Category Archives: Biology

Fun Fact about your diet…

Spoiler alert: I usually start my seminars by talking about how we are all in a continual flux of our constituent cells. Don’t tell me that “people never change”… yes, they do, in fact every day a huge chunk of every person dies and is reborn. For instance, perhaps 84% of our cells are red blood cells, and each one of those cells only lives about 100-120 days (meaning that 2.4 million new cells need to be produced every second)! Not only that, our entire intestinal epithelium is completely renewed every few days, and we lose (and gain) about a Billion (Carl Sagan emphasis added here) cells in our small intestine every 20 minutes.  Woah.  OK, … so what happens to the cells that “leave” our intestines? They enter the part of the gut where the “food” goes. So, do we eat them? Do we eat our own cells? Are we constantly, every day, digesting ourselves?

Yes.

According to the Food and Nutrition Encyclopedia, every day 25% of the protein in our diet comes from digesting our own intestinal cells! Think about that. Today, perhaps one fourth of the protein in your diet came from digesting your own flesh!

And then I can start talking about my research.

Dragonflies are awesome.

Alright, so my wife and I both think dragonflies are really cool. We never really thought about exactly why we think this, it’s just this inherent neatness about them. Maybe it’s how they hover like brightly colored silent helicopters and then quickly dart about like… I don’t know, some sort of alien spacecraft. And, unlike some of our other backyard insect friends (I’m talking about mosquitoes and red imported fire ants, both of which seem to have an affinity for my skin in particular), dragonflies don’t bother us.

This last weekend I was fortunate enough to have a dragonfly interaction that got me falling down the wikipedia rabbit hole learning about our flying friends, so I figured I’d share some of what I found here. First, for the fateful interaction:

I was grilling up a batch of beer in preparation for the summer…

You read that right. Cannataro’s Brewery Summer Saison will go on tap June 2015.

… and I was joined by a male blue dasher!

20150516_143557

He hung out for a while, flew to different perches, and even let me get a few close-ups.

IMG_20150516_144501

Smiling for the camera. Which, by the way, was just my cell phone (galaxy s4).

Eventually my wort was ready to start cooling and he was done patrolling the garden so we exchanged our goodbyes and went our separate ways.  Little did I know the carnage that was awaiting me the next morning. Warning, dear reader, the next image is graphic.

IMG_20150517_101944

My dragonfly friend had been decapitated! By one of his own! Well, kind of. That new, green, living dragonfly is (I believe) a female eastern pondhawk. After I took that picture she flew off, taking the body with her, leaving just his head as evidence. Woah. Talk about cool backyard biology! Down the wikipedia rabbit hole I went. Time for some rapid fire fun dragonfly facts.

Dragonflies have been on Earth in pretty much their present form for over 300 million years. In fact, the largest insect to ever exist was an ancient dragonfly (with an estimated wingspan of 28 inches!). They can spend years in their underwater nymph form, which has extending and retractile lower jaws (remind you of any alien characters?) and can feed on vertebrates (small fish, tadpoles) and mosquito larvae (thank you).

The adults enjoy mosquitoes as well (told you they were awesome).

The nymph crawls out of the water and transforms directly into the adult in a process called ecdysis. They have a unique mating system where the male grabs the female behind her head with the claspers at the end of his abdomen and they form a heart-shaped mating pair. Their wings are self-cleaning and water repellant due to the lotus effect. I can go on and on, but if you want to learn more you should check out this video:

So next time you look at a dragonfly think about how you’re looking at the 300 million year old body plan of a ruthless killing machine with a 95% hunting success rate. Dragonflies are awesome!

 

Generating Biology

I’m taking a Teaching Careers/Methods course and our first assignment was to develop a class we’d like to teach and give a little mini-lesson to convey some learning objectives and outcomes of the class. I proposed a class dubbed “Programming and Quantitative Methods in Biology” (or should it be quantitative methods and programming in biology?). Regardless, it’s meant for upper level undergraduates, and the idea is to give students the means to model and simulate biological systems and interpret the underlying biological phenomena at play. I wanted to turn the teaching of biology on its head a bit, instead of learning words and formulae (for example: drift, selection, p+q=1) and then trying to associate them to some dynamics in your head, you “generate” the biology, observe and manipulate the dynamics, and then learn the corresponding biological concepts. I guess I spent a lot of time in college memorizing terms instead of understanding concepts and I didn’t realize the difference until I was in graduate school. Anyway, I’ll give a synopsis of my mini-lesson below. Please feel free to expand and improve or implement these ideas yourself.

Towards the end of the semester students are tasked with creating a simulation of an evolving diploid population with constant population size. Ideally, their simulation has input parameters of the initial population size and the initial distribution of genotypes at a particular allele (AA,Aa,aa). It would also be nice to define the relative propensity for specific genotypes to have offspring and the ability for an allele to mutate into another allele at some specified rate. I coded this simulation up myself for the mini-lesson I gave so that the class could play along. You can find the code here:

https://github.com/vcannataro/HW_dynamics

(again, please feel free to expand and improve on this!)

You have to save both .R files into the same folder and then open R, open the HW_dynamics_master.R script, and set the folder you saved the files to as your working directory. Then you can manipulate the parameters, run the whole script, and see the resultant evolutionary dynamics.

What do you think will happen to the genotype distribution if you run the simulation with these initial parameters?

#Number of each genotype in the population initially:
AA <- 0
Aa <- 2000
aa <- 0

#Generations to run the simulation:
Generations <- 50


#Chance of allele mutations per reproduction event:
A.to.a <- 0
a.to.A <- 0

#Some measure of relative fitness. 
AA.fit <- 1
Aa.fit <- 1
aa.fit <- 1

Do you think the population will remain as 100% heterozygote? Do you think any allele will go extinct? Do you think it will continually fluctuate, or reach an equilibrium? Well, here’s an example of what happened for me:

Initial_conditionsAfter a single generation the population snapped in to an equilibrium and remained hovering around that for the rest of the simulation. This is known as the Hardy-Weinberg Equilibrium. (This is a good opportunity to derive the HW formulas on the board and discuss what assumptions are key to maintaining these genotype frequencies). The code spits out the expected HW equilibrium given the initial p and q and the actual average equilibrium after each run, here’s what it looks like for those initial parameters:

"Initial 'p': 0.5"
"Initial 'q': 0.5"
"Expected AA= 0.25 | Expected Aa= 0.5 | Expected aa= 0.25"
"Average AA= 0.26205 | Average Aa= 0.50067 | Average aa= 0.23728       
*(averages after first generation)"

 

Now the fun begins. What would happen if we started violating these “key assumptions” underlying the Hardy-Weinberg principle? Let’s see. What do you think might happen if we started with 20 heterozygotes instead of 2000?

#Number of each genotype in the population initially:
AA <- 0
Aa <- 20
aa <- 0

20_hets

"Initial 'p': 0.5"
"Initial 'q': 0.5"
"Expected AA= 0.25 | Expected Aa= 0.5 | Expected aa= 0.25"
"Average AA= 0.55918 | Average Aa= 0.30918 | Average aa= 0.13163      
 *(averages after first generation)"

 

Woah woah woah, our equilibrium is all off! In fact, an allele went completely extinct after 38 generations. It’s almost like one of the alleles drifted towards fixation in this population.

What if the heterozygote left, on average, twice as many offspring as either homozygote?

#Number of each genotype in the population initially:
AA <- 0
Aa <- 20
aa <- 0

#Generations to run the simulation:
Generations <- 50


#Chance of allele mutations per reproduction event:
A.to.a <- 0
a.to.A <- 0

#Some measure of relative fitness. 
AA.fit <- 1
Aa.fit <- 2
aa.fit <- 1

hets_2xfit

"Initial 'p': 0.5"
"Initial 'q': 0.5"
"Expected AA= 0.25 | Expected Aa= 0.5 | Expected aa= 0.25"
"Average AA= 0.28469 | Average Aa= 0.49898 | Average aa= 0.21633       
*(averages after first generation)"

 

All of the genotypes remain in the population! This is a good spot to bring up fitness, overdominance, and underdominance.

Plus, you can play with the mutation rate between alleles (what happens if the whole population is AA but there is some chance of a spontaneous A–>a mutation? What happens if this ‘a’ allele confers some fitness advantage?)

#Number of each genotype in the population initially:
AA <- 1000
Aa <- 0
aa <- 0

#Generations to run the simulation:
Generations <- 100


#Chance of allele mutations per reproduction event:
A.to.a <- 0.0001
a.to.A <- 0

#Some measure of relative fitness. 
AA.fit <- 1
Aa.fit <- 2
aa.fit <- 2.5

 

muts

Chances are that whatever resultant dynamics you observe from the model have already been described by population geneticists. And that’s the point-  you generate the biology, figure out what’s going on to lead you to the dynamics you observe, and learn how these biological phenomena have been previously described. There will also be a focus on the limitations of models and simulations.

 

Anyway, that’s my idea. Your thoughts are appreciated!

 

 

 

Mind controlling parasites- how sci-fi are zombies anyway?

 

Halloween weekend is drawing to a close, and as I type this (looking out a coffee shop window) I can still see the zombie makeup on the faces of those passing by. It’s understandable why the whole zombie thing can be pretty terrifying. In the movies the protagonist usually watches their once fully autonomous friends and loved ones fall prey to some microscopic parasite and become a mindless vessel, obeying the will of their neural captors, tasked with ensuring the survival of the parasite and oblivious to their own health. Good thing it’s science fiction! Right? Well, anyone studying parasitology can tell you that in some cases it’s less fiction and more science.

Whenever I teach the lab on species interaction I always spend a good bit of time on mind controlling parasites. First off- they’re just cool. Plus, there’s a lot of captivating videos out there! One of my favorite being:

(p.s. larva emerging from a caterpillar body below, viewer discretion advised!)

Great music and sound effects aside, it’s always interesting and sort of mind-blowing to see the caterpillar actively defend the larva that just busted through its skin. It really gives you a sense of just how possessed an organism can become at the whim of a parasite. Another zombie-state-inducing parasite infects snails:

And another favorite, the inspiration for the zombie-survival game The Last of Us, infects and alters the behavior of entire forests full of insects:

 

Ok, so mind controlling parasites might actually be all around us, but at least they only infect invertebrates. Right?! Well, no.

Rats have a natural (and understandable) aversion to cats. When they smell cat urine they feel fear and head in the other direction. However, rats infected with the protozoan Toxoplasma gondii, which only reproduces in the cat intestine, are actually drawn to cat urine. The parasite hijacks the sexual arousal pathway in the rat brain, and instead of feeling fear the rat feels sexual attraction to the cat odor. So, just like the snails in the video above, the rats search out their natural predators for the benefit of their parasite.

 

Ok, so mind controlling parasites can infect and manipulate the behavior of mammals as well. But, certainly humans, with their giant and complex brains, don’t have to worry about being influenced and controlled by the whims of a tiny microscopic organism. Right?! Well…

I have a habit of bringing up the universe that exists within multicellular organisms. It’s easy to think of this as a one way interaction- a large organism goes about their business and the little organisms tag along for the ride. But the survival and wellbeing of the microbiome is extremely important- so important that hosts even synthesize food for their microbiome during periods of illness to ensure that their microbial friends stay happy.

Is it possible that some of our microbial friends could be manipulating our behavior for their benefit? Some scientists have recently suggested that might be the case- we might be at the whims of a microbial puppet master. More research is needed to test these hypotheses, but I look forward to the day where taking a microbe-filled pill can change my appetite for the better and bolster my microbiome.

Outside of our bacterial microbiome, we also house a vast virome. Research published in PNAS this week has shown that humans can be infected with an algal virus, and this virus was associated with a 10% decrease in performance on visual processing exams. Additionally, mice infected with the virus took about 10% longer to navigate a maze and explored 20% less.

So, maybe we’re not so autonomous after all. Spooky! Happy Halloween!