PhD course: Introduction to recombinant DNA and NGS techniques and applications

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 4 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

Language

English

Form

4 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 Żylicz, 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

19^th November 2024              

26^th November 2024              

3^rd December 2024                

10^th 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