Search

Your search keyword '"Honemann, M."' showing total 6 results
Start Over Author "Honemann, M."
6 results on '"Honemann, M."'

1. Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II

Author

Vries, J.J.C. de, Brown, J.R., Couto, N., Beer, M., Mercier, P. le, Sidorov, I., Papa, A., Fischer, N., Munnink, B.B.O., Rodriquez, C., Zaheri, M., Sayiner, A., Honemann, M., Cataluna, A.P., Carbo, E.C., Bachofen, C., Kubacki, J., Schmitz, D., Tsioka, K., Matamoros, S., Hoper, D., Hernandez, M., Puchhammer-Stockl, E., Lebrand, A., Huber, M., Simmonds, P., Claas, E.C.J., Lopez-Labrador, F.X., ESCV Network Next-Generation Seque, and Virology

Subjects
0301 basic medicine, Viral metagenomics, NGS/HTS, Standardization, Computer science, Bioinformatics, 030106 microbiology, Computational biology, Sensitivity and Specificity, DNA sequencing, 03 medical and health sciences, 0302 clinical medicine, SDG 3 - Good Health and Well-being, Virology, Pipeline, Humans, 030212 general & internal medicine, Diagnostics, Network on, Computational Biology, High-Throughput Nucleotide Sequencing, Infectious Diseases, Metagenomics, NGS, Viruses, Metagenome, HTS, Pathogens, Clinical virology
Abstract

Metagenomic next-generation sequencing (mNGS) is an untargeted technique for determination of microbial DNA/RNA sequences in a variety of sample types from patients with infectious syndromes. mNGS is still in its early stages of broader translation into clinical applications. To further support the development, implementation, optimization and standardization of mNGS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mNGS for viral diagnostics to share methodologies and experiences, and to develop application guidelines. Following the ENNGS publication Recommendations for the introduction of mNGS in clinical virology, part I: wet lab procedure in this journal, the current manuscript aims to provide practical recommendations for the bioinformatic analysis of mNGS data and reporting of results to clinicians.

Published
2021

2. Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure

Author

Lopez-Labrador, F.X., Brown, J.R., Fischer, N., Harvala, H., Boheemen, S. van, Cinek, O., Sayiner, A., Madsen, T.V., Auvinen, E., Kufner, V., Huber, M., Rodriguez, C., Jonges, M., Honemann, M., Susi, P., Sousa, H., Klapper, P.E., Perez-Cataluna, A., Hernandez, M., Molenkamp, R., Hoek, L. van der, Schuurman, R., Couto, N., Leuzinger, K., Simmonds, P., Beer, M., Hoper, D., Kamminga, S., Feltkamp, M.C.W., Rodriguez-Diaz, J., Keyaerts, E., Nielsen, X.C., Puchhammer-Stockl, E., Kroes, A.C.M., Buesa, J., Breuer, J., Claas, E.C.J., Vries, J.J.C. de, ESCV Network Next-Generation Seque, Virology, Medicum, Eeva Auvinen / Principal Investigator, Biosciences, HUSLAB, Department of Virology, University of Helsinki, and Helsinki University Hospital Area

Subjects
0301 basic medicine, Pathogen detection, Standardization, Computer science, 030106 microbiology, Recommendations, INFLUENZA-A VIRUS, DIAGNOSIS, VALIDATION, DNA sequencing, 03 medical and health sciences, 0302 clinical medicine, SDG 3 - Good Health and Well-being, Virology, Wet lab, Viral metagenomics, 030212 general & internal medicine, 11832 Microbiology and virology, Laboratory methods, High-throughput sequencing, Quality assessment, Network on, High-Throughput Nucleotide Sequencing, DNA, EFFICIENT TRANSLATION, Data science, 3. Good health, Infectious Diseases, Metagenomics, Viruses, Next-generation sequencing, 3111 Biomedicine, DEPLETION, MESSENGER-RNA, Clinical virology, PATHOGEN DETECTION
Abstract

Metagenomic high-throughput sequencing (mHTS) is a hypothesis-free, universal pathogen detection technique for determination of the DNA/RNA sequences in a variety of sample types and infectious syndromes. mHTS is still in its early stages of translating into clinical application. To support the development, implementation and standardization of mHTS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mHTS for viral diagnostics to share methodologies and experiences, and to develop application recommendations. This manuscript aims to provide practical recommendations for the wet lab procedures necessary for implementation of mHTS for virus diagnostics and to give recommendations for development and validation of laboratory methods, including mHTS quality assurance, control and quality assessment protocols.

Published
2021
Full Text
View/download PDF

4. B-brick bare in 5 mM Mg2+

Author

Bertosin, E., primary, Stoemmer, P., additional, Feigl, E., additional, Wenig, M., additional, Honemann, M., additional, and Dietz, H., additional

Published
2021
Full Text
View/download PDF

6. A low-cost fluorescence reader for in vitro transcription and nucleic acid detection with Cas13a.

Author

Katzmeier F, Aufinger L, Dupin A, Quintero J, Lenz M, Bauer L, Klumpe S, Sherpa D, Dürr B, Honemann M, Styazhkin I, Simmel FC, and Heymann M

Subjects
Green Fluorescent Proteins, In Vitro Techniques, Limit of Detection, Transcription, Genetic, Bacterial Proteins genetics, Biosensing Techniques instrumentation, CRISPR-Associated Proteins genetics, CRISPR-Cas Systems, Fluorescence, RNA, Bacterial analysis, RNA, Bacterial genetics
Abstract

Point-of-care testing (POCT) in low-resource settings requires tools that can operate independently of typical laboratory infrastructure. Due to its favorable signal-to-background ratio, a wide variety of biomedical tests utilize fluorescence as a readout. However, fluorescence techniques often require expensive or complex instrumentation and can be difficult to adapt for POCT. To address this issue, we developed a pocket-sized fluorescence detector costing less than $15 that is easy to manufacture and can operate in low-resource settings. It is built from standard electronic components, including an LED and a light dependent resistor, filter foils and 3D printed parts, and reliably reaches a lower limit of detection (LOD) of ≈ 6.8 nM fluorescein, which is sufficient to follow typical biochemical reactions used in POCT applications. All assays are conducted on filter paper, which allows for a flat detector architecture to improve signal collection. We validate the device by quantifying in vitro RNA transcription and also demonstrate sequence-specific detection of target RNAs with an LOD of 3.7 nM using a Cas13a-based fluorescence assay. Cas13a is an RNA-guided, RNA-targeting CRISPR effector with promiscuous RNase activity upon recognition of its RNA target. Cas13a sensing is highly specific and adaptable and in combination with our detector represents a promising approach for nucleic acid POCT. Furthermore, our open-source device may be used in educational settings, through providing low cost instrumentation for quantitative assays or as a platform to integrate hardware, software and biochemistry concepts in the future., Competing Interests: The authors have declared that no competing interests exist.

Published
2019
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results