Biology subjects

Sala, S.

Publications and source records attributed to Sala, S..

10 recordsLinked to original sources

bioRxiv2026

A dependency-free, streamable format and cross-language toolkit for scalable LC-MS feature detection: reading only what you need

Mass spectrometry generates data faster than it can be read, and the exchange standard, mzML, is text-based and must be parsed in full before any spectrum is accessible. Binary alternatives are smaller but depend on storage engines such as HDF5, so access is dictated by the engine, not the file. We present Ionic (.ion), an open-source, compact, streamable binary format, and Quant{middle dot}ion, a processing toolkit built on the former. Ionic stores spectra, chromatograms and metadata as independently compressed, indexed blocks, so a reader retrieves only the bytes it needs, even inside a web browser, and converts losslessly to and from mzML. Ionic was smaller than compressed mzMLb on every acquisition type tested, and extracting one compound took under 40 ms, 35 to 90 times faster than an mzML reader. Quant{middle dot}ion exposes one core to R, Python, and JavaScript with identical results, and recovered 97% of true features on a ground-truth benchmark.

bioinformatics↗

bioRxiv2025

LIM Domain Proteins link molecular and global tension by recognizing strained actin in adhesions

Mechanotransduction is fundamental to cell signaling and depends on force-sensitive adhesion proteins. How these proteins differentiate and integrate their responses to tension remains an open question. We show mechanosensitive LIM domain proteins like zyxin detect global adhesion tension by recognizing strained actin within these structures. In sharp contrast, vinculin localization and intramolecular tension remain unchanged, despite vinculins well-documented role in mechanotransduction. This reveals a stark disconnect between molecular tension and global tension in adhesions. We further show tension-dependent localization is specific to LIM domain proteins that recognize strained actin and extends to LIM proteins at cell-cell junctions, suggesting a common mechanotransduction mechanism. Finally, we show zyxins tension-dependent adhesion localization stabilizes actin and recruits VASP to promote stress fiber polymerization, identical to its role in stress fiber repair. Our findings reveal a fundamental role for LIM domain protein force-sensing in adhesions and highlight the non-linear connection between molecular and global tension.

cell biology↗

bioRxiv2025

Functionalized Calcium Carbonate Microparticles in Ethyl Cellulose Films: A Vehicle for Sustained Amoxicillin Release for Medical Applications

The continuous quest for materials capable of providing extended release of antimicrobial drugs is particularly important for indwelling medical applications. In this study, we utilized amoxicillin as a model active pharmaceutical ingredient (API) to investigate the feasibility of using porous media - specifically, functionalized calcium carbonate (FCC) microparticles - as a primary drug carrier embedded within an ethyl cellulose (EC) polymer film. Our main objective was to prolong and sustain the release of the API. The fabrication process of the microparticle containing film involved two key steps: loading the model API into the FCC particles and then embedding these loaded particles into the polymeric film. Amoxicillin was loaded into the FCC particles using a solvent evaporation method. Detailed characterization through Scanning Electron Microscopy (SEM), lab- and synchrotron-based XRD revealed that amoxicillin precipitated both inside and on the surface of the FCC particles, predominantly in an amorphous form. Additionally, ultraviolet-visible (UV-vis) spectroscopic data demonstrated an increased release rate from the particles compared to pure amoxicillin powder. Embedding amoxicillin pre-loaded porous FCC particles in the EC film led to a more rational sustained release compared with powder amoxicillin embedded directly in the film, advantageously delivering the same amount of amoxicillin over a longer period; a result that may be relevant for indwelling medical devices such as urinary catheters, vascular access devices or wound drains.

bioengineering↗

bioRxiv2025

In vivo Morphological Dynamics of Single Laser-Axotomized Corneal Nerve Fibers in Sarm1-Null Adult Mice

Axonal regeneration represents a pivotal aspect of the adult peripheral nervous system (PNS). When an injury occurs, peripheral axons are able to regenerate and reestablish connections with their original targets. Although several precision techniques for severing axons in various non-mammalian model organisms have allowed to study the dynamics of regeneration after injury, similar axonal injury models have yet to be fully developed in mammals. In this study, we introduced a novel experimental method for laser-induced axotomy of single corneal sensory subbasal nerve fibers. This method enables the in vivo monitoring and quantification of axonal degeneration and regeneration morphological dynamics in adult mice. Results revealed that the degeneration of the distal stump of the subbasal fiber was delayed in mice lacking the protein SARM1, which promotes degenerative process after injury. Meanwhile, the proximal stump maintained the regenerative dynamics of the subbasal fiber, but regeneration of its nerve terminals was impaired. The present study introduces a valuable model for the in vivo study of the morphological plasticity dynamics of peripheral axons after injury in genetically tractable adult mammals.

neuroscience↗

bioRxiv2024

Non-muscle myosin 2 can incorporate into established filaments in cells without an assembly competence domain

Myosin 2 dynamically assembles into filaments that exert force on the actin cytoskeleton. To form filaments, myosin 2 monomers transition between folded and unfolded states. Monomer unfolding exposes an extended coiled-coil that interacts with other monomers in parallel and antiparallel fashions, enabling bipolar filament formation. A C-terminal domain of the coiled-coil, termed assembly competence domain (ACD), has been repeatedly identified as necessary for filament assembly. Here, we revisit ACD contribution when full-length filaments are present. Non-muscle myosin 2A lacking the ACD ({Delta}ACD) initially appears diffuse, but triton extraction of cytosolic fraction reveals cytoskeletal association. Disruption of the folded monomer enhances the cytoskeletal fraction, while inhibition of endogenous filament assembly appears to reduce it. Finally, high resolution imaging of endogenous and exogenous bipolar filamentous structures reveals highly coincident signal, suggesting {Delta}ACD constructs co-assemble with endogenous myosin 2A filaments. Our data demonstrate that while the ACD is required for de novo filament assembly, it is not required for monomers to recognize and associate with established filaments in cells. More broadly, this highlights the existence of distinct mechanisms governing myosin 2 monomer assembly into nascent filaments, and monomer recognition and association with established filaments to maintain steady-state contractile networks.

cell biology↗

bioRxiv2024

The ion channel TRPM8 is a direct target of the immunosuppressant rapamycin in primary sensory neurons

Background and PurposeThe mechanistic target of rapamycin (mTOR) signaling pathway is a key regulator of cell growth and metabolism. Its deregulation is implicated in several diseases. The macrolide rapamycin (RAP), a specific inhibitor of mTOR, has immunosuppressive, anti-inflammatory and antiproliferative properties. Recently, we identified tacrolimus, another macrolide immunosuppressant, as a novel activator of TRPM8 ion channels, involved in cold temperature sensing, thermoregulation, tearing and cold pain. We hypothesized that RAP may also have agonist activity on TRPM8. Experimental approachUsing calcium imaging and electrophysiology in transfected HEK293 cells and wildtype or Trpm8 KO mouse DRG neurons, we characterized RAP effects on TRPM8. We also examined the effects of RAP on tearing in mice. Key ResultsMicromolar concentrations of RAP activate rat and mouse TRPM8 directly and potentiate cold-evoked responses. These effects were also observed in human TRPM8. In cultured mouse DRG neurons, RAP evoked an increase in intracellular calcium almost exclusively in cold-sensitive neurons. Responses were drastically blunted in Trpm8 KO mice or by TRPM8 antagonists. Cutaneous cold thermoreceptor endings were also activated by RAP. Topical application of RAP to the eye surface evokes tearing in mice by a TRPM8-dependent mechanism. Conclusion and implicationsThese results identify TRPM8 cationic channels in sensory neurons as novel molecular targets of the immunosuppressant RAP. These findings may help explain some of its therapeutic effects after topical application to the skin and the eye surface. Moreover, RAP could be used as an experimental tool in the clinic to explore cold thermoreceptors. Bullet point summaryWHAT IS ALREADY KNOWN O_LITRPM8 is a polymodal channel involved in cold detection, thermoregulation, tearing and cold pain C_LIO_LITacrolimus, a macrolide immunosupressor, is an agonist of cold-activated TRPM8 channels C_LI WHAT THIS STUDY ADDS O_LIThe macrolide rapamycin also activates directly TRPM8 channels in mouse sensory neurons and human TRPM8 C_LIO_LIRapamycin stimulates tearing in mice in a TRPM8-dependent manner CLINICAL SIGNIFICANCE C_LIO_LIRapamycin, an FDA-approved drug, shows agonist activity on TRPM8 channels C_LIO_LIBeneficial effects of rapamycin and other macrolides on inflammatory ocular disorders may involve TRPM8 activation C_LI

neuroscience↗

bioRxiv2022

Smooth Muscle Myosin 2 Filaments Dynamically Assemble and Stabilize During Induced Contractility

BackgroundVascular smooth muscle cells (SMCs) dynamically tune blood vessel diameter to regulate blood pressure, provide vessel wall structural integrity, and absorb shock on a beat-to-beat timescale. Smooth muscle myosin 2 (SMII) is the dominant motor protein driving SMC contraction. To function, SMII monomers dynamically assemble into filaments, which associate with the actin cytoskeleton to drive contractility. Precisely how SMII filaments assemble and exchange in living SMCs, however, both at steady-state and during induced contractility, remains poorly defined. MethodsWe used a single-cell filament assembly assay to determine SMII assembly into filaments at steady-state and upon induced contractility in rat aortic SMCs (A7R5) transiently-expressing EGFP-tagged SM1A isoform of SMII. We then used fluorescence recovery after photobleaching (FRAP) to characterize SMII exchange kinetics at steady-state and upon induced contractility, and measured changes in force production using traction force microscopy. Finally, we developed a CRISPR knock-in EGFP-SMII murine model to quantify SMII dynamics at endogenous expression in primary SMCs and intact arterioles. ResultsWhile predominantly filamentous at baseline, induced contraction rapidly increased SMII filament assembly. FRAP revealed rapid SMII exchange kinetics, more similar to non-muscle myosin II than striated myosin II, and induced contractility consistently stabilized SMII filaments. Super-resolution imaging revealed SMII and non-muscle myosin II filament structures consistent with co-assembly. Endogenous EGFP-SMII in primary SMCs and intact arterioles paralleled cell culture studies with similar baseline exchange kinetics and activation-dependent stabilization. ConclusionsTogether, these data support a model in which SMII is surprisingly dynamic and co-assembles with non-muscle myosin II. Vascular SMC activation further increases SMII filament assembly while reducing filament exchange, consistent with stabilization of a dynamic SMII pool during force generation, which allows cells to dynamically adapt their overall contractility in response to environmental conditions. CLINICAL IMPLICATIONSSmooth muscle myosin II (SMII) is the principal contractile motor protein of vascular smooth muscle tissue, but its molecular behavior in living differentiated SMCs remains poorly defined. Here, we show that SMII is not a static contractile scaffold but highly dynamic. SMII exhibits dynamic exchange between the filament and monomeric forms at baseline, but becomes acutely stabilized during agonist-induced contraction, including in primary SMCs and intact arterioles at endogenous Myh11 expression. These findings suggest that vascular tone is tuned not only by activating pre-existing myosin filaments, but also by rapidly shifting SMII filament assembly levels and exchange rates. This framework is relevant to diseases in which SMC contractility and arterial wall mechanics are abnormal, including MYH11-associated thoracic aortic disease and related disorders of arterial stiffness or maladaptive vasomotor regulation. Although this study is mechanistic, it identifies SMII filament dynamics as a measurable layer of vascular regulation and a potential readout for future studies of pathogenic MYH11 variants, disease modeling, and therapies that alter myosin activation and/or cytoskeletal stability. O_FIG O_LINKSMALLFIG WIDTH=192 HEIGHT=200 SRC="FIGDIR/small/511341v2_ufig1.gif" ALT="Figure 1"> View larger version (78K): org.highwire.dtl.DTLVardef@d64a8forg.highwire.dtl.DTLVardef@b9000corg.highwire.dtl.DTLVardef@1b24a91org.highwire.dtl.DTLVardef@3d81be_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2021

RhoA mediates stress fiber strain site recognition by the LIM protein testin

The actin cytoskeleton is a key regulator of mechanical processes in cells. The family of LIM domain proteins have recently emerged as important mechanoresponsive cytoskeletal elements capable of sensing strain in the actin cytoskeleton. The mechanisms regulating this mechanosensitive behavior, however, remain poorly understood. Here we show that the LIM domain protein testin is peculiar in that despite the full-length protein primarily appearing diffuse in the cytoplasm, the C-terminal LIM domains alone recognize focal adhesions and strained actin while the N-terminal domains alone recognize stress fibers. Phosphorylation mutations in the dimerization regions of testin, however, reveal its mechanosensitivity and cause it to relocate to focal adhesions and sites of strain in the actin cytoskeleton. Finally, we demonstrate activated RhoA causes testin to adorn stress fibers and become mechanosensitive. Together, our data show that testins mechanoresponse is regulated in cells and provide new insights into LIM domain protein recognition of the actin cytoskeleton mechanical state.

cell biology↗

bioRxiv2020

The ubiquitin ligase Hecw controls oogenesis and neuronal homeostasis by promoting the liquid state of ribonucleoprotein particles

Specialised ribonucleoprotein (RNP) granules are a hallmark of germ cells. Among their main function is the spatial and temporal modulation of the activity of specific mRNA transcripts that allow specification of primary embryonic axes. While RNPs composition and role are well established, their regulation is poorly defined. Here, we demonstrate that Hecw, a newly identified Drosophila ubiquitin ligase, is a key modulator of RNPs in oogenesis. Loss of Hecw activity results in the formation of enlarged granules that transition from a liquid to a gel-like state. At the molecular level, Hecw depletion leads to reduced ubiquitination and activity of the translational repressor Fmrp, resulting in premature Orb expression/recruitment in nurse cells. In addition to defective oogenesis, flies lacking Hecw show neurodegenerative traits with premature aging and climbing defects due to neuronal loss that are linked to RNPs condensation. Our findings reveal an unprecedented function of ubiquitin in modulating RNP fluidity and activity.Competing Interest StatementThe authors have declared no competing interest.View Full Text

animal behavior and cognition↗

bioRxiv2018

The Notch and EGFR signaling regulate caspase inhibitor Diap1 to match supply with intestinal demand

The regenerative activity of adult stem cells carries a high risk of cancer, particularly in highly renewable tissues. To guarantee that the correct organ size is attained and to cope with the continual risk of cancer, developing tissues often use programmed cell death (PCD) as an adaptive mechanism to cull excess and abnormal cells. Members of the family of Inhibitor of Apoptosis Proteins (IAPs) inhibit caspases and cell death and are often overexpressed in cancer. Here, we show that Diap1 is expressed in committed progenitor (enteroblast) cells in the adult Drosophila intestine. Blocking endogenous caspases uncovered that more than half of enteroblasts produced by intestinal stem cells (ISCs) are actively eliminated by apoptosis in the physiological intestine and also led to tumorigenesis. We find that antagonistic interplay between the Notch and EGFR signaling on Diap1 regulation governs the enteroblast cell death or survival decision via the conserved Klumpfuss/WT1-Lozenge/RUNX axis, which also regulates of differentiation plasticity of enteroblasts. These data provide new insights into how apoptosis drives adult tissue renewal and protection against tumors.

cell biology↗