Our ongoing research concerns the relationship between growth, cell cycle, cell size control, and cell death in bacteria. This is the field that has generated some of the most fundamental, unsolved questions in biology, and we as a multidisciplinary team are actively working to solve them. We are currently working on three organisms: E. coli, B. subtilis, and cyanobacteria. Our collaborators include Susan Golden (UCSD) and Petra Levin (Washington University, St Louis), Andrew Wright (Tufts Medical School). There are active interactions and joint weekly group meetings with the group of Terry Hwa (UCSD) and Massimo Vergassola (UCSD).
Those who want to join the team may wish to read our first paper:
Every now and then, we start doing "A" and find interesting "B's". One of these “B” questions is the relationship between growth and cell shape in bacteria. This project was born as a summer research project for two undergrad students and one high-school student in 2009. Their pioneering fun work has been (completed by senior researchers and) published here:
Bending stresses plastically deform growing bacterial cell walls
Ariel Amir, Farinaz Babaeipour, Dustin McIntosh, David Nelson, and Suckjoon Jun
Proc. Nat. Acad. Sci. USA (Early Edition, 2014)
[open access full article]
We understand “from A to B” is the nature of making unexpected, exciting discoveries, and we are always open to such possibilities.
Our lab has long been working on chromosome organization and segregation in bacteria. Some of the lessons we have learned in the past ten years can be found below. Our focus is shifting towards understanding the extent to which the basic physical mechanisms underlying the bacterial chromosomes are relevant in higher eukaryotes.
Some of our collaborators include Stuart Austin (NCI/NIH), Jean-Yves Bouet (CNRS, Toulous), Bae-Yeun Ha (Univ. Waterloo), Sue Lovett (Brandeis), Kees Murre (UCSD), Conrad Woldringh (Univ. Amsterdam).
For background information, read the following three papers:
James Pelletier, Ken Halvorsen, Bae-Yeun Ha, Raffaella Paparcone, Steven Sandler, Conrad Woldringh, Wesley Wong, and Suckjoon Jun
Physical manipulation of the bacterial chromosome reveals its soft nature
PNAS Plus 109(40), E2649-E2656, 2012.
[open access full article] [PNAS highlight] [Nature Methods highlight]
The multifork Escherichia coli chromosome is a self-duplicating and self-segregating thermodynamic ring polymer
Brenda Youngren, Henrik Jork Nielsen, Suckjoon Jun, and Stuart Austin.
Genes & Development 28:71-84, 2014
[open access full article]
Notes on "entropy":
In Movie 1 below we show a simple molecular dynamics simulation, where two species of particles are initially separated by a wall in a rectangular box. As we remove the wall from the box, the two species of particles mix. The driving force of this process is the well-known "entropy of mixing."
Movie 1. Mixing of particles
Entropy, however, is more subtle than a simple measure of disorder. To see this, let's consider a mixed state of the particles and connect those particles of the same species to create two long linear chains, one painted with blue and the other with red. Importantly, the chains cannot cross each other. The reader is encouraged to perform this simple computer simulation (Movie 2 below), and s/he will see a "miracle" -- the two chains demix, that "order" emerges out of disorder.
Movie 2. Segregation of chains
While the real cell is much more complex, this emergence of order from disorder due to chain-connectivity and excluded-volume interactions is our starting point for understanding chromosome organization and segregation from early life to bacteria and eukaryotes.