Biology subjects

Waters, E.

Publications and source records attributed to Waters, E..

6 recordsLinked to original sources

bioRxiv2026

Carbon-negative biosynthesis of pyrone and pyridine dicarboxylic acids from terephthalic acid via continuous mixotrophic gas fermentation in Cupriavidus necator H16

Industrial defossilisation requires carbon-negative routes for sustainable chemical production. Bioprocesses based on renewable feedstocks are often constrained by biogenic CO2 emissions, reducing yields and undermining environmental performance. Here, we report a mixotrophic gas fermentation strategy using the chemolithoautotroph Cupriavidus necator H16 that simultaneously assimilates CO2 for cell growth and biocatalyst generation while converting the PET monomer terephthalic acid (TPA) into value-added biopolymer precursors. This process achieved complete conversion of TPA to 2-pyrone-4,6-dicarboxylic acid (PDC) with titres of 24.5 g/L and a productivity of 0.47 g/L{middle dot}h. Conversion to pyridine dicarboxylic acids (2,4- and 2,5-PDCA) was less efficient ([~]22% and [~]4% respectively) due to metabolic limitations such as intermediate toxicity, pH and ammonia-dependent spontaneous cyclisation. Our results establish the first carbon-negative route coupling simultaneous CO2 assimilation with plastic monomer valorisation, providing a blueprint for sustainable biomanufacturing aligned with global climate and circular economy goals.

bioengineering↗

bioRxiv2024

Perfusion-Independent Tissue Hypoxia in Cardiac Hypertrophy in Mice Measured by 64Cu-CTS PET Imaging

BackgroundHypoxia is central to many cardiac pathologies, but clinically its presence can only be inferred by indirect biomarkers including hypoperfusion and energetic compromise. Imaging hypoxia directly could offer new opportunities for the diagnosis and sub-stratification of cardiovascular diseases. ObjectivesTo determine whether [64Cu]CuCTS Positron Emission Tomography (PET) can identify hypoxia in a murine model of cardiac hypertrophy. MethodsMale C57BL/6 mice underwent abdominal aortic constriction (AAC) to induce cardiac hypertrophy, quantified by echocardiography over 4 weeks. Hypoxia and perfusion were quantified in vivo using [64Cu]CuCTS and [64Cu]CuGTSM PET, respectively, and radiotracer biodistribution was quantified post-mortem. Cardiac radiotracer retention was correlated with contractile function (measured by echocardiography), cardiac hypertrophy (measured by histology), HIF-1 stabilization and NMR-based metabolomics. The effect of anesthesia on [64Cu]CuCTS uptake was additionally investigated in a parallel cohort of mice injected with radiotracer while conscious. ResultsHearts showed increased LV wall thickness, reduced ejection fraction and fractional shortening following AAC. [64Cu]CuCTS retention was 317% higher in hypertrophic myocardium (p<0.001), despite there being no difference in perfusion measured by 64CuGTSM. Radiotracer retention correlated on an animal-by-animal basis with severity of hypertrophy, contractile dysfunction, HIF1 stabilization and metabolic signatures of hypoxia. [64Cu]CuCTS uptake in hypertrophic hearts was significantly higher when administered to conscious animals. Conclusions[64Cu]CuCTS PET can quantify cardiac hypoxia in hypertrophic myocardium, independent of perfusion, suggesting the hypoxia is caused by increased oxygen diffusion distances at the subcellular level. Alleviation of cardiac workload by anesthesia in preclinical models partially alleviates this effect.

bioengineering↗

bioRxiv2023

Uropathogenic Escherichia coli population structure and antimicrobial susceptibility in Norfolk, UK

SynopsisO_ST_ABSBackgroundC_ST_ABSHalf of all women have experienced a urinary tract infection (UTI) in their lifetime and this remains a persistent issue in rural counties like Norfolk, UK. In alignment globally, Uropathogenic E. coli (UPEC) are the main etiological agent for UTIs in Norfolk and are increasingly difficult to treat due to multi-drug resistance (MDR). ObjectiveWe set out to identify which clonal groups and resistance genes are disseminating in the community and hospitals in Norfolk, the first study of its kind for UPEC in this region. MethodsWe collected 217 clinical E. coli isolates causing UTIs in the community and hospital from the Clinical Microbiology laboratory at Norfolk and Norwich University Hospital. These were whole genome sequenced using the Illumina and MinION platforms for in silico multi-locus sequence typing and antibiotic resistance determinant detection. ResultsThe isolates were composed of 74 sequence types (STs); 8 lineages represented 57% of this population: ST73, ST12, ST69, ST131, ST404, ST95, ST127, and ST1193. Importantly, primary UTI screening deemed 8% of isolates to be MDR, with high rates of resistance to ampicillin (52.1%) and trimethoprim (36.2%) in hospitals. Of concern is the probable clonal expansion of MDR groups ST131 and ST1193 in hospitals and community settings with chromosomally encoded blaCTX-M-15, blaOXA-1, and aac(6)-Ib-cr5. ConclusionsThe burden of reported UTIs in Norfolk is largely caused by non-MDR isolates. The UPEC population is continually evolving, and monitoring samples with consideration of sources will help reduce burden of disease.

microbiology↗

bioRxiv2022

CTLA-4 regulates PD-L1-PD-1 interactions via transendocytosis of CD80

CTLA-4 and PD-1 are key immune checkpoints that are targeted in the treatment of cancer. Recently it has emerged that there is a physical interaction between the ligands of these pathways (CD80 and PD-L1), which can prevent PD-L1 inhibitory functions. Since CTLA-4 captures and degrades its ligands via transendocytosis, we investigated how transendocytosis of CD80 is impacted by PD-L1 interaction. We find that transendocytosis of CD80 results in a time-dependent recovery of PD-L1 availability that correlates with CD80 removal. Moreover, CD80 transendocytosis is highly specific in that only CD80 is removed, and its heterodimeric PD-L1 partner remains on the APC. We found no evidence that CTLA-4 interactions with CD80 were inhibited by PD-L1, however efficient removal of CD80 required an intact CTLA-4 cytoplasmic domain, distinguishing this process from more general trogocytosis. We also show that simple binding of CTLA-4 to the CD80-PD-L1 heterodimer is insufficient to liberate PD-L1-PD-1 interactions, suggesting that transendocytosis of CD80 is required to effectively control PD-L1-PD-1 interactions.

immunology↗

bioRxiv2021

Long term nasopharyngeal colonization by Staphylococcus aureus determinants of adaptation

Staphylococcus aureus nasal colonization is a risk factor for infection. A large proportion of the population are identified as potential S. aureus carriers yet we only partially understand the repertoire of genetic factors that promote long-term nasal colonization. Here we present a novel murine model of nasopharyngeal colonization that requires a low S. aureus inoculum and is amenable to experimental evolution approaches. We used this model to experimentally evolve S. aureus using successive passages in the nasopharynx to identify those genetic loci under selection. After 3 cycles of colonization, mutations were identified in mannitol, sorbitol, arginine, nitrite and lactate metabolism genes promoting key pathways in nasal colonization. Stress responses were identified as being under selective pressure, with mutations in DNA repair genes including dnaJ and recF and key stress response genes clpL, rpoB and ahpF. Peptidoglycan synthesis pathway genes also revealed mutations indicating potential selection for alteration of the cell surface. The infection model used here is versatile to assist decolonization and persistence studies.

microbiology↗

bioRxiv2019

An alanine permease mutation or exposure to D-cycloserine re-sensitizes MRSA to beta-lactam antibiotics

Prolonging the clinical effectiveness of {beta}-lactams, which remain first-line antibiotics for many infections, is an important part of efforts to address antimicrobial resistance. We report here that inactivation of the predicted D-cycloserine (DCS) transporter gene cycA re-sensitized MRSA to {beta}-lactam antibiotics. The cycA mutation also resulted in hyper-susceptibility to DCS, an alanine analogue antibiotic that inhibits alanine racemase and D-alanine ligase required for D-alanine incorporation into cell wall peptidoglycan (PG). Alanine transport was impaired in the cycA mutant and this correlated with increased susceptibility to oxacillin and DCS. The cycA mutation or exposure to DCS were both associated with the accumulation of muropeptides with tripeptide stems lacking the terminal D-ala-D-ala and reduced PG crosslinking, prompting us to investigate synergism between {beta}-lactams and DCS. DCS re-sensitised MRSA to {beta}-lactams in vitro and significantly enhanced MRSA eradication by oxacillin in a mouse bacteraemia model. These findings reveal alanine transport as a new therapeutic target to enhance the susceptibility of MRSA to {beta}-lactam antibiotics.

microbiology↗