Course DNA based identification of fungi 2018 by Webmaster Courses 2018-07-13 13:01:58
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October 11-12 2018   Registration

Venue: Westerdijk Fungal Biodiversity Institute, Utrecht, Uppsalalaan 8, The Netherlands.
Price: € 999,-

In the course “DNA based identification of fungi” (11-12 October 2018) we aim to give insight in the recent development in this field. Besides in-depth presentations of various topics (see below), the course gives insight in ways to generate high quality sequence data from a culture (theoretical) and a hands-on training in DNA based identification, sequence data interpretation and analysis.

  • Molecular based detection and identification
  • Trends and developments in food diagnostics
  • Next generation sequencing for food quality and safety
  • Fungal phylogeny
  • MALDI-TOF and other proteomics approaches
  • Bioinformatics

Day 1. Thursday, October 11, 2018

  • 09:30   Welcome and general introduction
  • 09:45   Trends and developments in food diagnostics – dr. Aart van Amerongen (WUR, Wageningen, NL)
    Food diagnostics is a relatively new and emerging area fuelled in large part by the ever-increasing demand for food safety and security. Traditional microbiological detection and identification methods for micro-organisms are well known to be time consuming and laborious and they are increasingly being perceived as insufficient to meet the demands of rapid food testing. Recently, various kinds of rapid detection, identification, and monitoring methods have been developed for foodborne micro-organisms, including nucleic-acid-based methods, immunological methods, and biosensor-based methods, etc. In this presentation an overview the principles, characteristics, and applications of rapid detection methods is given.
  • 10: 15  Coffee & tea
  • 10:45   Molecular-based identification of food and indoor fungi – dr. Jos Houbraken (Westerdijk Institute, Utrecht, NL)
    Identification of unknown isolates is of importance and a name will unlock a huge amount of additional information. Information on the ecology of the species and data on e.g. heat- or preservative resistance, ability to grow at low temperatures and mycotoxin production can be retrieved with a correct identification, and this information can directly affect decision making. Identification based on phenotypic characters can be time consuming and well-trained staff is needed, and is therefore more prone to erroneous identifications than a sequence-based identification. One or more genes or loci are being sequenced for identification and which target to sequence depends on the genus/species. Furthermore, the result of a sequence-based identification heavily depends on the quality of the database. In this presentation, information on how to get a reliable species identification using sequences is given. Additionally, information is given on strain typing. Strain typing – distinguishing between different strains of the same species – is used to get insight in the genetic diversity of spoilage agents (is contamination caused by the same strain) or can be used to trace the source of a contamination. Identification and typing are two overlapping fields, and fields and typing often follows identification. Over the years, many different typing methods are developed and an overview of the advantages and disadvantages of the most commonly used typing methods (amplified fragment length polymorphism (AFLP) typing, multilocus sequence typing (MLST) and short tandem repeat (STR) analysis) is given.
  • 11:30   MALDI-TOF MS and other proteomics approaches for identification of food and indoor fungi and yeasts – t.b.a.
    The matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) technique can be used to identify bacteria, yeasts and filamentous fungi. MALDI-TOF MS has a short turnaround time, is robust and can be reliable. The technique measures the difference in size of biomolecules (e.g. proteins, peptides, glycoproteins biomarkers, sugars) and organic molecules. MALDI-TOF MS has been successfully applied for the routine identification of foodborne yeasts and has applications for the identification of filamentous fungi. An important step in the identification process using MALDI-TOF MS is the comparison of the generated spectrum against the reference database with mass spectra. The quality and species/strains diversity within the database are essential for a correct identification. Next to the database, the technical variation resulting from the sample preparation procedure is of importance. These can affect negatively the spectra quality and consequently fungal identification. During the presentation information on extraction procedures and other relevant steps in the procedure is given.
  • 12:15   Lunch
  • 13:00   Practical explanation of DNA extraction, PCR, Sanger sequencing and data quality
  • 15:00 Hands-on workshop: BLAST analysis, sequence-based identification

Day 2. Friday, October 12 2018

  • 09:30   Application of next generation sequencing in food quality and safety – t.b.a.
    Molecular methods for the detection and identification of fungi and yeasts from spoiled foods or indoor environments can be faster than conventional methods. One of the advantages of molecular based methods, especially in PCR-based methods, is the specific detection of small amounts of target organisms by amplifying their DNA in a considerably short time frame. The most common used methods are conventional and real-time PCR assays, but next generation DNA sequencing is becoming more common. A compact overview of these methods with their advantages and disadvantages is given in this presentation.
  • 10: 15  Coffee & tea
  • 10:45   DNA sequence alignment and tree building – dr. Ewald Groenewald (Westerdijk Institute, Utrecht, NL)
  • 10:30 Hands-on workshop: DNA sequence alignment and phylogenetic analysis.
    Multiple sequence alignment (MSA) is generally the alignment of two or more biological sequences (protein or nucleic acid). From the output, homology can be inferred and the evolutionary relationships between the sequences studied. Various algorithms can be used to align sequences and those have different effects on the final result, the phylogram.
  • 12:15   Lunch
  • 13:00   Continuation of hands-on workshop: DNA sequence alignment and phylogenetic analysis.
  • 16:00   Closure and general remarks – dr. Jos Houbraken (Westerdijk Institute, Utrecht, NL)

Dr. J. Houbraken and Dr. J. Dijksterhuis. Lectures will be presented by specialists from Westerdijk Institute and invited speakers.

Language of instruction:
The course is taught in English.

The course will take place at Westerdijk Fungal Biodiversity Institute, Utrecht, Uppsalalaan 8, The Netherlands.

Course Food and Indoor Mycology: € 1299,-
DNA based identification of fungi: € 999,-
Course Food and Indoor Mycology package: € 1949,-

Lunches and the course book “Food and Indoor Fungi” by Samson et al. are included in the course fee; accommodation excluded