Biology subjects

Garcia, M.

Publications and source records attributed to Garcia, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Commensal taxa in gut microbiota limit antibiotic resistance during extended oral antibiotic use

Certain bacterial infections, such as those involving prosthetics, can require antimicrobial therapy over months to years, potentially increasing the burden of antimicrobial resistance. Here we longitudinally track the antimicrobial resistome in mice during continuous antibiotic dosing over 21 months. The burden of antibiotic resistance genes (ARGs) initially increases, but, surprisingly, declines in later months, approaching levels observed in untreated animals. ARG burden is regulated by taxonomy and declines as ARG-harboring taxa that initially bloom are replaced by commensals. Furthermore, we find that the dynamics of antibiotic-induced ARG burden are influenced by age-related differences in microbial taxonomy and can be removed by fecal microbiota transplantation. We show that commensals may regulate the resistome by limiting the growth of ARG-harboring taxa, thereby providing antimicrobial expansion resistance.

microbiology↗

bioRxiv2025

Evaluating zero-shot prediction of protein design success by AlphaFold, ESMFold, and ProteinMPNN

De novo protein design has enabled the creation of proteins with diverse functionalities that are not found in nature. Despite recent advances, experimental success rates remain inconsistent and context-dependent, posing a bottleneck for broader applications of de novo design. To overcome this, structure and sequence prediction models have been applied to assess design quality prior to experimental testing to save time and resources. In this study, we aimed to determine the extent to which AlphaFold2, Protein MPNN, and ESMFold can discriminate between experimentally successful and unsuccessful designs. For this, we curated a benchmark dataset of 614 experimentally characterized de novo designed monomers from 11 different design studies between 2012 and 2021. All predictive models demonstrated moderate ability to discriminate experimental successes (expressed, soluble, monomeric, and fold into the intended design structure) from failures, with many failed designs having better confidence metrics than successful designs. Among all computational models evaluated, ESMFold average pLDDT yielded the best individual performance at distinguishing between successful and unsuccessful designs. A logistic regression model combining all confidence metrics provided only modest improvement over ESMFold pLDDT alone. Overall, these results show that these models can serve as an initial filtering strategy prior to experimental validation; however, their utility at accurately predicting experimental successful designs remains limited without task-specific training.

bioinformatics↗

bioRxiv2025

Modular cyanobacterial regulatory architecture enables dynamic graded responses to oxidative stress

A fundamental paradox of oxygenic photosynthesis: growth-essential energy machinery generates reactive oxygen species (ROS) threatening survival, yet the systems-level regulatory networks balancing the growth-survival trade-off remain unclear. Through integrative experimental-computational analysis combining steady-state transcriptomics with independent component analysis across 0-78.4% oxygen, we decoded the regulatory architecture driving progressive transitions in Synechococcus elongatus PCC 7942 from ROS sensing through defense to growth shutdown. Integration of 407 transcriptome samples identified 78 regulatory modules (iModulons) explaining 72.3% of expression variance and revealed calibrated responses: low stress triggers metalloregulators (SufR, PerR) for ROS sensing and primary antioxidants; moderate stress activates RpaB operating through four distinct regulatory states redirecting metabolism to defense; severe stress induces growth arrest via stringent response pathway convergence. This quantitative regulatory framework enables precise growth-defense calibration through modular network architecture: RpaB coordinates genome-wide resource reallocation (RpaB[~]P growth-promoting, RpaB ROS defense-activating, RpaABC circadian-integrating, RpaB ycf46 checkpoint activation), offering systematic strategies for engineering stress-tolerant bioplatforms and predictive models for environmental stress responses.

systems biology↗

bioRxiv2025

In vivo exposure of mixed microplastic particles in mice and its impacts on the murine gut microbiome and metabolome

Microplastics (MPs) are emerging environmental contaminants due to increasing global plastic production and waste. Microplastics, defined as plastic particles less than 5 mm in diameter, are formed through degradation of larger plastics via sunlight, weathering, and microbes. These plastic compounds are widely detected in water, soil, food, as well as human stool and blood. The gut microbiome, often referred to as our second genome, is important in human health and is the primary point of contact for orally ingested microplastics. To investigate the impact of ingested MPs on the gut microbiome and the metabolome, 8 weeks-old male and female C57/BL6 mice were orally gavaged mixed plastic (5 um) exposure consisting of polystyrene, polyethylene, and the biodegradable/biocompatible plastic, poly-(lactic-co-glycolic acid) twice a week for 4 weeks at 0, 2, or 4 mg/week (n = 8/group). Fecal pellets were collected for bacterial DNA extraction and metagenomic shotgun sequencing, and serum was subjected to targeted and untargeted metabolomics. MPs exposure resulted in significant sex-specific and dose-dependent changes to the gut microbiome composition along with substantial regulation of the predicted metabolic pathways. Untargeted metabolomics in serum showed that a low MPs dose displayed a more prominent effect on key metabolic pathways such as amino acid metabolism, mitochondrial function, and inflammation. Additionally, SCFA-targeted metabolomics showed significant changes in neuroprotective SCFAs levels in both sexes by MPs exposure. In conclusion, our study has demonstrated that microplastics dysregulate the gut microbiome and serum metabolome, providing critical insights into potential human disease risks associated with microplastic contamination.

pharmacology and toxicology↗

bioRxiv2025

Virion encapsidation and cell attachment function of the reovirus attachment protein is influenced by its structural flexibility

The reovirus {sigma}1 attachment protein mediates virus interaction with host cell receptors that is critical for cell entry. Reovirus tropism is controlled by properties of {sigma}1. {sigma}1 is present as trimers that are held within turrets at the icosahedral vertices of reovirus virions. However, because {sigma}1 has not been visualized on reovirus virions in high resolution structures and because the fulllength structure of purified {sigma}1 protein has not been solved, it is not clear how {sigma}1 is presented on virions. What properties of {sigma}1 are essential for its incorporation on virions is also not known. In this study, we used ColabFold to model the structure of reovirus serotype 1 (T1) and serotype 3 (T3) {sigma}1 proteins. We find that these proteins fold into similar structures with regions of flexibility between the head and body domains of {sigma}1. We also predicted the structures of chimeric {sigma}1 proteins comprised of domain swaps between T1 and T3 {sigma}1 proteins. Our analyses indicate that chimeric proteins with mismatched body and head domain have increased flexibility in this region. Characterization of particles expressing such chimeric {sigma}1 proteins demonstrated that deviation from the flexibility of parental {sigma}1 leads to a reduction in {sigma}1 incorporation on to the virion. Further, we find that even when incorporation is not affected, virus attachment to host cell receptors is influenced by altered {sigma}1 flexibility. Finally, our work demonstrates that 1 protein impacts the encapsidation pattern and receptor engagement properties of {sigma}1 and that this effect is influenced by properties of the N-terminal portion of {sigma}1. ImportanceAttachment to host cell receptors is a critical step in initiation of virus infection. Some viruses attach to cellular receptors via dedicated viral proteins. Both the number of attachment factors present on the virus and whether they are present on the virus particle in the correct form can influence cell attachment. Here, using reovirus as a model, we use a protein structure prediction algorithm to model the as yet unknown structure of full-length reovirus attachment protein {sigma}1. We find predicted regions of flexibility in the protein and identify how this flexibility is regulated. We find that the flexibility of {sigma}1 independently regulates whether it is stably incorporated into particles and if can efficiently interact with host receptors.

microbiology↗

bioRxiv2025

Large-scale discovery, analysis, and design of protein energy landscapes

All folded proteins continuously fluctuate between their low-energy native structures and higher energy conformations that can be partially or fully unfolded. These rare states influence protein function, interactions, aggregation, and immunogenicity, yet they remain far less understood than protein native states. Although native protein structures are now often predictable with impressive accuracy, conformational fluctuations and their energies remain largely invisible and unpredictable, and experimental challenges have prevented large-scale measurements that could improve machine learning and physics-based modeling. Here, we introduce a multiplexed experimental approach to analyze the energies of conformational fluctuations for hundreds of protein domains in parallel using intact protein hydrogen-deuterium exchange mass spectrometry. We analyzed 5,778 domains 28-64 amino acids in length, revealing hidden variation in conformational fluctuations even between sequences sharing the same fold and global folding stability. Site-resolved hydrogen exchange NMR analysis of 13 domains showed that these fluctuations often involve entire secondary structural elements with lower stability than the overall fold. Computational modeling of our domains identified structural features that correlated with the experimentally observed fluctuations, enabling us to design mutations that stabilized low-stability structural segments. Our dataset enables new machine learning-based analysis of protein energy landscapes, and our experimental approach promises to reveal these landscapes at unprecedented scale.

biophysics↗

bioRxiv2025

Risk preferences depend on environmental richness in rats performing a patch-foraging task

Risk, or variance over outcomes, features prominently in many decisions, but the factors that determine when and how risk modulates decision making remain unclear. We tested how risk affected rats strategies for exploiting a diminishing food source as the overall richness of the environment was manipulated. Long-Evans rats earned food by sequentially visiting two foraging patches with different reward schedules--a low-variance standard option and a high-variance risky option--that provided the same average rate of reward. When rats switched between options, they encountered either a long or short delay during which no food was available to simulate the cost of travelling between patches. When the travel delay was short rats allocated more time to the low-variance standard reward schedule than the high-variance risky option. When the travel time was long rats spent the same amount of time in risky and standard patches. Consistent with previous work, rats "overharvested" patches, remaining for longer than the optimal patch residence duration. Overharvesting was prevalent in both risky and standard patches, and the magnitude of overharvesting increased with successive visits to the same patch, suggesting that overharvesting was not driven by uncertainty about the reward statistics of patches.

animal behavior and cognition↗

bioRxiv2025

Blood-borne sphingosine 1-phosphate maintains vascular resistance and cardiac function.

G protein-coupled receptors (GPCRs) are key regulators of cardiovascular function that provide targets for the treatment of cardiovascular disease. Sphingosine 1-phosphate (S1P) is an erythrocyte- and platelet-derived lipid mediator with cognate GPCRs on endothelial cells (EC), vascular smooth muscle cells (VSMC) and cardiomyocytes. S1P circulates in plasma bound to apolipoprotein M (ApoM)-containing high-density lipoproteins (HDL) and to albumin. Circulating S1P levels correlate positively with systolic blood pressure in hypertension and negatively with severity in septic shock and with left ventricular (LV) function in coronary heart disease. In mice, impaired S1P binding to HDL or signaling to EC both trigger hypertension, supporting an essential role for HDL-S1P in supporting endothelial function. The roles of albumin-S1P and myocyte S1PRs in cardiovascular homeostasis remain incompletely defined. Contrasting isolated HDL-S1P deficiency, we report that non-selective depletion of circulating S1P pools in mice impairs LV contractile function and induces hypotension and resistance to the spontaneous increase in blood pressure with age. Cardiac output was preserved in naive S1P deficient mice by compensatory LV dilation, but cardiac reserve reduced in a dobutamine stress test. These phenotypes tracked with hematopoietic cell S1P production and were partially or fully reversed by erythrocyte transfusion. Hypotension was accompanied by reduced peripheral resistance, and S1P infusion dose-dependently increased vascular resistance in isolated perfused kidneys from wild-type mice but not mice with compound deficiency in S1PR2&3. Epistatic analysis supported a critical role for S1PR3 in S1P-dependent blood pressure regulation and pointed to a distinct origin of the cardiac phenotype. Although circulating S1P is elevated in hypertensive mice and humans, increasing circulating S1P was not sufficient to induce hypertension in naive mice. These observations suggests that albumin-S1P crosses the endothelium in resistance arteries to gain access to contractile VSMC S1P receptors, and that myocyte S1PR signaling is essential for vascular resistance and blood pressure maintenance in mice. They also highlight the role for plasma chaperones in specifying vascular responses to S1P and the relevance of S1P as a biomarker and potential therapeutic target for blood pressure regulation and heart failure.

physiology↗

bioRxiv2024

Improving the monitoring of the invasive Blue Crab (Callinectes sapidus): combining environmental DNA and citizen observations

O_LIEarly detection is a crucial tool for identifying the spread of invasive species. C_LIO_LIIn this study, we validated a probe-based quantitative polymerase chain reaction (qPCR) assay for the detection of the invasive Blue Crab, Callinectes sapidus, in the Mediterranean Sea, using 22 initial eDNA environmental samples (eDNA) collected from three coastal lagoons. C_LIO_LIA subsequent large-scale eDNA sampling campaign (61 samples in 31 sites), conducted in collaboration with local stakeholders, was carried out to map the distribution of Callinectes sapidus along the Occitanie coastline (Western Mediterranean, France). C_LIO_LIUsing eDNA probe-based qPCR, Callinectes sapidus was detected in 32 out the 61 samples (52%), confirming its presence in 24 out of 31 sites surveyed, including the 13 lagoons where its occurrence had already been reported, as well as two additional lagoons and at sea where no prior records existed. C_LIO_LIOur results demonstrate the utility of eDNA probe-based qPCR for effective monitoring the invasive Blue Crab. The integration of eDNA analysis with citizen science observations enhances the monitoring framework, facilitating early detection and contributing to improved management strategies at the very beginning of species colonization when practical actions could be implemented. C_LI

ecology↗

bioRxiv2024

Quality assessment and control of unprocessed anatomical, functional, and diffusion MRI of the human brain using MRIQC

Quality control of MRI data prior to preprocessing is fundamental, as substandard data are known to increase variability spuriously. Currently, no automated or manual method reliably identifies subpar images, given pre-specified exclusion criteria. In this work, we propose a protocol describing how to carry out the visual assessment of T1-weighted, T2-weighted, functional, and diffusion MRI scans of the human brain with the visual reports generated by MRIQC. The protocol describes how to execute the software on all the images of the input dataset using typical research settings (i.e., a high-performance computing cluster). We then describe how to screen the visual reports generated with MRIQC to identify artifacts and potential quality issues and annotate the latter with the "rating widget" - a utility that enables rapid annotation and minimizes bookkeeping errors. Integrating proper quality control checks on the unprocessed data is fundamental to producing reliable statistical results and crucial to identifying faults in the scanning settings, preempting the acquisition of large datasets with persistent artifacts that should have been addressed as they emerged. RELATED LINKSO_ST_ABSKey reference(s) using this protocolC_ST_ABSEsteban, O. et al. (2017), PLoS ONE 12(9): e0184661. [10.1371/journal.pone.0184661] Esteban, O. et al. (2019), Sci Data 6, 30. [10.1038/s41597-019-0035-4] Esteban, O. et al. (2020), Nat Prot 15, 2186-2202. [10.1038/s41596-020-0327-3] Provins, C. et al. (2023), Front. Neuroinform. 1, 2813-1193. [10.3389/fnimg.2022.1073734] Bissett P. et al. (2024) Sci Data 11: 809. [10.1038/s41597-024-03636-y] Key data used in this protocolAmsterdam Open MRI Collection: Population Imaging of Psychology1 (AOMIC-PIOP1; ds002785 [https://openneuro.org/datasets/ds002785]).

neuroscience↗

bioRxiv2024

deadtrees.earth - An Open-Access and Interactive Database for Centimeter-Scale Aerial Imagery to Uncover Global Tree Mortality Dynamics

Excessive tree mortality is a global concern and remains poorly understood as it is a complex phenomenon. We lack global and temporally continuous coverage on tree mortality data. Ground-based observations on tree mortality, e.g., derived from national inventories, are very sparse, not standardized and not spatially explicit. Earth observation data, combined with supervised machine learning, offer a promising approach to map tree mortality over time. However, global-scale machine learning requires broad training data covering a wide range of environmental settings and forest types. Drones provide a cost-effective source of training data by capturing high-resolution orthophotos of tree mortality events at sub-centimeter resolution. Here, we introduce deadtrees.earth, an open-access platform hosting more than a thousand centimeter-resolution orthophotos, covering already more than 300,000 ha, of which more than 58,000 ha are fully annotated. This community-sourced and rigorously curated dataset shall serve as a foundation for a global initiative to gather comprehensive reference data. In concert with Earth observation data and machine learning it will serve to uncover tree mortality patterns from local to global scales. This will provide the foundation to attribute tree mortality patterns to environmental changes or project tree mortality dynamics to the future. Thus, the open and interactive nature of deadtrees.earth together with the collective effort of the community is meant to continuously increase our capacity to uncover and understand tree mortality patterns.

ecology↗

bioRxiv2024

A functional interleukin-4 homolog is encoded in the genome of infectious laryngotracheitis virus: unveiling a novel virulence factor

Herpesviruses have evolved numerous immune evasion tactics, persisting within their hosts through self-perpetuating strategies. One such tactic involves acquiring functional copies of host genes encoding cytokines such as IL-6 (HHV-8), IL-10 (HHV-4, HHV-5), and IL-17 (SaHV-2). These viral mimics, or virokines, can bind to cellular receptors, modulating the natural cytokine signaling to manipulate the immune response in favor of the virus or stimulate target cell growth to enhance virus replication. In the course of full-length cDNA sequencing of infectious laryngotracheitis virus (ILTV) transcripts, a previously unknown highly-spliced gene was discovered in the viral genome predicted to encode a 147 amino acid protein with similarity to vertebrate interleukin-4. The three-intron gene structure was precisely conserved with chicken and other vertebrate IL-4 homologs, and the amino acid sequence displayed structural conservation with vertebrate homologs at the primary, secondary, and tertiary levels based on computational modeling. The viral IL-4 gene was subsequently identified in all sequenced ILTV genomes. The mature transcript was highly expressed both in vitro and in vivo, and protein expression in infected cells was confirmed using LC-MS/MS. Phylogenetic analyses, along with the conserved gene structure, suggested direct capture from a Galliformes host. Functionally, an LPS-stimulation assay showed that the expressed viral IL-4 homolog stimulated nitric oxide production in a macrophage cell line at comparable levels to recombinant chicken IL-4. A recombinant virus lacking vIL-4 exhibited slightly higher titers in cell culture compared to the parental strain. In vivo bird studies demonstrated reduced pathogenicity of the vIL-4 knockout compared to wildtype. These results represent the first report of a previously unknown virokine encoded in the ILTV genome expressing a functional IL-4 homolog and virulence factor. Author SummaryHerpesviruses are large DNA viruses, several of which express proteins that are homologous to host cytokines (termed virokines) and are thought to modulate the host immune response in favor of the virus. We report the identification of a novel virokine in the genome of infectious laryngotracheitis virus (ILTV) that is structurally and functionally similar to avian interleukin-4. The significance of this finding is threefold: O_LINovel mechanism: The identification of vIL-4 expands our understanding of the strategies employed by viruses to evade the host immune response, including through the acquisition, adaptation, and expression of cellular genes for their own advantage. C_LIO_LIImplications for disease pathogenesis: We demonstrate that vIL-4 plays a functional role in ILTV virulence. Understanding the mechanisms by which this happens could lead to the development of novel therapeutic strategies. C_LIO_LIEvolutionary insights: The presence of the highly spliced vIL-4 gene in the ILTV genome suggests direct genomic capture of a host gene, providing insights into the evolutionary history of ILTV and its interactions with avian theropods. C_LI Overall, this research represents a significant contribution to our understanding of viral immunology and has potential implications for the development of improved vaccines for ILTV infection.

microbiology↗

bioRxiv2024

Larval motility assay using WMicrotracker: a high throughput test to discriminate between resistance and susceptibility to anthelmintic drugs in nematodes

Grazing ruminants suffer from various helminth infections particularly those caused by gastrointestinal nematode (GIN) parasites, which have a considerable impact on their welfare and productivity. Treatment predominantly relies on macrocyclic lactone (ML) anthelmintics, but their widespread application has led to the emergence of drug-resistant parasite populations worldwide. The standard method for detecting resistance, the Faecal Egg Count Reduction Test (FECRT), is susceptible to misinterpretation, leading to flawed management decisions that undermine parasite control efforts. Thus, there is a pressing need for robust resistance detection methods in field parasites. We investigated the potential of the WMicrotrackerTM (WMi) motility assay, previously unexplored in ML resistance assessment. The assay first compared ivermectin (IVM) susceptibility among wild-type Bristol N2 (N2B), IVM-selected (IVR10), and nhr-8 loss-of-function (AE501; nhr8(ok186)) Caenorhabditis elegans strains. Dose-response curves indicated differences in IVM susceptibility among strains, with IVR10 exhibiting a 2.12-fold decrease in sensitivity compared to N2B. Cross-resistance between IVM, moxidectin (MOX), and eprinomectin (EPR) was explored, demonstrating reduced susceptibility in IVR10 across all drugs compared to N2B. Further investigation was conducted using Haemonchus contortus (H. contortus) to assess the assays applicability in discriminating susceptible from resistant isolates. Results revealed significant differences in drug potency between susceptible and resistant isolates, with MOX demonstrating the highest efficacy. Resistance factors (RF) highlighted the substantial resistance of the resistant isolate to EPR. The motility assay effectively discriminated susceptible from resistant isolates in both C. elegans and H. contortus. Our findings demonstrate, for the first time, the relevance of the motility assay by WMi as a functional indicator of resistance in nematodes, offering a promising avenue for detecting resistance to MLs. This research sheds light on a novel approach for monitoring drug resistance, vital for effective parasite management strategies.

pharmacology and toxicology↗

bioRxiv2024

Involvement of ArlI, ArlJ, and CirA in Archaeal Type-IV Pilin-Mediated Motility Regulation

Many prokaryotes use swimming motility to move toward favorable conditions and escape adverse surroundings. Regulatory mechanisms governing bacterial flagella-driven motility are well-established, however, little is yet known about the regulation underlying swimming motility propelled by the archaeal cell surface structure, the archaella. Previous research showed that deletion of the adhesion pilins (PilA1-6), subunits of the type IV pili cell surface structure, renders the model archaeon Haloferax volcanii non-motile. In this study, we used EMS mutagenesis and a motility assay to identify motile suppressors of the {Delta}pilA[1-6] strain. Of the eight suppressors identified, six contain missense mutations in archaella biosynthesis genes, arlI and arlJ. Overexpression of these arlI and arlJ mutant constructs in the respective multi-deletion strains {Delta}pilA[1-6]{Delta}arlI and {Delta}pilA[1-6]{Delta}arlJ confirmed their role in suppressing the {Delta}pilA[1-6] motility defect. Additionally, three suppressors harbor co-occurring disruptive missense and nonsense mutations in cirA, a gene encoding a proposed regulatory protein. A deletion of cirA resulted in hypermotility, while cirA overexpression in wild-type cells led to decreased motility. Moreover, qRT-PCR analysis revealed that in wild-type cells, higher expression levels of arlI, arlJ, and the archaellin gene arlA1 were observed in motile early-log phase rod-shaped cells compared to non-motile mid-log phase disk-shaped cells. Conversely, {Delta}cirA cells, which form rods during both early and mid-log phases, exhibited similar expression levels of arl genes in both growth phases. Our findings contribute to a deeper understanding of the mechanisms governing archaeal motility, highlighting the involvement of ArlI, ArlJ, and CirA in pilin- mediated motility regulation. ImportanceArchaea are close relatives of eukaryotes and play crucial ecological roles. Certain behaviors, such as swimming motility, are thought to be important for archaeal environmental adaptation. Archaella, the archaeal motility appendages, are evolutionarily distinct from bacterial flagella, and the regulatory mechanisms driving archaeal motility are largely unknown. Previous research has linked the loss of type IV pili subunits to archaeal motility suppression. This study reveals three Haloferax volcanii proteins involved in pilin-mediated motility regulation, offering a deeper understanding of motility regulation in this understudied domain while also paving the way for uncovering novel mechanisms that govern archaeal motility. Understanding archaeal cellular processes will help elucidate the ecological roles of archaea as well as the evolution of these processes across domains.

microbiology↗

bioRxiv2024

Microbiome-induced Increases and Decreases in Bone Tissue Strength can be Initiated After Skeletal Maturity

Recent studies in mice have indicated that the gut microbiome can regulate bone tissue strength. However, prior work involved modifications to the gut microbiome in growing animals and it is unclear if the same changes in the microbiome, applied later in life, would change matrix strength. Here we changed the composition of the gut microbiome before and/or after skeletal maturity (16 weeks of age) using oral antibiotics (ampicillin + neomycin). Male and female mice (n=143 total, n=12-17/group/sex) were allocated into five study groups:1) Unaltered, 2) Continuous (dosing 4-24 weeks of age), 3) Delayed (dosing only 16-24 weeks of age), 4) Initial (dosing 4-16 weeks of age, suspended at 16 weeks), and 5) Reconstituted (dosing from 4-16 weeks following by fecal microbiota transplant from Unaltered donors). Animals were euthanized at 24 weeks of age. In males, bone matrix strength in the femur was 25-35% less than expected from geometry in mice from the Continuous (p= 0.001), Delayed (p= 0.005), and Initial (p=0.040) groups as compared to Unaltered. Reconstitution of the gut microbiota, however, led to a bone matrix strength similar to Unaltered animals (p=0.929). In females, microbiome-induced changes in bone matrix strength followed the same trend as males but were not significantly different, demonstrating sex-related differences in the response of bone matrix to the gut microbiota. Minor differences in chemical composition of bone matrix were observed (Raman spectroscopy). Our findings indicate that microbiome-induced impairment of bone matrix in males can be initiated and/or reversed after skeletal maturity. The portion of the femoral cortical bone formed after skeletal maturity (16 weeks) is small; however, this suggests that microbiome-induced changes in bone matrix occur without osteoblast/osteoclast turnover using an, as of yet unidentified mechanism. These findings add to evidence that the mechanical properties of bone matrix can be altered in the adult skeleton.

bioengineering↗

bioRxiv2024

Effects of long-term high dose aspartame on body mass, bone strength, femoral geometry, and microbiota composition in a young and aged cohort of male and female mice

BackgroundRecent reassessment of the safety of aspartame has prompted increased evaluation of its effect on the health of a range of tissues. The gut microbiome is altered by oral aspartame. One prior study suggested that changes in the microbiome caused by aspartame could influence the strength of bone in young skeletally developing mice. Here we ask how aspartame influences bone in mice of different age and sex. ObjectiveThe objective of this study was to determine the effect of aspartame on the bone strength and gut microbiota of young and aged mice. MethodsMale and female C57Bl/6J mice were untreated or treated with a high dose of aspartame in their drinking water from 1 month of age until 4 (young cohort; n = 80) or 22 months (aged cohort; n = 52). ResultsIn aged males, mice treated with aspartame had greater body mass, whole bone strength, and femoral geometry relative to untreated. Specifically, in aged males, aspartame led to 9% increase in body mass (p < 0.001), 22% increase in whole bone strength (p = 0.006), and 17% increase in section modulus (p < 0.001) relative to untreated mice. Aged males and females receiving aspartame had a different microbiota than untreated mice and a decreased abundance of Odoribacter. No differences in body mass, whole bone strength, or femoral geometry were associated with aspartame dosing in young males or young or aged females. ConclusionsAspartame treated aged males had greater whole bone strength and the effect appeared to be explained by greater body mass. Aspartame treatment did not alter whole bone strength in young males or young or aged females despite the aspartame having a similar effect on the microbiota of both aged males and females.

bioengineering↗

bioRxiv2023

Non-viral CRISPR/Cas9 Mutagenesis for Streamlined Generation of Mouse Lung Cancer Models

Functional analysis in mouse models is necessary to establish the involvement of a set of genetic variations in tumor development. Many lung cancer models have been developed using genetic techniques to create gain- or loss-of-function alleles in genes involved in tumorigenesis; however, because of their labor- and time-intensive nature, these models are not suitable for quick and flexible hypothesis testing. Here we introduce a lung mutagenesis platform that utilizes CRISPR/Cas9 RNPs delivered via cationic polymers. This approach allows for the simultaneous inactivation of multiple genes. We validate the effectiveness of this system by targeting a group of tumor suppressor genes, specifically Rb1, Rbl1, Pten, and Trp53, which were chosen for their potential to cause lung tumors, namely Small Cell Lung Carcinoma (SCLC). This polymer-based delivery platform enables the modeling of lung tumorigenesis independently of the genetic background, thus simplifying and expediting the process without the need for modifying the mouse germline or creating custom viral vectors. SignificanceThe development of models to rapidly introduce gene mutations into lung tissue to study their impact on tumor growth is critical for advancing the functional genomics of lung cancer. While previous methods using viral vectors and genetic manipulation in mice have been time-consuming and expensive, here we describe a new technique using cationic polymers as non-viral carriers for CRISPR/Cas9 delivery to induce cancer driving mutations that streamlines this process. This approach mimics natural mutations in lung cancer and accelerates the generation of accurate tumor models. Our study demonstrates the effectiveness of this method in generating small cell lung cancer (SCLC) by modifying four tumor suppressor genes in different mouse genetic backgrounds. This innovative strategy holds promise for faster and more cost-effective cancer modeling. Graphical AbstracSmall Cell Lung Cancer (SCLC) tumors are rapidly generated in any mouse genetic background by using cationic polymers to simultaneously deliver Cas9 and gRNAs targeting the Rb1, Rbl1, Pten and Trp53 tumor-suppressor genes to the adult airway respiratory system in vivo. Addition of the frt guide in the RC::FLTG mice provides a tdTomato gene editing reporter. This study shows the feasibility of rapidly generating lung cancer mouse models via somatic genome engineering through delivery of all CRISPR components in the form of nanoparticles. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/572771v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@d12eeeorg.highwire.dtl.DTLVardef@160472corg.highwire.dtl.DTLVardef@1e0c371org.highwire.dtl.DTLVardef@13f33c1_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2023

Unravelling neuronal and glial differences in ceramide composition, synthesis, and sensitivity to toxicity

Ceramides are lipids that play vital roles in complex lipid synthesis, membrane function, and cell signaling. Disrupted ceramide homeostasis is implicated in cell-death and several neurologic diseases. Ceramides are often analyzed in tissue, but this approach fails to resolve cell-type differences in ceramide homeostasis that are likely essential to understanding cell and non-cell autonomous contributions to neurodegeneration. We show that human iPSC-derived neurons and glia differ in their rate of ceramide synthesis, ceramide isoform composition, and responses to altered ceramide levels. RNA-sequencing of cells treated to increase or decrease ceramides revealed connections to inflammation, ER stress, and apoptosis. Moreover, introducing labeled sphinganine showed that glia readily synthesize ceramide de novo and that neurons are relatively more sensitive to ceramide toxicity. Our findings provide a framework for understanding neurologic diseases with sphingolipid alternations and insights in to designing therapeutics that target ceramide for treating them.

neuroscience↗