6 results on '"Zakharkina, Tetyana"'
Search Results
2. TD/GC–MS analysis of volatile markers emitted from mono- and co-cultures of Enterobacter cloacae and Pseudomonas aeruginosa in artificial sputum
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Lawal, Oluwasola, Knobel, Hugo, Weda, Hans, Nijsen, Tamara M.E., Goodacre, Royston, Fowler, Stephen J., Ahmed, Waqar M., Artigas, Antonio, Bannard-Smith, J., Bos, Lieuwe D.J., Camprubi, Marta, Coelho, Luis, Dark, Paul, Davie, Alan, Diaz, Emili, Goma, Gemma, Felton, Timothy, Leopold, Jan Hendrik, van Oort, Pouline M.P., Povoa, Pedro, Portsmouth, Craig, Rattray, Nicholas J.W., Rijnders, Guus, Schultz, Marcus J., Steenwelle, Ruud, Sterk, Peter J., Valles, Jordi, Verhoeckx, Fred, Vink, Anton, White, Iain R., Winters, Tineke, Zakharkina, Tetyana, Inorganic Materials Science, Intensive Care Medicine, ACS - Heart failure & arrhythmias, AII - Infectious diseases, APH - Methodology, Amsterdam Gastroenterology Endocrinology Metabolism, Graduate School, Pulmonology, ACS - Diabetes & metabolism, ACS - Pulmonary hypertension & thrombosis, and ACS - Microcirculation
- Subjects
0301 basic medicine ,Microbiological culture ,Endocrinology, Diabetes and Metabolism ,030106 microbiology ,Clinical Biochemistry ,UT-Hybrid-D ,medicine.disease_cause ,Biochemistry ,Gas Chromatography-Mass Spectrometry ,RS ,Microbiology ,03 medical and health sciences ,Manchester Institute of Biotechnology ,Enterobacter cloacae ,medicine ,Volatile organic compounds ,Axenic ,biology ,Bacteria ,Pseudomonas aeruginosa ,Chemistry ,biology.organism_classification ,Antimicrobial ,ResearchInstitutes_Networks_Beacons/manchester_institute_of_biotechnology ,3. Good health ,030104 developmental biology ,Sputum ,Gas chromatography–mass spectrometry ,medicine.symptom ,Infection - Abstract
Introduction: Infections such as ventilator-associated pneumonia (VAP) can be caused by one or more pathogens. Current methods for identifying these pathogenic microbes often require invasive sampling, and can be time consuming, due to the requirement for prolonged cultural enrichment along with selective and differential plating steps. This results in delays in diagnosis which in such critically ill patients can have potentially life-threatening consequences. Therefore, a non-invasive and timely diagnostic method is required. Detection of microbial volatile organic compounds (VOCs) in exhaled breath is proposed as an alternative method for identifying these pathogens and may distinguish between mono- and poly-microbial infections. Objectives: To investigate volatile metabolites that discriminate between bacterial mono- and co-cultures. Methods: VAP-associated pathogens Enterobacter cloacae and Pseudomonas aeruginosa were cultured individually and together in artificial sputum medium for 24 h and their headspace was analysed for potential discriminatory VOCs by thermal desorption gas chromatography–mass spectrometry. Results: Of the 70 VOCs putatively identified, 23 were found to significantly increase during bacterial culture (i.e. likely to be released during metabolism) and 13 decreased (i.e. likely consumed during metabolism). The other VOCs showed no transformation (similar concentrations observed as in the medium). Bacteria-specific VOCs including 2-methyl-1-propanol, 2-phenylethanol, and 3-methyl-1-butanol were observed in the headspace of axenic cultures of E. cloacae, and methyl 2-ethylhexanoate in the headspace of P. aeruginosa cultures which is novel to this investigation. Previously reported VOCs 1-undecene and pyrrole were also detected. The metabolites 2-methylbutyl acetate and methyl 2-methylbutyrate, which are reported to exhibit antimicrobial activity, were elevated in co-culture only. Conclusion: The observed VOCs were able to differentiate axenic and co-cultures. Validation of these markers in exhaled breath specimens could prove useful for timely pathogen identification and infection type diagnosis.
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- 2018
3. Next-Generation Sequencing of the BRCA1 and BRCA2 Genes for the Genetic Diagnostics of Hereditary Breast and/or Ovarian Cancer
- Author
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Trujillano, Daniel, primary, Weiss, Maximilian E.R., additional, Schneider, Juliane, additional, Köster, Julia, additional, Papachristos, Efstathios B., additional, Saviouk, Viatcheslav, additional, Zakharkina, Tetyana, additional, Nahavandi, Nahid, additional, Kovacevic, Lejla, additional, and Rolfs, Arndt, additional
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- 2015
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4. BreathDx - molecular analysis of exhaled breath as a diagnostic test for ventilator-associated pneumonia: protocol for a European multicentre observational study.
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van Oort, Pouline M. P., Nijsen, Tamara, Weda, Hans, Knobel, Hugo, Dark, Paul, Felton, Timothy, Rattray, Nicholas J. W., Lawal, Oluwasola, Ahmed, Waqar, Portsmouth, Craig, Sterk, Peter J., Schultz, Marcus J., Zakharkina, Tetyana, Artigas, Antonio, Povoa, Pedro, Martin-Loeches, Ignacio, Fowler, Stephen J., Bos, Lieuwe D. J., and BreathDx Consortium
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VENTILATOR-associated pneumonia ,PNEUMONIA diagnosis ,VOLATILE organic compounds ,MICROBIAL metabolism ,MICROBIAL physiology ,THERMAL desorption ,ORGANIC compound analysis ,ACADEMIC medical centers ,BIOCHEMISTRY ,BODY fluids ,BREATH tests ,COMPARATIVE studies ,EXPERIMENTAL design ,GAS chromatography ,INTENSIVE care units ,LONGITUDINAL method ,MASS spectrometry ,RESEARCH methodology ,MEDICAL cooperation ,RESEARCH ,LOGISTIC regression analysis ,EVALUATION research ,DIAGNOSIS - Abstract
Background: The diagnosis of ventilator-associated pneumonia (VAP) remains time-consuming and costly, the clinical tools lack specificity and a bedside test to exclude infection in suspected patients is unavailable. Breath contains hundreds to thousands of volatile organic compounds (VOCs) that result from host and microbial metabolism as well as the environment. The present study aims to use breath VOC analysis to develop a model that can discriminate between patients who have positive cultures and who have negative cultures with a high sensitivity.Methods/design: The Molecular Analysis of Exhaled Breath as Diagnostic Test for Ventilator-Associated Pneumonia (BreathDx) study is a multicentre observational study. Breath and bronchial lavage samples will be collected from 100 and 53 intubated and ventilated patients suspected of VAP. Breath will be analysed using Thermal Desorption - Gas Chromatography - Mass Spectrometry (TD-GC-MS). The primary endpoint is the accuracy of cross-validated prediction for positive respiratory cultures in patients that are suspected of VAP, with a sensitivity of at least 99% (high negative predictive value).Discussion: To our knowledge, BreathDx is the first study powered to investigate whether molecular analysis of breath can be used to classify suspected VAP patients with and without positive microbiological cultures with 99% sensitivity.Trial Registration: UKCRN ID number 19086, registered May 2015; as well as registration at www.trialregister.nl under the acronym 'BreathDx' with trial ID number NTR 6114 (retrospectively registered on 28 October 2016). [ABSTRACT FROM AUTHOR]- Published
- 2017
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5. Next-Generation Sequencing of the BRCA1and BRCA2Genes for the Genetic Diagnostics of Hereditary Breast and/or Ovarian Cancer
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Trujillano, Daniel, Weiss, Maximilian E.R., Schneider, Juliane, Köster, Julia, Papachristos, Efstathios B., Saviouk, Viatcheslav, Zakharkina, Tetyana, Nahavandi, Nahid, Kovacevic, Lejla, and Rolfs, Arndt
- Abstract
Genetic testing for hereditary breast and/or ovarian cancer mostly relies on laborious molecular tools that use Sanger sequencing to scan for mutations in the BRCA1and BRCA2genes. We explored a more efficient genetic screening strategy based on next-generation sequencing of the BRCA1and BRCA2genes in 210 hereditary breast and/or ovarian cancer patients. We first validated this approach in a cohort of 115 samples with previously known BRCA1and BRCA2mutations and polymorphisms. Genomic DNA was amplified using the Ion AmpliSeq BRCA1and BRCA2panel. The DNA Libraries were pooled, barcoded, and sequenced using an Ion Torrent Personal Genome Machine sequencer. The combination of different robust bioinformatics tools allowed detection of all previously known pathogenic mutations and polymorphisms in the 115 samples, without detecting spurious pathogenic calls. We then used the same assay in a discovery cohort of 95 uncharacterized hereditary breast and/or ovarian cancer patients for BRCA1and BRCA2. In addition, we describe the allelic frequencies across 210 hereditary breast and/or ovarian cancer patients of 74 unique definitely and likely pathogenic and uncertain BRCA1and BRCA2variants, some of which have not been previously annotated in the public databases. Targeted next-generation sequencing is ready to substitute classic molecular methods to perform genetic testing on the BRCA1and BRCA2genes and provides a greater opportunity for more comprehensive testing of at-risk patients.
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- 2015
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6. Levels of cytokines in broncho-alveolar lavage fluid, but not in plasma, are associated with levels of markers of lipid peroxidation in breath of ventilated ICU patients.
- Author
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Boshuizen M, Leopold JH, Zakharkina T, Knobel HH, Weda H, Nijsen TM, Vink TJ, Sterk PJ, Schultz MJ, and Bos LD
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- Adult, Aged, Biomarkers analysis, Breath Tests methods, Critical Care, Cytokines blood, Exhalation, Female, Humans, Intensive Care Units, Lung physiopathology, Male, Middle Aged, Reactive Oxygen Species, Respiration, Artificial, Bronchoalveolar Lavage Fluid chemistry, Cytokines analysis, Lipid Peroxidation physiology
- Abstract
Alkanes and alkenes in the breath are produced through fatty acid peroxidation, which is initialized by reactive oxygen species. Inflammation is an important cause and effect of reactive oxygen species. We aimed to evaluate the association between fatty acid peroxidation products and inflammation of the alveolar and systemic compartment in ventilated intensive care unit (ICU) patients.Volatile organic compounds were measured by gas chromatography and mass spectrometry in the breath of newly ventilated ICU patients within 24 h after ICU admission. Cytokines were measured in non-directed bronchial lavage fluid (NBL) and plasma by cytometric bead array. Correlation coefficients were calculated and presented in heatmaps.93 patients were included. Peroxidation products in exhaled breath were not associated with markers of inflammation in plasma, but were correlated with those in NBL. IL-6, IL-8, IL-1β and TNF-α concentration in NBL showed inverse correlation coefficients with the peroxidation products of fatty acids. Furthermore, NBL IL-10, IL-13, GM-CSF and IFNγ demonstrated positive associations with breath alkanes and alkenes. Correlation coefficients for NBL cytokines were high regarding peroxidation products of n-6, n-7 and particularly in n-9 fatty acids.Levels of lipid peroxidation products in the breath of ventilated ICU patients are associated with levels of inflammatory markers in NBL, but not in plasma. Alkanes and alkenes in breath seems to be associated with an anti-inflammatory, rather than a pro-inflammatory state in the alveoli.
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- 2015
- Full Text
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