Laboratory of Biosystem Dynamics (LBD)

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Laboratory for Single Cell Biology studies

In 2011, we established a Laboratory for Single Cell Biology studies. This laboratory makes use of multiple Molecular Biology techniques, ranging from qPCR, plate reading and western blotting, combined with extensive usage of live time-lapse microscopy. The study of natural and synthetic genes and circuits, via the collection of time-lapse, gene expression data in-house, gives us the ability to test models and to, from the data, propose new models. The lab is also used to boost the development of signal processing methods, such as image analysis, and of models and simulation tools of biological phenomena.

One of the methods most used in our lab is the RNA tagging by MS2-GFP, generously provided by Ido Golding (Baylor College of Medicine). It has allowed us to conduct several studies on transcription dynamics, under various environmental conditions. Based on this system, we have been studying various gene expression related processes in Escherichia coli, among other.

Golding cells
In vivo detection of individual RNA molecules in live E. coli cells by the MS2-GFP RNA tagging system.

The core tool of our lab is the microscope system. It is capable of imaging cells in multiple ways, such as confocal and epifluorescence microscopy, and Phase contrast. The system is fully motorized, thus allowing automatic time-series imaging.

Microscope

We also have a Flow-Cytometer with 2 lasers (488 nm and 561 nm), 6 PMTs, able to gather information on 12 parameters (2 light scatters, 10 fluorescence channels). Using this system, we collect a variety of information from a large amount of cells at a given point in time. The information is both on the fluorescent proteins (or bioluminescence) also detected using microscopy, as well as on biophysical properties of each cell (e.g. cell size, granularity, etc.). We combine this information with that obtained from the microscope.


This lab has allowed us to test novel ideas. For example, we engineered our very own system for creating unique temperature conditions for the cells while under microscope observation. It allows observing cells at temperatures ranging from 5 to 50 C, and to alter it at runtime very rapidly. We used it to study effects of changing temperature on the ability of cells to segregate unwanted aggregates to the poles. This is combined with a system that allows to perfuse cells with fresh or altered media, while under microscope observation.

Low_T system

Additionally, the lab is equipped with several common measurement devices in this research area, such as qPCR, plate reader, spectrophotometer, and western blot, that provide independent methods of validation of the data obtained by microscopy and flow-cytometry, among other. Finally, the lab has all required devices to grow and mantain bacterial cells and perform standard molecular biology techniques.