Print Syllabus

Syllabus

P000046 Phenotypic Microarray of Microbes, 3.0 Credits

Subjects

Horticulture Plant Protection Biology

Education cycle

Postgraduate level

Grading scale

Prior knowledge

Admitted to the PhD education.

Basic knowledge in biology, microbiology, horticulture, ecology, plant protection biology or related fields. Basic knowledge in R studio is mandatory.

Objectives

After completion of the course, the students should be able to:

- Demonstrate understanding of the physiological principles behind phenotypic microarray and associated ecological principles

- Demonstrate a good practical knowledge of the phenotypic microarray methodology and its limitations

- Demonstrate ability to be in command of planning and conducting phenotypic microarray as well as calculate and analyse obtained data

- Demonstrate ability to foresee pitfalls and develop solutions

- Demonstrate capacity to independently develop ideas for additional applications

Content

The course deals with microbial physiology and introduces students at postgraduate level to phenotyping of bacteria, fungi and human cell lines based on their capacity to metabolize sole nutrient sources. The course is divided into four sections: (i) theoretical (physiological background of phenotyping based on nutritional preferences, associated ecological principles), (ii) practical (preparing and running phenotypic micoarray using own isolates), (iii) calculation of data output and (iv) additional applications.

The course consist of a remote part and a laboratory training part conducted on the SLU campus in Alnarp. Laboratory training is alternated with lectures and workshops on basics and concepts related to phenotypic microarray. Both the remote and the on-site part are mandatory.

The remote part consists of literature preparations (3 days) and compiling of a study report (2 days). Each student will do hand-on training of phenotypic microarray using a bacterial pure culture, and participants are invited to bring a bacterial pure culture from their experimental work on the course. Retrieved data is analysed using R. The on-site part lasts 5 days.

There are two exams: the literature exam is given as a digital quiz prior to the hands-on training; the study report is handed in at the end of the course.

Formats and requirements for examination

Examination

Passed quiz

Approved laboratory report

According to the grading criteria the student has passed if:

The candidate is in good command of the basic fact within the framework of the stipulated content

- 75% of the given answers in the digital quiz is correct.

The candidate is in good command of the basic fact and considerations for conducting phenotypic microarray

- 75% of the given answers in the digital quiz is correct.

Evaluate, calculate and discuss lab results using phenotypic microarray and present procedures and analysis in a writing in a scientific way.

Critically assess and analyze pitfalls and limitations as well as develop decisive solutions and present them in writing in a scientific way.

Present a graphical abstract for a future theme/problem applying phenotypic microarray as a technique.

Additional information

**Pedagogical form**

The course is based on

- Literature studies
- Laboratory training
- Data analysis workshops
- Selected on-site lectures
- Future application workshops

**Time table**

3 days own work (remote literature studies, plus quiz)

5 days on site laboratory training, data analysis, lectures, future application workshop

2 days own work (laboratory report, remote)

**PhD students from other Universities than SLU**

The course is also open for PhD students at other Universities. A fee of 3800 SEK per participant will be charged.

**Contact person for application and further information**

Beatrix Alsanius beatrix.alsanius@slu.se

Maria Karlsson maria.e.karlsson@slu.se

Responsible department

Department of Biosystems and Technology