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LBIK10207U  Synthetic Biology Volume 2016/2017

Course information

LanguageEnglish
Credit7,5 ECTS
LevelFull Degree Master
Duration1 block
Placement
Block 3
Schedule
B
Course capacityNo limitation
Continuing and further education
Study boardStudy Board of Biomolecular Sciences and Technology
Contracting departments
  • Department of Plant and Environmental Sciences
  • Department of Media, Cognition and Communication
  • Department of Neuroscience and Pharmacology
  • Department of Chemistry
  • The Niels Bohr Institute
Course responsible
  • Sotirios Kampranis (4-77736f654474706972326f7932686f)
Lecturers
Science; Department of Plant and Environmental Sciences: Birger Lindgerg Møller, Thomas Günther-Pomorski
Irini Pateraki, Poul Erik Jensen, Krutika Bavishi, Agnieszka Janina Zygadlo Nielsen
Science: Department of Chemistry: Nikos Hatzakis, Emma Hooley
The Niels Bohr Institute
Humanities; Department of Media, Cognition and Communication: Sune Holm
Health; Department of Neuroscience and Pharmacology: Søren G.F. Rasmussen,Claus J. Leland
Saved on the 02-12-2016
Education

MSc Programme in Biology-Biotechnology
MSc Programme in Biochemistry
MSc Programme in Molecular Biomedicine

Content

The course is interdisciplinary and will be guided by the strong scientific groups of the UNIK center for Synthetic Biology of Copenhagen University. Synthetic biology is an emerging technology that applies biological science as a basis for new developments within medicine, pharmaceutics, plant biology and materials sciences using combined concepts developed in biotechnology and nano-science. Foundational tools to meet this challenge include: Ready access to off-the-shelf standardized biological parts and devices as well as advanced tools that enable the integration of basic biological and synthetic units into multi component systems. Further, a variety of modern measuring techniques and computational tools are applied in the design and tests of new systems. The richness and versatility of biology is the basis for the great potential of synthetic biology, and it is foreseen that several of the world’s most pressing challenges may be addressed by these methods.

The course will focus on topics in the frontier of synthetic biology. This will be guided by updated literatures. Examples of selected topics are:

1. Lipid membrane nanotechnology for synthetic biology
2. Light-driven synthesis: Charging the future
3. Synthesis of terpene compounds and manipulation
4. Applications of silver nano-cluster technology
5. Single molecule fluorescence microscopy and spectroscopy
6. Biophysical analysis for synthetic biology using scattering methods (light, X-ray) and thermal methods (DSC, ITC)
7. Intact Mammalian Cell Function on Semiconductor

Examples of experiments are:

Interface 1: Biology + Chemistry

1. Single molecule fluorescence microscopy
Demonstration of how we can record the emission of a single molecule. Pyrelenemonoimide dyes will be excited with Argon-ion laser and an image will be formed by a piezo scanner on top of an inverted confocal microscope.

2. Application of silver nano-cluster probe
Students will study how DNA fragment forms silver nano-clustering for a very strong fluorescence and possible applications of the DNA/silver nano-cluster probe for the detection of biological materials, e.g. miRNAs, nucleic acid binding proteins.

Interface 2: Biology + Physics

1. Nano-disc assembly
Self-assembly of monodisperse membrane nanoparticles is an extremely useful tool to study membrane proteins in a controlled native-like environment. Students will study how to make nano-disc (protein self assembly) and its biological applications.

2. Biophysical analysis for synthetic biology
a. Scattering methods (eg. Dynamic light scattering (DLS) and Small-angle X-ray scattering (SAXS)) can be used to elucidate the structure and size of biomelocules and bimolecular complexes. Students will study scattering methods using nanodiscs.
b. Thermal methods (eg. Isothermal titration calorimetry (ITC) and Differential Scanning Calorimetry (DSC)) wil be used to study the interaction of biomolecules as well as molecular transition and aggregation properties.

Fundamentals: Core concepts, Definitions.
Tools: Introduction to major experimental tool applied for synthetic biology.
Recent advances and future trends
Industry Applications: Linking theory and business
Ethical Issues: Public concerns and official debate

Learning Outcome

Participants will obtain broad interface insights on the main subject areas of synthetic biology with emphasis on interdisciplinary studies. A wide variety of topics in biotechnology, nano-technology, neuroscience, structure biology and more will have been covered on completion of the course. These insights will develop creativity for the merging to other subjects. By delivering advanced techniques from various disciplines, students will acquire practical skills that can be applied to other research fields. Group collaboration and interdisciplinary communication will be enhanced by the course.

Knowledge
1. The basic concepts and perspectives of synthetic biology, e.g. conventional synthetic biology and newly emerging synthetic biology.
2. Acquire a common vocabulary useful for synthetic biology (e.g. standard part, chassis, etc.).
3. Identify main current focus and hesitations concerning scientific, ethical and regulatory aspects.
4. The prospects of combining biology to engineer and/or technology.
5. Broad insights on coherent knowledge based on interdisciplinary research.
6. Knowledge of the most recent published literature in the field and insight into ongoing research.

Skills
1. Understand foundational tools applied to the engineering of biology.
2. Identify aspects of biotechnology that inhibit and enable the faster, reliable programming of natural systems.
3. Comprehend current and future applications for synthetic biology.
4. Apply fundamental laboratory approaches for engineering biology.
5. Ability to join in combinatorial interdisciplinary research, e.g. communication and knowledge delivery.
6. Structure reports and handle scientific literature in the proper way.

Competence
1. Able to discuss the issues of public concerns and ethical dilemmas and the potential solutions offered by synthetic biology.
2. Able to prepare and present oral and written work.
3. Capability to find a solution for a problem and work independently.
4. Able to apply the concepts and techniques of synthetic biology to other subjects at a high academic level.
5. Able to work efficiently in a collaborative work situation.

Literature

A combination of original research papers, review articles and laboratory manual

Teaching and learning methods
Lecture: Delivery of material in a lecture format (40%) Discussion or Group work (30%) Lab works: Demonstrations, experiments, simulations (30%)
Academic qualifications
The equivalent of a BSc in natural science (biology, biochemistry, biotechnology, chemistry, physics or medical science).
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Exam
Credit7,5 ECTS
Type of assessment
Oral examination, 25 min. (no preparation)
Description of Examination: Individual oral examination based on a group work report, 25min for presentation, discussion and question.

Weight: Oral examination 100%
Exam registration requirements

An approved written report. For the report, a group can select one of the topics of the course and be supervised by the lecturers of relevant topic.

AidAll aids allowed
Marking scale7-point grading scale
Censorship formNo external censorship
Several internal examinators
Re-exam

A report on a given topic need to be handed in 2 weeks before signing up for the re-exam if the requirements is not met.

Reexam as ordinary exam.

Criteria for exam assesment

See learning outcome

Workload
CategoryHours
Lectures40
Theory exercises20
Practical exercises50
Exam0,5
Preparation95,5
Total 206,0
Saved on the 02-12-2016

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