University of Minnesota
School of Physics & Astronomy

Spotlight

Synthetic Biology

Filippo Caschera
Filippo Caschera
                                                       

Filippo Caschera is a Research Associate working on synthetic biology with Professor Vincent Noireaux. Synthetic biology is a multidisciplinary field that combines physics, biology and chemistry. Caschera has a Ph.D. in chemistry, but has always worked in physics because he likes the approach. ‘We build things from the bottom up, like legos, using pieces to build a system that will evolve. We are building to understand.”

The goal of Caschera’s work is to create a life-like system that can replicate itself. The hope is to create an artificial cell that can mimic Darwinian evolution using a process like natural selection. The artificial cells that the Noireaux lab has built have life-like components such as metabolism. To mimic metabolism, they take pieces from a real cell and reassemble them to control the properties. First they crack open the cell, take cytoplasm, and use it to determine the metabolic pathways. They then add other molecules, such as enzymes to try to design a new module that can be exploited to form the energy needed for self-maintenance of the cell.

Noireaux’s lab has developed a cell-free expression system based on endogenous RNA polymerase, a self-expressing system that contains the necessary molecular machines to build a complex gene circuit. With a complex gene circuit they no longer need to rely on something that exists within the cell. They can go to the computer, and program a sequence of DNA for the gene of interest and put it in the cellular extract that they have developed. Caschera says the biggest achievement of Noireaux’s lab has been to regulate and design new circuits.

One new experimental avenue has been to express complex gene circuits in a lipid vesicle. A lipid vesicle is the boundary material that makes up most cells. This makes it an ideal container in which to experiment. Previously the lab used dynamic oil droplets as the medium to contain their samples. However, the lipid vesicle has the advantage of mimicking the condition of an organic cell. They reproduce this cell boundary through the self-assembly properties of lipids to form the vesicle.

Another direction of the work is to induce division of the vesicle, which is important for evolution of the artificial cell. If there is division they can be applied the population. Division is always driven by a DNA program that encodes for the proteins needed for the self-assembly of the cytoskeleton. The division is encoded in the DNA program, which is expressed through the cellular extract that synthesizes those proteins that self-assemble and drive the division of the vesicles, through the cytoskeleton.

Caschera says that the next level will be to optimize their cell-free expression system to be more efficient. They have created a “fitness landscape”, a term which describes all the interactions in a complex system and assess them in order to find the best combinations. The exploitation of computer modeling will drive the discovery of optimal interactions in the experimental space of combinations. To further automate the process, the group will eventually use a machine learning approach based on liquid handling robotic workstation to efficiently assemble the modules of the artificial cell.