Biology subjects

Ross, B.

Publications and source records attributed to Ross, B..

11 recordsLinked to original sources

bioRxiv2026

The Estuary Effect: Variations in Temperature and Salinity Alter msh Promoter Activity in Vibrio cholerae

Vibrio cholerae, the facultative pathogen underlying cholera, naturally inhabits warm aquatic estuaries. Environmental persistence is enhanced by the ability of V. cholerae to colonize host reservoirs and form multicellular biofilms, causing seasonally endemic outbreaks in many tropical regions. Most toxigenic strains utilize the type IVa mannose-sensitive hemagglutinin (MSHA) pilus for host reservoir colonization and biofilm formation. Temperature and salinity can alter V. cholerae biofilm formation, yet their impact on MSHA production specifically remains largely unknown. Here, we utilized transcriptional reporters of predicted msh promoters (msh-P1/msh-P2/msh-P3) and functional assays, to determine temperature and salinity impacts on msh expression and pilus biogenesis. Under standard laboratory conditions (30{degrees}C, 1% NaCl) only msh-P1/P2 are active and inversely-coordinated with one another. Both msh-P1/P2 activity were elevated by high temperature (37{degrees}C) and low salinity (0.25%/0.5% NaCl), and reduced by low temperature (20{degrees}C/25{degrees}C) and high salinity (2%/3% NaCl). Temperature-mediated alterations in promoter activity were not immediately reflected in changes to cell-surface MSHA levels, whereas high salinity led to decreased MSHA production. Combining high temperature (37{degrees}C) and high salinity (2%/3% NaCl), attenuated the salinity-mediated reduction of msh-P1/P2 activity. Biofilm biomass levels were only substantially heightened at 25{degrees}C and 20{degrees}C, likely a result of no temperature-dependent changes in cell-surface MSHA, and additional temperature-controlled biofilm regulation previously described. We also found msh-P1/P2 promoter activity and MSHA production varies widely across toxigenic O1 and O139 serogroups despite complete sequence homology. These results shed new light on how key signals regulate MSHA pilus production to support V. cholerae persistence in aquatic environments.

microbiology↗

bioRxiv2026

Intrinsic antifungal activity of curli nanofibers expands the design space for programmable antimicrobial biomaterials

The rise of antifungal resistance and limited antifungal drug classes creates an urgent need for biomaterials with localized, programmable activity. Here, we engineered curli nanofibers displaying the antifungal peptide heliomicin and unexpectedly discovered that wild-type CsgA itself exhibits intrinsic antifungal activity against Candida albicans, reducing fungal viability by approximately 2 log units. Heliomicin fusion enhanced this activity to a 3.5-log fungicidal reduction while preserving nanofiber self-assembly, hydrogel formation, mechanical properties, and 3D printability. Mechanistic analyses linked enhanced activity to membrane disruption and expansion of the cationic surface of CsgA. Heliomicin-CsgA hydrogels further reduced fungal burden and suppressed hyphal development in an ex vivo porcine skin infection model. These findings reveal that extracellular protein nanofibers can harbor intrinsic biological activities that can be uncovered and enhanced through protein engineering, establishing a strategy for developing intrinsically bioactive, programmable biomaterials for localized therapeutic applications against fungal pathogens and potentially other microbial infections.

bioengineering↗

bioRxiv2024

Accumulated reserves hold back age-related neural compensation in speech-in-noise perception

During cognitive tasks, increased frontoparietal neural activity and functional connectivity are commonly observed in older adults. Cognitive reserves accrued from positive life choices can provide additional neural resources to cope with aging. However, how cognitive reserves interact with upregulated neural activity in older adults is poorly understood. We measured brain activity with fMRI during a speech-in-noise task and assessed whether cognitive reserve accumulated from long-term musical training bolsters or holds back age-related upregulated activity. Older musicians exhibited less upregulation of task-induced functional connectivity than older non-musicians in auditory dorsal regions, which predicted better behavioral performance in older musicians. These results suggest that cognitive reserve may hold back neural recruitment. Besides functional connectivity strength, we also found that older musicians showed more youth-like fine spatial patterns of functional connectivity than older non-musicians. Our findings enlightened the intricate interplay between cognitive reserve and age-related upregulated activity during speech in noise perception. Significance StatementUnderstanding the interplay between cognitive reserve and age-related neural changes is vital for developing strategies to mitigate cognitive decline in older adults. This study reveals that long-term musical training, which provides cognitive reserve for speech perception, helps older musicians preserve youth-like levels of functional connectivity and fine-scale activity patterns in the auditory dorsal stream during speech-in-noise perception. Unlike older non-musicians, who exhibit age-related neural upregulation, older musicians maintain youth-like connectivity patterns akin to those of younger adults, resulting in superior speech-in-noise perception. These findings support the "Hold-back upregulation" hypothesis and suggest that musical training counteracts age-related declines by preserving youthful brain function. The results offer valuable insights for designing interventions to enhance aging populations cognitive function and communication abilities.

neuroscience↗

bioRxiv2024

Neurophysiology of effortful listening: Decoupling motivational modulation from task demands

In demanding listening situations, a listeners motivational state may affect their cognitive investment. Here, we aim to delineate how domain-specific sensory processing, domain-general neural alpha power, and pupil size as a proxy for cognitive investment encode influences of motivational state under demanding listening. Participants performed an auditory gap-detection task while pupil size and the magnetoencephalogram (MEG) were simultaneously recorded. Task demand and a listeners motivational state were orthogonally manipulated through changes in gap duration and monetary-reward prospect, respectively. Whereas task difficulty impaired performance, reward prospect enhanced it. Pupil size reliably indicated the modulatory impact of an individuals motivational state. At the neural level, the motivational state did not affect auditory sensory processing directly but impacted attentional post-processing of an auditory event as reflected in the late evoked-response field and alpha power change. Both pre-gap pupil dilation and higher parietal alpha power predicted better performance at the single-trial level. The current data support a framework wherein the motivational state acts as an attentional top-down neural means of post-processing the auditory input in challenging listening situations. Significance StatementHow does an individuals motivational state affect cognitive investment during effortful listening? In this simultaneous pupillometry and MEG study, participants performed an auditory gap-detection task while their motivational state was manipulated through varying prospect of a monetary reward. The pupil size directly mirrored this motivational modulation of the listening demand. The individuals motivational state also enhanced top-down attentional post-processing of the auditory event but did neither change auditory sensory processing nor pre-gap parietal alpha power. These data suggest that a listeners motivational state acts as a late attentional top-down effect on auditory neural processes in challenging listening situations.

neuroscience↗

bioRxiv2023

Rocket-miR, a Translational Launchpad for miRNA-based Antimicrobial Drug Development

Developing software tools that leverage biological datasets to accelerate drug discovery is an important aspect of bioinformatics research. Here we present a novel example: a web application called Rocket-miR that applies an existing bioinformatics algorithm (IntaRNA) to predict cross-species miRNA-mRNA interactions and identify human miRNAs with potential antimicrobial activity against antibiotic resistant bacterial infections. Rocket-miR is the logical extension of our prior finding that human miRNA let-7b-5p impairs the ability of the ubiquitous opportunistic pathogen P. aeruginosa to form biofilms and resist the bactericidal effect of beta lactam antibiotics. Rocket-miRs point and click interface enables researchers without programming expertise to predict additional human-miRNA-pathogen interactions. Identified miRNAs can be developed into novel antimicrobials effective against the 24 clinically relevant pathogens, implicated in diseases of the lung, gut and other organs, that are included in the application. The manuscript incorporates three case studies contributed by microbiologists that study human pathogens to demonstrate the usefulness and usability of the application. Rocket-miR is accessible at the following link: http://scangeo.dartmouth.edu/RocketmiR/. ImportanceAntimicrobial resistant infections contribute to millions of deaths worldwide every year. In particular, the group of bacteria collectively known as ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter sp.) pathogens are of considerable medical concern due to their virulence and exceptional ability to develop antibiotic resistance. New kinds of antimicrobial therapies are urgently needed to treat patients for whom existing antibiotics are ineffective. The Rocket-miR application predicts targets of human miRNAs in bacterial and fungal pathogens, rapidly identifying candidate miRNA-based antimicrobials. The applications target audience is microbiologists that have the laboratory resources to test the applications predictions. The Rocket-miR application currently supports 24 recognized human pathogens that are relevant to numerous diseases including CF, COPD, urinary tract infections and pneumonia. Furthermore, the application code was designed to be easily extendible to other human pathogens that commonly cause hospital-acquired infections.

bioinformatics↗

bioRxiv2022

Intestinal Bacteroides Modulates Systemic Inflammation and the Microbial Ecology in a Mouse Model of CF: Evidence for Propionate and other Short Chain Fatty Acids Reducing Systemic Inflammatory Cytokines

Persons with cystic fibrosis, starting in early life, have intestinal microbiome dysbiosis characterized in part by a decreased relative abundance of the genus Bacteroides. Bacteroides is a major producer of the intestinal short chain fatty acid (SCFA) propionate. We demonstrate here that CFTR-/- Caco-2 intestinal epithelial cells are responsive to the anti-inflammatory effects of propionate. Furthermore, Bacteroides isolates inhibit the IL-1{beta}-induced inflammatory response of CFTR-/- Caco-2 intestinal epithelial cells and do so in a propionate-dependent manner. Bacteroides isolates also produce low levels of butyrate; this SCFA is positively correlated with inhibition of the inflammatory response. Finally, the introduction of Bacteroides-supplemented stool from infants with CF into the gut of CftrF508del mice results in an increase in propionate in the stool as well as the reduction in several systemic pro-inflammatory cytokines. Bacteroides supplementation also reduced the fecal relative abundance of E. coli, indicating a potential interaction between these two microbes, consistent with previous clinical studies. Together, our data indicate the important role of Bacteroides and Bacteroides-derived propionate in the context of the developing microbiome in infants and children with CF, which could help explain the observed gut-lung axis in CF.

microbiology↗

bioRxiv2021

Natural variation in Arabidopsis ISR1 affects iron localization and induced systemic resistance

Beneficial root-associated bacteria can induce systemic resistance (ISR) to foliar pathogens and there is known transcriptional and genetic overlap in the root response to iron deficiency and ISR. A previous study found that there is natural variation in ISR among Arabidopsis accessions. The Ws accession is deficient in ISR, and the responsible recessive genetic locus, named ISR1, was mapped to chromosome 3. To find candidate genes that may underlie ISR deficiency in Ws, we identified genes that are induced in response to the ISR-triggering bacterium Pseudomonas simiae WCS417 and to iron stress and that have non-synonymous mutations in the Ws genome with respect to the ISR-responsive Col-0. We identified a kelch-domain containing protein encoded by At3g07720 that has a genomic rearrangement in Ws. We found that overexpression of Col-0 At3g07720 restores ISR to Ws, indicating that At3g07720 encodes ISR1. Isr1 loss of function mutants do not affect plant growth under iron limiting conditions but have increased levels of apoplastic iron. We found that iron supplementation, P. simiae WCS417, or a loss of isr1 enhance ROS production in a non-additive manner, suggesting they work through the same mechanism to enhance resistance. Our findings show that ISR1 is required for iron localization, immunity, and ISR, and suggest that increased iron uptake induced by ISR-eliciting bacteria may directly contribute to immunity through increased reactive oxygen production.

plant biology↗

bioRxiv2020

Dipeptidyl peptidase 9 triggers BRCA2 degradation by the N-degron pathway to promote DNA-damage repair

Dipeptidyl peptidase 9 (DPP9) is a serine protease cleaving N-terminal dipeptides preferentially post-proline with (patho)physiological roles in the immune system and cancer. Only few DPP9 substrates are known. Here we identify an association of human DPP9 with the tumour suppressor BRCA2, a key player in repair of DNA double-strand breaks that promotes the formation of RAD51 filaments. This interaction is triggered by DNA-damage and requires access to the DPP9 active-site. We present crystallographic structures documenting the N-terminal Met1-Pro2 of a BRCA21-40 peptide captured in the DPP9 active-site. Mechanistically, DPP9 targets BRCA2 for degradation by the N-degron pathway, and promotes RAD51 foci formation. Both processes are phenocopied by BRCA2 N-terminal truncation mutants, indicating that DPP9 regulates both stability and the cellular stoichiometric interactome of BRCA2. Consistently, DPP9-deprived cells are hypersensitive to DNA-damage. Together, we identify DPP9 as a regulator of BRCA2, providing a possible explanation for DPP9 involvement in cancer development.

biochemistry↗

bioRxiv2020

Spatially compartmentalized phase regulation of a Ca2+-cAMP-PKA oscillatory circuit

Signaling networks are spatiotemporally organized in order to sense diverse inputs, process information, and carry out specific cellular tasks. In pancreatic {beta} cells, Ca2+, cyclic adenosine monophosphate (cAMP), and Protein Kinase A (PKA) exist in an oscillatory circuit characterized by a high degree of feedback, which allows for specific signaling controls based on the oscillation frequencies. Here, we describe a novel mode of regulation within this circuit involving a spatial dependence of the relative phase between cAMP, PKA, and Ca2+. We show that nanodomain clustering of Ca2+-sensitive adenylyl cyclases drives oscillations of local cAMP levels to be precisely in-phase with Ca2+ oscillations, whereas Ca2+-sensitive phosphodiesterases maintain out-of-phase oscillations outside of the nanodomain, representing a striking example and novel mechanism of cAMP compartmentation. Disruption of this precise in-phase relationship perturbs Ca2+ oscillations, suggesting that the relative phase within an oscillatory circuit can encode specific functional information. This example of a signaling nanodomain utilized for localized tuning of an oscillatory circuit has broad implications for the spatiotemporal regulation of signaling networks.

cell biology↗

bioRxiv2019

A Pairwise Distance Distribution Correction (DDC) algorithm for blinking-free super-resolution microscopy

In single-molecule localization based super-resolution microscopy (SMLM), a fluorophore stochastically switches between fluorescent- and dark-states, leading to intermittent emission of fluorescence, a phenomenon known as blinking. Intermittent emissions create multiple localizations belonging to the same molecule, resulting in blinking-artifacts within SMLM images. These artifacts are often interpreted as true biological assemblies, confounding quantitative analyses and interpretations. Multiple methods have been developed to eliminate these artifacts, but they either require additional experiments, arbitrary thresholds, or specific photo-kinetic models. Here we present a method, termed Distance Distribution Correction (DDC), to eliminate blinking-caused repeat localizations without any additional calibrations. The approach relies on the finding that the true pairwise distance distribution of different fluorophores in an SMLM image can be naturally obtained from the imaging sequence by using distances between localizations separated by a time much longer than the average fluorescence survival time. We show that using the true pairwise distribution we can define and then maximize the likelihood of obtaining a particular set of localizations void of blinking-artifacts, generating an accurate reconstruction of the underlying cellular structure. Using both simulated and experimental data, we show that DDC surpasses all previous existing blinking-artifact correction methodologies, resulting in drastic improvements in obtaining the closest estimate of the true spatial organization and number of fluorescent emitters in a wide range of applications. The simplicity and robustness of DDC will allow it to become the field standard in SMLM imaging, enabling the most accurate reconstruction and quantification of SMLM images to date.

biophysics↗

bioRxiv2017

The Landscape Of Type VI Secretion Across Human Gut Microbiomes Reveals Its Role In Community Composition

While the composition of the human gut microbiome has been well defined, the forces governing its assembly are poorly understood. Recently, prominent members of this community from the order Bacteroidales were shown to possess the type VI secretion system (T6SS), which mediates contact-dependent antagonism between Gram-negative bacteria. However, the distribution of the T6SS in human gut microbiomes and its role have not yet been characterized. To address this challenge, we construct an extensive catalog of T6SS effector/immunity (E-I) genes from three genetic architectures (GA1-3) found in Bacteroidales genomes. We then use metagenomic analysis to assess the abundances of these genes across a large set of gut microbiome samples. We find that despite E-I diversity across reference strains, each individual microbiome harbors a limited set of E-I genes representing a single E-I genotype. Importantly, for GA1-2, these genotypes are not associated with a specific species, suggesting selection for compatibility. GA3, in contrast, is restricted to B. fragilis, and its low diversity reflects a single B. fragilis strain per sample. We further show that in infant microbiomes GA3 is enriched and B. fragilis strains are replaced over time, suggesting competition for dominance in developing microbiomes. Finally, we find a strong association between the presence of GA3 and increased abundance of Bacteroides, indicating that this system confers a selective advantage in vivo in Bacteroides rich ecosystems. Combined, our findings provide the first comprehensive characterization of the T6SS landscape in the human microbiome, implicating it in both intra- and inter-species interactions.

microbiology↗