Stay on top of the literature by automating PubMed feeds

Piles of scientific papers.

Despite the ever-rising bar to publish scientific papers, it seems that the scientific community is accelerating with the rate of publication, rather than slowing down or even maintaining pace. This is no doubt due to the increasing numbers of online-only journals that promise rapid acceptance times with minimal formatting and production overhead. At times it may feel impossible to actually keep track of where a field is going because by the time you’ve read last week’s hotlist papers, there are suddenly another five showing up on PubMed, Google Scholar or Web of Science. On top of that, if you haven’t checked “that one” journal in a while, you may end up missing an important paper until its already old news because you didn’t choose just the right keywords in your search.

Well, suffer no more. The following how-to guide will help you to stay on top of papers in your field by utilizing two important resources: PubMed’s search engine (without question the most trustable source for legitimate primary sources for the biological [and other] sciences) and IFTTT (“If This, then That”), a website that helps you to automate tasks through the internet. The best part: it’s all free. Continue reading “Stay on top of the literature by automating PubMed feeds”

Remembering Michael Davidson, a champion for microscopy

There are, of course, famous microscopists. The big names of the past like Antonie van Leeuwenhoek and Robert Hooke are remembered for their contributions to the beginnings of biological microscopy as a field: developing the principle of microscopy optics and turning them back onto the natural world. Then, in the early and mid-20th century important advancements like coherent lasers and innovative prisms by Ted Maiman, Gordon Gould, and Georges Nomarski allowed for a more informative and specific glimpse at the biological microcosm under the lens. Recently, microscopy made headlines when super-resolution approaches developed by Eric Betzig, Stefan Hell, and William Moerner won the 2014 Nobel Prize in Chemistry.

Michael W. Davidson. Image: Nikon Small World

As can be expected, there are also extremely important microscopists who never found the sort of fame afforded by winning a Nobel Prize. Sadly, we lost one of these microscopists last week when FSU’s Michael Davidson passed away from lung cancer at the age of 65. Davidson made tremendous contributions to cell biology and microscopy, as illustrated by his presence on the author list of hundreds of papers related the development and application of an impressive number of fluorescent proteins. It may come as a surprise that such a prolific and successful group-leading scientist never finished his PhD due to, according some interviews, growing tired of graduate student life (well… pay). With this perspective, Davidson had a unique and highly respected approach to mentoring; he took in (and paid) “troubled” students and other young hopefuls, taught them the art of microscopy and instilled in them an appreciation for the micro-world, then set them off to produce some astounding images and papers. In fact, I first learned of Davidson in conversation with my a mentor of mine a few years ago, as she spoke beautifully and admiringly of his mentoring approach.

You may not know Michael Davidson by name, but it’s likely you’ve encountered his impact on microscopy. To start, Nobel Laureate Eric Betzig attributes the realization that fluorescent proteins were what was “missing” to make super-resolution microscopy a reality to a visit to Davidson’s lab. But beyond his personal influence, Davidson personally championed huge resources for fluorescence microscopy:

Nikon MicroscopyU

If you’ve never been to MicroscopyU, do yourself a favor and do it now. This is without a doubt the best way to learn about the principles of optics and microscopic imaging methods relevant for biological science, as well as some aspects of materials sciences. The gorgeous illustrations of optical paths and dynamic demonstrations of imaging parameters make what would otherwise be a highly complex methodology extremely accessible. Davidson spearheaded the development of the website, as well as a similar website for Zeiss. This resource is the wildcard up many microscopists sleeve when they find themselves needing to teach a new user the basic principles of advanced imaging methods.

Bonus: Many, many incredible videos of live, fluorescent cells.

Nikon Small World/Olympus BioScapes

Microscopy is a valuable science, but also an art. Davidson knew this, which is why many of his images have been displayed in public galleries and museum shows. He also helped to develop microscopy as an appreciated art with the public. The two main microscopy competitions, Nikon Small World and Olympus BioScapes are a direct result of Davidson’s passion for the beauty of microscopy as an exciting an visually stimulating look at the dynamic micro-scale world around us.

Molecular Expressions

Moving slightly away from the hard-science of biological microscopy, Molecular Expressions provides an interesting view into the not-necessarily-biological world around us. With polarization microscopy images of beer and fragrances, Molecular Expressions helps us to realize there is microscopic beauty in the synthetic, as well as natural.

Michael Davidson Fluorescent Protein Collection at Addgene

This last resource is the most incredible in my opinion simply because of how useful it is for a scientist in my position. A few years ago Michael Davidson with a team of 1350 scientists from more than 275 institutions put together a catalog of over 3300 plasmids encoding for a huge array of fluorescent fusion proteins and empty backbones. The result is the Michael Davidson Fluorescent Protein Collection at Addgene. The collection is unbelievably extensive, with plasmids organized and individually searchable by spectrum, and with many proteins having a dominant-negative mutation to jump-start the viability of a study. On top of that, most of the plasmids have a datasheet with specific nucleotide compositions, spectra and example micrographs of protein localization. The collection is truly jaw-dropping in magnitude and will certainly serve as a long-lived reminder to the efforts of Davidson and his colleagues.

I want to close with one of my favorite images on Davidson’s MicroscopyU, a HeLa cell stained with markers for peroxisomes, mitochondria and nuclear DNA:

HeLa cell from Michael Davidson's website, Nikon MicroscopyU.
HeLa cell with fluorescently marked peroxisomes, mitochondria and nuclear DNA. Image: Nikon MicroscopyU, an effort of Michael Davidson.

Why a HeLa cell? Because of all of the numerous and varied cell lines used in research labs, HeLa are probably the most broadly recognizable due in major part to a recent popular book discussing its history. But even though HeLa cells are so well known and easily recognizable, I find it interesting that it would take the effort of such a disproportionately important scientist and unsung hero of microscopy such as Michael Davidson to reveal its beauty in a way that many people, including scientists, could not have expected.


A 2016 Chromosome wallpaper to jump-start your year

In past years I really enjoyed making wallpapers that played off the numbering of human chromosomes in karyotypes to make wallpapers for the New Year. I didn’t get to do this during the 2014/2015 New Year because I was drowning in a pile of writing and data analysis.

But, I made it out of grad school alive!

So, below you’ll find a 2016 Chromosome wallpaper to dress up your desktop for the New Year, displaying cartoon representations of chromosomes 20 and 16. I’ve made it in most sizes and at high enough resolution that, should you have a device with normal proportions but super high resolution (e.g., retina displays), it should still look good. Click the thumbnail for the wallpaper you want and save the image to your computer, per usual.


2016-01-24 Update: By request, I have added an additional wallpaper at a resolution of 2560×1440.

Happy New Year!

The Biology Blog is back!

A lot has happened in the past year that kept me from actively working on the site, the most exhausting of which was finishing my PhD. I’ve published some papers, started a postdoc and am already waist-deep in a whole new field.

Despite (or because of?) all of these changes, I think the time is right to refresh the blog start anew.

I look forward to breathing new life into The Biology Blog. It’s always been a fun outlet to discuss recent events in the MCB fields, and has proven to be a valuable way to connect to the community outside of my benchwork.

I hope 2016 will be an exciting year, scientifically and otherwise, for all of the readers of The Biology Blog!

Happy New Year!,