Biology subjects

Schmitt, S.

Publications and source records attributed to Schmitt, S..

At least 19 recordsLinked to original sources

bioRxiv2026

scIRES-seq reveals multimodal molecular heterogeneity in CTCs from small cell cervical cancer

Circulating tumor cells (CTCs) can provide a window into cellular and molecular mechanisms of cancer dissemination. However, the rarity and heterogeneity of CTCs complicate reliable identification and molecular characterization. Here, we introduce scIRES-seq, a framework linking immunophenotype, genetic variation, epigenomic profiles and gene expression within individual cells. In this proof-of-concept study, we coupled scIRES-seq to real-time imaging spectral flow cytometry and applied it to CTCs from a patient with metastatic cervical small cell neuroendocrine carcinoma. Tumor-matched copy-number alterations and targeted somatic variants established CTC identity, supported by DNA methylation profiles concordant with metastatic tissue and transcriptional features consistent with neuroendocrine differentiation. Genetic and DNA methylation analyses identified two largely concordant CTC subpopulations that were not clearly distinguished by their transcriptomes, highlighting the complementary information gained through single-cell multi-omics profiling. These findings demonstrate the feasibility of integrated CTC identification and characterization and provide a framework for investigating relationships between genetic diversity and molecular states in rare, heterogeneous cell populations.

cancer biology↗

bioRxiv2026

Induced Estrogen Receptor SUMOylation drives SERD activity

The ligand dependent transcription factor estrogen receptor (ER) is a key driver of and important drug target in breast cancer. Patients with advanced disease are typically treated with selective ER degraders (SERDs), whose therapeutic activity is commonly attributed to induced ER protein degradation. Yet the exact mechanism and relevance of degradation for clinical efficacy remain unclear. We show that SERDs directly induce ER SUMOylation, thereby triggering degradation via SUMO-targeted ubiquitin ligases (STUbLs). Inactivation of STUbLs prevents ER degradation and counterintuitively further sensitizes breast cancer cells to SERDs, rather than conferring resistance. SERD efficacy is independent of ER degradation, challenging the degradation-centric model of SERD action. Instead, SUMOylation recruits transcriptional co-repressors, turning SUMOylated ER into a dominant-negative repressor. Thus, SUMOylation rather than degradation is the direct consequence and driver of SERD activity. Our findings position SUMO-inducing drugs as a hitherto underappreciated yet clinically validated therapeutic modality with broad applicability.

Cancer Biology↗

bioRxiv2026

Generative AI designs functional thiolation domains for reprogramming non-ribosomal peptide synthetases

Large language models and generative protein design promise to accelerate biotechnology, but it remains unclear whether they can engineer dynamic megasynth(et)ases whose activity depends on transient, context-specific domain interfaces. Non-ribosomal peptide synthetases (NRPSs) are an especially demanding target, yet a high-value one because they produce many clinically important natural products and offer a route to analogs that are often difficult or impractical to access by chemical synthesis. Here we integrate pretrained generative models (ESM3, ProteinMPNN and EvoDiff) with design-build-test-learn cycles and data-guided prioritization to generate 76 de novo thiolation (T) domains. We built and tested 578 recombinant NRPS variants in vivo spanning minimal, full-length and hybrid assembly lines. AI-designed T-domains supported product formation across architectures, enabled catalytically active hybrids at recombined junctions and increased yields by up to [~]3-fold relative to NRPSs carrying the native T-domain. A representative design showed improved soluble expression, refolding, and a 12 {degrees}C higher melting temperature, while molecular dynamics simulations indicated preserved global stability but reshaped, state-dependent interdomain contact networks. Together, these results establish generative design as an effective route to context-conditioned optimization and reprogramming of biosynthetic assembly lines.

synthetic biology↗

bioRxiv2026

Integrating coastal microbiome observations for human, oyster and environmental protection

The Reseau dObservatoires de Microbiologie Environnementale integree (ROME) was a pilot study conducted in France from September 2020 to August 2023 aiming to establish a network of eDNA-based observatories across four estuarine ecosystems associated with oyster farming: the Bay of Veys (Normandy), the Bay of Brest (Brittany), Marennes-Oleron (Nouvelle-Aquitaine), and the Thau Lagoon (Occitania). Within a One Health framework, the study assessed the influence of river inputs on estuarine microbiome structuring and the emergence of microbiological hazards affecting human, aquaculture, and ecosystem health. Over 2,000 samples were collected during the study, including biweekly surface water and monthly adult oyster samples. Environmental nucleic acids were analysed using metabarcoding (bacterial and protist communities) and metagenomics (human RNA viruses). The coastal microbiome, including pathogenic and harmful taxa relevant to humans and aquatic invertebrates, was characterized. River influence on microbial community composition was examined through spatial comparisons of stations exposed to varying levels of freshwater runoff, while oysters acted as bio-integrators of local microbial diversity. Results revealed coherent coastal-to-offshore microbiome structuring across all ecosystems, with local variations linked to riverine inputs. eDNA metabarcoding allowed to detect a wide range of prokaryotic and eukaryotic pathogens, as well as harmful algal bloom (HAB) genera, several not captured by conventional monitoring. These findings demonstrate the potential of the ROME eDNA observatory network for high-resolution, integrative surveillance of microbial biodiversity and early detection of biological risks in estuarine environments.

genomics↗

bioRxiv2026

Vitamin B12 Improves Skeletal Muscle Mitochondrial Biology in Aged Mice

Age-related skeletal muscle deterioration is a commonly reported disability among older adults, attributed to several factors including mitochondrial dysfunction, a major hallmark of aging. Therapies to attenuate or reverse mitochondrial decline are limited. Despite identified positive relationships between vitamin B12 (B12) and mitochondrial biology, the impact of B12 supplementation on skeletal muscle mitochondria, in advanced aged, has not been examined. Thus, the impact of B12 supplementation on skeletal muscle mitochondrial biology was examined in (i) aged female mice, given 12 weeks of B12 supplementation (SUPP) or vehicle control, and (ii) in human primary myotubes. In the mouse model, mitochondrial DNA and content were measured with PCR and citrate synthase activity, respectively; mitochondrial morphology was examined using transmission electron microscopy; mitochondrial function was examined using extracellular metabolic flux analysis; and proteins and pathway enrichment was identified with proteomics. In the cell model, ROS and glutathione was measured using luminescent assays. The results demonstrated that SUPP in aged mice increased muscle mitochondrial content and improved morphology. Further, differentially expressed proteins were enriched in TCA cycle, OXPHOS, and oxidative stress pathways. In the cell model, B12 supplementation reduced ROS levels. This is the first study, to our knowledge, examining the impact of B12 supplementation on skeletal muscle mitochondrial biology in aged female mice. Results suggest that B12 supplementation improves mitochondrial biology in aged female mice.

molecular biology↗

bioRxiv2025

Glutamine deficiency enhances nuclear localization of TCA cycle enzymes and epigenetic modifications, impairing myogenesis

ObjectiveSkeletal muscle myogenesis, during development and regeneration, are primarily facilitated by the progeny of resident muscle stem cells, the muscle progenitor cells (MPCs). Intriguingly, extracellular glutamine (Gln) is required by MPCs. Disruptions in Gln availability or metabolism, impair MPC function and hinder skeletal muscle regeneration. Gln, a nutritionally non-essential amino acid (NEAA), which is most abundant in skeletal muscle, becomes conditionally essential during advancing age and catabolic states like sepsis, trauma, and strenuous situations. The intracellular mechanisms through which extracellular Gln availability affects MPC proliferation are poorly understood. Therefore, this study was aimed to examine how extracellular supply of Gln influences myogenesis through the spatial distribution of TCA-cycle enzymes. MethodsHuman primary muscle myoblasts (HSKM2) and murine MPCs (C2C12) were utilized for in-vitro experiments. To investigate the impact of Gln availability on MPC proliferation, proliferation assays, confocal imaging, succinyl-proteomics, and single-cell nuclei ATAC sequencing were used. ResultsGln (2 mM) significantly enhanced MPC viability and cell cycle progression, while Gln depletion (0 mM) reduced cell number and induced G0/G1 arrest. Gln deficiency downregulated MyoD expression, impairing myogenic potential. Inhibiting intracellular Gln metabolism also limited proliferation, indicating the necessity of Gln catabolism for cell proliferation. Gln deficiency increased nuclear localization of TCA cycle enzymes (DLST, OGDH), elevated histone succinylation, and restricted chromatin accessibility of the myogenic regulatory factor, MyoD1, highlighting a Gln dependent metabolic-epigenetic nexus in myogenic regulation. ConclusionThese findings demonstrate that extracellular Gln availability is a key regulator of myogenesis through its influence on metabolism, epigenetic modifications, and chromatin accessibility.

developmental biology↗

bioRxiv2025

A Highly Potent Human Antibody Neutralizing All Serotypes of BK Polyomavirus

BK polyomavirus infection poses a significant risk to kidney transplant recipients. Reactivation of dormant virus in the transplanted kidney, triggered by immunosuppression, can lead to BK polyomavirus-associated nephropathy in up to 10% of transplants, often resulting in loss of graft function or even graft loss. Currently, there is no specific treatment that reliably prevents BK polyomavirus-associated nephropathy or halts its progression. Standard of care relies on reducing immunosuppression, allowing the immune system to gradually control the infection but at the risk of provoking rejection episodes and compromising kidney function. This study describes the discovery and characterization of an ultra-potent BK polyomavirus-neutralizing antibody, identified from a kidney transplant recipient who displayed rapid clearance of high-level BK viremia. Antibody mAb 319C07 (USAN potravitug) neutralizes all four BK polyomavirus serotypes and recognizes an epitope critical for viral cell attachment. mAb 319C07 is in clinical development for the treatment of BKPyV infection in renal transplant patients (NCT05769582).

immunology↗

bioRxiv2025

A simple network of proprioceptive reflexes can produce a variety of bipedal gaits

Proprioception is crucial for movement, yet the role of proprioceptive reflexes in legged locomotion is still poorly understood. While previous simulation studies have shown great potential for reflex-based control strategies, these controllers are typically catered to specific gaits, using hand-crafted feedback pathways that are linked to specific gait phases. In this work, we explore the control capabilities of a simple reflex controller that consists of only monosynaptic and antagonistic length and force feedback pathways with constant gains. Despite its simplicity, we found our control framework capable of producing a wide variety of natural gaits, including walking and hopping, forwards and backwards, and running in different variations and at different velocities - without requiring any rhythmic inputs or high-level state machines modulating the feedback gains. Our work highlights the important role and flexibility of proprioceptive reflexes and suggests a necessary re-evaluation of their role in locomotion. Due to its simplicity and flexibility, our control framework provides a solid basis for the development of higher level neuromuscular control systems. Author summaryHuman locomotion is characterized by an impressive versatility and humans transition naturally between different gaits. However, the neural mechanisms underlying human motor control are not fully understood and remain controversial. The two widely accepted basic components of the neural circuitry involved in locomotion are central pattern generators (CPG) and spinal reflexes, leading to a long-standing debate on their respective roles. Neuromusculoskeletal models can be employed to study the role of these neural control structures in simulation. Until now, these models mostly focus on walking and require an additional component like a state-machine or CPG besides reflexes to generate rhythmic activation of muscles. In this work, we propose a controller that can generate different rhythmic gaits like walking and hopping, forwards and backwards, as well as running, based solely on simple reflexes known to exist in the mammalian spinal cord. We challenge the current view of the role of rhythm-generating components and show the remarkable potential of reflexes for locomotion control. To our knowledge, this is the first work showing that versatile locomotion can be achieved solely based on reflexes without the need of a CPG. Our results contribute to the understanding of human motor control and are relevant for the control of robots, exoskeletons, prostheses and ortheses.

biophysics↗

bioRxiv2025

TUB-010, a novel anti-CD30 antibody-drug conjugate based on Tub-tag technology, widens the therapeutic window by reducing toxicity while maintaining high efficacy

TUB-010 is a next-generation antibody-drug conjugate (ADC) targeting CD30, which is expressed on various hematopoietic malignancies such as Hodgkin lymphoma and anaplastic large cell lymphoma. Patients with refractory and relapsed CD30-positive cancers often lack effective and tolerable therapy options. Among the therapeutic options for these patients is brentuximab vedotin (Adcetris), a monomethyl auristatin E (MMAE)-delivering anti-CD30 ADC with a mean drug-to antibody ratio (DAR) of 4. Adcetris exhibits a high response rate at the cost of significant toxicities, among which neutropenia and peripheral neuropathy are the most prevalent adverse events, which are likely driven by the payload MMAE and instability of the maleimide conjugation chemistry. TUB-010 uses the same antibody brentuximab and payload MMAE as Adcetris, but instead of maleimide chemistry, TUB-010 is based on the Tub-tag conjugation strategy, which enables the generation of a homogenous and site-specific DAR 2 ADC with unique biophysical properties. This new technology stably attaches MMAE to the hydrophilic Tub-tag peptides on the light chains via chemoenzymatic conjugation using the enzyme tubulin tyrosine ligase. TUB-010 demonstrates similar binding affinity, internalization and lysosomal release characteristics as Adcetris in CD30-positive cells. When normalized to the MMAE concentration, TUB-010 shows comparable in vitro cytotoxic efficacy as well as similar bystander activity compared to Adcetris on established cancer cell lines. Importantly, TUB-010 exhibits higher stability with neglectable premature deconjugation in circulation and reduced high molecular weight species formation as well as lower non-specific cytotoxicity on target-negative cells compared to Adcetris. As a consequence, TUB-010 induces superior tumor control compared to Adcetris when dosed at equal MMAE concentrations in vivo and also shows lower toxicity and higher tolerability in rodents and non-human primates. Taken together, TUB-010 is a novel and potential best-in-class anti-CD30 ADC with improved biophysical properties designed to deliver the cytotoxic payload with higher precision and with a wider therapeutic window than Adcetris using Tub-tag conjugation technology. Therefore, TUB-010 may increase the clinical benefit of ADC therapies for patients with CD30-positive malignancies.

cancer biology↗

bioRxiv2025

Multi-omics profiling of cross-resistance between ceftazidime-avibactam and meropenem identifies common and strain-specific mechanisms in Pseudomonas aeruginosa clinical isolates

Pseudomonas aeruginosa is a highly versatile and resilient pathogen that can infect different tissues and rapidly develop resistance to multiple drugs. Ceftazidime-avibactam (CZA) is an antibiotic often used to treat multidrug resistant infections, however, the knowledge on the CZA resistance mechanisms in P. aeruginosa is limited. Here we performed laboratory evolution of eight clinical isolates of P. aeruginosa exposed to either CZA or meropenem (MEM) in sub-inhibitory concentrations, and used multi-omics profiling to investigate emerging resistance mechanisms. The majority of strains exposed to MEM developed high resistance (83%, 20/24 strains from eight clinical isolates), with only 17% (4/24) acquiring cross-resistance to CZA. The rate of resistance evolution to CZA was substantially lower (21%, 5/24), while 38% (9/24) acquired cross-resistance to MEM. Whole-genome sequencing revealed strain heterogeneity and different evolutionary paths, with three genes mutated in three or more strains: dacB in CZA-treated strains and oprD and ftsI in MEM-treated strains. Transcriptomic and proteomic analysis underlined heterogeneous strain response to antibiotic treatment with few commonly regulated genes and proteins. To identify genes potentially associated with antibiotic resistance, we built a machine learning model that could separate CZA- and MEM-resistant from sensitive strains based on gene expression and protein abundances. To test some of the identified associations, we performed CRISPR/Cas9 genome editing that demonstrated that mutations in dacB, ampD, and to a lesser extent in mexR directly affected CZA resistance. Overall, this study provides novel insights into the strain-specific molecular mechanisms regulating CZA resistance in Pseudomonas aeruginosa. ImportancePseudomonas aeruginosa is one of the most difficult-to-treat pathogens in the hospital, which often acquires resistance to multiple antibiotics. Ceftazidime-avibactam (CZA) is an essential antibiotic used to treat multidrug resistant infections, but its resistance mechanisms are not well understood. Here we investigated the evolution of resistance to CZA and meropenem (MEM) in eight clinical bacterial isolates from patients blood, urine, and sputum. While the rate of resistance evolution to MEM was higher than to CZA, MEM-resistant strains rarely acquired cross-resistance towards CZA. To identify changes at the genome, transcriptome and proteome levels during antibiotic exposure, we performed multi-omics profiling of the evolved strains, and confirmed the effect of several genes on antibiotic resistance with genetic engineering. Altogether, our study provides insights into the molecular response of P. aeruginosa to CZA and MEM and informs therapeutic interventions, suggesting that CZA could still be effective for patients infected with MEM-resistant pathogens.

microbiology↗

bioRxiv2024

Calcium-based input timing learning

AO_SCPLOWBSTRACTC_SCPLOWStimulus-triggered synaptic long-term plasticity is the foundation of learning and other cognitive abilities of the brain. In general, long-term synaptic plasticity is subdivided into two different forms: homosynaptic plasticity describes synaptic changes at stimulated synapses, while heterosynaptic plasticity summarizes synaptic changes at non-stimulated synapses. For homosynaptic plasticity, the Ca2+-hypothesis pinpoints the calcium concentration within a stimulated dendritic spine as key mediator or controller of underlying biochemical and -physical processes. On the other hand, for heterosynaptic plasticity, although theoretical studies attribute important functional roles to it, such as synaptic competition and cooperation, experimental results remain ambiguous regarding its manifestation and biological basis. By integrating insights from Ca2+-dependent homosynaptic plasticity with experimental data of dendritic Ca2+-dynamics, we developed a mathematical model that describes the complex temporal and spatial dynamics of calcium in dendrites.We show that the influx of calcium into a stimulated spine can lead to its diffusion to neighboring spines, triggering heterosynaptic effects such as synaptic competition or cooperation. By considering different input strengths, our model explains the ambiguity of reported experimental results of heterosynaptic plasticity, suggesting that the Ca2+-hypothesis of homosynaptic plasticity can be extended to also model heterosynaptic plasticity. Furthermore, our model predicts thata synapse can modulate the expression of homosynaptic plasticity at a neighboring synapse in an input-timing-dependent manner, without the need of postsynaptic spiking. The resulting sensitivity of synaptic plasticity on input-spike-timing can be influenced by the distance between involved spines as well as the local diffusion properties of the connecting dendritic shaft, providing a new way of dendritic computation.

neuroscience↗

bioRxiv2024

Nanoliter-scale selection of optimized bioengineered peptide antibiotics that rescue mice with bacterial lung infection

Increasing numbers of multi-drug resistant pathogens call for new chemical scaffolds, addressing novel targets, that can serve as lead structures for the development of life-saving drugs. For antibiotics, natural product-inspired molecules represent a most promising resource. Natural products evolved to high chemical complexity and occupy a chemical space different than synthetic libraries. However, clinical translation of promising natural products is often impeded by their relative inaccessibility to medicinal chemistry optimization, e.g. iterative synthesis of large series of derivatives. Here, this limitation is addressed with a randomized library of bicyclic heptapeptides based on the natural product darobactin that hits the clinically not addressed target BamA. Variants of the ribosomally synthesized and post-translationally modified peptides were generated using heterologous mutasynthesis. A parallelized screening assay is adapted in nanoliter-scale beads to test the darobactin derivatives against our sensor strain. Loss of fluorescence sorting prioritized 563 events out of the analyzed [~]500k beads. Re-testing confirmed 48 hit events, of which 40 proved to produce distinct darobactin-type molecules. Most promising structures were isolated and the growth inhibitory effects against Gram-negative pathogens validated. One of our current frontrunner compounds (i.e., darobactin B) was reinforced by the randomized screen. While microbiological investigations of the new derivatives is ongoing, darobactin B was profiled in later tier assays and compared to another promising, rationally-designed analog (i.e., darobactin B9, "D22"). Early ADMET profiling and efficacy tests in a mouse pneumonia model were performed. Darobactin B reduced bacterial load of Pseudomonas aeruginosa and Klebsiella pneumoniae by intraperitoneal, as well as intratracheal administration. Our study showcases the potential of mutasynthetic libraries for high-throughput screening and identification of functional peptides for drug lead discovery.

microbiology↗

bioRxiv2024

Using muscle-tendon load limits to assess unphysiological musculoskeletal model deformation and Hill-type muscle parameter choice

Musculoskeletal simulations are a useful tool for improving our understanding of the human body. However, the physiological validity of predicted kinematics and forces is highly dependent upon the correct calibration of muscle parameters and the structural integrity of a models internal skeletal structure. In this study, we show how ill-tuned muscle parameters and unphysiological deformations of a models skeletal structure can be detected by using muscle elements as sensors with which modelling and parameterization inconsistencies can be identified through muscle and tendon strain injury assessment. To illustrate our approach, two modelling issues were recreated. First, a model repositioning simulation using the THUMS AM50 occupant model version 5.03 was performed to show how internal model deformations can occur during a change of model posture. Second, the muscle material parameters of the OpenSim gait2354 model were varied to illustrate how unphysiological muscle forces can arise if material parameters are inadequately calibrated. The simulations were assessed for muscle and tendon strain injuries using previously published injury criteria and a newly developed method to determine tendon strain injury threshold values. Muscle strain injuries in the left and right musculus pronator teres were detected during the model repositioning. This straining was caused by an unphysiologically large gap (12.92 mm) that had formed in the elbow joint. Similarly, muscle and tendon strain injuries were detected in the modified right-hand musculus gastrocnemius medialis of the gait2354 model where an unphysiological reduction of the tendon slack length introduced large pre-strain of the muscle-tendon-unit. The results of this work show that the proposed method can quantify the internal distortion behaviour of musculoskeletal human body models and the validity of Hill-type muscle parameter choice via strain injury assessment. Furthermore, we highlight possible actions to avoid the presented issues and inconsistencies in literature data concerning the material characteristics of human tendons.

biophysics↗

bioRxiv2024

Transcranial Focused Ultrasound Remotely Modulates Extrastriate Visual Cortex with Subregion Specificity

Low-intensity transcranial focused ultrasound (tFUS) has emerged as a powerful neuromodulation tool characterized by its deep penetration and precise spatial targeting to influence neural activity. Our study directed low-intensity tFUS stimulation onto a region of prefrontal cortex (the frontal eye field, or FEF) of a rhesus macaque to examine its impact on a remote site, the extrastriate visual cortex (area V4). This pair of cortical regions form a top-down modulatory circuit that has been studied extensively with electrical microstimulation. To measure the impact of tFUS stimulation, we recorded local field potentials (LFPs) and multi-unit spiking activities from a multi-electrode array implanted in the visual cortex. To deliver tFUS stimulation, we leveraged a customized 128-element random array ultrasound transducer with improved spatial targeting. We observed that tFUS stimulation in FEF produced modulation of V4 neuronal activity, either through enhancement or suppression, dependent on the pulse repetition frequency of the tFUS stimulation. Electronically steering the transcranial ultrasound focus through the targeted FEF cortical region produced changes in the level of modulation, indicating that the tFUS stimulation was spatially targeted within FEF. Modulation of V4 activity was confined to specific frequency bands, and this modulation was dependent on the presence or absence of a visual stimulus during tFUS stimulation. A control study targeting the insula produced no effect, emphasizing the region-specific nature of tFUS neuromodulation. Our findings shed light on the capacity of tFUS to modulate specific neural pathways and provide a comprehensive understanding of its potential applications for neuromodulation within brain networks.

neuroscience↗

bioRxiv2023

Estimation of contemporary effective population size in plant populations: limitations of genomic datasets

Effective population size (Ne) is a pivotal evolutionary parameter with crucial implications in conservation practice and policy. Genetic methods to estimate Ne have been preferred over demographic methods because they rely on genetic data rather than time-consuming ecological monitoring. Methods based on linkage disequilibrium, in particular, have become popular in conservation as they require a single sampling and provide estimates that refer to recent generations. A software programme based on the linkage disequilibrium method, GONE, looks particularly promising to estimate contemporary and recent-historical Ne (up to 200 generations in the past). Genomic datasets from non-model species, especially plants, may present some constraints to the use of GONE, as linkage maps and reference genomes are seldom available, and SNP genotyping is usually based on reduced-representation methods. In this study, we use empirical datasets from four plant species to explore the limitations of plant genomic datasets when estimating Ne using the algorithm implemented in GONE, in addition to exploring some typical biological limitations that may affect Ne estimation using the linkage disequilibrium method, such as the occurrence of population structure. We show how accuracy and precision of Ne estimates potentially change with the following factors: occurrence of missing data, limited number of SNPs/individuals sampled, and lack of information about the location of SNPs on chromosomes, with the latter producing a significant bias, previously unexplored with empirical data. We finally compare the Ne estimates obtained in GONE for the last generations with the contemporary Ne estimates obtained in the programmes currentNe and NeEstimator.

evolutionary biology↗

bioRxiv2023

Plant mutations: slaying beautiful hypotheses by surprising evidence

Somatic mutations potentially play a role in plant evolution, but common expectations pertaining to plant somatic mutations remain insufficiently tested. Unlike in most animals, the plant germline is assumed to be set aside late in development, leading to the expectation that plants accumulate somatic mutations along growth. Therefore, several predictions were made on the fate of somatic mutations: mutations have generally low frequency in plant tissues; mutations at high frequency have a higher chance of intergenerational transmission; branching topology of the tree dictates mutation distribution; and, exposure to UV radiation increases mutagenesis. To provide new insights into mutation accumulation and transmission in plants, we produced two high-quality reference genomes and a unique dataset of 60 high-coverage whole-genome sequences of two tropical tree species, Dicorynia guianensis (Fabaceae) and Sextonia rubra (Lauraceae). We identified 15,066 de novo somatic mutations in D. guianensis and 3,208 in S. rubra, surprisingly almost all found at low frequency. We demonstrate that: 1) low-frequency mutations can be transmitted to the next generation; 2) mutation phylogenies deviate from the branching topology of the tree; and 3) mutation rates and mutation spectra are not demonstrably affected by differences in UV exposure. Altogether, our results suggest far more complex links between plant growth, ageing, UV exposure, and mutation rates than commonly thought. Significance StatementThe origin and fate of new mutations have received less attention in plants than in animals. Similarly to animals, plant mutations are expected to accumulate with growth and time, and under exposure to UV light. However, contrary to animals, plant reproductive organs form late in an individuals development, allowing the transmission to the progeny of mutations accumulated along growth. Here, we resequenced DNA from different branches differentially exposed to sunlight of two tropical tree species. We showed that new mutations are generally rare in plant tissues and do not mimic branching patterns but can nevertheless be transmitted to the progeny. Our findings provide a new perspective on heritable plant mutation and its pivotal role as the engine of evolution.

genomics↗

bioRxiv2022

High intraspecific growth variability despite strong evolutionary heritage in a neotropical forest

Individual tree growth is a key determinant of species performance and a driver of forest dynamics and composition. Previous studies on tree growth unravelled the variation in species growth as a function of demographic trade-offs that are partially predicted using functional traits. They have explored the environmental determinants of species growth potential and the variation of intraspecific growth over space and time due to environment and biotic factors. However, variation in individual growth within species remains underexplored for a whole community and the relative role of species evolutionary heritage and of local environments remains unquantified. Here, based on 36 years of diameter records for thousands of mapped individuals belonging to 138 species, we assessed individual tree growth potential in a local neotropical forest community in the Amazon basin. We further related variation in individual growth potential with taxonomic levels, local topography, and neighbourhood crowding, before exploring species growth potential link to functional traits and distribution along the phylogeny. We found that most of the variation in growth potential was individual, and that taxonomic structure explained a third of the observed variation. Species growth potential was phylogenetically conserved with positive conservatism up to the genus level in the vast majority of species. Functional traits of roots, wood and leaves together predicted species growth potential. Phylogeny suggested joint selection of species growth strategies and associated functional traits during convergent evolutions. Finally, neighbourhood crowding had a significant effect on individual growth potential, although much of this inter-individual variation remains largely unexplained and the underlying ecological and evolutionary factors are still little explored. The high intraspecific variation observed could allow individuals in these hyperdiverse ecosystems to respond to the variable light and competitive conditions offered by successional niches during forest gap dynamics.

ecology↗

bioRxiv2022

{Pi}-{Pi} Interactions Stabilize PeptoMicelle-Based Formulations of Pretomanid Derivatives Leading to Promising Therapy Against Tuberculosis in Zebrafish and Mouse Models

Tuberculosis is the deadliest bacterial disease globally, threatening the lives of millions every year. New antibiotic therapies that can shorten the duration of treatment, improve cure rates, and impede the development of drug resistance are desperately needed. Here, we used polymeric micelles to encapsulate four second-generation derivatives of the antitubercular drug pretomanid that had previously displayed much better in vivo activity against Mycobacterium tuberculosis than pretomanid itself. Because these compounds were relatively hydrophobic, we expected that such micellar formulations would increase drug bioavailability, reduce toxicities, and improve therapeutic outcomes. The polymeric micelles were based on polypept(o)ides (PeptoMicelles) and were stabilized in their hydrophobic core by {pi}-{pi} interactions, allowing the efficient encapsulation of aromatic pretomanid derivatives. The stability of these {pi}-{pi}-stabilized PeptoMicelles was demonstrated in water, blood plasma, and lung surfactant by fluorescence cross-correlation spectroscopy and was further supported by prolonged circulation times of several days in the vasculature of zebrafish larvae. The pretomanid derivative with the best in vitro potency against Mycobacterium marinum ("drug D") was also the most efficacious PeptoMicelle formulation tested in the zebrafish larvae infection model, almost completely eradicating the bacteria at non-toxic doses. This lead formulation was further assessed against Mycobacterium tuberculosis in the susceptible C3HeB/FeJ mouse model, which develops human-like necrotic granulomas. Following intravenous administration, the drug D micellar formulation significantly reduced bacterial burden and inflammatory responses in the lungs and spleens of infected mice.

bioengineering↗