WARNING: Digressions may occur. Wee knight illustration courtesy of the magnificent Jon Hoehn II.

Tuesday, December 16, 2014

Where do animals go in the winter? The tale of the wood frog

I spent the first 18 years of my life in North Carolina, and I can count the number of times it snowed in my hometown (village, really) on one hand. Now that I've moved to Wisconsin, deep in the frigid North, I find myself wondering every year around November where all the little critters go in anticipation of the impending deluge of snowflakes. Birds obviously migrate South, and bears hibernate in cozy holes, but what about squirrels and rabbits?
Optional digression: Earlier this year I met two baby bunnies! There are a ton of rabbits around my apartment complex. One evening I was walking up to the front door when I noticed some movement. Being a nature enthusiast, I stopped immediately because I suspected there might be an interesting critter in the vicinity. Sure enough, two little bunlets (if that's not the term, it should be) and their mama were in the grass right in front of my building. I crouched down to try to look less threatening, and one of the little fellows hopped right up to my foot! He (or she) touched me! I have high hopes for that bunlet and his family.

HE'S SO CUTE

Back to original story! It's entirely possible, I suppose, that other furry creatures also migrate in the harsher months, but what about snakes and frogs and insects? Surely they don't ALL migrate. So, I've been curious for several winters and I finally bothered to do some in-depth research (i.e., I googled it). Because this topic has already been covered by other intrepid bloggers, I've included a bonus look into the life of the wood frog!
It turns out that two of the animals I mentioned before, squirrels and rabbits, actually stay active in the winter and just do their best to find food and keep warm in trees and burrows [1]. Chipmunks, on the other hand, hibernate like bears [2].
Reptiles like snakes will also take shelter in burrows. Fish will move to the bottom of lakes and ponds where the water won't freeze, and turtles and frogs hide out in water bodies too, entering a dormant state and absorbing oxygen from the water through their skin [3].
Some insects, such as the silkworm Bombyx mori, will enter a hibernation-like state called diapause during the winter [4]. Others lay eggs which will hatch in the spring, then die. Still others simply hang out in various hidey-holes (tree bark, fallen logs, dirt). An interesting variation on this theme is the gall. You've probably seen plants that seemed to have warts, like so:

Ewwwwwwww

This is actually a wee insect's home. Bugs like eriophyid mites secrete compounds that bulge out the plant tissues, then live there and munch on the plant throughout the winter like a bunch of degenerates [5].
And then there's the wood frog. Rana sylvatica, much like Geobacter sulfurreducens (I have a blog post on that, too!), just doesn't give a fuck.

Pretty cool background, huh? Even if it's not as cool as Arya. I got it here.

These frogs can survive being frozen in the winter, so when it starts to get nippy they just hunker down under some dead leaves near a woodland pool (gotta be ready to start making babies in the spring) and turn into frog cubes.
Like this. Except, you know, frog.
Yeeeeeaaaahhhhh.

They are able to do this because they accumulate cryoprotectants--antifreeze*, basically--in their blood and tissues to decrease the formation of ice crystals that would rip their cells open. Soooper cool (that was a pun).
I'll leave you with this video of scientists playing with frozen wood frogs because...science?







*Not technically true. Antifreeze prevents freezing, while these compounds minimize the size of ice crystals that form, which reduces the stress on the cells (less stabby stabby = good). They do also prevent freezing to some extent because of freezing point depression, but that does not seem to be their main purpose. There ARE critters that have antifreeze in their blood (some Antarctic fishes come to mind), but those are a topic for another day :)




References:

  1. http://wdfw.wa.gov/living/rabbits.html
  2. http://animals.nationalgeographic.com/animals/mammals/chipmunk/
  3. http://www.newton.dep.anl.gov/natbltn/400-499/nb485.htm
  4. Okitsugu Yamashita (1996). Diapause hormone of the silkworm, Bombyx mori: Structure, gene expression and function. Journal of Insect Physiology 42(7):669-679.
  5. Robert Wawrzynski, Jeffrey Hahn, and Mark Ascerno (2005). Insect and mite galls. University of Minnesota. http://www.extension.umn.edu/garden/insects/find/insect-and-mite-galls/

Wednesday, December 10, 2014

Self-medication in animals

Hi there! Did you know that when your dog eats grass, it's probably because it has an upset stomach and is trying to puke/poop out the problem? Apparently other animals do that too! I found this neat article while traversing the interwebs this morning.Give it a read!

News Feature: Animals that self-medicate by Joel Shurkin

Friday, December 5, 2014

Dianne Newman is awesome

So, yesterday I had breakfast with Dr. Dianne Newman, who is a professor at Cal Tech, and OMGOSH SHE'S SO AMAZING!!

I think her science is pretty cool, but really I like her just because she is such a nice person. I and the other students at the breakfast were asking her a bunch of questions about the usual, how did you become a professor, how do you choose post-docs, how do you feel about the funding climate, etc. Her answers were definitely helpful, and they gave a lot of insight into what kind of person she really is. One thing she said regarding how she chooses post-docs that resonated with me was (paraphrasing), "It's not enough to be intelligent, you have to be nice, too."

Yes!!! Yes! All of my yes! This is so true, especially in this context. Honestly, almost everyone in grad school was at the top of their class in college. We are all smart, and that is not special. It seems like so many professors choose post-docs because they have 5 first author papers or they got a Nature paper or they got this award or that, and completely disregard their character. Along those lines, she also said that she expects her post-docs to help other students in the lab and really be a mentor to other people. Also fabulous. Many, many post-docs are going to look for a faculty job at some point, and the whole point of these positions is to have your own lab, which means you're going to have to mentor people! I just think it's silly when post-docs focus super hard on their research and don't give a sh*t about their labmates.

AND (seriously love this woman), another thought she expressed reminds me of my undergrad advisor, Antje Almeida (who is also awesome and will probably be featured in a future blog post). One thing that I really loved about Antje was that her door was always open--not just for help with research or classes, but also if I just found a funny cat video and wanted to share. Since then, I haven't met a professor that I felt I could ever be friends with. Friendly acquaintances, sure, but not an actual I-send-you-Christmas-presents-and-invite-you-to-my-wedding friend. I was getting that same friendly vibe from Dr. Newman. In fact, she explicitly said that she wants to be a part of the group in her lab, and have people stop by her office just to say "hi" sometimes instead of always for business.

Of course I also respect her so much for being a successful, tenured professor at a respected university and having a family at the same time. You hear so much on the interwebs about gender discrimination; it's nice to see a success story now and then.

I almost want to do a postdoc just so I can work in her lab...

Friday, November 21, 2014

Sea star wasting: what is it and why do we care?

Sea star wasting syndrome (SSWS). What the heck is that? It's this:

Holy crap. If you want to skip straight to the sad parts, check out around 4:20. I couldn't find the video to post it here, but somewhere out there is a video of starfish literally walking themselves apart; two arms going in opposite directions, then *boop* three-armed starfish! Awful.

Obviously, that kind of sucks for starfish, but who really cares? They're not pretty like this lovely critter:
Pictured: a male violet-crowned woodnymph. Thanks for the photo, Joseph C Boone of Wikipedia land!
And they eat and poop through the same hole, so they can't be contributing to global IQ levels too much.

Luckily, you don't need brains to eat, and these dudes eat a lot. They are in many ecosystems what is called a keystone species: a species whose effect on its ecosystem is disproportionate to its population size in that ecosystem. Starfish eat shellfish like sea urchins and mussels, keeping their population in check. If you take starfish out of the equation, the shellfish population explodes. This throws the ecosystem out of balance--suddenly you have a plethora of clams roving around, eating all the food and taking all the nice rocks for themselves. But wait, there's more!

Getting rid of the starfish also destroys a food source for several predators: sharks, rays, and sea anemones. Sharks in particular could just eat more regulat, fish-shaped fish, but that would cause the fish, but that would cause the fish population to plummet and the price of tuna would go up and next thing you know Chicken of the Sea costs $20 a can. It's not a great scenario.
Pictured: not worth it.
So why are all the sea stars dying? What is causing this disease, and can you get it by kissing a starfish?

The cause of SSWS has been a mystery since it was first observed in January of this year, but this month research groups at Cornell (among other places) showed some pretty decent evidence that the condition is caused by a kind of virus called a densovirus. The researchers ground up some diseased sea stars and filtered everything larger than a virus out of the sea star puree (mmmm, tasty), then infected healthy starfish with this virus soup. Within a couple weeks, most of the healthy starfish started showing symptoms of SSWS.
The control is boiled starfish puree. From Hewson et al. 2014, PNAS
They also found these little guys in diseased starfish:
From Hewson et al. 2014, PNAS
Using genetic analysis, they determined that this was a type of virus called a densovirus. Densoviruses are small, icosahedral DNA viruses; icosahedral just means they are shaped like an icosahedron, pictured below.
I'm poor, so you'll have to deal with the watermark.
Now that we are reasonably sure what is causing SSWS, what do we do about it? Well, science fans, that question is still unanswered. But at least we know where to start!



Pictures?
I realized that when I link to a picture here, you can just click on it to get to the original source, so I've decided to stop including the links down here. It only took me three blog posts to figure that out!

Wednesday, November 5, 2014

How do you cool something?

I think we can all agree that refrigerators are made of magic. But, it may surprise you to know that there is also some science sprinkled in for funsies. Since I never got my letter from Hogwarts, I can't tell you about the first point, but I have journeyed far and wide (to the other side of the lab where the physicist--my co-blogger!--sits) to discover the secrets of

Let us begin with a quick refresher on thermodynamics. Hey, get back here! I swear it's not scary or hard. What it is is a great word to use to make your friends think you're smart. Look, we're just going to use this teensy equation, very harmless...

PV = nRT
where P is pressure, V is volume, T is temperature, n is number of molecules and R is the gas constant.

Super easy, right? Pressure, volume and temperature are proportional to each other! So, if we increase the pressure, either volume will decrease or temperature will increase--or, more likely, a little bit of both. Let's pop some numbers in there so you believe me. I'm going to ignore n and R for simplicity.
Let P = 5, V = 6, T = 30

P*V = T, therefore 5*6 = 30 (woo!)

Now, P = 6. Three options:
(1) V decreases to 5
(2) T increases to 36
(3) Mix of 1 and 2

What's that? You'd like a real world example? Alright, science fans, I whipped this one up just for you! Let us turn to our faithful friend, water.
Is that not just fabulous? Doesn't it make you feel good just looking at it?
As you know, if you take a room temperature pot of water and increase the temperature until it boils, it will turn to steam. Now, the temperature of the steam won't rise until all of the water evaporates (for reasons I will not get into because they aren't that interesting to most people). However, you will note that steam takes up a LOT more space than water does, which--oh my goodness here it comes--decreases the pressure.
Did you see what I did there?!
Why does it decrease the pressure? Because the molecules are farther apart! If you take a packed bus full of people and spread them out among 5 buses, those people feel less pressure on them from fellow bus-goers. Same deal with water and steam. Boom. We just proved that PV = nRT, the ideal gas equation, works in real life.

Now, armed with this thermodynamical knowledge, we are fully prepared to battle understand

If you have a refrigerator and you ever bothered to look at the back of it, you probably saw something like this:

What's going on there? I have made this very detailed, scientific, post-modern illustration to explain.


What a great invention. Science!


Pictures!

Friday, October 24, 2014

Bioremediation by bacterial badasses part 2: How do bacteria digest toxic waste?

If you haven't checked out part 1, you should! Unless you know how heavy metals are poisonous, then you're already caught up.

Ok, so stuff like radioactive waste and oil are bad for the environment. Thus, it might be a good idea to clean that stuff up if it gets where it's not supposed to be. Unfortunately, you can't just mop it up with a paper towel like that time you spilled wine all over your grandmother's new carpet (you drunkard, you). There are some very smart people trying to design materials that can act like paper towels and sop up bad stuff, and I'll include some links at the end if you want to read more about that business. However, I promised you bacteria, and bacteria you shall have! Let me introduce you to my friend Geobacter. You can call him Geo.
Don't mind me. I'm just chillin', saving the environment and stuff.
Geo is kind of an oddball. Like many bacteria (and higher organisms such as ourselves), Geo likes to eat sugars and/or small, sugar-like molecules (e.g., acetate, malate), because sugar is delicious.
Take a break if you need to and go find some candy.
But, Geo also eats metal and petroleum, because he doesn't care about your rules.
Imagine a bacterium sitting in that swing seat, if you would.
You see, most (possibly all) organisms make high-energy molecules using what is called an electron transport chain. We can think of it this way: in general, organisms receive energy (eat) from a lot of different sources. That is apparent just by looking around us. Humans eat pretty much anything that stands still long enough; chickens, broccoli, termites (check this out!) Dogs are so anti-picky, they eat their own puke--among other things...

But wouldn't it be kind of a pain if we had to build cars that ran on gasoline, natural gas, electricity, hydrogen, solar power, wind power, etc.? That would be pretty silly, so most cars are powered by just gasoline.

Cells are the same as cars. A lot of proteins--our handy-dandy molecular machines--are powered by ATP (adenosine triphosphate).
You have about 250 grams of me right now. Picture--Ben Mills
Alright, back to the electron transport chain (ETC). The basic idea isn't really intuitive to me, even though I've worked in biological sciences for several years now, so I'm going to do my best to break it down into something simple but still fairly accurate.

ATP is a way for you to store energy. Returning to the car analogy, you probably fill up your tank when it starts getting low, but most of the time you don't use all that gas at once. You drive to work, you go to the grocery store, you visit your friend's house a few minutes away. And you can do this because gasoline is a source of energy that can be stored. Sunlight is a form of energy, too, but if you don't have a solar panel to soak it up and put it inside a battery, you can't use the sunlight later. So, ATP is one of the reasons why you don't need to constantly eat to power your body.

The way the ETC works is kind of like this: you have a vehicle that you want to drive down a hill at midnight. The vehicle can only run when the sun is shining on it. So, you drive the vehicle to the top of the hill during the day, then later that night you can just give it a little nudge and it will roll down the hill. ETC is how your cells get the vehicle up the hill.

That's great, but what does this have to do with our old friend Geo? Geo has the neat ability to use nasty stuff like oil and uranium as steps in the ETC. It can bounce electrons through them to other molecules to make ATP.

Why can't we do that? We just don't have the machinery! Like I said earlier, proteins do everything for us. We don't have the same proteins that Geo uses to eat up toxic waste.

Geo has already been useful in cleaning up the streets, and a lot of people are trying to figure out how he does his job and maybe how to help him do it better, like a bunch of Commissioner Gordons rooting for Batman.
I am the night!
Some people are even thinking about using him to make batteries! But let me not leave you thinking that Geo is the only quicker-picker-upper out there. He has friends like Pseudomonas putida and Deinococcus radiodurans. I've heard they like to have parties and talk about all the seagulls they've saved.
Like a boss.


Pictures!

Tuesday, October 14, 2014

Bioremediation by bacterial badasses part I: Why are heavy metals toxic?

We all know that heavy metals like uranium and arsenic, as well as hydrocarbons such as crude oil and plastics are pretty bad for the environment, since they have this weird tendency to kill things. Most people know how oil kills innocent critters: it gets all over their feathers, gills, fur and fins, weighing them down so that they can't use their locomotory method of choice, which often results in them drowning. They probably get eaten sometimes, too, since they're slow, easy prey, and I'm sure that gives some unlucky predator a lingering foul (or fowl, ha) taste and a nasty bout of indigestion.

But how are heavy metals toxic? And what the heck is a heavy metal? Are there metals that aren't heavy? I think those are questions not many folks know the answers to. I didn't, until my junior (senior? It's been a while) year of college.

It all comes down to proteins. Proteins are not, contrary to bodybuilder popular opinion, just a post-workout necessity. Actually, we are all made up of a vast number and diversity of proteins that basically do everything for us. Yes, even plants. Don't be racist, plants are people too. Here are a few examples of cool proteins:

actin keeps your cells in their proper shape, and makes those sexy muscles contract
They look weird, but they're supposed to. That green stuff is actin, and the blue is DNA.

DNA polymerase copies your DNA, in conjunction with DNA helicase, which unzips your genes

Hank Green is my hero. Watch all of his videos.


I'm a little disappointed that I'm already in a relationship and can't use this pickup line on somebody.
trypsin breaks up them food proteins
amylase breaks up them food sugars
rhodopsin eyeballs! I'm actually not 100% sure what this one does, but I do know it's important for seein'.
Pretty. I got this from Petr Novák, Wikipedia - Own work.
I learned what rod and cone cells are from this. I never knew! You should look it up if you don't know already.

Proteins are great. Wouldn't it be sad if they stopped working? Or if something stopped them from working? Like heavy metals?

That's right, sports fans, that huge tangent had a purpose. Coming back around, let's talk about metalloproteins. A lot of super important proteins require metals to function.

Most metalloproteins use lighter metals like sodium (Na), potassium (K), magnesium (Mg), and calcium (Ca). Some use slightly heavier metals like manganese (Mn), cobalt (Co), or zinc (Zn). Heavy metals are elements like silver (Ag), gold (Au), and mercury (Hg). Those metals like proteins, too. They actually like them more than the lighter metals. You can think of heavy metals as bullies. Gold comes up and sees magnesium playing with a DNA polymerase, and he's like "I want to play with that protein!" Since he's bigger, he pushes magnesium in the dirt and takes the polymerase.

Of course, it's not quite that simple, but that's the general idea. You can also imagine that sticking a bigger blob where a smaller one used to be would change the shape of something. Since a protein needs to have a certain shape to work, heavy metals cause problems and basically break whichever protein they attach to.

The title of this post mentions bacteria. Odd, I didn't mention bacteria at all in this article, did I? I guess that will be in part 2!
This is like a trailer, except it's not a video!



I can't do art, so let me tell you where I got all those neat pictures, in order of appearance: