Science can cure disease and make things adorable at the same time!

A recent study by the University of Rochester Medical Center has found that the same chemical used to color blue M&Ms and blue Gatorade can also be used to heal spine injuries. The chemical, Brilliant Blue G (BGG) blocks P2X7, known as the “Death Receptor.” This stops the signal that tells motor neurons to undergo apoptosis (cell death). When rats with spinal cord injuries were injected with BGG, they were able to walk again with a limp.

How awesome is that?

And BGG has the added benefit of making rats extra adorable. They go from this:
To this:Want. Now.

I'm a scientist! Pt 5

So the previous project I described is what I worked on most of my junior year and is in the process of being transformed into a paper (which I’ll likely get to be first author on – huzzah!). What other lab work have I been doing recently?

This wasn’t even meant to be a full project, but really started out of curiosity (like all good science does). One of my professors, Prof W, was doing some collection in the krat’s breeding season (Novemberish) instead of our usual July. During his trapping he was lucky enough to discover some copulatory plugs.

What the hell are copulatory plugs, you ask? Basically it’s a secretion the male deposits during mating that hardens into…well, a plug that takes time to remove. This makes it harder for the female to mate with another male later for obvious reasons. Or to steal a good analogy from Wikipedia, it’s a biological chastity belt.

Most rodents and some insects use copulatory plugs but they’re still a bit of a mystery. There’s not much literature on them in rodents, and virtually none on kangaroo rats. So we thought, what the heck can we do these things? Hmmm, let’s chop them up and genotype them!

We cut the plug into four segments, so one segment 1 would be the most internal in the female, and segment 4 would be the most external. We digested the plug and extracted DNA, then genotyped the DNA using various genetic markers. We then compared the results for these markers to the genotypes of the females we retrieved the plugs from. The tricky thing here is that you have a mixed sample, something they have to deal with a lot in forensic cases. Think of a rape case – you may have a semen sample, but it’ll have DNA from the female in it too. How do you know which belongs to which when you’re looking at something on a screen?

This is an example of what you would see (each number represents an allele):

Female: 130, 142
Mixed sample: 130, 136, 138, 142

You know that 130 and 142 most likely came from the female, and the new 136 and 138 came from the male. So the male is 136, 138 right? Well…it’s a bit more complicated. Maybe there are two males, and one is 130, 136 and the other is 138, 142. Or maybe one is 136, 138, and the other is 138, 142. What if there are three males?

Thankfully, there are ways around this. One is by comparing the relative strengths of each allele (not going to explain that, sorry). Another is using multiple markers. Another is assessing the probability of the combination using statistics. And finally, you can use the exclusion principle – see what males absolutely cannot possibly have contributed those alleles, and see who’s left and how the puzzle fits together.

I think you can imagine that this project is the ultimate puzzle. It can be a pain in the butt deciphering everything, but it’s really rewarding once you crack the code. And what have we figured out so far? Well, we have a pretty good guess of what male contributed to the plug, and in some cases more than one male appears to have contributed to the same plug, with their contributions separated by location in plug. Aka, the male that got their first formed the most internal part of the plug, and the second male formed the most external.

And before I start talking too much about rodent sex, I’m going to leave the implications of that up to your imagination.

This is post 29 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.

I’m a scientist! Pt 5

So the previous project I described is what I worked on most of my junior year and is in the process of being transformed into a paper (which I’ll likely get to be first author on – huzzah!). What other lab work have I been doing recently?

This wasn’t even meant to be a full project, but really started out of curiosity (like all good science does). One of my professors, Prof W, was doing some collection in the krat’s breeding season (Novemberish) instead of our usual July. During his trapping he was lucky enough to discover some copulatory plugs.

What the hell are copulatory plugs, you ask? Basically it’s a secretion the male deposits during mating that hardens into…well, a plug that takes time to remove. This makes it harder for the female to mate with another male later for obvious reasons. Or to steal a good analogy from Wikipedia, it’s a biological chastity belt.

Most rodents and some insects use copulatory plugs but they’re still a bit of a mystery. There’s not much literature on them in rodents, and virtually none on kangaroo rats. So we thought, what the heck can we do these things? Hmmm, let’s chop them up and genotype them!

We cut the plug into four segments, so one segment 1 would be the most internal in the female, and segment 4 would be the most external. We digested the plug and extracted DNA, then genotyped the DNA using various genetic markers. We then compared the results for these markers to the genotypes of the females we retrieved the plugs from. The tricky thing here is that you have a mixed sample, something they have to deal with a lot in forensic cases. Think of a rape case – you may have a semen sample, but it’ll have DNA from the female in it too. How do you know which belongs to which when you’re looking at something on a screen?

This is an example of what you would see (each number represents an allele):

Female: 130, 142
Mixed sample: 130, 136, 138, 142

You know that 130 and 142 most likely came from the female, and the new 136 and 138 came from the male. So the male is 136, 138 right? Well…it’s a bit more complicated. Maybe there are two males, and one is 130, 136 and the other is 138, 142. Or maybe one is 136, 138, and the other is 138, 142. What if there are three males?

Thankfully, there are ways around this. One is by comparing the relative strengths of each allele (not going to explain that, sorry). Another is using multiple markers. Another is assessing the probability of the combination using statistics. And finally, you can use the exclusion principle – see what males absolutely cannot possibly have contributed those alleles, and see who’s left and how the puzzle fits together.

I think you can imagine that this project is the ultimate puzzle. It can be a pain in the butt deciphering everything, but it’s really rewarding once you crack the code. And what have we figured out so far? Well, we have a pretty good guess of what male contributed to the plug, and in some cases more than one male appears to have contributed to the same plug, with their contributions separated by location in plug. Aka, the male that got their first formed the most internal part of the plug, and the second male formed the most external.

And before I start talking too much about rodent sex, I’m going to leave the implications of that up to your imagination.

This is post 29 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.

I’m a scientist! Pt 2

If you want to read some news articles about my lab’s research, here are some links:

Scientists are learning more about big birds from feathers
Study shows animal mating choices more complex than once thought
Sex lives of wild fish: genetic techniques provide new insights
Random picks better than complicated process in gene indentification
DNA from feathers tells tale of eagle fidelity
Road losses add up, taxing amphibians and other animals
Study rules out inbreeding as cause of amphibian deformities
Genetically modified fish could damage ecology

Speaking of our amphibian road kill project…to give you an idea of how bad it gets, here’s the carnage on a road in West Lafayette after it rains:The town literally has sweepers that come through and remove all of the frog bodies. Thousands die after a single rainfall.

This is why road planners need to talk to biologists before building a major road that bisects a marsh.

This is post 22 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.

I'm a scientist! Pt 2

If you want to read some news articles about my lab’s research, here are some links:

Scientists are learning more about big birds from feathers
Study shows animal mating choices more complex than once thought
Sex lives of wild fish: genetic techniques provide new insights
Random picks better than complicated process in gene indentification
DNA from feathers tells tale of eagle fidelity
Road losses add up, taxing amphibians and other animals
Study rules out inbreeding as cause of amphibian deformities
Genetically modified fish could damage ecology

Speaking of our amphibian road kill project…to give you an idea of how bad it gets, here’s the carnage on a road in West Lafayette after it rains:The town literally has sweepers that come through and remove all of the frog bodies. Thousands die after a single rainfall.

This is why road planners need to talk to biologists before building a major road that bisects a marsh.

This is post 22 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.

I’m a scientist!

I figured I’ve been blogging long enough with vague references to lab work and research and biology conferences that I should actually tell you guys what my research is. I’m not going to go super in depth for two reasons: one, if you’re not a biologist, you probably wouldn’t know what the heck I was talking about, and two, we’re still trying to publish my work, so I don’t want to give it all away before it’s officially out there.

So before I get into specifics, let me give you a little background information about what I do.

My official job title is not “Undergraduate Slave Technician” but a Forestry & Natural Resources Signature Area Fellow in Ecological Genetics (phew, try saying that three times fast). That’s really just a fancy way of saying I get paid slightly more because FNR had a special fund for smarty pants undergraduates doing more than one year of lab work. I’m actually a student of the Biology Department, which is in the College of Science, while FNR is part of the College of Agriculture. The only difference? Ag gets better funding at Purdue. Genetics is genetics no matter what department you’re in.

The laboratory I work in is pretty diverse as far as projects go. Most of our research is on ecological genetics and using genetics to answer questions about conservation. While a lot of labs have only one or two study organisms, we basically have everything. Birds (a ton of species from Hispanola, Eastern Imperial Eagles from Kazakhstan), amphibians (from Tiger Salamanders to whatever we find squished on the road), fish (Lake Sturgeon, my favorite sexually ambiguous fish), and mammals (hurray for Kangaroo Rats!). And our actual research is just as diverse: investigating long term population histories, genetic diversity and the effects of human structures, noninvasive ways to monitor population densities, discovering the genetic mechanisms for sex determination, the genetic basis for mate choice, dispersal…we’ve basically done it all.

When I started research, I have to admit that I really didn’t see the point of conservation projects. I didn’t know much about the fragile nature of ecosystems or why we need to protect our wealth of resources on earth, even at the very least for selfish reasons. After working in the lab for a while, I have a new appreciation for conservation. Personally, it’s not the kind of research I want to be doing – I’m still a bit of a cynic about conservation, and I’m not passionate enough to devote my life to it. My cynicism doesn’t make my the best spokeswoman for it, either. But regardless, I do appreciate the work done much more than I did before, and I’m glad I got what’s going to be a diverse lab experience before I go devoting my life to human genetics or something (or who knows what).

This is post 20 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.

I'm a scientist!

I figured I’ve been blogging long enough with vague references to lab work and research and biology conferences that I should actually tell you guys what my research is. I’m not going to go super in depth for two reasons: one, if you’re not a biologist, you probably wouldn’t know what the heck I was talking about, and two, we’re still trying to publish my work, so I don’t want to give it all away before it’s officially out there.

So before I get into specifics, let me give you a little background information about what I do.

My official job title is not “Undergraduate Slave Technician” but a Forestry & Natural Resources Signature Area Fellow in Ecological Genetics (phew, try saying that three times fast). That’s really just a fancy way of saying I get paid slightly more because FNR had a special fund for smarty pants undergraduates doing more than one year of lab work. I’m actually a student of the Biology Department, which is in the College of Science, while FNR is part of the College of Agriculture. The only difference? Ag gets better funding at Purdue. Genetics is genetics no matter what department you’re in.

The laboratory I work in is pretty diverse as far as projects go. Most of our research is on ecological genetics and using genetics to answer questions about conservation. While a lot of labs have only one or two study organisms, we basically have everything. Birds (a ton of species from Hispanola, Eastern Imperial Eagles from Kazakhstan), amphibians (from Tiger Salamanders to whatever we find squished on the road), fish (Lake Sturgeon, my favorite sexually ambiguous fish), and mammals (hurray for Kangaroo Rats!). And our actual research is just as diverse: investigating long term population histories, genetic diversity and the effects of human structures, noninvasive ways to monitor population densities, discovering the genetic mechanisms for sex determination, the genetic basis for mate choice, dispersal…we’ve basically done it all.

When I started research, I have to admit that I really didn’t see the point of conservation projects. I didn’t know much about the fragile nature of ecosystems or why we need to protect our wealth of resources on earth, even at the very least for selfish reasons. After working in the lab for a while, I have a new appreciation for conservation. Personally, it’s not the kind of research I want to be doing – I’m still a bit of a cynic about conservation, and I’m not passionate enough to devote my life to it. My cynicism doesn’t make my the best spokeswoman for it, either. But regardless, I do appreciate the work done much more than I did before, and I’m glad I got what’s going to be a diverse lab experience before I go devoting my life to human genetics or something (or who knows what).

This is post 20 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.

Galapagos Tortoise Gets His Freak On

…That title is what happens when I’m listening to dance music in order to stay alert. Anyway.

90 year old Galapagos Tortoise, Lonesome George, may soon be a daddy.

“No wonder they were amazed – a team of scientists have been doggedly coaxing the sullen creature to mate since 1993, when they introduced two female tortoises of a different subspecies into his pen. Until now, George, the last known Pinta Island tortoise had shown little interest in his companions.”

There…there are too many possible jokes to make about this! Here, choose your favorite:

a) But with the advent of Pfizer’s new Tortoise Viagra, there’s now hope for George.

b) Unfortunately for the species, Lonesome George has finally come out as being homosexual. His main keeper isn’t surprised.

c) 90 year old virgin? But who could resist a face like this?

“But at age 90, George, now said to be in his sexual prime, was finally spurred into action.

…Galapagos Tortoises, among the species Charles Darwin observed to formulate his theory of evolution in the 19th century, were hunted for their meat by sailors and fishermen to the point of extinction, while their habitat has been eaten away by goats introduced from the mainland.”

It always saddens me when people do something so extraordinarily stupid, and then we have to desperately try and fix it a hundred years later. Of course, that seems to be a prevalent pattern in human history. Good luck, George!

This is post 7 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.

I’ve been podcasted!

Hm, is podcasted a word?

Anyway, you may remember one of my older posts, Natural Sexuality, which was a satire in the form of a script. Well it turns out the podcast Polyamory Weekly liked it so much that they did a mini reenactment of it. It’s not the entire thing, but I do like the guy’s voice for Lion. Too bad it took me almost two months to accidentally discover that they did it.

If you’re interested, the mp3 is here. It’s the first thing they talk about on the show.

I feel pretty special. I don’t think even PZ’s had voice actors for his post (and now I know someone will give me a link to prove me wrong…shhhhhhh).

I've been podcasted!

Hm, is podcasted a word?

Anyway, you may remember one of my older posts, Natural Sexuality, which was a satire in the form of a script. Well it turns out the podcast Polyamory Weekly liked it so much that they did a mini reenactment of it. It’s not the entire thing, but I do like the guy’s voice for Lion. Too bad it took me almost two months to accidentally discover that they did it.

If you’re interested, the mp3 is here. It’s the first thing they talk about on the show.

I feel pretty special. I don’t think even PZ’s had voice actors for his post (and now I know someone will give me a link to prove me wrong…shhhhhhh).