User talk:Andy Maloney/Kinesin & Microtubule Page

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If you do not have an account with Open Wet Ware, you can obtain one from here. I would like to have people format their questions and comments in the following manner:

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   • '''~~~~:''' The output of this looks like: Andy Maloney 12:29, 7 February 2011 (EST):.

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As much as I would like to keep my dissertation completely open and in the media wiki format, I will have to at some point format it to the guidelines dictated by my university. This will necessitate putting a final "snap shot" of the dissertation in a book format of which, all comments will have their own special appendix in each chapter.

Thanks for looking at my open dissertation!

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Frank Wicker

• Professor Emeritus of Education Psychology at the University of Texas

Via email.

1. I see that you're in a field where just establishing the conditions to start doing the experiment is a tremendously complex and elusive thing, so it seems to me to be a really important contribution to help other researchers understand those complexities and overcome those barriers.
2. I think your definition of the word "tool" is a little different from my own, because e.g., I would have said that the first person who came up with and used, say, the wheel, was being very creative but it was instantly a tool. That is, I guess a tool is to me more or less anything that is useful and I don't normally separate that from creativity. However, I think we all have a right to come up with our own definitions of words, and I can see how your definition is just right for allowing you to make the point you want to make and for clarifying what your dissertation is about.
3. I liked your use of the cooking analogy -- it seemed right on target to me. Again some committees in my day might have frowned on the use of any non-formal analogies but if that is no longer true it's all to the better. I think the analogy is especially helpful for outsiders like me to get a clear sense of the plans and purposes of your study.
4. There are a few places where I might make a minor quibble about wording, such as somewhere you say that something "works best" for you whereas I think "works well" would be better, since one probably never knows for sure what works best.

Cesar A. Rodriguez-Rosario

• Cesar's Blog.
• Cesar's Lab Page.

1. Ha! Your first reference is Ace of Cakes!
2. This is very detailed and sharp, very nice. I think you might need a broader Introduction to engage the reader before spelling out the tools. This might be done as an introductory chapter (Chapter 0?), or as an overview of the different tools before you describe them in detail.

Steve Koch

Steve Koch 19:59, 1 April 2011 (EDT): Can you work out a way to cite the Kinesin Home Page in this chapter? Even if you didn't use it, I used it when @ Sandia, and I'm sure passed along a lot of the information to you. Thanks! http://www.cellbio.duke.edu/kinesin/Methods/

• Andy Maloney 18:50, 7 April 2011 (EDT): Done.
• Steve Koch 12:18, 9 April 2011 (EDT):
  • Ackn. are ambiguous now about Gabe Montano, it could look like she gave him kinesin. Try "...Dr. Haiqing Liu (while in the lab of Dr. Gabriel Montano)..."
    • Andy Maloney 01:24, 10 April 2011 (EDT): Done.
  • Typo: stociometric
    • Andy Maloney 01:24, 10 April 2011 (EDT): Done.
  • "Apparently no one else..." I would not say this. Surely some people know, but we haven't met them on that thread limited to just a few people and our literature search. I would say instead, "BRB80 and no explanation...the origin of the name remains ambiguous to us."
    • Andy Maloney 01:24, 10 April 2011 (EDT): Yes, this is true and for completeness, I will change it.
  • Some people do use the "PEM" acronym, so I wouldn't call it "the naming convention I have proposed." I would say, "...naming convention I have adopted."
    • Andy Maloney 01:24, 10 April 2011 (EDT): Yes, this is very true and should be clearer.
  • I don't like the sentence, "...so much so that it will basically put itself into solution." Is that true? Like the whole crystal will dissolve? If not, I'd just delete the whole sentence.
    • Andy Maloney 01:24, 10 April 2011 (EDT): Well, I think I have seen it before. I think it takes a long time but I'm pretty sure it will do this. I remember cleaning out the lab and I found an old container of MgCl₂ from the previous lab owner in there. The bottle was closed tightly and there was a ton of water in it. The contents weren't completely in solution but I could tell that the liquid in it was not from someone putting it there. You do make a good point though and I will reword it. NaOH definitely will suck up moisture from the atmosphere enough to make a puddle of water around it.
  • "...in the flavor of NaOH." Now that I'm reading carefully (finally! sorry!), I can see some issues with too much conversational tone. Especially for someone reading with English as a second language. It would be much clearer to say that "these ions come from NaOH." Whereas what you have could lead someone to believe there's a special kind of NaOH, a certain "flavor." Up to you.

• • One reason people don't specify the amount of pH added is because they don't measure it. Another reason is that in principle is is predictable if you know the final pH. Definitely specifying what was used is useful, but of course in the old-school journals there was not enough space to do this every time.
    • Andy Maloney 01:24, 10 April 2011 (EDT): Good point.
  • I realize now I'm commenting on outdated version so I'll stop!
  • "does not have a secondary..." the word structure is missing. Also, I don't believe it doesn't have secondary structure. Just maybe it's not important.
    • Andy Maloney 01:24, 10 April 2011 (EDT): You are correct. Whole bovine casein has little secondary or tertiary structure. Some does occur but not a lot and you have to get up there in temperature to find it.
  • I know you've already made the PDF, but for the web version, I would add a sentence at the top saying something like, "I am going to be as detailed as possible, in case people with very little experience read this page. Many of the steps I describe are considered "obvious" to experts and can be ignored by them." I say this because I think there's a real risk of someone reading this wondering what kind of expertise you had when you started. For example, when talking about 2M dextrose as if it's surprising that you can make a 2M sugar solution or that it takes up substantial volume. It would be surprising to a novice, but it wasn't surprising to you. Just thinking about the risk of a postdoc advisor thinking this.
  • I would guess that you don't know that DMSO helps taxol be soluble in PEM. Unless you mean it's better to have it dissolved in DMSO and then put into PEM so that it's temporarily "soluble" in PEM. That is, now we know that it's not soluble at that concentration in PEM, which is worth highlighting for sure, as you do farther down with the wonderful article from PLoS ONE.
    • Andy Maloney 01:24, 10 April 2011 (EDT): Nope. I know this. Taxol is insoluble in aqueous environments, hence the need for an organic solvent that is soluble in both polar and non polar environments, i.e. DMSO. The DMSO is used to put the Taxol in a solution so that it is easy to add into the motility solution.
  • That is really interesting about the not freezing at 3C taxol solution. Good observation, very surprising.
    • Andy Maloney 01:24, 10 April 2011 (EDT): Yep. I noticed more Taxol crystals in solution when this occurred.
  • That's worrisome about the ATP precipitate, especially if we start doing lower ATP concentrations. Great that you note this fact and I don't think an issue for high-ATP experiments.
    • Andy Maloney 01:24, 10 April 2011 (EDT): I suppose we can send it to someone with an HPLC to determine the constituents of the precipitate.
  • done