Biology subjects

Myers, M.

Publications and source records attributed to Myers, M..

12 recordsLinked to original sources

bioRxiv2026

A switch-rheostat circuit governs quorum sensing homeostasis in a phytopathogen

Pseudomonas fuscovaginae, a wide-host-range plant pathogen of several cereal and grass species, possesses two canonical N-acyl homoserine (AHL)-based quorum sensing (QS) systems called PfsI/R and PfvI/R, both of which are inactive under laboratory conditions but active in planta. The pfsI-pfsR intergenic region encodes for RsaM, a putative protein that has since been hypothesized to act as a repressor switch of this QS circuit. In the present study, we demonstrate that the stringent repression exerted on the PfsI/R system depends entirely on the divergent promoter/intergenic pfsR-rsaM region rather than RsaM itself. Remarkably, this regulatory switch element stringently represses the expression of both the pfsR and rsaM genes. We further show for the first time that RsaM is endogenously expressed and functions as a negative regulator modulating the PfsI/R circuit instead of preventing its activation. Taken together, our results evidence a unique two-tiered/hierarchical repression of a QS system, provided by a master repressor switch and a repressor modulator. ImportancePseudomonas fuscovaginae is a globally occurring plant pathogen that employs AHL QS to regulate virulence. In this bacterium, QS signaling circuits display a rather unusual feature: the lack of activation at high cell densities under standard laboratory conditions. A hypothetical regulator named RsaM was previously linked to this phenomenon as a repressor switch acting on the PfsI/R AHL QS system in the absence of an unknown signal or stimulus. In this study, we show that a regulatory element within the pfsR-rsaM intergenic region acts as the primary switch of the PfsI/R QS system, independently of RsaM. Conversely, RsaM functions as a post-activation modulator that fine-tunes the QS response. This study advances our understanding of the regulatory configurations of unconventional QS systems by revealing a two-tier control mechanism in which a master regulatory switch governs circuit activation, while the previously uncharacterized protein RsaM controls signaling output once the system is engaged.

microbiology↗

bioRxiv2026

Performance of pathogen identification and resistance gene expression tests using ASTar(R) remnant bacterial suspension in Gram-negative contrived positive blood cultures

IntroductionRapid pathogen identification, resistance detection, and susceptibility profiling improve antimicrobial prescribing and associated outcomes, but fragmented workflows lead to inefficiencies and are costly. We evaluated a research-use-only (RUO) approach using ASTar(R) remnant bacterial suspension from routine AST for MALDI-TOF MS pathogen identification and Lateral Flow Assay (LFA)-based detection of targeted resistance mechanisms. MethodsGram-negative (GN) bacterial strains from reference and curated resistance collections (CDC1, ARLG2, ATCC3) [n=119] were contrived into blood culture bottles and processed in the ASTar System using the ASTar BC G-Kit (Q-linea AB, Sweden). Under RUO conditions, remnant bacterial suspensions were collected ~1-2 h after ASTar run initiation and analyzed using NG Test CTX-M Multi, NG Test CARBA-5, NG Test Acineto-5 RUO, and MALDI-TOF MS. ResultsMean ({+/-} SD) remnant suspension volume was 2722 L ({+/-} 300 L). All samples yielded high-confidence MALDI-TOF MS scores (>2.0), with five initially scoring <2.0 and resolving on repeat testing. LFA results showed full agreement with reference isolates for blaCTX-M positive/negative (30/30) and with 60 or 61 target carbapenemase-positive/negative isolates. Testing of a subset of samples to mimic reflex workflows with ASTar phenotypic results did not affect LFA performance (n=26; 23 Enterobacterales, 3 P. aeruginosa and 9 A. baumannii). Cost savings can be realised versus commercial multiplex PCR. ConclusionThis integrated approach of ~6 h rapid phenotypic AST with same-run identification and resistance detection (1-2 h from instrument start) or reflex testing upon availability of ASTar results may support earlier susceptibility results and offer cost savings to current workflows.

microbiology↗

bioRxiv2026

HARMONY: A large-scale harmonized neuroimaging dataset for research on anxious misery disorders

Patterns of brain circuit dysfunction underlying depression and anxiety have been increasingly characterized, including dimensional and subtype variation. A key challenge is determining how such patterns generalize across populations and measurement frameworks. Here, we introduce HARMONY, a harmonized multimodal neuroimaging dataset supporting large-scale investigation of brain-behavior associations across symptom-defined dimensions. HARMONY integrates four Human Connectome Project-style Connectomes Related to Human Disease cohorts spanning adolescence to later adulthood and capturing anxious misery symptoms. The resource combines standardized HCP-style preprocessing, quality control, imaging-derived phenotypes, and harmonized symptom measures into a clinically enriched public dataset. Proof-of-concept analyses using HARMONY showed that pooling heterogeneous cohorts increased statistical power for detecting associations between imaging-derived phenotypes and anhedonia and depression severity. Effect sizes remained modest, consistent with symptom-based measures across heterogeneous samples. Functional imaging-derived phenotypes showed the strongest multivariate predictive performance. In summary, HARMONY provides a large multi-cohort resource for reproducible mental health neuroimaging research.

neuroscience↗

bioRxiv2026

Molecularly defined subpopulations of leptin receptor neurons dissociate the control of food intake from blood pressure

While previous studies have suggested that leptin regulates cardiovascular function independently of body weight, the specific leptin receptor (Lepr)-expressing neurons that mediate these distinct effects remain unknown. We found that genes located in blood pressure (BP)-associated genome-wide association study loci were regulated by leptin in Lepr and glucagon-like peptide-1 receptor (Glp1r)-expressing (LeprGlp1r) neurons. Ablating Lepr from these cells decreased BP despite causing hyperphagic obesity. Single-cell and spatial transcriptomics revealed that LeprGlp1r neurons segregate into two distinct subpopulations of cells located in the arcuate nucleus (ARC) and dorsomedial hypothalamic nucleus (DMH). Activating ARC LeprGlp1r neurons suppressed food intake without impacting energy expenditure or cardiovascular function. Conversely, DMH LeprGlp1r neurons increased energy utilization and BP without altering food intake. Our results identify distinct LeprGlp1r neuron subpopulations that dissociate the control of food intake from outputs related to sympathetic tone, including BP, suggesting the potential therapeutic utility of targeting of these subpopulations independently.

physiology↗

bioRxiv2026

RsaM is not a switch but a built-in modulator of quorum sensing in Pseudomonas fuscovaginae

Pseudomonas fuscovaginae, a wide host-range plant pathogen of several cereal and grass species, possesses two canonical N-acyl homoserine (AHL)-based quorum sensing (QS) systems called PfsI/R and PfvI/R, both of which are inactive under laboratory conditions but active in planta. A Tn5 mutant insertion in the pfsI and pfsR intergenic region was previously reported to trigger the PfsI/R system. This region contains coding sequences for RsaM, a putative protein that has since been hypothesized to play a central role in imposing repression on the PfsI/R system. Putative rsaM genes/RsaM proteins negatively controlling AHL QS systems have also been reported in several other bacterial species. In the present study, we report for the first time the endogenous expression of an RsaM family protein and determine its position within the PfsI/R regulatory circuit. We found that RsaM is not produced in the wild-type P. fuscovaginae and does not play a role in keeping the PfsI/R system in a quiescent state. The expression of RsaM is instead triggered upon targeted mutations in the pfsR-rsaM intergenic region, which concomitantly activate the transcription of both the pfsI and pfsR genes. Moreover, we demonstrated that RsaM attenuates the PfsI/R circuit upon its activation. Taken together, our results evidenced that RsaM does not function as a repressor switch of the PfsI/R system, but behaves as a built-in modulator that prevents overactivation of this circuit once it is triggered. ImportancePseudomonas fuscovaginae is a globally occurring plant pathogen that employs AHL QS to regulate virulence. In this bacterium, QS signalling circuits display a rather unusual feature; the lack of activation at high cell densities under standard laboratory conditions. A hypothetical regulator named RsaM was previously linked to this phenomenon as a possible repressor switch acting on the PfsI/R AHL QS system in the absence of an unknown signal or stimulus. In this study, we demonstrated that the expression of RsaM and activation of the PfsI/R system both depend on the disruption of the rsaM and pfsR divergent intergenic region, and that RsaM functions as a negative modulator of this circuit, rather than as its master repressor. This study unveils the functional position of a novel protein regulator and broadens our understanding of regulatory configurations governing QS circuits.

microbiology↗

bioRxiv2024

Early Life Neuroimaging: The Generalizability of Cortical Area Parcellations Across Development

The cerebral cortex consists of distinct areas that develop through intrinsic embryonic patterning and postnatal experiences. Accurate parcellation of these areas in neuroimaging studies improves statistical power and cross-study comparability. Given significant brain changes in volume, microstructure, and connectivity during early life, we hypothesized that cortical areas in 1- to 3-year-olds would differ markedly from neonates and increasingly resemble adult patterns as development progresses. Here, we parcellated the cerebral cortex into putative areas using local functional connectivity gradients in 92 toddlers at 2 years old. We demonstrate high reproducibility of these cortical regions across 1- to 3-year-olds in two independent datasets. The area boundaries in 1- to 3-year-olds were more similar to those in adults than those in neonates. While the age-specific group area parcellation better fit the underlying functional connectivity in individuals during the first 3 years, adult area parcellations might still have some utility in developmental studies, especially in children older than 6 years. Additionally, we provide connectivity-based community assignments of the parcels, showing fragmented anterior and posterior components based on the strongest connectivity, yet alignment with adult systems when weaker connectivity was included.

neuroscience↗

bioRxiv2023

Fecal microbiomes of laboratory beagles receiving antiparasitic formulations in an experimental setting

Here we describe the fecal microbiome of laboratory beagles in a non-invasive and humane experiment designed to contrast in vivo versus invitro bioequivalence in response to antiparasitic drug administration. The experiment provided a unique opportunity to describe the fecal microbiota of dogs in an experimental setting prior to their adoption. These data are contributed as a resource for the scientific community by the Center for Veterinary Medicine (CVM) of the U.S. Food and Drug Administration (FDA).

microbiology↗

bioRxiv2023

Improvements to the Gulf Pipefish Syngnathus scovelli Genome

The Gulf pipefish Syngnathus scovelli has emerged as an important species in the study of sexual selection, development, and physiology, among other topics. The fish family Syngnathidae, which includes pipefishes, seahorses, and seadragons, has become an increasingly attractive target for comparative research in ecological and evolutionary genomics. These endeavors depend on having a high-quality genome assembly and annotation. However, the first version of the S. scovelli genome assembly was generated by short-read sequencing and annotated using a small set of RNA-sequence data, resulting in limited contiguity and a relatively poor annotation. Here, we present an improved genome assembly and an enhanced annotation, resulting in a new official gene set for S. scovelli. By using PacBio long-read high-fidelity (Hi-Fi) sequences and a proximity ligation (Hi-C) library, we fill small gaps and join the contigs to obtain 22 chromosome-level scaffolds. Compared to the previously published genome, the gaps in our novel genome assembly are smaller, the N75 is much larger (13.3 Mb), and this new genome is around 95% BUSCO complete. The precision of the gene models in the NCBIs eukaryotic annotation pipeline was enhanced by using a large body of RNA-Seq reads from different tissue types, leading to the discovery of 28,162 genes, of which 8,061 were non-coding genes. This new genome assembly and the annotation are tagged as a RefSeq genome by NCBI and thus provide substantially enhanced genomic resources for future research involving S. scovelli.

genomics↗

bioRxiv2022

Recruitment of TRiC chaperonin in rotavirus viroplasms directly associates with virus replication.

Rotavirus replication takes place in the viroplasms, cytosolic inclusions that allow the synthesis of virus genome segments and their encapsidation in the core shell followed by the addition of the second layer of the virion. The viroplasms are composed of several viral proteins, including NSP5, which is the main building block. Microtubules, lipid droplets, and miRNA-7 are among the host components recruited in viroplasms. To investigate the relationship between rotavirus proteins and host components of the viroplasms, we performed a pull-down assay of lysates from rotavirus-infected cells expressing NSP5-BiolD2. Subsequent tandem mass spectrometry identified all eight subunits of the TRiC complex, a cellular chaperonin responsible for folding at least 10% of the cytosolic proteins. Our validated results show that TRiC is recruited in viroplasms and specifically surrounds newly formed double-layered particles (DLPs). Chemical inhibition of TRiC and silencing of its subunits drastically reduced virus progeny production. Interestingly, TRiC-inhibited RV-infected cells lacked triple-layered particles (TLPs) but harbored empty DLPs. Through sequence-specific direct RNA nanopore sequencing, we show that TRiC is critical for RV replication by controlling dsRNA genome segment synthesis, particularly (-)ssRNA. Moreover, TRiC associates and regulates the folding of VP2, a cofactor allowing dsRNA synthesis. This study provides in-cell culture evidence of the regulatory mechanism by which dsRNA genome segment replication is controlled and coordinated in the rotavirus viroplasms. ImportanceThe replication of rotavirus takes place in cytosolic inclusions termed viroplasms. In these inclusions, the eleven double-stranded RNA genome segments are synthesized and packaged individually into the newly generated virus particles. In this study, we show for the first time that the TRiC complex, a cellular chaperonin responsible for the folding of at least 10% of the cytosolic proteins, is a component of viroplasms and is required for the synthesis of the viral (-)ssRNA. Specifically, TRiC interacts and assists in folding VP2, the cofactor involved in RNA replication. Our study adds a new component to the current model of rotavirus replication, where TRiC is recruited in viroplasm to assist replication.

microbiology↗

bioRxiv2022

Dissecting the Genetic Architecture of Carbon Partitioning in Sorghum using Multiscale Phenotypes

Carbon partitioning in plants may be viewed as a dynamic process composed of the many interactions between sources and sinks. The accumulation and distribution of fixed carbon is not dictated simply by the sink strength and number but is dependent upon the source, pathways, and interactions of the system. As such, the study of carbon partitioning through perturbations to the system or through focus on individual traits may fail to produce actionable developments or a comprehensive understanding of the mechanisms underlying this complex process. Using the recently published sorghum carbon-partitioning panel, we collected both macroscale phenotypic characteristics such as plant height, above-ground biomass, and dry weight along with microscale compositional traits to deconvolute the carbon-partitioning pathways in this multipurpose crop. Multivariate analyses of traits resulted in the identification of numerous loci associated with several distinct carbon-partitioning traits, which putatively regulate sugar content, manganese homeostasis, and nitrate transportation. Using a multivariate adaptive shrinkage approach, we identified several loci associated with multiple traits suggesting that pleiotropic and/or interactive effects may positively influence multiple carbon-partitioning traits, or these overlaps may represent molecular switches mediating basal carbon allocating or partitioning networks. Conversely, we also identify a carbon tradeoff where reduced lignin content is associated with increased sugar content. The results presented here support previous studies demonstrating the convoluted nature of carbon partitioning in sorghum and emphasize the importance of taking a holistic approach to the study of carbon partitioning by utilizing multiscale phenotypes.

plant biology↗

bioRxiv2021

tTARGIT AAVs: A sensitive and flexible method to manipulate intersectional neuronal populations

While Cre-dependent viral systems permit the manipulation of many neuron types, some cell populations cannot be targeted by a single DNA recombinase. Although the combined use of Flp and Cre recombinases can overcome this limitation, insufficient recombinase activity can reduce the efficacy of existing Cre+Flp-dependent viral systems. We developed a sensitive dual recombinase-activated viral approach: tTA-driven Recombinase-Guided Intersectional Targeting (tTARGIT) AAVs. tTARGIT AAVs utilize a Flp-dependent tetracycline transactivator (tTA) "Driver" AAV and a tetracycline response element (TRE)-driven, Cre-dependent "Payload" AAV to express the transgene of interest. We employed this system in Slc17a6FlpO;LeprCre mice to manipulate LepRb neurons of the ventromedial hypothalamus (VMH; LepRbVMH neurons) while omitting neighboring LepRb populations. We defined the circuitry of LepRbVMH neurons and roles for these cells in the control of food intake and energy expenditure. Thus, the tTARGIT system mediates robust recombinase-sensitive transgene expression, permitting the precise manipulation of previously intractable neural populations.

physiology↗

bioRxiv2019

Modeling adaptive therapy in non-muscle invasive bladder cancer

Bladder cancer is the 9th most commonly diagnosed cancer. Nearly half of patients with early stage bladder cancer treated with the immune-stimulating agent BCG have disease recurrence, while 13% progress to invasive bladder cancer. Here we explored the potential of tumor mutational heterogeneity and the role of pro- and anti-inflammatory cytokines to identify different subtypes of bladder cancer that may predict therapeutic response to BCG. Further, we used mathematical modeling of dosing strategies to infer tumor response to varying doses and time schedules f BCG administration. As a proof-of-concept, present adaptive therapy scheduling of BCG as a viable strategy to control tumor size and minimize recurrence.

cancer biology↗