Overordnede kursusmål
Microorganisms are unique sources for diverse chemistry that can be
exploited in biotechnology (e.g. as pharmaceuticals) or feared as
contaminants in food or feed (e.g. mycotoxins). The aim of the
course is to give the students a fundamental insight into this
chemical diversity produced by microorganisms and how they are
analyzed. More specifically the course will introduce i) how the
various types of natural products are biosynthesized; ii) the
different types of unique enzymes that catalyzes their
biosynthesis; iii) the nature of the underlying gene clusters; iv)
how bioinformatics tools can be used to link genes to chemical
structures and vice versa; v) and the analytical methods and
strategies to profile, characterize and quantitate such
metabolites.
Læringsmål
En studerende, der fuldt ud har opfyldt kursets mål, vil kunne:
- Define and describe the major classes of natural products
(secondary metabolites).
- Recognize a common polyketide, non-ribosomal peptide or
terpenoid type of natural product and predict a likely biosynthetic
pathway based on a given structure and retro biosynthetic
considerations.
- Be able to predict the composition of the related biosynthetic
gene cluster, based on structural analysis of a given natural
product.
- Advanced user knowledge of bioinformatic tools, such as
antiSMASH, for analysis of secondary metabolite gene clusters.
- Advanced knowledge of bioinformatics tools such as BLAST,
HMMer, Interproscan for prediction of enzyme activities.
- Basic knowledge on analysis and handling of microbial whole
genome sequence data.
- Advanced skills in prediction of types of natural product based
on genome analysis.
- Present one of the major pathways leading to secondary
metabolites in some details.
- Explain the principles of different types of chromatography
(RP, HILIC, IC) and pH considerations.
- Interpret data from mass spectrometry (spectra and
chromatograms), isotope and adduct patterns, including
interpretation of simple MS/MS spectra and their use in
dereplication.
- Within a short timeframe write a report and prepare a
scientific presentation.
Kursusindhold
With onset in microbial metabolites especially fungal, the course
will focus on the following topics: a) the biochemistry of the
chemodiversity in microorganisms including the biosynthesis of
important classes of compounds such as polyketides, terpenoids and
alkaloids; b) concept and strategies of metabolite profiling and
metabolomics, c) the core analytical methodologies used for
detection and analysis of natural products including LC and GC and
detectors e.g. UV (diode array detection), fluorescence,
evaporative light scattering and especially mass spectrometry (MS),
d) data analysis of unit resolution MS and high resolution (TOF) MS
atmospheric pressure ionization spectra; e) data interpretation for
database searching; f) tentative identification of compounds based
on LC-MS data, LogD consideration and ion-exchange sample
preparation strategy, and g) Target analysis of known compounds and
their metabolites based on LC-MS/MS (triple quadrupole data)
including the scan functions of this instrument; h) Solid Phase
Extraction (SPE) purification strategies.
If possible we encourage and facilitate that the students work on
their own data during the course (microbial genome sequence and
natural product containing extracts). Please contact us beforehand
to arrange this.
Bemærkninger
Course fee
1) 2,500 DKK for PhD students (The course is free for all PhD
students from Denmark and other EU/EEA countries. However, these
pay a fee for course materials of 2,000 DKK)
2) 2,500 DKK for other participants from academia
3) DKK 12,500 for participants from industry
The course fee includes course materials, lab expenses and meals
during the day.
Sidst opdateret
19. november, 2018