The Center for Nanoscience and Nanotechnology

Nathalie Questembert-Balaban

The Racah Institute of Physics
Faculty of Science
The Hebrew University, Jerusalem 91904, Israel
Tel: +972-2-6585400; Fax: +972-2-6585474
E-mail: nathalieqb@phys.huji.ac.il

Website: www.phys.huji.ac.il/bio_physics/nathalie/#1

Noise in Biological Systems

Biological systems are notoriously complex. Each gene interacts with a multitude of components in the cell. Biological physics' goal is to find new ways to deal with this complexity. We focus on extracting meaningful information on different biological systems by quantitative studies on the variability in those systems. Our aim is to develop an experimental and theoretical framework for the variation in populations of genetically identical single cells. For this purpose, we have developed new devices, based on soft lithography technology, in which single cells can be trapped and studied while controlling the environmental conditions (Fig. 1). Soft lithography relies on micro- and nano- lithography for the patterning of a soft biocompatible transparent polymer. Very narrow channels can be designed to trap single cells and study them down to the molecular level. These devices are then placed under automated microscopy observation and the variability of the biological system quantified. In order to understand the mechanisms responsible for the observed variability, we develop simple mathematical models and compare them with our experimental results. This approach has lead to the inditification of new developmental steps in bacteria (Fig. 2), as well as on quantitative data on the importance of variability on the interaction between bacteria and phage-particles. We now extended our techniques and approach to study the source of variability in the response of single cancer cells to treatment (Fig.3).

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Fig. 1: Single persister bacteria observed in a microfluidic device. Top: schematic layout of the microfluidic device. Bottom: Typical experiment where single E.coli bacteria are observed before, during and after an antibiotic treatment. The red arrow points to the location of a persister bacterium. It can be seen that it was not growing before the exposure to antibiotics.

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Fig. 2 : Automated quantitative analysis of single-cell induction curves
(a-d) High magnification microscopy of single bacteria. Simultaneous pictures of the same field of view. (a) Phase contrast. (b) YFP fluorescence (here shown in green) (c) mCherry induced fluorescence. (d) Automatic detection and tracking of the fluorescent bacteria in pseudo-colors. Each new cell is assigned an arbitrary color by the detection algorithm. Bar: 5 micrometers

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Fig. 3: Observing cancer cells growth and division process. Cancerous cells were engineered to express different colours of fluorescent proteins depending on their position in the cell-cycle. Cells turn on the red fluorescence at the beginning of the cell cycle (G1) and switch to green at the onset of S-phase. These markers allow us to follow both cell-cycle progression and response to anti-cancer agents at the single cells levels.

Specific research topics related to Nanoscience and Nanotechnology:

Design and fabrication of novel microfluidic devices for analysis of single cells.
Automated analysis system for single bacteria characterization
Quantification of the response of single cancer cells to drugs in microfluidic devices
Mathematical analysis of noise

List of publications in Nanoscience and Nanotechnology (2011-2012)

Friedman O, Goldberg A, & Balaban NQ (2012) Whack-an-E.coli with the morbidostat. Genome Biology.
Balaban NQ (2011) Persistence: mechanisms for triggering and enhancing phenotypic variability. Curr Opin Genet Dev 21(6):768-775.

Five most significant publications:

Balaban, N.Q., U.S. Schwarz, D. Riveline, P. Goichberg, G. Tzur, I. Sabanay, D. Mahalu, S. Safran, A. Bershadsky, L. Addadi, and B. Geiger, Force and focal adhesion assembly: a close relationship studied using elastic micropatterned substrates. Nat Cell Biology, 2001. 3(5): p. 466-472
Balaban, N.Q., J. Merrin, R. Chait , L. Kowalik, and S. Leibler, Bacterial persistence as a phenotypic switch. Science, 2004. 305(5690): p. 1622-1625.
Gefen, O., Gabay, C., Mumcuoglu, M., Engel, G., & Balaban, N. Q. (2008) Single-cell protein induction dynamics reveals a period of vulnerability to antibiotics in persister bacteria Proc Natl Acad Sci U S A 105, 6145-6149.
Rotem, E., Loinger, A., Ronin, I., Levin-Reisman, I., Shoresh, N., Biham, O., and Balaban N.Q., (2010) Regulation of phenotypic variability by a threshold based mechanism underlies bacterial persistence PNAS 107 , 12541-12546
Levin-Reisman, I., Gefen, O. Fridman, O., Ronin, I., Shwa, D., Seftel, H., and Balaban, N. Q., (2010) Automated imaging using ScanLag reveals previously undetectable growth phenotypes Nature Methods epub Aug. 1

Distinctions and awards:

2009 Krill Prize for Excellence in Science from the Wolf Foundation

Cooperation with other universities in Israel:

Within Hebrew University:

Prof. Oded Agam, Racah Institute of Physics.
Prof. Ofer Biham, Racah Institute of Physics.
Prof. Gadi Glaser, Hassasah Medical School.
Dr. Itamar Simon, Hadassah Medical School.

Research grants:

2010-2015: European Research Council ERC Consolidator Starting Grant.
2010-2014: Israel Science Foundation
2011-2013: Ministry of Health

Students, postdocs and researchers (include those graduated in 2009-2010):

Staff scientist: Irine Ronin
Post Doc: Orit Gefen.
Ph.D. students: Eitan Rotem, Ofer Fridman, Sivan Pearl, Irit Levin-Reisman.
M.Sc students: Amir Goldberg, Noga Weiss