How It's Made - derivatized carbohydrates

I've been wanting to do a drawing like this for a long time, and finally a project came along that was perfect for it. It's for cover art, so I can use quite a bit of artistic license, and the article it highlights is about metabolic engineering, or hijacking a biosynthetic assembly line to put a modified sugar on the cell surface. I left off some details on the rough sketch here since it's not published yet, but I'll post the final image when it is. The plan is for this drawing to be done in white and overlaid on top of a sweet image of a glowing zebrafish head from the paper.  As a side note, I watched some clips of "How It's Made" for a bit of inspiration. We love that show around here.

Running Interference

This animation goes along with a video of a postdoc describing her research in RNA interference. She starts by explaining that a short stretch of double-stranded RNA is complementary to a stretch of DNA in the genome. When the interfering RNA enters the cell, it binds to and is separated into single strands by a multi-protein complex called RISC. RISC tosses one strand out and then uses the remaining one to guide it to mRNA that bears complementarity to the short interfering RNA strand. Once that mRNA is found, a protease within the complex destroys it so that it can no longer be translated into protein. The hope is that this could be used to combat diseases that are manifested by overexpression of certain proteins.

Please take a moment for reflection...

First project on my new computer! As you can see, the reflection of this molecule is not exactly true. I am wondering how recognizable this image is, so if you would be so kind as to help me out, please leave a comment here or send me a message through the contact page to tell me what you think the molecule in the reflection is made of. Thanks!

Update on 2012-04-04 03:22 by Mary

With some help from a facebook poll, I found that most people recognized it as what it is - corkscrew pasta, aka tricolor rotini. The molecule itself is folic acid, which is found in pasta and bread, among other foods. One person guessed Twizzlers. Another thought it was DNA, which makes sense considering that the rotinis are right-handed helices. Perhaps these rotini will be of use for a future project.

A Matrix-inspired cover design

Last week my computer completely died and although I had backed up recently, I lost two days worth of work on projects that are both due tomorrow (above is one of four designs being submitted as possible cover art for one of the two projects). Also last week, the baby forgot how to take naps. As Steve McCroskey in Airplane! says, it looks like I picked the wrong week to stop sniffing glue. Thankfully I married some sort of wizard, because I met both deadlines, keeping a perfect record intact, the naps are back, and now I am going to sleep too.

Bringing grunge back

This started as a really simple mock-up design for a cover art project, and turned into a lesson in giving images that weathered, vintage look. When I decided to grunge it up, I turned off the meter so that my client wouldn't have to pay for the lesson, and searched for different techniques for doing this. What I ended up doing involved downloading some free splatter brushes for photoshop, adding noise and some eraser strokes, and incorporating a photo of our bathroom tile that I snapped with my phone. 

I Second That Stop Motion

This is a story about how urea-based compounds can sense ketones such as acetone and cyclohexanone, which are used in the purification of certain explosives and whose high vapor pressure make them useful for detection. Over the past few days I made this stop motion animation to play as the narrator (aka the graduate student working on this research) describes how ketones interact with urea. She explains that the lone pairs of electrons on the ketone's carbonyl oxygen "grab" urea's hydrogens. My collaborators suggested the arms literally reaching out and grabbing the H's, which then set the tone for the rest of the animation. The ensuing hydrogen bond between oxygen and hydrogen leaves the N-H bond to exist in a "lone pair-like" state. As my former Chem 151 students hopefully remember, a lone pair is believed to take up more space than a bond, therefore creating more repulsion of the neighboring bonds. The bond angles adjust to accommodate this change, and voila. This subtle change in structure is amplified through the connected polymer in such a way that both the fluorescence and refractive index properties of the compound are changed, and these changes can be measured. I never considered lone pairs to be such bullies but I guess they are kind of lone rebels. I'll bet Mala Radhakrishnan could write a poem about this...

No thanks, I couldn't eat another electron

This is a very simplified animation to show how molecular oxygen acts as the final electron acceptor after the food we eat is metabolized and turned into energy. I know what you're thinking, and yes, electrons are South Beach Diet-approved.

Work-in-progress

These days I've been working on this cover art piece highlighting a review article on photolyzable caging molecules. The one shown above binds to (cages) zinc until it's hit with light at a particular wavelength, which leads to bond cleavage. With the molecule split in two, it no longer binds zinc. This is a neat trick for releasing zinc at a specific time and place as controlled by the researcher, and may be a particularly useful tool in neurobiology due to the role of zinc in the central nervous system. The products of photolysis are shown as having been taken out of commission, lying helplessly on the floor.

Earlier today, I was responding to an e-mail from a graduate student I've been corresponding with who is interested in possibly pursuing a career in science illustration. She showed me a piece she had done as cover art and asked for feedback. I told her that when doing cover art, I start by looking at several covers from recent issues of the journal it's going to in order to get a sense of the style. More often than not, the editors seem to be looking for the most eye-catching graphic, not an image that seeks to tell a story or show details of the research it is highlighting. I admitted that it is a challenge for me to remember this, and had to laugh at myself when I finished the e-mail and then opened up the image above to work on.  I guess it's easier to give advice than take it, even when it's my own.

Stymied by X-rays

Here is an animation I made last week for the MIT/HHMI video series for undergraduates. In this video, a professor describes her work in X-ray crystallography, and in doing so explains the principles of light wave diffraction. That is where I come in. I make these animations in Flash, but create many of the images in Illustrator. Here I'm apparently approaching the limits of this strategy. These waves of X-rays brought in from Illustrator don't obey the timeline, but rather appear only when they are good and ready. Luckily the person who assembles this into the video can control the timing, but that's not an ideal solution. I'm still deciding what is the best way around this without compromising the quality of the images, probably by rasterizing or flattening the transparency, but in the background I am hearing the call of 3D animation software growing louder and louder.

When snapshots don't tell the full story

Here are a couple of images I made for a client to submit as cover art for his article, which just came out, so I can show these now. The idea is that a certain ligand undergoes a conformational change in the binding pocket of a protein, but this change happens too rapidly to see it by X-ray crystallography. Instead, they used nuclear magnetic resonance spectroscopy (NMR) to capture this interesting behavior. In X-ray structures, the ligand always appears to be in the same conformation. The time scale of NMR enabled the authors to observe two different binding modes of the ligand, and show that the switching between these two binding modes happens in the binding site. Pretty cool stuff.

On the fruits of my sleep deprivation

This image will show up soon on the back cover of a review journal and is the first project I did after having the baby. In my sleep-deprived state I have no idea where the idea came from, though now that I'm thinking about it, I am reading Haruki Murakami's new novel, 1Q84, which has to do with a cult. Could that be why it looks like a bunch of trans-azobenzenes just drank the Kool-Aid, but only one was chosen for salvation? In fact, it is supposed to demonstrate the light-activated isomerization of a substituted azobenzene from trans to cis. The review deals with various substitutions on the rings and the different mechanisms of isomerization. In case you are wondering, cis-azobenzene does not then ascend into heaven. It just thermally relaxes anti-climactically back to the trans conformation.

Hijacking pathways to make way for biofuels

This is how a certain bacterium uses carbon sources in two different biosynthetic pathways.

And this is how you can get more biofuel made by deleting a competing pathway!

Bringing the prostate into focus

I made this image from an actual photograph of a mouse prostate in hopes of getting the cover of a journal for a client who investigates imaging technologies for cancer diagnostics.  The idea is that with better imaging, a better picture of prostate cancers can be deciphered. Hence, the manually pixelated image (I know, I could do it with a click in photoshop but I didn't like the results so I did it manually box by box, with a slightly transparent version of the original photo overlaid). The groovy 70's background was made, surprisingly, with only colors taken directly from the prostate photo.

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.

There's no shame in loving your favorite protein

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.