Archive for the 'Science' category

Teflon for Teeth

Nov 15 2013 Published by under Science


I may come to regret the title of this post given the chemophobia and fear surrounding fluoride and water fluoridation, but recent research suggests that fluoride may help prevent bacteria from causing cavities by creating a non-stick surface on teeth.

Read more at PLOS Blogs.

No responses yet

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.

One response so far

Condemned to a Skeletal Prison

Feb 28 2013 Published by under Science

*Re-blogged from Amasian Science for Rare Disease Day.

Imagine going to sleep and waking up the next morning not able to bend your elbow or knee. Or imagine having difficulty drawing breath because your rib cage is starting to fuse. Imagine being unable to enjoy your favorite cut of steak because your jaw has locked into place. Even worse, imagine having a limb amputated because you've been misdiagnosed with cancer. This is the harsh reality facing patients with fibrodysplasia ossificans progressiva (FOP), a rare, genetic disease affecting 1 in 2 million people (700 known cases worldwide, 185 in the US), where soft tissues--like muscle and connective tissue--are progressively replaced by bone. Often beginning in the neck, ribbons of bone spread through the shoulders, along the back, trunk, and limbs of the body eventually freezing patients in a skeletal cage.

Curiously, FOP patients are born by and large symptom free, the only consistent tell-tale sign being malformed great toes:

Extraskeletal bone formation occurs sometime in the first two decades of life, usually during childhood. Bone formation is preceded by a painful, inflammatory flareup, the cause of which is unknown. A particularly insidious feature of the disease is that trauma or injury can induce these flareups, meaning that undergoing surgery to remove the extra bone only exacerbates the problem. Bumps and bruises we typically overlook cause alarm for FOP patients. Even injections, such as vaccinations, are a source of concern. Currently, while there is no cure, treatment revolves around reducing inflammation and controlling pain using corticosteriods, NSAIDS, or COX-2 inhibitors such as Vioxx (before it was pulled from the market).

A mystery unraveled

While the earliest description of FOP dates back to the late 17th century, the cause of the disease remained an enigma for centuries until 2006, when researchers at the University of Pennsylvania linked the disease to a mutation found in FOP patients (1). The mutation affects one copy of the ACVR1(ALK2) gene, which encodes a protein important in relaying communication between cells. In the body, cells can send signals to instruct other cells to start forming bone via Bone Morphogenetic Proteins (BMP)--thus named for their ability to induce bone growth. ACVR1 is a type I receptor for BMPs and, with the help of the BMP type II receptor, acts like an antenna that receives these signals and transmits the encoded instructions to the cell.

Cellular messaging. Cells communicate with each other by sending proteins "messages" that are received by receptors on the cell surface. BMPs are just one of many types of different protein messages. These messages can instruct other cells to grow, divide, transform into other types of cells, or even self-destruct. This is analogous to people communicating by text message. BMPs and the ACVR1 receptor can be thought of as the text message and the cell phone receiving the text message, respectively.* 

Studies in zebrafish, fruit flies and mammalian cell culture all indicate that the mutant ACVR1 receptor linked to FOP has gone rogue, capable of transmitting the instructions without having to receive the initial BMP signal (2-4). The mutant receptor acts as though its power switch has been permanently flipped to the "on" position. More recently, scientists have provided even more direct evidence that the mutant form of ACVR1 is responsible for FOP. Through a trick of genetic engineering known as "gene knock-in", the researchers at UPenn were able to replace one copy of the normal ACVR1 gene in mice with the mutant form associated with FOP. The resulting mutant mice displayed many of the hallmarks of FOP: "malformed first digits in the hind limbs and post-natal extra-skeletal bone formation" that occurs both spontaneously and as a result of injury (5).

Adapted from Figure 2 (5). (A) Characteristic great toe malformation in FOP patient. (B) FOP mutant mice (right panels) displayed malformation of the first digits of the hind-limbs (circled) at birth. (C) Skeleton of FOP mouse with arrows to indicate extra-skeletal bone formation. Fusion of cervical vertebrae (C3-C5) (D), fusion of costovertebral malformations and fusion of vertebrae (asterisks) (E), and abnormal bone growth (arrows) (F) are observed in the mouse and FOP patients.

One of the limitations of their knock-in technique, however, was that the replacement of the normal ACVR1 gene with the mutant version was incomplete--it occured in most, but not all, of the cells in the mice. This produced chimeric mice, which were mosaics of cells that had one copy of the mutated ACVR1 gene ("FOP" cells) and cells that had two normal copies of the ACVR1 gene. Exploiting this mixed nature of the mice, the researchers were able to study how "FOP" cells interacted with normal cells. Surprisingly, they found that in the presence of "FOP" cells even normal cells were turning into bone. This suggests that cells that have the faulty ACVR1 receptor can also instruct normal cells to turn into bone through an unidentified mechanism.

Marching toward a cure

With these findings scientists are beginning to devise strategies and design drugs that can either specifically turn off the expression of the mutant ACVR1 gene or turn off the aberrant activity of the mutant, providing hope that a cure or, at very least, an effective treatment is on the horizon. While some of these avenues are promising, a viable treatment is far from reaching the market. To find a cure will require more research, which in turn requires money. Because FOP is such a rare disease it often flies under the radar when it comes to research funding. Currently, an estimated $1.5 million a year is spent on FOP research, 25% of which is funded by institutions like the NIH and the Orthopaedic Research and Education Foundation. Incredibly, the remaining 75% is generated through donations and FOP family fundraising. If you would like to help or find out more about FOP, please visit the International FOP Association website.

Featured Image: Harry Eastlack, a man who lived with FOP, donated his skeleton to science. His skeleton is on display at the Mütter Museum.

1. Shore EM, Xu M, Feldman GJ, Fenstermacher DA, Cho TJ, Choi IH, Connor JM, Delai P, Glaser DL, LeMerrer M, Morhart R, Rogers JG, Smith R, Triffitt JT, Urtizberea JA, Zasloff M, Brown MA, Kaplan FS. A recurrent mutation in the BMP type I receptor ACVR1 causes inherited and sporadic fibrodysplasia ossificans progressiva. Nat Genet. 2006 May;38(5):525-7

2. Shen Q, Little SC, Xu M, Haupt J, Ast C, Katagiri T, Mundlos S, Seemann P, Kaplan FS, Mullins MC, Shore EM. The fibrodysplasia ossificans progressiva R206H ACVR1 mutation activates BMP-independent chondrogenesis and zebrafish embryo ventralization. J Clin Invest. 2009 Nov;119(11):3462-72. doi: 10.1172/JCI37412

3. Le VQ, Wharton KA. Hyperactive BMP signaling induced by ALK2(R206H) requirestype II receptor function in a Drosophila model for classic fibrodysplasiaossificans progressiva. Dev Dyn. 2012 Jan;241(1):200-14. doi: 10.1002/dvdy.22779

4. van Dinther M, Visser N, de Gorter DJ, Doorn J, Goumans MJ, de Boer J, ten Dijke P. ALK2 R206H mutation linked to fibrodysplasia ossificans progressiva confers constitutive activity to the BMP type I receptor and sensitizes mesenchymal cells to BMP-induced osteoblast differentiation and bone formation. J Bone Miner Res. 2010 Jun;25(6):1208-15

5. Chakkalakal, S., Zhang, D., Culbert, A., Convente, M., Caron, R., Wright, A., Maidment, A., Kaplan, F., & Shore, E. (2012). An Acvr1 R206H knock-in mouse has fibrodysplasia ossificans progressiva Journal of Bone and Mineral Research DOI: 10.1002/jbmr.1637

*7.10.12 - Updated figure. See this post.

No responses yet

Sabotaging the “Warning Beacons” to Prevent Immune Cells from Attacking the Body

Jan 25 2013 Published by under Science

I'm over at Amasian Science today blogging about how proteins that bacteria use to slip past our defenses might be exploited to control the behavior of immune cells...with a little shout out to LoTR.

Human immune cells are remarkably adaptable. These foot soldiers of the immune system can be harvested from the body, retrained to recognize and fight different diseases, and then redeployed in the body. This process, known as adoptive cell transfer, has incredible potential for treating cancer or chronic infections–particularly in individuals whose immune systems have been weakened by diseases like AIDS. There is, however, a big problem with this technique. Immune cells that have been harvested and engineered to fight specific diseases can often go haywire and turn their weapons on host cells. As a result, healthy cells and tissues in the body that aren’t supposed to be attacked by immune cells get caught up in the crossfire and end up as casualties. As a solution, biologists want to keep these immune cells in line by reprogramming their behavior using the very tools that bacteria employ to slip past our immune system. Read more

No responses yet

Is there a bamboo ceiling for Asians in science?

Jan 18 2013 Published by under Asian Americanism, Science

First let me say that I've never liked the term "bamboo ceiling." It always sounded a little too culturally forced* to me. And in terms of imagery, it flat out sucks. Glass ceiling? At least with glass you walk away with the impression that you can shatter through it. But bamboo? That shit is hard. Like indestructible hard. Doesn't quite inspire much confidence in breaking through it now does it?

Earlier this month in Nature Jobs, Lilian Gomory Wu and Wei Jing argue that the path to leadership roles in science is impeded for Asians in the US:

In academia, just 42% of Asian men are tenured, compared with 58% of white men, 49% of black men and 50% of Hispanic men. Just 21% of Asian women in academia are tenured, the lowest proportion for any ethnicity or gender. They are also least likely to be promoted to full professor.

Similar numbers exist for industry and the federal workforce they report, and this graph was included in the tl;dr blog post:

The take home: Asians were attaining leadership positions (like PI-ships) at a lower clip than other ethnicities (although, I wonder at what rate do Asians apply or seek out managerial positions, comparatively speaking). Wu and Jing identify several possible reasons for this disparity that mainly derive from the "model minority" stereotype:

hardworking and patient, family oriented, good at maths and science and having a strong work ethic, but also humble, non-confrontational and lacking the passion to be charismatic leaders.

Many of these have been used to explain the relative absence of Asians in company boardrooms, CEOs, and the like, so it's not totally unreasonable for these explanations to apply to the sciences as well. Take, for example, how Eastern ideas of leadership--where Asians are more likely to let their actions do the talking over...well talking--are lost in translation. This can give the impression that Asians are passive or indifferent. Another possible reason is the language barrier, which can be prohibitive in writing successful grants and papers. These issues, of course, are biased towards our foreign-born, transplanted colleagues, of which there are many in science.

In 2009, Asians — defined as people from the Far East, southeast Asia and the Indian subcontinent — made up 78% of doctoral recipients with temporary visas who were planning to work in the United States.

Looking at 2008 demographic numbers from the NSF, there were 2,038,000 Asians employed as scientists and engineers: 58.9% were naturalized US citizens while 21.3% were non-US citizens. For comparison, of Black or Hispanic scientists and engineers, only 3.3% and 7.4% were non-US citizens, respectively. That being said, and particularly concerning to me, Wu and Jing also point to the perception that Asians are "forever foreign." Meaning that no matter how acculturated Asians are or become, these standards might still be unfairly applied.

As for solutions, they suggest re-evaluating cultural differences in leadership and communication skills--which basically sounds like cultural sensitivity training to me. Yet, they also put the onus on Asians to "seek training in communication, assertiveness and leadership skills." Soooo...which is it?

And what does it say about the fact that under the Comments section of the blog post it reads: "There are currently no comments"? Now, I wasn't exactly expecting my Asian colleagues to tear it up in the comments (hell, I don't know if anyone comments on Nature blog posts). It's quite possible that neither the article nor the blog post isn't reaching an Asian audience--and without social sharing/altmetrics-like data available, how am I to gauge dissemination? But that no one has voiced any opinion at all certainly doesn't help silence any of the Asian stereotypes.


Ceiling With Mud and Bamboo

Is this my view when I look up?

*Someone recently suggested to me that the phrase be changed to "glass noodle ceiling."

Related Reading:

How committed is NIH to addressing its race problem? Hint: kinda sorta



9 responses so far