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  • ItemPublished versionOpen Access
    In vivo imaging of hepatic neutrophil migration in severe alcoholic hepatitis with 111In-radiolabelled leucocytes.
    (Portland Press Ltd., 2018-08-31) Potts, Jonathan R; Farahi, Neda; Howard, Mark R; Taylor, Mark R; Heard, Sarah; Shankar, Arun N; Alexander, Graeme J; Chilvers, Edwin R; Verma, Sumita; Peters, A Michael; Chilvers, Edwin [0000-0002-4230-9677]
    The study's aim was to image severe alcoholic hepatitis (SAH) using 111In-labelled leucocytes with two objectives in mind: firstly for non-invasive diagnosis and secondly to provide a platform for experimental therapies aiming to inhibit intrahepatic neutrophil migration. 111In-leucocyte scintigraphy was performed 30 min and 24 h post-injection in 19 patients with SAH, 14 abstinent patients with alcohol-related cirrhosis and 11 normal controls. Eleven with SAH and seven with cirrhosis also had 99mTc-nanocolloid scintigraphy. Change in hepatic 111In radioactivity was expressed as decay-corrected 24 h:30 min count ratio and, in SAH, compared with histological grading of steatohepatitis and expression of granulocyte marker, CD15. Hepatic microautoradiography on biopsy specimens obtained 24 h post-injection of 111In-leucocytes was performed in one patient. Median 24 h:30 min hepatic 111In activity ratio was higher in SAH (2.5 (interquartile range (IQR): 1.7-4.0) compared with cirrhotics and normal controls (1.0 (0.8-1.1) and 0.8 (0.7-0.9) respectively, P<0.0001). In SAH, it correlated with CD15 expression (r = 0.62, P=0.023) and was higher in marked compared with mild/moderate steatohepatitis (4.0 (3.0-4.6) compared with 1.8 (1.5-2.6), P=0.006). Hepatic-to-splenic 99mTc count rate ratio was reduced in SAH (0.5 (0.4-1.4)) compared with cirrhotics (2.3( 0.6-3.0)) and three historic normal controls (4.2 (3.8-5.0); P=0.003), consistent with impaired hepatic reticuloendothelial function. Scintigraphic findings in SAH included prominent lung radioactivity at 30 min, likely the result of neutrophil primimg. Microautoradiography demonstrated cell-associated 111In in areas of parenchymal neutrophil infiltration. In conclusion, 111In-leucocyte scintigraphy can non-invasively diagnose SAH and could provide a platform for evaluation of novel treatments aiming to inhibit intrahepatic neutrophil migration.
  • ItemPublished versionOpen Access
    Gut microbiota trajectory in early life may predict development of celiac disease.
    (Springer Science and Business Media LLC, 2018-02-20) Olivares, Marta; Walker, Alan W; Capilla, Amalia; Benítez-Páez, Alfonso; Palau, Francesc; Parkhill, Julian; Castillejo, Gemma; Sanz, Yolanda; Olivares, Marta [0000-0002-7966-2781]
    BACKGROUND: To investigate whether alterations in the developing intestinal microbiota and immune markers precede celiac disease (CD) onset in infants at familial risk of developing the disease. METHODS: A nested case-control study was carried out as part of a larger prospective cohort study, which included healthy full-term newborns (> 200) with at least one first relative with biopsy-verified CD. The present study includes cases of CD (n = 10) and the best-matched controls (n = 10) who did not develop the disease after 5-year follow-up. Fecal microbiota, assessed by high-throughput 16S rRNA gene amplicon sequencing, and immune parameters were profiled at 4 and 6 months of age and related to CD onset. RESULTS: The microbiota of infants who remained healthy showed an increase in bacterial diversity over time, characterized by increases in Firmicutes families, but not those who developed CD. Infants who subsequently developed CD showed a significant reduction in sIgA levels over time, while those who remained healthy showed increases in TNF-α correlated to Bifidobacterium spp. An increased relative abundance of Bifidobacterium longum was associated with control children while increased proportions of Bifidobacterium breve and Enterococcus spp. were associated with CD development. CONCLUSION: The findings suggest that alterations in the early trajectory of gut microbiota in infants at CD risk could influence the immune maturation process and predispose to CD, although larger population studies are warranted to confirm this hypothesis.
  • ItemAccepted versionOpen Access
    Massively parallel C. elegans tracking provides multi-dimensional fingerprints for phenotypic discovery.
    (Elsevier BV, 2018-08-01) Perni, Michele; Challa, Pavan K; Kirkegaard, Julius B; Limbocker, Ryan; Koopman, Mandy; Hardenberg, Maarten C; Sormanni, Pietro; Müller, Thomas; Saar, Kadi L; Roode, Lianne WY; Habchi, Johnny; Vecchi, Giulia; Fernando, Nilumi; Casford, Samuel; Nollen, Ellen AA; Vendruscolo, Michele; Dobson, Christopher M; Knowles, Tuomas PJ; Perni, Michele [0000-0001-7593-8376]; Challa, Pavan [0000-0002-0863-381X]; Limbocker, Ryan [0000-0002-6030-6656]; Sormanni, Pietro [0000-0002-6228-2221]; Saar, Kadi [0000-0002-5926-3628]; Vendruscolo, Michele [0000-0002-3616-1610]; Knowles, Tuomas [0000-0002-7879-0140]
    BACKGROUND: The nematode worm C. elegans is a model organism widely used for studies of genetics and of human disease. The health and fitness of the worms can be quantified in different ways, such as by measuring their bending frequency, speed or lifespan. Manual assays, however, are time consuming and limited in their scope providing a strong motivation for automation. NEW METHOD: We describe the development and application of an advanced machine vision system for characterising the behaviour of C. elegans, the Wide Field-of-View Nematode Tracking Platform (WF-NTP), which enables massively parallel data acquisition and automated multi-parameter behavioural profiling of thousands of worms simultaneously. RESULTS: We screened more than a million worms from several established models of neurodegenerative disorders and characterised the effects of potential therapeutic molecules for Alzheimer's and Parkinson's diseases. By using very large numbers of animals we show that the sensitivity and reproducibility of behavioural assays is very greatly increased. The results reveal the ability of this platform to detect even subtle phenotypes. COMPARISON WITH EXISTING METHODS: The WF-NTP method has substantially greater capacity compared to current automated platforms that typically either focus on characterising single worms at high resolution or tracking the properties of populations of less than 50 animals. CONCLUSIONS: The WF-NTP extends significantly the power of existing automated platforms by combining enhanced optical imaging techniques with an advanced software platform. We anticipate that this approach will further extend the scope and utility of C. elegans as a model organism.
  • ItemPublished versionOpen Access
    Phenotypic screening reveals TNFR2 as a promising target for cancer immunotherapy.
    (Impact Journals, 2016-10-18) Williams, Geoffrey S; Mistry, Bina; Guillard, Sandrine; Ulrichsen, Jane Coates; Sandercock, Alan M; Wang, Jun; González-Muñoz, Andrea; Parmentier, Julie; Black, Chelsea; Soden, Jo; Freeth, Jim; Jovanović, Jelena; Leyland, Rebecca; Al-Lamki, Rafia S; Leishman, Andrew J; Rust, Steven J; Stewart, Ross; Jermutus, Lutz; Bradley, John R; Bedian, Vahe; Valge-Archer, Viia; Minter, Ralph; Wilkinson, Robert W; Wang, Jun [0000-0003-3667-3760]; Bradley, John [0000-0002-7774-8805]
    Antibodies that target cell-surface molecules on T cells can enhance anti-tumor immune responses, resulting in sustained immune-mediated control of cancer. We set out to find new cancer immunotherapy targets by phenotypic screening on human regulatory T (Treg) cells and report the discovery of novel activators of tumor necrosis factor receptor 2 (TNFR2) and a potential role for this target in immunotherapy. A diverse phage display library was screened to find antibody mimetics with preferential binding to Treg cells, the most Treg-selective of which were all, without exception, found to bind specifically to TNFR2. A subset of these TNFR2 binders were found to agonise the receptor, inducing iκ-B degradation and NF-κB pathway signalling in vitro. TNFR2 was found to be expressed by tumor-infiltrating Treg cells, and to a lesser extent Teff cells, from three lung cancer patients, and a similar pattern was also observed in mice implanted with CT26 syngeneic tumors. In such animals, TNFR2-specific agonists inhibited tumor growth, enhanced tumor infiltration by CD8+ T cells and increased CD8+ T cell IFN-γ synthesis. Together, these data indicate a novel mechanism for TNF-α-independent TNFR2 agonism in cancer immunotherapy, and demonstrate the utility of target-agnostic screening in highlighting important targets during drug discovery.
  • ItemOpen Access
    Interaction between a MAPT variant causing frontotemporal dementia and mutant APP affects axonal transport.
    (Elsevier BV, 2018-08) Adalbert, Robert; Milde, Stefan; Durrant, Claire; Ando, Kunie; Stygelbout, Virginie; Yilmaz, Zehra; Gould, Stacey; Brion, Jean-Pierre; Coleman, Michael P; Gould, Stacey [0000-0003-4374-0300]; Coleman, Michael [0000-0002-9354-532X]
    In Alzheimer's disease, many indicators point to a central role for poor axonal transport, but the potential for stimulating axonal transport to alleviate the disease remains largely untested. Previously, we reported enhanced anterograde axonal transport of mitochondria in 8- to 11-month-old MAPTP301L knockin mice, a genetic model of frontotemporal dementia with parkinsonism-17T. In this study, we further characterized the axonal transport of mitochondria in younger MAPTP301L mice crossed with the familial Alzheimer's disease model, TgCRND8, aiming to test whether boosting axonal transport in young TgCRND8 mice can alleviate axonal swelling. We successfully replicated the enhancement of anterograde axonal transport in young MAPTP301L/P301L knockin animals. Surprisingly, we found that in the presence of the amyloid precursor protein mutations, MAPTP301L/P3101L impaired anterograde axonal transport. The numbers of plaque-associated axonal swellings or amyloid plaques in TgCRND8 brains were unaltered. These findings suggest that amyloid-β promotes an action of mutant tau that impairs axonal transport. As amyloid-β levels increase with age even without amyloid precursor protein mutation, we suggest that this rise could contribute to age-related decline in frontotemporal dementia.
  • ItemAccepted versionOpen Access
    Optimizing medical management in peripheral artery disease.
    (Oxford University Press (OUP), 2018-08) Coughlin, PA; Rudd, JHF; Coughlin, PA [0000-0003-1342-1114]
    Changing times
  • ItemPublished versionOpen Access
    Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in a long-term care facility in the United Kingdom.
    (2017-07-25) Brodrick, Hayley J; Raven, Kathy E; Kallonen, Teemu; Jamrozy, Dorota; Blane, Beth; Brown, Nicholas M; Martin, Veronique; Török, M Estée; Parkhill, Julian; Peacock, Sharon; Kallonen, Teemu [0000-0003-1741-6486]; Török, M Estée [0000-0001-9098-8590]; Parkhill, Julian [0000-0002-7069-5958]; Peacock, Sharon [0000-0002-1718-2782]
  • ItemPublished versionOpen Access
    Convergent evolution and topologically disruptive polymorphisms among multidrug-resistant tuberculosis in Peru.
    (Public Library of Science (PLoS), 2017) Grandjean, Louis; Gilman, Robert H; Iwamoto, Tomatada; Köser, Claudio U; Coronel, Jorge; Zimic, Mirko; Török, M Estee; Ayabina, Diepreye; Kendall, Michelle; Fraser, Christophe; Harris, Simon; Parkhill, Julian; Peacock, Sharon J; Moore, David AJ; Colijn, Caroline; Grandjean, Louis [0000-0002-1457-8327]; Iwamoto, Tomatada [0000-0002-2650-0308]; Köser, Claudio U [0000-0002-0232-846X]; Török, M Estee [0000-0001-9098-8590]; Harris, Simon [0000-0003-1512-6194]; Parkhill, Julian [0000-0002-7069-5958]; Peacock, Sharon J [0000-0002-1718-2782]; Colijn, Caroline [0000-0001-6097-6708]
    BACKGROUND: Multidrug-resistant tuberculosis poses a major threat to the success of tuberculosis control programs worldwide. Understanding how drug-resistant tuberculosis evolves can inform the development of new therapeutic and preventive strategies. METHODS: Here, we use novel genome-wide analysis techniques to identify polymorphisms that are associated with drug resistance, adaptive evolution and the structure of the phylogenetic tree. A total of 471 samples from different patients collected between 2009 and 2013 in the Lima suburbs of Callao and Lima South were sequenced on the Illumina MiSeq platform with 150bp paired-end reads. After alignment to the reference H37Rv genome, variants were called using standardized methodology. Genome-wide analysis was undertaken using custom written scripts implemented in R software. RESULTS: High quality homoplastic single nucleotide polymorphisms were observed in genes known to confer drug resistance as well as genes in the Mycobacterium tuberculosis ESX secreted protein pathway, pks12, and close to toxin/anti-toxin pairs. Correlation of homoplastic variant sites identified that many were significantly correlated, suggestive of epistasis. Variation in genes coding for ESX secreted proteins also significantly disrupted phylogenetic structure. Mutations in ESX genes in key antigenic epitope positions were also found to disrupt tree topology. CONCLUSION: Variation in these genes have a biologically plausible effect on immunogenicity and virulence. This makes functional characterization warranted to determine the effects of these polymorphisms on bacterial fitness and transmission.
  • ItemPublished versionOpen Access
    The Microevolution and Epidemiology of Staphylococcus aureus Colonization during Atopic Eczema Disease Flare.
    (Elsevier, 2018-02) Harkins, Catriona P; Pettigrew, Kerry A; Oravcová, Katarina; Gardner, June; Hearn, RM Ross; Rice, Debbie; Mather, Alison E; Parkhill, Julian; Brown, Sara J; Proby, Charlotte M; Holden, Matthew TG; Parkhill, Julian [0000-0002-7069-5958]
    Staphylococcus aureus is an opportunistic pathogen and variable component of the human microbiota. A characteristic of atopic eczema (AE) is colonization by S. aureus, with exacerbations associated with an increased bacterial burden of the organism. Despite this, the origins and genetic diversity of S. aureus colonizing individual patients during AE disease flares is poorly understood. To examine the microevolution of S. aureus colonization, we deep sequenced S. aureus populations from nine children with moderate to severe AE and 18 non-atopic children asymptomatically carrying S. aureus nasally. Colonization by clonal S. aureus populations was observed in both AE patients and control participants, with all but one of the individuals carrying colonies belonging to a single sequence type. Phylogenetic analysis showed that disease flares were associated with the clonal expansion of the S. aureus population, occurring over a period of weeks to months. There was a significant difference in the genetic backgrounds of S. aureus colonizing AE cases versus controls (Fisher exact test, P = 0.03). Examination of intra-host genetic heterogeneity of the colonizing S. aureus populations identified evidence of within-host selection in the AE patients, with AE variants being potentially selectively advantageous for intracellular persistence and treatment resistance.
  • ItemPublished versionOpen Access
    Erythrocytes lacking the Langereis blood group protein ABCB6 are resistant to the malaria parasite Plasmodium falciparum.
    (Springer Science and Business Media LLC, 2018) Egan, Elizabeth S; Weekes, Michael P; Kanjee, Usheer; Manzo, Jale; Srinivasan, Ashwin; Lomas-Francis, Christine; Westhoff, Connie; Takahashi, Junko; Tanaka, Mitsunobu; Watanabe, Seishi; Brugnara, Carlo; Gygi, Steven P; Tani, Yoshihiko; Duraisingh, Manoj T; Weekes, Michael P [0000-0003-3196-5545]; Brugnara, Carlo [0000-0001-8192-8713]
    The ATP-binding cassette transporter ABCB6 was recently discovered to encode the Langereis (Lan) blood group antigen. Lan null individuals are asymptomatic, and the function of ABCB6 in mature erythrocytes is not understood. Here, we assessed ABCB6 as a host factor for Plasmodium falciparum malaria parasites during erythrocyte invasion. We show that Lan null erythrocytes are highly resistant to invasion by P. falciparum, in a strain-transcendent manner. Although both Lan null and Jr(a-) erythrocytes harbor excess porphyrin, only Lan null erythrocytes exhibit a P. falciparum invasion defect. Further, the zoonotic parasite P. knowlesi invades Lan null and control cells with similar efficiency, suggesting that ABCB6 may mediate P. falciparum invasion through species-specific molecular interactions. Using tandem mass tag-based proteomics, we find that the only consistent difference in membrane proteins between Lan null and control cells is absence of ABCB6. Our results demonstrate that a newly identified naturally occurring blood group variant is associated with resistance to Plasmodium falciparum.
  • ItemAccepted versionOpen Access
    Patients with perianal Crohn's fistulas experience delays in accessing anti-TNF therapy due to slow recognition, diagnosis and integration of specialist services: lessons learned from three referral centres.
    (Wiley, 2018-09) Lee, MJ; Freer, C; Adegbola, S; Elkady, S; Parkes, M; Hart, A; Fearnhead, NS; Lobo, AJ; Brown, SR; Lee, MJ [0000-0001-9971-1635]
    AIM: Crohn's anal fistula should be managed by a multidisciplinary team. There is no clearly defined 'patient pathway' from presentation to treatment. The aim of this study was to describe the patient route from presentation with symptomatic Crohn's anal fistula to starting anti-tumour necrosis factor (anti-TNF) therapy. METHOD: Case note review was undertaken at three hospitals with established inflammatory bowel disease services. Patients with Crohn's anal fistula presenting between 2010 and 2015 were identified through clinical coding and local databases. Baseline demographics were captured. Patient records were interrogated to identify route of access, and clinical contacts during the patient pathway. RESULTS: Seventy-nine patients were included in the study, of whom 54 (68%) had an established diagnosis of Crohn's disease (CD). Median time from presentation to anti-TNF therapy was 204 days (174 vs 365 days for existing and new diagnosis of CD, respectively; P = 0.019). The mean number of surgical outpatient attendances, operations and MRI scans per patient was 1.03, 1.71 and 1.03, respectively. Patients attended a mean of 1.49 medical clinics. Seton insertion was the most common procedure, accounting for 48.6% of all operations. Where care episodes ('clinical events per 30 days') were infrequent this correlated with prolongation of the pathway (r = -0.87; P < 0.01). CONCLUSION: This study highlights two key challenges in the treatment pathway: (i) delays in diagnosis of underlying CD in patients with anal fistula and (ii) the pathway to anti-TNF therapy is long, suggesting issues with service design and delivery. These should be addressed to improve patient experience and outcome.
  • ItemAccepted versionOpen Access
    Asthma: From Diagnosis to Endotype to Treatment.
    (2018-04) Lodge, Katharine M; Knolle, Martin D; Jha, Akhilesh; Jha, Akhilesh [0000-0002-8413-7738]
  • ItemPublished versionOpen Access
    Detection of human disease conditions by single-cell morpho-rheological phenotyping of blood.
    (eLife Sciences Publications, Ltd, 2018-01-13) Toepfner, Nicole; Herold, Christoph; Otto, Oliver; Rosendahl, Philipp; Jacobi, Angela; Kräter, Martin; Stächele, Julia; Menschner, Leonhard; Herbig, Maik; Ciuffreda, Laura; Ranford-Cartwright, Lisa; Grzybek, Michal; Coskun, Ünal; Reithuber, Elisabeth; Garriss, Geneviève; Mellroth, Peter; Henriques-Normark, Birgitta; Tregay, Nicola; Suttorp, Meinolf; Bornhäuser, Martin; Chilvers, Edwin R; Berner, Reinhard; Guck, Jochen; Rosendahl, Philipp [0000-0002-9545-5045]; Kräter, Martin [0000-0001-7122-7331]; Coskun, Ünal [0000-0003-4375-3144]; Garriss, Geneviève [0000-0002-5361-0975]; Chilvers, Edwin R [0000-0002-4230-9677]; Guck, Jochen [0000-0002-1453-6119]
    Blood is arguably the most important bodily fluid and its analysis provides crucial health status information. A first routine measure to narrow down diagnosis in clinical practice is the differential blood count, determining the frequency of all major blood cells. What is lacking to advance initial blood diagnostics is an unbiased and quick functional assessment of blood that can narrow down the diagnosis and generate specific hypotheses. To address this need, we introduce the continuous, cell-by-cell morpho-rheological (MORE) analysis of diluted whole blood, without labeling, enrichment or separation, at rates of 1000 cells/sec. In a drop of blood we can identify all major blood cells and characterize their pathological changes in several disease conditions in vitro and in patient samples. This approach takes previous results of mechanical studies on specifically isolated blood cells to the level of application directly in blood and adds a functional dimension to conventional blood analysis.
  • ItemAccepted versionOpen Access
    Exploring the Human Side of Meteorology: A Brief Report on the Psychology of Meteorologists
    (National Weather Association, 2018) Bolton, Matthew J; Ault, Lara K; Greenberg, David M; Baron-Cohen, Simon; Baron-Cohen, Simon [0000-0001-9217-2544]
    Links between autism spectrum conditions and scientific aptitude were first investigated twenty years ago. Since then, associations between autism and STEM (science, technology, engineering, and math) aptitude have been established and discussed via the empathizing-systemizing (E-S) theory. E-S theory hypothesizes that autistic individuals are naturally driven to create and analyze sets of logical rules, or “systems,” related to and constructed around things in the world. This is at the expense of cognitive, but not affective, empathy. Here, we not only extend previous work in testing the similarity of meteorologists, engineers, and physicists with respect to empathizing, systemizing, and autistic traits; we also report the first examination of meteorologists’ personality and mental health relative to other representative physical scientists. Meteorologists in this sample were higher in empathizing and systemizing, extraversion, conscientiousness, and agreeableness, and less stressed, depressed, and anxious, than were engineers and physicists. Implications for the meteorological workplace are discussed.
  • ItemAccepted versionOpen Access
    Clinical imaging in dementia with Lewy bodies.
    (BMJ, 2018-05) Surendranathan, Ajenthan; O'Brien, John Tiernan; Surendranathan, Ajenthan [0000-0003-3809-1545]
    Dementia with Lewy bodies (DLB) is a common neurodegenerative dementia in older people; however, the clinical features, particularly cognitive fluctuations and rapid eye movement sleep disorder, are often hard to elicit, leading to difficulty in making the diagnosis clinically. Here we examine the literature for the evidence behind imaging modalities that could assist in making the diagnosis. Dopamine transporter (DAT) imaging remains the best modality for differentiation from dementia of Alzheimer's type with high sensitivity and specificity reported based on pathological diagnoses. 123Iodine-metaiodobenzylguanidine myocardial scintigraphy (MIBG) however is rapidly becoming an alternative imaging modality for the diagnosis of DLB, though studies assessing its accuracy with postmortem verification are still awaited. However, there are suggestions that MIBG may be better in the differentiation of vascular parkinsonism from DLB than DAT scans but may have lower sensitivity for detecting DLB compared with the 80% sensitivity seen in DAT imaging. Structural MRI scans have long been used for the diagnosis of dementia; however, their utility in DLB is limited to revealing the presence of coexisting Alzheimer's disease. Fluorodeoxyglucose (FDG) PET is an alternative biomarker that can also differentiate Alzheimer's disease and DLB but lacks the evidence base of both DAT and MIBG scans.
  • ItemPublished versionOpen Access
    Metabolomic Profiling in Acute ST-Segment-Elevation Myocardial Infarction Identifies Succinate as an Early Marker of Human Ischemia-Reperfusion Injury.
    (Ovid Technologies (Wolters Kluwer Health), 2018-04-06) Kohlhauer, Matthias; Dawkins, Sam; Costa, Ana SH; Lee, Regent; Young, Timothy; Pell, Victoria R; Choudhury, Robin P; Banning, Adrian P; Kharbanda, Rajesh K; Oxford Acute Myocardial Infarction (OxAMI) Study; Saeb-Parsy, Kourosh; Murphy, Michael P; Frezza, Christian; Krieg, Thomas; Channon, Keith M; Saeb-Parsy, Kourosh [0000-0002-0633-3696]; Murphy, Mike [0000-0003-1115-9618]; Frezza, Christian [0000-0002-3293-7397]; Krieg, Thomas [0000-0002-5192-580X]
    BACKGROUND: Ischemia-reperfusion injury following ST-segment-elevation myocardial infarction (STEMI) is a leading determinant of clinical outcome. In experimental models of myocardial ischemia, succinate accumulation leading to mitochondrial dysfunction is a major cause of ischemia-reperfusion injury; however, the potential importance and specificity of myocardial succinate accumulation in human STEMI is unknown. We sought to identify the metabolites released from the heart in patients undergoing primary percutaneous coronary intervention for emergency treatment of STEMI. METHODS AND RESULTS: Blood samples were obtained from the coronary artery, coronary sinus, and peripheral vein in patients undergoing primary percutaneous coronary intervention for acute STEMI and in control patients undergoing nonemergency coronary angiography or percutaneous coronary intervention for stable angina or non-STEMI. Plasma metabolites were analyzed by targeted liquid chromatography and mass spectrometry. Metabolite levels for coronary artery, coronary sinus, and peripheral vein were compared to derive cardiac and systemic release ratios. In STEMI patients, cardiac magnetic resonance imaging was performed 2 days and 6 months after primary percutaneous coronary intervention to quantify acute myocardial edema and final infarct size, respectively. In total, 115 patients undergoing acute STEMI and 26 control patients were included. Succinate was the only metabolite significantly increased in coronary sinus blood compared with venous blood in STEMI patients, indicating cardiac release of succinate. STEMI patients had higher succinate concentrations in arterial, coronary sinus, and peripheral venous blood than patients with non-STEMI or stable angina. Furthermore, cardiac succinate release in STEMI correlated with the extent of acute myocardial injury, quantified by cardiac magnetic resonance imaging. CONCLUSION: Succinate release by the myocardium correlates with the extent of ischemia.
  • ItemPublished versionOpen Access
    Monitoring Ca2+ elevations in individual astrocytes upon local release of amyloid beta in acute brain slices.
    (Elsevier BV, 2018-01) Tyurikova, Olga; Zheng, Kaiyu; Rings, Annika; Drews, Anna; Klenerman, David; Rusakov, Dmitri A; Klenerman, David [0000-0001-7116-6954]
    The pathogenesis of Alzheimer's disease (AD) is thought to involve acute neurotoxic effects exerted by oligomeric forms of amyloid-β 1-42 (Aβ). Application of Aβ oligomers in physiological concentrations have been shown to transiently elevate internal Ca2+ in cultured astroglia. While the cellular machinery involved has been extensively explored, to what degree this important signalling cascade occurs in organised brain tissue has remained unclear. Here we adapted two-photon excitation microscopy and calibrated time-resolved imaging (FLIM), coupled with patch-clamp electrophysiology, to monitor Ca2+ concentration ([Ca2+]) inside individual astrocytes and principal neurons in acute brain slices. Inside the slice tissue local micro-ejection of Aβ in sub-micromolar concentrations triggered prominent [Ca2+] elevations in an adjacent astrocyte translated as an approximately two-fold increase (averaged over ∼5min) in basal [Ca2+]. This elevation did not spread to neighbouring cells and appeared comparable in amplitude with commonly documented spontaneous [Ca2+] rises in astroglia. Principal nerve cells (pyramidal neurons) also showed Ca2+ sensitivity, albeit to a lesser degree. These observations shed light on the extent and dynamics of the acute physiological effects of Aβ on brain cells in situ, in the context of AD.
  • ItemPublished versionOpen Access
    ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads.
    (Microbiology Society, 2017-10) Hunt, Martin; Mather, Alison E; Sánchez-Busó, Leonor; Page, Andrew J; Parkhill, Julian; Keane, Jacqueline A; Harris, Simon R; Parkhill, Julian [0000-0002-7069-5958]
    Antimicrobial resistance (AMR) is one of the major threats to human and animal health worldwide, yet few high-throughput tools exist to analyse and predict the resistance of a bacterial isolate from sequencing data. Here we present a new tool, ARIBA, that identifies AMR-associated genes and single nucleotide polymorphisms directly from short reads, and generates detailed and customizable output. The accuracy and advantages of ARIBA over other tools are demonstrated on three datasets from Gram-positive and Gram-negative bacteria, with ARIBA outperforming existing methods.
  • ItemPublished versionOpen Access
    Emergence and genomic diversification of a virulent serogroup W:ST-2881(CC175) Neisseria meningitidis clone in the African meningitis belt.
    (Microbiology Society, 2017-08) Lamelas, Araceli; Hauser, Julia; Dangy, Jean-Pierre; Hamid, Abdul-Wahab M; Röltgen, Katharina; Abdul Sater, Mohamad R; Hodgson, Abraham; Sie, Ali; Junghanss, Thomas; Harris, Simon R; Parkhill, Julian; Bentley, Stephen D; Pluschke, Gerd; Parkhill, Julian [0000-0002-7069-5958]
    Countries of the African 'meningitis belt' are susceptible to meningococcal meningitis outbreaks. While in the past major epidemics have been primarily caused by serogroup A meningococci, W strains are currently responsible for most of the cases. After an epidemic in Mecca in 2000, W:ST-11 strains have caused many outbreaks worldwide. An unrelated W:ST-2881 clone was described for the first time in 2002, with the first meningitis cases caused by these bacteria reported in 2003. Here we describe results of a comparative whole-genome analysis of 74 W:ST-2881 strains isolated within the framework of two longitudinal colonization and disease studies conducted in Ghana and Burkina Faso. Genomic data indicate that the W:ST-2881 clone has emerged from Y:ST-175(CC175) bacteria by capsule switching. The circulating W:ST-2881 populations were composed of a variety of closely related but distinct genomic variants with no systematic differences between colonization and disease isolates. Two distinct and geographically clustered phylogenetic clonal variants were identified in Burkina Faso and a third in Ghana. On the basis of the presence or absence of 17 recombination fragments, the Ghanaian variant could be differentiated into five clusters. All 25 Ghanaian disease isolates clustered together with 23 out of 40 Ghanaian isolates associated with carriage within one cluster, indicating that W:ST-2881 clusters differ in virulence. More than half of the genes affected by horizontal gene transfer encoded proteins of the 'cell envelope' and the 'transport/binding protein' categories, which indicates that exchange of non-capsular antigens plays an important role in immune evasion.
  • ItemPublished versionOpen Access
    Bifunctional fluorescent probes for detection of amyloid aggregates and reactive oxygen species.
    (Royal Society Publishing, 2018-02) Needham, Lisa-Maria; Weber, Judith; Fyfe, James WB; Kabia, Omaru M; Do, Dung T; Klimont, Ewa; Zhang, Yu; Rodrigues, Margarida; Dobson, Christopher M; Ghandi, Sonia; Bohndiek, Sarah E; Snaddon, Thomas N; Lee, Steven F; Needham, Lisa-Maria [0000-0002-8139-5862]; Bohndiek, Sarah [0000-0003-0371-8635]; Lee, Steven [0000-0003-4492-5139]
    Protein aggregation into amyloid deposits and oxidative stress are key features of many neurodegenerative disorders including Parkinson's and Alzheimer's disease. We report here the creation of four highly sensitive bifunctional fluorescent probes, capable of H2O2 and/or amyloid aggregate detection. These bifunctional sensors use a benzothiazole core for amyloid localization and boronic ester oxidation to specifically detect H2O2. We characterized the optical properties of these probes using both bulk fluorescence measurements and single-aggregate fluorescence imaging, and quantify changes in their fluorescence properties upon addition of amyloid aggregates of α-synuclein and pathophysiological H2O2 concentrations. Our results indicate these new probes will be useful to detect and monitor neurodegenerative disease.