Archive for: April, 2013

(data not shown) Hypocrite

Apr 25 2013 Published by under Issues in Science, Late-stage PhD student

Earlier this week, I spent a good chunk of time complaining about data not being shown in two papers I had read. Normally, I'd be apt to take their word for it because "data not shown" results tend to be inconsequential footnotes to the larger story and conclusions. This time it was different, though. The data not being shown was being used to make claims that were pertinent to a little thing I've been working on called my thesis. It didn't help matters that the results that were published were less than convincing. I really would have liked to see the data--I mean, isn't that what Supplemental Information is for? Some have suggested that I contact the authors to see if they'd send me the data but I'm not sure how to craft that correspondence without broadcasting a big, fat "Yo, I don't believe you."

Well anyway, now's a good time as any to check myself since I'm totally guilty of pulling the "data now shown" card, too.



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Staying Boston Strong

Apr 20 2013 Published by under Potpourri

I’m going to the Bruins game today. It was originally scheduled for last night but was postponed in light of the manhunt for Dzhokhar Tsarnaev, “suspect #2” in the Boston Marathon bombing. Am I nervous about going? I won’t lie. I don’t see how anyone couldn't be. It’s been less than a week since two bombs went off at the finish line of the marathon. Less than 48 hours since gunfire filled one of the streets of Watertown.

But it’s a game I’ve been looking forward to since we bought tickets several months ago. When the schedule for the shortened season came out I circled this game against the Penguins as one of the must-sees of the year. It’d be a chance to see one of the league's best, if not best, players in the game, Sidney Crosby, even though I find him to be a little on the whiny side (although, he’s since been injured and won’t be playing after a puck to the face broke his jaw). The game became even more interesting when the Penguins swooped-in in the last seconds to pilfer Jarome Iginla before he was to be traded to the Bruins. The Bruins ended up traded for ex-Penguin Jaromir Jagr instead.

At today’s game, I don’t know how those who’ve died, those who were injured, or the men and women who protect us and heal us will be honored. I don’t know if there’ll be a rousing, audience-led, rendition of the Star-Spangled Banner. I don’t know if my team will even win today. But I do know that these are the steps we take to bring a city and life back to normalcy.

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Two Bombs Prevented Me from Saying Thank You

Apr 16 2013 Published by under Potpourri

I sat down to write a blog post yesterday, only to have my day derailed by two bombs exploding by the finish line of the Boston Marathon. An attack like yesterday's isn't just about harming and maiming as many people as possible as it did in killing three and injuring more than a hundred people. It also knocks the rest of us off our psychological tracks. I spent the rest of my afternoon distracted and glued to my computer searching for answers. Reasons. Rationalizations for what happened. More information. Always looking for more information. Judging by my Facebook and Twitter feeds, I wasn't alone.

Invariably, you think about 9/11. About where you were, what you were doing. This time was different. New York City felt close. This was my backyard. I've sat a countless number of times on the steps of the Boston Public Library. Had drinks at the Mandarin. The shock I was feeling wasn't the same as it was 11 years ago. It was the sobering realization that that thing you were quietly fearful of happening again...was happening. And maybe that it took this long.

I thought of my organic chemistry professor, who refused to cancel class just hours after the planes hit on 9/11. His rationale? "If we let them disrupt our lives, then they win and we lose." But I didn't have it in me to write what I had wanted to write yesterday. Even if I had my professor's resolve, it would have been lost in all of the din of yesterday's explosions.

Which is unfortunate, really, since it was a message of appreciation (unrelated to the bombings) that I had sat down to write. And when the smoke cleared from the explosions and victims were shuttled to hospitals, I started seeing that same spirit of appreciation as people were thanking the first responders, volunteers, doctors and nurses. Everyone who tended to the needs of the injured. Everyone who was opening their homes to runners and others who needed places to stay for the night. Thank you.

Here is what I wanted to say yesterday:

Earlier today, DM sent out a tweet thanking US taxpayers for funding science research:

I was preparing cell culture media at the time and thought to myself, "$100? That just about pays for a case of powdered cell culture media that lasts me about 10-12 months." While buying it in powdered form means there's added labor in dissolving the media and sterilizing it, it's a hell of a lot more economical this way since it's about 1/10 the cost of premade liquid media (hey, I'm looking out for you, US taxpayer!). More importantly, it allows me to customize the media for my purposes (e.g. pH, other nutritive supplements, etc.).

M3 media

$10 worth of cell culture media

Anyway, the media is used to grow cells derived from fruit flies (Drosophila) and has been instrumental for my research. So, let me take a moment and join DM in thanking you for your support!

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Never Touch a Grad Student's Radio

Apr 11 2013 Published by under Late-stage PhD student

I know. The title should probably say Winamp Pandora or Spotify or something a little bit more current. But, this was a mistake I made years ago during my pregrad school days when as a tech I had anointed myself lab DJ. I walked around like I owned the place--playing my CDs (remember those?) and changing the radio station at whim with so little as a peep of protestation from other lab members. Since no one ever said anything--at least, not to my face--I just assumed people were cool with my music choices.

On this particular occasion, the offending song was a cover of Roxette's Listen to your, I don't think you can really blame me for changing the station.

No, but this song was different, you see, because as soon as I touched the dial I heard this:

""Excuuuuuse me. Were you raised in a barn? I was listening to that."

I froze. Things got real quiet in the lab. I don't think I had ever been admonished like that in my life. Caught somewhere between the urge to start bah-ing like a sheep and actually feeling sheepish, I mumbled through an apology and told the grad student that I didn't really appreciate the dig at how my parents raised me. Then, I backed out of the room mad tentatively.

Anyway, moral of the story: Not everyone has impeccable tast Don't be an inconsiderate jerk. And have a democratic process in place for electing the lab DJ.

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An "Acceptable" GMO?

Apr 05 2013 Published by under Issues in Science, Science

Soybean Field

For many opponents of genetically modified foods, the idea of fiddling with an organism’s genome doesn’t quite sit well in their stomachs. The type of genetic tweaking that renders soybean plants resistant to the herbicide Roundup strikes some not only as unnatural but something that borders on playing God. Similarly, another common objection to genetic engineering is that the transfer of genetic material/DNA genes violates a so-called “species barrier.” Such is the case for Bt corn, which harbors the bacterial gene for Bt toxin, a compound that is poisonous to insect pests. This argument, however, disregards the fact that Nature ignores this barrier all the time. In the wild, DNA is often transferred between species through processes collectively known as horizontal gene transfer. So, not even Nature plays by antiGMO rules.

But what if an already existing gene variant with a desired trait from one organism is genetically engineered into another organism of the same species? Would this make GMOs a little bit more palatable to their detractors?

Soy is one of the most important crops grown in the US and it is nearly ubiquitous in the market. It’s in our food, drinks, biodiesel fuel, even cosmetics. If you rummage through my mom’s kitchen you’ll find soy sauce in the pantry, tofu in the fridge, and edamame in the freezer. Back in the day, she used to keep soybeans on hand for when she’d press her own soy milk.

Soybean cyst nematode and egg SEM

"Low-temperature scanning electron micrograph of soybean cyst nematode and its egg. Magnified 1,000 times."

Latte drinkers, vegetarians, and us Asians aren’t the only ones who love soy, however. Lurking underground are parasitic worms known as soybean cyst nematodes, which find the roots of the soybean plant irresistible. These agricultural pests invade the roots of the soybean plant where they do a bit of their own agriculturing. These nematodes are capable of inducing the root cells on which they feed to divide thereby creating a steady supply of food for themselves. Whereas males leave the comforts of their “root homes” in order to find mates, females remain there where they continue to feed and swell in size until eventually their bodies burst through the root. Once mated and having laid her eggs, the female dies and her cuticle hardens to form characteristic the cysts on the roots of the soybean plant. The damage to soy crops is damages to the tune of $500 million to $1 billion annually in the US alone.

Segment of soybean root infected with soybean cyst nematode. Signs of infection are brown-white females or cysts with egg masses that are attached to root surfaces.

"Segment of soybean root infected with soybean cyst nematode. Signs of infection are brown-white females or cysts with egg masses that are attached to root surfaces."

Soybean plants aren’t entirely defenseless, however, as there are soybean plant strains, such as the Forrest cultivar, that are resistant to nematode attack. In this cultivar, the feeding cells that the nematodes “cultivate” in the roots of the soybean plant die off and the worms starve before they can reproduce. (Conversely, there are also soybean cyst nematodes that are resistant to resistant soybean plants. It wouldn’t be Nature without the wrinkles, now would it?)

While exactly how the feeding cells in the Forrest cultivar degenerate in response to soybean cyst nematode is unknown, a team of scientists led by Shiming Liu (Southern Illinois University) and Pramod Kandoth (University of Missouri) has recently identified mutations in the serine hydroxymethyltransferase (SHMT) gene that are responsible for nematode resistance. Serine hydroxymethyltransferase is an enzyme involved in the shuttling of one-carbon units between molecules--folate in particular--until the carbon is ultimately freed up for the cell to use in important processes such as DNA and protein synthesis. For instance, one of the consequences of serine hydroxymethyltransferase activity is the conversion of the serine to glycine, both of which are amino acids found in proteins.

One of the reactions that serine hydroxymethyl transferase catalyzes is the conversion of the amino acid serine to glycine.

One of the reactions that serine hydroxymethyl transferase catalyzes is the conversion of the amino acid serine to glycine.

Since the mutations in the Forrest SHMT gene are located near the active site, or the “business end” of the SHMT protein where the shuttling of carbons occurs, it’s possible that the mutations affect the activity of the SHMT protein. Since To test this model, Liu and Kandoth expressed the mutated SHMT Forrest gene to see if it could restore the growth of an E. coli strain that is unable to survive because it can’t manufacture it’s own glycine. They found that the mutated version of SHMT was less effective than the unmutated form of SHMT in restoring growth of the E. coli strain indicating that the activity of the Forrest SHMT protein was probably reduced due to mutations.

More importantly, soybean plants that were susceptible to SCN infection became resistant when Liu and Kandoth transferred the Forrest SHMT gene in the susceptible plants. This demonstrated that the mutated Forrest SHMT was responsible for soybean cyst nematode resistance. The scientists speculate that the decreased activity of the mutated SHMT reduces either the “nutritiousness” of the feeding cells or their ability to divide, and as a result the nematodes that infect the Forrest cultivar starve to death.

So, this brings me back to my original question of what, if anything, would constitute an “acceptable” GMO to opponents of genetic engineering? Would detracters object to a scenario where an already existing mutation* that confers resistance to an agricultural pest is engineered into other soybean plants. Directly transferring the existent Forrest SHMT variant would be more efficient over traditional methods of breeding, since only the Forrest SHMT gene would be introduced into another soybean plant without carrying over any unwanted traits or genes. There are, after all, many different cultivars of soybean plants used for different applications that may benefit from nematode resistance.

*I’ll avoid saying “naturally-occurring” since the Forrest cultivar was developed by a USDA breeding program.



Liu, S., Kandoth, P., Warren, S., Yeckel, G., Heinz, R., Alden, J., Yang, C., Jamai, A., El-Mellouki, T., Juvale, P., Hill, J., Baum, T., Cianzio, S., Whitham, S., Korkin, D., Mitchum, M., & Meksem, K. (2012). A soybean cyst nematode resistance gene points to a new mechanism of plant resistance to pathogens Nature, 492 (7428), 256-260 DOI: 10.1038/nature11651

Crossposted at Amasian Science.

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