Biology subjects

Moser, C.

Publications and source records attributed to Moser, C..

10 recordsLinked to original sources

bioRxiv2026

Evolutionary Trajectories of Ciprofloxacin Resistance in P. aeruginosa Lung Biofilms: Mutation Dynamics, Metabolomic Shifts, and Collateral Sensitivity

The evolution of antimicrobial resistance (AMR) in chronic biofilms is often viewed as a unidirectional path toward higher fitness, yet the metabolic constraints governing these trajectories remain poorly understood. We performed a four-passage evolution experiment using a murine lung biofilm model to assess the impact of prolonged ciprofloxacin (CIP) exposure on resistance and host response. This approach integrated population-level adaptive dynamics, whole-genome sequencing (WGS), and NMR-based metabolomics, alongside histopathology and cytokine analysis. Prolonged CIP treatment accelerated resistance, with isolates reaching MICs of 8-12 mg/L (a 32- to 48-fold increase) by the fourth passage. WGS revealed distinct evolutionary trajectories: control isolates accumulated metabolic and regulatory mutations without susceptibility changes, while CIP-treated isolates exhibited a stepwise progression from metabolic adaptation to high-level resistance, marked by early nfxB and late gyrA mutations. Metabolomic profiling revealed progressive divergence, with PCA identifying the nfxB genotype as the primary driver of variation (49.1% of variance). This resistant metabolic state was characterized by the depletion of central carbon metabolites, including glucose and tyrosine, alongside the accumulation of essential amino acids. Importantly, these changes were accompanied by a distinct trade-off; high-level CIP resistance triggered collateral sensitivity to tobramycin and aztreonam. While CIP treatment ultimately reduced neutrophilic inflammation (p = 0.011) and mucin production (p = 0.0496), early-passage lungs exhibited transient elevations in pro-inflammatory cytokines (CXCL2, MMP2, TNF-). In conclusion, the adaptive trajectory to CIP resistance involves metabolic rewiring and collateral sensitivity, offering a framework to exploit the evolutionary costs of resistance in chronic biofilm infections.

microbiology↗

bioRxiv2026

Tomographic Printing in a Chip: A Versatile Platform for Biomimetic 3D Organ-on-Chip

Abstract textOrgan-on-chip (OoC) platforms are increasingly adopted for predictive in vitro testing. However, most remain limited by soft-lithography-derived 2.5D microfluidic architectures and non-physiological rigid materials, or bioprinting approaches that require complex and failure-prone post-fabrication assembly. Here, we present a versatile approach that integrates tomographic volumetric additive manufacturing (TVAM) directly within preassembled microfluidic chips, enabling rapid, contactless fabrication of freeform 3D OoCs. Leveraging our open-source optical simulation framework, Dr.TVAM, we perform TVAM in custom-designed chips, eliminating post-printing manual assembly steps that commonly lead to leakage, contamination, and poor reproducibility. This strategy, termed TVAM-in-a-chip, supports the generation of diverse 3D channel architectures in multiple biocompatible photoresins spanning a wide range of chemistries and mechanical properties, including cell-laden formulations. We demonstrate multi-channel designs, compatibility with confocal imaging, and dynamic culture of epithelial and endothelial models. Overall, TVAM-in-a-chip overcomes key limitations of current OoC technologies and paves the way for a new generation of scalable, biomimetic 3D platforms for advanced in vitro modeling.

bioengineering↗

bioRxiv2024

Pharmacodynamic modeling of colistin and imipenem against in vitro Pseudomonas aeruginosa biofilms

IntroductionAntibiotic treatment of chronic biofilm-associated infections can be challenging. Characterization of pharmacokinetic-pharmacodynamic (PK-PD) relationships for biofilm-associated infections may be relevant to inform the design of antibiotic treatment regimens for biofilm-associated infections. To this end, we aim to develop a mathematical PK-PD model for planktonic and biofilm bacterial infections and demonstrate how PK-PD simulations can be used to design optimized dosing schedules, using imipenem and colistin as proof-of-concept examples. MethodsPharmacodynamic models were developed using time-kill assay data from planktonic and alginate-bead biofilm cultures of Pseudomonas aeruginosa exposed to imipenem or colistin. The PD models were coupled to population PK models for plasma and epithelial lining fluid (ELF) to translate PD relationships for clinical dosing schedules and PK-PD indices. ResultsThe developed models incorporated sensitive and resistant bacterial subpopulations and were able to adequately capture the observed time-kill data. Simulation studies identified differences in suppression of bacterial growth dynamics for multiple clinical intravenous and inhalation-based treatment regimens and were used to infer biofilm-specific PK-PD indices associated with ELF target site concentrations. ConclusionIn conclusion, we demonstrate the utility of mathematical modeling for the characterization of PK-PD relationships underlying time-kill kinetic profiles in biofilm-associated infections and their utility in translating experimental findings to inform the optimization of clinical dosing schedules.

pharmacology and toxicology↗

bioRxiv2023

SARS-CoV-2 monoclonal antibody treatment followed by vaccination shifts human memory B cell epitope recognition suggesting antibody feedback

Therapeutic anti-SARS-CoV-2 monoclonal antibodies (mAbs) have been extensively studied in humans, but the impact on immune memory of mAb treatment during an ongoing immune response has remained unclear. Here, we evaluated the effect of infusion of the anti-SARS-CoV-2 spike receptor binding domain (RBD) mAb bamlanivimab on memory B cells (MBCs) in SARS-CoV-2-infected individuals. Bamlanivimab treatment skewed the repertoire of memory B cells targeting Spike towards non-RBD epitopes. Furthermore, the relative affinity of RBD memory B cells was weaker in mAb-treated individuals compared to placebo-treated individuals over time. Subsequently, after mRNA COVID-19 vaccination, memory B cell differences persisted and mapped to a specific defect in recognition of the class II RBD site, the same RBD epitope recognized by bamlanivimab. These findings indicate a substantial role of antibody feedback in regulating human memory B cell responses, both to infection and vaccination. These data indicate that mAb administration can promote alterations in the epitopes recognized by the B cell repertoire, and the single administration of mAb can continue to determine the fate of B cells in response to additional antigen exposures months later. SIGNIFICANCE STATEMENTEvaluating the therapeutic use of monoclonal antibodies during SARS-CoV-2 infection requires a comprehensive understanding of their impact on B cell responses at the cellular level and how these responses are shaped after vaccination. We report for the first time the effect of bamlanivimab on SARS-CoV-2 specific human memory B cells of COVID-19 infected humans receiving, or not, mRNA immunization.

immunology↗

bioRxiv2023

Early antiviral CD4 and CD8 T cell responses are associated with upper respiratory tract clearance of SARS-CoV-2

T cells are involved in protective immunity against numerous viral infections. Data regarding functional roles of human T cells in SARS-CoV-2 (SARS2) viral clearance in primary COVID-19 are limited. To address this knowledge gap, samples were assessed for associations between SARS2 upper respiratory tract viral RNA levels and early virus-specific adaptive immune responses for 95 unvaccinated clinical trial participants with acute primary COVID-19 aged 18-86 years old, approximately half of whom were considered high risk for progression to severe COVID-19. Functionality and magnitude of acute SARS2-specific CD4 and CD8 T cell responses were evaluated, in addition to antibody responses. Most individuals with acute COVID-19 developed SARS2-specific T cell responses within 6 days of COVID-19 symptom onset. Early CD4 T cell and CD8 T cell responses were polyfunctional, and both strongly associated with reduced upper respiratory tract SARS2 viral RNA, independent of neutralizing antibody titers. Overall, these findings provide evidence for protective roles for circulating SARS2-specific CD4 and CD8 T cells during acute COVID-19.

immunology↗

bioRxiv2023

An actor-model framework for visual sensory encoding

A fundamental challenge in neuroengineering is determining a proper input to a sensory system that yields the desired functional output. In neuroprosthetics, this process is known as sensory encoding, and it holds a crucial role in prosthetic devices restoring sensory perception in individuals with disabilities. For example, in visual prostheses, one key aspect of image encoding is to down-sample the images captured by a camera to a size matching the number of inputs and resolution of the prosthesis. Here, we show that down-sampling an image using the inherent computation of the retinal network yields better performance compared to a learning-free down-sampling encoding. We validated a learning-based approach (actor-model framework) that exploits the signal transformation from photoreceptors to retinal ganglion cells measured in explanted retinas. The actor-model framework generates down-sampled images eliciting a neuronal response in-silico and ex-vivo with higher neuronal reliability to the one produced by original images compared to a learning-free approach (i.e. pixel averaging). In addition, the actor-model learned that contrast is a crucial feature for effective down-sampling. This methodological approach could serve as a template for future image encoding strategies. Ultimately, it can be exploited to improve encoding strategies in visual prostheses or other sensory prostheses such as cochlear or limb.

bioengineering↗

bioRxiv2023

Tomographic volumetric bioprinting of 3D pancreatic cancer models

1.Pancreatic ductal adenocarcinoma (PDAC) is the most frequent type of pancreatic cancer, one of the leading causes of cancer-related deaths worldwide. The first lesions associated with PDAC occur within the functional units of exocrine pancreas. The crosstalk between PDAC cells and stromal cells plays a key role in tumor progression. Thus, in vitro, fully human models of the pancreatic cancer microenvironment are needed to foster the development of new, more effective therapies. However, it is challenging to make these models anatomically and functionally relevant. Here, we used tomographic volumetric bioprinting, a novel method to fabricate three-dimensional cell-laden constructs, to produce a portion of the complex convoluted exocrine pancreas in vitro. Human fibroblast-laden gelatin methacrylate-based pancreatic models were processed to reassemble the tubuloacinar structures of the exocrine pancreas and, then human pancreatic ductal epithelial (HPDE) cells overexpressing the KRAS oncogene (HPDE-KRAS) were seeded in the acinar lumen to reproduce the pathological exocrine pancreatic tissue. The growth and organization of HPDE cells within the structure was evaluated and the formation of a thin epithelium which covered the acini inner surfaces in a physiological way inside the 3D model was successfully demonstrated. Interestingly, immunofluorescence assays revealed a significantly higher expressions of alpha smooth muscle actin (-SMA) vs. actin in the fibroblasts co-cultured with cancerous than with wild-type HPDE cells. Moreover, -SMA expression increased with time, and it was found to be higher in fibroblasts that laid closer to HPDE cells than in those laying deeper into the model. Increased levels of interleukin (IL)-6 were also quantified in supernatants from co-cultures of stromal and HPDE-KRAS cells. These findings correlate with inflamed tumor-associated fibroblast behavior, thus being relevant biomarkers to monitor the early progression of the disease and to target drug efficacy. To our knowledge, this is the first demonstration of a 3D bioprinted portion of pancreas that recapitulates its true 3-dimensional microanatomy, and which shows tumor triggered inflammation.

bioengineering↗

bioRxiv2022

Vitis vinifera plants edited in DMR6 genes show improved resistance to downy mildew.

The production and cultivation of vines (Vitis vinifera) tolerant or resistant to diseases such as downy mildew (DM) is a promising strategy to reduce fungicides and help viticulture sustainability. In many crops, generation of knock-out mutants in host genes controlling susceptibility to DM, such as Downy Mildew Resistant 6 (DMR6) is a strategy of proven success to obtain resistant plants, while the effect of mutations in DMR6 genes has yet to be demonstrated in grapevine. In addition, small mutations in genes governing important traits can be obtained by gene-editing while maintaining the genetic background of commercially important clones. Moreover, very recent advances in the technology of gene-editing allowed to produce non-transgenic grapevine mutants, by regeneration of protoplasts previously edited with the CRISPR-Cas9 ribonucleoprotein. This approach may revolutionize the production of new grapevine varieties and clones, but it requires knowledge on the targets, and an extensive evaluation of the impact of their mutation on plant phenotype and fitness. In this work we generated single and double knock-out mutants in DMR6 susceptibility (S) genes in multiple grapevine cultivars with improved resistance to DM.

plant biology↗

bioRxiv2021

Regeneration of Plants from DNA-free Edited Grapevine Protoplasts

CRISPR-Cas technology has widely extended the application fields of genome editing in plant breeding, making possible specific and minimal mutations within a genetic pool. With respect to standard genome editing technologies, CRISPR-Cas machinery can be introduced in the form of ribonucleoproteins (RNPs), thus avoiding the introduction of exogenous DNA into cells. The interest on the application of DNA-free delivery into plant cells is constantly increasing, especially in the case of valuable woody plants elite varieties where CRISPR-Cas9 technology would preserve their genotype, while still resulting into targeted genetic modifications. The use of single cells fits well the requirements of New Breeding Technologies, by ensuring both the CRISPR-Cas DNA-free delivery as RNPs and, since every plant will be regenerated from a single edited cell, the absence of chimerism. However, the use of protoplasts cell culture from woody plants is generally hampered by low editing efficiencies and an unsuccessful regenerative process. We here describe a successful DNA-free methodology to obtain fully edited grapevine plants, regenerated from protoplasts obtained from V. vinifera cv. Crimson seedless L. embryogenic callus. The transfected protoplasts were edited on the Downy Mildew susceptibility gene VvDMR6-2. The regenerated edited plants exhibited homozygous deletions of 1bp or 2bp, and homozygous insertion of 1bp.

plant biology↗

bioRxiv2020

Mining downy mildew susceptibility genes: a diversity study in grapevine.

Several pathogens continuously threaten viticulture worldwide. Until now, the investigation on resistance loci has been the main trend to understand the interaction between grapevine and mildew causal agents. Dominantly inherited gene-based resistance has shown to be race-specific in some cases, to confer partial immunity and to be potentially overcome within a few years since its introgression. Recently, on the footprint of research conducted on Arabidopsis, the putative hortologues of genes associated with downy mildew susceptibility in this species, have been discovered also in the grapevine genome. In this work, we deep-resequenced four putative susceptibility genes in 190 highly genetically diverse grapevine genotypes to discover new sources of broad-spectrum recessively inherited resistance. The scouted genes are VvDMR6-1, VvDMR6-2, VvDLO1, VvDLO2 and predicted to be involved in susceptibility to downy mildew. From all identified mutations, 56% were Single Nucleotide Polymorphisms (SNPs) in heterozygosity, while the remaining 44% were homozygous. Regarding the identified mutations with putative impact on gene function, we observed ~4% genotypes mutated in VvDMR6-1 and ~8% mutated in VvDMR6-2, only a handful of genotypes that were mutated in both genes. ~2% and ~7% genotypes showed mutations in VvDLO1 and VvDLO2 respectively, and again a few genotypes resulted mutated in both genes. In particular, 80% of impacting mutations were heterozygous while 20% were homozygous. The current results will inform grapevine genetics and corroborate genomic-assisted breeding programs for resistance to biotic stresses. Significance statementA survey on the genetic diversity of downy mildew susceptibility genes in grapevine varieties and wild species reveals a potential valuable for genomic-assisted breeding as well as tailored gene editing to induce disease resistance.

plant biology↗