Parts characterization: Difference between revisions

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#What are the current available methods for characterization of parts?
#What are the current available methods for characterization of parts?
#Which characterization methods are particularly relevant to certain parts?
#Which characterization methods are particularly relevant to certain parts?
#How can we ensure that these methods can easily be applied in a standardized way across labs?
#How can we ensure that these methods can easily be applied in a standardized way across labs? i.e. how do we make the information produced by an experiment be independent of the particular experiment?
#What information does each characterization method provide about a part?
#What information does each characterization method provide about a part?
#Are standard operating conditions important?
#Are standard operating conditions important?
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==Meetings==
==Meetings==


'''Based on earlier voting, the parts characterization meeting will be on Wednesday, Oct 26, 2005 at 1pm in 68-474.'''
===Wednesday, Oct 26, 2005 at 1pm in 68-474===


'''I can attend'''
====Attending====


*[[Austin Che | Austin]]
*[[Austin Che | Austin]]
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*[[Reshma Shetty | RS]]
*[[Reshma Shetty | RS]]
*[[Caitlin Conboy|cmc]]
*[[Caitlin Conboy|cmc]]
*[[User:Jkm|JM]]
*[[Samantha Sutton|Samarita]]
*[[Samantha Sutton|Samarita]]
*[[Jason Kelly|JK]]
*[[Jason Kelly|JK]]
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*[[User:Randy|Randy]]
*[[User:Randy|Randy]]
*[[Meagan Lizarazo|Meagan]]
*[[Meagan Lizarazo|Meagan]]
*[[Tom Knight | Tom]]
*[[Alex Mallet | Alex]]


'''I would like to attend but can't make it, please reschedule'''
====Notes====
 
'''Short term to do list'''
#F plasmids - [[Reshma Shetty | Reshma]]
#Antibiotic resistance cassettes - [[Tom Knight | Tom]]
#Terminators - [[Jason Kelly | Jason]]
#FCS - [[Caitlin Conboy|Caitlin]] and [[Reshma Shetty | Reshma]]
#pheS (PCR or synthesize) - [[Tom Knight | Tom]]


==Substrate for discussion==
==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.
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==
*[[Parts characterization/Measurement techniques]]
When is measuring the aggregate behavior or population average behavior sufficient?
*[[Parts characterization/Characterization approaches]]
*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====
*[[MIT Flow Cytometer Core Facility | 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...


====RNA====
==Notes==
*[[Endy: Journal Club: Le et al 2005]]
*[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15277674&query_hl=3 Ido Golding approach]


====Protein====
*[[Standard E. coli Strain for BioBricks]]
*[http://www.biophysics.org/education/schwille.pdf Fluorescence correlation spectroscopy]
*[[Synthetic Biology:Vectors | Vectors for Synthetic Biology]]
*[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15790856&query_hl=1 Michael Elowitz approach]
*[[Bacterial artificial chromosomes]]

Latest revision as of 15:25, 3 January 2006

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

  1. What are the current available methods for characterization of parts?
  2. Which characterization methods are particularly relevant to certain parts?
  3. How can we ensure that these methods can easily be applied in a standardized way across labs? i.e. how do we make the information produced by an experiment be independent of the particular experiment?
  4. What information does each characterization method provide about a part?
  5. Are standard operating conditions important?
  6. When is the characterization of a part finished? i.e. What would a characterization standard look like?

Meetings

Wednesday, Oct 26, 2005 at 1pm in 68-474

Attending

Notes

Short term to do list

  1. F plasmids - Reshma
  2. Antibiotic resistance cassettes - Tom
  3. Terminators - Jason
  4. FCS - Caitlin and Reshma
  5. pheS (PCR or synthesize) - Tom

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.

Notes