Biology subjects

Parry, C.

Publications and source records attributed to Parry, C..

9 recordsLinked to original sources

bioRxiv2026

Beyond Navigation - Tissue-contacting Fluorescent Lifetime Imaging reveals a pathology-linked lung cancer phenotype at the point of biopsy

Background: Accurate sampling of suspected peripheral lung cancers depends on access to the lesion and confirmation that the biopsy tool is in contact with target tissue. Current bronchoscopic navigation and imaging techniques can guide instruments to a target but do not provide real-time biological confirmation at the point of sampling. Fluorescence lifetime imaging microscopy (FLIM) provides molecular contrast by measuring fluorescence decay - how long photons continue to be emitted from fluorescent molecules. In the Precision Lung clinical study (ISRCTN15093468), the Prothea Imaging System (Generation 1) identified a candidate tumour-associated phenotype of spatially overlapped low fluorescence lifetime and low intensity (LLLI) from in-vivo imaging. We used this observation as the basis for a reverse-translational study to determine whether the LLLI phenotype is linked to cancer pathology; reproducible with the Imaging System (Generation 2); and distinguishable from normal lung tissue. Methods: Previously reported Precision Lung findings were used as the clinical starting observation and were not re-analysed. Validation was then performed using: (i) pathology linked benchtop FLIM of early-stage non-small-cell lung tissue microarrays encompassing malignant cell clusters of approximately 300 um2, matched to the EoT imaging scale; (ii) five sequential fresh lung-cancer resections imaged at tumour and comparator regions, including visibly blood-rich contact sites, using the (Generation 2) Imaging System; and (iii) systematic mapping of two ventilated non-cancer donor lungs, one from a smoker and one from a non-smoker, across all available lobes. The LLLI phenotype was defined as spatial co-localisation of low intensity and short lifetime. Results: Using a real time fibre based FLIM system, capable of deployment through a working channel of a bronchoscope, the LLLI tumour phenotype was optically identified in freshly resected tumour tissue. The same phenotype was identified in fixed tissue samples with known pathology, and with images taken in the Precision Lung clinical study. Whole human lung controls did not show evidence of the tumour phenotype. Conclusions: This evidence forms a reverse-translational chain that supports the concept of the Prothea Imaging System - as a platform that confirms that the tool is in contact with a region of cancer in the lesion, while preserving continuous access for biopsy or intervention.

cancer biology↗

bioRxiv2026

Population bottlenecks shape laboratory evolution of piperacillin-tazobactam resistance in Klebsiella grimontii and reveal a shared within-patient evolutionary trajectory

Laboratory-based experimental evolution is widely used to investigate how antimicrobial resistance (AMR) emerges and to identify resistance-associated trade-offs that could inform treatment strategies. However, there is limited understanding of how in vitro AMR evolution reflects the complexity of resistance evolution within the human host, where selective pressures, and therefore evolutionary pathways, are more variable. Here, we investigated the effect of population bottleneck size and growth environment on the evolution of piperacillin-tazobactam (TZP) resistance in Klebsiella grimontii and compared this to resistance evolution observed during a recurrent bloodstream infection. Three clonal K. grimontii isolates cultured from one patient over four months included a TZP-susceptible ancestor and a within-patient evolved TZP-resistant isolate. The susceptible ancestor was evolved under TZP selection using either a small 0.1% bottleneck or a larger 5% bottleneck, and under a second environment, LB supplemented with 5% sheep blood, using a 0.1% bottleneck. Evolved isolates were assessed for TZP susceptibility, {beta}-lactamase activity, fitness, and genomic changes. A single nucleotide polymorphism (SNP) in the promoter region of the chromosomally located {beta}-lactamase gene blaOXY-6-4 was identified in the within-patient evolved isolate and was replicated in all 0.1% bottleneck lineages across both environments. In contrast, the larger 5% bottleneck lineages exhibited greater phenotypic variation and genetic diversity, including multiple blaOXY-6-4 promoter variants and variable TZP MICs. These findings show that laboratory evolution can reproduce key within-patient resistance mechanisms, but that bottleneck size strongly shapes the resistance phenotypes and mutational landscapes observed in vitro. ImportanceAdaptive laboratory evolution is increasingly used to predict how antimicrobial resistance emerges and to identify trade-offs associated with resistance acquisition that could inform future treatment strategies. Here, we directly compared piperacillin-tazobactam resistance evolution in the laboratory with resistance that emerged within a patient during a recurrent bloodstream infection. We show that a small population bottleneck reproducibly selected the same blaOXY-6-4 promoter mutation observed in the patient, whereas a larger bottleneck produced more diverse evolutionary outcomes. These findings build on previous work showing that experimental conditions shape laboratory evolution outcomes and highlight population bottleneck size as an important experimental parameter when designing laboratory evolution studies that intend to model clinically relevant resistance evolution.

evolutionary biology↗

bioRxiv2025

Polli-markers: spectral and chemical biomarkers for detecting cryptic early plant pollination responses

O_LIPollination is essential for plant reproduction, ecosystem resilience and human health. Yet, our capability to map pollination service delivery in real-time across large areas remains poor. Determining where and when flowers are pollinated is vital to mitigate widespread pollination deficits, increase plant health and yield, and support pollinator management. Hence, innovative approaches are urgently needed for establishing scalable predictive bioindicators of plant pollination status with the goal of achieving real-time landscape-scale monitoring. C_LIO_LIHere we present two parallel controlled pollination assays in which we characterise the post-pollination petal physiology of a world leading flowering crop, Brassica napus, using in-situ close-range hyperspectral reflectance and semi-untargeted metabolomics. C_LIO_LIThis multiomics approach coupled with supervised machine learning and biomarker detection reveals cryptic changes in the UV petal reflectance spectrum which are predictive of pollination status, representing a novel set of candidate pollination bioindicators ( polli-markers), and our high-resolution time series enables prediction of when this pollination event occurred. It also reveals an associated set of candidate metabolites, including flavonoids and senescence markers, shedding light on the functional pathways related to our polli-markers. C_LIO_LIThis study provides key insights into floral development, enabling a transformative step towards predicting, mapping and quantifying pollination service delivery at the landscape scale. C_LI

ecology↗

bioRxiv2025

Interplay Between Pulmonary Membrane Properties and Lung Disease: a Study of Seven Bottlenose Dolphins

Pneumonia is the leading cause of morbidity and mortality of bottlenose dolphins Tursiops truncatus. We investigate a series of rare and opportunistic samples of pulmonary surfactant membranes (PSMs) extracted from lungs of seven dolphins in the care of the U.S. Navy Marine Mammal Program. We found a striking correlation between PSM structure, lipidome, and mechanical properties with the severity of lung injury. Specifically, lipidomics reveals exacerbated contents of cardiolipins, confirming a result obtained for terrestrial mammals afflicted by experimental pneumonia. Employing a battery of X-ray scattering, atomic force, and electron microscopy, we evaluate how the altered lipid composition impairs the structural integrity of the PSM and leads to dehydration and enhanced rigidity. Our findings demonstrate that the function of pulmonary surfactant membranes goes far beyond lowering alveolar surface tension, regulating their biochemical and biophysical properties with lung pathology progression. This knowledge will be useful to the development of future diagnostics and therapeutics of respiratory diseases targeting lung membranes.

biophysics↗

bioRxiv2024

IL-1β-driven NF-κB transcription of ACE2 as a Mechanism of Macrophage Infection by SARS-CoV-2

Coronavirus disease 2019 (COVID-19), caused by infection with the enveloped RNA betacoronavirus, SARS-CoV-2, led to a global pandemic involving over 7 million deaths. Macrophage inflammatory responses impact COVID-19 severity; however, it is unclear whether macrophages are infected by SARS-CoV-2. We sought to identify mechanisms regulating macrophage expression of ACE2, the primary receptor for SARS-CoV-2, and to determine if macrophages are susceptible to productive infection. We developed a humanized ACE2 (hACE2) mouse whereby hACE2 cDNA was cloned into the mouse ACE2 locus under control of the native promoter. We validated the susceptibility of hACE2 mice to SARS-CoV-2 infection relative to wild-type mice and an established K18-hACE2 model of acute fulminating disease. Intranasal exposure to SARS-CoV-2 led to pulmonary consolidations with cellular infiltrate, edema, and hemorrhage, consistent with pneumonia, yet unlike the K18-hACE2 model, hACE2 mice survived and maintained stable weight. Infected hACE2 mice also exhibited a unique plasma chemokine, cytokine, and growth factor inflammatory signature relative to K18-hACE2 mice. Infected hACE2 mice demonstrated evidence of viral replication in infiltrating lung macrophages, and infection of macrophages in vitro revealed a transcriptional profile indicative of altered RNA and ribosomal processing machinery as well as activated cellular antiviral defense. Macrophage IL-1{beta}-driven NF-{kappa}B transcription of ACE2 was an important mechanism of dynamic ACE2 upregulation, promoting macrophage susceptibility to infection. Experimental models of COVID-19 that make use of native hACE2 expression will allow for mechanistic insight into factors that can either promote host resilience or increase susceptibility to worsening severity of infection.

immunology↗

bioRxiv2023

Differential expression of RET and GDNF family receptor, GFR-α1, between striatum and substantia nigra following nigrostriatal lesion: a case for diminished GDNF-signaling

Although glial cell line-derived neurotrophic factor (GDNF) showed efficacy in preclinical and early clinical studies to alleviate parkinsonian signs in Parkinsons disease (PD), later trials did not meet primary endpoints, giving pause to consider further investigation. While GDNF dose and delivery methods may have contributed to diminished efficacy, one crucial aspect of these clinical studies is that GDNF treatment across all studies began [~]8 years after PD diagnosis; a time point representing several years after near 100% depletion of nigrostriatal dopamine markers in striatum and at least 50% in substantia nigra (SN), and is later than the timing of GDNF treatment in preclinical studies. With nigrostriatal terminal loss exceeding 70% at PD diagnosis, we utilized hemi-parkinsonian rats to determine if expression of GDNF family receptor, GFR-1, and receptor tyrosine kinase, RET, differed between striatum and SN at 1 and 4 weeks following a 6-hydroxydopamine (6-OHDA) lesion. Whereas GDNF expression changed minimally, GFR-1 expression decreased progressively in striatum and in tyrosine hydroxylase positive (TH+) cells in SN, correlating with reduced TH cell number. However, in nigral astrocytes, GFR-1 expression increased. RET expression decreased maximally in striatum by 1 week, whereas in the SN, a transient bilateral increase occurred that returned to control levels by 4 weeks. Expression of brain-derived neurotrophic factor (BDNF) or its receptor, TrkB, were unchanged throughout lesion progression. Together, these results reveal that differential GFR-1 and RET expression between the striatum and SN, and cell-specific differences in GFR-1 expression in SN, occur during nigrostriatal neuron loss. Targeting loss of GDNF receptors appears critical to enhance GDNF therapeutic efficacy against nigrostriatal neuron loss. Significance StatementAlthough preclinical evidence supports that GDNF provides neuroprotection and improves locomotor function in preclinical studies, clinical data supporting its efficacy to alleviate motor impairment in Parkinsons disease patients remains uncertain. Using the established 6-OHDA hemi-parkinsonian rat model, we determined whether expression of its cognate receptors, GFR-1 and RET, were differentially affected between striatum and substantia nigra in a timeline study. In striatum, there was early and significant loss of RET, but a gradual, progressive loss of GFR-1. In contrast, RET transiently increased in lesioned substantia nigra, but GFR-1 progressively decreased only in nigrostriatal neurons and correlated with TH cell loss. Our results indicate that direct availability of GFR-1 may be a critical element that determines GDNF efficacy following striatal delivery. HighlightsGDNF expression was minimally affected by nigrostriatal lesion GDNF family receptor, GFR-1, progressively decreased in striatum and in TH neurons in SN. GFR-1 expression decreased along with TH neurons as lesion progressed GFR-1 increased bilaterally in GFAP+ cells suggesting an inherent response to offset TH neuron loss RET expression was severely reduced in striatum, whereas it increased in SN early after lesion induction

neuroscience↗

bioRxiv2022

Nigral-specific increase in ser31 tyrosine hydroxylase phosphorylation offsets dopamine loss and forestalls hypokinesia onset during progressive nigrostriatal neuron loss

Mechanisms that augment dopamine (DA) signaling to compensate for tyrosine hydroxylase (TH) loss and delay motor impairment in Parkinsons disease remain unidentified. The rat nigrostriatal pathway was unilaterally-lesioned by 6-OHDA to determine whether differences in DA content, TH protein, TH phosphorylation, or D1 receptor expression in striatum or substantia nigra (SN) aligned with onset of hypokinesia at two time points. At 7 days, DA and TH loss in striatum exceeded 95%, whereas DA was unaffected in SN, despite [~]60% TH loss. At 28 days, hypokinesia was established. At both time points, ser31 TH phosphorylation increased only in SN, corresponding to less DA versus TH loss. ser40 TH phosphorylation was unaffected in striatum or SN. By day 28, D1 receptor expression increased only in lesioned SN. These results indicate that increased ser31 TH phosphorylation and D1 receptor in the SN, not striatum, augment DA signaling against TH loss to mitigate hypokinesia. Highlights-Despite >90% TH and DA loss in striatum, open-field locomotor activity did not decrease -Early after lesion, DA and TH loss in striatum exceeded 90%. In contrast, DA loss did not occur despite 60% TH loss in substantia nigra (SN). -TH loss was progressive in the SN, with loss also spreading contralateral to lesion. -Loss of TH protein in SN preceded cell loss ipsilateral and contralateral to lesion, indicating first stages of nigrostriatal neuron loss begin with loss of TH protein loss. -TH phosphorylation at ser31 in SN was associated with less, if any, DA loss compared to TH protein loss. -TH phosphorylation at ser40 did not change in either region and at any time during TH loss, suggesting no contribution to differences in DA loss against TH loss. -Expression of the D1 receptor increased 2.5-fold in the SN late, but not early, after lesion, suggesting a post-synaptic receptor response to offset DA loss in SN. -No increases in TH phosphorylation or D1 receptor expression in striatum at any time after lesion induction, indicating that compensatory mechanisms occur only in substantia nigra, but not in striatum, to delay onset of hypokinesia.

neuroscience↗

bioRxiv2020

Reproductive Compatibility in Capsicum is not Reflected in Genetic or Phenotypic Similarity Between Species Complexes

Wild relatives of domesticated Capsicum represent substantial genetic diversity and thus sources of traits of potential interest. Furthermore, the hybridization compatibility between members of Capsicum species complexes remains unresolved. Improving our understanding of the relationship between Capsicum species relatedness and their ability to form hybrids is a highly pertinent issue. Through the development of novel interspecific hybrids in this study, we demonstrate interspecies compatibility is not necessarily reflected in relatedness according to established Capsicum genepool complexes. Based on a phylogeny constructed by genotyping using single sequence repeat (SSR) markers and with a portion of the waxy locus, and through principal component analysis (PCA) of phenotypic data, we clarify the relationships among wild and domesticated Capsicum species. Together, the phylogeny and hybridization studies provide evidence for the misidentification of a number of species from the World Vegetable Center genebank included in this study. The World Vegetable Center holds the largest collection of Capsicum genetic material globally, therefore this may reflect a wider issue in the misidentification of Capsicum wild relatives. The findings presented here provide insight into an apparent disconnect between compatibility and relatedness in the Capsicum genus, which will be valuable in identifying candidates for future breeding programs.

plant biology↗

bioRxiv2017

Epidemiology of paediatric gastrointestinal colonisation by extended spectrum cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolates in north-west Cambodia

Extended-spectrum cephalosporin resistance (ESC-R) in Escherichia coli and Klebsiella pneumoniae is a healthcare threat; high gastrointestinal carriage rates are reported from South-east Asia. Colonisation prevalence data in Cambodia are lacking. We determined gastrointestinal colonisation prevalence of ESC-resistant E. coli (ESC-R-EC) and K. pneumoniae (ESC-R-KP) in Cambodian children/adolescents and associated risk factors; characterised relevant resistance genes, their genetic contexts, and the genetic relatedness of ESC-R strains using whole genome sequencing (WGS). Faeces and questionnaire data were obtained from individuals <16 years in northwestern Cambodia, 2012. WGS of cultured ESC-R-EC/KP was performed (Illumina). Maximum likelihood phylogenies were used to characterise relatedness of isolates; ESC-R-associated resistance genes and their genetic contexts were identified from de novo assemblies using BLASTn and automated/manual annotation. 82/148 (55%) of children/adolescents were ESC-R-EC/KP colonised; 12/148 (8%) were co-colonised with both species. Independent risk factors for colonisation were hospitalisation (OR: 3.12, 95%, CI [1.52-6.38]) and intestinal parasites (OR: 3.11 [1.29-7.51]); school attendance conferred decreased risk (OR: 0.44 [0.21-0.92]. ESC-R strains were diverse; the commonest ESC-R mechanisms were blaCTX-M 1 and 9 sub-family variants. Structures flanking these genes were highly variable, and for blaCTX-M-15, -55 and -27, frequently involved IS26. Chromosomal blaCTX-M integration was common in E. coli. Gastrointestinal ESC-R-EC/KP colonisation is widespread in Cambodian children/adolescents; hospital admission and intestinal parasites are independent risk factors. The genetic contexts of blaCTX-M are highly mosaic, consistent with rapid horizontal exchange. Chromosomal integration of blaCTX-M may result in stable propagation in these community-associated pathogens.

microbiology↗