27815 Analytisk mikrobiel naturstofkemi og biosyntese

2018/2019

Kurset udbydes hvet andet år - næste gang i januar 2019.
Kursusinformation
Analytical microbial natural product chemistry and biosynthesis
Engelsk
5
Ph.d., Fagligt fokuseret kursus
Kurset udbydes som enkeltfag
Januar
2 uger i januar hvert år.
I 2019: 16.-25. januar (kursets varighed: 10 dage ca. 9 timer/dag inkl. 1 weekend og hjemme arbejde).
Campus Lyngby
Forelæsninger, seminarer og gruppediskussioner samt opgaver
[Kurset følger ikke DTUs normale skemastruktur]
Umiddelbart efter undervisningen (3-ugers-kursus), Umiddelbart efter undervisningen (3-ugers-kursus), Kursets sidste dag
Bedømmelse af opgave(r)/rapport(er)
Evaluering af opgaver, præsentationer og en endelig rapport
Skriftlige hjælpemidler er tilladt
bestået/ikke bestået , intern bedømmelse
Minimum 10 Maksimum: 24
Thomas Ostenfeld Larsen , Bygning 221, Tlf. (+45) 4525 2632 , tol@bio.dtu.dk
Ling Ding , Lyngby Campus, Bygning 221 , lidi@dtu.dk
Tilmann Weber , tiwe@biosustain.dtu.dk

27 Institut for Bioteknologi og Biomedicin
DTU Biosustain
http://www.bio.dtu.dk/english/Stud...D/Courses/27815
På instituttet
14 december 2019
Pr. email til Thomas Ostenfeld Larsen (tol@bio.dtu.dk) med CV og kort beskrivelse af hvorfor du vil deltage i kurset.
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