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Printable Handouts
Navigable Slide Index
- Introduction
- Reductionist strategy to characterize mechanisms
- Chose a favorable organism
- Genetic model organisms
- Cell culture methods
- Reductionist strategy to understand mechanisms: Question and inventory
- Strategies for the molecular inventory
- Reductionist strategy to understand mechanisms: Localizing molecules
- Localization of molecules in cells and tissues (1)
- Localization of molecules in cells and tissues (2)
- Optical path through light microscopes
- Producing contrast in light microscopy
- Example staining in light micrographs
- Comparison of methods to produce contrast
- Methods to produce contrast in light microscopy
- Fluorescence
- Optics in a fluorescence microscope
- Sources of fluorescence
- Micrographs of stained cells
- Sources of fluorescence
- Fluorescence miscroscopy of live yeast cells
- Fluorescence microscopy
- Thin optical sections for fluorescence microscopy (1)
- Thin optical sections for fluorescence microscopy (2)
- Localization microscopy
- Reductionist strategy to understand mechanisms: Concentrations and structures
- Structure determination
- X-ray crystallography
- Transmission electron micrograph
- Reductionist strategy to understand mechanisms: Molecular patterns
- Identification of molecular partners
- Yeast two hybrid assays
- Reductionist strategy to understand mechanisms: Rate and constants
- Reductionist strategy to understand mechanisms Process and physiological tests
- Tests of physiological function
- Genome engineering
- RNA-guided DNA cleavage by CRISPR/Cas9
- Genome engineering by CRISPR/Cas9
- Reductionist strategy to understand mechanisms: Simulating models
- Mathematical models
- Reductionist strategy to understand mechanisms: Recap
Topics Covered
- Genetic model organisms
- Light microscopy
- Fluorescence microscopy
- Structure determination
- Identification of molecular partners
- Genome engineering
- Physiological tests
- Mathematical modelling
Talk Citation
Pollard, T.D. (2021, May 30). Introduction to research strategies in cell biology [Video file]. In The Biomedical & Life Sciences Collection, Henry Stewart Talks. Retrieved November 21, 2024, from https://doi.org/10.69645/VSPD8834.Export Citation (RIS)
Publication History
Financial Disclosures
- There are no commercial/financial matters to disclose.
A selection of talks on Cell Biology
Transcript
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0:00
Hello, I'm Tom Pollard from Yale University,
Department of Molecular, Cellular and Developmental Biology.
Today I'm going to discuss how complimentary approaches are
used to understand molecular mechanisms of cellular processes.
0:16
This strategy is called the reductionist strategy.
It starts off by defining a biological question which can come from
clinical medicine or natural history or observations of cells and other organisms.
Once a good biological question is defined.
Then the next question is finding an inventory of parts,
some molecules that operate the system of interest.
Then there are three major types of research that needs to be done
to understand how these parts are used in the biological process.
One is the structural agenda that involves light and electron microscopy,
X-ray crystallography, nuclear magnetic resonance spectroscopy,
and molecular dynamics simulations.
Secondly, there is a bio-chemical agenda.
This is used to establish interactions among the molecules and to
measure the rate constants and equilibrium constants for the reactions.
This research results in hypothesis yet to be
formulated into mathematical models and tested by computer simulations.
Third part of the agenda deals with cells. One needs
to measure the concentrations of the molecules of interest in cells,
document their dynamics in live cells.
Then what one does is take
one's biochemical ideas from the chemical part of this work and
test whether simulations of
these biochemical hypotheses can reproduce and predict cellular behavior,
both in normal cells and perturbed cells.
Usually at this point, the process fails because the models aren't good enough.
One wants to go back and look to see whether parts are missing,
whether the biochemical measurements are good enough.
Then cycle back to the cells to see whether
the mathematical models can reproduce the behavior in the cells.
So on circles around the right-hand side of this diagram,
getting closer and closer to understanding the underlying mechanism.
This approach requires facile genetic editing in
order to make cells that can be used to test the hypotheses.
So we'll come back to how to edit genes later in the talk.