(from B. Wong 2011)

That moment during lab meeting when I demand from an undergrad if he's convinced whether 2 proteins really are colocalized based on overlapping red-green immunofluorescence and he frustratingly replies, "I can't tell you that...because I'm color blind."

Neuropolarwife and I use those nights to recover from the week .

And by Sunday evening we are feeling cabin fever and want to go out and do something.

Are we the only ones too tired to go out Fri and Sat??

The editor did a new thing.

They said, You only get one chance. If the paper is not satisfactory after this it will be rejected.

One of the papers had essentially one small remaining problem and it was about stats. And it got rejected. (Of course, who knows what the reviewers said behind the scenes).

The other one is being revised currently.

Is this a thing?

Are editors getting obsessive about this all of a sudden? Is it because they are being pressured to reduce time to acceptance? Is this the journals equivalent of the NIH going from 3 rounds to 2?

I liked being able to go back and forth with the reviewers. Especially because the reviewers were often maddeningly vague about what they wanted. I have had many experiences where my paper was improved by comments late in the process. And experiences where I convinced a recalcitrant reviewer to accept the paper after even 4/5 rounds.  Reviewers who are careful look a lot to an editor like reviewers who are just plain stubborn.

Enjoy some funny Father's Day videos.

Studying scat is not just about where an animal has been. Yes, it can tell you a lot about the distribution of populations, but it can also give you a rough idea of population size, what they eat, where they've been before, and even where an animal might be in its life cycle. Clearly, it's important to know your crap.

Many poop samples are pretty easy to tell apart (if you can mix up a wolf and a squirrel, it's safe to say that one of those species is having some tummy trouble), but what about species that are very closely related? One species of squirrel from another? Or...one type of kangaroo from another?

Wadley et al. "Rapid species identification of eight sympatric northern
Australian macropods from faecal-pellet DNA" Wildlife Research, 2013.

(This 'roo wants to know the deal with its poo. Source)

The savannahs of Australia boast 9 of the 13 species of macropods (the marsupial group that includes wallabies and kangaroos). Environmental scientists and ecologists have become very worried about the animal diversity on the savannah, as things like mining and farming encroach on the land that the macropods usually use to survive. It's possible that some species may be more affected than others.

But how to tell? You can go over in a plane (if you have the money), you can drive all over the savannah counting (if you have the time and the gas), you can maybe hunker down in a blind for a very, very, very long time. Or, you can take a look at the local crap.

But when you're dealing with kangaroos and wallabies, you are dealing with species that have very similar diets and that are usually very similar in size, and often which occupy a similar range. And if they are similar species that are sized alike and eat alike, it's a good bet they poop alike. It's probably relatively simple to tell squirrel scat from panther poo, but a kangaroo from a wallaby?

So how do you tell? Well, why just look at and puzzle over your roo poo, when you can bring it in to the lab and...look at its DNA.

Yes, there's DNA in poop. And not just the DNA of the stuff the animal was eating. When we digest, some of our stomach and intestinal cells end up as a sacrifice to a good meal, and will get incorporated into your poop. If you can isolate the DNA from those cells (preferably with a DNA bit that is not going to be mixed up in what the animal was eating), that differs between the species, you might be able to amplify that up with polymerase chain reaction (which uses an enzyme to copy a specific set of DNA over and over and over), and then be able to tell what species you have.

And that's what this group did. They took a segment of mitochondrial DNA that differs between the species. They took 8 different species of wallabies and kangaroos, and PCRd up the DNA. Then they used enzymes to cut it at the places where it differed between species, resulting in DNA bands of different sizes.

Above in Fig 1 you can see the bands, a different size for each species. Using this, the authors took a large number of samples (406) from all over the savannah, and PCRd them up, and were able to identify the vast majority (except for a couple of really bad samples, and three that were accidentally from sheep. Oops).

You can see in table 2 you've got your kangaroos, your wallabies, but the big winner was the "wallaroo". Kangaroos are big. Wallabies are small. Wallaroos are right in the middle.

(But also, apparently, a species of severe cuteness. Source)

Hopefully, this method can be used to keep an eye on the macropod populations in Australia. A little s**t can go a long way.

"In Myriad, the high court held cDNA is patentable, because it involves actual work in the laboratory and inverts the normal process found in nature. The synthetic DNA is an edited version of a gene, stripped of non-coding regions that the court said makes it “not naturally occurring.”

Critics say even the edited sequences are directly analogous to naturally occurring DNA."

In many labs, cDNAs are routinely made, manipulated, and used for research. cDNA is DNA that is engineered in reverse using messenger RNA (mRNA) as the template. As the above quote alludes, a cDNA is not a carbon copy of its corresponding gene. Interspersed along the length of a gene are regions of non-coding DNA sequence. These are segments of DNA that aren't represented in the sequence of the encoded protein. When a gene is initially transcribed into mRNA some of these non-coding regions, called introns, are included. Introns, however, are ultimately removed by the cell before the mRNA is translated into protein. Since mRNA is used to make cDNA, the introns are excluded from the cDNA sequence.

During gene expression, a gene is first transcribed into a primary RNA transcript, which includes non-coding introns (blue). Through a process called splicing the introns are removed from the transcript resulting in a mature mRNA molecule. The sequences found in mRNA are called exons (red and yellow). The mRNA is  then translated into protein. Since cDNA is made from mature mRNA, it will consist only of exon sequences.

Although gene and cDNA are different, they both carry essentially the same DNA sequence for a protein. (It should be noted, however, that many genes encode multiple forms of a protein, for which each form has its own corresponding cDNA.) So, I'm not sure why the "patentable" emphasis is on cDNAs as opposed to making mutations* to the underlying sequence that result in say, new or altered function of a protein. At least there I could see an inventive process happening--or am I missing something here?

*I'm talking about generating novel mutations. Of course, I'm not sure what should happen if said mutations are discovered to be "naturally occurring" after the fact.

Love the gold fish!

Of course, this post is not really about desserts. It considers the purposes of mentoring.  I suspect that every job in the US above the fast-food server includes some sort of mentoring. Corporations and academia noted the role of informal mentoring in career success many years ago, and mentoring programs have become commonplace. Gender inequity in the workplace has been attributed, in part, to the lack of mentoring for women.  Make the Most of Mentoring: Capitalize on Mentoring and Take Your Career to the Next Level explores the components of common formal mentoring programs and contrasts them with the informal mentoring that inspired them. It's author, Susan Colantuono, founded Leading Women™.

According to Colantuono, women have not benefitted from these formal programs because they get too much CAKE and not enough PIE. Mentoring, informal or through formal programs, can provide a lot of different types of support. Most formal programs focus on CAKE:

• Confidence
• Aptitude/Attitude/Advice
• Konnection to resources (yes, this took a twist to make the acronym work; get over it)
• Encouragement

These aspects of career development are important. Too many women take themselves out of competition for new positions and assignments because they are missing these components. However, to really crack through the glass ceiling to the next level, you need PIE:

• Performance
• Image
• Exposure

Performance is not just how someone performs; it also considers the performance of the business. Someone may be doing a great job, but they will never scale the heights of a corporation until they have responsibilities and demonstrate competency in operations and strategic capabilities for the core business.

Image incorporates appearance and attitude. Unless you look and act like a competent, confident professional, others will not see you moving up to the next level of leadership. This competency is more than wearing the correct clothes; vocabulary, body language, and other personal traits influence how a person is seen by others.

Exposure involves seeing how work is done at higher levels. Who makes strategic decisions? If you aspire to these positions, you need to be at the table for these sorts of activities.

The book paints a vivid picture of these differences, using real-life examples from the work world. Making the jump to academia is a bit problematic; given the broad mission of an academic health center, what is our core mission? How do I position myself close to key operations and strategy?

Buyers of the book also get access to a number of free online resources, including worksheets for those entering into mentoring relationships.

Make the Most of Mentoring provides a quick read with a new perspective on the process of grooming new leaders. Click here to learn more about Leading Women™ and the books of Susan Colantuono.