Happy holidays!

December 18, 2013 § Leave a comment


Wild Types will be taking a short holiday break. To tide you over the holidays, check out the science versions of holiday songs that I, ASBMB editor’s Angela Hopp and ASBMB’s two science policy fellows, Chris Pickett and Shaila Kotadia came up with (we call them “Lab Carols”):

http://www.asbmb.org/asbmbtoday/asbmbtoday_article.aspx?id=49835

Wishing my readers the very best for 2014 🙂

Reporter’s notebook: the pizza that launched 3,000 words

November 4, 2013 § Leave a comment

Naked Pizza graces my pizza parties.

Naked Pizza graces my parties.

In January, there was an email waiting for me from an ASBMB member when I got back from vacation. Congratulating me on my story on omega-6 fatty acids in the American diet that had appeared in the December 2012 issue of ASBMB Today, the member told me that there was another nutrition controversy that needed to be explored: the glycemic index.

I’d never heard of the glycemic index. My dietary attitude is simple and reflects my life motto: Embrace all good things and avoid fakes.  Besides, I felt it was too soon for me to do another nutrition story. So I filed the email away.

Early in the summer, after a crazy work day and with no meals ready in the fridge, I declared it to be pizza night. Over the years, I flirted with various local artisanal pizza deliveries, and Naked Pizza is my latest love. There aren’t too many outlets in the region so I consider myself lucky to live in an area with one. I love the taste of the “Ancestral Blend” crust. The pizza isn’t a grease pool. I can’t resist the garlic, cilantro and artichoke combo in the “Superbiotic.”

The Naked Pizza box is, in it of itself, reading material. The box is covered with little comments. While munching on a slice of “Superbiotic” that night, I idly twisted the box around to continue reading. There is was: A box explaining that Naked Pizza pies have a low glycemic index.

I stopped mid-munch—my favorite pizza place seemed to endorse the glycemic index. The next day at work, I pulled up the email I received in January and reread it. The member had sent me a scientific paper that explored the impact of high and low glycemic index diets on chronic metabolic conditions. I began to search PubMed for papers about the index. One of my first hits was a white paper by Health Canada saying that the authority would not use the index on food labels. The paper had just been published. So the discussion over whether or not the glycemic index was a useful measure was still ongoing and seemed to indicate that the controversy was not laid to rest.

I searched the Internet to see if any magazines had covered the index. Except for a few blog posts, my searches didn’t show up anything. Did I have a story here?

Like the omega-6 story, the glycemic index story wasn’t an easy one to write. Because the topic is controversial, it was very important that I came to understand the nuances of the science being disputed. There were times I doubted I had a story to tell. But with firm urging and cajoling by ASBMB Today’s intrepid editor, Angela Hopp, the story began to take shape over the course of three months. You can see the result in this month’s ASBMB Today.

Has reporting on the glycemic index changed my opinion of my favorite pizza? No. I still regularly order it (I now alternate between “Greenhouse” and “Mediterranean” as my favorites),  and I’ve gotten friends hooked onto it. Indeed, every time I invite folks over for wine-and-pizza nights, they ask, “Are we getting Naked?”

Finally getting an answer to a question (and a profile on an interesting scientist)

August 9, 2013 § 3 Comments

Virginia Lee

Some stories just take a long time to be born. This month’s issue of ASBMB Today has a profile I did on Virginia Lee, the director at the Center for Neurodegenerative Disease Research at the University of Pennsylvania. This profile was more than 10 years in the making.

I first met Virginia when I was a green-behind-the-ears graduate student at Johns Hopkins University. I don’t recall the exact year, but I’m guessing it was around 2000, and so I must have been in my second year of graduate school.

My thesis adviser, Jan Hoh, had invited Virginia to give a seminar at our department because Virginia was working on a protein called tau, which belongs to the family of microtubule-associated proteins and forms neurofibrillary tangles in a number of neurodegenerative diseases.  My thesis project focused on deciphering the biophysical properties of tau and another microtubule-associated protein called MAP2.

We had a hypothesis that these two proteins were intrinsically unstructured and formed polymer brushes on microtubules to keep microtubules properly spaced apart from one another in neurons. (Note that I was working on intrinsically unstructured proteins way before they became the hot topic they are today.)

I don’t recall a word of Virginia’s seminar, but I never forgot the impression she made. She commands attention in a room. She is articulate, sharp and charming. As a young and inexperienced graduate student, I was intimidated by her because I felt I couldn’t measure up to this confident and charismatic woman.

Lee already had spent some time chatting with Jan about the work we were doing on intrinsically unstructured proteins, so, when Jan brought her over to meet the members of the lab, I immediately clammed up (very unusual for me, as my family and friends will attest). I was terrified I’d say something stupid, so I let the more senior graduate students and postdocs do all the talking.  I simply sat there, to her left, watching her in profile as she talked.

I don’t remember how the subject came up, but the only thing I do recall Lee saying was that she trained as a concert pianist in London before becoming a scientist. She said it in passing, and the conversation moved on.

But I did a double-take and stared at Lee. I trained in piano for 10 years, going through the U.K.’s Royal Schools of Music syllabus and exams. I got as far as grade 7 before I quit.  I knew how rigorous and hard it was to get even as far as the last grade, grade 8, of the syllabus, let alone beyond. At that point, I was awestruck and even more intimidated by Virginia.

But my curiosity was aroused. How do you go one route and then switch to a different route that is seemingly unconnected to the first?

Fast-forward now by 10 or so years to March of this year. Virginia’s group published a Journal of Biological Chemistry paper that was selected as a Paper of the Week. I am responsible for writing the summaries of these papers. Seeing Virginia’s name on the paper took me back to that day in graduate school when I heard her say she once trained as a pianist.

On a whim, I looked up Virginia in ASBMB’s member directory. There she was, a member of the society, giving me the green light to approach her to do a profile for the membership magazine.

And finally, more than a decade later, I learned how she went from being a pianist to a scientist.

Name ASBMB’s knockout mouse!

April 1, 2013 § Leave a comment

The mascot for the American Society for Biochemisty and Molecular Biology needs a name for the upcoming Experimental Biology 2013 meeting. Who better to select one than you? Post your favorite name to ASBMB’s Facebook page.

ASBMB’s Valentine’s Day summed up in tweets

February 15, 2013 § Leave a comment

  1. Let’s ditch these chaperone proteins and see what unfolds. #mybiovalentine
  2. The best way to stay healthy through the flu season is to get inoculated..together. #mybiovalentine
  3. Oh, oxygenated hemoglobin, I am blue without you. #mybiovalentine
  4. You know the other definition of ATP? All That Passion #mybiovalentine
  5. If you think you’re wearing that on date night, you must be trypsin. #mybiovalentine
  6. Why don’t we go back to my place for something I like to call recombination. #mybiovalentine
  7. #mybiovalentine Roses are red/violets are blue/lets transcribe a love message/with RNA Pol2

Funny #SoGodMadeAScientist Tweets

February 4, 2013 § 3 Comments

  1. “I need someone who will endure failure, failure, failure in the lab and still not quit.” #SoGodMadeAScientist
  2. It may have taken me 7 days to create the universe but it’ll be a while before you guys figure this stuff out. #SoGodMadeAScientist
  3. God got annoyed watching people admiring the universe without even seeing the coolest parts of it. #SoGodMadeAScientist
  4. “Billions of years ago I made protons…and magnetism. Gonna be wicked cool when someone figures out NMR!” #SoGodMadeAScientist
  5. God realized that the only thing to do with some people was put them on reality TV. But there were no televisions #SoGodMadeAScientist
  6. “I need someone to come into lab at 5 am, start a Western blot, run stats on yesterday’s data, & code behavior videos” #SoGodMadeAScientist
  7. I needed someone to work out that the pork prohibition was about trichinosis…and fix it so farmers could make bacon #SoGodMadeAScientist
  8. God knew DNA looked pretty cool at the EM level, but needed someone to invent an electron microscope #SoGodMadeAScientist
  9. Needed: someone to devote their life to one protein, in one cell type, with no real KO phenotype, and no western blot #SoGodMadeAScientist
  10. I need someone who can look at a harsh world and not recoil in fear but ask how to make things better for all of us. #SoGodMadeAScientist

Teen wins Intel science prize for pancreatic cancer detector

May 25, 2012 § Leave a comment

Andraka gets first prize at the 2012 Intel ISEF, which was held in Pittsburgh.

A 15-year-old won the big prize at this year’s Intel International Science and Engineering Fair for designing a paper-based diagnostic test for pancreatic cancer, the fourth most common cause for cancer-related deaths worldwide. In collaboration with Anirban Maitra at the Sol Goldman Pancreatic Cancer Research Center at the Johns Hopkins Medical Institutions, Jack Andraka of Colesville, Md., developed a simple dip-stick sensor for early stage pancreatic cancer that is over 400 times more sensitive than current tests.

The sensor detects mesothelin, a biomarker that is overexpressed in the blood and urine of patients with pancreatic cancer but absent in patients with chronic pancreatitis or other conditions.

Andraka explains his sensor has single-walled carbon nanotubes and monoclonal antibodies that recognize mesothelin. He made an uniform dispersion of nanotubes and antibodies and then dip-coated filter paper strips with the dispersion. A nanotube network, with the antibodies on the surface, formed on the paper substrate.

The sensor worked on a microliter, literally a drop, of blood or urine. When mesothelin was present in a sample, it bound to the antibodies and pushed apart the nanotubes, increasing the tunneling gap between them.  “As the tunneling gap of a nanotube network highly affects how electricity is transferred between carbon nanotubes and how it flows through the network, the addition of mesothelin greatly altered the electrical properties of the sensor,” explains Andraka.

Andraka tested the sensor on buffers and healthy human serum samples spiked with mesothelin. He used keratin as a negative control. He also tested the sensor on mouse models and is now starting to work on human samples.

Andraka’s test beats current methods for early pancreatic cancer detection on several fronts. It’s over 90 percent accurate. It takes 5 minutes to run, which is 168 times faster than an ELISA. Andraka estimates that each sensor will cost 3 cents to manufacture.

“The sensor really has unlimited applications, as you simply switch the antibody and detect an entirely different protein. It could be used for other cancers, cancer drug resistance, and infectious diseases in food and water safety,” says Andraka. Because of its simplicity, Andraka suggests that the sensor can be used as a home test, like the ones found at drugstores for diabetes and pregnancy.

Maitra says Andraka’s story holds a great teaching moment for high school students because it has three important messages. The first is that a passion for science goes a long way. The second is the power of perserverence.  “Jack emailed over 190 professors before he got a ‘yes’ from me,” says Maitra.  Finally, adds Maitra, there is no substitute for hard work. “Jack spent long hours every day after school and on weekends getting the work done.”

As the winner of the Intel competition, Andraka received the $75,000 Gordon E. Moore Award, named in honor of Intel’s co-founder and retired chairman and CEO.

Biology in watercolor

May 17, 2012 § Leave a comment

Gold mitochondria” caught my eye as I was scrolling through Twitter one day. By clicking on the link, I discovered the art of Michele Banks,  an artist based in Washington, D.C., who has the online store artologica on Etsy.  She bases a lot of her work on science and medical themes. Just check out her colorful renditions of Petri dishes, neurons, viruses and mitosis. As she says in her Etsy profile, “I’m not a scientist, I just love and am fascinated by the natural world, especially at the microscopic level.”

I reached out to Banks to find out more about who she is and how she blends science and medicine with art. Below are excerpts of the interview, edited for length and clarity.

What’s your day job? Tell us a little bit about how you got to where you are today.

I’m a full-time artist. Of course, that doesn’t mean I paint 40 hours a week. It’s a business: I have to order supplies, photograph my work, list it online, mount, frame, package and ship paintings, apply for shows, set up at festivals, do the taxes and much more.

I became an artist in a very circuitous way. I studied political science and Russian, and I got a job as a management consultant in Russia, working on privatization and economic-development projects. After five years of that, I was pretty bored and disillusioned, and I got married and came back to D.C. Shortly after that, my husband got offered a job in Bermuda, so I went along, but I was not given a work permit. I used the free time to have a baby and mess around with some artwork. After we moved back to Washington, I started showing my work in the usual places that beginning artists do — coffee shops and community festivals. And I basically plugged away at it in a small way for years, until about two years ago, when I started selling online, http://www.etsy.com/shop/artologica  and my business expanded a lot.

So there you have it — I don’t have a background in either art or science. Life is funny sometimes.

 

What gave you the inspiration to create art from biology?

I started out making abstract paintings using the wet-in-wet watercolor technique, and so many people told me they looked like things under a microscope that I decided to investigate. I read books and articles about basic biology, and I was amazed at the visual forms of cells, bacteria and viruses.

Many of my paintings use a wet-in-wet technique, which means that I put down a background color and then add another color while the first one is still wet. The paint “bleeds” naturally and forms amazing fractal patterns, just like tree branches, blood vessels and brain cells. This quality makes it ideal for mimicking forms in science and nature.

Watercolor is also good for biology because it can be translucent, which allows you to show things that are going on beneath the surface.

 

When and how did you learn to paint?

I taught myself, just messing around with watercolor until I got what I wanted. I took a few classes to learn some basic techniques, and then I just practiced a lot. Apparently there are a lot of “rules” for watercolor painting. I don’t really even want to know them.

There’s one exception to my no-rules policy: I do use high-quality archival paper and paints. It makes a huge difference in how paintings look and how long they will last.

 

How do you keep up with advances in biology? Do you consult with any scientists?

Many of my paintings deal with really basic stuff like cell division, which has been known for ages. I do incorporate more current ideas into my work thematically, though. A lot of what I’ve been doing lately has been influenced by work on the microbiome, the idea that living creatures are not just a collection of our own cells but an ecosystem for millions of microbes.

I read a lot of articles in science magazines and on blogs. I love the Nikon Small World site and The Cell Library for images. I do talk to scientists a lot online, but more about ideas than about technical stuff. I’m not an illustrator — I don’t have that responsibility to get the details perfect. I simplify forms a lot in my work.

That said, the “brainbows” work of Jeff Lichtman, Jean Livet and Joshua Sanes has been a big influence on me. It’s just fantastic how their techniques have “lit up” brain cells, showing the structure and functions while creating gorgeous images.

 

Has anything from the biological world frustrated you in trying to render it in paint?

Yes! One of the coolest shapes in biology is the ribbon. I think they’re beautiful and amazing, and unfortunately I stink at painting them. Mine always look stiff, never flowing!

 

How much does your artwork go for, and how much have you sold so far?

My work is very reasonably priced, ranging from $40 to a few thousand for a large piece. Between Etsy, art shows and commissions, I sell a couple hundred pieces a year now.

 

What are you working on next?

Exciting things! One of my paintings, of malaria in red blood cells, is on the cover of a novel coming out this fall.   Another one is on the cover of the EMBO Journal.

Last year I made petri dish Christmas ornaments with bacteria and parasites in them — they were a hit, and I plan on bringing them back even better this year. I’m also working on some other new products incorporating my images. Stay tuned!

In January, I went to the 2012 Science Online conference in North Carolina, where I met hundreds of inspiring scientists, writers, artists, illustrators and science communicators. I learned a lot, made great contacts and got tons of ideas. I can’t wait to go back next year.

In the meantime, I’m writing about science and art for Guru magazine, blogging at my site and at the Finch and Pea  doing shows locally and painting, painting, painting. Oh, and Twitter. Way too much Twitter.

 

What do you love about science? Where do you see art and science coming together?

What I love about science is the opportunity to understand how things work.  Artists and scientists have very different approaches, but fundamentally we’re doing the same thing — trying to understand and explain the world around us. Also, the world inside us!

If you are in Washington, D.C., between May 18 and June 24, you can check out Bank’s work in person at Artomatic 2012, the area’s biggest free arts event.

All image rights and permission go to Michele Banks

Protein structure caught in sculpture: the art of Mike Tyka

March 29, 2012 § 1 Comment

KscA potassium channel. Photo by Mike Tyka

The shiny gold twists caught my eye one day as I quickly scrolled through a social media site. What were those?

In stopping to look more closely, I discovered the gorgeous work of Mike Tyka, who makes sculptures of protein structures. He has so far made sculptures of a potassium channel and ubiquitin. It was the helices of the potassium channel that had caught my attention. It is a model of the KcsA channel, a membrane-spanning potassium channel with eight alpha helices.

I emailed Tyka to ask him about his work. Below are his answers to my questions, which have been lightly edited for style, length and clarity.

1) What’s your day job?

I’m a postdoc at the University of Washington in Seattle, with professor David Baker. I work on computational protein structure prediction, writing algorithms for conformational space search on large parallel computers.

2) What gave you the inspiration to make sculptures of protein  structures?

I’ve been working on proteins for nearly a decade, concentrating on structural aspects. I’ve seen a great number of crystal structures and have grown to love and appreciate the beauty of protein folds. They are graceful and complicated, regular but often surprising, and often symmetric or pseudo-symmetric.

I’ve been curating a small blog called beautifulproteins.blogspot.com, collecting pretty proteins I come across. At some point, it evolved into the idea of making physical, artistic expressions of the folds.

3) How did you learn to work with metal for sculpting?

I’ve been involved with art/tech making for a while in my spare time. I co-founded GroovLabs, which built a 30-foot, playable Rubik’s cube that is currently on display at the Pacific Science Center in Seattle. During that project, I taught myself how to work with metal.

I had a really good time, so I decided to start a community art workshop in Seattle with some friends of mine, which has grown into a reasonably large shop and art community by now. That’s where I started studying metal in my spare time and where I do all my work [now]. Metal is a fascinating material once you dig below the surface.

4) What do you look for in a protein structure to to render it into metal?

Ubiquitin. Photo by Mike Tyka

The choice is determined by a number of factors. The process of making these is something I developed over time and that is still evolving. I typically aim for the most interesting structure I can find that is within my currently manageable size and complexity range.

For example, right now I’m working on a beta-barreled porin molecule, which is larger and has more individual secondary structure elements than my previous two pieces. This would not have been possible to make in a reasonable time without a bunch of custom tools that I only made this winter after learning much about the process during the first two pieces, which were made summer of 2011.

I’m thinking about larger proteins now and ones involving symmetry. Symmetry is difficult because you have to make  exact copies of the subunits; otherwise, the brain of the viewer has a hard time spotting the symmetry. I need more jigs and custom tools before I embark on that.

The KcsA channel *is* fourfold symmetrical and was done by eye and hand. It has OK symmetry, but I think it could be a lot better.

Other than technical issues, I look for both aesthetic beauty as well as medical or human relevance. I can’t always satisfy all requirements, but I try to find proteins that intersect at least most of my criteria.

5) How large are your sculptures?

The scale is roughly 4 Angstroms to an inch. The two sculptures I made last year are about 16 to 24 inches tall roughly, including the base.

I hope to make ones as big as 3 to 4 feet by the end of the year at the same scale.

6) Is there anything you’ve learned about yourself as a  sculptor or a scientist?

That’s a hard question. I’ve only been doing it for a little over a year.

I work exclusively with computers for my scientific work, and I realize that I’ve really missed working with my hands. I love the tactility of making art. A huge area of our brains is devoted to our hands and, in the modern world, we really underuse them.

Ubiquitin's close-up. Photo by Mike Tyka

Ubiquitin's close-up. Photo by Mike Tyka

I also learned that the process of science and art are much closely related then most people realize. But that is a whole other conversation!

7) What are you working on next?

I’m currently working on a porin molecule. There are some pictures of the process here

8) Any thoughts on selling?

Yes, I would absolutely sell them or even make sculptures on request.

It would be awesome to be able to install a few at universities’ or pharmaceutical companies’ lobbies or even public places.

A major motivating factor of my work is that I want to make the public more aware of just how stunningly gorgeous the machines of life are.

I’m inspired by people like Drew Berry or David Goodsell. I think education of the public by making science accessible is really important. Science is moving way too fast these days for most people to keep up.

Public perception ultimately decides the fate and funding of science. It’s vital for science itself to keep the world inspired and informed.

Leaf-cutter ants and their marvelous microbiomes

March 8, 2012 § 1 Comment

Earlier this week, I showed up for The Social Biology of Microbial Communities meeting at the National Academies. The Institute of Medicine’s Forum on Microbial Threats hosted this two-day event to discuss all the ways that microbes communicate and work together in all kinds of ecosystems. One of the ecosystems discussed was leaf-cutter ants. A talk by Cameron Currie from the University of Wisconsin-Madison about these ants gave me a newly found appreciation for insect microbiomes.

By now, we’ve come to appreciate that as humans, we have microbiomes, such as the ones in our guts and skin. Currie has shown that insects, too, benefit from microbes that cozily live inside them.

Leaf-cutter ants, natives of South and Central America, clip off leaves, flowers and grasses and scurry back to their nests, wielding the vegetation above their heads. The ants feed fungus farms in their nests with the vegetation. The fungi, in turn, are made into food for the ant queen and the larvae.

But the fungus farm that the ants loving care for and make food out of are susceptible to attacks by pathogens. An example of a pathogen is escovopsis.

Leaf-cutter ants were originally thought to be coated in a wax. But as Currie explained in his talk, this “wax” turned out to be colonies of actinobacteria. These bacteria produce antibiotics that fend off escovopsis. (It turns out we too benefit from actinobacteria because two-thirds of the antibiotics we use are made by Streptomyces, a kind of actinobacteria).

Because these bacteria are useful for the ants in keeping their fungus gardens alive with their antibiotic production, the ants have specialized crypts with exocrine glands in their bodies to house and support these bacteria. Currie and his colleagues have demonstrated the presence of these crypts by electron microscopy and other techniques.

Currie said that the relationship between actinobacteria (which, in the case of these ants, is pseudonocardnia)  and leaf-cutter ants is ancient, stretching to 50 million years and perhaps older. Leaf-cutter ants aren’t the only insects to have friendly bacteria live on them — wasps, honey bees and Southern pine beetles are other examples of insects that get a helping hand from bacteria.

In looking up Currie’s publications, I discovered that Currie’s group has also done genomic and proteomic analyses on the bacterial diversity within the fungal gardens themselves. In gardens harvested by field and lab-based leaf-cutter ants, Currie and his colleagues showed that the fungi coexist with bacteria that help fungi feed on the plant material hauled in by the ants.

As Currie pointed out at the end of his talk at the IOM event, understanding insect-bacterial relationships can help us find natural products against pathogens.

You can watch Currie collect ants on his recent Costa Rica trip here.

Enjoy!

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