The Story Behind a Potential Protein Treatment for Achondroplasia

Injecting sFGFR3 induces bone growth in wildtype mice (WT) and achondroplastic mice (Fgfr3ach/+). Adapted from Fig. 2 (1).
Injecting sFGFR3 induces bone growth in wildtype mice (WT) and achondroplastic mice (Fgfr3 ach/+). Adapted from Fig. 2 (1).

Earlier this week, several news outlets reported on a decoy protein as a potential treatment for achondroplasia or, more commonly, dwarfism, but made no mention of its origins.

From the New York Times:

Injections of a decoy protein can restore normal bone growth in mice with dwarfism characteristics, according to a new study, suggesting a possible treatment for humans with the condition.

People born with achondroplasia, the most common form of dwarfism, tend to be short in stature with short arms and legs and a relatively larger head, sometimes resulting in problems with the spine and with hearing and breathing. The condition is caused by a single mutation in the gene Fgfr3, which provides instructions for making a protein involved in the development of bone and brain tissue.

The Fgfr3 gene codes for fibroblast growth factor receptor 3 (FGFR3), a protein found on the surface of cells that in essence serves as an antenna that cells use to communicate with each other.  Continue reading

Dog-day Cicada

Found this little bugger on my tire this morning.

A photo posted by Viet Le (@amasianv) on

This past spring, my girlfriend and I were in Virginia for a wedding when the 17-year Brood II cicadas were just starting to emerge. We were excited by the possibility of seeing some on our trip, but unfortunately, we didn’t spot any–I think we were too early?

Well, I can rest easy now after finding this lil’ bugger perched on the tire of my car yesterday morning. I believe this is a “dog-day” cicada, or annual cicada, which is different from the 13- and 17-year periodic cicadas that have been all up in the news. Dog-day cicadas typically have a 2-5 year life cycle and their broods are not synchronized. Overlapping broods ensure that dog-days cicadas appear every summer, usually in July and August, but it also means they don’t swarm like their periodic cousins.

Still pretty cool looking nonetheless.

Photo 51

Rosalind Franklin doodle

Today’s Google Doodle honors Rosalind Franklin, whose work on X-ray diffraction was instrumental in determining the double helix structure of DNA. In the Doodle she’s staring at an X-ray diffraction image, known as Photo 51, that got the ball rolling. If you’d like to learn more about how the structure of DNA was determined, Nova has a great interactive dissection of Photo 51 that helps unravel the double helix structure from what looks like just an “X.”

After her work on DNA, she “conducted pioneering work into the structure of viruses.” Sadly, she died due to complications of ovarian cancer in 1958–four years before the Nobel Prize was awarded to Watson and Crick for their research on nucleic acids, and at the time much of her contribution was overlooked.

I can’t help but wonder what else she would have accomplished had she not passed away.

Alien Faces or Larval Butts?

Crane Flies  spiracles
Image credit: Chen Young

These might look like mugshots of unsavory patrons that frequent the Mos Eisley Cantina, but they’re actually the posterior ends of larvae from 6 different species of crane flies. The dark circles that resemble eyes are in fact breathing holes called spiracles. Instead of lungs, insects have a respiratory system made of a network of tubes and ducts, called trachea and tracheaoles, connected directly to the outside world by spiracles. These breathing holes are used by both the larva and adult forms of insects and can be found running along the length of the insect’s body.

Spiracles
Spiracles on the side of catepillar.

Just below the spiracles is the larva’s anus surrounded by anal pads, which give the “alien face” the appearance of a mouth or teeth (imagine having a set of nostrils right above your anus!).

Ponda Baba and Muftak meme

The larvae of many crane fly species are aquatic or are found in wet environments. Since crane fly larvae do the majority of their breathing through their posterior spiracles the odd, tentacle-like protrusions may be adaptations that  help them breathe. For instance,  the hairs and bristles covering the protrusions can trap air when the larvae are submerged in water.

cranefly larva posterior
Posterior spiracles of a crane fly larva.

Adult crane flies are often confused for being male mosquitos or even mosquito hunters, despite the fact that they generally feed on nectar or in some cases nothing at all–the adult flies of some species exist only to mate. You’ve all probably seen crane flies before, wobbly flittering around looking like drunk daddy longlegs with wings.

Tipula paludosa
Adult Tipula paludosa crane fly
The Mos Eisley Cantina scene from Star Wars Episode IV – A New Hope:

Related Reading

It’s An Evolutionary Trap!!!

Snyder-frog-banner-990x603
“A Cuban Tree Frog tries to eat a Christmas light. Photo by James Snyder. National Geographic My Shot”

You might be wondering why a frog would eat a Christmas light, but it may have simply confused the glowing bulb for a luminescent insect it normally feasts on. This is just one example of how even the mundane ways we’ve changed the environment can trip up other creatures–and sometimes with evolutionary consequences. As Carl Zimmer explains in a blog post over at The Loom,

We have altered the environment in a vast number of ways, both small and large. And when animals try to read the cues from our human environment, they can get tricked. They can end up doing something that kills them, loses them the opportunity to reproduce, or simply wastes their time. Scientists call these situations evolutionary traps.

Hydropsyche pellucidula
Caddisfly species Hydropsyche pellucidula
While the Cuban tree frog ultimately spit out its mistaken meal and survived its run-in with holiday lighting, other organisms are not as fortunate.

When caddis flies become adults and are ready to mate, they need to get to a body of water. Without Google Maps to help them, they do what their ancestors have done for countless generations: they take advantage of the fact that ponds and streams change the reflection of moonlight, altering its polarization. Unfortunately, large plate glass windows can polarize light in the same way, with the result that caddis flies will sometimes blanket the glass, mate, and lay their eggs there.

Carl Zimmer goes on to mention several other examples of evolutionary traps, like the Australian beetles that vigorously try to mate with empty beer bottles, and also discusses ways that we might disarm them. Head over there and have a read.

It's an evolutionary trap

I couldn’t resist.

 

Blight-Resistant Potato: an “Acceptable” GMO?

1280px-Phytophtora_infestans-effects
“Potato Blight Effects”

Last week, I wrote about a disease-causing nematode that infects the roots of soybean plants and  a mutation in one strain of soybeans that makes them resistant to these nematodes. In the post I mused,

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?

While intended to be more of a thought experiment, a commenter alerted me to a very similar scenario playing out in Ireland, where potato crops are still affected by blight–yes, as in the blight responsible for the Great Famine of the mid-1840s. Blight makes potatoes rot and is caused by infestation of a fungus-like organism (oomycetes) called Phytophthora infestans.

In recent years, scientists have developed blight-resistant GMO strains of potato plants by introducing a blight-resistance gene called RB into the potato’s genome. This gene was identified in Solanum bulbocastanum, a wild potato plant native to Mexico that is closely-related to potatoes. Resistance to blight most likely developed as a result of coevolving with P. infestans, which is considered to be native to Mexico as well.

The scenario facing GMO potatoes, however, is a little bit different from the question I posed earlier since the RB gene isn’t found in cultivated potato plants. Furthermore, traditional breeding methods have been unsuccessful in making hybrids between cultivated potatoes and S. bulbocastanum, therefore necessitating genetic engineering. There are, however, other blight-resistant wild Solanum plants, such as Solanum venturii, that can be hybridized with cultivated potatoes. But using the RB gene from S. bulbocastanum remains the most attractive option because S. bulbocastanum is resistant to the most number of blight-causing P. infestans strains

The response from one anti-GM campaigner to using genetic engineering in this case?

It is just there to make GM more palatable to the general public. The fact that it comes from a related plant doesn’t make it any different. The real danger is the process.

I guess that answers my question.

An “Acceptable” GMO?

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 kept soybeans on hand to 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 (SCN), which find the roots of the soybean plant irresistible. These agricultural pests invade the roots of the soy plant where they do a bit of their own agriculturing. These nematodes can create a steady supply of food for themselves by coaxing the root cells that they feed on to divide. 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, forming characteristic cysts on the roots of the soybean plant. The damage to soy crops comes in at $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 soybean plant roots 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 just 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 identifiedmutations 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 important functions of serine hydroxymethyltransferase is to convert serine into 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 cause changes near the active site of the SHMT protein, or the “business end” where the shuttling of carbons occurs, it’s possible that the mutations affect the activity of the SHMT protein. To test this model, Liu and Kandoth compared the ability of the normal and mutant forms of SHMT to make glycine by expressing these genes in an E. coli bacteria strain that can’t make its own glycine.  This particular strain of bacteria dies when glycine is removed from its diet, but was able to survive when Liu and Kandoth engineered the strain to express the normal form of SHMT. This indicated that expressing the normal SHMT protein restored the bacteria’s ability to make glycine. However, the bacteria didn’t survive as well when the mutant form of SHMT protein was expressed which suggested to the scientists that the mutant protein was less efficient in making glycine.

More importantly, soybean plants that were susceptible to SCN infection became resistant when Liu and Kandoth transferred the mutated Forrest SHMT gene into 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 protein in the feeding cells of the soybean plant root reduces either their “nutritiousness” or their ability to divide. As a result the nematodes that infect the Forrest cultivar starve.

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.

Reference
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

Battle of the Sperms

Inside every Drosophila melanogaster (fruit fly) female is a battleground where sperm can jockey with each other for the honor of fertilizing her eggs. By sequentially mating females with males genetically-engineered to produce sperm that glow either green or red (see video below), scientists have been able to directly observe sperm from two different males competing in what resembles a fruit fly version of Tron. Color coding the sperm in this way allows researchers to distinguish one male’s sperm from another’s and determine who the winners are.

“Sperm from two different males genetically-engineered to express either green or red fluorescent proteins compete within the female reproductive tract of the fruit fly Drosophila melanogaster.”

Surprisingly, it’s not always the fastest sperm that wins.

Continue reading

Drug Resistance in MRSA is Finely-tuned

Cross-posted at PLOS Public Health Perspectives.

In hindsight, shoving my hand into a narrow drinking glass wasn’t such a good idea.  I learned this the hard way a few years ago while vigorously scrubbing the inside of a glass with a sponge. When the glass shattered in my hands, one of the shards cut the base of my index finger–right by the the knuckle–and required a trip to the local urgent care center. After being stitched up, I was sent home with some antibiotic ointment, extra gauze, and instructions to keep the wound clean. And that’s when things got worse.

Several days later, my finger became red, inflamed, and tender to the touch. There was also stomach-turning pus oozing out of the wound. Fearing that it was infected, I went back to the the urgent care center where the doctor took one look at my wound and then stated the obvious, “That looks infected.” A swab sample was taken from my wound to start a bacterial culture, which would be used to identify the nature of the infection. Since it would take a few days for the results to come back from the lab, she preemptively started me on a course of antibiotics. At the end of the week, there was a message left on my voicemail. The culture was positive for methicillin-resistant Staphylococcus aureus (MRSA).

MRSA-infected finger

This was cause for concern because MRSA is a bacterial pathogen that, once it enters the bloodstream, can cause severe to life-threatening infections. MRSA is also notoriously difficult to treat because it is resistant to β-lactams, a class of antibiotics generally prescribed as the first line of defense against normal staph infections. β-lactams, which include drugs like penicillin, oxacillin, and methicillin, kill bacteria by preventing the synthesis of bacterial cell walls–without which bacteria cannot survive. These drugs accomplish this by glomming onto and inactivating penicillin-binding protein (PBP), an enzyme that makes an essential component of bacterial cell walls. MRSA strains, however, are resistant to β-lactam drugs because they carry a gene called mecA. The mecA gene encodes a different form of penicillin-binding protein, PBP2a, which β-lactam drugs cannot inactivate, thus allowing normal cell wall synthesis to occur even in the presence of these drugs.

Methicillin-resistant Staphylococcus aureus (MRSA) Bacteria2
Scanning electron micrograph of methicillin-resistant Staphylococcus aureus bacteria (yellow) killing and escaping from a human white cell.

MRSA infections have long been associated with health care settings such as hospitals and nursing homes. These settings, characterized by a sick general population coupled with high antibiotic usage which selects for drug-resistance, are a perfect environment for MRSA strains to gain a foothold. Given that I had my stitches done at an urgent care center I just assumed that’s where I came into contact with MRSA.

In recent years, however, community-acquired MRSA (CA-MRSA) infections have been on the rise. These are infections contracted from settings like schools, childcare centers, gyms, and prisons. Infections caused by CA-MRSA strains are a particular concern because they are more virulent, spread more rapidly, and can cause more severe infections than its healthcare-acquired MRSA (HA-MRSA) counterparts. What’s worse is the line between the two are blurring as HA-MRSA strains move out into the community and CA-MRSA moves into the hospitals. Because of the increased virulence of CA-MRSA strains there are fears that these strains will eventually replace HA-MRSA strains in healthcare settings–although a recent model published in PLOS Pathogens suggests otherwise[1].

How MRSA developed β-lactam resistance is still unclear. While there are quite a few different strains of MRSA (some of which have also developed resistance to other classes of drugs) they all carry the mecA gene. The mecA gene, in turn, is part of a larger piece of foreign DNA known as the SCCmec element, which is not normally found in S. aureus. Since bacteria are quite adept at exchanging DNA with each other, scientists speculate that the SCCmec element found its way into a normal staph strain from an as-of-yet identified trading partner. This process of swapping and transferring DNA is known as horizontal gene transfer.

Interestingly, MRSA has a finely-tuned, “on-demand system” that turns mecA expression on in the presence of β-lactam drugs, while keeping expression turned off in the absence of these drugs. This regulation is carried out by proteins whose genes are also found on the SCCmec element. In the absence of β-lactams–when the bacteria doesn’t need the drug-resistant PBP2a protein around– the expression of mecA is kept in check by the protein MecI. MecI binds to the DNA promoter region of mecAand prevents gene transcription. However, in the presence of β-lactam drugs the bacteria needs PBP2a around in order to survive. In this case, expression of mecA is turned on through the action of the cell surface protein MecR1 whose job is to keep an eye out for β-lactams. When MecR1 detects the presence of β-lactams, it instructs the bacterial cell to break down the MecI inhibitor. This allows expression of the mecA gene that is essential for the bacteria’s survival to occur.

journal.ppat.1002816.g010460
Figure 10. Model for the mecA induction by MecR1-MecI-MecR2.In the presence of a β-lactam antibiotic, MecR1 is activated and rapidly induces the expression of mecA and mecR1-mecI-mecR2. The anti-repressor activity of MecR2 is essential to sustain the mecA induction since it promotes the inactivation of MecI by proteolytic cleavage. In the absence of β-lactams, MecR1 is not activated and a steady state is established with stable MecI-dimers bound to the mecA promoter and residual copies of MecR1 at the cell membrane [2].

Recently, researchers from Portugal have identified and characterized another gene on the SCC element called mecR2 [2]. As it turns out the MecR2 protein is another component of the finely-tuned, “on-demand system”that regulates mecA expression. When MRSA bacteria encounter β-lactam drugs it starts ramping up the production of MecR2 protein. MecR2, in turn, knocks the MecI inhibitor protein off of the mecA gene promoter, thereby increasing mecA expression. The researchers speculate that the dislodged MecI protein becomes unstable and is then degraded inside the bacterial cell.

Importantly, the researchers demonstrated that in order to get the optimal expression of mecA that would confer resistance to β-lactam drugs, the bacteria needed MecR2 protein around. When they removed the mecR2 gene, the bacteria once again became sensitive to the β-lactam drug oxacillin, which coincided with a decrease in mecA expression. This research not only helps further our understanding of drug resistance in MRSA but also highlights new targets for therapeutics. For instance, drugs could be designed that either short circuit the ability of MecR1 to alert the bacterial cell to the presence of β-lactam drugs or prevent MecR2 from dislodging the MecI inhibitor from the mecA promoter, thereby keeping mecAexpression in check.

As for my finger and me, we made it out of the MRSA scare relatively unscathed–other than a barely noticeable scar at the base of my index finger. Once the lab results came back positive for MRSA, the doctor switched my prescription to Bactrim. Luckily for me, I wasn’t dealing with one of the multi-drug resistant varieties of the bug so the infection cleared in a few days.

Featured image: Scanning electron micrograph of methicillin-resistant Staphylococcus aureus (MRSA, yellow) surrounded by cellular debris. Credit: NIAID

References:

1. Kouyos R, Klein E, & Grenfell B (2013). Hospital-Community Interactions Foster Coexistence between Methicillin-Resistant Strains of Staphylococcus aureus. PLoS Pathogens, 9 (2) PMID: 23468619 doi:10.1371/journal.ppat.1003134

2. Arêde P, Milheiriço C, de Lencastre H, & Oliveira DC (2012). The anti-repressor MecR2 promotes the proteolysis of the mecA repressor and enables optimal expression of β-lactam resistance in MRSA. PLoS Pathogens, 8 (7) PMID: 22911052 doi:10.1371/journal.ppat.1002816