At Long Last, Freezable Fruit Flies

From Apartment Therapy.comIf you have ever done any research with the model organism Drosophila, you will immediately understand what an incredibly big deal this latest paper from PNAS is.


Conversion of the chill susceptible fruit fly larva (Drosophila melanogaster) to a freeze-tolerant organism
http://www.pnas.org/content/early/2012/02/06/1119986109.abstract
PNAS, 2012 


Kostal et al report a protocol for preserving fruit fly larvae at -5 degrees C. Freezing time was pretty short (75 minutes according to the Materials and Methods) but this is a significant step toward the long-term-storage promised land currently dominated by worms (C. elegans), bacteria, and cultured mammalian cells.


A little more context for those who don’t get how cool this is. Let’s say you spend a couple of years creating a genetically engineered fruit fly that expresses human huntington disease proteins, which allows you to do ground-breaking world-saving research (test new drugs and dissect how the disease works) in an easy-to-grow little organism. All you have to do is keep this genetically modified “species” (or strain) alive for, say, five more years.


Problem is, after keeping flies in a plastic bottle “fly house” for three weeks, fly carcasses accumulate, fungus starts growing, and the flies’ numbers start declining. The easy solution is to take a few flies and start a new fly bottle. Problem solved! Until a few weeks later, when you have to restart a new fly bottle. This “fly passaging” approach is fine if you don’t plan on ever stopping, being away for more than three weeks, doing non-fly experiments, or if you only have one or two genetically modified strains.


Try 50. That’s about how many unique fly strains I had to maintain during the last couple years of my Ph.D. thesis work. How about 38,424…that’s how many are maintained at the Bloomington Drosophila Stock Center (as of 2011). In the mean time, my C. elegans, human cell culture, and bacteria research neighbors got to keep their organisms in the  freezer until they were ready to use them again.


Colleagues: Hey Karmella, why don’t you come out to happy hour with us? You won’t believe it…Mos Def is D.J.ing and Dave Chapelle is doing impromptu stand-up with Justin Timberlake! 
Me: Can’t go. Passaging flies.
~sad trombone~ 


Why is freezing flies so hard? They are tropical insects. Evolution didn’t deal them cryopreservation cards. A 7 degree drop in temperature from the optimal 25 degrees will slow down their metabolism significantly (that’s actually a trick Drosophologists use to extend the life cycle clock).


How did Kostal et al do it? It appears that the secret is diet. They took cues from the biology of the subarctic fly Chymomyza costata, and fed Drosophila fly larvae a proline-, trehalose-, and glycerol-enriched diet. Glycerol, by the way, is what you add to bacterial cultures to prevent ice crystals from damaging the cells when they are frozen. Preliminary tests show that the thawed Drosophila larvae grow into healthy adults.


Even though I don’t do fly work anymore, I’m anxious to see how long the larvae can be cryogenically preserved. So far this is really cool, and time will tell (I owe the pun-ishment jar a dollar for that one).

How To Create a Cool iGEM Project

One summer, a team of undergraduate students decided they were going to win the grand prize at the International Genetically Engineered Machines competition (iGEM). They figured that doing this would be challenging, but the approach was straightforward. They set out to simply create the coolest project that any of the judges or competing teams had ever seen. Alas, after weeks and weeks of hard work, their project turned into a spin-off of their advisor’s work, ended up looking too much like someone else’s project, and suffered from lack of team morale which dissolved by the end of the summer. In the end, another team with a really cool project won the grand prize at the jamboree.

This proverbial team made two critical mistakes. First, they decided at the beginning of the summer that they were going to win the grand prize at iGEM. Second, and perhaps most importantly, they attempted to deliberately create a cool project.

When we set out to make something “cool” we often look for an impressive precedent and imitate it. The idea, then, is inspired entirely by something that has been done already, or some external person’s idea. When we deliberately try to make something creative, we sometimes ironically default to copying a creative thing. Why do so many of us default to this behavior? It’s easy to fall back when you are not propped up by a genuine passion or purpose.

What’s more, we try to win when we are afraid of losing.

This doesn’t just happen to iGEM students, it also happens to professional scientists in academia and industry.

So what makes a project really cool, instead of just an attempt to win something? Inspiration. Ask yourself this, what else besides the desire to impress the judges and win a trophy is motivating your project? If you don’t win anything, will your project change the world? When your supporters abandon it, will you still want it to succeed? If you aren’t being driven by an urgent cause, are you having fun?

Take a look at major pioneers and leaders in Synthetic Biology today. What was Drew Endy doing before he became a synthetic biologist? How about Tom Knight, Pam Silver, Randy Rettburg, or Craig Venter? I mention these scientists because while learning about their backgrounds, I keenly remember my delight at discovering some unexpected fact about their path, a moment of inspiration, or a huge risk they took because they knew that what they would accomplish would change the world. The result of their work was something really cool.

Should we just give up on competition and ignore all the rules? No, just understand what the rules are there for. Although the iGEM track titles and some awards suggest inspirational grand challenges, for the most part the rules are not there to inspire you. In iGEM, the rules help you to package your work so that diverse projects can be compared fairly and measurable success can be rewarded by the organization. Furthermore, some iGEM rules are tailored to help you make comprehensible, meaningful, and useful contributions to open-source bioengineering (i.e., The MIT Registry of Standard Biological Parts).

Don’t work on an iGEM project because it will get you an award. Do it because you know it’s the only real way you are going to make a positive impact on the world. If you don’t feel in your heart that this is true, you need to shift directions or work on a different project.

Be inspired.

Learning by building…a new lab

September 5th marked my official transition from a postdoctoral research fellow to an assistant professor with my own lab. A very empty lab. No equipment, no students, not even one of those ubiquitous half-sized refrigerators or a biohazard waste bin.

So I figured I’d just dive into my big pile of start-up cash and go shopping for equipment and supplies.

"Oh wait, how do I order stuff?"

Every school has it’s own system. Fortunately, the culture of my program and department encourages undergraduate students to volunteer for professors to help the student warm up to lab culture and to give the professor an opportunity to get to know his/her potential future undergrad research fellows. I got an undergrad registered to use the online ordering system and she orders everything I add to a Google doc spreadsheet we share. My student rocks.

"What brand of gloves was I using back at my old lab? I loved those gloves."

It dawned on me that making an inventory of all of he stuff I loved but took for granted at the old homestead would have been really helpful.

"An ice bucket costs HOW much? You’ve got to be f****ing kidding me."

I’m sure my sticker shock provides my undergrad volunteer with endless entertainment.

"This thing looks kind of odd. This isn’t what I was expecting."

I learned not to expect to reproduce the old lab. There are a million slightly different versions of the generic things you use in lab and items get outdated or discontinued.

Some interesting stuff (that you’ll probably never learn as a student or postdoc) happens during the complicated dance involving medium/ large equipment purchases.

- Meet your sales representative out on the floor
- Schedule an instrument demo
- Plan the trial run, don’t forget to invite your lab neighbors
- Negotiate length of time to keep the machine, new machine pricing, spin your partner round and round
- Explain why you’re not buying from a local or small business by writing a sole source justification (e.g., This company is the only one in the universe that makes this machine and I need it)
- Submit your quote, tax exempt form, and justification to the buyer
- Wait and wait…5 6 7 8

Don’t get me wrong, I do appreciate that just having the opportunity to build a lab from scratch is exciting. If this process turns out to be the most exciting part of my career for a while, I shouldn’t ruin it by focusing too much on the process.

"Greetings, new -150 C cryogenic freezer! I christen thee, Burrrt. Burrrt Reynolds."

I’m going to have fun with this.

The lead author of the paper featured in this article is Christina Agapakis, a graduate student and a colleague of mine in Pam Silver’s lab at harvard. She’s artist/scientist after my own heart.

She has posted a blog article that very nicely places her work into context. 

I’m a big fan of using colorful metaphors to explain dry scientific factoids. Not only is it entertaining, it makes the concepts more accessible by taking physical properties of the universe that we cannot quite grasp with our hands and eyes, and connecting them to familiar objects that exist on a more conceivable scale.

Take this Wordpress.com blog about a “human scale” cell nucleus, for instance.

… the 150 foot nucleus contains just 15,000,000 feet of double stranded DNA and water. … In our model nucleus, DNA is a cylinder 20 Angstroms (3/8 of an inch) thick. … You can visualize DNA at this level of magnification as two strands of linguini wrapped around each other every 10/16ths of an inch forming a right handed helix.

Magically, one of the world’s most recognizable macromolecules scales up to a size you can imagine holding between your fingers. As a chromatin biologist by training, I absolutely love the following part…

What do you do with this much linguini? Well, an Italian friend (uncle Tom) showed me how to eat it properly by using a spoon to curl it around a fork. So does the cell. Except that fork is a set of 8 proteins (called histones) packed together.

Thanks luysii! I’m now inspired to create a physical rubbery DNA double helix (but perhaps with meatballs instead of forks to wrap it around).

Sneakers for Geeks and Hackers Are Made form Recycled Computer Chips : TreeHugger 
This article is over a year old, but I just ran across it and had to post it. Now if only they made high-heeled peep-toe booties.

Sneakers for Geeks and Hackers Are Made form Recycled Computer Chips : TreeHugger 

This article is over a year old, but I just ran across it and had to post it. Now if only they made high-heeled peep-toe booties.

"When we sent a copy of our article about the Knox brothers to a chemistry colleague with historical interests, he responded, “Just think of all the black talent that was wasted over the benighted decades. … Our country has a toxic legacy in that area.” That is certainly one of the messages of this story, but there is another. With help at critical moments from established figures — Paul Bartlett, Willard Libby, William Doering — both Knox brothers managed to make important contributions to chemistry. They showed what perseverance, courage, and commitment can accomplish."

Perspective: Stumbling Through History: Discovering Unsung African-American Chemists - Science Careers - Biotech, Pharmaceutical, Faculty, Postdoc jobs on Science Careers

iGEM 2010: and the human practices award goes to…

Like a nervous parent in the bleachers at a little league softball game, I sat at the edge of my seat, trying my best to keep my composure as the awards were announced for this year’s International Genetically Engineered Machines Competition. Like any competitive player, I was rooting for my home team, but I also had a good feeling of who among the many contestants was a true competitor.

Then the results were announced and I was left perplexed.

The Human Practices award honors the efforts to bring synthetic biology closer to people’s lives in a tangible and meaningful way. For that reason, I was utterly confused that the award-winning project consisted of a privileged group coming down from the hillside, so to speak, to save underprivileged brown people from their tragic lot in life, and snapping public relations photos for display. A clever new technology to save the victims from disease was proposed, which basically leaves those people dependent upon on the graciousness of the privileged scientists.

What kind of message do we send when “touch and go” style humanitarian efforts, notoriously common and convenient to privileged people, are rewarded on an international stage, while in the very same competition projects that aim to actually empower people to participate in science go unrecognized? It’s a bit twisted and unsettling in my opinion.

It’s the 21st century and colonialism is old news. Do we really still think that approach is noble? This critique may seem harsh, but I am very concerned about this and it really needs to be said. The iGEM award decisions influence how future teams will do science and how they will approach human practices. We need to make sure we’re steering budding scientists in the right direction.

With that said, I’m inspired to recognize the three human practices that I feel truly reflected the spirit of empowering people by allowing them to choose what to do with science to better or sustain their own well-being.

1. Art Science Bangalore: This group presented their efforts to spark a “jugaad biology” movement in their local community in India. Jugaad is defined as ‘a hack to get around or deal with a lack of or limited resources…things poor but clever people do to make the most of the resources they have.’ This is the true spirit of empowerment.

2. Harvard University (conflict of interest disclosure: my home team): The iGarden, a personalized genetic toolkit for creating your own hypoallergenic and nutritionally enhanced veggies, had implications for taking control of genetically modified foods from the hands of large companies and putting it into the hands of the people who need it. The idea was so powerful and so tangible, a USDA official who had volunteered as a judge struggled with the implications as he spent a very long time discussing the project with the students.

3. University of Alberta: This is the closest I’ve seen any team come to making and distributing an affordable toolkit that allows high school students to do gene splicing. They put a lot of thought into every detail, from DNA assembly to liquid measuring pipettes.

Perhaps these ideas were just a little too big and a little too real for iGEM. Over the past four years I’ve been a participant, I’ve noticed that the big award winners tend to look the same. It’s unlikely that things will change much. Perhaps this is a sign that the time has come for other student bioengineering competitions…and what an interesting human practices project that would be.

What if you had the ability to genetically engineer your own vegetables in quick, safe, and natural way for your own benefit? Help Harvard students understand your opinions by voting in their public opinion survey. Be sure to check out all of the cool stuff on their 2010 Interntional Genetically Engineered Machines Competition (iGEM) page.

The 2010 Harvard iGEM team will compete with teams from around the world at the international jamboree on November 5 - 7. Good luck iGardeners!

Public science education is one of those very fun and exciting challenges that stretches your mind to invent new ways to communicate the deeper relevance of science. It’s more than just “dummying down” the content and erasing jargon. It takes real innovation to do it well. Every research scientist can benefit from this exercise and should take opportunities to do so.

This is why I’m excited about this year’s PopTech event “Noise in the System: Brilliant Accidents, Necessary Failures, and Improbable Breakthroughs.” PopTech brings together thinkers and doers from multiple areas aroudn the globe to explore the social impact of new technologies. Harvard’s very own Don Ingber will be part of an exciting line up of event speakers including filmmaker Laura Poitras, MoveOn.org’s Eli Pariser, and R&B artist John Legend…John Legend? You read it right.

I won’t be able to make it to Maine in time, but I’ll be checking out the webcast. I can’t wait to see how synthetic biology mashes up with R&B ballads.

Artoo by Black Milk

Does the pattern look familiar? Any person who calls themselves a real Star Wars fan will recognize it as R2D2’s hardware. How awesome is this? Now if only they can make a gold one for C3PO…

Learn Molecular Biology the Jersey Shore Way!!! (via harvardigem)

The Harvard International Genetically Engineered Machines (iGEM) team shows you how to do science and be a chick magnet at the same time. “DTL,” it’s more than just a schedule, it’s a life style.

I want one! I think…

BeforeAfter

A group of seventh graders were asked to describe scientists before and after a visit to a research lab. The results are heart-warming, sometimes funny, and surprisingly insightful. For the most part, these kids get it…scientists are pretty normal folks!

Meet the Tiger Dog: Chinese owners dye pets to look like wild animals | Mail Online Well, it’s probably much friendlier than a real panda bear.

Meet the Tiger Dog: Chinese owners dye pets to look like wild animals | Mail Online Well, it’s probably much friendlier than a real panda bear.