Bitesize Bio profiles

on Using Enzymes at the Bench — Keep it in the cooler? On ice? or... 10th of May, 2013

I agree!!! We are scientists, aren't we? Can we not have evidence-based research, rather than assertions?

on How To Get Organized With Reference Managers for Science – Mendeley 3rd of May, 2013

Thanks for this post, Matthias. I was not aware that so many of the other programs were backed by publishers. (I use Jabref, so I'm in the clear.)

I also think this article is oddly-timed to write about Mendeley without mentioning the uproar over the recent buy-out by Elsevier. I think you've touched on good points with this comment. As a scientist, open-source is extremely important, not only for ideology, but also full-disclosure of what the program does.

on How To Get Organized With Reference Managers for Science – An... 25th of April, 2013

To expand on Kurt's point about "no guarantee for long term usage", an example is Elsevier's recent purchase of Mendeley. Some critics suggest that Elsevier might shut down Mendeley, and I've read others suggest they Elsevier might introduce anti-competitive philosophies into the product. Hopefully this will be addressed in the next article, though!

on How To Get Organized With Reference Managers for Science – An... 24th of April, 2013

It would have been be nice to mention which run on Linux or other platforms. And another field for "owned by Elsevier" (i.e. Mendeley).

Jabref is excellent, and is also free (as in freedom, as well as "doesn't cost anything") and integrates excellently with LyX.

Bibdesk is/was also excellent if you are using OS X.

on Three Tips (and Two Tricks) for Using BLAST 16th of January, 2013

I agree. The title of this article is misleading, as it's really about using NCBI BLAST, not BLAST per se. BLAST is so much larger and more powerful than just what NCBI's web interface allows! Similarly, my organism isn't in NCBI, so it's irrelevant. Another good option for checking primer specificity is ipcress.

on How To Deal With People Stealing Your Reagents 21st of December, 2012

Put radiation stickers on everything?

on BioNumbers: An Online Database of Useful Biological Numbers 10th of December, 2012

"How many cells are in a single colony of Escherichia coli?" What does that even mean? Is that like "how long is a piece of string"?

on How to Lyse Cells for Protein Extraction 4th of July, 2012

I just resuspend my cells in sample buffer, then boil them in an eppy...

on What Can Mendeley Do For You? 1st of June, 2012

Have you ever tried Jabref? It seems to share all the features of Mendeley, and seems very powerful. Unlike Mendeley, it's open source, which is nice. I use it with LyX, and it integrates well. The Jabref devs are very open to feedback as well.

on How Do Buffers Work? 21st of April, 2012

Well, in the absence of a reply, I've researched this some more... From your first reference link, "increasing the OH- concentration of an aqueous solution has the effect of decreasing the H+ concentration, because the product of these two concentrations must remain constant", which contradicts your paragraph.

on How Do Buffers Work? 16th of April, 2012

"If you were to add more H+ to this solution, more H2O would dissociate to generate a matching amount of OH-. The more H+ you add, the more dissociation of water occurs, moving the equation to the right."

Is this correct? AFAIK it works that other way around. If you add more H+, it would drive your equation to the LEFT. K_w, the ionization constant of water, must stay constant. K_w = [H+][OH-] = 10^-14. Hence, if you add [H+], [OH-] must decrease, creating more H2O.

on How To Preserve Your Samples In Western Blotting 19th of March, 2012

If your primary concern is consistency, then working *quickly* is inconsistent with that aim. This would amplify the difference between samples, as proportional (linear or logarithmic) time has a greater effect when the numbers are small. The difference in protease activity between 1 and 2 minutes is much different than 20 and 21 minutes.

on How To Keep Your Mammalian Cells Happy And Healthy 3rd of February, 2012

Thanks for that. I do enjoy reading your website, but as a protist biologist, I often feel maligned!
Cheers.

on How To Keep Your Mammalian Cells Happy And Healthy 3rd of February, 2012

I'm used to a bias toward Homo sapiens in science reporting generally, but this is ridiculous! What about all the other "cells" that scientists culture? Parasites, algae, amoebae, etc., etc. I'm sure most varieties of "cells" do NOT want 37°C, nor 5% carbon dioxide. I don't mind if most articles are directed toward human-orientated scientists, but don't assume that encompasses everyone!

on LibreOffice: A Free Office Suite to Rival Microsoft’s 19th of September, 2011

For scientists particularly, I think TeX is a much more versatile and powerful word processor (also free/open source). It's a fairly steep learning curve, but ticks all the boxes. If you use a frontend such as LyX, it's very easy to learn. On the Mac, LyX syncs excellently with a fabulous reference utility called BibDesk, which is worth a look even if you don't use LyX/TeX. Better than Papers, and free!

on How to Get Perfect Protein Transfer in Western Blotting 17th of August, 2011

My understanding is that if smaller proteins are running through the membrane, then you need to transfer at a lower voltage, not for less time (assuming the time is correct for the larger molecules). The theory is that lower voltage will not allow the transferring proteins from becoming "unstuck" from the front face of the membrane.
Also, most commercial sample buffers include Coomassie G250, which tracks the ion front when running the SDS-PAGE gel. Hence, you can just stop the electrophoresis run when the dye front reaches the bottom of the gel.

on 5 ways to destroy your Western blot 1st of April, 2011

I've not heard of having to fill empty lanes with loading buffer. What is the theory behind this? I did sometimes get smiling even when all lanes are loaded, but changed to pre-casts, which seemed to fix it.

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