Archive for November, 2008

Classic papers on signaling and aggregation of amoebae

Over the next few months/years I’d like to use this website to build up a repository of information on the various topics that we study in the lab. Today as a beginning I am introducing 4 classic papers that pioneered a system-level description and quantitative understanding of this spectacular phenomenon:

Video not available

In this movie roughly 200 starved amoebae of the species Dictyostelium discoideum are shown over 8 hours during which they find each other and culminate in a cellular slime mould. This process is seen as a survival strategy because individual amoebae would die under starvation whereas as in the multi-cellular organism 80% of the cells can survive as spores. (more…)

Lab Drawings Finished

The drawings for the new lab are finally done.

Here is a sneak preview:


About the tools we use

For starters, some images:

Laser Scanning Two-Photon Microscope

Laser Scanning Two-Photon Microscope

Detail of a custom built Two-Photon Microscope

Illustration of custom-built two-photon microscope with trans- and epi-detection (also note embryo in special holder).

Illustration of custom-built two-photon microscope with trans- and epi-detection (also note embryo in special holder).

Can we fit all of the data?

W. Bialek, T. Gregor, D.W. Tank, E.F. Wieschaus, Cell 132, 17-18 (2008).

Shape and function of the Bicoid morphogen gradient in dipteran species with different sized embryos.

T. Gregor, A. P. McGregor, E. F. Wieschaus, Dev. Biol. 316, 350-358 (2008).

The role of input noise in transcriptional regulation.

G. Tkačik, T. Gregor, W. Bialek, PLoS One 3, e2774 (2008).


Probing the limits to positional information.

T. Gregor, E. F. Wieschaus, D. W. Tank, W. Bialek, Cell 130, 153-164 (2007).


Stability and nuclear dynamics of the Bicoid morphogen gradient.

T. Gregor, E. F. Wieschaus, A. P. McGregor, W. Bialek, D. W. Tank, Cell 130, 141-152 (2007).


Diffusion and scaling during early embryonic pattern formation.

T. Gregor, W. Bialek, R. R. deRuyter van Steveninck, D. W. Tank, E. F. Wieschaus, PNAS 102, 18403-18407 (2005).


Minimization of the potential energy surface of Lennard-Jones clusters by quantum optimization

T. Gregor and R. Car, Chem. Phys. Lett. 412, 125-130 (2005).


A comparison of methods for the calculation of NMR chemical shifts

T. Gregor, F. Mauri and R. Car, J. Chem. Phys. 111, 1815-1822 (1999).


Lab construction underway

The new lab is being built on the first floor of Jadwin Hall. During my last campus visit mid-October it looked like this:

Let’s hope for the best!

Introducing a new biophysics laboratory in Princeton’s physics department

Starting February 2009 I will join the Physics Department at Princeton as a new faculty member. I will also be associate faculty of the Lewis-Sigler Institute for Integrative Genomics and of the Molecular Biology Department.

I will teach classes both for the Physics Department and for the Lewis-Sigler Institute. My research is highly interdisciplinary, and my hope is to work closely with students from many science departments across campus, mainly physics, biology, computer science, engineering and applied mathematics.

The research focus of the lab is at the interface of biological physics and systems biology. In particular, understanding embryonic development from the perspective of a physicist that views this highly complex process as a self-assembly problem: How do the different parts and ingredients that originate as a single cell work together to develop into a fully-functioning living animal?

This process of biological self-assembly I am also trying to tackle by looking at the emergence of collective behavior in starved amoebae populations. Here, originally autonomous amoebae display a survival strategy in the face of starvation that leads to a multi-cellular organism that produces spores. This system is very accessible experimentally to understand cell signaling, early stages of cell differentiation and pattern formation and the emergence of collective behavior that leads to multicellularity.

Our research will be mainly experimental, but with a strong theoretical influence, both within the lab and in close collaborations with theorists on campus and elsewhere. On the experimental side the goal is to watch life unfolds, i.e. in vivo measurements and manipulations. We build state-of-the-art microscopes and microfluidics devices, and we make heavy use of tools from molecular biology and genetics. On the theoretical side we design analytical and numerical models both to test and guide our experiments, and we take advantage of tools from computer science to analyze images and large data sets.

A new laboratory is under construction at the moment in 125 Jadwin Hall, the first floor of the physics building next to the stadium. My office will be located on the same floor.