768 research outputs found
MCC-IMS data analysis using automated spectra processing and explorative visualisation methods
No full textBunkowski A. MCC-IMS data analysis using automated spectra processing and explorative visualisation methods. Bielefeld: Bielefeld University; 2012.Ion Mobility Spectrometry (IMS) is a method to characterise chemical substances on the basis of velocity of gas-phase ions in an electrical field. The data resulting from an IMS measurement is a number of spectra sorted by retention time. Each spectrum contains a series of values and each value represents the amount of ionised molecules at one specific drift time. Recent advantages in the field of Ion Mobility Spectrometry lead to an highly increased amount of data per measurement as well as measurements per experiment. Due to the usage of a Multi-capillary Chromatographic Column (MCC) as pre-separation technique the task of analysing and interpreting the resulting data completely changed and now includes a pseudo coloured image in addition to the classic spectra data. Analysing and comparing a high number of these images and their corresponding spectra is almost impossible and extremely time consuming with the methods used so far.
Different methods for spectra processing, data analysis, visualisation and project management were developed and combined in one software called ’IMS Peaklist & Heatmap Explorer’ (IPHEx) to challenge this task. IPHEx is the first software system supporting the analysis, management, and visualisation of large amounts of MCC-IMS measurements in parallel. It is currently used for the investigation of metabolomics experiments with a focus on the analysis of exhaled air, headspace samples of cell and bacteria cultures, as well as general screening of ambient air. While the main methods of IPHEx are designed to process three dimensional data obtained from different MCC-IMS devices,it also handles GC-MS based data for comparison and substance identification as well as several other information obtained from flat and Excel files. It became the standard analysis platform at the Leibniz-Institut für Analytische Wissenschaften ISAS e.V. for MCC-IMS data and showed its potential during the examination of experiments performed in cooperation with the Lungenklinik Hemer - Zentrum für Pneumologie und Thoraxchirurgie, the University Göttingen - Department of Anesthesiology, Emergency and Intensive Care Medicine, the Charité – Universitätsmedizin Berlin and several others. It is also used for experimental purposes at the Korea Institute of Science and Technology, Saarbrücken and the B&S Analytik GmbH, Dortmund.
The application to many different experiments and tasks demonstrates that the requirements have successfully been addressed and the software and therefore the underlying methods and concepts are suited to analyse large amounts of IMS data in an efficient way. With IPHEx, a complete analysis environment exists, which offers a solution for all analysis, management, and visualisation tasks which are necessary to perform a comprehensive investigation of large amounts of MCC-IMS data
Software tool for coupling chromatographic total ion current dependencies of GC/MSD and MCC/IMS
No full textBunkowski A. Software tool for coupling chromatographic total ion current dependencies of GC/MSD and MCC/IMS. Int. J. Ion Mobil. Spectrom. 2010;13(3-4):169-175
MCC/IMS signals in human breath related to sarcoidosis-results of a feasibility study using an automated peak finding procedure
No full textBunkowski A, Bödeker B, Bader S, Westhoff M, Litterst P, Baumbach JI. MCC/IMS signals in human breath related to sarcoidosis-results of a feasibility study using an automated peak finding procedure. Journal of Breath Research. 2009;3(4):046001
One-year time series of investigations of analytes within human breath using ion mobility spectrometry
No full textBunkowski A, Maddula S, Davies AN, et al. One-year time series of investigations of analytes within human breath using ion mobility spectrometry. Int. J. Ion Mobility Spectrometry. 2010;13(3-4):141-148
Web2.0 paves new ways for collaborative and exploratory analysis of Chemical Compounds in Spectrometry Data
No full textLoyek C, Bunkowski A, Vautz W, Nattkemper TW. Web2.0 paves new ways for collaborative and exploratory analysis of Chemical Compounds in Spectrometry Data. Journal of Integrative Bioinformatics. 2011;8(2):158.In nowadays life science projects, sharing data and data interpretation is becoming increasingly important. This considerably calls for novel information technology approaches, which enable the integration of expert knowledge from different disciplines in combination with advanced data analysis facilities in a collaborative manner. Since the recent development of web technologies offers scientific communities new ways for cooperation and communication, we propose a fully web-based software approach for the collaborative analysis of bioimage data and demonstrate the applicability of Web2.0 techniques to ion mobility spectrometry image data. Our approach allows collaborating experts to easily share, explore and discuss complex image data without any installation of software packages. Scientists only need a username and a password to get access to our system and can directly start exploring and analyzing their data
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IMS2- An integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath
No full textBaumbach J, Bunkowski A, Lange S, et al. IMS2- An integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath. Journal of Integrative Bioinformatics. 2007;4(3):75.IMS2 is an Integrated Medical Software system for the analysis of Ion Mobility Spectrometry (IMS) data. It assists medical staff with the following IMS data processing steps: acquisition, visualization, classification, and annotation. IMS2 provides data analysis and interpretation features on the one hand, and also helps to improve the classification by increasing the number of the pre-classified datasets on the other hand. It is designed to facilitate early detection of lung cancer, one of the most common cancer types with one million deaths each year around the world. After reviewing the IMS technology, we first describe the software architecture of IMS2 and then the integrated classification module, including necessary pre-processing steps and different classification methods. The Lung Hospital Hemer (Germany) provided IMS data of 35 patients suffering from lung cancer and 72 samples of healthy persons. IMS2 correctly classifies 99% of the samples, evaluated using 10-fold cross-validation
Bacterial Cytolysin during Meningitis Disrupts the Regulation of Glutamate in the Brain, Leading to Synaptic Damage
No full textAbstract
Streptococcus pneumoniae (pneumococcal) meningitis is a common bacterial infection of the brain. The cholesterol-dependent cytolysin pneumolysin represents a key factor, determining the neuropathogenic potential of the pneumococci. Here, we demonstrate selective synaptic loss within the superficial layers of the frontal neocortex of post-mortem brain samples from individuals with pneumococcal meningitis. A similar effect was observed in mice with pneumococcal meningitis only when the bacteria expressed the pore-forming cholesterol-dependent cytolysin pneumolysin. Exposure of acute mouse brain slices to only pore-competent pneumolysin at disease-relevant, non-lytic concentrations caused permanent dendritic swelling, dendritic spine elimination and synaptic loss. The NMDA glutamate receptor antagonists MK801 and D-AP5 reduced this pathology. Pneumolysin increased glutamate levels within the mouse brain slices. In mouse astrocytes, pneumolysin initiated the release of glutamate in a calcium-dependent manner. We propose that pneumolysin plays a significant synapto- and dendritotoxic role in pneumococcal meningitis by initiating glutamate release from astrocytes, leading to subsequent glutamate-dependent synaptic damage. We outline for the first time the occurrence of synaptic pathology in pneumococcal meningitis and demonstrate that a bacterial cytolysin can dysregulate the control of glutamate in the brain, inducing excitotoxic damage.
Author Summary
Bacterial meningitis is one of the most devastating brain diseases. Among the bacteria that cause meningitis, Streptococcus pneumoniae is the most common. Meningitis predominantly affects children, especially in the Third World, and most of them do not survive. Those that do survive often suffer permanent brain damage and hearing problems. The exact morphological substrates of brain damage in Streptococcus pneumoniae meningitis remain largely unknown. In our experiments, we found that the brain cortex of patients with meningitis demonstrated a loss of synapses (the contact points among neurons, responsible for the processes of learning and memory), and we identified the major pneumococcal neurotoxin pneumolysin as a sufficient cause of this loss. The effect was not direct but was mediated by the brain neurotransmitter glutamate, which was released upon toxin binding by one of the non-neuronal cell types of the brain – the astrocytes. Pneumolysin initiated calcium influx in astrocytes and subsequent glutamate release. Glutamate damaged the synapses via NMDA-receptors – a mechanism similar to the damage occurring in brain ischemia. Thus, we show that synaptic loss is present in pneumococcal meningitis, and we identify the toxic bacterial protein pneumolysin as the major factor in this process. These findings alter our understanding of bacterial meningitis and establish new therapeutic strategies for this fatal disease
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