Biology subjects

Bowden, S.

Publications and source records attributed to Bowden, S..

13 recordsLinked to original sources

bioRxiv2026

Gain-of-function CCaMK in rice overrides genetic and anatomical barriers to arbuscular mycorrhizal colonisation

Arbuscular mycorrhizal (AM) symbiosis is conserved across land plants and is the default nutrient uptake strategy in nature. Within roots, AM colonisation is tightly patterned and dynamically tuned by nutritional cues. Multiple genetic modules contribute to this regulation, including the phosphate starvation response, DWARF14-LIKE (D14L) karrikin signalling, and the common symbiosis signalling pathway (CSSP). Transcriptional overlap among these has led to the hypothesis that phosphate starvation and D14L signalling act upstream of the CSSP. Here, we examined the epistatic relationship between D14L and CSSP in rice. Overexpression of an autoactive gain-of-function CCaMK (gofCCaMKox) restored AM colonisation and symbiosis marker gene expression in d14l mutants to wild-type levels or above, whereas overexpression of wild-type CCaMK did not, confirming that CSSP operates downstream of D14L signalling. However, gofCCaMKox did not rescue the d14l mesocotyl elongation phenotype, supporting a bifurcation of D14L into developmental and symbiotic outputs. Unexpectedly, gofCCaMKox also expanded fungal access to normally restrictive tissue domains (the meristematic zone and endodermis) assigning a role for CCaMK activation in defining root zone and cell-type competence for AM colonisation. Despite restored colonisation, introduction of gofCCaMKox into d14l produced arbuscules, which however were less developed and had increased hyphal septation, revealing a CCaMK-independent role for D14L in intraradical colonisation and arbuscule development. Transcriptome profiling resolved AM-relevant genes into modules controlled by CCaMK activation alone, in combination with D14L, or requiring additional colonisation-associated cues, and further suggested CCaMK primarily acts through AP2 transcription factors. Together, these findings reinforce CCaMK as a master regulator of AM symbiosis at the genetic, transcriptomic and anatomical levels while uncovering CCaMK-independent functions of D14L in arbuscule development.

plant biology↗

bioRxiv2025

A conserved sRNA regulates mucin adhesion and gut colonization across the Enterococcaceae

Enterococci, particularly E. faecalis, can survive in diverse settings within and outside human hosts. The capacity of E. faecalis to colonize these locations relies on its ability to adapt by altering gene expression in response to environmental exposures. One mechanism for quickly altering gene expression is through regulation by small noncoding RNAs (sRNAs); sRNAs can regulate one or many target genes and either up- or down-regulate transcript stability and protein expression. While many sRNAs have been predicted in E. faecalis, few have experimentally established target mRNAs or physiological functions. Here, we investigate the targets, function, and mechanism of Enterococcus sRNA 84. We found that sRNA 84 is conserved within the family Enterococcaceae, suggesting that it plays a role in the regulation of core genes and functions. RNA sequencing and proteomic analysis revealed that the absence of sRNA 84 led to downregulation of many cell surface proteins, including mucin-binding proteins. Consistent with these findings, an sRNA 84 knockout strain had reduced binding to mucin in vitro and impaired intestinal colonization of specific-pathogen-free mice. Taken together, these data support a model whereby sRNA 84 upregulates cell surface adhesins, which subsequently facilitate host colonization through binding to mucin. sRNA 84 is one of the first sRNAs in enterococci with demonstrated targets and function. This finding establishes the conserved sRNA 84 as a potential key regulator of enterococcal host adaptation, providing insight into how these organisms adapt their gene expression to survive both within and outside animal hosts.

microbiology↗

bioRxiv2025

Replicative selfish genetic elements are driving rapid pathogenic adaptation of Enterococcus faecium

Understanding how healthcare-associated pathogens adapt in clinical environments can inform strategies to reduce their burden. Here, we investigate the hypothesis that insertion sequences (IS), prokaryotic transposable elements, are a dominant mediator of rapid genomic evolution in healthcare-associated pathogens. Among 28,207 publicly available pathogen genomes, we find high copy numbers of the replicative ISL3 family in healthcare-associated Enterococcus faecium, Streptococcus pneumoniae and Staphylococcus aureus. In E. faecium, the ESKAPE pathogen with the highest IS density, we find that ISL3 proliferation has increased in the last 30 years. To enable better identification of structural variants, we long read-sequenced a new, single hospital collection of 282 Enterococcal infection isolates collected over three years. In these samples, we observed extensive, ongoing structural variation of the E. faecium genome, largely mediated by active replicative ISL3 elements. To determine if ISL3 is actively replicating in clinical timescales in its natural, gut microbiome reservoir, we long read-sequenced a collection of 28 longitudinal stool samples from patients undergoing hematopoietic cell transplantation, whose gut microbiomes were dominated by E. faecium. We found up to six structural variants of a given E. faecium strain within a single stool sample. Examining longitudinal samples from one individual in further detail, we find ISL3 elements can replicate and move to specific positions with profound regulatory effects on neighboring gene expression. In particular, we identify an ISL3 element that upon insertion replaces an imperfect -35 promoter sequence at a folT gene locus with a perfect -35 sequence, which leads to substantial upregulation of expression of folT, driving highly effective folate scavenging. As a known folate auxotroph, E. faecium depends on other members of the microbiota or diet to supply folate. Enhanced folate scavenging may enable E. faecium to thrive in the setting of microbiome collapse that is common in HCT and other critically ill patients. Together, ISL3 expansion has enabled E. faecium to rapidly evolve in healthcare settings, and this likely contributes to its metabolic fitness and may strongly influence its ongoing trajectory of genomic evolution.

microbiology↗

bioRxiv2024

Foxi1 regulates multiple steps of mucociliary development and ionocyte specification through transcriptional and epigenetic mechanisms

Foxi1 is a master regulator of ionocytes (ISCs / INCs) across species and organs. Two subtypes of ISCs exist, and both -and {beta}-ISCs regulate pH-and ion-homeostasis in epithelia. Gain and loss of FOXI1 function are associated with human diseases, including Pendred syndrome, male infertility, renal acidosis and cancers. Foxi1 was predominantly studied in the context of ISC specification, however, reports indicate additional functions in early and ectodermal development. Here, we re-investigated the functions of Foxi1 in Xenopus laevis embryonic mucociliary epidermis development and found a novel function for Foxi1 in the generation of Notch-ligand expressing mucociliary multipotent progenitors (MPPs). We demonstrate that Foxi1 has multiple concentration-dependent functions: At low levels, Foxi1 maintains ectodermal competence in MPPs through transcriptional and epigenetic mechanisms, while at high levels, Foxi1 induces a multi-step process of ISC specification and differentiation in cooperation with Ubp1 and Dmrt2. We further describe how foxi1 expression is affected through auto-and Notch-regulation, and how this developmental program affects mucociliary patterning. Together, we reveal novel functions for Foxi1 in Xenopus mucociliary epidermis formation, relevant to our understanding of vertebrate development and human disease.

developmental biology↗

bioRxiv2024

Dual quorum-sensing control of purine biosynthesis drives pathogenic fitness of Enterococcus faecalis

Enterococcus faecalis is a resident of the human gut, though upon translocation to the blood or body tissues, it can be pathogenic. Here we discover and characterize two peptide-based quorum-sensing systems that transcriptionally modulate de novo purine biosynthesis in E. faecalis. Using a comparative genomic analysis, we find that most enterococcal species do not encode this system; E. moraviensis, E. haemoperoxidus and E. caccae, three species that are closely related to E. faecalis, encode one of the two systems, and only E. faecalis encodes both systems. We show that these systems are important for the intracellular survival of E. faecalis within macrophages and for the fitness of E. faecalis in a murine wound infection model. Taken together, we combine comparative genomics, microbiological, bacterial genetics, transcriptomics, targeted proteomics and animal model experiments to describe a paired quorum sensing mechanism that directly influences central metabolism and impacts the pathogenicity of E. faecalis.

microbiology↗

bioRxiv2023

Temporal Notch signaling regulates mucociliary cell fates through Hes-mediated competitive de-repression

Mucociliary epithelia are found across different organs in animals, where they release bioactive substances and generate extracellular fluid flows. One key function of mucociliary epithelia is the clearance of pathogens, e.g. in the vertebrate lung and the epidermis of amphibian tadpoles. Mucociliary clearance relies on the correct balance between secretory cells that release mucus, ciliated cells that generate fluid flow as well as specialized cell types, including pH-regulating ionocytes and basal stem cells. Notch signaling, Hes repressors and cell type-inducing transcription factors (e.g. Foxi1, Mcidas, Spdef and Tp63) regulate cell fates and cell type proportions across mucociliary systems. Lateral inhibition was proposed to control mucociliary cell fates, but current models cannot explain how more than two cell types are generated and how Hes genes are employed as mediators during patterning. Using the Xenopus tadpole epidermis, we addressed these open questions in mucociliary biology through a combination of in vivo and organoid experiments, time-resolved transcriptomic studies and mathematical modeling. This revealed that ionocytes, ciliated cells, secretory cells and basal cells are preferentially specified at different time points and Notch signaling levels via sequentially expressed Hes factors. We termed this mode of patterning "competitive de-repression", because cell fates are selected by suppression of alternative fate choices, and demonstrate that this relies on differential active repression of cell fate transcription factors. Mathematical modeling further indicated the need for a positively Notch-regulated patterning factor, and we provide evidence that Spdef mediates Notch input for secretory and basal cell specification. Collectively, this work presents a coherent model for Notch- and Hes-mediated mucociliary cell fate specification in a vertebrate tissue, which allows for the specification of more than two cell fates within the Notch lateral-inhibition paradigm.

developmental biology↗

bioRxiv2022

OsPSTOL but not TaPSTOL can play a role in nutrient use efficiency and works through conserved pathways in both wheat and rice

There is a large demand to reduce inputs for current crop production, particularly phosphate and nitrogen inputs which are the two most frequently added supplements to agricultural production. Gene characterization is often limited to the native species from which it was identified, but may offer benefits to other species. To understand if OsPSTOL, a gene identified from rice which improves tolerance to low P growth conditions, might improve performance and provide the same benefit in wheat, OsPSTOL was transformed into wheat and expressed from a constitutive promoter. The ability of OsPSTOL to improve nutrient acquisition under low phosphate or low nitrogen was evaluated. Here we show that OsPSTOL works through a conserved pathway in wheat and rice to improve yields under both low phosphate and low nitrogen. This increase is yield is mainly driven by improved uptake from the soil driving increased biomass and ultimately increased seed number, but does not change the concentration of N in the straw or grain. Overexpression of OsPSTOL in wheat modifies N regulated genes to aid in this uptake whereas the putative homolog TaPSTOL does not suggesting that expression of OsPSTOL in wheat can help to improve yields under low input agriculture.

plant biology↗

bioRxiv2022

Wheat cells show positional responses to invasive Zymoseptoria tritici

The stomatal complex of grasses consists of two guard cells and two adjacent subsidiary cells that cooperate during stomatal closure. Zymoseptoria tritici, the main causal agent of Septoria tritici blotch in wheat, enters the host via stomata. Here we test the hypothesis that the stomatal complex shows focused sub-cellular responses to invading Z. tritici hyphae. We have combined live-cell transmission light microscopy, immunofluorescence and CRS microscopy to identify cell wall modifications triggered by hyphal invasion. Furthermore, we have used confocal fluorescence microscopy and automated quantitative image analysis to assess whether host cells respond to hyphae through spatial redistribution of organelles. We find that subsidiary cells construct papillae that are accurately aligned with hyphal position even when hyphae are occluded by guard cells. These are distinct from those induced by powdery mildew, with callose restricted to a crust that surrounds content with a high-amplitude Raman signal in the CH-band. Peroxisome populations in subsidiary cells show distributions with modes weakly correlated with hyphal position but do not differ significantly between compatible and incompatible interactions. Our data suggest local changes to cell wall architecture and focal accumulation of organelles in subsidiary cells could play roles in crop defence during host leaf penetration by Z. tritici. Molecular strategies to amplify these responses may provide novel routes for crop protection.

plant biology↗

bioRxiv2021

Over-expression of the brassinosteroid gene TaDWF4 increases wheat productivity under low and sufficient nitrogen through enhanced carbon assimilation

There is a strong pressure to reduce nitrogen (N) fertiliser inputs while maintaining or increasing current cereal crop yields. Brassinosteroids, (BR), are a group of phytohormones essential for plant growth and development, that have been demonstrated to regulate several agronomic traits. DWF4 encodes a cytochrome P450 that catalyses a rate-limiting step in BR synthesis. We show that overexpression of the dominant shoot expressed homoeologue TaDWF4-B in wheat can increase plant productivity by up to 105% under a range of N levels on marginal soils, resulting in increased N use efficiency (NUE). We show that a two to four-fold increase in TaDWF4 transcript levels enhances the responsiveness of genes regulated by N. The productivity increases seen were primarily due to the maintenance of photosystem II operating efficiency and carbon assimilation in plants when grown under limiting N conditions and not an overall increase in photosynthesis capacity. The increased biomass production and yield per plant in TaDWF4 OE lines could be linked to modified carbon partitioning and changes in expression pattern of the growth regulator Target Of Rapamycin, offering a route towards breeding for sustained yield and lower N inputs.

plant biology↗

bioRxiv2021

Spatial spread of white-nose syndrome in North America, 2006-2018

White-nose syndrome has caused massive mortality in multiple bat species and spread across much of North America, making it one of the most destructive wildlife diseases on record. This has also resulted in it being one of the most well-documented wildlife disease outbreaks, making it possible to look for changes in the pattern of spatial spread over time. We fit a series of spatial interaction models to the United States county-level observations of the pathogenic fungus, Pseudogymnoascus destructans, that causes white-nose syndrome. Models included the distance between caves, cave abundance, measures of winter length and winter onset, and species richness of all bats and hibernating bats only. We found that the best supported models included all of these factors, but that the particular structure and most informative covariates changed over the course of the outbreak, with winter length displacing winter onset as the most informative measure of winter conditions, and evidence for the effects total species richness and hibernation varying from year to year. We also found that weather had detectable effects on spread. While the effect sizes for cave abundance and species richness were relatively stable over the length of the outbreak, distance became less important as time went on. These findings indicate that although models produced early in the outbreak captured important and consistent aspects of the spatial spread of white-nose syndrome, there were also changes over time in the factors associated with spread, suggesting that forecasts may be improved by iterative model refinement.

ecology↗

bioRxiv2018

Quantifying individual differences in brain morphometry underlying symptom severity in Autism Spectrum Disorders

The neurobiology of heterogeneous neurodevelopmental disorders such as autism spectrum disorders (ASD) are still unclear. Despite extensive efforts, most findings are difficult to reproduce due to high levels of individual variance in phenotypic expression. To quantify individual differences in brain morphometry in ASD, we implemented a novel subject-level, distance-based method on subject-specific attributes. In a large multi-cohort sample, each subject with ASD (n=100; n=84 males; mean age: 11.43 years; mean IQ: 110.58) was strictly matched to a control participant (n=100; n=84 males; mean age: 11.43 years; mean IQ: 110.70). Intrapair Euclidean distance of MRI brain morphometry and symptom severity measures were entered into a regularised machine learning pipeline for feature selection, with rigorous out-of-sample validation and bootstrapped permutation testing. Subject-specific structural morphometry features significantly predicted individual variation in ASD symptom severity (19 cortical thickness features, p=0.01, n=5000 permutations; 10 surface area features, p=0.006, n=5000 permutations). Findings remained robust across subjects and were replicated in validation samples. Identified cortical regions implicate key hubs of the salience and default mode networks as neuroanatomical features of social impairment in ASD. Present results highlight the importance of subject-level markers in ASD, and offer an important step forward in understanding the neurobiology of heterogeneous disorders.

neuroscience↗

bioRxiv2018

A fungal ribonuclease-like effector protein inhibits plant host ribosomal RNA degradation

The biotrophic fungal pathogen Blumeria graminis causes the powdery mildew disease of cereals and grasses. Proteins with a predicted ribonuclease (RNase)-like fold (termed RALPHs) comprise the largest set of secreted effector candidates within the B. graminis f. sp. hordei genome. Their exceptional abundance suggests they play crucial functions during pathogenesis. We show that transgenic expression of RALPH CSEP0064/BEC1054 increases susceptibility to infection in monocotyledenous and dicotyledonous plants. CSEP0064/BEC1054 interacts in planta with five host proteins: two translation elongation factors (eEF1 and eEF1{gamma}), two pathogenesis-related proteins (PR5 and PR10) and a glutathione-S-transferase. We present the first crystal structure of a RALPH, CSEP0064/BEC1054, demonstrating it has an RNase-like fold. The protein interacts with total RNA and weakly with DNA. Methyl jasmonate levels modulate susceptibility to aniline-induced host RNA fragmentation. In planta expression of CSEP0064/BEC1054 reduces the formation of this RNA fragment. We propose that CSEP0064/BEC1054 is a pseudoenzyme that binds to host ribosomes, thereby inhibiting the action of plant ribosome-inactivating proteins that would otherwise lead to host cell death, an unviable interaction and demise of the fungus.

plant biology↗

bioRxiv2017

Different Brain Networks Underlying Intelligence In Autism Spectrum Disorders And Typically Developing Children

BackgroundThere has been sustained clinical and cognitive neuroscience research interest in how network correlates of brain-behaviour relationships might be altered in Autism Spectrum Disorders (ASD) and other neurodevelopmental disorders. As previous work has mostly focused on adults, the nature of whole-brain connectivity networks underlying intelligence in pediatric cohorts with abnormal neurodevelopment requires further investigation.\n\nMethodsWe used network-based statistics (NBS) to examine the association between resting-state functional Magnetic Resonance Imaging (fMRI) connectivity and fluid intelligence ability in male children (n=50) with Autism Spectrum Disorders (ASD; M=10.45, SD=1.58 years and in controls (M=10.38, SD=0.96 years) matched on fluid intelligence performance, age and sex. Repeat analyses were performed in independent sites for validation and replication.\n\nResultsDespite being equivalent on fluid intelligence ability to strictly matched neurotypical controls, boys with ASD displayed a subnetwork of significantly increased associations between functional connectivity and fluid intelligence. Between-group differences remained significant at higher edge thresholding, and results were validated in independent-site replication analyses in an equivalent age and sex-matched cohort with ASD. Regions consistently implicated in atypical connectivity correlates of fluid intelligence in ASD were the angular gyrus, posterior middle temporal gyrus, occipital and temporo-occipital regions.\n\nConclusionDevelopment of fluid intelligence neural correlates in young ASD males is aberrant, with an increased strength in intrinsic connectivity association during childhood. Alterations in whole-brain network correlates of fluid intelligence in ASD may be a compensatory mechanism that allows equal task performance to neurotypical peers.

neuroscience↗