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Synthetic Biology 2

Module PH2235

This module handbook serves to describe contents, learning outcome, methods and examination type as well as linking to current dates for courses and module examination in the respective sections.

Module version of SS 2018 (current)

There are historic module descriptions of this module. A module description is valid until replaced by a newer one.

available module versions
SS 2018SS 2016

Basic Information

PH2235 is a semester module in German or English language at Master’s level which is offered in winter semester.

This Module is included in the following catalogues within the study programs in physics.

  • Specific catalogue of special courses for Biophysics
  • Elective Modules Natural Sciences in the Master Program Matter to Life
  • Complementary catalogue of special courses for condensed matter physics
  • Complementary catalogue of special courses for nuclear, particle, and astrophysics
  • Complementary catalogue of special courses for Applied and Engineering Physics

If not stated otherwise for export to a non-physics program the student workload is given in the following table.

Total workloadContact hoursCredits (ECTS)
150 h 30 h 5 CP

Responsible coordinator of the module PH2235 is Friedrich Simmel.

Content, Learning Outcome and Preconditions

Content

In contrast to the first part, the lecture Synthetic Biology deals with special topics, in particular with recent technological developments, which are used in synthetic biology.

These include:

- Gene assembly & gene editing

- Microfluidics (single-cell studies in microfluidics, droplet microfluidics for screening)

- Sequencing, especially Next Generation Sequencing

- RNA-based synthetic biology

- Metabolic engineering

Learning Outcome

After successfully completion of the module, students have knowledge of:

     1. the physical fundamentals of microfluidic systems
     2. about modern methods of gene and genome engineering
     3. the experimental and theoretical foundations of Next GEneration Sequencing methods
     4. modern genetic procedures, in particular CRISPR
     5. principles of metabolic engineering and associated analysis methods (flux balance analysis, etc)

     and the application of appropriate procedures in synthetic biology.

In addition, students are able to understand and use appropriate computational tools.

Preconditions

Background knowledge in biophysics / biochemistry / molecular biology is desirable, also the previous attendance of the lecture Synthetic Biology 1 would be helpful.

Courses, Learning and Teaching Methods and Literature

Courses and Schedule

TypeSWSTitleLecturer(s)Dates
VO 2 Synthetic Biology 2 Simmel, F. Thu, 10:00–12:00, ZNN 2.003

Learning and Teaching Methods

The contents will be presented by lecture, media/powerpoint presentation and occasional work on the blackboard.

The lecture introduces basic concepts and discusses them scientifically using a variety of examples from current research. The students should try to understand and penetrate these examples in moredetail at home. Here, the students should actively apply the contents of the lecture,

In addition, the students will use corresponding textbooks (or sections in the textbooks) as well as special literature to deepen the knowledge necessary for the contents of the lecture.

Media

Transparencies, additional literature, online tools for biophysics/synthetic biology. Literature will be provided via moodle.

Literature

Milo & Phillips, Biology by the Numbers (Garland Science)

Phillips, Kondev, Theriot, Garcia, Physical Biology of the Cell (Garland Science)

Uri Alon, Systems Biology (Chapman & Hall)

Alberts, Molecular Biology of the Cell (Garland Science)

Strogatz, Nonlinear Dynamics and Chaos (Westview Press)

Module Exam

Description of exams and course work

There will be an oral exam of 25 minutes duration. Therein the achievement of the competencies given in section learning outcome is tested exemplarily at least to the given cognition level using comprehension questions and sample calculations.

For example an assignment in the exam might be:

  • Explain classical, Gibson & golden gate cloning.
  • Explain CRISPR/Cas9 gene editing and other applications of CRISPR systems.
  • Generation of droplets in microfluidics (capillary number, interfacial and viscous tension).
  • Explain one of the modern (next generation) sequencing techniques.
  • Explain general concept of metabolic control analysis.
  • Discuss in vivo sensing/computing with RNA molecules.
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