Tuesday, April 23, 2019

Ten simple rules for better figures!

I might just be leaving this paper here for me and my lab as we continue frantically preparing posters, talks and preprints for conference season....worth checking out, though!!

Monday, April 22, 2019

Nonsense Induced Transcriptional Compensation (NITC)!

A bunch of new studies just dropped in Nature this month that go a long way toward explaining a lot of results that seemed like nonreproducible nonsense.

The best place to start is this summary!

Here is the paradox mentioned above in my dummies view of it: in higher organisms you can "knock out" a gene by messing up it's structure or you can "knock down" a gene/gene product by messing with it's regulator or silencing it's RNA production.

You'd think that decreasing the amount of gene by either mechanism would have the same effects (cause, obviously, the gene doesn't actually do anything --- only the protein and how much of it is around is what is important) -- and sometimes it does.

But, other times the knockout and the knockdown will have VERY different effects on the phenotype. This will look like
1) Either the knockdown or the knockout didn't work
2) The person measuring the phenotype is:

 But  now there appears to be a mechanism -- it looks like short "nonfunctional" products from knockouts (often called nonsense mutations) may lead to compensation by causing upregulation of similar genes. Which -- from an evolutionary standpoint seems to make a lot of sense, right? Why have 30,000 genes or whatever if one single amino acid variant could call a stop codon and shut the whole organism down?

The evidence is described in zebrafish in this and this great new study(ies?).

Sunday, April 21, 2019

Sci-Hub -- a terrible illegal misuse of the internet you should never ever use.

If Shaq can't convince you not to do it, maybe I probably have no chance, but I'm going to try.

Never ever ever use SciHub. It's totally illegal and bad for publisher profits and we need healthy academic journals making money in order for science as we know it to work today.

What is SciHub? Oh -- it's a way to get any article from any journal in a free way via illegal unethical means that you should never ever use.

How do you use it?

You don't. But if you were to, you'd

1) Find a paper that you can't get access to without doing it the right way (the right way being -- giving Elfsevier $42 for a research study performed by the U.S.A. HHS (which is -- by US law -- REQUIRED to be open access)

2) You'd definitely (for real, I'm not joking, this is just for helping you not make the mistake of accidentally doing it) never Google the words "where is SciHub now"

3) If you didn't listen to my advice and actually did this you'd get a link that would lead you to these unethical criminal's website. Where you'd be asked told to enter the paper identifier or direct link.

4) Then this criminal website would provide you this study PDF that US taxpayers had already funded completely so that anyone in the world should have access to it, but of course it would be a total crime for you to access without paying the publisher for it.

Again -- this was for purely 100% scientific inquiry. I would never endorse the use of this service. I strongly recommend that you not use it. I encourage your report anyone who does to the proper authorities.

Keep science ethical, yo.

Tuesday, April 2, 2019

Reliable identification of lactic acid bacteria in food products!

Microbial identification in complex matrices by LC-MS/MS isn't new. I know people within an hour of my house that have published papers on this going back 10 or 15 years (APG, FTW!)

However -- it never seems to make it into routine usage. Part of it might be the technical aspects, but part of it might be that you need to really understand your matrix and what you're looking for. This great new study provides an awesome twist on microbial ID and a way that I could envision LC-MS/MS really going into daily use! 

What's the twist? There are bacteria that we do want around -- particularly in food preparation. But when you've got large populations of bacteria making yogurt or cheese for you it can be hard to tell those from the ones you don't want.

By clever selection of peptides from the extremely well characterized organisms of interest that should never exist in your starting material (or, presumably, in the bacteria you don't want) you can use either untargeted or targeted nLC-QE methods to identify good vs bad microbes.

The reason I'm thinking this is a great example of one that we can adapt to routine analysis is that the signal for these peptides is off the charts -- the XICs on the nanoLC allow you to see even the M+4, maybe even the M+5 isotope on these peptides! You're only getting that when you've got TONS of signal. If you can make out an M+4 at 200nL/min nLC -- this is an ion that you can EASILY find 3 isotopes for using analytical level flow rates (200uL/min)!!!

Yes, I've been pretty hard on the ElfSeverers this week. Good science still ends up there, though, right now and this is one example.

Monday, April 1, 2019


If you do have an ElfSeverer account you might want to check your Spam folder. I just got this email this week and should change my password.

For your information, Little Bunny FooFoo was already in use.

This is not an April Fool's day thing, btw.