Alfred Wegener Institute (AWI): Workshop on real time quantitative PCR
Workshop on real time quantitative PCR to develop climate services for monitoring harmful microorganisms in their marine environment
21th to 25th October 2019 at Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
This workshop is aimed at giving participants an understanding of real time quantitative PCR and its applications in harmful algal bloom (HAB) monitoring. The course includes presentations, discussions, and hands-on demonstrations and covers all aspects of qPCR development and application, from designing a qPCR assay and preparation of defined samples to data analysis and trouble shooting. SYBR green and TaqMan assays will be applied with focus on key species groups of HAB microalgae (e.g., Alexandrium, Ostreopsis, Phaeocystis and Pseudo-nitzschia spp.). After completing the course participants will be able to design qPCR assays specific for their individual needs and perform qPCR experiments as well as to interpret and analyze the gained data. Furthermore, the workshop will give insights into fluorescence in situ hybridization (FISH) as a validation tool for quantitative real time PCR.
The workshop is intended for persons working in or planning to initiate harmful algal monitoring programs, and are interested in and equipped to applying this molecular technology. Participation is limited to 10 participants, with a documented professional interest in phytoplankton identification by molecular biological methods. Applications should be sent by email to: Kerstin Klemm (Kerstin.Klemm@awi.de; cc: Allan.Cembella@awi.de, Uwe.John@awi.de, Raffaele.Siano@ifremer.fr) before the 15th of May 2019. A short letter justifying the participation of the applicant and details of the proposed application of the knowledge gained to HAB monitoring should be submitted. A brief CV of the applicant’s experience and qualifications must also be provided. The course will be taught in English and a good knowledge of English is therefore required. There will be no registration fee, but participants will have to provide for their own travel and accommodation expenses.
Goals of the Workshop
- To give participants a deeper understanding of qPCR and its applications
- To improve harmful algal bloom detection by using molecular tools
- To explore the potential application of qPCR for the monitoring and forecasting of harmful algal blooms in (own) monitoring programs
- To provide guidance for developing own qPCR assays for desired target species
- To validate qPCR achieved results by applying light microscopy and fluorescence in situ hybridization (FISH) on selected samples
Workshop agenda
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1st day Monday, 21 October 2019 |
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9:00- 9:10 |
Welcome and Workshop Overview
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Uwe John, Kerstin Klemm, Raffaele Siano, Allan Cembella |
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9:10-9:30 |
Presentation of the hosting institute and introduction of workshop attendees |
Uwe John
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9:30 - 10:00 Theoretical session |
Introduction to project CoCliME Harmful algal blooms, and coastal ecosystem status indicators in the project CoCliME |
Kerstin Klemm |
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10:00-10:30 Theoretical session
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Introduction to PCR: a general overview
Detection chemistries |
Uwe John |
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10:30-10:45 |
Recreational break |
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10:45-11:15 Theoretical session
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Different sampling methods of field samples Quantitative PCR applications in detecting harmful microalgae and their use in HAB monitoring programs with focus on the HAB species involved in monitoring programs of CoCliME endusers
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Raffaele Siano, Kerstin Klemm |
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11:15-12:00 Theoretical session
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Primer and probe design for qPCR applications General overview:
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Uwe John |
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12:00-13:00 |
Lunch at AWI canteen |
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13:00-17:00 Practical session
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Kerstin Klemm, Uwe John, Raffaele Siano |
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17:00 |
End of Workshop day 1 |
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2nd day Tuesday, 22nd October 2019 |
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9:00 – 09:30 Theoretical session |
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Uwe John |
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9:30-9:45 |
Recreational break |
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9:45-12:00 Practical session
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Kerstin Klemm, Uwe John |
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12:00-13:00 |
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13:00-14:30 Practical session |
Data analysis
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Kerstin Klemm, Uwe John |
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14:30-17:00 Practical session |
Analysis of performed qPCR experiments |
Kerstin Klemm, Uwe John, Raffaele Siano, |
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17:00 |
End of Workshop day 2 |
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3rd day Wednesday, 23 October 2019 |
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9:00 – 12:00 |
qPCR analysis of field samples using SYBR Green or TaqMan assays |
Kerstin Klemm, Uwe John, Raffaele Siano |
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12:00-13:00 |
Lunch at AWI canteen |
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13:00-17:00 |
End of Workshop day 3 |
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4th day Thursday, 24 October 2019 |
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9:00-9:15 Theoretical session
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Introduction to alternative analysis methods in detecting harmful algal blooms with focus on fluorescence in situ hybridization techniques |
Kerstin Klemm |
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9:15-12:00 Practical session |
Practical demonstration of FISH experiments and analysis of data
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Kerstin Klemm, Uwe John |
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12:00-13:00 |
Lunch at AWI canteen |
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13:00-17:00 Combined theoretical and practical session |
Further qPCR analysis of field samples, analysis of performed qPCR experiments |
Kerstin Klemm, Uwe John, Raffaele Siano, |
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17:00 |
End of Workshop day 4 |
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5th day Friday, 25 October 2019 |
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9.30-12:00 Combined theoretical and practical session
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Ongoing analysis of performed qPCR experiments, optimization strategies, trouble shooting
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Kerstin Klemm, Uwe John, Raffaele Siano |
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12:30 |
End of workshop |
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