Biology subjects

Webb, M.

Publications and source records attributed to Webb, M..

10 recordsLinked to original sources

bioRxiv2025

Discovery and biosynthesis of biffamycin A, a novel glycotetrapeptide antibiotic

The clinical deployment of antibiotics is undermined by antimicrobial resistance. Without new agents to treat antibiotic resistant bacterial infections, mortality rates are predicted to reach 10 million people per year by 2050. Most antibiotics are derived from natural products (NPs) produced by bacteria; however, this resource was abandoned by industry because of high rediscovery rates. We are amid a natural product renaissance fuelled by inexpensive access to genome sequencing and sophisticated bioinformatic tools, which have highlighted that most of the biosynthetic pathways for NPs are not expressed in the laboratory. Here, we engineered the expression of a silent biosynthetic gene cluster harboured by an environmental isolate of Streptomyces albidoflavus. By using a bioinformatics-guided approach, we isolated and structurally characterised a novel glycopeptide antibiotic (GPA) named biffamycin A, which is the smallest GPA known and harbours unprecedented 5-chloro-4-methoxy tryptophan and 3-hydroxy(-O_SCPLOWDC_SCPLOW-mannoysl)-O_SCPLOWDC_SCPLOW-lysine moieties. Biffamycin A possesses antimycobacterial and antistaphylococcal bioactivity, including methicillin-vancomycin-resistant Staphylococcus aureus.

biochemistry↗

bioRxiv2025

Passive acoustic monitoring of Tasmanian masked owls and swift parrots: an effective tool for conservation actions

The Tasmanian masked owl (Tyto novaehollandiae subsp. castanops) and swift parrot (Lathamus discolor), both endangered species, rely on old forest features that are declining across their ranges in Tasmania, Australia. Their elusive behavior and high mobility make monitoring difficult, hindering conservation actions. Passive acoustic monitoring can greatly increase spatial and temporal survey coverage, though the identification of the species vocalisations within large audio datasets remains challenging. We deployed automated recording units at 108 sites in Tasmanias native forests to collect a large and representative acoustic dataset. We trained a neural network model to automate call detection for both the Tasmanian masked owl and the swift parrot. Our model demonstrated high performance, with a sensitivity of 97.7% and specificity of 96.5% for the Tasmanian masked owl, and a sensitivity of 87.5% and specificity of 83.3% for the swift parrot. Through two real-world applications, we illustrated how our method provides detailed quantitative insights into habitat use patterns over extended spatial and temporal scales. This innovative approach enhances both site-specific and population monitoring, enabling more effective and targeted conservation actions for these endangered species.

ecology↗

bioRxiv2024

Centromeres are Hotspots for Chromosomal Inversions and Breeding Traits in Mango

Chromosomal inversions can preserve combinations of favorable alleles by suppressing recombination. Simultaneously, they reduce the effectiveness of purifying selection enabling deleterious alleles to accumulate. This study explores how areas of low recombination, including centromeric regions and chromosomal inversions, contribute to the accumulation of deleterious and favorable loci in 225 Mangifera indica genomes from the Australian Mango Breeding Program. Here, we identify 17 chromosomal inversions that cover 7.7% (29.7Mb) of the M. indica genome: eight pericentric (inversion includes the centromere) and nine paracentric (inversion is on one arm of the chromosome). Our results show that these large pericentric inversions are accumulating deleterious loci, while the paracentric inversions show deleterious levels above and below the genome wide average. We find that despite their deleterious load, chromosomal inversions contain small effect loci linked to variation in crucial breeding traits, indicating that chromosomal inversions have likely facilitated their selection. The results from this study have important implications for selective breeding of favorable combinations of alleles in regions of low recombination. Significance StatementChromosomal inversions and other low recombination regions of the genome can drive trait evolution. Fewer recombination events can assist in maintaining favorable combinations of alleles, but it can also make disentangling favorable and deleterious alleles difficult. Understanding whether these low recombination regions contain favorable or deleterious loci could drive our decision to increase or decrease the frequency of these regions in target breeding populations. Breeding for large segments of the genome based on presence or absence of an inversion can rapidly drive large trait differences within few generations. Harnessing the impact of large low recombination regions of the genome could have major implications for future genetic improvement in breeding.

genomics↗

bioRxiv2023

Olfaction regulates peripheral mitophagy and mitochondrial function

The central nervous system is a master regulator of peripheral homeostasis and cellular-stress responses; however, the contexts for which this regulatory capability evolved remain unknown. The olfactory sensory nervous system has access to privileged information about environmental conditions and can signal to the periphery to prepare for potential metabolic perturbations. The unfolded protein response of the mitochondria (UPRMT) is upregulated upon infection by many pathogens and in metabolic flux, and pathogenic infection and metabolic byproducts are a present hazard in consuming nutrients. Therefore, we asked whether the olfactory nervous system in C. elegans regulates the UPRMT cell nonautonomously. We found that loss of a single olfactory neuron pair, AWC, led to robust induction of the UPRMT downstream of enhanced, serotonin-dependent mitophagy. Further, AWC ablation confers resistance to the pathogenic bacteria Pseudomonas aeruginosa partially dependent on the UPRMT transcription factor atfs-1, and fully dependent on mitophagy machinery pdr-1/Parkin. These data demonstrate a novel role for the olfactory nervous system in regulating whole-organism mitochondrial dynamics, perhaps in preparation for postprandial metabolic stress or pathogenic infection.

neuroscience↗

bioRxiv2023

A collaboration between immune cells and the choroid plexus epithelium in brain inflammation

The choroid plexus (ChP) is a vital brain barrier and source of cerebrospinal fluid (CSF). Here, we use chronic two-photon imaging in awake mice and single-cell transcriptomics to demonstrate that in addition to these roles, the ChP is a complex immune organ that regulates brain inflammation. In a mouse meningitis model, neutrophils and monocytes accumulated in ChP stroma and surged across the epithelial barrier into the CSF. Bi-directional recruitment of monocytes from the periphery and, unexpectedly, macrophages from the CSF to the ChP helped eliminate neutrophils and repair the barrier. Transcriptomic analyses detailed the molecular steps accompanying this process, including the discovery of epithelial cells that transiently specialized to nurture immune cells, coordinate their recruitment, survival, and differentiation, and ultimately, control the opening/closing of the ChP brain barrier. Collectively, we provide a new conceptual understanding and comprehensive roadmap of neuroinflammation at the ChP brain barrier.

neuroscience↗

bioRxiv2022

Potent, Gut-Restricted Inhibitors of Divalent Metal Transporter 1 (DMT1): Preclinical Efficacy Against Iron Overload and Safety Evaluation

Divalent metal transporter 1 (DMT1) cotransports ferrous iron and protons and is the primary mechanism for uptake of non-heme iron by enterocytes. Inhibitors are potentially useful as therapeutic agents to treat iron overload disorders such as hereditary hemochromatosis or {beta}-thalassemia intermedia, provided that inhibition can be restricted to the duodenum. We used a calcein quench assay to identify human DMT1 (hDMT1) inhibitors. Dimeric constructs were made to generate more potent compounds with low systemic exposure. Direct block of DMT1 was confirmed by voltage clamp measurements. The lead compound, XEN602, strongly inhibits dietary iron uptake in both rats and pigs, yet has negligible systemic exposure. Efficacy is maintained for >2 weeks in a rat subchronic dosing assay. Doses that lowered iron content in the spleen and liver by >50% had no effect on the tissue content of other divalent cations except for cobalt. XEN602 represents a powerful pharmacological tool for understanding the physiological function of DMT1. SIGNIFICANCE STATEMENTThis report introduces methodology to develop potent, gut-restricted inhibitors of DMT1 and identifies XEN602 as a suitable compound for in vivo studies. We also report novel animal models to quantify the inhibition of dietary uptake of iron in both rodents and pigs. This research shows that inhibition of DMT1 is a promising means to treat iron overload disorders.

pharmacology and toxicology↗

bioRxiv2021

Psychological stress disrupts intestinal epithelial cell function and mucosal integrity through microbe and host-directed processes

Psychological stress alters the gut microbiota and predisposes individuals to increased risk for enteric infections and chronic bowel conditions. Intestinal epithelial cells (IECs) are responsible for maintaining homeostatic interactions between the gut microbiota and its host. In this study, we hypothesized that disruption to colonic IECs is a key factor underlying stress-induced disturbances to intestinal homeostasis. Conventionally raised (CONV-R) and germ-free (GF) mice were exposed to a social disruption stressor (Str) to ascertain how stress modifies colonic IECs, the mucosal layer, and the gut microbiota. RNA sequencing of IECs isolated from CONV-R mice revealed a robust pro-inflammatory (Saa1, Il18), pro-oxidative (Duox2, Nos2), and antimicrobial (Reg3b/g) transcriptional profile as a result of Str. This response occurred concomitant to mucus layer thinning and signs of microbial translocation. In contrast to their CONV-R counterparts, IECs from GF mice or mice treated with broad spectrum antibiotics exhibited no detectable transcriptional changes in response to Str. Nevertheless, IECs from Str-exposed GF mice exhibited an altered response to ex vivo bacterial challenge (increased dual Oxidase-2 [Duox2] and nitric oxide synthase-2 (Nos2)), indicating that STR primes host IEC pro-oxidative responses. In CONV-R mice stress-induced increases in colonic Duox2 and Nos2 (ROS generating enzymes) strongly paralleled changes to microbiome composition and function, evidencing Str-mediated ROS production as a primary factor mediating gut-microbiota dysbiosis. In conclusion, a mouse model of social stress disrupts colonic epithelial and mucosal integrity, a response dependent on an intact microbiota and host stress signals. Together these preclinical findings may provide new insight into mechanisms of stress-associated bowel pathologies in humans.

immunology↗

bioRxiv2020

GABA AND GLUTAMATE CHANGES IN PEDIATRIC MIGRAINE

Despite migraine being one of the top five most prevalent childhood diseases, a lack of knowledge about pediatric migraine limits effective treatment strategies; standard adult pharmaceutical therapies are less effective in children and can carry undesirable side-effects. Non-pharmacological therapies have shown some success in adults; however, to appropriately apply these in children we need to understand pediatric migraines underlying biology. One theory is that migraine results from an imbalance in cortical excitability. Magnetic resonance spectroscopy (MRS) studies show changes in GABA and glutamate levels (the primary inhibitory and excitatory neurotransmitters in the brain, respectively) in multiple brain regions. Although there is indirect evidence of abnormal excitability in pediatric migraine, GABA and glutamate levels have yet to be assessed. The purpose of this study was to measure levels of GABA and glutamate in the thalamus, sensorimotor cortex and visual cortex of children with migraine using MRS. We found that children with migraine and aura had significantly lower glutamate levels in the visual cortex as compared to control children, opposite to results seen in adults. Additionally, we found significant correlations between metabolite levels and migraine characteristics; higher GABA levels were associated with a higher migraine burden. We also found that higher glutamate in the thalamus and higher GABA/Glx ratios in the sensorimotor cortex were associated with duration since diagnosis, i.e., having migraines longer. Lower GABA levels in the sensorimotor cortex were associated with being closer to their next migraine attack. Together this indicates that GABA and glutamate disturbances occur early in migraine pathophysiology and emphasizes that evidence from adults with migraine cannot be immediately translated to paediatric sufferers. This highlights the need for further mechanistic studies of migraine in children, to aid in the development of more effective treatments.

neuroscience↗

bioRxiv2019

Resolving sub-clonal heterogeneity within cell-line growths by single cell sequencing genomic DNA

We performed shallow single-cell sequencing of genomic DNA across 1,475 cells from a well-studied cell-line, COLO829, to resolve overall tumor complexity and clonality. This melanoma tumor-line has been previously characterized by multiple technologies and provides a benchmark for evaluating somatic alterations, though has exhibited conflicting and indeterminate copy number states. We identified at least four major sub-clones by discriminant analysis of principal components (DAPC) of single cell copy number data. Break-point and loss of heterozygosity (LOH) analysis of aggregated data from sub-clones revealed a complex rearrangement of chromosomes 1, 10 and 18 that was maintained in all but two sub-clones. Likewise, two of the sub-clones were distinguished by loss of 1 copy of chromosome 8. Re-analysis of previous spectral karyotyping data and bulk sequencing data recapitulated these sub-clone hallmark features and explains why the original bulk sequencing experiments generated conflicting copy number results. Overall, our results demonstrate how shallow copy number profiling together with clustering analysis of single cell sequencing can uncover significant hidden insights even in well studied cell-lines.

genomics↗

bioRxiv2017

Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle

In North America, antibiotic feed additives such as monensin and tylosin are added to the finishing diets of feedlot cattle to counter the ill-effects of feeding diets with rapidly digestible carbohydrates. While these feed additives have been proven to improve feed efficiency, and reduce liver abscess incidence, how these products impact the gastrointestinal microbiota is not completely understood. Furthermore, there are concerns that antibiotic feed additives may expand the antibiotic resistome of feedlot cattle by enriching antimicrobial resistance genes in pathogenic and nonpathogenic bacteria in the gut microbiota. In this study, we analyzed the impact of providing antibiotic feed additives to feedlot cattle using metagenome sequencing of treated and untreated animals. Our results indicate that use of antibiotic feed additives does not produce discernable changes at the phylum level however treated cattle had reduced the abundance of gram-positive bacteria at the genus level. The abundance of Ruminococcus, Erysipelotrichaceae and Lachanospira in the gut of treated steers was reduced. This may impact the ability of these animals to exclude pathogens from the gut. However, our results did not show any correlation between the presence of antimicrobial resistance genes in the gut microbiota and the administration of antibiotic feed additives.

microbiology↗