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Publikationsliste Dr. Silvia Calabrese
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Originalarbeiten in wissenschaftlichen Fachzeitschriften Jahre: 2023 |
2022 |
2020 | alle anzeigen zurück zur Übersicht aller Publikationen Y.-K. Lai, Y.-T. Kao, J. Hess, S. Calabrese, F. von Stetten, N. PaustInterfacing centrifugal microfluidics with linear-oriented 8-tube strips and multichannel pipettes for increased throughput of digital assays 2023 Lab on a Chip , Band : 23, Seiten : 2623 - 2632 S. Calabrese, A. M. Markl, M. Neugebauer, S. J. Krauth, N. Borst, F. von Stetten, M. LehnertReporter emission multiplexing in digital PCRs (REM-dPCRs): direct quantification of multiple target sequences per detection channel by population specific reporters 2023 Analyst , Band : 148, Seiten : 5243 - 5254 Y.-T. Kao, S. Calabrese, N. Borst, M. Lehnert, Y.-K. Lai, F. Schlenker, P. Juelg, R. Zengerle, P. Garstecki, F. von StettenMicrofluidic One-Pot Digital Droplet FISH Using LNA/DNA Molecular Beacons for Bacteria Detection and Absolute Quantification 2022 Biosensors , Band : 12, Nummer : 4, Seite : 237 J. F. Hess, M. Kotrová, S. Calabrese, N. Darzentas, T. Hutzenlaub, R. Zengerle, M. Brüggemann, N. PaustAutomation of amplicon-based library preparation for next generation sequencing by centrifugal microfluidics 2020 Anal Chem , Band : 92, Nummer : 19, Seiten : 12833 - 12841» Kurzfassung anzeigen « Kurzfassung verbergen Kurzfassung Next generation sequencing has become a mainstream method in bioanalysis. Improvements in sequencing and bioinformatics turned the complex and cumbersome library preparation to the bottle neck in terms of reproducibility and costs in the complete NGS workflow. Here, we introduce an automated library preparation approach based on a generic centrifugal microfluidic car-tridge. Multiplex polymerase chain reaction amplification and subsequent clean-up were processed with all reagents pre-stored on disk, including cell line-based DNA as quality control. Exchange of pre-stored reagents allows to apply the cartridge to different target genes. Sequencing of automatically prepared libraries from T-cell receptor and immunoglobulin gene rearrangements in context of lymphoproliferative disorders demonstrated excellent clean-up performance between 91.9% and 99.9% of target DNA reads and successful amplification of all target regions by up to 15 forward combined with four reverse primers. The fully auto-mated library preparation by centrifugal microfluidics thus offers attractive automation options in diagnostic settings. M. Schulz, S. Calabrese, F. Hausladen, H. Wurm, D. Drossart, K. Stock, A. M. Sobieraj, F. Eichenseher, M. J. Loessner, M. Schmelcher, A. Gerhardts, U. Goetz, M. Handel, A. Serr, G. Haecker, J. Li, M. Specht, P. Koch, M. Meyer, P. Tepper, R. Rother, M. Jehle, S. Wadle, R. Zengerle, F. von Stetten, N. Paust, N. BorstPoint-of-care testing system for digital single cell detection of MRSA directly from nasal swabs 2020 Lab Chip , Band : 20, Seiten : 2549 - 2561» Kurzfassung anzeigen « Kurzfassung verbergen Kurzfassung We present an automated point-of-care testing (POCT) system for rapid detection of species- and resistance markers in methicillin-resistant Staphylococcus aureus (MRSA) at the level of single cells, directly from nasal swab samples. Our novel system allows clear differentiation between MRSA, methicillin-sensitive S. aureus (MSSA) and methicillin-resistant coagulase-negative staphylococci (MR-CoNS), which is not the case for currently used real-time quantitative PCR based systems. On top, the novel approach outcompetes the culture-based methods in terms of its short time-to-result (1 h vs. up to 60 h) and reduces manual labor. The walk-away test is fully automated on the centrifugal microfluidic LabDisk platform. The LabDisk cartridge comprises the unit operations swab-uptake, reagent pre-storage, distribution of the sample into 20 000 droplets, specific enzymatic lysis of Staphylococcus spp. and recombinase polymerase amplification (RPA) of species (vicK) – and resistance (mecA) -markers. LabDisk actuation, incubation and multi-channel fluorescence detection is demonstrated with a clinical isolate and spiked nasal swab samples down to a limit of detection (LOD) of 3 ± 0.3 CFU μl−1 for MRSA. The novel approach of the digital single cell detection is suggested to improve hospital admission screening, timely decision making, and goal-oriented antibiotic therapy. The implementation of a higher degree of multiplexing is required to translate the results into clinical practice. M. Schulz, S. Probst, S. Calabrese, A. Homann, N. Borst, M. Weiss, F. von Stetten, R. Zengerle, N. PaustVersatile Tool for Droplet Generation in Standard Reaction Tubes by Centrifugal Step Emulsification 2020 Molecules , Band : 25, Nummer : 8, Seite : 1914» Kurzfassung anzeigen « Kurzfassung verbergen Kurzfassung We present a versatile tool for the generation of monodisperse water-in-fluorinated-oil droplets in standard reaction tubes by centrifugal step emulsification. The microfluidic cartridge is designed as an insert into a standard 2 mL reaction tube and can be processed in standard laboratory centrifuges. It allows for droplet generation and subsequent transfer for any downstream analysis or further use, does not need any specialized device, and manufacturing is simple because it consists of two parts only: A structured substrate and a sealing foil. The design of the structured substrate is compatible to injection molding to allow manufacturing at large scale. Droplets are generated in fluorinated oil and collected in the reaction tube for subsequent analysis. For sample sizes up to 100 µL with a viscosity range of 1 mPa·s–4 mPa·s, we demonstrate stable droplet generation and transfer of more than 6 × 105 monodisperse droplets (droplet diameter 66 µm ± 3 µm, CV ≤ 4%) in less than 10 min. With two application examples, a digital droplet polymerase chain reaction (ddPCR) and digital droplet loop mediated isothermal amplification (ddLAMP), we demonstrate the compatibility of the droplet production for two main amplification techniques. Both applications show a high degree of linearity (ddPCR: R2 ≥ 0.994; ddLAMP: R2 ≥ 0.998), which demonstrates that the cartridge and the droplet generation method do not compromise assay performance.
Konferenzbeiträge Jahre: 2023 |
2021 |
2020 |
2018 | alle anzeigen zurück zur Übersicht aller Publikationen S. Murad, M. Heyer, F. Lickert, J. Menges, S. Calabrese, T. Hutzenlaub, N. Paust, P. JuelgFast and bubble-free filling of nano-imprinted high-density picoliter well arrays for digital assays enabled by centrifugal microfluidics 2023 MicroTAS 2023, Katovice/Poland, 15.-19.10.2023 Y.-T. Kao, S. Calabrese, N. Borst, M. Lehnert, Y.-K. Lai, F. Schlenker, R. Zengerle, P. Garstecki, F. von StettenOne-step amplification-free bacteria detection by optimizes LNA/DNA molecular beacons in droplets 2021 MicroTAS 2021, Palm Springs/USA, 10.-14.10.2021, online J. F. Hess, M. Kotrová, S. Calabrese, T. Hutzenlaub, R. Zengerle, M. Brüggemann, N. PaustAutomated library preparation for next generation sequencing of immunoglobulin gene rearrangements by centrifugal microfluidics 2020 MicroTAS 2020, 04.-09.10.2020, virtual M. Schulz, N. Borst, M. Specht, S. Calabrese, F. von Stetten, R. Zengerle, N. PaustFrom nasal swab to digital answer: unit operations for antibiotic resistance screening on a single cell level 2018 MicroTAS 2018, 11. -15. November 2018, Kaohsiung / Taiwan Credits: SILK Icons by http://www.famfamfam.com/lab/icons/silk/