Dysregulated metabolism and Lolita

Here is a website graphic I made for a brand new professor at Berkeley. He studies how perturbations, or dysregulation, in metabolic pathways can lead to inflammation, cancers, and neurodegenerative diseases. By using liquid chromatography-mass spectrometry he can study the collection of metabolites in a biological sample at any given time, also known as the metabolome. He can probe one node and see how the levels of different metabolites in the vast network are affected. This concept reminded me of a passage in Nabokov's "Lolita" in which Humbert likens himself to a spider who spins a web throughout the entire house so he can pluck one strand and locate the exact whereabouts of Lolita, then guess at her activities. Creepy... but very memorable.

nano-MRI

Once again I'm been remiss in posting, so I'll make up for it with a three video series. These go along with a video in which an MIT grad student talks about a technique called nano-MRI. It's like atomic force microscopy meets nuclear magnetic resonance, and instead of brain scans of humans, these MRIs measure structures on the molecular (nano to be precise) scale. One of the long term goals is to use it to look at whole viruses in action and see exactly how they work. I wonder if they need the viruses to lay perfectly still to get the scan as humans do. I suppose they could just tether them to the surface, which I would imagine would not be nearly as anxiety-inducing to a virus.

The videos would make more sense if you could hear the narration, but hopefully before long all of the videos will be freely available. I can't wait to show them to my own students.

Have you thanked your free radicals today?

We hear so much about the havoc that can be wreaked in our bodies by free radicals running amok that it's easy to forget why they're there in the first place. They're actually pretty useful in protecting us from foreign invaaders like bacteria, and maybe even cancer cells that crop up within us. This animation is about how oxygen can trigger the generation of a whole host of reactive oxygen and nitrogen species that our immune cells, like the macrophage shown in this video, can use to destroy pathogens.

A nickel for your ulcers?

Here's the latest animation for the educational video series. This draft is still a little artifact-y but will be in tip top shape soon.  It describes how the bacterium Helicobacter pylori, the causative agent of ulcers, survives the harsh acidic environment of the stomach. Using a nickel-dependent enzyme that catalyzes the production of ammonia, it can neutralize the acid in its immediate environment and cloak itself within a buffer zone. In this way it swims through even the most acidic parts of the stomache unscathed. Since we humans don't have much need for nickel, processes like this one that require nickel have become attractive targets for antibacterial intervention.

 

Flashy Proteins

This is a Flash animation I made for an educational series of videos in which researchers describe their work. Very fun project. This one shows an enzyme transfering a fluorescent probe to a target protein, sort of like hanging a cow bell around the protein's neck so that one can keep track of it while it grazes the intracellular milieu.

A return to my multivalent roots

 

Here's a project I did this week for a company in the UK. They attach growth factors to a flexible and biologically compatibe backbone to improve efficiency and bioactivity. I spent most of my postdoc thinking about multivalency so it was neat for me to see this technology put to use to dramatically (by orders of magnitude) reduce the numbers of growth factors necessary to do the same job - just by stringing them together.

For most projects I rely almost entirely on Adobe Illustrator, but this one called for some Photoshop, which allowed me a self-refresher in the methods I learned in that segment of my digital design certificate program. To make the red growth factors look like are are really embedded into the orange receptors, I used the same techniques that magazines use to remove pimples, wrinkles, and dimples (not the good kind) from celebrities. So I guess I've got that to fall back on.

Congratulations Bruce Beutler

In honor of Bruce Beutler, one of the recipients of this year's Nobel Prize in Physiology or Medicine, here is an illustration of Toll-Like Receptor (blue) signaling that I did years ago for a company whose scientific advisory board includes Dr. Beutler.

I wish I had an image related to quasicrystals in my back pocket for the winner in Chemistry, Daniel Shechtman, but since no one even really knows what they look like, that'll have to wait.

Toying with Zinc

Today I spent some time on a draft of one of my cover art projects, which is going to be submitted with an article to the Journal of Inorganic Biochemistry. What's happening is that this big honking molecule acts like a cage for zinc that can distract it from its usual biological endeavors. However, if the molecule is exposed to a certain wavelength of light, photolysis occurs, which means that a bond breaks and the molecule separates into fragments that are no longer strong enough to contain zinc. Being able to control zinc concentration in a time-dependent manner can hopefully answer some interesting questions about neurobiology!

More animation: quantum dots

It still needs some polishing but here's another draft animation (the slow version) for the project I mentioned in the last post. This one goes with a video about quantum dots, and describes how their super small stature gives them properties similar to atoms. Namely, they can absorb and emit light. Electrons get promoted to higher energy levels upon absorption of light, and the difference in energy levels corresponds to the energy, and thus the frequency, of light emitted. What is cool about quantum dots is that they absorb/emit different colors based on their size. So smaller dots glow blue, larger ones red, etc. Coincidentally, this week I taught my student about atomic line spectra, the same concept but just for atoms, not quantum dots. At least this week my brain didn't have to switch wavelenths.

Works-in-progress: Helpful microbes turn pollutant to fuel

Since I've been remiss in posting, I'll make this a double post. The still image and animation are both part of a project in which short video clips have been recorded of researchers talking about their work. My job is to add images and animations that illustrate what they are describing. The two items below both have to do with bugs that can gobble up carbon dioxide, a potentially useful trait in itself, and then proceed to convert the carbon source into something that can be used as fuel. The animation is creepily slow here because of the frame speed I had to use to convert it from Flash to Quicktime. Once embedded into the video, it will be quicker and less hypnotic.

Untitled from Mary O'Reilly on Vimeo.

 

Balancing equations: the movie

 

This afternoon I spent a little time putting together an idea for an animation to describe balancing equations. It would ultimately be interactive, with the students hitting the "Add a mole" buttons themselves, but this is just meant to be a simple demo. I wish I could say that I am such a devoted adjunct assistant professor that I spend my Sundays making interactive Flash animations for my students (if you've been following for awhile then you've seen that I do make animations for them, but they're low-budget Keynote jobbies), but in actuality this is brainstorming for an all-digital general chemistry textbook that I am lucky to have been asked to contribute to. The challenge for this particular animation is that the students using this textbook will not have seen molecular structures before, so I can't use them to demonstrate the reaction stoichiometry as I usually do. Never have my two jobs been so overlapping, but I think that's why I was chosen for this book. More animations to come soon!

Design challenge: simplicity

Some months ago I was hired by my undergraduate research advisor to create a figure for a paper she was preparing to submit, and here it is, now that the manuscript has been accepted. As an undergraduate I worked in her lab for over two years, where I fell in love with research and learned everything from how to run a dry reaction to the difference between a sipping tequila and the kind you make margaritas with. She is the reason I went to MIT, and her example greatly influenced my career goals. After everything she's done for me, I told her I couldn't take any money for the project, but she refused to give it to me unless I charged her what I would charge anyone else. Her vision for the figure was to keep it very simple, in a sort of Japanese minimalist style. I actually find this more challenging than the typical style I use. Every mark really counts, as well as the precise placement of every element. It is an important style to master when the main goal is communicating, as it almost always is, and it is something I am continuing to practice. Here, an inhibitor of reverse transcriptase, a target for HIV-1 therapy, has been synthesized as a dimer through a disulfide bridge. The dimerized version acts as an inhibitor of the transmembrane P-glycoprotein, which captures small organic molecules non-specifically and transports them out of the cell, foiling attempts to deliver drugs to cells. While holding up the P-glycoprotein, other dimers get into the cell, where the reducing environment breaks the disulfide bond and intracellular esterases chew off the linker. Monomers of the drug are then free to inhibit the reverse transcriptase. It is an elegant system that deserved an elegant visual representation. I am no Piet Mondrian, but then in art I've always favored abstract expressionism, which is exactly what the minimalist movement rebeled against. So therein lies the challenge. But what's a good career without any challenges?

What next?

Two weeks ago I was drawing zebras and cross-dressing horses. Last week I was reading up on Boolean logic. Now I'm making figures to describe the statistical analysis of mass spectrometry-based proteomics experiments. Here's one of them, which mainly describes how subjects are chosen from healthy and diseased populations. This is the second of four figures, and they just keep getting more and more complicated. This project definitely put my design skills to the test. It's not done, but it is close. And next week? Next up is a graphical abstract that invokes the mythological story of Cupid shooting an arrow into Apollo's heart, causing him to fall hard for Daphne. The client had this idea as a metaphor for his system. It's my job to find a way to represent a huge honking natural product as an arrow. Should be a fun one.

Guess which one we're going for

Not only has this been a fun project for me, complete departure as it is from my usual subjects, the TA trainng illustrations hold some good lessons for me in my own teaching. With only a year under my belt, I am still learning how best to encourage and motivate students. Turns out it's not only the students who don't care or don't try who get C's, and when they come looking for help, it's really important not to scare them away. Sometimes it feels like the most challenging part of the job takes place outside of the classroom. I may never get used to the tears, but hopefully I will grow to respond without an awkwardness akin to watching a commercial for feminine hygiene products with one's father.

Another take on the imposter syndrome

This is a different take on the same idea described in the July 18 post. Instead of an owl feeling like a turkey, it's a horse trying to pass itself off as a zebra. It's a subtle difference, but the point is still the same - that almost everyone feels like an imposter at some point. It's best not to feed into these fears in other people, or yourself.

This series of six illustrations is almost finished, and then I'll be back to the nano-scale again. It's been a really fun departure from the usual material, but I'm excited about some new projects on the horizon as well. More on those soon.

Misperceptions in the absense of feedback

This cartoon was done for the HHMI-funded training program I talked about on July 13 and 18. The scenario depicted was inspired by actual events described to the PI on the grant by a female student. She felt that she got zero feedback from her advisor, as opposed to her male colleagues, which led her to think that he didn't even care enough about her or her project to be angry at her. More likely, he wanted data from the male student for a particular reason, but when no feedback is given, imaginations are given free reign to fill in the gaps. The training is about giving feedback, but giving it wisely, and not just to certain students. As a side note, it has obviously been awhile since I ran a column. Now that I think about it, I doubt she would have collected that many fractions in only 15 minutes without pushing air through the column. As fueled as she is by disappointment and resentment, these forces cannot contend with gravity. I may need to edit this a bit.

Girl with Bowler Hat & the North County Coastal Businessman

In an effort to ward off cabin fever, I've taken my work out of the house a couple of times this week. The work I've been doing over the past few days isn't really worth showing yet, so instead I'll show you what I did during my breaks. Because one of my current projects involves illustrating humans, it's a good time to get some fresh practice drawing people. From my perch next to the window inside a cafe, I had a great view of people sitting outside. The hardest part of doing sketches like these is the hands. Not only are hands notoriously hard to draw, they are the parts that we seem to most often move, even when we're sitting still. So cut me a little slack on the weird looking hands, they are partially drawn from memory. And lest there be any misinterpretation, that is a pen in the man's hand. The young lady is texting, I believe.

The truth about my inspiration

Like the post on July 2nd, this figure is for a systems biology textbook that a client is writing and I am glad to be involved in. For this one, he sketched out roughly what he wanted to go into it and I turned it into this. At this point we'll probably make some decisions about the style of the illustrations that will go into the book, since we'll want to keep them consistent. For instance, I've been using my two-toned shaded but sort of 2D representations of proteins. I have a few different ways of representing proteins, but when I can't use real X-ray crystal structures, this is probably my favorite. I'd like to say that my style was influenced by Picasso or Cassandre. The truth is, it is inspired by watching the cartoon Aqua Teen Hunger Force on TV (particularly the character Meatwad). I was looking to strike the balance between simplicity and aesthetics, and this is what happened. We'll see if it sticks.

 

Ever feel like a turkey?

This sketch, illustrating imposter syndrome, is in the same series as the sketch from the previous post. This training session is given broadly, but is in large part designed for teaching assistants at MIT. When I was a TA at MIT for freshman chemistry, I was surprised to find that my students were not robot geniuses speaking in a secret language of differential equations, but rather they were for the most part 18 and 19 year olds terrified of not living up to expectations. I could relate, because as a 1st year grad student, I was still a little nervous about whether or not I belonged there too. An extreme form of this is called imposter syndrome, in which one believes that he or she doesn't belong, and lives in fear of being "found out". Hence the wise but self-doubting owl in the illustration, seeing itself in the reflection as a decidedly less clever species of bird. This is why educators should be careful to use "wise criticism" when talking to struggling students, as opposed to saying things like, "So... your family must have a strong alumni connection to this school?"