The Art of Basic Science #6

This month I thought I'd try a New Yorker cartoon-style piece. My seventeen-year old niece who is crushing her pre-college summer biology course approves.

Seven-day cross-country catch-up: Day 6

Today we arrived in Boston. Ever since I left here 11 years ago I've missed it terribly, so when the hubs joined a small start-up that would ultimately lead us here, it was a dream come true. Before the move I borrowed "Make Way for Ducklings" from the library to read to the boys. As the moving truck was getting unloaded and I led the ducklings from Indiana today I thought of Mr. Mallard frantically getting the boys' rooms ready for them. The boys did not follow after me in a neat line, and no policeman helped me, but we survived. And they were very excited about their rooms.

While I'm feeling wistful I'll share this cover that I made for the Bundle lab, which is possibly the last one after years of making covers for them, as I'm losing this venerated client to a well deserved retirement. I felt a little better when I learned that my former lab-mate and current friend will be taking over the lab space in the fall to start his independent career.

Here is the paper the cover highlights:

Synthetic glycoconjugates characterize the fine specificity of Brucella A and M monoclonal antibodies.

Mandal SS, Ganesh NVSadowska JMBundle DR.

Org Biomol Chem. 2017 May 10;15(18):3874-3883. doi: 10.1039/c7ob00445a.

Seven-day cross-country catch-up: Day 5

Here's a JACS Table of Contents graphic that I made for the Pratt Lab at USC. They made a new metabolic chemical reporter that gets incorporated into O-GlcNAcylated proteins preferentially over cell surface glycoproteins, making it a handy tool for identifying more proteins that have the O-GlcNAc modification. Using it, they discovered not only that Caspase-8 gets modified with O-GlcNAc, but that the modification slows down the self-cleavage event that can lead a cell down the path to apoptosis. Which is very exciting, because apoptotic cells are so much fun to draw. And I guess also because they discovered a potential anti-apoptotic mechanism. Read all about it here:

The New Chemical Reporter 6-Alkynyl-6-deoxy-GlcNAc Reveals O-GlcNAc Modification of the Apoptotic Caspases That Can Block the Cleavage/Activation of Caspase-8.

Chuh KNBatt ARZaro BWDarabedian NMarotta NPBrennan CKAmirhekmat APratt MR.

J Am Chem Soc. 2017 May 31. doi: 10.1021/jacs.7b02213. [Epub ahead of print]

Seven-day cross-country catch-up: Day 4

We are still a couple of days from arriving in Boston but to follow on yesterday's theme of Harvard post docs, this piece was commissioned by a post doc (Rio Sugimura) in George Q. Daley's lab at Harvard Med School/Children's Hospital Boston for a press release on their recent Nature paper. They describe taking one big step closer to creating blood stem cells from a patient's own cells. Shown in the illustration are blood stem cells emerging from hemogenic endothelial cells. You can find all of the details here:

Haematopoietic stem and progenitor cells from human pluripotent stem cells. Sugimura RJha DKHan ASoria-Valles Cda Rocha ELLu YFGoettel JASerrao E7, Rowe RG1, Malleshaiah M8, Wong ISousa PZhu TNDitadi AKeller GEngelman ANSnapper SBDoulatov SDaley GQ.

Nature. 2017 May 25;545(7655):432-438. doi: 10.1038/nature22370. Epub 2017 May 17.

Seven-day cross-country catch-up: Day 3

This is a project I just finished up a couple of weeks ago for a young up and coming assistant professor who came from a post doc at Harvard and Mass. General Hospital and is starting his independent career at Rutgers. These illustrations were made for his website, where you can find the captions and more details of his research program: www.izgulab.com

Seven-day cross-country catch-up: Day 2

Today I'm sharing some PowerPoint slides I made for Prof. Shana Sturla at ETH. Since we had plenty of time I really got to sink my teeth into this project and after some great discussions we came up with these new slides for her talks. In related news, another client recently asked me for a gif of illustrations I made for them. So now I make gifs, evidently. 

Seven-day cross-country catch-up: Day one

Because we are in the process of moving from San Diego to Boston and because my computer is in a truck trailer somewhere in the middle of the country, I'm doing something a little different in lieu of The Art of Basic Science this month. I realized I've been remiss in posting actual client work so I'm going to post something every day for a week to share some of the projects I've been doing over the past few months. 

This is another cover I did for the Mankad Lab at University of Illinois at Chicago, highlighting the power of bimetallic systems in selectivity. Here it is used to favor one transformation over another. You can read more about it here:

Fundamental organometallic chemistry under bimetallic influence: driving β-hydride elimination and diverting migratory insertion at Cu and Ni.

Mazzacano TJ1, Leon NJWaldhart GWMankad NP.

Dalton Trans. 2017 May 2;46(17):5518-5521. doi: 10.1039/c6dt04533b

The Art of Basic Science will return in July, and I'm feeling particularly inspired after I finally made it to LACMA (Los Angeles County Museum of Art) the day before I left California. 

The Art of Basic Science #5

For the fifth installment of this series, I chose a paper from the labs of Donna Blackmond and Alan Aspuru-Guzik in the current issue of ACS Central Science. It deals with the age-old question of how chirality arose in the origins of life, and finds that chiral pentose sugars are capable of tipping the scales toward specific enrichment of L-amino acid precursors. I won't go into the details since that isn't what this series is for, but you can see for yourself here:

Chiral Sugars Drive Enantioenrichment in Prebiotic Amino Acid Synthesis. Alexander J. Wagner, Dmitry Yu. Zabarev, Alan Aspuru-Gusik, and Donna G. Blackmond. ACS Cent. Sci., 2017, 3 (4), pp 322–328.

Rather, it is just meant to be a celebration of basic science, the anything-but-basic folks who dedicate themselves to the craft, and, in this case, open access to it, thanks to journals like ACS Central Science. If you look at it long enough you should see two distinct alpha helices along with ribose, one of the featured (and notably pre-biotically plausible) stars of the show. If you look at it even longer a 3D dolphin will pop out. Oh no wait that's magic eye posters. Never mind.

If at first you don't succeed, try again three and a half years later

The recent Chemical Science cover below was developed from a concept I used for candidate cover art three and a half years ago with the same client, the Mankad Lab at The University of Illinois - Chicago. It was originally made for a JACS cover (see bottom image), but as I now understand, JACS editors generally seem to prefer eye-catching images of chemical structures, with minimal interest in the metaphorical, whimisical, or comical. My client had the idea to reprise it and lo and behold it worked!

The Art of Basic Science #4

On this April Fool's Day I decided to feature a guest post for the fourth installment of this series. The guest is my 5-year old son, who stated his intention to grow up to be a scientist, and then someone who draws science to explain it to other people. This was quite a departure from fire-fighting astronaut, but I suspect he began to realize that the lack of oxygen in space might impact his employment prospects. 

I sometimes take advantage of time spent "coloring" with the kids to sketch out ideas for projects. But it was just a week ago that my 5-year old wanted to start copying what I was drawing. Which is how he came to be a guest illustrator for this series. This drawing comprises DNA polymerases, nucleotide triphosphates, methylated template DNA, PCR products (both pictorial and in-gel), and the hydrogen-bonding pattern of a DNA adduct to a cognate non-natural nucleoside. My sketches are pretty rough so I must admit that it isn't a very big stretch from my version. 

This installment is inspired by work in Shana Sturla's lab at ETH.

The Art of Basic Science #3

Flexibility of substrates has been found to play a key role in the action of Fatty Acid Amide Hydrolase (FAAH), a critical enzyme of the endocannabanoid system. This image was inspired by the work of Marco DeVivo's lab at the Molecular Modeling & Drug Discovery Lab, which is part of the Istituto Italiano di Tecnologia in Genoa, Italy,

The Art of Basic Science #2

Here is the second installment of the series I introduced here on January 1st. Recently I became briefly obsessed with patterns, related perhaps to the nostalgic feeling I get any time I see 1970's wallpaper. In spite of my most earnest efforts toward minimalism, sometimes I have to give in to the urge. In my defense, I thought this might be a good way to evoke a sense of the complexity of cellular systems.

In the pattern above, the Pac-men are enzymes that use reactive cysteines in their active sites to carry out their jobs. The triangles are groups that latch onto cysteine if its thiol is available and sufficiently reactive, and these groups are tagged with tracers that are either heavy (red) or light (blue) so when used in parallel, changes in reactivity within the same enzyme upon treatment of some sort can be revealed. It is a clever method for making mass spectrometry, a technique that is not necessarily quantitative by nature, quantitative. If there was a way to do that for humans, maybe I would still be at the bench. Anyway, for the vast majority of enzymes that react with the probe, there will be equal amounts with heavy and light tracers, meaning there was no change in reactivity associated with the treatment. But, when you discover enzymes that have blue:red ratios other than 1, like in the overlaid trace above, then you may have just discovered a previously unknown function for an enzyme, a clue to a regulatory mechanism, or even a new drug target. 

The inspiration for this comes from a plethora of papers from the Weerapana Lab at Boston College, which has pioneered the method for this purpose. 

Check back March 1st for the next installment!

Publishing in style

Here are a couple of figures I made for recent papers out of the Soh Lab at Stanford. I've been fortunate to do a number of projects with them, and what's nice about developing a relationship with a lab like this is that I can try to develop a consistent and recognizable style for their figures. There's a precipitous drop in cost after the first one or two figures since I have become familiar with their science and the aesthetic style has been established. And besides, I get to know the grad students and post docs with whom I hope to populate my future client pipeline, mwah ha ha.

Angew Chem Int Ed Engl. 2016 Dec 9. doi: 10.1002/anie.201608880. [Epub ahead of print] Multiparameter Particle Display (MPPD): A Quantitative Screening Method for the Discovery of Highly Specific Aptamers. Wang J, Yu J, Yang Q, McDermott J, Scott A, Vukovich M, Lagrois R, Gong Q, Greenleaf W, Eisenstein M, Ferguson BS, Soh HT.

Angew Chem Int Ed Engl. 2016 Dec 9. doi: 10.1002/anie.201608880. [Epub ahead of print]

Multiparameter Particle Display (MPPD): A Quantitative Screening Method for the Discovery of Highly Specific Aptamers.

Wang J, Yu J, Yang Q, McDermott J, Scott A, Vukovich M, Lagrois R, Gong Q, Greenleaf W, Eisenstein M, Ferguson BS, Soh HT.

High-Throughput Discovery of Aptamers for Sandwich Assays. Csordas AT, Jørgensen A, Wang J, Gruber E, Gong Q, Bagley ER, Nakamoto MA, Eisenstein M, Soh HT. Anal Chem. 2016 Nov 15;88(22):10842-10847.

High-Throughput Discovery of Aptamers for Sandwich Assays.

Csordas AT, Jørgensen A, Wang J, Gruber E, Gong Q, Bagley ER, Nakamoto MA, Eisenstein M, Soh HT.

Anal Chem. 2016 Nov 15;88(22):10842-10847.

The Art of Basic Science

Happy New Year everybody! Usually at this time of year I post about the O'Reilly Science Art holiday party of two, but the hubs and I couldn't secure a sitter this year. Instead, I am eager to announce a new series for this website. While I love doing The Short Answer and would be thrilled if anyone commissioned me to do one for their work, I had a feeling that after two years here it had run its course. So lately, I've been cooking up a new series that uses a more fine art-inspired brand of illustration to celebrate everyday discoveries in chemistry and biology. They won't be the stories you see in the New York Times or on Nova, but the indispensable yet unsung advances upon which those larger discoveries are built. So I give you, The Art of Basic Science. 

The inaugural piece was inspired by a new tool that helps to show us what de-ubiquitylating enzymes are doing (see reference to paper below image). For a long time we thought of ubiquitylation as a simple tag for proteins on the way to the cellular landfill, but we are beginning to understand the dynamic and modular nature of this post-translational modification and its importance in a number of disorders. The artwork, loosely inspired by the likes of Klee and Kandinsky, is meant to illustrate the beauty of ubiquitin itself, its propensity for forming chains which are typically represented as a series of circles, and to invite you to imagine these circles being removed and replaced in a dynamic fashion. 

Selenocysteine as a Latent Bioorthogonal Electrophilic Probe for Deubiquitylating Enzymes

Samuel D. Whedon, Nagula Markandeya, Ambar S. J. B. Rana, Nicholas A. Senger, Caroline E. Weller, Frantisek Tureček, Eric R. Strieter, and Champak Chatterjee

J. Am. Chem. Soc., 2016138 (42), pp 13774–13777

Saving clients money one carbon footprint at a time

This is a graphical abstract I did for a paper published by a group at the La Jolla Institute for Allergy and Immunology (see reference below image). Since the lab is local, I was able to meet with them in person to talk about the project, and here is how this entire project was completed in only 6 hours. The night before we met, I read their paper. The next morning, I drove down to La Jolla, and on the way I had an idea. Getting there a little early, I was able to sketch it out in my car before I went in. We fleshed it out on the white board and I was back in the car 25 minutes later. I went home and drew it. That was pretty much it. As much as I dislike driving, I know that it is a great time to get ideas, much like being in the shower, which is the primary way that I come up with them. But if someone could just tell me one way to get ideas without wasting natural resources I would be much obliged. Thanks.

 

Deleting an Nr4a1 Super-Enhancer Subdomain Ablates Ly6Clow Monocytes while Preserving Macrophage Gene Function.

Thomas GD, Hanna RN, Vasudevan NT, Hamers AA, Romanoski CE, McArdle S, Ross KD, Blatchley A, Yoakum D, Hamilton BA, Mikulski Z, Jain MK, Glass CK, Hedrick CC.

Immunity. 2016 Nov 15;45(5):975-987. doi: 10.1016/j.immuni.2016.10.011.

Anderson Lab feature article gets the cover

This cover that I made for Jared Anderson's group at Iowa State University just came out. It highlights a feature article they wrote about sample preparation for bioanalytical and pharmaceutical analysis. I learned that we've come a long way from phenol-chloroform extractions as the main way we get DNA from cells. For anyone who knows anything about this, I am dating myself, but the first experiment I ever did in a non-classroom laboratory started with doing mini-preps using phenol-chloroform extraction. By the time I got to grad school we used these adorable little centrifuge tubes equipped with filters to do mini-preps, and you could finish one before your coffee got cold on your desk. Now they're using microfluidics to separate DNA from proteins and other flotsam and jetsam. I know very little about microfluidics, but I am always reminded of a seminar I saw over a decade ago at MIT from an up and coming Rustem Ismagilov, a professor at CalTech. It was common for researchers to photograph their microfluidic devices next to a penny to demonstrate the impossibly small size they were able to achieve. Professor Ismagilov told us how, as he embarked on this field of research, the first thing he did was to go out and get a really really big penny. Maybe the funniest thing I've ever heard in a seminar. 

Below are the sketches I presented to the Anderson Lab for consideration. They discuss many techniques in the paper (magnetic ionic liquids, solid phase extraction, etc.) so it was a challenge to try to work in as many as I could. They chose the second sketch. I don't know the reason, but maybe having the bacteria and pills looking like so many college freshman was a bit much.

Weerapana Lab website gets a long overdue upgrade

When my good pal Eranthie started her lab in Boston College's chemistry department, I illustrated a home page image for her (below). It lived there for 6 years. 

It's pretty generic and outdated, way too superhero comic-y, and frankly I generally don't like to look at anything I made that long ago. But because she is way too loyal I knew she would never change it unless I made something to replace it. So as a gift to congratulate her on getting tenure, I came up with three new designs. Her students voted and chose the one below.  I like it now but I'm sure I'll be ashamed to look at it by the time she gets promoted to full professor. At least I hope so. 

A throwback in honor of the 2016 Nobel Prize in Chemistry

When I was a postdoc in Jim Paulson's lab studying multivalency in protein-carbohydrate interactions, I was invited to the Frie Universitat in Berlin to give two talks, one about multivalency in nature and chemical methods to mimic it, and one specific to my own research. I made the illustration below for the former, to describe a self-assembled pseudopolyrotaxane, often described as the molecular equivalent of beads on a string. It was developed in the lab of Fraser Stoddard, one of the three winners of the Nobel Prize in Chemistry that was just announced. In this collaboration with Linda Baum's group, they built a scaffold of the pseudopolyrotaxane that multivalently displayed a carbohydrate ligand (in yellow), and precipitated its dimeric cognate lectin, galectin (in gray), by forming cross-links like you see in the illustration. The circles you see in between the "beads" are positive charges that act as speed bumps, to stall the beads from just falling off of the string. I remember thinking that this was incredibly cool, and in retrospect apparently just the kind of ingenuity that puts you in line for a Nobel Prize. Looking back on this illustration reminds me of how immensely satisfying I found it to create all of these new illustrations for my talks. I was just on the cusp of letting go of the idea of an academic career in favor of, for lack of a less cliché phrase, following my dream. But at the time I was my only client, and I didn't pay well. Somehow I didn't enjoy it any less. 

Transcription factors: the high school guidance counselors of the cells

I was commissioned by the DeVal Lab at the Ludwig Institute in Oxford to create this little animation that explains very simply for a general audience how different transcription factors trigger cells to become either arterial or venous cells. The lab was an absolute dream to work with and the animation has been a lot of fun to make. And how lovely is it with the British-accented voiceover done by the client? People pay good money for that here!