Parts characterization
Characterization of standard biological parts is an essential step in enabling construction of more complicated devices and systems based on these parts. A standard method of characterization (or several standards) will better enable sharing of parts between different laboratories, as well as improve our ability to design devices.
Discussion Topics
- What are the current available methods for characterization of parts?
- Which characterization methods are particularly relevant to certain parts?
- How can we ensure that these methods can be applied in a standardized way across labs?
- What information does each characterization method provide about a part?
- Are standard operating conditions important?
- When is the characterization of a part finished? i.e. What would a characterization standard look like?
Meetings
Based on the voting below, the parts characterization will be on Wednesday, Oct 26, 2005 at 1pm in 68-474.
Proposed meeting on Wednesday Oct 26, 2005
5pm-6pm
Location 68-574.
See the discussion topics above for substrate for the meeting. Feel free to annotate/add to them.
I can attend
I would like to attend but can't make it, please reschedule
- Austin (1-2pm on this day would work for me, 5pm on any other day of this week would also work)
- cmc, I will be ~40 min late... if we had the mtg at 5 pm.
- AL That week I can make only Friday. I can make most times week after that.
Alternate meeting time Wednesday Oct 26, 2005
1-2pm
Location 68-474
I can attend
I would like to attend but can't make it, please reschedule
Substrate for discussion
This is an attempt to organize some of the available characterization methodologies as well as the type of information that they generate. It might help us formulate the beginnings of a characterization standard(s). Feel free to edit and revise since this is very preliminary and likely has errors and is missing useful techniques.
Population average measurements
When is measuring the aggregate behavior or population average behavior sufficient?
- We only care about the behavior of the majority of cells?
- single population
- can offer time dependent behavior (via the plate reader)
DNA
- Plasmid copy number measurements (Caitlin and Jen)
RNA
- Northerns (Caitlin)
- RT-PCR (Heather)
Proteins
- Quantitative westerns (Jen)
- Plate reader (Barry)
Population distributions
When do you care about the population distributions of a large number of cells?
- multiple populations
- want to examine 1000s of cells rather than 10s or 100s
- only need static behavior (you can do a time course, but it is somewhat painful)
DNA
- Can you stain DNA with DAPI or something else and characterize DNA content in living E. coli cells? Plasmid copy number?
RNA
both of these methods require intensive method development
- merge reporters from single cells measurements with flow cytometry
- develop a high throughput microscopy version of one of the single cell techniques below
Proteins
- Flow Cytometry using a fluorescent protein
Single cell measurements
When do we want to know the behavior in a single cell?
- stochastic effects are important
- single molecule resolution
- dynamic behavior (want time resolved behavior of each cell lineage)
DNA
- how do you measure the plasmid copy number in a single cell?
- Perhaps you could use FCS with a DNA binding protein specific to your plasmid, conjugated to GFP. This would require a lot of work on the method...
