Graduate School of health and Medical Sciences

Intro to recombinant DNA and NGS technologies
Provider: Faculty of Health and Medical Sciences

Activity no.: 3688-24-00-00
	Enrollment deadline: 05/11/2024

Date and time	19.11.2024, at: 09:00 - 10.12.2024, at: 12:15
Regular seats	12
Course fee	3,960.00 kr.
Lecturers	Jan Zylicz
ECTS credits	2.50

Contact person	MoMed Team E-mail address: momed@bric.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 from NorDoc member faculties. 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 NorDoc member faculties. After the enrollment deadline, available seats will be allocated to applicants on the waiting list. Learning objectives A student who has met the objectives of the course will be able to: 1. demonstrate a functional understanding of the latest approaches to molecular cloning and recombinant DNA technologies. 2. apply this knowledge to a set of common experimental tools used in contemporary molecular biology and troubleshoot common experimental pitfalls. 3. critically evaluate the experimental design of published projects and understand the extent to which they may be prone to artefacts. 4. identify various bioinformatic resources required for effective experimental design and use simple analysis pipelines for processing small scale sequencing data. 5. design next generation sequencing projects for expression analysis and protein-DNA interaction analysis. Content The fundamental principles of molecular cloning will be explained with an emphasis on common applications in molecular and cellular biology. The course will build on foundation principals governing how DNA can be manipulated in a laboratory to generate bespoke molecules for a wide range of purposes. Specific applications of these concepts will cover 1. plasmid cloning, and the generation of transgenic mammalian cell lines using CRISPR/Cas9 technologies 2. experimental workflows for NGS projects 3. analytical workflows for NGS projects The course is designed with early-stage researchers in mind and is specifically structured to cover a wide field of knowledge, and help alleviate, many of the common pitfalls when working with recombinant DNA. The course is not targeted towards clinical PhDs unless they have or will have direct laboratory experience. The topics that will be covered in a lecture setting that will include group discussions and workshop style interactions which will draw from participants experiences. The 6 lessons will be followed by a project period of 4 weeks. (equivalent to 32 hours of work), where the participants will design an experiment they wish to pursue for their own research interests, from the topics covered in the lectures, and submit it for evaluation with the course directors. During the project period, the participants will have additional three 1-hour feedback/discussion sessions with the course director. During these sessions participants will present a graphical abstract of their experiment and highlight their research questions. These sessions are designed to provide constructive feedback and increase the quality of the written assignment. The assignment is done individually, and a satisfactory evaluation is needed to pass the course. The course will be evaluated based on how well the student displayed an understanding of the course material, and how well that was applied to the chosen experimental setting. As this course is intended as an introduction to the topics, there should be clear evidence that students read more in-depth about their chosen experiment approach, and this reading should be referenced in the final proposal. Self-directed research should take up approximately 75% of the allocated project workload (i.e. 15 hours) Participants All students must have significant prior laboratory or bioinformatic experience. Junior PhD students; Required qualifications: Undergraduate Course in Genetics 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: Molecular Mechanisms of Disease Neuroscience Cellular and Genetic Medicine Language English Form 6 Lectures Individual assignments, equivalent to 32 hours of workload. The assignment will be divided into 4 sections (word count given as a guideline only), to be delivered within 4-week of completion of the lectures. 1) Aim of the project (~100 words) 2) Graphical abstract of the project (max 1A4, accepted formats: pdf, png) 3) Justification for the experimental approach (~300 words) 4) An experimental outline that should contain a step-by-step workflow for the experimental approach (~1500 words) 5) Expected results and contingency plan (~500 words) Additional obligatory group discussion and feedback sessions (3hrs) will be organized during the project writing phase. Each participant will have to pitch their project with clear research questions and approach. Detailed feedback from other participants and course director will be provided to help structure the written assignment. Final feedback on assignments will be in written form. Course director Jan Zylicz, Associate Professor, reNEW, jan.zylicz@sund.ku.dk Teachers Jan Zylicz, Associate Professor, reNEW Molly Pleasants Lowndes, Assistant Professor, reNEW Alberto Dinarello, PostDoc Daniela Mayer, PostDoc, reNEW Naz Salehin, PostDoc, reNEW Silvia Raineri, Postdoc, reNEW Cecilia Lövkvist, Assistant Professor, reNEW Bob Hersbach, PostDoc, reNEW Dates 19th November 2024 26th November 2024 3rd December 2024 10th December 2024 All days 9:00-12:15 Course location Panum, room 31.01.26a / 13.1.37 Registration Please register before 19 October 2024 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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