Biology subjects

Preston, A.

Publications and source records attributed to Preston, A..

8 recordsLinked to original sources

bioRxiv2024

A Novel Adhesin of B. pertussis is Key to Colonisation of Epithelial Cells

Despite effective vaccines to protect against Whooping cough, or pertussis, the disease is resurgent in many countries. A switch from acellular to whole-cell vaccines has resulted in waning protective immunity, likely contributing to increases in infection prevalence, underlining the need to better understand B. pertussis virulence. As a respiratory pathogen, B. pertussis colonises the upper respiratory tract utilising an array of adhesins, four of which (FHA, pertactin, Fim2/3) are included in the acellular vaccine. In this study, we identified two Bvg regulated genes that are upregulated during virulence conditions and thus potentially involved in pathogenesis. bp1251 and bp1252 encode orphan toxin B subunits, with homology to AB toxin B subunits. Mutation of bp1251 and bp1252 reduced the in vitro adherence of B. pertussis to A549 and BEAS-2B alveolar and bronchial epithelial-like cells. In a murine model of infection, bp1251 and bp1252 mutant strains were recovered from the nasal cavity and lungs at lower levels than WT. In vitro no effect of mutation of bp1251 or bp1252 on cell invasion or toxicity was found suggesting that these proteins do not form part of a toxin. Given their homology to B subunits of AB toxins, and their role in colonisation, we propose that BP1251 and BP1252 are novel adhesins. Our data suggests that these proteins play a significant role in Bordetella infection and have the potential to further the understanding of B. pertussis pathogenesis.

microbiology↗

bioRxiv2023

Development of human hippocampal subfield microstructure and relation to associative inference

The hippocampus is a complex brain structure composed of subfields that each have distinct cellular organizations. While the volume of hippocampal subfields displays age-related changes that have been associated with inference and memory functions, the degree to which the cellular organization within each subfield is related to these functions throughout development is not well understood. We employed an explicit model testing approach to characterize the development of tissue microstructure and its relationship to performance on two inference tasks, one that required memory (memory-based inference) and one that required only perceptually available information (perception-based inference). We found that each subfield had a unique relationship with age in terms of its cellular organization. While the subiculum (SUB) displayed a linear relationship with age, the dentate gyrus (DG), cornu ammonis field 1 (CA1), and cornu ammonis subfields 2 and 3 (combined; CA2/3) displayed non-linear trajectories that interacted with sex in CA2/3. We found that the DG was related to memory-based inference performance and that the SUB was related to perception-based inference; neither relationship interacted with age. Results are consistent with the idea that cellular organization within hippocampal subfields might undergo distinct developmental trajectories that support inference and memory performance throughout development.

neuroscience↗

bioRxiv2021

Comparative genomics of Bordetella pertussis isolates from New Zealand, a country with an uncommonly high incidence of whooping cough

2.Whooping cough, the respiratory disease caused by Bordetella pertussis, has undergone a wide-spread resurgence over the last several decades. Previously, we developed a pipeline to assemble the repetitive B. pertussis genome into closed sequences using hybrid nanopore and Illumina sequencing. Here, this sequencing pipeline was used to conduct a more high-throughput, longitudinal screen of 66 strains isolated between 1982 and 2018 in New Zealand. New Zealand has a higher incidence of whooping cough than many other countries; usually at least twice as many cases per 100,000 people as the USA and UK and often even higher, despite similar rates of vaccine uptake. To the best of our knowledge, these strains are the first New Zealand B. pertussis isolates to be sequenced. The analyses here show that, on the whole, genomic trends in New Zealand B. pertussis isolates, such as changing allelic profile in vaccine-related genes and increasing pertactin deficiency, have paralleled those seen elsewhere in the world. At the same time, phylogenetic comparisons of the New Zealand isolates with global isolates suggest that a number of strains are circulating in New Zealand which cluster separately from other global strains, but which are closely related to each other. The results of this study add to a growing body of knowledge regarding recent changes to the B. pertussis genome, and are the first genetic investigation into B. pertussis isolates from New Zealand. 3. Impact statementSince the 1990s, whooping cough has been resurgent in many countries around the world, despite the wide availability of vaccines. New Zealand has often had a higher incidence of whooping cough than other countries such as the USA, UK and Australia, both during outbreak periods and in the intervening years. One potential reason for the resurgence of whooping cough is genetic changes to the causative bacterium, Bordetella pertussis, with several recently identified, ongoing global genetic trends. No B. pertussis isolates from New Zealand have previously been sequenced, however. Here, we used hybrid sequencing to investigate the genomes of 66 New Zealand B. pertussis isolates, collected between 1982 and 2018. This revealed that genetic trends in New Zealand B. pertussis match those observed elsewhere, but over the years a number of highly similar or identical strains appear to have circulated (or are currently circulating) in the country, a phenomenon not commonly noted elsewhere. This first study of B. pertussis isolates from New Zealand contributes to the global understanding of B. pertussis genomics, as well as providing the groundwork for any future whole genome sequencing of New Zealand B. pertussis isolates. 4. Data summaryO_LINanopore and Illumina fastq sequence files for all strains have been deposited in NCBIs Sequence Read Archive, BioProject PRJNA556977. A full list of accession numbers for all sequence read files is provided in Supplementary Table S1. C_LIO_LIGenome sequences for 63 strains have been deposited in NCBIs GenBank, BioProject PRJNA556977, accession numbers in Supplementary Table S1. C_LIO_LIGenome assemblies for 3 strains assembled using only nanopore data (NZ1, NZ5 and NZ29), which had a high number of pseudogenes, were not deposited in GenBank, but are available from Figshare: https://doi.org/10.6084/m9.figshare.12640463 C_LIO_LISource code and full commands used are available from Github: https://github.com/nataliering/Comparative-genomics-of-Bordetella-pertussis-isolates-from-New-Zealand C_LI The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

genomics↗

bioRxiv2021

Are some commercial diets inadequate in essential nutrients?

BackgroundCommercial manufacturers have formulated diets to promote not only weight reduction but also to reduce risks of chronic diseases. The objective of this study is to determine if these formulations satisfy requirements for essential nutrients. MethodsWe have selected two established commercial diets, one low fat, high carbohydrate (diet 1) and the other, high fat, low carbohydrate (diet 2) and determined "representative meals" through use of recipes suggested in the manufacturers manuals. Nutrition Data System for Research (NDSR) software has been used to perform the most extensive nutrient analysis to date of these diets. Tables report macronutrients (energy), vitamins, minerals, essential amino acids, essential lipids and nutrient-related components for a total of 62entries. ResultsDiet 1 satisfied requirements for 50 of these (81%) with only vitamin B12, vitamin D, and essential fatty acids not reaching recommended levels, while fiber and glycemic load exceeded suggested values. Diet 2 satisfied requirements for 46 of the components (71%) but had excess percentage of fat, especially saturated fat, sodium and cholesterol as well as decreased percentage of carbohydrate resulting in suboptimal intake of B-complex vitamins (B1, niacin and total folate) as well as fiber. ConclusionsNeither diet satisfied adequacy for all reported nutrients. However, based on nutrient content alone diet 1, if supplemented or modified, could be sustained over the long term whereas diet 2 should not be encouraged for long term adaptation

scientific communication and education↗

bioRxiv2020

Cobalt(III) Schiff Base complexes stabilize non-fibrillar amyloid-β aggregates with reduced toxicity

The aggregation of A{beta} is believed to be foundational to the pathogenesis of Alzheimers disease (AD). In vitro aggregation kinetics have been shown to correlate with rates of disease progression in both AD patients and animal models, thus proving to be a useful metric for testing A{beta}-targeted therapeutics. Here we present evidence of Cobalt(III) Schiff base complex (Co(III)-sb) modulation of A{beta} aggregation kinetics by a variety of complementary techniques. These include Thioflavin T (ThT) fluorescence, circular dichroism (CD) spectroscopy, transmission electron microscopy (TEM), and atomic force microscopy (AFM). Our data was fitted to kinetic rate laws using a mathematical model developed by Knowles et al. in order to extract mechanistic information about the effect of Co(III)-sb on aggregation kinetics. Our analysis revealed that Co(III)-sb significantly decreases the kinetic parameter k+, and significantly increases the polymerization rate kn, suggesting that Co(III)-sb causes A{beta} to rapidly form stable oligomeric species that are unable to elongate into mature fibrils. This result was corroborated by TEM and AFM of A{beta} aggregates in vitro. We also demonstrate that A{beta} aggregate mixtures produced in the presence of Co(III)-sb exhibit decreased cytotoxicity compared to untreated samples. Statement of SignificanceAmyloid-{beta} is thought to be a key mediator in the pathology of Alzheimers disease, yet its precise mechanisms of toxicity are poorly understood. The interaction of A{beta} with endogenous metal ions via its N terminal Histidine residues has been shown to alter the peptides aggregation and toxicity. As such, metal-based complexes have been developed both as therapeutic agents as well as tools for investigating the role of metal binding in the pathogenesis of AD. This work expands on our previous studies developing Cobalt(III) Schiff base complexes as amyloid inhibitors. Here we demonstrate effective inhibition of aggregation by various complementary modalities. Additionally we show that Co(III)-sb reduces the toxicity of A{beta} aggregates to cells in culture.

neuroscience↗

bioRxiv2020

Duplications drive diversity in Bordetella pertussis on an underestimated scale.

Bacterial genetic diversity is often described using solely base pair changes despite a wide variety of other mutation types likely being major contributors. Tandem duplications of genomic loci are thought to be widespread among bacteria but due to their often intractable size and instability, comprehensive studies of the range and genome dynamics of these mutations are rare. We define a methodology to investigate duplications in bacterial genomes based on read depth of genome sequence data as a proxy for copy number. We demonstrate the approach with Bordetella pertussis, whose insertion sequence element-rich genome provides extensive scope for duplications to occur. Analysis of genome sequence data for 2430 B. pertussis isolates identified 272 putative duplications, of which 94% were located at 11 hotspot loci. We demonstrate limited phylogenetic connection for the occurrence of duplications, suggesting unstable and sporadic characteristics. Genome instability was further described in-vitro using long read sequencing via the Nanopore platform. Clonally derived laboratory cultures produced heterogenous populations containing multiple structural variants. Short read data was used to predict 272 duplications, whilst long reads generated on the Nanopore platform enabled the in-depth study of the genome dynamics of tandem duplications in B. pertussis. Our work reveals the unrecognised and dynamic genetic diversity of B. pertussis and, as the complexity of the B. pertussis genome is not unique, highlights the need for a holistic and fundamental understanding of bacterial genetics.

microbiology↗

bioRxiv2019

A qPCR assay for Bordetella pertussis cells that enumerates both live and dead bacteria.

Bordetella pertussis is the causative agent of whooping cough, commonly referred to as pertussis. Although the incidence of pertussis was reduced through vaccination, during the last thirty years it has returned to high levels in a number of countries. This resurgence has been linked to the switch from the use of whole-cell to acellular vaccines. Protection afforded by acellular vaccines appears to be short-lived compared to that afforded by whole cell vaccines. In order to inform future vaccine improvement by identifying immune correlates of protection, a human challenge model of B. pertussis colonisation has been developed. Accurate measurement of colonisation status in this model has required development of a qPCR-based assay to enumerate B. pertussis in samples that distinguishes between viable and dead bacteria. Here we report the development of this assay and its performance in the quantification of B. pertussis from human challenge model samples. This assay has future utility in diagnostic labs and in research where a quantitative measure of both B. pertussis number and viability is required.

microbiology↗

bioRxiv2018

Resolving the complex Bordetella pertussis genome using barcoded nanopore sequencing

The genome of Bordetella pertussis is complex, with high GC content and many repeats, each longer than 1,000 bp. Short-read DNA sequencing is unable to resolve the structure of the genome; however, long-read sequencing offers the opportunity to produce single-contig B. pertussis assemblies using sequencing reads which are longer than the repetitive sections. We used an R9.4 MinION flow cell and barcoding to sequence five B. pertussis strains in a single sequencing run. We then trialled combinations of the many nanopore-user-community-built long-read analysis tools to establish the current optimal assembly pipeline for B. pertussis genome sequences. Our best long-read-only assemblies were produced by Canu read correction followed by assembly with Flye and polishing with Nanopolish, whilst the best hybrids (using nanopore and Illumina reads together) were produced by Canu correction followed by Unicycler. This pipeline produced closed genome sequences for four strains, revealing inter-strain genomic rearrangement. However, read mapping to the Tohama I reference genome suggests that the remaining strain contains an ultra-long duplicated region (over 100 kbp), which was not resolved by our pipeline. We have therefore demonstrated the ability to resolve the structure of several B. pertussis strains per single barcoded nanopore flow cell, but the genomes with highest complexity (e.g. very large duplicated regions) remain only partially resolved using the standard library preparation and will require an alternative library preparation method. For full strain characterisation, we recommend hybrid assembly of long and short reads together; for comparison of genome arrangement, assembly using long reads alone is sufficient.\n\nDATA SUMMARYO_LIFinal sequence read files (fastq) for all 5 strains have been deposited in the SRA, BioProject PRJNA478201, accession numbers SAMN09500966, SAMN09500967, SAMN09500968, SAMN09500969, SAMN09500970\nC_LIO_LIA full list of accession numbers for Illumina sequence reads is available in Table S1\nC_LIO_LIAssembly tests, basecalled read sets and reference materials are available from figshare: https://figshare.com/projects/Resolving_the_complex_Bordetella_pertussis_genome_using_barcoded_nanopore_sequencing/31313\nC_LIO_LIGenome sequences for B. pertussis strains UK36, UK38, UK39, UK48 and UK76 have been deposited in GenBank; accession numbers: CP031289, CP031112, CP031113, QRAX00000000, CP031114\nC_LIO_LISource code and full commands used are available from Github: https://github.com/nataliering/Resolving-the-complex-Bordetella-pertussis-genome-using-barcoded-nanopore-sequencing\nC_LI\n\nIMPACT STATEMENTOver the past two decades, whole genome sequencing has allowed us to understand microbial pathogenicity and evolution on an unprecedented level. However, repetitive regions, like those found throughout the B. pertussis genome, have confounded our ability to resolve complex genomes using short-read sequencing technologies alone. To produce closed B. pertussis genome sequences it is necessary to use a sequencing technology which can generate reads longer than these problematic genomic regions. Using barcoded nanopore sequencing, we show that multiple B. pertussis genomes can be resolved per flow cell. Use of our assembly pipeline to resolve further B. pertussis genomes will advance understanding of how genome-level differences affect the phenotypes of strains which appear monomorphic at nucleotide-level.\n\nThis work expands the recently emergent theme that even the most complex genomes can be resolved with sufficiently long sequencing reads. Additionally, we utilise a more widely accessible alternative sequencing platform to the Pacific Biosciences platform already used by large research centres such as the CDC. Our optimisation process, moreover, shows that the analysis tools favoured by the sequencing community do not necessarily produce the most accurate assemblies for all organisms; pipeline optimisation may therefore be beneficial in studies of unusually complex genomes.

microbiology↗