Christopher Dieni

Hi Jennifer,
Thanks a lot for the answer and additional advice.
Best,
Chris

Hi Jennifer,
Amongst your points of advice, you list that one should find a way to get back into the classroom. My Ph.D. is long over. Does this mean that I would need to go back to school and get a whole other degree in Policy?

3.5 of those things happened for me back at an interview in July 2010, and I didn't get the job. What was missing was that my referees weren't contacted prior to the interview, and there was some doubt as to when the decision would be made (though there was a general idea). That said, the interview was for a faculty position, and these steps/signs are fairly standard for interviews in academia, I think.

Well, although Canada is neither in the US or Europe *ahem* I guess the analogue over here is to have positions that are simply "lecturers" or "instructors" which are positions as professors, but do not involve running a teaching lab.
I would be very happy to do a teaching-only position but what I don't like is that, according to the advertisements I see, more often than not these teaching-only positions are by no means permanent. They are referred to as contract, temporary or the specialized term is "sessional." These can range anywhere from one semester of about four months to a maximum, typically, of three years- but I've never seen any longer than that. It gives me pause to wonder what will happen at that three-year mark (if not earlier); do you then find yourself no longer employed and once again looking for a job?
It's grim to think of one's self moving from position to position- albeit enjoying the teaching that you're doing- but without any permanence and with an overall very transient life. If these teaching fellowships are more permanent in the UK, you definitely have a wisdom that has eluded us over here.

I'm just guessing, but I would think that the prestained ladder is useful for knowing the correct orientation of your gel when you removed it from your electrophoretic tank. That's been the case with me- I always hate it when I pre-soak my gel in transfer buffer and then lose track of its orientation.

Well, just as was the case with your agarose gels, breaking your acrylamide gel into many tiny pieces also works really well for destroying your in-progress westerns!

Also, as far as 2D westerns are concerned: any slight slip of the wrist with that thin, tiny, delicate capillary 1st dimension IEF, and that'll be game over too!

I'm sure we've all encountered, in our own labs, things that our labmates do that really make us scratch our heads. We don't know why, and oftentimes- just as is the case right here- they seem to defy the logic that we as scientists should be well-attuned to.

I think one of the only ways to combat this is to just lead by example. Use your chemicals and expose them to as light as you see fit, then, SHOW your colleagues that the chemicals still work in spite of that light exposure. Once they receive proof, they- as scientists- should accept it. If you prove that the chemicals work in spite of light exposure, and your labmates still insist on covering tubes with foil, then there's nothing further that you can do to change their minds. This is something that we in my graduate lab used to refer to as "voodoo science" and it can manifest itself in a number of ways, including this one. One guy who used to be a Ph.D. candidate in my old lab was convinced- I emphasize convinced- that protein purification would only work properly if only done in a certain corner of a certain lab room, even though the column and fractionator could easily be moved and clamped virtually anywhere!

Hopefully it'll pass, but if not, it's one of those things you need to live with. Sorry if this isn't more helpful.

Interesting! Then why is it okay to autoclave media containing sugars and peptone? For example, on almost a daily basis, I autoclave MRS media (named after its inventors, de Man, Rogosa and Sharpe) for Lactobacillus growth. This media contains 1% peptone (proteolytic digests of animal milk or meat resulting in a variety of peptides) and 2% glucose, yet it's perfectly safe to autoclave.

Jode, thanks so much for writing this. This has answered so many questions I had about why certain components just couldn't be autoclaved together! I just grumbled and followed the directions without being adventurous, but if I had, now I know what would've happened.
Just a chemistry question, more out of curiosity than anything else. Plenty of components of media have free amino groups. In fact, the peptides found in various formulations of peptides have N-terminal amino groups, just like an amino acid would. Why are these not undergoing the Maillard reaction as well?

Well said!

I like this Jode, and it's actually a really great follow-up to my enzyme article of yesterday. Obviously I'm setting myself up for a bias, but what I would love to see in this article (or maybe future ones) are some of the enzyme-specific details of concentrating proteins. Can you over-concentrate and precipitate? What are the best way to ensure your enzyme remains properly natured and active during your concentration process? What are some of the risks and "don'ts" associated with concentrating your protein?

Author's postscript note: a friend of mine just informed me that I left out ribozymes. When I gave it further thought, I also realized that even if I had included ribozymes, someone else might have just as easily argued that I left out abzymes, too.

I admit that at the time, I found mentoring undergrads to be a bit of a hassle and distraction while I was a grad student. But I nonetheless did a LOT (not necessarily out of my own volition) and eventually it became quasi-enjoyable. 

Hey JMG, sorry I'm only just reading your comment now! Thanks a lot for the great feedback. Part V is already available and helps wrap up the series. In the future- I'm not sure exactly when but it'll definitely happen at some point- I'll be covering some more intermediate topics on protein phosphorylation.

Excellent article Emily!

Hi Silas. Apologies for the delay, I didn't notice your comment until just now. We need an email alert system to indicate when someone has commented after us in a particular thread.

I'm going to ask the dreaded question that a lot of people might be thinking.

Yup, that's what I would've said. Your characteristic "frown" which usually happens when the upper buffer leaks, where proteins on the edges migrate somewhat, but not in the middle.

I'd really like to see some topics corresponding to the basic concepts of epigenetics, and methods for studying epigenetic-based modifications of proteins (I guess mostly histones) and DNA.

Thanks Nick!

Absolutely, go ahead. Thanks Alex!