Experiment
Without experiment there is little theory and in biology this is particularly
so. The complexity of the system; its asymmetries and inhomogeneities
make direct physical observation the absolutely necessary as a precursor
to making any calculations. Further, theories need to be tested. So
we are involved with designing and implementing experiments at all levels.
What follows is general discussion of these four levels. For discussions
of specific projects start from the Research
Page.
Molecular Biology and Genetics of Target Systems
We are ultimately driven by our desire to understand how particular
cells and their regulatory networks function to control the development
and behavior of an organism. We choose organisms based on a number of
criteria ranging from genetic tractability (so we can manipulate the
organism easily) to whether or not they express a model of an important
complex behavior (such as conditional development of an asymmetric cell
division).
Once we have chosen a target system (say comparative analysis of chemotaxis
in E. coli and B. subtilis) we will dig into the literature
to find out everything about these systems and begin to create a quantitative
framework on which to ask questions about these systems. Working withing
this framework invariably leads to questions that have not been addressed
in the current literature. At this point we will generally hook up with
a laboratory expert in the problem area and one or more of us will learn
how to work with the system and do the experiments necessary to fill
in the data needed or to test a specific model hypothesis.
For information on specific projects see the Biosystems
Page.
Biosensors for Concentration, Kinetic and Thermodynamic
Data
The ultimate biosensor is able to measure quantitative kinetics and
thermodynamics of molecular interaction in living single cells. Rarely
is this possible. In the last decade or so, technologies that have come
close are 1) the use of green fluorescent protein to get qualitative
measures of when, where and how much of a particular protein is made
and localized and 2) the use of fluorescent sensing molecules that change
spectrum when bound to an intracellular ion such as calcium. However,
use of these technologies is still a tricky thing and are relatively
low throughput. High throughput techniques, such as DNA chips and microarrays
can measure thousands of RNA and DNA concentrations (semi-quantitatively)
at once, but only if amplified from relatively large populations of
cells that have been killed. Nonetheless, such "molecular profiling"
techniques are the best genome-scale biosensors we have.
RNA transcript levels are very useful, but the correlation between
protein levels and RNA levels is not so good. Further, post-translation
modifications of proteins and small molecules also play a role. Thus,
this laboratory is interested in the development of high-throughput
measurement devices that can create molecular profiles for proteins,
their modifications and metabolites in a population of cells.
We are also interested in the development of cell-based biosensors
(see the next section as well) and devices for measuring cell-cell interactions
as well.
For information on specific projects see the Biosensors
Page.
Design and Implementation of Artificial Genetic
Circuits in Microbes
One of our major theoretical efforts is in understand how cells control
their development. This means developing theories for biological chemistry
could possibly implement switches, pulse generators, oscillators, etc.
and then intersecting this physical set with what is found experimentally
(finding regulatory motifs). When we identify real biological regulatory
network that we think of as a representative of a motif (for example
a futile cycle, see the Theory Page)
we try to understand why the cell implemented the particulars of this
instance. From this we learn how the cell does robust engineering. This
leads us to want to build our own circuitry inside cells to test our
theories for biological robust control circuit design.
Thus, there are three basic reasons we develop intracellular circuitry:
- To test theories of biochemical regulatory circuit design and control
- To use such circuitry to query the state of the cell (reporter constructs)
- To use such circuitry to instrument the cell as an active sensor
of the environment
- To use such circuitry as an way of actively controling the cellular
environment.
For more details see the Biomolecular
Engineering Page.
Large Multidisciplinary Team Projects
We are interested in promoting cross-disciplinary biological research
wherein many laboratories combine efforts to understand the entirety
of a particular biological process or set of processes. For example,
the Alliance for Cellular Signaling (click here
for our pages, click here for the
Alliance website) is combining many different experimental laboratories
collecting data on G-protein coupled signal transduction in B-cell and
cardiomyocytes in order to understand how these pathway are regulated
in healthy and disease cells and how these pathways respond to pharmaceuticals.
They are designing standardized protocols and measurement pipelines
so that all the experiments may be cross-compared. This laboratory in
interested in optimal experimental design for this sort of project,
designing new measurement techniques that aid such projects, perform
experiments on the project systems, and most central to our research,
develop the data and analysis infrastructure for this sort of data.
The figure below is the data analysis workflow we envision for such
efforts.
Readings in Central Biology
Biology
These are mostly the central textbook for Biology
| Title |
Authors |
Link |
| Genes VII |
Benjamin Lewin |
[amazon] |
| Molecular Biology of the Cell |
Bruce Alberts (Editor), Bray Alberts |
[amazon] |
| Gene Structure and Transcription (In Focus Series)
|
Trevor Beebee, J. Burke |
[amazon] |
| Protein Biosynthesis (In Focus Series) |
H. R. V. ARNSTEIN and R. A. COX |
[oxford] |
| Protein Structure (In Focus Series) |
N. J. DARBY and T. E. CREIGHTON, |
[oxford] |
| Regulation of Enzyme Activity (In Focus Series) |
J. H. OTTAWAY |
[oxford] |
| The Machinery of Life |
David S. Goodsell |
[amazon] |
Biosensors
These are mostly the central textbook for Biology
