Biology subjects

Villa, F.

Publications and source records attributed to Villa, F..

9 recordsLinked to original sources

bioRxiv2026

Sedimentary ancient DNA reveals rhizosphere-like plant-microbe association signals in a 2-million-year-old Arctic ecosystem

Plant-microbe interactions in the rhizosphere are central to nutrient cycling and ecosystem functioning. Sedimentary ancient DNA (sedaDNA) is a promising yet underexplored tool for reconstructing past microbial communities and investigating ecological interactions among plants, animals, and microorganisms. Here, we reanalyse the previously published Kap Kobenhavn Formation (Northern Greenland) sedaDNA dataset to move beyond taxonomic ecosystem reconstruction and test whether ancient sediments preserve structured, rhizosphere-compatible plant-microbe association signals. Our results show that this ancient boreal ecosystem hosted several rhizosphere-associated taxa, comparable to those in modern boreal soils. Several bacterial genera co-occurred repeatedly with specific plant families, forming a rhizosphere-like taxonomic core with predicted plant-growth-promoting traits related to nutrient acquisition, colonisation, and stress tolerance. Although sedaDNA co-occurrence cannot demonstrate direct symbiosis, the consistency of taxonomic, network, and functional signals suggests that ancient sediments preserve interconnected ecological structure. Our findings extend sedaDNA-based ecosystem reconstruction beyond taxonomy and provide a possibility for investigating plant-microbe association signals in deep time.

plant biology↗

bioRxiv2026

Preclinical validation of AAV9-TECPR2 gene therapy in a novel knock-in model of TECPR2-related disorder

TECPR2-related disorder is a rare, autosomal recessive neurodevelopmental and neurodegenerative disease characterized by early-onset motor dysfunction, sensory- and autonomic neuropathy, and progressive neurological decline with early mortality. Currently, there are no effective treatments for individuals affected by this debilitating condition. To advance our understanding of disease mechanisms and explore therapeutic strategies, we developed and then characterized a knock-in (KI) mouse model carrying the human TECPR2 c.1319delC frameshift mutation. TECPR2-KI mice exhibit a subset of disease-relevant phenotypes, most prominently abnormal gait, along with reduced body weight and altered tactile sensitivity. We additionally observe a reduction in acoustic startle responses, consistent with dysfunction of brainstem-associated sensorimotor pathways. Histopathological analyses reveal progressive accumulation of axonal spheroids in the dorsal column nuclei, together with abnormalities in autophagy-related markers, features previously reported in individuals with TECPR2-related disorder. To assess the therapeutic potential of gene replacement, we delivered TECPR2 via intracisternal infusion of AAV9/TECPR2 in neonatal KI mice. Gene therapy restored mechanosensory function, normalized gait and startle responses, maintain autophagic homeostasis, and partially reduced axonal pathology. These findings demonstrate that TECPR2-associated deficits are not only replicable in this new mouse model but are also amenable to postnatal intervention. Our study introduces a genetically accurate murine model of TECPR2 deficiency, identifies brainstem-associated phenotypes, and provides preliminary evidence supporting the feasibility of AAV9-mediated TECPR2 gene delivery, establishing a foundation for future translational research in a currently untreatable disease. One-Sentence Key MessageTECPR2 deficiency disrupts brainstem sensory-motor circuits, impairing autophagy and tactile, gait, and startle function and is prevented by neonatal AAV9.

neuroscience↗

bioRxiv2024

USP37 protects mammalian cells during DNA replication stress by counteracting CUL2-LRR1 and TRAIP

The USP37 deubiquitylase is important for mammalian cells to survive DNA replication stress but the underlying mechanisms are unknown. Here we demonstrate that USP37 binds the CDC45-MCM-GINS (CMG) helicase, which forms the stable core of the replisome and is regulated by ubiquitylation. The Pleckstrin-Homology Domain of USP37 binds CDC45 and structure-guided mutations that displace USP37 from CMG are sufficient to phenocopy loss of USP37 catalytic activity. Importantly, USP37 counteracts CMG helicase ubiquitylation by the CUL2LRR1 ligase, which induces helicase disassembly during termination. We show that depletion of CUL2LRR1 suppresses the sensitivity of Usp37 mutants to DNA synthesis defects and to ATR checkpoint kinase inhibitors. In contrast, mutation of the TRAIP ubiquitin ligase specifically suppresses the sensitivity of Usp37 mutants to topological stress during chromosome replication. We propose that USP37 evolved to reverse the untimely action of the two ubiquitin ligases that regulate the CMG helicase during chromosome replication in metazoa.

molecular biology↗

bioRxiv2021

Cooled SPAD array detector for low light-dose fluorescence laser scanning microscopy

The single-photon timing and sensitivity performance and the imaging ability of asynchronous-readout single-photon avalanche diode (SPAD) array detectors have opened up enormous perspectives in fluorescence (lifetime) laser scanning microscopy (FLSM), such as super-resolution image scanning microscopy and high-information content fluorescence fluctuation spectroscopy (FFS). However, the strengths of these FLSM techniques depend on the many different characteristics of the detector, such as dark-noise, photon-detection efficiency, after-pulsing probability, and optical-cross talk, whose overall optimization is typically a trade-off between these characteristics. To mitigate this trade-off, we present a novel SPAD array detector with an active cooling system, which substantially reduces the dark-noise without significantly deteriorating any other detector characteristics. In particular, we show that lowering the temperature of the sensor to -15{degrees}C significantly improves the signal-to-noise ratio due to a 10-fold decrease in the dark-count rate compared to room temperature. As a result, for imaging, the laser power can be decreased by more than a factor of three, which is particularly beneficial for live-cell super-resolution imaging, as demonstrated in fixed and living cells expressing GFP-tagged proteins. For FFS, together with the benefit of the reduced laser power, we show that cooling the detector is necessary to remove artifacts in the correlation function, such as spurious negative correlations observed in the hot elements of the detector, i.e., elements whose dark-noise is substantially higher than the median value. Overall, this detector represents a further step towards the integration of SPAD array detectors in any FLSM system. SIGNIFICANCESingle-photon avalanche diode (SPAD) array detectors are revolutionizing fluorescence laser-scanning microscopy (FLSM). Thanks to their single-photon timing and sensitivity ability and their imaging faculty, a SPAD array detector transforms any FLSM into a super-resolution microscope, and opens a whole range of possibilities for the study of sample dynamics by means of fluorescence fluctuation spectroscopy (FFS). However, dark-noise can be a severe problem for both imaging and FFS. For imaging, the signal overcomes noise only for a relatively high illumination intensity, which can be detrimental for live-cell experiments. For FFS, the noise leads to artifacts in the correlation curves, potentially leading to wrong conclusions about the sample. We show that lowering the temperature of the detector to -15{degrees}C solves both problems

biophysics↗

bioRxiv2021

Scientific modelling can be accessible, interoperable and user friendly: An example for pasture and livestock modelling

This article describes the adaptation of a non-spatial model of pastureland dynamics, including vegetation life cycle, livestock management and nitrogen cycle, for use in a spatially explicit and modular modelling platform (k.LAB) dedicated to make data and models more interoperable. The aim is to deliver an existing, locally successful monolithic model, into a more modular, transparent and accessible approach to potential end users, regional managers, farmers and other stakeholders. This allows better usability and adaptability of the model beyond its originally intended geographical scope (the Cantabrian Region in the North of Spain). The original model, named Puerto, is developed in the R language and includes 1,491 lines of code divided into 13 script files and linked to 19 input tables. The spatiotemporal rewrite is structured around a set of 10 namespaces called PaL (Pasture and Livestock), which includes 198 interoperable but independent models. The end user chooses the spatial and temporal context of the analysis through an intuitive web-based user interface called k.Explorer. Each model can be called individually or in conjunction with the others, by querying any PaL-related concepts in a search bar. A scientific workflow is built as a response, which is run to produce result datasets and a report with information on the data sources and modelling processes used, delivering results with full transparency. We argue that this work demonstrates key steps needed to create more Findable, Accessible, Interoperable and Reusable (FAIR) models. This is particularly essential in environments as complex as agricultural systems, where multidisciplinary knowledge needs to be integrated across diverse spatial and temporal scales in order to understand complex and changing problems.

ecology↗

bioRxiv2020

Proteus software for physics-based protein design

We describe methods and software for physics-based protein design. The folded state energy combines molecular mechanics with Generalized Born solvent. Sequence and conformation space are sampled with Replica Exchange Monte Carlo, assuming one or a few fixed protein backbone structures and discrete side chain rotamers. Whole protein design and enzyme design are presented as illustrations. Full redesign of three PDZ domains was done using a simple, empirical, unfolded state model. Designed sequences were very similar to natural ones. Enzyme redesign exploited a powerful, adaptive, importance sampling approach that allows the design to directly target substrate binding, reaction rate, catalytic efficiency, or the specificity of these properties. Redesign of tyrosyl-tRNA synthetase stereospecificity is reported as an example.Competing Interest StatementThe authors have declared no competing interest.View Full Text

biophysics↗

bioRxiv2019

Easy Two-Photon Image Scanning Microscopy with SPAD Array and Blind Image Reconstruction

Two-photon excitation (2PE) microscopy is the imaging modality of choice, when one desires to work with thick biological samples, possibly in-vivo. However, the resolution in two-photon microscopy is poor, below confocal microscopy, and the lack of an optical pinhole becomes apparent in complex samples as reduced quality of optical sectioning. Here, we propose a straightforward implementation of 2PE image scanning microscopy (2PE-ISM) that, by leveraging our recently introduced ISM platform - based on a new single-photon avalanche diode array detector - coupled with a novel blind image reconstruction method, is shown to improve the optical resolution, as well as the overall image quality in various test samples. Most importantly, our 2PE-ISM implementation requires no calibration or other input from the user - it works like any old and familiar two-photon system, but simply produces higher resolution images (in real-time). Making the complexity disappear, in our view, is the biggest novelty here, and the key for making 2PE-ISM mainstream.

bioengineering↗

bioRxiv2018

Image Scanning Microscopy with Single-Photon Detector Array

Image scanning microscopy (ISM) improves the spatial resolution of conventional confocal laser-scanning microscopy (CLSM), but current implementations reduce versatility and restrict its combination with fluorescence spectroscopy techniques, such as fluorescence lifetime. Here, we describe a natural design of ISM based on a fast single-photon detector array, which allows straightforward upgrade of an existing confocal microscope, without compromising any of its functionalities. In contrast to all-optical ISM implementations, our approach provides access to the raw scanned images, opening the way to adaptive reconstruction methods, capable of considering different imaging conditions and distortions. We demonstrate its utility in the context of fluorescence lifetime, deep, multicolor and live-cell imaging. This implementation will pave the way for a transparent and massive transition from conventional CLSM to ISM.\n\nconfocal microscopy | time-resolved spectroscopy | image scanning microscopy | single-photon detector array

bioengineering↗

bioRxiv2017

Conformational Dynamics In TRPV1 Channels Reported By An Encoded Coumarin Amino Acid

Transient Receptor Potential Vanilloid (TRPV1) channels support the detection and integration of nociceptive input. Currently available functional and structural data suggest that that TRPV1 channels have two potential gates within their cation selective permeation pathway: a barrier formed by a bundle crossing at the intracellular entrance and a second constriction created by the ion selectivity filter. To describe conformational changes associated with channel gating within the pore, the fluorescent non-canonical amino acid (f- ncAA) coumarin-tyrosine was genetically encoded at Y671, a residue proximal to the selectivity filter. TRPV1 channels expressing coumarin at either site displayed normal voltage- and agonist-dependent gating. Next, total internal reflection microscopy (TIRF) was performed to enable ultra-rapid, millisecond imaging of the conformational dynamics in single TRPV1 channels in live cells. Here, the data obtained from channels expressed in human derived cells show that optical fluctuations, photon counts, and variance of noise analysis from Y671 coumarin encoded in TRPV1 tetramers correlates closely with channel activation by capsaicin, thus providing an direct optical marker of channel activation at the selectivity filter. In companion molecular dynamics simulations, Y671 displays alternating solvent exposure between the closed and open states, giving support to the optical data. These calculations further suggest a direct involvement of Y671 in controlling the relative position of the pore helix and its role in supporting ionic conductance at the TRPV1 selectivity filter.

biophysics↗