Tuesday, August 20, 2013

Programmed Cell Death

I know education is a unique experience for everyone, but for me, I LOVE being in school. It keeps me stimulated and challenged, which is something that I think goes away when we start working, sometimes even if you work in a challenging environment. A part of me died a little when I graduated and started working full time. Honestly, it took me a long time to adjust to not having to study, and to all the free time I suddenly had (I can read for fun? Psh! Yeah, okay pal. Whatever you say.).

It effected me so strongly that I've found myself desperately searching for classes to take for free online. We live in an amazing time where education is starting to become more available, and I think everyone should take advantage of it. There are sites like Coursera and EdX, that both have a number of scientific classes (some of which overlap) that are taught by leading professors and professionals from major universities... and it's all FREE.

I'm plugging these websites because I recently published a paper, and when I posted the abstract on facebook for my family and friends to read, if they wished (ok fine, it was to brag, whatever.), I found a number of people actually saying "Wow, cool, but I don't understand it", which, to be terribly honest, really bugged me. I've found that the trend among my peers is to veer away from scientific literature, and instead, read articles that are easier to digest (things on huffington post, reddit, etc.). The truly sad thing about this is that most people just don't believe in themselves enough to try and read these scientific articles. They don't want to put in the effort to look up words that they don't understand, or concepts that are foreign to them.

Sure, I'm a bit hypocritical because I use this blog to make the science of diseases fun and interesting to my peers. But the way I see it, these posts should be the gateway to higher learning. Reading only minor articles that skip over some of the most important facts in a study or paper and ignoring the true publications is like subsiding only on 100-calorie snack bags instead of entire meals.

With that being said, I've really jumped into these sites because I think it's important to keep learning. One of my favorite courses that I've taken so far was Programmed Cell Death taught by Dr. Barbara Conradt at LMU.

In 6 weeks, Dr. Conradt simply explains the pathways involved in apoptosis, which is a process practically all living organisms rely on. Apoptosis is the way our body destroys infected or diseased cells, avoids tumorigenesis (the development of tumors via uncontrolled cell proliferation), and controls tissue and system development. While it's used ubiquitously throughout living systems, my favorite use is in our immune systems. Without apoptosis, our bodies wouldn't be able to stop the proliferation of infectious diseases that take over our immune system. Without apoptosis, some viruses and chronic diseases wouldn't be able to evade our immune system responses. Really, it's quite fascinating.

Towards the end of the course, she posted a link to a video (imbedded below for your viewing pleasure) that summarizes the actions of apoptosis (aka Programmed Cell Death) in a little over 4 minutes. The only words used are labels, and the entire video is a computer animation of the steps our bodies take to destroy diseased cells.

This is what I love about science. You might skip the video (if you do, you are really missing out), or you might watch it, but either way, apoptosis is happening inside of you RIGHT NOW. Sure, studying pathways can be tedious, and is not for everyone, but this video summarizes it beautifully. The soundtrack is perfectly eerie, as well.

My point is, when I see things like this video, I know I'm in the right field. It weirds me out that apoptosis is occuring inside of me while I watch the video explaining it, but it also fascinates me. It makes me want to learn even more. I don't know, maybe I'm crazy.

So, without further rambling, here is "Apoptosis" by The Walter and Eliza Hall Institute of Medical Research.

Side note: I apologize for the absence of my posts lately. I've been completely consumed with work, publishing the paper I mentioned, presenting it at an international conference, and also I'm getting married in 2 months. Please excuse my absence.

Friday, March 1, 2013

Still alive, still kicking, and so are viruses, too.

The last few months for me have been a total whirl-wind, and have caused me to neglect my blog! I feel terrible! I'm sure that, since then, all of my (not so) dedicated readers have turned to bland multi-topic science quick-fixes, like those posted by the "I fucking love science" page on Facebook, or io9, who tried to say that NASA was covering up knowledge of alien existence a few months ago. Laughable! Anyway, we'll just forget I abandoned my blog as I planned out the next few steps in my life. It's not important!

Let's jump right in, shall we?

The hottest topic in virology these days is the sudden reemergence of the age old "are viruses alive?" debate. The basic properties used to describe something as "living" are:
  • Does it have the ability to grow? 
  • Does it have the ability to reproduce? 
  • Can it maintain an internal homeostasis
  • Can it respond to stimuli, and carry out various metabolic processes? 
  • Has it, and can it evolve over time?
 Such criteria make sense when you apply them to things that we've already determined to be alive, but when it comes to viruses, we're still searching for some solid answers. The most common quest to find an answer to whether or not viruses can be classified as living things is to consider the origin of viruses.

There are three theories for the origin of viruses that have been respectfully agreed-upon: (1) the progressive hypothesis, (2) the regressive hypothesis, and (3) the virus-first hypothesis. Let's discuss, shall we?

The progressive hypothesis:
The progressive hypothesis states that mobile genetic elements found the ability to leave one cell and enter another, progressively picking up additions as they traveled, forming infectious agents. The progressive hypothesis is supported by the existence and they behaviors of retrotransposons. Retrotransposons are the essence of the progressive hypothesis, as they are genes that move along the genome with the aid of RNA intermediates. While transitive within a single cell's genome, retrotransposons are currently limited to the confines of that cell. We've seen retrotransposons in many eukaryotic genomes, and attribute them to assisting with evolution.

The progressive hypothesis, which leans so heavily on retrotransposons for support, also has a viral example: retroviruses (which as you know, are some of my favorites). The single stranded RNA genome of a retrovirus utilizes a number of enzymes to fuel reverse transcription and integration into the host's genome. But, while retrotransposons are limited to one cell, retroviruses are able to bud from the host cell and move to another.

The regressive hypothesis:
The regressive hypothesis states that the formation of viruses occurred due to reductive evolution. Regressive evolution is not as common, but is supported. On a singular cell level, the best example of regressive evolution is that of the mitochondria. Mitochondria are organelles in eukaryotic cells that are responsible for the generation of most of the cell's energy. Mitochondria are comprised of multiple layers and membranes, and have their own set of DNA that is handed down through maternal ties. Due to their complex structure and their individual set of DNA, researchers believe that mitochondria were once bacteria that devolved to become an organelle.

The virus-first hypothesis:
The virus-first hypothesis takes a completely different approach to the origin of viruses, as it suggests that viruses originated before other cellular life. This hypothesis is really hard for some people to grasp, since we currently identify viruses by their dependency on a host for continued replication and existence. But what if viruses existed first? The simplistic design of a virus and the high rate of mutations that occur within viral replication are both promising reasons for the virus-first hypothesis.

Why am I talking about this?

A study published in Nature seems to have illustrated an adaptive quality in bacteriophages, wherein they begin to express somewhat of an "immune response" to the host's innate immune response. Researchers have shown that specific short palindromic repeats and associated proteins (CRISPR/Cas, for those who are interested) protect vital regions of the bacteriophage genome when exposed to potential threats, like invading amino acids or other bacteriophages.

Now, this article on Discovery News jumps the gun a little bit in the headline alone. "Viruses Pass Major Test to Enter Ranks of Living"? Now just hold on a gosh darned second.

Well, actually, I think I might let you decide. What do you think? Does this mean viruses are living things? Additionally, how do you think people will react to hearing that viruses may be living?

Or do you even care?