even narrower core interval of 2.0-1.8 Ga, for the origin of eukaryotes, a period closely aligned with the rise in oxygen. We further reconstructed the history of biological complexity across the tree of life using three universal measures: cell types, genes, and genome size. We found that the rise in complexity was temporally consistent with and followed a pattern similar to the rise in oxygen. This suggests a causal relationship stemming from the increased energy needs of complex life fulfilled by oxygen.},
}

@article {pmid37727086,
year = {2023},
author = {Kalambokidis, M and Travisano, M},
title = {Multispecies interactions shape the transition to multicellularity.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {2007},
pages = {20231055},
doi = {10.1098/rspb.2023.1055},
pmid = {37727086},
issn = {1471-2954},
abstract = {The origin of multicellularity transformed the adaptive landscape on Earth, opening diverse avenues for further innovation. The transition to multicellular life is understood as the evolution of cooperative groups which form a new level of individuality. Despite the potential for community-level interactions, most studies have not addressed the competitive context of this transition, such as competition between species. Here, we explore how interspecific competition shapes the emergence of multicellularity in an experimental system with two yeast species, Saccharomyces cerevisiae and Kluyveromyces lactis, where multicellularity evolves in response to selection for faster settling ability. We find that the multispecies context slows the rate of the transition to multicellularity, and the transition to multicellularity significantly impacts community composition. Multicellular K. lactis emerges first and sweeps through populations in monocultures faster than in cocultures with S. cerevisiae. Following the transition, the between-species competitive dynamics shift, likely in part to intraspecific cooperation in K. lactis. Hence, we document an eco-evolutionary feedback across the transition to multicellularity, underscoring how ecological context is critical for understanding the causes and consequences of innovation. By including two species, we demonstrate that cooperation and competition across several biological scales shapes the origin and persistence of multicellularity.},
}

@article {pmid37722687,
year = {2023},
author = {Kulkarni, M and Hardwick, JM},
title = {Programmed Cell Death in Unicellular Versus Multicellular Organisms.},
journal = {Annual review of genetics},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-genet-033123-095833},
pmid = {37722687},
issn = {1545-2948},
abstract = {Programmed cell death (self-induced) is intrinsic to all cellular life forms, including unicellular organisms. However, cell death research has focused on animal models to understand cancer, degenerative disorders, and developmental processes. Recently delineated suicidal death mechanisms in bacteria and fungi have revealed ancient origins of animal cell death that are intertwined with immune mechanisms, allaying earlier doubts that self-inflicted cell death pathways exist in microorganisms. Approximately 20 mammalian death pathways have been partially characterized over the last 35 years. By contrast, more than 100 death mechanisms have been identified in bacteria and a few fungi in recent years. However, cell death is nearly unstudied in most human pathogenic microbes that cause major public health burdens. Here, we consider how the current understanding of programmed cell death arose through animal studies and how recently uncovered microbial cell death mechanisms in fungi and bacteria resemble and differ from mechanisms of mammalian cell death. Expected final online publication date for the Annual Review of Genetics, Volume 57 is November 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
}

@article {pmid37699344,
year = {2023},
author = {Azimzadeh, J and Durand, B},
title = {Evolution: The ancient history of cilia assembly regulation.},
journal = {Current biology : CB},
volume = {33},
number = {17},
pages = {R898-R900},
doi = {10.1016/j.cub.2023.07.053},
pmid = {37699344},
issn = {1879-0445},
abstract = {A new study identifies a conserved regulatory mechanism for cilia assembly in the closest unicellular relatives of animals, suggesting that this mechanism was already present in a common unicellular ancestor and was repurposed during the transition to multicellularity.},
}

@article {pmid37679778,
year = {2023},
author = {Johnson, GA and Burghardt, RC and Bazer, FW and Seo, H and Cain, JW},
title = {Integrins and their potential roles in mammalian pregnancy.},
journal = {Journal of animal science and biotechnology},
volume = {14},
number = {1},
pages = {115},
pmid = {37679778},
issn = {1674-9782},
support = {98-35203-6337//National Institute of Food and Agriculture/ ; 2006-35203-17199//National Institute of Food and Agriculture/ ; 2012-67011-19892//National Institute of Food and Agriculture/ ; 2016-67015-24955//National Institute of Food and Agriculture/ ; 1-F32-HDO 8501 O1A1//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; 1R21HD071468-01//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; },
abstract = {Integrins are a highly complex family of receptors that, when expressed on the surface of cells, can mediate reciprocal cell-to-cell and cell-to-extracellular matrix (ECM) interactions leading to assembly of integrin adhesion complexes (IACs) that initiate many signaling functions both at the membrane and deeper within the cytoplasm to coordinate processes including cell adhesion, migration, proliferation, survival, differentiation, and metabolism. All metazoan organisms possess integrins, and it is generally agreed that integrins were associated with the evolution of multicellularity, being essential for the association of cells with their neighbors and surroundings, during embryonic development and many aspects of cellular and molecular biology. Integrins have important roles in many aspects of embryonic development, normal physiology, and disease processes with a multitude of functions discovered and elucidated for integrins that directly influence many areas of biology and medicine, including mammalian pregnancy, in particular implantation of the blastocyst to the uterine wall, subsequent placentation and conceptus (embryo/fetus and associated placental membranes) development. This review provides a succinct overview of integrin structure, ligand binding, and signaling followed with a concise overview of embryonic development, implantation, and early placentation in pigs, sheep, humans, and mice as an example for rodents. A brief timeline of the initial localization of integrin subunits to the uterine luminal epithelium (LE) and conceptus trophoblast is then presented, followed by sequential summaries of integrin expression and function during gestation in pigs, sheep, humans, and rodents. As appropriate for this journal, summaries of integrin expression and function during gestation in pigs and sheep are in depth, whereas summaries for humans and rodents are brief. Because similar models to those illustrated in Fig. 1, 2, 3, 4, 5 and 6 are present throughout the scientific literature, the illustrations in this manuscript are drafted as Viking imagery for entertainment purposes.},
}

@article {pmid37675460,
year = {2023},
author = {Chevalier, RL},
title = {Why is chronic kidney disease progressive? Evolutionary adaptations and maladaptations.},
journal = {American journal of physiology. Renal physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajprenal.00134.2023},
pmid = {37675460},
issn = {1522-1466},
abstract = {Despite significant advances in renal physiology, the global prevalence of chronic kidney disease (CKD) continues to increase. The emergence of multicellular organisms gave rise to increasing complexity of life resulting in tradeoffs reflecting ancestral adaptations to changing environments. Three evolutionary traits shape CKD over the lifespan: 1) variation in nephron number at birth, 2) progressive nephron loss with aging, and 3) adaptive kidney growth in response to decreased nephron number. Although providing plasticity in adaptation to changing environments, the cell cycle must function within constraints dictated by available energy. Prioritized allocation of energy available through the placenta can restrict fetal nephrogenesis, a risk factor for CKD. Moreover, nephron loss with aging is a consequence of cell senescence, a pathway accelerated by adaptive nephron hypertrophy that maintains metabolic homeostasis at the expense of increased vulnerability to stressors. Driven by reproductive fitness, natural selection operates in early life, but diminishes thereafter, leading to an exponential increase in CKD with aging, a product of antagonistic pleiotropy. A deeper understanding of the evolutionary constraints on the cell cycle may lead to manipulation of the balance between progenitor cell renewal and differentiation, regulation of cell senescence, and modulation of the balance between cell proliferation and hypertrophy. Application of an evolutionary perspective may enhance understanding of adaptation and maladaptation by nephrons in the progression of CKD, leading to new therapeutic advances.},
}

@article {pmid37668864,
year = {2023},
author = {Garte, S},
title = {Targeted Hypermutation as a Survival Strategy: A Theoretical Approach.},
journal = {Acta biotheoretica},
volume = {71},
number = {4},
pages = {20},
pmid = {37668864},
issn = {1572-8358},
abstract = {Targeted hypermutation has proven to be a useful survival strategy for bacteria under severe stress and is also used by multicellular organisms in specific instances such as the mammalian immune system. This might appear surprising, given the generally observed deleterious effects of poor replication fidelity/high mutation rate. A previous theoretical model designed to explore the role of replication fidelity in the origin of life was applied to a simulated hypermutation scenario. The results confirmed that the same model is useful for analyzing hypermutation and can predict the effects of the same parameters (survival probability, replication fidelity, mutation effect, and others) on the survival of cellular populations undergoing hypermutation as a result of severe stress.},
}

@article {pmid37666963,
year = {2023},
author = {Clark, JW and Hetherington, AJ and Morris, JL and Pressel, S and Duckett, JG and Puttick, MN and Schneider, H and Kenrick, P and Wellman, CH and Donoghue, PCJ},
title = {Evolution of phenotypic disparity in the plant kingdom.},
journal = {Nature plants},
volume = {},
number = {},
pages = {},
pmid = {37666963},
issn = {2055-0278},
support = {NE/N002067/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/P013678/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N002067/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N002067/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N002067/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N002067/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N002067/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N002067/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N002067/1//RCUK | Natural Environment Research Council (NERC)/ ; BB/N000919/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/T012773/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; RF-2022-167//Leverhulme Trust/ ; RPG-2019-004//Leverhulme Trust/ ; JTF 62574//John Templeton Foundation (JTF)/ ; },
abstract = {The plant kingdom exhibits diverse bodyplans, from single-celled algae to complex multicellular land plants, but it is unclear how this phenotypic disparity was achieved. Here we show that the living divisions comprise discrete clusters within morphospace, separated largely by reproductive innovations, the extinction of evolutionary intermediates and lineage-specific evolution. Phenotypic complexity correlates not with disparity but with ploidy history, reflecting the role of genome duplication in plant macroevolution. Overall, the plant kingdom exhibits a pattern of episodically increasing disparity throughout its evolutionary history that mirrors the evolutionary floras and reflects ecological expansion facilitated by reproductive innovations. This pattern also parallels that seen in the animal and fungal kingdoms, suggesting a general pattern for the evolution of multicellular bodyplans.},
}

@article {pmid37664459,
year = {2023},
author = {Marotta, P and Ruggiero, A and Bilcke, G},
title = {Editorial: Unicellular organisms as an evolutionary snapshot toward multicellularity.},
journal = {Frontiers in cell and developmental biology},
volume = {11},
number = {},
pages = {1254636},
pmid = {37664459},
issn = {2296-634X},
}

@article {pmid36993598,
year = {2023},
author = {Barker-Clarke, RJ and Gray, JM and Tadele, DS and Hinczewski, M and Scott, JG},
title = {Maintaining, masking, and mimicking selection: the interplay of cell-intrinsic and cell-extrinsic effects upon eco-evolutionary dynamics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.03.15.532871},
pmid = {36993598},
support = {R37 CA244613/CA/NCI NIH HHS/United States ; },
abstract = {Evolution is a stochastic yet inevitable process that lies at the heart of biology yet in the multi-cellular environments within patients, ecological complexities arise via heterogeneity and microenvironments. The interplay of ecology and mutation is thus fundamental to predicting the evolution of complex diseases and engineering optimal treatment solutions. As experimental evidence of ecological interactions between disease agents continues to grow, so does the need for evolutionary theory and modeling that incorporates these interaction effects. Inspired by experimental cell biology, we transform the variables in the interaction payoff matrix to encode cell-cell interactions in our mathematical approach as growth-rate modifying, frequency-dependent interactions. In this way, we can show the extent to which the presence of these cell-extrinsic ecological interactions can modify the evolutionary trajectories that would be predicted from cell-intrinsic properties alone. To do this we form a Fokker-Planck equation for a genetic population undergoing diffusion, drift, and interactions and generate a novel, analytic solution for the stationary distribution. We use this solution to determine when these interactions can modify evolution in such ways as to maintain, mask, or mimic mono-culture fitness differences. This work has implications for the interpretation and understanding of experimental and patient evolution and is a result that may help to explain the abundance of apparently neutral evolution in cancer systems and heterogeneous populations in general. In addition, the derivation of an analytical result for stochastic, ecologically dependent evolution paves the way for treatment approaches requiring knowledge of a stationary solution for the development of control protocols.},
}

@article {pmid37649301,
year = {2023},
author = {Borg, M and Krueger-Hadfield, SA and Destombe, C and Collén, J and Lipinska, A and Coelho, SM},
title = {Red macroalgae in the genomic era.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.19211},
pmid = {37649301},
issn = {1469-8137},
support = {//Bettencourt Schuller Foundation/ ; //Gordon and Betty Moore Foundation/ ; 864038//H2020 European Research Council/ ; DEB-2141971//National Science Foundation/ ; //Max Planck Society/ ; },
abstract = {Rhodophyta (or red algae) are a diverse and species-rich group that forms one of three major lineages in the Archaeplastida, a eukaryotic supergroup whose plastids arose from a single primary endosymbiosis. Red algae are united by several features, such as relatively small intron-poor genomes and a lack of cytoskeletal structures associated with motility like flagella and centrioles, as well as a highly efficient photosynthetic capacity. Multicellular red algae (or macroalgae) are one of the earliest diverging eukaryotic lineages to have evolved complex multicellularity, yet despite their ecological, evolutionary, and commercial importance, they have remained a largely understudied group of organisms. Considering the increasing availability of red algal genome sequences, we present a broad overview of fundamental aspects of red macroalgal biology and posit on how this is expected to accelerate research in many domains of red algal biology in the coming years.},
}

@article {pmid37645274,
year = {2022},
author = {Hall, G and Kelly, S and Schaap, P and Schilde, C},
title = {Phylogeny-wide analysis of G-protein coupled receptors in social amoebas and implications for the evolution of multicellularity.},
journal = {Open research Europe},
volume = {2},
number = {},
pages = {134},
pmid = {37645274},
issn = {2732-5121},
abstract = {G-protein coupled receptors (GPCRs) are seven-transmembrane proteins and constitute the largest group of receptors within eukaryotes. The presence of a large set of GPCRs in the unicellular Amoebozoa was surprising and is indicative of the largely undiscovered environmental sensing capabilities in this group. Evolutionary transitions from unicellular to multicellular lifestyles, like we see in social amoebas, have occurred several times independently in the Amoebozoa, and GPCRs may have been co-opted for new functions in cell-cell communication. Methods We have analysed a set of GPCRs from fully sequenced Amoebozoan genomes by Bayesian inference, compared their phylogenetic distribution and domain composition, and analysed their temporal and spatial expression patterns in five species of dictyostelids. Results We found evidence that most GPCRs are conserved deeply in the Amoebozoa and are probably performing roles in general cell functions and complex environmental sensing. All families of GPCRs (apart from the family 4 fungal pheromone receptors) are present in dictyostelids with family 5 being the largest and family 2 the one with the fewest members. For the first time, we identify the presence of family 1 rhodopsin-like GPCRs in dictyostelids. Some GPCRs have been amplified in the dictyostelids and in specific lineages thereof and through changes in expression patterns may have been repurposed for signalling in multicellular development. Discussion Our phylogenetic analysis suggests that GPCR families 1, 2 and 6 already diverged early in the Amoebozoa, whereas families 3 and 5 expanded later within the dictyostelids. The family 6 cAMP receptors that have experimentally supported roles in multicellular development in dictyostelids (carA-carD; tasA/B) originated at the root of all dictyostelids and only have weakly associated homologs in Physarum polycephalum. Our analysis identified candidate GPCRs which have evolved in the dictyostelids and could have been co-opted for multicellular development.},
}

@article {pmid37628687,
year = {2023},
author = {Zamani-Dahaj, SA and Burnetti, A and Day, TC and Yunker, PJ and Ratcliff, WC and Herron, MD},
title = {Spontaneous Emergence of Multicellular Heritability.},
journal = {Genes},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/genes14081635},
pmid = {37628687},
issn = {2073-4425},
support = {GM138030/GM/NIGMS NIH HHS/United States ; NNA17BB05A/NASA/NASA/United States ; },
abstract = {The major transitions in evolution include events and processes that result in the emergence of new levels of biological individuality. For collectives to undergo Darwinian evolution, their traits must be heritable, but the emergence of higher-level heritability is poorly understood and has long been considered a stumbling block for nascent evolutionary transitions. Using analytical models, synthetic biology, and biologically-informed simulations, we explored the emergence of trait heritability during the evolution of multicellularity. Prior work on the evolution of multicellularity has asserted that substantial collective-level trait heritability either emerges only late in the transition or requires some evolutionary change subsequent to the formation of clonal multicellular groups. In a prior analytical model, we showed that collective-level heritability not only exists but is usually more heritable than the underlying cell-level trait upon which it is based, as soon as multicellular groups form. Here, we show that key assumptions and predictions of that model are borne out in a real engineered biological system, with important implications for the emergence of collective-level heritability.},
}

@article {pmid37620617,
year = {2023},
author = {Savageau, MA},
title = {Phenotype Design Space Provides a Mechanistic Framework Relating Molecular Parameters to Phenotype Diversity Available for Selection.},
journal = {Journal of molecular evolution},
volume = {},
number = {},
pages = {},
pmid = {37620617},
issn = {1432-1432},
support = {MCB 1716833//National Science Foundation/ ; },
abstract = {Two long-standing challenges in theoretical population genetics and evolution are predicting the distribution of phenotype diversity generated by mutation and available for selection, and determining the interaction of mutation, selection and drift to characterize evolutionary equilibria and dynamics. More fundamental for enabling such predictions is the current inability to causally link genotype to phenotype. There are three major mechanistic mappings required for such a linking - genetic sequence to kinetic parameters of the molecular processes, kinetic parameters to biochemical system phenotypes, and biochemical phenotypes to organismal phenotypes. This article introduces a theoretical framework, the Phenotype Design Space (PDS) framework, for addressing these challenges by focusing on the mapping of kinetic parameters to biochemical system phenotypes. It provides a quantitative theory whose key features include (1) a mathematically rigorous definition of phenotype based on biochemical kinetics, (2) enumeration of the full phenotypic repertoire, and (3) functional characterization of each phenotype independent of its context-dependent selection or fitness contributions. This framework is built on Design Space methods that relate system phenotypes to genetically determined parameters and environmentally determined variables. It also has the potential to automate prediction of phenotype-specific mutation rate constants and equilibrium distributions of phenotype diversity in microbial populations undergoing steady-state exponential growth, which provides an ideal reference to which more realistic cases can be compared. Although the framework is quite general and flexible, the details will undoubtedly differ for different functions, organisms and contexts. Here a hypothetical case study involving a small molecular system, a primordial circadian clock, is used to introduce this framework and to illustrate its use in a particular case. The framework is built on fundamental biochemical kinetics. Thus, the foundation is based on linear algebra and reasonable physical assumptions, which provide numerous opportunities for experimental testing and further elaboration to deal with complex multicellular organisms that are currently beyond its scope. The discussion provides a comparison of results from the PDS framework with those from other approaches in theoretical population genetics.},
}

@article {pmid37620056,
year = {2023},
author = {Li, XG and Dai, J and Zhang, WJ and Jiang, AJ and Li, DH and Wu, LF},
title = {Genome analysis of Tepidibacter sp. SWIR-1, an anaerobic endospore-forming bacterium isolated from a deep-sea hydrothermal vent.},
journal = {Marine genomics},
volume = {71},
number = {},
pages = {101049},
doi = {10.1016/j.margen.2023.101049},
pmid = {37620056},
issn = {1876-7478},
abstract = {Tepidibacter sp. SWIR-1, a putative new species isolated from deep-sea hydrothermal vent field on the Southwest Indian Ridge (SWIR), is an anaerobic, mesophilic and endospore-forming bacterium belonging to the family Peptostreptococcaceae. In this study, we present the complete genome sequence of strain SWIR-1, consists of a single circular chromosome comprising 4,122,966 nucleotides with 29.25% G + C content and a circular plasmid comprising 38,843 nucleotides with 29.46% G + C content. In total, 3861 protein coding genes, 104 tRNA genes and 46 rRNA genes were obtained. SWIR-1 genome contains numerous genes related to sporulation and germination. Compared with the other three Tepidibacter species, SWIR-1 contained more spore germination receptor proteins. In addition, SWIR-1 contained more genes involved in chemotaxis and two-component systems than other Tepidibacter species. These results indicated that SWIR-1 has developed versatile adaptability to the Southwest Indian Ridge hydrothermal vent environment. The genome of strain SWIR-1 will be helpful for further understanding adaptive strategies used by bacteria dwelling in the deep-sea hydrothermal vent environments of different oceans.},
}

@article {pmid37609247,
year = {2023},
author = {Kasimatis, KR and Willis, JH and Phillips, PC},
title = {Post-insemination sexual selection in males indirectly masculinizes the female transcriptome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.08.09.552689},
pmid = {37609247},
abstract = {UNLABELLED: Sex-specific regulation of gene expression is the most plausible way for generating sexually differentiated phenotypes from an essentially shared genome. However, since genetic material is shared, sex-specific selection in one sex can have an indirect response in the other sex. From a gene expression perspective, this tethered response can move one sex away from their wildtype expression state and impact potentially many gene regulatory networks. Here, using experimental evolution in the model nematode Caenorhabditis elegans , we explore the coupling of direct sexual selection on males with the transcriptomic response in females over microevolutionary timescales to uncover the extent to which post-insemination reproductive traits share a genetic basis between the sexes. We find that differential gene expression is driven by female ancestral or evolved generation alone and that male generation has no impact on changes in gene expression. Almost all differentially expressed genes were downregulated in evolved females. Moreover, 80% of these gene were located on the X chromosome and have wildtype female-biased expression profiles. Changes in gene expression profiles were likely driven through trans -acting pathways that are shared between the sexes. We found no evidence that the core dosage compensation machinery was impacted by experimental evolution. Together these data suggest masculinization of the female transcriptome driven by direct selection on male sperm competitive ability. Our results indicate that on short evolutionary timescales sexual selection can generate sexual conflict in expression space.

LAY SUMMARY: Sexual selection drives the evolution of some of the most dramatic phenotypic differences between the sexes. Such sexual dimorphism is so common across multicellular organisms that we often overlook how remarkable it is for shared genetic material to create numerous and complex sex differences. At an evolutionary level, sexual dimorphism furthers the opportunity for sex-specific selection to optimize the fitness of a given sex. As a consequence, sex-specific selection, such as sexual selection, can have an indirect evolutionary response in the other sex due to genetic associations created by the sexes sharing the same genome. This correlated evolutionary response can create sexual conflict by shifting a sex away from their fitness optimum. At the functional level, sexual dimorphism is generated is through sex-specific regulation of gene expression. Bridging the evolutionary response to sexual selection with the evolution of sex-specific gene regulation during post-mating interactions has proved challenging. We previously used experimental evolution to increase male fertility by directly selecting for increased sperm competitive ability. In this study, we examined the effect of this direct selection on males on gene expression patterns in females. Differential gene expression was determined by whether a female was ancestral or evolved generation, indicating that gene expression changes were an evolved response due to indirect selection on females. Significantly differentially expressed genes were downregulated in evolved females. These genes tended to be female-biased in wildtype individuals and located on the X chromosome. The downregulation of X-linked genes suggests expression levels in females equal to or lower than that in males. Together these results indicate a less female-like transcriptome after experimental evolution. This supports a sexual conflict scenario by which direct sexual selection on males indirectly masculinizes the female transcriptome over short evolutionary timescales.},
}

@article {pmid37337232,
year = {2023},
author = {Sarkar, MMH and Rahman, MS and Islam, MR and Rahman, A and Islam, MS and Banu, TA and Akter, S and Goswami, B and Jahan, I and Habib, MA and Uddin, MM and Mia, MZ and Miah, MI and Shaikh, AA and Khan, MS},
title = {Comparative phylogenetic analysis and transcriptomic profiling of Dengue (DENV-3 genotype I) outbreak in 2021 in Bangladesh.},
journal = {Virology journal},
volume = {20},
number = {1},
pages = {127},
pmid = {37337232},
issn = {1743-422X},
mesh = {Humans ; Phylogeny ; Bangladesh/epidemiology ; *Transcriptome ; *Dengue/epidemiology ; Disease Outbreaks ; Genotype ; Serogroup ; },
abstract = {BACKGROUND: The next-generation sequencing (NGS) technology facilitates in-depth study of host-pathogen metatranscriptome. We, therefore, implicated phylodynamic and transcriptomic approaches through NGS technology to know/understand the dengue virus (DENV) origin and host response with dengue fever.

METHODS: In this study, blood serum RNA was extracted from 21 dengue patients and 3 healthy individuals. Total transcriptomic data were analyzed for phylogenetic, phylodynamic, differential express gene (DEG), and gene ontology (GO) using respective bioinformatics tools.

RESULTS: The viral genome sequence revealed dengue viral genome size ranges 10647 to 10707 nucleotide. Phylogenetic and phylodynamic analysis showed that the 2021 epidemic isolates were DENV-3 genotype-I and maintained as a new clade in compared to 2019 epidemic. Transcriptome analysis showed a total of 2686 genes were DEG in dengue patients compared to control with a q-value < 0.05. DESeq2 plot counts function of the top 24 genes with the smallest q-values of differential gene expression of RNA-seq data showed that 11 genes were upregulated, whereas 13 genes were downregulated. GO analysis showed a significant upregulation (p = < 0.001) in a process of multicellular organismal, nervous system, sensory perception of chemical stimulus, and G protein-coupled receptor signaling pathways in the dengue patients. However, there were a significant downregulation (p = < 0.001) of intracellular component, cellular anatomical entity, and protein-containing complex in dengue patients. Most importantly, there was a significant increase of a class of immunoregulatory proteins in dengue patients in compared to the controls, with increased GO of immune system process. In addition, upregulation of toll receptor (TLR) signaling pathways were found in dengue patients. These TLR pathways were particularly involved for the activation of innate system coupled with adaptive immune system that probably involved the rapid elimination of dengue virus infected cells. These differentially expressed genes could be further investigated for target based prophylactic interventions for dengue.

CONCLUSION: This is a first report describing DENV complete genomic features and differentially expressed genes in patients in Bangladesh. These genes may have diagnostic and therapeutic values for dengue infection. Continual genomic surveillance is required to further investigate the shift in dominant genotypes in relation to viral pathogenesis.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12985-023-02030-1.},
}

Humans
Phylogeny
Bangladesh/epidemiology
*Transcriptome
*Dengue/epidemiology
Disease Outbreaks
Genotype
Serogroup

@article {pmid37592065,
year = {2023},
author = {Shen, J and Paterson, GA and Wang, Y and Kirschvink, JL and Pan, Y and Lin, W},
title = {Renaissance for magnetotactic bacteria in astrobiology.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {37592065},
issn = {1751-7370},
support = {T2225011//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42293293//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42202339//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023M733478//China Postdoctoral Science Foundation/ ; NE/P017266/1//RCUK | Natural Environment Research Council (NERC)/ ; },
abstract = {Capable of forming magnetofossils similar to some magnetite nanocrystals observed in the Martian meteorite ALH84001, magnetotactic bacteria (MTB) once occupied a special position in the field of astrobiology during the 1990s and 2000s. This flourish of interest in putative Martian magnetofossils faded from all but the experts studying magnetosome formation, based on claims that abiotic processes could produce magnetosome-like magnetite crystals. Recently, the rapid growth in our knowledge of the extreme environments in which MTB thrive and their phylogenic heritage, leads us to advocate for a renaissance of MTB in astrobiology. In recent decades, magnetotactic members have been discovered alive in natural extreme environments with wide ranges of salinity (up to 90 g L[-1]), pH (1-10), and temperature (0-70 °C). Additionally, some MTB populations are found to be able to survive irradiated, desiccated, metal-rich, hypomagnetic, or microgravity conditions, and are capable of utilizing simple inorganic compounds such as sulfate and nitrate. Moreover, MTB likely emerged quite early in Earth's history, coinciding with a period when the Martian surface was covered with liquid water as well as a strong magnetic field. MTB are commonly discovered in suboxic or oxic-anoxic interfaces in aquatic environments or sediments similar to ancient crater lakes on Mars, such as Gale crater and Jezero crater. Taken together, MTB can be exemplary model microorganisms in astrobiology research, and putative ancient Martian life, if it ever occurred, could plausibly have included magnetotactic microorganisms. Furthermore, we summarize multiple typical biosignatures that can be applied for the detection of ancient MTB on Earth and extraterrestrial MTB-like life. We suggest transporting MTB to space stations and simulation chambers to further investigate their tolerance potential and distinctive biosignatures to aid in understanding the evolutionary history of MTB and the potential of magnetofossils as an extraterrestrial biomarker.},
}

@article {pmid37588220,
year = {2024},
author = {Luo, H and Birjandi, AA and Ren, F and Sun, T and Sharpe, PT and Sun, H and An, Z},
title = {Advances in oral mesenchymal stem cell-derived extracellular vesicles in health and disease.},
journal = {Genes & diseases},
volume = {11},
number = {1},
pages = {346-357},
pmid = {37588220},
issn = {2352-3042},
abstract = {Extracellular vesicles (EVs) are nano-size vesicles secreted naturally by all cells into the extracellular space and have been recognized as important cell-cell mediators in multicellular organisms. EVs contain nucleic acids, proteins, lipids, and other cellular components, regulating many basic biological processes and playing an important role in regenerative medicine and diseases. EVs can be traced to their cells of origin and exhibit a similar function. Moreover, EVs demonstrate low immunogenicity, good biocompatibility, and fewer side effects, compared to their parent cells. Mesenchymal stem cells (MSCs) are one of the most important resource cells for EVs, with a great capacity for self-renewal and multipotent differentiation, and play an essential role in stem cell therapy. The mechanism of MSC therapy was thought to be attributed to the differentiation of MSCs after targeted migration, as previously noted. However, emerging evidence shows the previously unknown role of MSC-derived paracrine factors in stem cell therapy. Especially EVs derived from oral tissue MSCs (OMSC-EVs), show more advantages than those of all other MSCs in tissue repair and regeneration, due to their lower invasiveness and easier accessibility for sample collection. Here, we systematically review the biogenesis and biological characteristics of OMSC-EVs, as well as the role of OMSC-EVs in intercellular communication. Furthermore, we discuss the potential therapeutic roles of OMSC-EVs in oral and systemic diseases. We highlight the current challenges and future directions of OMSC-EVs to focus more attention on clinical translation. We aim to provide valuable insights for the explorative clinical application of OMSC-EVs.},
}

@article {pmid37586948,
year = {2023},
author = {Shalev, O and Ye, X and Ratzke, C},
title = {Replaying the evolution of multicellularity.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2023.07.007},
pmid = {37586948},
issn = {1872-8383},
abstract = {The first organisms on Earth were presumably unicellular. At one point, evolution shaped these individual cells into multicellular organisms, which was a significant transition in the history of life on Earth. To investigate how this change happened, Bozdag et al. re-ran evolution in the lab and observed how single-celled yeast forms large multicellular aggregates.},
}

@article {pmid37565532,
year = {2023},
author = {Cervantes, S and Kesälahti, R and Kumpula, TA and Mattila, TM and Helanterä, H and Pyhäjärvi, T},
title = {Strong purifying selection in haploid tissue-specific genes of Scots pine supports the masking theory.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msad183},
pmid = {37565532},
issn = {1537-1719},
abstract = {The masking theory states that genes expressed in haploid stage will be under more efficient selection. In contrast, selection will be less efficient in genes expressed in diploid stage, where the fitness effects of recessive deleterious or beneficial mutations can be hidden from selection in heterozygous form. This difference can influence several evolutionary processes such as the maintenance of genetic variation, adaptation rate, and genetic load. Masking theory expectations have been confirmed in single-cell haploid and diploid organisms. However, in multicellular organisms, such as plants, the effects of haploid selection are not clear-cut. In plants, the great majority of studies indicating haploid selection have been carried out using male haploid tissues in angiosperms. Hence, evidence in these systems is confounded with the effects of sexual selection and intra-specific competition. Evidence from other plant groups is scarce and results show no support for the masking theory. Here we have used a gymnosperm Scots pine megagametophyte, a maternally-derived seed haploid tissue, and four diploid tissues to test the strength of purifying selection on a set of genes with tissue-specific expression. By using targeted resequencing data of those genes, we obtained estimates of genetic diversity, the site frequency spectrum of 0-fold and 4-fold sites, and inferred the distribution of fitness effects (DFE) of new mutations in haploid and diploid tissue-specific genes. Our results show that purifying selection is stronger for tissue-specific genes expressed in the haploid megagametophyte tissue, and that this signal of strong selection is not an artifact driven by high expression levels.},
}

@article {pmid37563336,
year = {2023},
author = {Mocarski, ES},
title = {Programmed Necrosis in Host Defense.},
journal = {Current topics in microbiology and immunology},
volume = {},
number = {},
pages = {},
doi = {10.1007/82_2023_264},
pmid = {37563336},
issn = {0070-217X},
abstract = {Host control over infectious disease relies on the ability of cells in multicellular organisms to detect and defend against pathogens to prevent disease. Evolution affords mammals with a wide variety of independent immune mechanisms to control or eliminate invading infectious agents. Many pathogens acquire functions to deflect these immune mechanisms and promote infection. Following successful invasion of a host, cell autonomous signaling pathways drive the production of inflammatory cytokines, deployment of restriction factors and induction of cell death. Combined, these innate immune mechanisms attract dendritic cells, neutrophils and macrophages as well as innate lymphoid cells such as natural killer cells that all help control infection. Eventually, the development of adaptive pathogen-specific immunity clears infection and provides immune memory of the encounter. For obligate intracellular pathogens such as viruses, diverse cell death pathways make a pivotal contribution to early control by eliminating host cells before progeny are produced. Pro-apoptotic caspase-8 activity (along with caspase-10 in humans) executes extrinsic apoptosis, a nonlytic form of cell death triggered by TNF family death receptors (DRs). Over the past two decades, alternate extrinsic apoptosis and necroptosis outcomes have been described. Programmed necrosis, or necroptosis, occurs when receptor interacting protein kinase 3 (RIPK3) activates mixed lineage kinase-like (MLKL), causing cell leakage. Thus, activation of DRs, toll-like receptors (TLRs) or pathogen sensor Z-nucleic acid binding protein 1 (ZBP1) initiates apoptosis as well as necroptosis if not blocked by virus-encoded inhibitors. Mammalian cell death pathways are blocked by herpesvirus- and poxvirus-encoded cell death suppressors. Growing evidence has revealed the importance of Z-nucleic acid sensor, ZBP1, in the cell autonomous recognition of both DNA and RNA virus infection. This volume will explore the detente between viruses and cells to manage death machinery and avoid elimination to support dissemination within the host animal.},
}

@article {pmid37559824,
year = {2023},
author = {Golenberg, EM and Popadić, A and Hao, W},
title = {Transcriptome analyses of leaf architecture in Sansevieria support a common genetic toolkit in the parallel evolution of unifacial leaves in monocots.},
journal = {Plant direct},
volume = {7},
number = {8},
pages = {e511},
pmid = {37559824},
issn = {2475-4455},
abstract = {Planar structures dramatically increase the surface-area-to-volume ratio, which is critically important for multicellular organisms. In this study, we utilize naturally occurring phenotypic variation among three Sansivieria species (Asperagaceae) to investigate leaf margin expression patterns that are associated with mediolateral and adaxial/abaxial development. We identified differentially expressed genes (DEGs) between center and margin leaf tissues in two planar-leaf species Sansevieria subspicata and Sansevieria trifasciata and compared these with expression patterns within the cylindrically leaved Sansevieria cylindrica. Two YABBY family genes, homologs of FILAMENTOUS FLOWER and DROOPING LEAF, are overexpressed in the center leaf tissue in the planar-leaf species and in the tissue of the cylindrical leaves. As mesophyll structure does not indicate adaxial versus abaxial differentiation, increased leaf thickness results in more water-storage tissue and enhances resistance to aridity. This suggests that the cylindrical-leaf in S. cylindrica is analogous to the central leaf tissue in the planar-leaf species. Furthermore, the congruence of the expression patterns of these YABBY genes in Sansevieria with expression patterns found in other unifacial monocot species suggests that patterns of parallel evolution may be the result of similar solutions derived from a limited developmental toolbox.},
}

@article {pmid37556606,
year = {2023},
author = {Majic, P and Payne, JL},
title = {Developmental selection and the perception of mutation bias.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msad179},
pmid = {37556606},
issn = {1537-1719},
abstract = {The notion that mutations are random relative to their fitness effects is central to the Neo-Darwinian view of evolution. However, a recent interpretation of the patterns of mutation accumulation in the genome of Arabidopsis thaliana has challenged this notion, arguing for the presence of a targeted DNA repair mechanism that causes a non-random association of mutation rates and fitness effects. Specifically, this mechanism was suggested to cause a reduction in the rates of mutations on essential genes, thus lowering the rates of deleterious mutations. Central to this argument were attempts to rule out selection at the population level. Here, we offer an alternative and parsimonious interpretation of the patterns of mutation accumulation previously attributed to mutation bias, showing how they can instead or additionally be caused by developmental selection, i.e., selection occurring at the cellular level during the development of a multicellular organism. Thus, the depletion of deleterious mutations in A. thaliana may indeed be the result of a selective process, rather than a bias in mutation. More broadly, our work highlights the importance of considering development in the interpretation of population genetic analyses of multicellular organisms, and it emphasizes that efforts to identify mechanisms involved in mutational biases should explicitly account for developmental selection.},
}

@article {pmid37551449,
year = {2023},
author = {Khan, AK and Muñoz-Castro, G and Muñoz, JJ},
title = {Single and two-cells shape analysis from energy functionals for three-dimensional vertex models.},
journal = {International journal for numerical methods in biomedical engineering},
volume = {},
number = {},
pages = {e3766},
doi = {10.1002/cnm.3766},
pmid = {37551449},
issn = {2040-7947},
support = {//Generalitat de Catalunya/ ; //Ministerio de Ciencia e Innovación/ ; //Ministry of Federal Education and Professional Training/ ; //Higher Education Commission (under the Ministry of Federal Education and Professional Training) of Pakistan/ ; CEX2018-000797-S//Spanish Ministry of Science and Innovation/ ; PID2020-116141GB-I00//Spanish Ministry of Science and Innovation/ ; 2021 SGR 01049//Catalan government Generalitat de Catalunya/ ; },
abstract = {Vertex models have been extensively used for simulating the evolution of multicellular systems, and have given rise to important global properties concerning their macroscopic rheology or jamming transitions. These models are based on the definition of an energy functional, which fully determines the cellular response and conclusions. While two-dimensional vertex models have been widely employed, three-dimensional models are far more scarce, mainly due to the large amount of configurations that they may adopt and the complex geometrical transitions they undergo. We here investigate the shape of single and two-cells configurations as a function of the energy terms, and we study the dependence of the final shape on the model parameters: namely the exponent of the term penalising cell-cell adhesion and surface contractility. In single cell analysis, we deduce analytically the radius and limit values of the contractility for linear and quadratic surface energy terms, in 2D and 3D. In two-cells systems, symmetrical and asymmetrical, we deduce the evolution of the aspect ratio and the relative radius. While in functionals with linear surface terms yield the same aspect ratio in 2D and 3D, the configurations when using quadratic surface terms are distinct. We relate our results with well-known solutions from capillarity theory, and verify our analytical findings with a three-dimensional vertex model.},
}

@article {pmid37546755,
year = {2023},
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 = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.07.25.550562},
pmid = {37546755},
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 and uncover a novel role for Hippo signaling in regulating cell density in a proliferation-independent manner.},
}

@article {pmid37540742,
year = {2023},
author = {Sartor, F and Xu, X and Popp, T and Dodd, AN and Kovács, ÁT and Merrow, M},
title = {The circadian clock of the bacterium B. subtilis evokes properties of complex, multicellular circadian systems.},
journal = {Science advances},
volume = {9},
number = {31},
pages = {eadh1308},
pmid = {37540742},
issn = {2375-2548},
mesh = {*Circadian Clocks ; Bacillus subtilis ; Circadian Rhythm ; Light ; Eukaryota ; },
abstract = {Circadian clocks are pervasive throughout nature, yet only recently has this adaptive regulatory program been described in nonphotosynthetic bacteria. Here, we describe an inherent complexity in the Bacillus subtilis circadian clock. We find that B. subtilis entrains to blue and red light and that circadian entrainment is separable from masking through fluence titration and frequency demultiplication protocols. We identify circadian rhythmicity in constant light, consistent with the Aschoff's rule, and entrainment aftereffects, both of which are properties described for eukaryotic circadian clocks. We report that circadian rhythms occur in wild isolates of this prokaryote, thus establishing them as a general property of this species, and that its circadian system responds to the environment in a complex fashion that is consistent with multicellular eukaryotic circadian systems.},
}

*Circadian Clocks
Bacillus subtilis
Circadian Rhythm
Light
Eukaryota

@article {pmid37511419,
year = {2023},
author = {Erenpreisa, J and Vainshelbaum, NM and Lazovska, M and Karklins, R and Salmina, K and Zayakin, P and Rumnieks, F and Inashkina, I and Pjanova, D and Erenpreiss, J},
title = {The Price of Human Evolution: Cancer-Testis Antigens, the Decline in Male Fertility and the Increase in Cancer.},
journal = {International journal of molecular sciences},
volume = {24},
number = {14},
pages = {},
pmid = {37511419},
issn = {1422-0067},
mesh = {Pregnancy ; Animals ; Humans ; Male ; Female ; *Testis/metabolism ; Placenta ; Spermatogenesis/genetics ; Reproduction ; *Neoplasms/genetics/metabolism ; Mammals ; Polyploidy ; Fertility/genetics ; },
abstract = {The increasing frequency of general and particularly male cancer coupled with the reduction in male fertility seen worldwide motivated us to seek a potential evolutionary link between these two phenomena, concerning the reproductive transcriptional modules observed in cancer and the expression of cancer-testis antigens (CTA). The phylostratigraphy analysis of the human genome allowed us to link the early evolutionary origin of cancer via the reproductive life cycles of the unicellulars and early multicellulars, potentially driving soma-germ transition, female meiosis, and the parthenogenesis of polyploid giant cancer cells (PGCCs), with the expansion of the CTA multi-families, very late during their evolution. CTA adaptation was aided by retrovirus domestication in the unstable genomes of mammals, for protecting male fertility in stress conditions, particularly that of humans, as compensation for the energy consumption of a large complex brain which also exploited retrotransposition. We found that the early and late evolutionary branches of human cancer are united by the immunity-proto-placental network, which evolved in the Cambrian and shares stress regulators with the finely-tuned sex determination system. We further propose that social stress and endocrine disruption caused by environmental pollution with organic materials, which alter sex determination in male foetuses and further spermatogenesis in adults, bias the development of PGCC-parthenogenetic cancer by default.},
}

Pregnancy
Animals
Humans
Male
Female
*Testis/metabolism
Placenta
Spermatogenesis/genetics
Reproduction
*Neoplasms/genetics/metabolism
Mammals
Polyploidy
Fertility/genetics

@article {pmid37498572,
year = {2023},
author = {Ma, X and Shi, X and Wang, Q and Zhao, M and Zhang, Z and Zhong, B},
title = {A reinvestigation of multiple independent evolution and Triassic-Jurassic origin of multicellular Volvocine algae.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evad142},
pmid = {37498572},
issn = {1759-6653},
abstract = {The evolution of multicellular organisms is considered to be a major evolutionary transition, profoundly affecting the ecology and evolution of nearly all life on earth. The volvocine algae, a unique clade of chlorophytes with diverse cell morphology, provide an appealing model for investigating the evolution of multicellularity and development. However, the phylogenetic relationship and timescale of the volvocine algae are not fully resolved. Here, we use extensive taxon and gene sampling to reconstruct the phylogeny of the volvocine algae. Our results support that the colonial volvocine algae are not monophyletic group, and multicellularity independently evolve at least twice in the volvocine algae, once in Tetrabaenaceae and another in the Goniaceae + Volvocaceae. The simulation analyses suggest that incomplete lineage sorting is a major factor for the tree topology discrepancy, which imply that the multispecies coalescent model better fits the data used in this study. The coalescent-based species tree supports that the Goniaceae is monophyletic, and Crucicarteria is the earliest diverging lineage, followed by Hafniomonas and Radicarteria within the Volvocales. By considering the multiple uncertainties in divergence time estimation, the dating analyses indicate that the volvocine algae occurred during the Cryogenian to Ediacaran (696.6-551.1 Ma), and multicellularity in the volvocine algae originated from the Triassic to Jurassic. Our phylogeny and timeline provide an evolutionary framework for studying the evolution of key traits and the origin of multicellularity in the volvocine algae.},
}

@article {pmid37494396,
year = {2023},
author = {Fichman, Y and Rowland, L and Oliver, MJ and Mittler, R},
title = {ROS are evolutionary conserved cell-to-cell stress signals.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {31},
pages = {e2305496120},
pmid = {37494396},
issn = {1091-6490},
support = {R01 GM111364/GM/NIGMS NIH HHS/United States ; GM111364/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Reactive Oxygen Species ; *Hydrogen Peroxide ; *Signal Transduction ; Cell Communication ; Plants ; Mammals ; },
abstract = {Cell-to-cell communication is fundamental to multicellular organisms and unicellular organisms living in a microbiome. It is thought to have evolved as a stress- or quorum-sensing mechanism in unicellular organisms. A unique cell-to-cell communication mechanism that uses reactive oxygen species (ROS) as a signal (termed the "ROS wave") was identified in flowering plants. This process is essential for systemic signaling and plant acclimation to stress and can spread from a small group of cells to the entire plant within minutes. Whether a similar signaling process is found in other organisms is however unknown. Here, we report that the ROS wave can be found in unicellular algae, amoeba, ferns, mosses, mammalian cells, and isolated hearts. We further show that this process can be triggered in unicellular and multicellular organisms by a local stress or H2O2 treatment and blocked by the application of catalase or NADPH oxidase inhibitors and that in unicellular algae it communicates important stress-response signals between cells. Taken together, our findings suggest that an active process of cell-to-cell ROS signaling, like the ROS wave, evolved before unicellular and multicellular organisms diverged. This mechanism could have communicated an environmental stress signal between cells and coordinated the acclimation response of many different cells living in a community. The finding of a signaling process, like the ROS wave, in mammalian cells further contributes to our understanding of different diseases and could impact the development of drugs that target for example cancer or heart disease.},
}

Animals
Reactive Oxygen Species
*Hydrogen Peroxide
*Signal Transduction
Cell Communication
Plants
Mammals

@article {pmid37492150,
year = {2023},
author = {Capp, JP and Thomas, F and Marusyk, A and M Dujon, A and Tissot, S and Gatenby, R and Roche, B and Ujvari, B and DeGregori, J and Brown, JS and Nedelcu, AM},
title = {The paradox of cooperation among selfish cancer cells.},
journal = {Evolutionary applications},
volume = {16},
number = {7},
pages = {1239-1256},
pmid = {37492150},
issn = {1752-4571},
abstract = {It is traditionally assumed that during cancer development, tumor cells abort their initially cooperative behavior (i.e., cheat) in favor of evolutionary strategies designed solely to enhance their own fitness (i.e., a "selfish" life style) at the expense of that of the multicellular organism. However, the growth and progress of solid tumors can also involve cooperation among these presumed selfish cells (which, by definition, should be noncooperative) and with stromal cells. The ultimate and proximate reasons behind this paradox are not fully understood. Here, in the light of current theories on the evolution of cooperation, we discuss the possible evolutionary mechanisms that could explain the apparent cooperative behaviors among selfish malignant cells. In addition to the most classical explanations for cooperation in cancer and in general (by-product mutualism, kin selection, direct reciprocity, indirect reciprocity, network reciprocity, group selection), we propose the idea that "greenbeard" effects are relevant to explaining some cooperative behaviors in cancer. Also, we discuss the possibility that malignant cooperative cells express or co-opt cooperative traits normally expressed by healthy cells. We provide examples where considerations of these processes could help understand tumorigenesis and metastasis and argue that this framework provides novel insights into cancer biology and potential strategies for cancer prevention and treatment.},
}

@article {pmid37481773,
year = {2023},
author = {Evans, JA and Schwartz, WJ},
title = {On the origin and evolution of the dual oscillator model underlying the photoperiodic clockwork in the suprachiasmatic nucleus.},
journal = {Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology},
volume = {},
number = {},
pages = {},
pmid = {37481773},
issn = {1432-1351},
support = {R01GM143545/NH/NIH HHS/United States ; },
abstract = {Decades have now passed since Colin Pittendrigh first proposed a model of a circadian clock composed of two coupled oscillators, individually responsive to the rising and setting sun, as a flexible solution to the challenge of behavioral and physiological adaptation to the changing seasons. The elegance and predictive power of this postulation has stimulated laboratories around the world in searches to identify and localize such hypothesized evening and morning oscillators, or sets of oscillators, in insects, rodents, and humans, with experimental designs and approaches keeping pace over the years with technological advances in biology and neuroscience. Here, we recount the conceptual origin and highlight the subsequent evolution of this dual oscillator model for the circadian clock in the mammalian suprachiasmatic nucleus; and how, despite our increasingly sophisticated view of this multicellular pacemaker, Pittendrigh's binary conception has remained influential in our clock models and metaphors.},
}

@article {pmid37481138,
year = {2023},
author = {Corallo, D and Dalla Vecchia, M and Lazic, D and Taschner-Mandl, S and Biffi, A and Aveic, S},
title = {The molecular basis of tumor metastasis and current approaches to decode targeted migration-promoting events in pediatric neuroblastoma.},
journal = {Biochemical pharmacology},
volume = {215},
number = {},
pages = {115696},
doi = {10.1016/j.bcp.2023.115696},
pmid = {37481138},
issn = {1873-2968},
abstract = {Cell motility is a crucial biological process that plays a critical role in the development of multicellular organisms and is essential for tissue formation and regeneration. However, uncontrolled cell motility can lead to the development of various diseases, including neoplasms. In this review, we discuss recent advances in the discovery of regulatory mechanisms underlying the metastatic spread of neuroblastoma, a solid pediatric tumor that originates in the embryonic migratory cells of the neural crest. The highly motile phenotype of metastatic neuroblastoma cells requires targeting of intracellular and extracellular processes, that, if affected, would be helpful for the treatment of high-risk patients with neuroblastoma, for whom current therapies remain inadequate. Development of new potentially migration-inhibiting compounds and standardized preclinical approaches for the selection of anti-metastatic drugs in neuroblastoma will also be discussed.},
}

@article {pmid37475643,
year = {2023},
author = {Kato, D and Aoyama, Y and Nishida, K and Takahashi, Y and Sakamoto, T and Takeda, I and Tatematsu, T and Go, S and Saito, Y and Kunishima, S and Cheng, J and Hou, L and Tachibana, Y and Sugio, S and Kondo, R and Eto, F and Sato, S and Moorhouse, AJ and Yao, I and Kadomatsu, K and Setou, M and Wake, H},
title = {Regulation of lipid synthesis in myelin modulates neural activity and is required for motor learning.},
journal = {Glia},
volume = {},
number = {},
pages = {},
doi = {10.1002/glia.24441},
pmid = {37475643},
issn = {1098-1136},
support = {JPMJCR1755//Core Research for Evolutional Science and Technology/ ; JPMJCR22P6//Core Research for Evolutional Science and Technology/ ; 20H05699//Grants-in-Aid for Transformative Research Areas (A)/ ; 21H05587//Grants-in-Aid for Transformative Research Areas (A)/ ; JP23gm1410011 h0002//Japan Agency for Medical Research and Development/ ; JP22ak0101150//Japan Agency for Medical Research and Development/ ; 26710004//Grants-in-Aid for Young Scientists (A)/ ; JPMJFR2145//FOREST program/ ; 20K16574//Grants-in-Aid for Young Scientists/ ; //Nagoya University CIBoG WISE program from MEXT/ ; 25110732//Grants-in-Aid for Scientific Research on Innovative Areas/ ; 19H05219//Grants-in-Aid for Scientific Research on Innovative Areas/ ; 19H04753//Grants-in-Aid for Scientific Research on Innovative Areas/ ; 20KK0170//Fostering Joint International Research (B)/ ; 21H02662//Grants-in-Aid for Scientific Research (B)/ ; 18H02598//Grants-in-Aid for Scientific Research (B)/ ; },
abstract = {Brain function relies on both rapid electrical communication in neural circuitry and appropriate patterns or synchrony of neural activity. Rapid communication between neurons is facilitated by wrapping nerve axons with insulation by a myelin sheath composed largely of different lipids. Recent evidence has indicated that the extent of myelination of nerve axons can adapt based on neural activity levels and this adaptive myelination is associated with improved learning of motor tasks, suggesting such plasticity may enhance effective learning. In this study, we examined whether another aspect of myelin plasticity-changes in myelin lipid synthesis and composition-may also be associated with motor learning. We combined a motor learning task in mice with in vivo two-photon imaging of neural activity in the primary motor cortex (M1) to distinguish early and late stages of learning and then probed levels of some key myelin lipids using mass spectrometry analysis. Sphingomyelin levels were elevated in the early stage of motor learning while galactosylceramide levels were elevated in the middle and late stages of motor learning, and these changes were correlated across individual mice with both learning performance and neural activity changes. Targeted inhibition of oligodendrocyte-specific galactosyltransferase expression, the enzyme that synthesizes myelin galactosylceramide, impaired motor learning. Our results suggest regulation of myelin lipid composition could be a novel facet of myelin adaptations associated with learning.},
}

@article {pmid37468829,
year = {2023},
author = {Vroomans, RMA and Colizzi, ES},
title = {Evolution of selfish multicellularity: collective organisation of individual spatio-temporal regulatory strategies.},
journal = {BMC ecology and evolution},
volume = {23},
number = {1},
pages = {35},
pmid = {37468829},
issn = {2730-7182},
mesh = {Animals ; *Biological Evolution ; *Reproduction ; Cell Differentiation ; },
abstract = {BACKGROUND: The unicellular ancestors of modern-day multicellular organisms were remarkably complex. They had an extensive set of regulatory and signalling genes, an intricate life cycle and could change their behaviour in response to environmental changes. At the transition to multicellularity, some of these behaviours were co-opted to organise the development of the nascent multicellular organism. Here, we focus on the transition to multicellularity before the evolution of stable cell differentiation, to reveal how the emergence of clusters affects the evolution of cell behaviour.

RESULTS: We construct a computational model of a population of cells that can evolve the regulation of their behavioural state - either division or migration - and study both a unicellular and a multicellular context. Cells compete for reproduction and for resources to survive in a seasonally changing environment. We find that the evolution of multicellularity strongly determines the co-evolution of cell behaviour, by altering the competition dynamics between cells. When adhesion cannot evolve, cells compete for survival by rapidly migrating towards resources before dividing. When adhesion evolves, emergent collective migration alleviates the pressure on individual cells to reach resources. This allows individual cells to maximise their own replication. Migrating adhesive clusters display striking patterns of spatio-temporal cell state changes that visually resemble animal development.

CONCLUSIONS: Our model demonstrates how emergent selection pressures at the onset of multicellularity can drive the evolution of cellular behaviour to give rise to developmental patterns.},
}

Animals
*Biological Evolution
*Reproduction
Cell Differentiation

@article {pmid37465696,
year = {2023},
author = {Narayanan, SA},
title = {Gravity's effect on biology.},
journal = {Frontiers in physiology},
volume = {14},
number = {},
pages = {1199175},
pmid = {37465696},
issn = {1664-042X},
abstract = {Gravity is a fundamental interaction that permeates throughout our Universe. On Earth, gravity gives weight to physical objects, and has been a constant presence throughout terrestrial biological evolution. Thus, gravity has shaped all biological functions, some examples include the growth of plants (e.g., gravitropism), the structure and morphology of biological parts in multicellular organisms, to its effects on our physiological function when humans travel into space. Moreover, from an evolutionary perspective, gravity has been a constant force on biology, and life, to our understanding, should have no reason to not experience the effects of gravity. Interestingly, there appear to be specific biological mechanisms that activate in the absence of gravity, with the space environment the only location to study the effects of a lack of gravity on biological systems. Thus, in this perspective piece, biological adaptations from the cellular to the whole organism levels to the presence and absence of gravity will be organized and described, as well as outlining future areas of research for gravitational biological investigations to address. Up to now, we have observed and shown how gravity effects biology at different levels, with a few examples including genetic (e.g., cell cycle, metabolism, signal transduction associated pathways, etc.), biochemically (e.g., cytoskeleton, NADPH oxidase, Yes-associated protein, etc.), and functionally (e.g., astronauts experiencing musculoskeletal and cardiovascular deconditioning, immune dysfunction, etc., when traveling into space). Based from these observations, there appear to be gravity-sensitive and specific pathways across biological organisms, though knowledge gaps of the effects of gravity on biology remain, such as similarities and differences across species, reproduction, development, and evolutionary adaptations, sex-differences, etc. Thus, here an overview of the literature is provided for context of gravitational biology research to-date and consideration for future studies, as we prepare for long-term occupation of low-Earth Orbit and cis-Lunar space, and missions to the Moon and Mars, experiencing the effects of Lunar and Martian gravity on biology, respectively, through our Artemis program.},
}

@article {pmid37461608,
year = {2023},
author = {Compton, Z and Harris, V and Mellon, W and Rupp, S and Mallo, D and Kapsetaki, S and Wilmot, M and Kennington, R and Noble, K and Baciu, C and Ramirez, L and Peraza, A and Martins, B and Sudhakar, S and Aksoy, S and Furukawa, G and Vincze, O and Giraudeau, M and Duke, E and Spiro, S and Flach, E and Davidson, H and Zehnder, A and Graham, T and Troan, B and Harrison, T and Tollis, M and Schiffman, J and Aktipis, A and Abegglen, L and Maley, C and Boddy, A},
title = {Cancer Prevalence Across Vertebrates.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {37461608},
abstract = {Cancer is pervasive across multicellular species, but what explains differences in cancer prevalence across species? Using 16,049 necropsy records for 292 species spanning three clades (amphibians, sauropsids and mammals) we found that neoplasia and malignancy prevalence increases with adult weight (contrary to Peto's Paradox) and somatic mutation rate, but decreases with gestation time. Evolution of cancer susceptibility appears to have undergone sudden shifts followed by stabilizing selection. Outliers for neoplasia prevalence include the common porpoise (<1.3%), the Rodrigues fruit bat (<1.6%) the black-footed penguin (<0.4%), ferrets (63%) and opossums (35%). Discovering why some species have particularly high or low levels of cancer may lead to a better understanding of cancer syndromes and novel strategies for the management and prevention of cancer.},
}

@article {pmid37459530,
year = {2023},
author = {Xu, H and Nejad, MR and Yeomans, JM and Wu, Y},
title = {Geometrical control of interface patterning underlies active matter invasion.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {30},
pages = {e2219708120},
pmid = {37459530},
issn = {1091-6490},
mesh = {*Bacteria ; },
abstract = {Interaction between active materials and the boundaries of geometrical confinement is key to many emergent phenomena in active systems. For living active matter consisting of animal cells or motile bacteria, the confinement boundary is often a deformable interface, and it has been unclear how activity-induced interface dynamics might lead to morphogenesis and pattern formation. Here, we studied the evolution of bacterial active matter confined by a deformable boundary. We found that an ordered morphological pattern emerged at the interface characterized by periodically spaced interfacial protrusions; behind the interfacial protrusions, bacterial swimmers self-organized into multicellular clusters displaying +1/2 nematic defects. Subsequently, a hierarchical sequence of transitions from interfacial protrusions to creeping branches allowed the bacterial active drop to rapidly invade surrounding space with a striking self-similar branch pattern. We found that this interface patterning is geometrically controlled by the local curvature of the interface, a phenomenon we denote as collective curvature sensing. Using a continuum active model, we revealed that the collective curvature sensing arises from enhanced active stresses near high-curvature regions, with the active length scale setting the characteristic distance between the interfacial protrusions. Our findings reveal a protrusion-to-branch transition as a unique mode of active matter invasion and suggest a strategy to engineer pattern formation of active materials.},
}

*Bacteria

@article {pmid37445995,
year = {2023},
author = {Endres, K and Friedland, K},
title = {Talk to Me-Interplay between Mitochondria and Microbiota in Aging.},
journal = {International journal of molecular sciences},
volume = {24},
number = {13},
pages = {},
pmid = {37445995},
issn = {1422-0067},
mesh = {*Gastrointestinal Microbiome/physiology ; *Microbiota ; Mitochondria ; Bacteria/metabolism ; },
abstract = {The existence of mitochondria in eukaryotic host cells as a remnant of former microbial organisms has been widely accepted, as has their fundamental role in several diseases and physiological aging. In recent years, it has become clear that the health, aging, and life span of multicellular hosts are also highly dependent on the still-residing microbiota, e.g., those within the intestinal system. Due to the common evolutionary origin of mitochondria and these microbial commensals, it is intriguing to investigate if there might be a crosstalk based on preserved common properties. In the light of rising knowledge on the gut-brain axis, such crosstalk might severely affect brain homeostasis in aging, as neuronal tissue has a high energy demand and low tolerance for according functional decline. In this review, we summarize what is known about the impact of both mitochondria and the microbiome on the host's aging process and what is known about the aging of both entities. For a long time, bacteria were assumed to be immortal; however, recent evidence indicates their aging and similar observations have been made for mitochondria. Finally, we present pathways by which mitochondria are affected by microbiota and give information about therapeutic anti-aging approaches that are based on current knowledge.},
}

*Gastrointestinal Microbiome/physiology
*Microbiota
Mitochondria
Bacteria/metabolism