A NOVEL METHOD FOR ACCELERATED CELL FACTORY
DEVELOPMENT AND INVESTIGATION OF ANTIBIOTIC RESISTANCE
-Master’s thesis or project at the Novo Nordisk Foundation Center for Biosustainability in
collaboration with Harvard University
The main goal of the project is to develop and apply a novel method for developing cell factories.
In collaboration with the George Church Lab at Harvard University we have established a proofof-concept for the method, which enables rapid and efficient genetic engineering at many
genomic sites of an organism to develop cell factories. This means that we can modify or
knockout whole pathways in bacteria instead of using time consuming traditional techniques. The
technique includes synthesis of several 1000’s of DNA oligos from DNA microchips, and using the
oligos to engineer genes with the novel and cool method MAGE. We are currently focused on E.
coli, but it is our goal to proceed to mammalian and stem cells at later stages of development. It is
the plan to publish high-impact articles in each project, some in collaboration with the researchers
at Harvard.
Project A: Introducing antibiotic resistance by 170 targeted chromosomal changes – a
proof of concept
As a proof of concept for the novel technique, we have modified 170 ribosome binding sites
upstream of genes encoding transcription factors, to identify how these genes affect antibiotic
resistance. The study is both interesting in itself, for the identification of novel genes related to
antibiotic resistance, and as a proof-of concept for the method. We have identified several
resistant mutants, some with several modifications, and the next step is to investigate the role of
the mutations in conferring resistance.
Project B: Accelerated cell factory optimization with massive targeted mutagenesis
The objective of this project is to apply the novel method to develop and optimize valuable cell
factories. We will order a custom-made inkjet printed DNA microchip by a process invented by our
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collaborator Sriram Kosuri . The microchip will contain DNA oligos targetting many E. coli genes
in several ways to 1) optimize cell factories for increased production and tolerance 2) investigate
genes related to resistance and 3) possibly other targets which could be influenced by your
interests. Your project would include the design of novel and efficient oligos for the new chip,
followed by its use in a series of experiments to develop the cell factory.
Project C: Accelerated cell factory development – combination of multiplex targeted
genome modification and a novel selection system
We are in the process of patenting a novel selection system, and therefore it cannot be described
in greater detail here. The project will combine the newly invented method described above with
the novel selection system, with the goal of developing and optimizing cell factories at a game
changing faster pace. If successful, this project will have a huge impact on the development
process of novel cell factories for e.g. medicine production.
Project D: Design of a novel inkjet printed DNA microchip architecture by applying
bioinformatics
We are planning to design a new logic for the DNA microchips, allowing subpools of
oligonucleotides to be extracted individually. This project focuses on the use of bioinformatics for
development of a DNA-chip design tool that will be used to generate microchips based on input
data of which oligos are desired. It is the vision that this tool will be widely used to design novel
smarter DNA chips, with oligos that e.g. target specific genes.
Project A, B and C includes a lot of lab-work, where project D mainly requires bioinformatics and
programming skills –however the projects can be tweaked to balance your interests of
experimental work with data analysis and bioinformatics. Combinations of projects might be
possible.
In the project, you have the possibility to work with
An exciting, high impact project with good publication possibilities
Cutting-edge molecular biology techniques including Next-generation sequencing, DNA
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synthesis from microchips, MAGE (developed by our collaborator Harris Wang )
Brand new equipment in a modern lab with good resources
Engaged supervisors and colleagues with focus on your professional development
Phd. student Mads Tvillinggaard Bonde (CV) is leading the project, supervised by Professor
Morten Sommer (Research group page).
Your role in the project
I believe that skilled students can contribute significantly to and perform real research, and I like
to spend the needed time to instruct and collaborate. As a student you will be an integral part of
the research group, regularly presenting at group meetings and with your own desk in our shared
post-doc/PhD-office.
Study abroad?
The project is in collaboration with Harvard University, and if you are interested in studying
abroad at Harvard or another interesting university, this could most likely be part of the project.
The Novo Nordisk Foundation Center for Biosustainability
The center has received 950 mio DKK to develop novel cell factories for production of tomorrow’s
medicine and chemicals. It is the ambition to be one of the best centers in the world within the
field and there are collaborations with the best universities in the world. The working environment
is extremely international and motivating.
When can I start and what is the time frame of the projects?
Projects can start immediately this fall semester or the spring 2013 semester. I highly recommend
performing projects spanning at least 1 year but don’t hesitate to contact me if you are interested
in a shorter timeframe.
Required skills
The most important is that you are ambitious, engaged and interested in learning fast by
performing real research. Lab experience is not a requirement, but of course positive.
Contact
If you are interested and/or would like more information, please contact Mads at [email protected]
You are welcome to send information about yourself such as CV.
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Kosuri, S., Eroshenko, N., Leproust, E. M., Super, M., Way, J., Li, J. B., & Church, G. M. (2010).
Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips.
Nature biotechnology, 28(12), 1295-9. doi:10.1038/nbt.1716
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Wang, H. H., Isaacs, F. J., Carr, P. A., Sun, Z. Z., Xu, G., Forest, C. R., & Church, G. M. (2009).
Programming cells by multiplex genome engineering and accelerated evolution. Nature, 460(7257),
894-8. Nature Publishing Group. doi:10.1038/nature08187