Author Archives: Peter

Favorite Links for Week 45 2019

What is the real, mathematical dog-year calculation?

Ok, so we all knew dog-years can’t be a linear translation to human years. So what is the real translation between human and dog age? There’s an “epigenetic clock” discovered by Steve Horvath. Basically, DNA gets little chemical modifications that help turn genes on and off. It turns out that some of those modifications accumulate with age. And this biochemical signature tracks age better than just about anything else. So is it the same in dogs? And can we use it to correlate dog-years to human-years? Yes. Tina Wang et al. figured it out (bioRxiv).

Personalized predictions of blood sugar based on poop bacteria

This 2019 paper, “Personalized Approach to Predicting Postprandial Glycemic Responses,” showed a predictive model for blood sugar spikes after meals. The composition of the food (carbohydrate content and calorie content) did not predict blood sugar spikes very well. On the other hand, food information PLUS information about a specific person’s gut microbiome did a very good job. So if you knew your gut microbiome, you could make better food choices.

Failure Found to be an “Essential Prerequisite” For Success

These folks used the NIH database of applications for grants to see what differentiates people who eventually succeeded from those who didn’t. The average was two failures before a successful grant application. I wish I could convey how incredibly hard it is to put together a proposal that gets rejected.

Philip Pullman on Children’s Literature and the Critics Who Disdain It

I read this essay a few days ago and loved it. It came up in conversation, too. The premise is that good literature is not accessible literature. That a book is something children enjoy just means that it is clear and accessible, not that it is simplistic. Generally, children don’t like simplistic. And if a book is enjoyable for children and has depth, it will be equally enjoyable for adults.

Atomic Force Microscope was used to look at single molecules and resolve details

The article, “Revisiting Kekulene: Synthesis and Single-Molecule Imaging,” is amazing. First, what a crazy molecule. Second, what an amazing technique to look at its structure and properties.

Little Things:

Can snakes use doorknobs? Wait for it to find out


Alternative to the Pyramid Scheme of “Aspirational content”

Youtube put out a caution about burnout. Penny arcade summed it up. “Creators: you’re feeling burned out because you are light bulbs. And there are always more light bulbs. You create young, energetic light bulbs with every video you make.”

Good educational content is distinct from aspirational content. As a chemistry professor, my primary job is to produce more chemists (and educate non-chemists who need the background). The point is not to generate a great many more chemistry professors. Complexly and the Scishow folks make great educational content. Aspirational content is the opposite: it endeavors to sell the idea that you too can become an aspirational content producer. Mostly by watching more aspirational content.

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Build video for the iron battery

I made a youtube video every weekday in 2017. That experience pulled me into the world of battery chemistry. Daily vlogging was hard but taught me something about social media, science outreach, and the topics that people are interested in. I was a little surprised to find that people were so interested in batteries. I like the opportunity to explore something that is of wide interest. Everyone has a battery in their pocket, and everyone wants them to last longer.

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qPCR and graphene for aptamer selection

We’ve been selecting aptamers in the lab for the last year. Having a qPCR on the bench has really helped, and so we wrote up a methods paper in ACS Combinatorial Science. The company that made our qPCR instrument has put up a blurb about it, too.

The qPCR function is great for cycle course optimization, and we have been using the melt curve analysis function of the Open qPCR (thermofluorimetry) to do a binding assay. It works pretty well. We put a dye in with the aptamer and measure the temperature at which the dye dye-DNA complex melts. The bound aptamer has a different melt temperature, so it gives a specific signal. We plot that specific signal as a function of concentration and to determine the binding constant. It’s based on the Easley lab’s method paper from 2015 with low-cost equipment.

The instrument simplifies some of the more touchy parts of the aptamer selection. Undergrads have been turning rounds pretty efficiently this year with the help of the open qPCR instrument.

We have also been using graphene oxide to try some selections. I have only heard of graphene oxide SELEX recently, but it grabs unstructured DNA to separate them from aptamers bound to target. It’s looking good. I hope to report on that soon.