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Johnston, C.

Publications and source records attributed to Johnston, C..

15 recordsLinked to original sources

Menstruation is associated with cyclical granulysin peaks in vaginal secretions despite stable expression by cervicovaginal immune cells

ProblemThe anti-microbial protein granulysin is present in vaginal secretions during the follicular phase of the menstrual cycle but nearly disappears during the luteal phase. The reason for this change is unknown. Method of studyParticipants (n = 23) with regular menstrual cycles collected daily vaginal swabs for granulysin ELISAs. Endocervical cytobrushes, ectocervical biopsies, vaginal biopsies, and PBMC were collected across the cycle to enumerate granulysin-expressing cells by flow cytometry. Cycle phase was determined by daily urinary luteinizing hormone testing and confirmed by serum progesterone levels. ResultsGranulysin levels in secretions were up to 10,000 times higher during menstruation than during the luteal phase (menstruation, median 3,924 pg/mL [IQR 400-17,280]; luteal, median and IQR undetectable [<7.81 pg/mL]). In the endocervical canal, granulysin-expressing cells were much more abundant during menstruation than during the mid-follicular or mid-luteal phases. In contrast, the number of granulysin-expressing cells in the ectocervix and vagina remained stable during the cycle. The most abundant granulysin-expressing cell types in the mucosa were CD8 T cells and NK cells. In a minority of participants, granulysin was consistently detected in luteal-phase swabs; this phenomenon was associated with parity. ConclusionsGranulysin in vaginal secretions is associated with menstruation and concomitant with a spike in granulysin-expressing cells in the endocervical canal. This result explains the much higher granulysin levels in secretions during the follicular than the luteal phase. In contrast, immune cells from ectocervical and vaginal biopsies express granulysin independently of the menstrual cycle, indicating their continuous ability to respond to microbial infection.

immunology↗

Ecology of mosquitoes in Scottish wetlands and confirmation of Culex molestus and hybrids in Scotland

BackgroundThe recent spread of mosquito-borne pathogens and their vectors within Europe highlights the impact of climate change on vector-borne disease (VBD) distributions. Mosquito surveillance has been implemented in many European countries to monitor expansion of vector populations and VBDs, but ability to predict disease risk is constrained by geographic data gaps, particularly in northern areas. In the United Kingdom, wetland mosquito surveillance has been conducted extensively in England, with a knowledge deficit for Scotland. Here, we addressed this gap through a nationwide survey of mosquitoes at Scottish wetlands, with aims of 1) confirming the geographic distribution and environmental drivers of mosquito occurrence and abundance, and 2) identifying the presence of vector species of epidemiological concern, including the Culex pipiens molestus biotype, an important vector of emerging VBDs in mainland Europe. MethodsMonthly mosquito sampling was conducted between June and October 2023 at 22 sites across Scotland comprising six wetland types: coastal saltmarsh, wet grassland, wet woodland, reedbeds, ponds and blanket bog. Adult and larval populations were sampled using Biogents BG-Pro traps and larval dipping respectively. Microclimatic and hydrological variables were recorded at collection sites and used in generalised linear mixed models to identify predictors of mosquito presence and abundance. Results1951 adults (17 species/ groups) and 860 larvae (six species/ groups) were collected from wetlands over 183 and 164 sampling events respectively. Mosquitoes were widely distributed across the Scottish mainland including up to the northern coast, being found at all but one site. Several potential vector species including Culex pipiens s.l. and Anopheles claviger were common. Amongst the adult Culex pipiens s.l. specimens, approximately 8% were Culex pipiens biotype molestus or hybrid forms. Total mosquito abundance and that of key vector species were positively associated with temperature and rainfall. ConclusionsWe report the widespread distribution of mosquitoes in wetlands throughout Scotland, including potential vector species previously unconfirmed in Scotland. Predicted associations between mosquito abundance, rainfall and temperature indicate that climate change could favour mosquito populations in Scotland. Our results provide the first comprehensive description of mosquito ecology in Scotland, as required to update assessment of VBD risk under climate change.

ecology↗

Targeted NAD+ Delivery for Intimal Hyperplasia and Re-endothelialization: A Novel Anti-restenotic Therapy Approach

Endovascular interventions often fail due to restenosis, primarily caused by smooth muscle cell (SMC) proliferation, leading to intimal hyperplasia (IH). Current strategies to prevent restenosis are far from perfect and impose significant collateral damage on the fragile endothelial cell (EC), causing profound thrombotic risks. Nicotinamide adenine dinucleotide (NAD+) is a co-enzyme and signaling substrate implicated in redox and metabolic homeostasis, with a pleiotropic role in protecting against cardiovascular diseases. However, a functional link between NAD+ repletion and the delicate duo of IH and EC regeneration has yet to be established. NAD+ repletion has been historically challenging due to its poor cellular uptake and low bioavailability. We have recently invented the first nanocarrier that enables direct intracellular delivery of NAD+ in vivo. Combining the merits of this prototypic NAD+-loaded calcium phosphate (CaP) nanoparticle (NP) and biomimetic surface functionalization, we created a biomimetic P-NAD+-NP with platelet membrane coating, which enabled an injectable modality that targets IH with excellent biocompatibility. Using human cell primary culture, we demonstrated the benefits of NP-assisted NAD+ repletion in selectively inhibiting the excessive proliferation of aortic SMC, while differentially protecting aortic EC from apoptosis. Moreover, in a rat balloon angioplasty model, a single-dose treatment with intravenously injected P-NAD+-NP immediately post angioplasty not only mitigated IH, but also accelerated the regeneration of EC (re-endothelialization) in vivo in comparison to control groups (i.e., saline, free NAD+ solution, empty CaP-NP). Collectively, our current study provides proof-of-concept evidence supporting the role of targeted NAD+ repletion nanotherapy in managing restenosis and improving re-endothelialization.

pathology↗

Combining Unity with machine vision to create low latency, flexible, and simple virtual realities

O_LIIn recent years, virtual reality arenas have become increasingly popular for quantifying visual behaviors. By using the actions of a constrained animal to control the visual scenery, the animal is provided the perception of moving through a simulated environment. As the animal is constrained in space, this allows detailed behavioral quantification. Additionally, as the world is generally computer-generated this allows for mechanistic quantification of visual triggers of behavior. C_LIO_LIWe created a novel virtual arena combining machine vision with the gaming engine Unity. For tethered flight, we enhanced an existing multi-modal virtual reality arena, MultiMoVR (Kaushik et al., 2020) but tracked hoverfly wing movements using DeepLabCut-live (DLC-live, Kane et al., 2020). For trackball experiments, we recorded the motion of a ball that a tethered crab was walking on using FicTrac (Moore et al., 2014). In both cases, real-time tracking was interfaced with Unity to control the movement of the tethered animals avatars in the virtual world. We developed a user-friendly Unity Editor interface, CAVE, to simplify experimental design and data storage without the need for coding. C_LIO_LIWe show that both the DLC-live-Unity and the FicTrac-Unity configurations close the feedback loop effectively with small delays, less than 50 ms. Our FicTrac-Unity integration highlighted the importance of closed-loop feedback by reducing behavioral artifacts exhibited by the crabs in open-loop scenarios. We show that Eristalis tenax hoverflies, using the DLC-live-Unity integration, navigate towards flowers. The effectiveness of our CAVE interface is shown by implementing experimental sequencing control based on avatar proximity to virtual structures. C_LIO_LIOur results show that combining Unity with machine vision tools such as DLC-live and FicTrac provides an easy and flexible virtual reality (VR) environment that can be readily adjusted to new experiments and species. This can be implemented programmatically in Unity, or by using our new tool CAVE, which allows users to design and implement new experiments without programming in code. We provide resources for replicating experiments and our interface CAVE via GitHub, together with user manuals and instruction videos, for sharing with the wider scientific community. C_LI

animal behavior and cognition↗

Improving bacterial metagenomic research through long read sequencing

Metagenomic sequencing analysis is central to investigating microbial communities in clinical and environmental studies. Short read sequencing remains the primary data type for metagenomic research, however, long read sequencing promises advantages of improved metagenomic assembly and resolved taxonomic identification. To assess the comparative performance of short and long read sequencing data for metagenomic analysis, we simulated short and long read datasets using increasingly complex metagenomes comprised of 10, 20, and 50 microbial taxa. In addition, an empirical dataset of paired short and long read data from mouse fecal pellets was generated to assess feasibility. We compared metagenomic assembly quality, taxonomic classification capabilities, and metagenome-assembled genome recovery rates for both simulated and real metagenomic sequence data. We show that long read sequencing data significantly improves taxonomic classification capabilities and assembly quality. For simulated long read datasets, metagenomic assemblies were completer and more contiguous with higher rates of metagenome-assembled genome recovery. This resulted in more precise taxonomic classifications. Analysis of empirical data demonstrated that sequencing technology directly affects compositional results. Overall, we highlight strengths of long read sequencing for metagenomic studies of microbial communities over traditional short read approaches. Long read sequencing improved the accuracy of classification and abundance estimation. These results will aid researchers when considering which sequencing platforms to use for metagenomic projects. Data descriptionThe experimental metagenomic sequence data used for comparison of short and long read data from the same source are available from NCBIs Sequence Read Archive (SRA) under Bioproject accession ID PRJNA1092431.

bioinformatics↗

The Drosophila cardiogenic transcription factors Myocyte enhancer factor-2 and Tinman contribute to heart lumen enlargement through direct activation of the collagen gene Multiplexin.

During embryogenesis, the Drosophila heart forms a lumen, the posterior region of which is increased in diameter and corresponds to the heart proper. To identify the transcriptional control of this morphogenetic process, we analyzed the formation and enlargement of the heart lumen in mutants for the myogenic transcription factor gene Myocyte enhancer factor-2 (Mef2). We found that Mef2 contributes to both lumen formation and lumen expansion, the latter through a requirement for both Mef2 and the cardiogenic gene tinman (tin) to activate the collagen gene Multiplexin (Mp). To determine if Tin and MEF2 act directly upon the Mp gene, we identified an enhancer whose activity recapitulates the cardiac expression of Mp. This enhancer contains binding sites for both Tin and MEF2 and is activated in tissue culture by MEF2 but not Tin. We did not observe synergistic activation of the enhancer when the factors were in combination, despite documenting a direct physical interaction between Tin and MEF2 in vitro. In vivo, the Tin sites are required for normal enhancer activity, whereas mutation of the MEF2 sites results in expanded expression of an enhancer-lacZ reporter, suggesting that transcriptional repression may also contribute to regulation of Mp. Our studies underline how transcription factors must utilize combinatorial interactions to achieve organ-specific and region-specific patterns of gene expression and cell morphogenesis.

developmental biology↗

Corticosterone enhances formation of non-fear but not fear memory during infectious illness

Survivors of critical illness are at high risk of developing post-traumatic stress disorder (PTSD) but administration of glucocorticoids during the illness can lower that risk. The mechanism is not known but may involve glucocorticoid modulation of hippocampal- and amygdalar-dependent memory formation. In this study, we sought to determine whether glucocorticoids given during an acute illness influence the formation and persistence of fear and non-fear memories from the time of the illness. We performed cecal ligation and puncture in male and female mice to induce an acute infectious illness. During the illness, mice were introduced to a neutral object in their home cage and separately underwent contextual fear conditioning. We then tested the persistence of object and fear memories after recovery. Glucocorticoid treatment enhanced object discrimination but did not alter the expression of contextual fear memory. During context re-exposure, neural activity was elevated in the dentate gyrus irrespective of fear conditioning. Our results suggest that glucocorticoids given during illness enhance hippocampal-dependent non-fear memory processes. This indicates that PTSD outcomes in critically ill patients may be improved by enhancing non-fear memories from the time of their illness.

neuroscience↗

Forebrain glucocorticoid receptor overexpression alters behavioral encoding of hippocampal CA1 pyramidal cells in mice

Stress hormone signaling via the glucocorticoid receptor (GR) modulates vulnerability to stress-related disorders, but whether GR influences how the brain encodes contextual experience is unknown. Mice with lifelong GR overexpression in forebrain glutamatergic neurons (GRov) show increased sensitivity to environmental stimuli. This phenotype is developmentally programmed and associated with profound changes in hippocampal gene expression. We hypothesized that GR overexpression influences hippocampal encoding of experiences. To test our hypothesis, we performed in vivo microendoscopic calcium imaging of 1359 dorsal CA1 pyramidal cells in freely behaving male and female WT and GRov mice during exploration of a novel open field. We compared calcium amplitude and event rate as well as sensitivity to center location and mobility between genotypes. GRov neurons exhibited higher average calcium activity than WT neurons in the novel open field. While most neurons showed sensitivity to center location and/or mobility, GRov neurons were more likely to be sensitive to center location and less likely to be sensitive to mobility, as compared to WT neurons. More than one-third of behavior-selective GRov neurons were uniquely sensitive to location without mobility sensitivity; these uniquely center-sensitive neurons were rare in WT. We conclude that dorsal CA1 pyramidal cells in GRov mice show increased activity in a novel environment and preferentially encode emotionally salient behavior. This heightened sensitivity to a novel environment and preferential encoding of emotionally salient elements of experience could underlie differential stress vulnerability in humans with increased glucocorticoid sensitivity. Significance Statement (120 words maximum)Endogenous stress hormones, glucocorticoids, are known to alter vulnerability to stress-related disorders. Here, we find that increased sensitivity to glucocorticoid via lifelong overexpression of glucocorticoid receptor in forebrain neurons (GRov) alters the encoding of environmental experiences in the hippocampus. GRov mice showed increased activity of dorsal CA1 hippocampal pyramidal cells during exploration of a novel environment and more sensitivity to emotionally relevant behaviors. These changes in how hippocampal neurons encode environmental experiences could underlie the differences in stress vulnerability in humans with genetic and epigenetic differences in glucocorticoid receptor signaling.

neuroscience↗

Herpes Simplex Virus Mistyping due to HSV-1 x HSV-2 Interspecies Recombination in Viral Gene Encoding Glycoprotein B

Human herpes simplex viruses (HSV) 1 and 2 are most often typed via molecular assays. Here we describe the first known case of HSV mistyping due to a previously undescribed HSV-1 x HSV-2 recombination event in UL27, the gene that encodes glycoprotein B. This is the first reported HSV interspecies recombination event impacting this gene, which is frequently used as a target for diagnostics and experimental therapeutics.

genomics↗

Microbial ecology of Atlantic salmon, Salmo salar, hatcheries: impacts of the built environment on fish mucosal microbiota

Successful rearing of fish in hatcheries is critical for conservation, recreational fishing, and commercial fishing through wild stock enhancements, and aquaculture production. Flow through (FT) hatcheries require more water than Recirculating-Aquaculture-Systems (RAS) which enable up to 99% of water to be recycled thus significantly reducing environmental impacts. Here, we evaluated the biological and physical microbiome interactions of the built environment of a hatchery from three Atl salmon hatcheries (RAS n=2, FT n=1). Six juvenile fish were sampled from tanks in each of the hatcheries for a total of 60 fish across 10 tanks. Water and tank side biofilm samples were collected from each of the tanks along with three salmon body sites (gill, skin, and digesta) to assess mucosal microbiota using 16S rRNA sequencing. The water and tank biofilm had more microbial richness than fish mucus while skin and digesta from RAS fish had 2x the richness of FT fish. Body sites each had unique microbial communities (P<0.001) and were influenced by the various hatchery systems (P<0.001) with RAS systems more similar. Water and especially tank biofilm richness was positively correlated with skin and digesta richness. Strikingly, the gill, skin and digesta communities were more similar to the origin tank biofilm vs. all other experimental tanks suggesting that the tank biofilm has a direct influence on fish-associated microbial communities. The results from this study provide evidence for a link between the tank microbiome and the fish microbiome with the skin microbiome as an important intermediate.\n\nIMPORTANCEAtlantic salmon, Salmo salar, is the most farmed marine fish worldwide with an annual production of 2,248 million metric tonnes in 2016. Salmon hatcheries are increasingly changing from flow through towards RAS design to accommodate more control over production along with improved environmental sustainability due to lower impacts on water consumption. To date, microbiome studies on hatcheries have focused either on the fish mucosal microbiota or the built environment microbiota, but have not combined the two to understand interactions. Our study evaluates how water and tank biofilm microbiota influences fish microbiota across three mucosal environments (gill, skin, and digesta). Results from this study highlight how the built environment is a unique source of microbes to colonize fish mucus and furthermore how this can influence the fish health. Further studies can use this knowledge to engineer built environments to modulate fish microbiota for a beneficial phenotype.

microbiology↗

Deep evolutionary origin of nematode SL2 trans-splicing revealed by genome-wide analysis of the Trichinella spiralis transcriptome

Spliced leader trans-splicing is intimately associated with the presence of eukaryotic operons, allowing the processing of polycistronic RNAs into individual mRNAs. Most of our understanding of spliced leader trans-splicing as it relates to operon gene expression comes from studies in C. elegans. In this organism, two distinct spliced leader trans-splicing events are recognised: SL1, which is used to replace the 5 ends of pre-mRNAs that have a nascent monomethyl guanosine cap; and SL2, which provides the 5 end to uncapped pre-mRNAs derived from polycistronic RNAs. Limited data on operons and spliced leader trans-splicing in other nematodes suggested that SL2-type trans-splicing is a relatively recent innovation, associated with increased efficiency of polycistronic processing, and confined to only one of the five major nematode clades, Clade V. We have conducted the first transcriptome-wide analysis of spliced leader trans-splicing in a nematode species, Trichinella spiralis, which belongs to a clade distantly related to Clade V. Our work identifies a set of T. spiralis SL2-type spliced leaders that are specifically used to process polycistronic RNAs, the first examples of specialised spliced leaders that have been found outside of Clade V. These T. spiralis spliced leader RNAs possess a perfectly conserved stem-loop motif previously shown to be essential for polycistronic RNA processing in C. elegans. We show that this motif is found in specific sets of spliced leader RNAs broadly distributed across the nematode phylum. This work substantially revises our understanding of the evolution of nematode spliced leader trans-splicing, showing that the machinery for SL2 trans-splicing evolved much earlier during nematode evolution than was previously appreciated, and has been conserved throughout the radiation of the nematode phylum.

genomics↗

The impact of interspecies recombination on human herpes simplex virus evolution and host immune recognition

Among the most ubiquitous of human pathogens, HSV-1 and HSV-2 are distinct viral species that diverged about six million years ago. At least four ancient HSV-1 x HSV-2 interspecies recombination events have affected the HSV-2 genome, with recombinants and non-recombinants at each locus circulating today. Though interspecies recombination has occurred in the past, its importance in HSV evolution remains incompletely defined. Using 255 newly-sequenced and 219 existing HSV genome sequences, we comprehensively assessed interspecies recombination in HSV. The novel recombinants we identify demonstrate that the sizes and locations of interspecies recombination events in HSV-2 are more variable than previously appreciated. One novel recombinant arose in its current host, showing for the first time that interspecies recombination occurs in contemporary HSV populations. We also demonstrate that interspecies recombination affects T-cell recognition of HSV. Our findings indicate that interspecies recombination can significantly influence genetic variation in and host immunologic response to HSV-2.

genomics↗

Ultrasensitive capture of human herpes simplex virus genomes directly from clinical samples reveals extraordinarily limited evolution in cell culture

Herpes simplex viruses (HSV) are difficult to sequence due to their large DNA genome, high GC content, and the presence of repeats. To date, most HSV genomes have been recovered from culture isolates, raising concern that these genomes may not accurately represent circulating clinical strains. We report the development and validation of a DNA oligonucleotide hybridization panel to recover near complete HSV genomes at abundances up to 50,000-fold lower than previously reported. Using copy number information on herpesvirus and host DNA background via quantitative PCR, we developed a protocol for pooling for cost-effective recovery of more than 50 HSV-1 or HSV-2 genomes per MiSeq run. We demonstrate the ability to recover >99% of the HSV genome at >100X coverage in 72 hours at viral loads that allow whole genome recovery from latently-infected ganglia. We also report a new computational pipeline for rapid HSV genome assembly and annotation. Using the above tools and a series of 17 HSV-1-positive clinical swabs sent to our laboratory for viral isolation, we show limited evolution of HSV-1 during viral isolation in human fibroblast cells compared to the original clinical samples. Our data indicate that previous studies using low passage clinical isolates of herpes simplex viruses are reflective of the viral sequences present in the lesion and thus can be used in phylogenetic analyses. We also detect superinfection within a single sample with unrelated HSV-1 strains recovered from separate oral lesions in an immunosuppressed patient during a 2.5-week period, illustrating the power of direct-from-specimen sequencing of HSV.\n\nImportanceHerpes simplex viruses affect more than 4 billion people across the globe, constituting a large burden of disease. Understanding global diversity of herpes simplex viruses is important for diagnostics and therapeutics as well as cure research and tracking transmission among humans. To date, most HSV genomics has been performed on culture isolates and DNA swabs with high quantities of virus. We describe the development of wet-lab and computational tools that enable the accurate sequencing of near-complete genomes of HSV-1 and HSV-2 directly from clinical specimens at abundances >50,000-fold lower than previously sequenced and at significantly reduced cost. We use these tools to profile circulating HSV-1 strains in the community and illustrate limited changes to the viral genome during the viral isolation process. These techniques enable cost-effective, rapid sequencing of HSV-1 and HSV-2 genomes that will help enable improved detection, surveillance, and control of this human pathogen.

genomics↗

Fine-tuning cellular levels of DprA ensures transformant fitness in the human pathogen Streptococcus pneumoniae

Natural genetic transformation is a widespread mechanism of bacterial horizontal gene transfer. Transformation involves the internalization of exogenous DNA as single strands, followed by chromosomal integration via homologous recombination, promoting acquisition of new genetic traits. Transformation occurs during a distinct physiological state called competence, during which all proteins required to transform are produced. In the human pathogen Streptococcus pneumoniae, competence is controlled by a two-component system ComDE, which is induced by an exported peptide pheromone. DprA is universal among transformable species, strongly and specifically induced during pneumococcal competence, and crucial for pneumococcal transformation. Pneumococcal DprA plays three crucial roles in transformation and competence. Firstly, DprA protects internalized single-stranded (ss) DNA from degradation. Secondly, DprA loads the homologous recombinase RecA onto transforming ssDNA to promote transformation. Finally, DprA interacts with the response regulator ComE to shut-off pneumococcal competence. Pneumococcal shut-off has been linked to physiology, with long growth delays in competent dprA- cells. Here, we explored the effect of altering the cellular levels of DprA on these three roles. High cellular levels of DprA were not required for the primary role of DprA as a transformation-dedicated recombinase loader or for protection of transforming ssDNA. In contrast, full expression of dprA was required for optimal competence shut-off. Full expression of dprA was also crucial for transformant fitness. High cellular levels of DprA in competent cells thus ensure the fitness of pneumococcal transformants by promoting competence shut-off. This promotes survival and propagation of transformants, thus maximizing the adaptive potential of this human pathogen.\n\nImportanceTransformation is a widespread mechanism of horizontal gene transfer that allows bacteria to acquire new genetic traits by internalizing foreign DNA and integrating it into their chromosomes. Transformation occurs during a transient physiological state called competence. DprA is conserved in transformable species and crucial for the protection and integration of transforming DNA. In the human pathogen Streptococcus pneumoniae, DprA is highly abundant and is also crucial for competence shut-off. Here, we show that high DprA expression is not required for transformation. In contrast, full expression of dprA was required for competence shut-off and transformant fitness. These findings thus link high cellular levels of DprA to survival and propagation of pneumococcal transformants, maximizing the adaptive potential of this human pathogen.

microbiology↗

Does genetic risk help to predict amyloid burden in a non-demented population? A Bayesian approach.

INTRODUCTIONIn this study we investigate the association between A{beta} levels in cerebrospinal fluid (CSF) and genetic risk in a non-demented population. This paper presents the first analysis to use a Bayesian methodology in this area.\n\nMETHODSData from the Alzheimers Disease Neuroimaging Initiative (ADNI) and the EDAR* and DESCRIPA** studies was used in a Bayesian logistic regression analysis. We modeled CSF A{beta} burden using age, diagnosis (healthy control or mild cognitive impairment), APOE and a polygenic risk score (PGRS) associated with Alzheimers Disease (AD). We compared models built using informative priors on age, diagnosis and APOE with non-informative priors on all variables.\n\nRESULTSThe use of informative priors did not improve model performance in the majority of cases. Models using only age, diagnosis and APOE genotype showed the best predictive ability.\n\nDISCUSSIONA previous study indicated that a PGRS of AD case/control status was associated with CSF A{beta} burden in healthy controls. The current study suggests that this association does not lead to models that are more predictive of amyloid positivity than already known factors such as age and APOE.\n\n* Beta amyloid oligomers in the early diagnosis of AD and as marker for treatment response\n\n** Development of screening guidelines and criteria for pre-dementia Alzheimers disease

bioinformatics↗