Endy:Measkit draft

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Revision as of 13:52, 12 August 2008 by Endy (talk | contribs) (Example 1. Gel Electrophoresis.)
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Ideas, Issues, & Questions Related to Measuring the Activity of a Promoter

  • PoPS, polymerase per second, is a derivative unit based on the SI base units of Mole and Second. PoPS represents the number of polymerase molecules that pass any specific position on a nucleic acid per unit time.
    • Q. Is derivative the right word? Compound feels like a better word. See here.
    • Jason R. Kelly 12:38, 12 August 2008 (EDT): yeah, not clear. Seems like it is pretty much equivalent to the katal (catalytic activity, mol/s) which is a derivative unit. I couldn't find any info about the bar to clear for being a derivative unit. it may actually mean it's been officially "cleared" by some official SI body, so we might not want to just use it w/o looking into it more.
      • I think that derivative units are simply officially named compound units, so we want to use the word compound not derivative.
      • I do not believe that you are correct about the katal. That is a really weird unit, having to do with the amount of a catalyst needed to carry out a reaction.
        • Jason R. Kelly:Agreed. Wasn't proposing a PoPS replacement, sounds like we should go with compound.
  • We are proposing that a relative measurement of promoter activity may be useful for reducing variation (across conditions and settings) in the observed absolute activity of promoters. In practical terms we are proposing that the activity of BBa_J23101 be used as a physical reference standard to which the activity of other promoters may be compared. Instead of measuring the absolute activity of a promoter in PoPS, the activity of the to-be-measured promoter and BBa_J23101 are both measured under the same conditions and a unitless ratio is taken (i.e., PoPS/PoPS []= unitless).
    • Q. What should the resulting, unitless number be called, if anything? Standard Promoter Units, SPUs? Or...
      • This specific question has been tricky to resolve. It may be useful (or dangerous) to make comparisons to other types of measurements, and to identify and discuss the issues which led to their success. Here goes...
    • 'Jason R. Kelly 12:43, 12 August 2008 (EDT):The term "absolute" may make things more confusing. All SI measurements are relative, for example the mol and second from which PoPS (the unit of promoter activity) is derived are relative measurements. So I worry about framing the discussion as absolute vs. relative.
      • OK. So, relative is a valid and safe word but we a replacement for absolute. How about physical or molecular?

Example 1. Gel Electrophoresis.

  • Slab gel electrophoresis (PMID 11116182) is now used routinely to separate and estimate the mass or length of proteins, RNA, and DNA. Molecules within samples are separated in space and then observed. Typically, the absolute distance that a molecule travels through a gel is not directly converted to the size of the molecule (with apologies to equipment that allows for direct model-based estimation of length or mass from distance traveled, run time length, or some other observable). Instead, reference standards of known length or mass are used, the distance traveled by both the sample and reference are measured and compared, allowing for a relative measure to be made (thereby accounting for differences in experimental conditions). However, since the length or mass of the reference standard is previously known the relative measure can be converted to an absolute measure of the sample such as base pairs or Daltons.
    • There is an important difference between the activity of a promoter and the length of a fragment of DNA. The actual distance that a fragment of DNA travels on a gel may vary from one experiment to the next but the absolute underlying length of the DNA molecule being characterized does not change. In contrast, the reported absolute activity of a promoter (as measured in PoPS) may vary greatly across experimental conditions, and such variation may reflect true changes in the underlying activity of the promoter.
      • Jason R. Kelly 14:31, 12 August 2008 (EDT): I'm going to restate this to make sure I have it right / clarify a little. The length of DNA in meters might change / length it runs on a gel might change in different conditions, however the number of base pairs doesn't change. This could be equivalently described as the number of atoms in an object being measured for length doesn't change depending on conditions (say temperature), however the length of the object changes at different temperatures as a function of the coefficient expansion for the material it is made of. In this case length (a property that changed as a function of measurement conditions) was preferred over atoms (a property that remained constant but was difficult/impossible to measure). In the case of DNA we could measure an unchanging "intrinsic" characteristic of the object (base pairs) so we went with that.
        • I find your text right above to be incredibly difficult to read and understand. Could you please edit?
    • Another point to ponder is that folks are familiar with (i.e., prefer to have knowledge of / use) the absolute length of DNA. 'Back in the day,' researchers didn't define the smallest band from a HindIII lambda DNA digest to have units of 1.0 "NEB" and then report everything in units of NEBs. Will gene expression engineers prefer to have promoter activity described in some reference term (i.e., relative to 1.0 standard promoter units, or SPUs)? Or, will absolute molecular activity defined in terms of well-defined base units be preferred (i.e., PoPS)?
      • Jason R. Kelly:Agree with this. Basepairs had value in that they fit into a "framework for understanding biology" that for instance DNA length as measured in meters wouldn't have fit into as easily. Seems like you would rather have promoter activity in terms of PoPS, but here's that "technical" reference on the Ohm I promised I would dig up that talks about defining the Ohm as a relative unit equivalent to a physical object (e.g. a "NEB"): First 10 pages of this (Reports of the Committee on Electrical Standards Appointed by the British Association for the Advancement of Science - Jenkin, Kelvin, Joule, Maxwell).
        • I'll start by noting that you don't actually state a conclusion or make a point here, you instead ask me to read a reference. Now having re-read this reference here are some questions:
          • Q1. Was the exact value of the Ohm defined under standard conditions of measurement (e.g., as was the prototypical meter)?
          • Q2. Is it true that there is no intrinsic value in naming a unit (e.g., THE OHM) other than convenience?
          • Q3. How is the world of standards different today compared to the 1860s? What is the significance of the fact that we now have well-established base standards for time and number?
    • It's interesting to consider the history of units of time: for example, "The Egyptians subdivided daytime and nighttime into twelve hours each since at least 2000 BC, hence their hours varied seasonally." Later, with the development of pendulum-based clocks, there was an transition from apparent time to observational or mean time. From there to the rotation of the earth, to it's rotation w/in a particular epoch, to atomic clocks under defined standard conditions.
      • As the second transitions from apparent to mean, other units of measure can be developed based on the definition of a second.
      • Imagine how things would be different if we used apparent time today. In the northern hemisphere winter, would meetings would last "longer" at night versus the day? Or, would daytime meetings be scheduled for a longer block of time? <boggle!>

Example 2. Length.

  • "The metre or meter is a measure of length." From this same reference, we find that on September 28 1889, the "first General Conference on Weights and Measures (CGPM) defines the length as the distance between two lines on a standard bar of an alloy of platinum with ten percent iridium, measured at the melting point of ice." Later, on October 6 1927, "the seventh CGPM adjusts the definition of the length to be the distance, at 0 °C, between the axes of the two central lines marked on the prototype bar of platinum-iridium, this bar being subject to one standard atmosphere of pressure and supported on two cylinders of at least one centimetre diameter, symmetrically placed in the same horizontal plane at a distance of 571 millimetres from each other." Most recently, on October 21 1983, "the seventeenth CGPM defines the length as equal to the distance travelled by light in vacuum during a time interval of 1⁄299,792,458 of a second."
    • So, if something heats up and becomes longer, it's length as defined in meters will be said to increase, because the definition of a meter is under some defined standard conditions.
    • Jason R. Kelly:Yes, that's right.

Big Question 1.

  • A Prototype or Reference Promoter? Should we have a reference promoter that embodies a standard, to the best of our ability? We can define promoter activity in terms of promoter clearance rate and more generically in terms of PoPS, both of which can be related to base SI units. Thus, one path forward would be to define 1.0 Standard Promoter Units to be embodied by a promoter whose activity is closest to 1.0 PoPS under some defined conditions.
    • Given that the activity of a promoter can be defined via a compound unit derived from base units that themselves already have well defined physical reference standards, it seems like a potential trap to attempt to define a new "Standard Promoter Unit" based on the activity of some new physical reference standard. Instead, we could do two things. First, we could declare that 1.0 PoPS under some defined conditions is 1.0 standard promoter unit (SPU). Second, people could simply make reference collections that are known to produce certain PoPS levels under various conditions. For convenience, over time, researchers could perhaps develop ever-improving promoters that are evermore closer to producing exactly 1.000000000 PoPS, and so on (this would be similar to how ever better DNA ladders are developed, with the 2-log ladder being pretty tasty!). If the SPU becomes a useful shorthand then terrific, otherwise no worries.
    • Jason R. Kelly: see note on this ref above. First 10 pages of this (Reports of the Committee on Electrical Standards Appointed by the British Association for the Advancement of Science - Jenkin, Kelvin, Joule, Maxwell).

Possible Big Conclusions.

    • We focus the paper as highlighting the utility of making relative measurements.
    • We discuss that 1.0 PoPS produced under standard conditions is 1.0 SPUs.
      • Is there something to say about the possible utility of the SPU?
    • We focus attention on the utility of (a) making improved promoter reference collections, and (b) making more accurate measurements of promoter activity.

Prev discussion

  • How should we measure promoters under varying measurement conditions?
    • There is likely an analogy here to measuring length using a meter stick with a different (or the same) coefficient of expansion (compared to what, the thing being measured?). An open question is whether J23101 when measured under any conditions should always = 1 SPU (even if the amount of PoPS produced is changing). As I understand this is not the way that it would be done when measuring length - if you measure a meter stick at a temperature where it expands 8X then it is 8 meters long, not 1 meter. However, there seems to still be value in treating J23101 as = 1 SPU across different measurement approaches in that it would allow you to rank order promoters measured in different environments by different researchers. So not sure how to reconcile these two different points.
  • How should the reference standard and unit be defined?
    • For instance, we could define the unit of the SPU as the # of PoPS from a reference standard promoter (i.e. J23101) under some standard operating conditions.
    • We could alternatively define the SPU as = 1 PoPS.
    • I think that the first option is likely to be the right one, but I think it could be influenced by the answer to the first question above.