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Simon, C.

Publications and source records attributed to Simon, C..

At least 37 records · Page 2Linked to original sources

Global genomics of the man-o'-war (Physalia) reveal biodiversity at the ocean surface

The open ocean is a vast, highly connected environment, and the organisms found there have been hypothesized to represent massive, well-mixed populations. Of these, the Portuguese man-o-war (Physalia) is uniquely suited to dispersal, sailing the ocean surface with a muscular crest. We tested the hypothesis of a single, panmictic Physalia population by sequencing 133 genomes, and found five distinct lineages, with multiple lines of evidence showing strong reproductive isolation despite range overlap. We then scored thousands of citizen-science photos and identified four recognizable morphologies linked to these lineages. Within lineages, we detected regionally endemic subpopulations, connected by winds and currents, and identified individual long-distance dispersal events. We find that, even in these sailing species, genetic variation is highly partitioned geographically across the open ocean. SummaryThe open ocean is a vast and highly connected environment. The organisms that live there have a significant capacity for dispersal and few geographic boundaries to separate populations. Of these, the Portuguese man-o-war or bluebottle (genus Physalia) is uniquely suited to long-distance travel, using its gas-filled float and muscular crest to catch the wind and sail the sea surface. Physalia are distributed across the globe, and like many pelagic organisms, have been hypothesized to represent a massive, well-mixed population that extends across ocean basins. We tested this hypothesis by sequencing whole genomes of 133 samples collected from waters of over a dozen countries around the globe. Our results revealed five distinct lineages, with multiple lines of evidence indicating strong reproductive isolation, despite regions of range overlap. We combined these data with an independent dataset of thousands of images of Physalia uploaded to the citizen-science website inaturalist.org, which we scored for morphological characters including sail size, tentacle arrangement, and color. From these images, we identified four recognizable morphologies, described their geographical distribution, and linked them to four of the lineages identified with genomic data. We conclude there are at least four species, three of which correspond to species proposed by scientists in the 18th and 19th centuries: P. physalis, P utriculus, and P. megalista, along with one as yet unnamed species Physalia sp. from the Tasman Sea. Within each species, we observe significant population structure, with evidence of persistent subpopulations at a regional scale, as well as evidence for individual long-distance dispersal events. Our findings indicate that, instead of one well-mixed, cosmopolitan species, there are in fact multiple Physalia species with distinct but overlapping ranges, each made up of regionally endemic subpopulations that are connected by major ocean currents and wind patterns.

zoology↗

The Radical Pair Mechanism Cannot Explain Telecommunication Frequency Effects on Reactive Oxygen Species

In order to investigate whether the radical pair mechanism (RPM) can explain the effects of telecommunication frequency radiation on reactive oxygen species production, we modelled the effects of oscillating magnetic fields on radical pair systems. Our analysis indicates that the RPM cannot account for the biological effects observed under exposure to telecommunication frequencies due to negligible effects under low-amplitude conditions used in experimental setups. Observable effects on radical pairs at these frequencies would require hyperfine coupling constants that are precisely fine-tuned to large values that far exceed those naturally occurring within biological systems. We conclude that some other mechanism must be responsible for the effects of telecommunication frequency fields in biological systems.

biophysics↗

Quantum theory of a potential biological magnetic field sensor: radical pair mechanism in flavin adenine dinucleotide biradicals

Recent studies in vitro and in vivo suggest that flavin adenine dinucleotide (FAD) on its own might be able to act as a biological magnetic field sensor. Motivated by these observations, in this study, we develop a detailed quantum theoretical model for the radical pair mechanism (RPM) for the flavin adenine biradical within the FAD molecule. We perform molecular dynamics simulations to determine the distance between the radicals on FAD, which we then feed into a quantum master equation treatment of the RPM. In contrast to previous semi-classical models which are limited to the low-field and high-field cases, our quantum model can predict the full magnetic field dependence of the transient absorption signal. Our models predictions are consistent with experiments.

biophysics↗

The recombination landscape of the barn owl, from families to populations

Homologous recombination is a meiotic process that generates diversity along the genome and interacts with all evolutionary forces. Despite its importance, studies of recombination landscapes are lacking due to methodological limitations and a dearth of appropriate data. Linkage mapping based on familial data gives unbiased sex-specific broad-scale estimates of recombination while linkage disequilibrium (LD) based inference based on population data provides finer resolution data albeit depending on the effective population size and acting selective forces. In this study, we use a combination of these two methods, using a dataset of whole genome sequences and elucidate the recombination landscape for the Afro-European barn owl (Tyto alba). Linkage mapping allows us to refine the genome assembly to a chromosome-level quality. We find subtle differences in crossover placement between sexes that leads to differential effective shuffling of alleles. LD based estimates of recombination are concordant with family-based estimates and identify large variation in recombination rates within and among linkage groups. Larger chromosomes show variation in recombination rates while smaller chromosomes have a universally high rate which shapes the diversity landscape. We also identify local recombination hotspots in accordance with other studies in birds lacking the PRDM9 gene. However these hotspots show very little evolutionary stability when compared among populations with shallow genetic differentiation. Overall, this comprehensive analysis enhances our understanding of recombination dynamics, genomic architecture, and sex-specific variation in the barn owl, contributing valuable insights to the broader field of avian genomics. Article summaryTo study recombination events we look either in family data or in population data, with each method having advantages over the other. In this study we use both approaches to quantify the barn owl recombination landscape. We find that differences exist between sexes, populations and chromosomes.

genomics↗

Radical pairs and superoxide amplification can explain magnetic field effects on planarian regeneration

Weak magnetic field exposure can affect many biological processes across a wide range of living organisms. Recently, it has been observed that weak magnetic fields can modulate reactive oxygen species (ROS) concentration, affecting regeneration in planaria. These effects show unusual nonlinear dependence on magnetic field strength, including a sign change. In another study by the same group, superoxide is identified as the particular ROS being modulated. We propose a radical pair mechanism based on a flavin-superoxide radical pair to explain the modulation of superoxide production and its effect on planarian regeneration. The results of our calculations favor a triplet-born radical pair. Our yield calculations can reproduce the observed magnetic field dependence, including the sign change. Moreover, to explain the size of the effect on ROS concentration, we suggest a simple amplification model inspired by known biochemical mechanisms and lay out the conditions for such a model to work. Further, we also make empirical predictions concerning the hypomagnetic field effects on planarian regeneration.

biophysics↗

Radical Pair Model for Magnetic Field Effects on NMDA Receptor Activity

The N-methyl-D-aspartate receptor is a prominent player in brain development and functioning. Perturbations to its functioning through external stimuli like magnetic fields can potentially affect the brain in numerous ways. Various studies have shown that magnetic fields of varying strengths affect these receptors. We propose that the radical pair mechanism, a quantum mechanical process, could explain some of these field effects. Radicals of the form [RO* Mg(H2O)n+*], where R is a protein residue that can be Serine or Tyrosine, are considered for this study. The variation in the singlet fractional yield of the radical pairs, as a function of magnetic field strength, is calculated to understand how the magnetic field affects the products of the radical pair reactions. Based on the results, the radical pair mechanism is a likely candidate for explaining the magnetic field effects observed on the receptor activity. The model predicts changes in the behaviour of the system as magnetic field strength is varied and also predicts certain isotope effects. The results further suggest that similar effects on radical pairs could be a plausible explanation for various magnetic field effects within the brain.

biophysics↗

SAMD1 suppresses epithelial-mesenchymal transition (EMT) pathways in pancreatic ductal adenocarcinoma

SAMD1 (SAM-domain containing protein 1), a CpG island-binding protein, plays a pivotal role in the repression of its target genes. Despite its significant correlation with outcomes in various tumor types, the role of SAMD1 in cancer has remained largely unexplored. In this study we focused on pancreatic ductal adenocarcinoma (PDAC) and revealed that SAMD1 acts as a repressor of genes associated with epithelial-mesenchymal transition (EMT). Upon deletion of SAMD1 in PDAC cells, we observed significantly increased migration rates. SAMD1 exerts its effects by binding to specific genomic targets, including CDH2, encoding N-cadherin, which emerged as a driver of enhanced migration upon SAMD1 knockout. Furthermore, we discovered the FBXO11-containing E3 ubiquitin ligase complex as an interactor of SAMD1. FBXO11 ubiquitinates SAMD1 within its DNA-binding winged helix domain and inhibits SAMD1 chromatin binding genome-wide. High FBXO11 expression in PDAC is associated with poor prognosis and increased expression of EMT-related genes, underlining an antagonistic relationship between SAMD1 and FBXO11. In summary, our findings provide new insights into the regulation of EMT-related genes in PDAC, shedding light on the intricate role of SAMD1 and its interplay with FBXO11 in this cancer type.

molecular biology↗

Effect of Aging on the Human Myometrium at Single-Cell Resolution

The myometrial dysfunction associated with aging can prompt complications during pregnancy and labor, causing a 7.8-fold increase in maternal mortality in women over 40. Using single-cell/single-nucleus RNA sequencing and spatial transcriptomics, we constructed a cellular atlas of the aging myometrium from 186,120 cells across twenty peri- and post-menopausal women. We identified 23 myometrial cell subpopulations, including novel contractile capillary, venous capillary, immune-modulated fibroblasts, and nervous system regulatory fibroblasts. Myometrial aging leads to fewer contractile capillary cells, a reduced level of ion channel expression in smooth muscle cells, and impaired gene expression in endothelial, smooth muscle, fibroblast, perivascular, and immune cells. We observed altered myometrial cell-to-cell communication as an aging hallmark associated with the loss of 25/229 signaling pathways, including those related to angiogenesis, tissue repair, contractility, immunity, and nervous system regulation. These insights may contribute to a better understanding of the complications faced by older women during pregnancy and labor.

cell biology↗

Nuclear lamin A/C phosphorylation by loss of Androgen Receptor is a global determinant of cancer-associated fibroblast activation.

Alterations of nuclear structure and function, and associated impact on gene transcription, are a hallmark of cancer cells. Little is known of these alterations in Cancer-Associated Fibroblasts (CAFs), a key component of the tumor stroma. Here we show that loss of androgen receptor (AR), which triggers early steps of CAF activation in human dermal fibroblasts (HDFs), leads to nuclear membrane alterations and increased micronuclei formation, which are unlinked from induction of cellular senescence. Similar alterations occur in fully established CAFs, which are overcome by restored AR function. AR associates with nuclear lamin A/C and loss of AR results in a substantially increased lamin A/C nucleoplasmic redistribution. Mechanistically, AR functions as a bridge between lamin A/C with the protein phosphatase PPP1. In parallel with a decreased lamin-PPP1 association, AR loss results in a marked increase of lamin A/C phosphorylation at Ser 301, which is also a feature of CAFs. Phosphorylated lamin A/C at Ser 301 binds to the transcription promoter regulatory region of several CAF effector genes, which are upregulated due to the loss of AR. More directly, expression of a lamin A/C Ser301 phosphomimetic mutant alone is sufficient to convert normal fibroblasts into tumor-promoting CAFs of the myofibroblast subtype, without an impact on senescence. These findings highlight the pivotal role of the AR-lamin A/C-PPP1 axis and lamin A/C phosphorylation at Ser 301 in driving CAF activation.

cancer biology↗

IRF2BP2 counteracts the ATF7/JDP2 AP-1 heterodimer to prevent inflammatory overactivation in acute myeloid leukemia (AML) cells

Acute myeloid leukemia (AML) is a hematological malignancy characterized by abnormal proliferation and accumulation of immature myeloid cells in the bone marrow. Inflammation plays a crucial role in AML progression, but excessive activation of cell-intrinsic inflammatory pathways can also trigger cell death. IRF2BP2 is a chromatin regulator implicated in AML pathogenesis, although its precise role in this disease is not fully understood. In this study, we demonstrate that IRF2BP2 interacts with the AP-1 heterodimer ATF7/JDP2, which is involved in activating inflammatory pathways in AML cells. We show that IRF2BP2 is recruited by the ATF7/JDP2 dimer to chromatin and counteracts its gene-activating function. Loss of IRF2BP2 leads to overactivation of inflammatory pathways, resulting in strongly reduced proliferation. Our research indicates that a precise equilibrium between activating and repressive transcriptional mechanisms creates a pro-oncogenic inflammatory environment in AML cells. The ATF7/JDP2-IRF2BP2 regulatory axis is likely a key regulator of this process and may therefore represent a promising therapeutic vulnerability for AML. Thus, our study provides new insights into the molecular mechanisms underlying AML pathogenesis and identifies a potential therapeutic target for AML treatment.

molecular biology↗

Delay of human early development via in vitro diapause

Many mammals can control the timing of gestation and birth by pausing embryonic development at the blastocyst stage. It is unknown whether the capacity to pause development is conserved, in general across mammals, and more specifically in humans. Activity of the growth regulating mTOR pathway governs developmental pausing in the mouse (1). Here we show a stage-specific capacity to delay the progression of human development via mTOR inhibition. In this context, human blastoids and pluripotent stem cells in naive and naive-like, but not primed, states can be induced to enter a dormant state, which is reversible at the functional and molecular level. Comparative analysis of mouse and human naive cells longitudinal response to mTORi revealed distinct temporal dynamics and metabolic requirements of dormancy in each species. Mouse and human blastocysts show similar tissue-specific patterns of mTOR pathway activity, suggesting that the mTOR pathway may be a conserved regulator of blastocyst development and timing in both species. Our results raise the possibility that the developmental timing of the human embryo may be controllable, with implications for reproductive therapies.

developmental biology↗

Vertical transmission of maternal mitochondrial DNA through extracellular vesicles modulates embryo bioenergetics

The transmission of DNA through extracellular vesicles (EVs) represents a novel genetic material transfer mechanism that may impact genome evolution and tumorigenesis. We aimed to investigate the potential for vertical DNA transmission within maternal endometrial EVs to the pre-implantation embryo and describe any effect on embryo bioenergetics. We discovered that the human endometrium secretes all three general subtypes of EV - apoptotic bodies (ABs), microvesicles (MVs), and exosomes (EXOs) - into the human endometrial fluid (EF) within the uterine cavity. EVs become uniformly secreted into the EF during the menstrual cycle, with the proportion of different EV populations remaining constant; however, MVs contain significantly higher levels of mitochondrial (mt)DNA than ABs or EXOs. During the window of implantation, MVs contain an eleven-fold higher level of mtDNA when compared to cells-of-origin within the receptive endometrium, which possesses a lower mtDNA content and displays the upregulated expression of mitophagy-related genes. Furthermore, we demonstrate the internalization of EV-derived nuclear-encoded (n)DNA/mtDNA by trophoblast cells of murine embryos, which associates with a reduction in mitochondrial respiration and ATP production. These findings suggest that the maternal endometrium suffers a reduction in mtDNA content during the preconceptional period, that nDNA/mtDNA become packaged into secreted EVs that the embryo uptakes, and that the transfer of DNA to the embryo within EVs occurs alongside the modulation of bioenergetics during implantation.

developmental biology↗

The genomic architecture of a continuous color polymorphism in the European barn owl (Tyto alba)

The maintenance of color polymorphism in populations has fascinated evolutionary biologists for decades. Studies of color variation in wild populations often focus on discrete color traits exhibiting simple inheritance patterns, while studies on continuously varying traits remain rare. Here, we studied the continuous white to rufous color polymorphism in the European barn owl (Tyto alba). Using a Genome Wide Association approach on whole-genome data of 75 barn owls sampled across Europe, we identified, in addition to a previously known MC1R mutation, two regions involved in this color polymorphism. We show that the combination of the three explains 80.37% (95% credible interval 58.45 to 100%) of the color variation. Among the two newly identified regions, the one on the sexual chromosome (Z) shows a large signal of differentiation in the Swiss population when contrasting individuals with different morph but the same MC1R genotype. We suggest it may play a role in the sexual dimorphism observed locally in the species. These results, uncovering two new genomic regions, provide keys to better understand the molecular bases of the color polymorphism as well as the mechanisms responsible for its maintenance in the European barn owl at both continental and local scales.

genomics↗

Optical polarization evolution and transmission inmulti-Ranvier-node axonal myelin-sheath waveguides

In neuroscience, it is of interest to consider all possible modes of information transfer between neurons in order to fully understand processing in the brain. It has been suggested that photonic communication may be possible along axonal connections, especially through the myelin sheath as a waveguide, due to its high refractive index. There is already a good deal of theoretical and experimental evidence for light guidance in the myelin sheath; however, the question of how the polarization of light is transmitted remains largely unexplored. It is presently unclear whether polarization-encoded information could be preserved within the myelin sheath. We simulate guided mode propagation through a myelinated axon structure with multiple Ranvier nodes. This allows both to observe polarization change and to test the assumption of exponentiated transmission loss through multiple Ranvier nodes for guided light in myelin sheath waveguides. We find that the polarization can be well preserved through multiple nodes and that transmission losses through multiple nodes are approximately multiplicative. These results provide an important context for the hypothesis of neural information transmission facilitated by biophotons, strengthening the possibility of both classical and quantum photonic communication within the brain.

neuroscience↗

Uptake of plant-derived carbon and proximity to the root determine differences in temporal and spatial stability among microbial groups

The interactions between plants and soil microorganisms are fundamental for ecosystem functioning. However, it remains unclear if seasonality of plant growth impacts plant-microbial interactions, such as by inducing shifts in the microbial community composition, their biomass, or changes in the microbial uptake of plant-derived carbon. Here, we investigate the stability of microbial biomass of different functional groups and their net assimilation of plant-derived carbon over an entire growing season. Using a C3-C4 vegetation change experiment, and taking advantage of natural abundances of 13C, we measured the plant-derived carbon in lipid biomarkers of soil microorganisms in rhizosphere and non-rhizosphere soil. We found that temporal and spatial stability was higher in bacterial than in fungal biomass, while the high temporal stability of all bacterial groups even increased in close proximity to roots. Moreover, differences in the association to plants, i.e., symbionts vs. free-living microorganisms, tend to determine the stability in the uptake of plant-derived carbon. Our results indicate, the inputs of plant-derived carbon over the growing season did not result in a shift in the microbial community composition, but instead, functional groups that are not in obligate symbiosis with plants showed a varying use of soil- and plant-derived carbon.

ecology↗

MICA: A multi-omics method to predict gene regulatory networks in early human embryos

Recent advances in single-cell-omics have been transformative to characterise cell types in challenging to study biological contexts. It is technically difficult to infer transcription factor-gene regulatory interactions from these datasets, especially in contexts with limited single-cell sample number such as the early human embryo. Here we systematically assessed the application of four different linear or non-linear gene regulatory network (GRN) prediction strategies to single-cell simulated and human embryo transcriptome datasets. We also compared how gene expression normalisation methods impact on regulatory network predictions, finding that TPM (transcripts per million reads) outperformed alternative methods. We identified more reproducible GRN inferences using a non-linear method based on mutual information (MI) applied to single-cell transcriptome datasets refined with chromatin accessibility (CA) (called MICA), compared to alternative network prediction methods tested. MICA captures complex non-monotonic dependencies and feedback loops. Using MICA, we generated the first GRN inferences in early human development. MICA predicted co-localisation of the AP-1 transcription factor subunit proto-oncogene JUND and the TFAP2C transcription factor AP-2{psi} in human preimplantation embryos. These interactions were supported by previous findings in other developmental and stem cell contexts. Overall, our comparative analysis of gene regulatory network prediction methods defines a pipeline that can be applied to single-cell multi-omics datasets in especially challenging contexts to infer interactions between transcription factor expression and target gene regulation.

developmental biology↗

Organelle-specific photoactivation and dual-isotope labeling strategy reveals phosphatidylethanolamine metabolic flux

Phosphatidylethanolamine metabolism plays essential roles in eukaryotic cells but has not been completely resolved due to its complexity. This is because lipid species, unlike proteins or nucleic acids, cannot be easily manipulated at the single molecule level or controlled with subcellular resolution, two of the key factors toward understanding their functions. Here, we use the organelle-targeting photoactivation method to study PE metabolism in living cells with a high spatiotemporal resolution. Containing predefined PE structures, we designed probes which can be selectively introduced to the ER or mitochondria to compare their metabolic products according to their subcellular localization. We combined photo-uncaging method with dual stable isotopic labeling to track PE metabolism in living cells by mass spectrometry analysis. Our results reveal that both mitochondrial- and ER-released PE participate in phospholipid remodeling, and that PE methylation can be detectable only under particular conditions. Thus, our method provides a framework to study phospholipid metabolism at subcellular resolution.

cell biology↗

Peptide-mediated inhibition of the transcriptional regulator Elongin BC induces apoptosis in cancer cells

Inhibition of protein-protein interactions (PPIs) via designed peptides is an effective strategy to interfere with their biological functions. The Elongin BC heterodimer (ELOB/C) is involved in transcription elongation and protein turnover by PPIs that involve the so-called BC-box. ELOB and ELOC are commonly upregulated in cancer and essential for cancer cell growth, making them attractive drug targets. However, no strategy has been established to inhibit their functions in cells, so far. Here, we report a peptide that mimics a high-affinity BC-box and tightly binds to the ELOB/C dimer (kD = 0.45 {+/-} 0.03 nM). Our peptide blocks the association of ELOB/C with its interaction partners, both in vitro and in the cellular environment. Cancer cells treated with this peptide inhibitor show decreased cell viability, altered cell cycle and increased apoptosis. Therefore, our work proposes that blocking the BC-box binding pocket of ELOB/C is a feasible strategy to impair the function of the ELOB/C heterodimer and inhibit cancer cell growth. Our peptide inhibitor promises novel mechanistic insights into the biological function of the ELOB/C dimer and offers a starting point for therapeutics linked to ELOB/C dysfunction.

cancer biology↗