Biology subjects

Summers, S.

Publications and source records attributed to Summers, S..

11 recordsLinked to original sources

bioRxiv2025

Targeted genomic surveillance of insecticide resistance in African malaria vectors

The emergence of insecticide resistance is threatening the efforts of malaria control programmes, which rely heavily on a limited arsenal of insecticidal tools, such as insecticide-treated bed nets. Importantly, genomic surveillance of malaria vectors can provide critical, policy-relevant insights into the presence and evolution of insecticide resistance, allowing us to maintain and extend the shelf life of these interventions. Yet the complex genetic architecture of resistance, combined with resource constraints in malaria-endemic settings, have thus far precluded the widespread use of genomics in routine surveillance. Meanwhile, stakeholders in sub-Saharan Africa are moving towards locally driven, decentralised generation of genomic data, underscoring the need for standardised and robust genomics workflows. To address this need, we demonstrate an approach to targeted genomic surveillance in Anopheles gambiae s.l with Illumina sequencing. We target 90 genomic loci in the Anopheles gambiae s.l genome, including 55 resistance-associated mutations and 35 ancestry informative markers. This protocol is coupled with advanced, automated software for accurate and reproducible variant analysis. We are able to elucidate population structure and ancestry in our cohorts and accurately identify most species in the An. gambiae species complex. We report frequencies of variants at insecticide-resistance loci and explore the continued evolution of the pyrethroid target site, the Voltage-gated sodium channel. Applying the platform to a recently established colony of field-caught resistant mosquitoes (Siaya, Kenya), we identified seven independent resistance-associated variants contributing to reduced efficacy of insecticide-treated nets in East Africa. Additionally, we leverage a machine learning algorithm (XGBoost) to demonstrate the possibility of predicting bioassay mortality using genotypes alone. This achieved high accuracy (75%), demonstrating the potential of targeted genomics to predictively monitor insecticide resistance. Together these tools provide a practical, scalable solution for resistance monitoring while advancing the goal of building local genomic surveillance capacity in sub-Saharan Africa.

genomics↗

bioRxiv2024

Rapid Nanopore cloud-based monitoring and analysis of commercial aquaculture microbiomes

Aquaculture stands as a crucial component of global food security and sustainable development, yet it faces challenges in disease management and ecological balance. Here, we present a novel approach using rapid nanopore sequencing, cloud-based monitoring and analysis for aquaculture microbiomes. Our study aimed to perform untargeted, agnostic biological monitoring of a commercial aquaculture facility, emphasizing rapidity, specificity, and sensitivity. We employed Oxford Nanopore Technologies MinION sequencer with an optimised rapid sequencing protocol, enabling on-site operation by facility staff. Three separate sampling efforts resulting in thirteen sequencing runs were conducted, revealing a representative microbiome baseline across aquaculture system components within a 24-hour timeframe. Our results demonstrated the feasibility of rapid monitoring and analysis of nitrogen-associated organisms, essential for same-day water quality management and infection event detection. Notably, Moving Bed Biofilm Reactor (MBBR media) or BioDiscs exhibited the highest diversity and abundance of nitrogen-associated organisms, confirming a pivotal role in nitrification processes. Critically, our approach addressed challenges in metagenomic sample purity and false positives, offering insights for future refinement and application. Our findings underscore the potential of rapid sequencing technologies in enhancing aquaculture management and sustainability. This approach holds promise for mitigating disease outbreaks, optimizing productivity, and advancing ecological balance in aquaculture systems.

microbiology↗

bioRxiv2024

HAF Prevents Hepatocyte Apoptosis and Hepatocellular Carcinoma through Transcriptional Regulation of the NF-κB pathway.

BackgroundHepatocellular carcinoma (HCC) incidence is increasing worldwide due to the obesity epidemic, which drives metabolic dysfunction-associated steatohepatitis (MASH) that can lead to HCC. However, the molecular pathways that lead to MASH-HCC are poorly understood. We have previously reported that male mice with global haploinsufficiency of hypoxia-associated factor, HAF (SART1+/-) spontaneously develop MASH/HCC. However, the cell type(s) responsible for HCC associated with HAF loss are unclear. ResultsSART1-floxed mice were crossed with mice expressing Cre-recombinase within hepatocytes (Alb-Cre; hepS-/-) or macrophages (LysM-Cre, macS-/-). Only hepS-/- mice (both male and female) developed HCC suggesting that HAF protects against HCC primarily within hepatocytes. HAF-deficient macrophages showed decreased P-p65 and P-p50 and in many major components of the NF-{kappa}B pathway, which was recapitulated using HAF siRNA in vitro. HAF depletion increased apoptosis both in vitro and in vivo, suggesting that HAF mediates a tumor suppressor role by suppressing hepatocyte apoptosis. We show that HAF regulates NF-{kappa}B activity by controlling transcription of TRADD and RIPK1. Mice fed a high-fat diet (HFD) showed marked suppression of HAF, P-p65 and TRADD within their livers after 26 weeks, but manifest profound upregulation of HAF, P-65 and TRADD within their livers after 40 weeks of HFD, implicating deregulation of the HAF-NF-{kappa}B axis in the progression to MASH. In humans, HAF was significantly decreased in livers with simple steatosis but significantly increased in HCC compared to normal liver. ConclusionsHAF is novel transcriptional regulator of the NF-{kappa}B pathway that protects against hepatocyte apoptosis and is a key determinant of cell fate during progression to MASH and MASH-HCC.

cancer biology↗

bioRxiv2023

Phospholipid isotope tracing reveals β-catenin-driven suppression of phosphatidylcholine metabolism in hepatocellular carcinoma

Background and AimsActivating mutations in the CTNNB1 gene encoding {beta}-catenin are among the most frequently observed oncogenic alterations in hepatocellular carcinoma (HCC). HCC with CTNNB1 mutations show profound alterations in lipid metabolism including increases in fatty acid oxidation and transformation of the phospholipidome, but it is unclear how these changes arise and whether they contribute to the oncogenic program in HCC. MethodsWe employed untargeted lipidomics and targeted isotope tracing to quantify phospholipid production fluxes in an inducible human liver cell line expressing mutant {beta}-catenin, as well as in transgenic zebrafish with activated {beta}-catenin-driven HCC. ResultsIn both models, activated {beta}-catenin expression was associated with large changes in the lipidome including conserved increases in acylcarnitines and ceramides and decreases in triglycerides. Lipid flux analysis in human cells revealed a large reduction in phosphatidylcholine (PC) production rates as assayed by choline tracer incorporation. We developed isotope tracing lipid flux analysis for zebrafish and observed similar reductions in phosphatidylcholine synthesis flux accomplished by sex-specific mechanisms. ConclusionsThe integration of isotope tracing with lipid abundances highlights specific lipid class transformations downstream of {beta}-catenin signaling in HCC and suggests future HCC-specific lipid metabolic targets. SynopsisIn this work, we show by lipid specific isotope tracing that mutations in the oncogene CTNNB1 leads to conserved changes in lipid metabolism in hepatocellular carcinoma. These include the stimulation of fatty acid oxidation and a suppression of phosphorylcholine synthesis.

cancer biology↗

bioRxiv2023

Identification of genetic drivers of plasma lipoproteins in the Diversity Outbred mouse population

Despite great progress in understanding lipoprotein physiology, there is still much to be learned about the genetic drivers of lipoprotein abundance, composition, and function. We used ion mobility spectrometry to survey 16 plasma lipoprotein subfractions in 500 Diversity Outbred (DO) mice maintained on a Western-style diet. We identified 21 quantitative trait loci (QTL) affecting lipoprotein abundance. To refine the QTL and link them to disease risk in humans, we asked if the human homologues of genes located at each QTL were associated with lipid traits in human genome-wide association studies (GWAS). Integration of mouse QTL with human GWAS yielded candidate gene drivers for 18 of the 21 QTL. This approach enabled us to nominate the gene encoding the neutral ceramidase, Asah2, as a novel candidate driver at a QTL on chromosome 19 for large HDL particles (HDL-2b). To experimentally validate Asah2, we surveyed lipoproteins in Asah2-/-mice. Compared to wild-type mice, female Asah2-/- mice showed an increase in several lipoproteins, including HDL. Our results provide insights into the genetic regulation of circulating lipoproteins, as well as mechanisms by which lipoprotein subfractions may affect cardiovascular disease risk in humans.

genetics↗

bioRxiv2022

Polypyrimidine Tract-Binding Protein 1 (PTBP1) regulates CD4 T cell Activation independent of its role in proliferation

Our previous work found that the RNA binding protein polypyrimidine tract-binding protein (PTBP1) is critical for regulating multiple events in T cell activation including changes in proliferation, and expression of activation markers and cytokines. These changes corresponded to the regulation of the ERK1/2 and NF-{kappa}B pathways as well as through changes in steady-state RNA levels. Because proliferation is critical for driving T cell activation, it was unclear whether PTBP1 was required for optimal activation per se or whether changes were secondary to a requirement for initiating/sustaining proliferation. To address this question, the human T cell lymphoma cell line, Jurkat, which recapitulates many of the molecular events of TCR-induced activation, was used to understand how PTBP1 impacts early events in T cell activation with ongoing proliferation. Using two phenotypically distinct Jurkat subclones (D1.1 and B2.7), we first profiled global RNA expression patterns using RNAseq analysis and found marked differences between the two cell lines with the D1.1 line giving a more antigen-experienced phenotype. Reducing PTBP1 by shPTB expression, to 60% WT levels resulted in no significant decrease in proliferation in the two subclones. However, we observed that PTBP1 was required for both optimal expression of activation markers, CD25, CD38, CD69, and CD40L, and signaling through the ERK1/2, P38 and AKT pathways. Importantly, limiting PTBP1 had different effects on the activation signals for each cell line suggesting that the differentiation state of the cell is a critical factor in understanding the role of PTBP1 in T cell activation. This was further reinforced by our finding that PTBP1 regulated distinct groups of genes specific for each line. Together, our findings suggest that PTBP1 regulates specific T cell activation responses independent of its role in proliferation and that the initial phenotype of the T cell plays an essential role in the dependency of the cell on PTBP1 for driving these changes.

immunology↗

bioRxiv2021

Convalescence from prototype SARS-CoV-2 protects Syrian hamsters from disease caused by the Omicron variant

The mutation profile of the SARS-CoV-2 Omicron variant poses a concern for naturally acquired and vaccine-induced immunity. We investigated the ability of prior infection with an early SARS-CoV-2, 99.99% identical to Wuhan-Hu-1, to protect against disease caused by the Omicron variant. We established that infection with Omicron in naive Syrian hamsters resulted in a less severe disease than a comparable dose of prototype SARS-CoV-2 (Australia/VIC01/2020), with fewer clinical signs and less weight loss. We present data to show that these clinical observations were almost absent in convalescent hamsters challenged with the same dose of Omicron 50 days after an initial infection with Australia/VIC01/2020. The data provide evidence for immunity raised against prototype SARS-CoV-2 being protective against Omicron in the Syrian hamster model. Further investigation is required to conclusively determine whether Omicron is less pathogenic in Syrian hamsters and whether this is predictive of pathogenicity in humans.

microbiology↗

bioRxiv2020

The effect of heat on SARS-CoV-2 viability and RNA integrity as determined by plaque assay, virus culture and real-time RT-PCR

The effect of heat on SARS-CoV-2/England/2/2020 viability was assessed by plaque assay and virus culture. Heating to 56{degrees}C and 60{degrees}C for 15, 30 and 60 minutes led to a reduction in titre of between 2.1 and 4.9 log10 pfu/ml but complete inactivation was not observed. At 80{degrees}C plaques were observed after 15 and 30 minutes of heating, however after 60 minutes viable virus was only detected following virus culture. Heating to 80{degrees}C for 90 minutes and 95{degrees}C for 1 and 5 minutes resulted in no viable virus being detected. At 56{degrees}C and 60{degrees}C significant variability between replicates was observed and the titre often increased with heat-treatment time. Nucleic acids were extracted and tested by RT-PCR. Sensitivity of the RT-PCR was not compromised by heating to 56{degrees}C and 60{degrees}C. Heating to 80{degrees}C for 30 minutes or more and 95{degrees}C for 1 or 5 minutes however, resulted in an increase of at least three Ct values. This increase remained constant when different dilutions of virus underwent heat treatment. This indicates that high temperature heat inactivation of clinical samples prior to nucleic acid extraction could significantly affect the ability to detect virus in clinical samples from patients with lower viral loads by RT-PCR.

microbiology↗

bioRxiv2020

Acquired fluoroquinolone resistance genes in corneal isolates of Pseudomonas aeruginosa

Fluroquinolones are widely used as an empirical therapy for pseudomonal ocular infections. Based on increasing reports on acquired fluroquinolone resistance genes in clinical isolates of Pseudomonas aeruginosa, we investigated 33 strains of P. aeruginosa isolated from the cornea of microbial keratitis patients in India and Australia between 1992 and 2018 to understand the prevalence of acquired fluroquinolone resistance genes in ocular isolates and to assess whether the possession of those genes was associated with fluoroquinolone susceptibility. We obtained the whole genome sequence of 33 isolates using Illumina MiSeq platform and investigated the prevalence of two fluoroquinolone resistance genes crpP and qnrVC1. To examine the associated mobile genetic elements of qnrVC1 positive strains, we obtained long read sequences using Oxford Nanopore MinION and performed hybrid assembly to combine long reads with Illumina short sequence reads. We further assessed mutations in QRDRs and antibiotic susceptibilities to ciprofloxacin, levofloxacin and moxifloxacin to examine the association between resistance genes and phenotype. Twenty strains possessed crpP in genetic islands characterised by possession of integrative conjugative elements. The qnrVC1 gene was carried by four isolates on class I integrons and Tn3 transposons along with aminoglycoside and beta-lactam resistance genes. We did not observe any evidence of plasmids carrying fluroquinolone resistance genes. Resistance to fluroquinolones was observed in those strains which possessed crpP, qnrVC1 and that had QRDRs mutations. The presence of crpP was not a sole cause of fluroquinolone resistance.

microbiology↗

bioRxiv2019

Mitochondrial pyruvate carrier is required for optimal brown fat thermogenesis

Brown adipose tissue (BAT) is composed of thermogenic cells that convert chemical energy into heat to help maintain a constant body temperature and counteract metabolic disease in mammals. The metabolic adaptations required for thermogenesis are not fully understood. Here we explore how steady state levels of metabolic intermediates are altered in brown adipose tissue in response to cold exposure. Transcriptome and metabolome analysis revealed changes in pathways involved in amino acid, glucose, and TCA cycle metabolism. Using isotopic labeling experiments, we found that activated brown adipocytes increased labeling of pyruvate and TCA cycle intermediates from U13C-glucose. Although glucose oxidation has been implicated as being essential for thermogenesis, its requirement for efficient thermogenesis has not been directly tested. Here we show that mitochondrial pyruvate uptake is essential for optimal thermogenesis, as conditional deletion of Mpc1 in brown adipocytes leads to impaired cold adaptation. Isotopic labeling experiments using U13C-glucose showed that loss of MPC1 led to impaired labeling of TCA cycle intermediates, while labeling of glycolytic intermediates was unchanged. Loss of MPC1 in BAT increased 3-hydroxybutyrate levels in blood and BAT in response to the cold, suggesting that ketogenesis provides an alternative fuel source that partially compensates for impaired mitochondrial oxidation of cytosolic pyruvate. Collectively, these studies highlight that complete glucose oxidation is essential for optimal brown fat thermogenesis.

biochemistry↗

bioRxiv2019

Respiratory Intervention Techniques Increase Selection Rate for Special Forces

O_LISpecial Forces Selection Rates have declined over recent years, partly due to reduced fitness rates of applications\nC_LIO_LIPostural changes incurred prior to the recruitment may contribute to compromised respiratory function, resulting in fatigue, overexertion, and Selection Course failure\nC_LIO_LIPerformance breathing training and respiratory muscle strengthening can reverse impaired respiratory function and optimize cardiopulmonary fitness.\nC_LIO_LIIn this study, a 6-week intervention program including performance breathing training improved fitness and performance of SF Selection Course participants.\nC_LIO_LIThe intervention program including performance breathing training increased the SF Selection Course pass rate from 0% to 30%, compared to prior years.\nC_LI

physiology↗