Towards synthetic hierarchical pattern
formation in heterogeneous microbial

Master of Science Thesis
Schaerli Lab UNIL

Visual aid to discuss the scope of the
project with my brother
Synthetic biology is a powerful field emerging from systems
biology, incorporating an engineering mind-set to solve
fundamental questions. Especially when investigating cellular
functions essential for survival, synthetic biology may provide the
tools for deeper insight. By reconstituting the supposed
functionality in a host cell independent of the function, heavy
perturbations and emerging phenotypes may be observed
otherwise inaccessible. This work incorporates different bio-
engineering methods to take the next step in achieving spatial
patterning resembling early Drosophila embryonal development.
The first layer of pattern formation is achieved by an incoherent
feed forward loop exposed to a spatial gradient of a morphogen.
The network processes the primary input and expresses a stripe of
downstream genes at intermediate morphogen concentrations as
output. Building on an analogous three node network for E. coli
previously constructed, I retrofitted multiple versions of sender and
receiver variants to connect a second network layer processing the
output of the primary network. To allow communication but avoid
crosstalk between layers, each network was designed to be
separately transformed and connected through quorum sensing.
The modifications at both the input and output nodes showcase
the challenges and design possibilities when faced with preexisting
network designs. Furthermore, the creation of multiple fluorescent
quorum sensing fusion proteins will allow closer monitoring of
quorum sensing in future projects.

Participatory performance at the trans-disciplinary seminar of ZHDK
Pieces of information regarding the sourcing and creation of the
supposed filling material are placed in the bags which are set on the
As people take the pieces to examine more clearly, they are removed
from the bag, monopolizing a part of the information. Each
participant gains particular insight but looses the whole picture in
the process. This immediately mirrors the global reality of
production. Through social engagement, the information is then
reassembled into a version of meaning.

Trash bags, min. 80% recycled PET
Print paper
Various information from the internet
Imre Banlaki, Njomza Dragusha
Giulia Prone

Single molecule fluorescent mRNA
tagging in C. elegans embryos
Project crash course
To observe dosage compensation of genes in vivo and over time,
single molecule tagging, followed by fluorescence microscopy, is a
neat and possibly well quantifiable approach. Specifically, the
tagging of mRNAs sheds light on the corresponding gene
The issue however is, that a single fluorophore tag is not
sufficiently detectable by our microscopes. To compensate for the
lack of sensitivity, multiple tags per molecule are required. This is
accomplished by recruiting fusion coat proteins borrowed from
RNA viruses that recognize specific RNA stem loops.
We use two stem loop repeats (MS2, PP7) with the corresponding
coat proteins (MCP, PCP) which allows us to either tag two
different genes at once or observe transcription velocity by cloning
one stem loop into the 5’ end and the other at the 3’ end of the
mRNA. If cloned into an intron even splicing events may be
To make sure we tag the correct mRNA, a dCas9 control is used,
where the sgRNA has a protruding MS2 or PP7 stem loop
sequence that is tagged by the marker. Here the dCas9 attaches to
the gene (DNA) itself, but due to a mutation does not induce
double strand breaks, but instead keeps attached for some time to
be imaged.

Explorative Research
Meister Lab UNIBE

Adult C. elegans and its embryos
Con-focal and Spinning Disc fluorescent