Summer School: Molecular Analysis of Environmental Samples
The MAnES course offers young scientists and established researchers a comprehensive introduction to molecular methods suitable for the analysis of trace amounts of DNA in environmental and dietary samples (i.e. environmental DNA, short: eDNA). In the research fields of conservation, species monitoring, and trophic ecology these methods enable scalability and the non-invasive acquisition of data. Thus, they are ideal for researching endangered species or complex communities and the interactions within them.
The MAnES course covers the entire workflow from the collection of environmental DNA samples to the statistical evaluation of results obtained via species-specific assays and metabarcoding. This includes laboratory work in a clean room environment, as well as bioinformatic sessions in the computer lab. Prior to the two week in-person course at the University of Innsbruck, the participants are introduced to software packages and key background information via online tutorials. The laboratory and bioinformatic sessions are supported by lectures covering the theoretical background and recent scientific findings. Additionally, the participants are given the opportunity to present their own research and discuss the potential for optimization in one-on-one sessions with the instructors.
The MAnES course includes online tutorials, a lecture series, a seminar, as well as practical work in the clean-room and computer laboratory (Σ 7.5 ECTS). The target audience includes undergraduate and graduate students, postdoctoral researchers, PIs and technicians who wish get into working with environmental DNA (eDNA) to study species distributions and trophic interactions.
A maximum of 16 participants will be allowed for the course. The course language is English.
Applicant must submit an informal letter of motivation and proof of their highest academic degree via manes@uibk.ac.at; we've extended the submission deadline until the second half of July.
The lecture series provides an overview of eDNA-based research and the field of trophic ecology. It covers common theoretical concepts and methodological approaches including the use of species-specific assays and metabarcoding approaches. Important procedures such as DNA extraction and PCR as well as study design, field sampling procedures and interpretation of DNA-based data will be covered.
The seminar is centered around participants’ own research projects. It provides participants with the opportunity to present their plans which will be discussed and evaluated with regard to practicability, cost- and time effectiveness.
The practical course includes the entire eDNA workflow from sampling to statistical analysis of the results obtained via species-specific assays and metabarcoding. The general concepts of primer design and assay development needed for diagnostic and metabarcoding approaches will be addressed as well as bioinformatic processing of raw metabarcoding data in a command-line environment. The lab work will be conducted in a clean-room laboratory specifically set up for the analysis of trace amounts of DNA. Groups of 3-4 people will work together to guarantee hands-on training at all times. The bioinformatic processing will be taught in a computer-lab setting and cover data analysis via common bioinformatic pipelines including taxonomic assignment, potential pitfalls, and statistical analysis of the generated OTU or ASV tables.
Participants will receive a certificate of the University of Innsbruck in Molecular Analysis of Environmental Samples (MAnES). Those participants who wish to obtain the ECTS credits (e.g. Master, PhD students) have to generate a protocol on the practical coursework and pass a final exam.
Meet your Instructors
Details and deadlines
Degree: Certificate for 7.5 ECTS-AP
Two weeks blocked in-person course supported by online preparation and online follow-up
Maximum number of participants: 16
Language: English
Laboratory work and bioinformatic analyses in Innsbruck: 16.-27. September 2024
Online tutorials open: 15th August - 15th September
Price: 2150 EUR
Application deadline: 2nd half of July 2024
Apply with an informal motivation letter and proof of your highest academic degree: manes@uibk.ac.at
Additional Information
From all major cities in Austria, Innsbruck, the capital of Tyrol province, has the most picturesque backdrop: nestled in the gorgeous deep valley of the River Inn, between the scenic Karwendel Mountains to the north and Tuxer Mountains to the south. The city offers a long list of outdoor activities, but it is most often visited by the skiing and mountain hiking lovers. A variety of mountain transportation facilities can be found in the city, providing numerous opportunities for skiing and walking. The main street of Innsbruck is the beautiful, lively and elegant Maria Theresien Street, which is a major transport artery but is closed for private vehicles.
Innsbruck is a pleasant and quiet city with down to earth atmosphere and citizens who enjoy a high standard of living. There are a great number of architectural monuments to discover and most of them are compactly located within the area of the historical city centre (Altstadt). The city is the third largest university centre of Austria and offers an intense night life and numerous entertainment venues.
If you need more information, you'll find it at the following websites:
http://www.innsbruck.info/en/innsbruck-city.html
Sightseeing and City Walks:
http://www.innsbruck.info/en/innsbruck-city/experience/sightseeing-in-innsbruck.html
http://www.gpsmycity.com/tours/innsbruck-museums-3650.html
http://www.innsbruck.info/en/experience/sightseeing/routes-tours/1-day-in-innsbruck.html
Travelling to Innsbruck
Innsbruck, the capital of Tyrol province, lies in the centre of the Alps and due to its well-developed touristic infrastructure it’s easy to access from round the world.
Innsbruck's international airport can be reached directly on numerous scheduled flights and charters. From Munich (200 km) or Salzburg airport (180 km) it is a 2-hour trip by either train or car. From Vienna and Zurich airport a direct train connection to Innsbruck is available serveral times per day (travel time 4.5 hours). Daily shuttle bus services are available from Munich airport. Alternatively, airport transfer shuttle services can be booked online.
Innsbruck Train Station is centrally located and internationally well connected. You can book train tickets here.
Public transport in Innsbruck
A two weeks public transport ticket for your personal use will be provided for all participants of the MAnES course. The tickets are valid for one person in Innsbruck.
More details regarding your trips within Innsbruck including time tables of busses and trams, a city map and a journey planner can be found on the IVB webpage.
An alternative journey planner is available on the webpage of the regional transport association VVT (includes Innsbruck, but currently only in German)
The costs for accommodation are not included in the course fees. Participants are required to book accommodation in Innsbruck for the two course weeks in September on their own. Upon demand, the MAnES team and the and the team of Continuing Education of the University of Innsbruck can help participants with finding appropriate and low-cost accommodation options.