Graduate School of health and Medical Sciences

Shape the world with phage biology
Provider: Faculty of Health and Medical Sciences

Activity no.: 3265-21-00-00
	Enrollment deadline: 28/02/2022

Date and time	28.03.2022, at: 09:00 - 08.04.2022, at: 16:00
Regular seats	20
Course fee	20,760.00 kr.
Lecturers	Hanne Ingmer Michela Gambino
ECTS credits	7.50

Contact person	Michela Gambino E-mail address: mgambino@sund.ku.dk

Enrolment Handling/Course Organiser	PhD administration E-mail address: phdkursus@sund.ku.dk

Aim and content This course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD students at graduate schools in the other Nordic countries. All other participants must pay the course fee. Anyone can apply for the course, but if you are not a PhD student at a Danish university, you will be placed on the waiting list until enrollment deadline. This also applies to PhD students from Nordic countries. After the enrollment deadline, available seats will be allocated to applicants on the waiting list. Course title *Shape the world with phage biology: isolation, sequencing, transduction and engineering of phages* Learning objectives A student who has met the objectives of the course will be able to: 1. To integrate and transfer experimental observations from phage isolation and propagation to the principles of infection mechanisms of viruses and their diversity in the environment 2. To analyse whole genome sequencing output and identify gene functions with biofinformatic tools to identify candidates for phage therapy and discover the molecular basis of phage-host interaction 3. To run and discuss protocols for engineering phages (CRISPR-Cas) useful to propose innovative alternative to antimicrobials 4. To run phage transduction experiments and explain phage role as mobile genetic elements and impact of horizontal gene transfer in the spread of antibiotic resistance and pathogenicity 5. To generalize the considered topics and discuss the use of phages as antimicrobials and molecular tools to shape our world Content The course is organized as 2-weeks hands-on course, divided into 4 main modules: 1) PHAGE DIVERSITY: Isolation, propagation and host range of phages 2) PHAGE-BACTERIUM INTERACTION: Genome analysis and annotation of phages that target bacterial human pathogens and prophages expressing virulence factors 3) PHAGE DERIVED ANTIMICROBIALS: Engineering of prophages using CRISPR-Cas to generate phage related antimicrobials 4) HORIZONTAL GENE TRANSFER: Phage transduction of antibiotic resistance and bacterial pathogenicity islands as models Each module is organized with a short introduction, an experimental part in the laboratory or working in silico and a seminar from an invited expert in the topic. Students will then work in teams to present an application of the learned concepts and techniques and will receive peer and teachers feedback. The laboratory and in silico work draws on running projects in the Section of Food Safety and Zoonosis, in which we study pathogenic bacteria such as Salmonella, E. coli and Staphylococcus aureus, investigate the molecular mechanisms of antimicrobial resistance and propose innovative alternatives to antibiotics such as phage therapy and biocontrol. Students will independently run real experiments of phage biology, using last generation molecular tools, relevant for any fields of microbiology (fundamental, environmental, clinical, veterinary, industrial), and attractive for careers in academy and in companies. The implementation of a constructive approach and an open dialogue with the teachers will allow students to learn-by-doing, partecipate actively to the cutting-edge research running at the department, and generalize their findings. Participants PhD students interested in biology, microbiology, molecular biology, genome engineering. Please contact the teachers if you are unsure if you meet the required qualifications. Relevance to graduate programmes The course is relevant to PhD students from the following graduate programmes at the Graduate School of Health and Medical Sciences, UCPH: All graduate programmes Language English Form Lectures and exercises in the laboratory and in silico. As preparation, the students will follow the short introductory videos (recorded, 30 min presentation max about the course) and read the protocols provided. At the course, the students will be organized in small teams (2-3 people max) and they will follow the planned exercises of microbiology/molecular biology and of bioinformatic, in an open dialogue with the teacher and helpers. After each experimental parts, they will follow seminars from an experts in the proposed topics. Then the students will discuss the results, put them into context and propose their interpretation. Results will be validated by the teachers, that will build on the students aquired knowledge by providing further details and presenting further explanations and applications, also using their own experience in the respective fields. The students will organize themselves a final seminar day to shortly present their results and their take home message. For each presentation, the other teams and the teachers team will have the chance to ask questions and discuss. Course director Assistant professor Michela Gambino and Professor Hanne Ingmer Teachers Michela Gambino, Cedric Woudstra, Janine Bowring Date Week 13: 28 March -1 April 2022 Week 14: 4 April - 8 April 2022 All days from 9am – 4pm. Course location Section of Food Safety and ZoonosisDepartment of Veterinary and Animal Sciences, University of Copenhagen Stigbøjlen 4, 1870 Frederiksberg C Registration Please register before 28 February 2022 Seats to PhD students from other Danish universities will be allocated on a first-come, first-served basis and according to the applicable rules. Applications from other participants will be considered after the last day of enrolment. Note: All applicants are asked to submit invoice details in case of no-show, late cancellation or obligation to pay the course fee (typically non-PhD students). If you are a PhD student, your participation in the course must be in agreement with your principal supervisor.

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