Sunday, November 2, 2014

Secret Benefits to Thalassemia, Round 2: Email Inquiry

I get emails from people asking for me to diagnose them based on images of maggots that they found on their skin, a peculiar rash they've had for years, or something they found in their poop. I have to say, I love these emails. If anyone is worried about the NSA spying on their email activity, it should probably be me, because my inbox is full of stuff that could be considered private medical information, and I am not an MD.

But sometimes I get legitimate questions, like this one that I featured on my blog forever ago (don't worry, I always ask if they mind if I post their questions). Recently, I got a really interesting and smart question from an anonymous reader. The email said:
Dear Doc,  is there an immunity of reduction of Ebola with people who have beta-thalassemia? Or is it just the opposite, a more susceptible case for those with beta-thalassemia?
If you don't remember what beta-thalassemia is, or why it might be "beneficial" (I say this loosely, as it's not necessarily a good thing to have), feel free to brush up by reading this old post about it and it's relationship with malaria.

Image from the American Society of Hematology
To recap, thalassemia is a disease associated with globin gene mutations (both α- and β-globin genes can be mutated, yet α-globin mutations are most common). Since your α- or β-globin gene is recessively mutated if you have active Thalassemia, your red blood cells develop into malformed, or "sickled", cells, thus inhibiting their affinity to bind and transport oxygen (see image above for a great example). This lower affinity can cause extreme cases of anemia. In major cases, treatments such as chronic blood transfusion therapy, splenectomy, transplantation and iron supplementation are used. Thalassemia would make a great potential candidate for genome editing therapies that are still in the research stage (yes, I know that article is about hemophilia, but it's a good example).

So, why is this anonymous question a great one? Simply put, it doesn't really have an answer. There isn't any research being done to look into populations that aren't as affected by Ebola right now, as far as my searches have illustrated. This might be because most research that's being done is to either understand the physiology of the virus, to identify all possible vectors (yes, most evidence point to bats as the vector, but I'm still not convinced), or to come up with therapies/treatments and vaccines.

But the submitted question addresses an important point: thalassemia, specifically β-thalassemia is really prevalent in Nigeria (25% of the population are carriers for Sickle Cell Disease, while another 25% is hemizygous for the G6PD gene), and other parts of Africa. So, why isn't this being looked into? I can't answer that. I don't know. All I can say is maybe it isn't yet. I'm sure now that Ebola is in the spotlight, there will be a new emphasis on funding down the line for exploratory research.

In my fervent literature search to find an answer for the anonymous email, I did find that similar research has been done to look at the effects of thalassemia on hemorrhagic fevers (specifically Dengue Hemorrhagic Fever), mostly in Thailand and Southeast Asian countries. It turns out that patients with thalassemia don't necessarily have any higher risk, or even less of a risk (as seen with malaria), of getting hemorrhagic fevers, as my anonymous email inquiry asked. But, they do present differently, meaning their symptoms may seem different than infected people without thalassemia. Most normal (non-thalassemia) patients show signs of hemoconcentration (or an increase of solids in the blood), but patients with thalassemia present anemia (which is the opposite). This is the main symptom that presents differently, but its a really important one. Other symptoms also reference changes in AST and ALT levels, which illustrate the concentration of enzyme in the liver, heart and muscle cells, and can indicate liver function.

Hemoconcentration is really important during the diagnostic phase, and to track how the infection is progressing. So, if, instead, your patient is presenting with the exact opposite, it might lead to misdiagnosis. Also, if a patient with thalassemia, who is also infected with dengue hemorrhagic fever, is showing anemia, it needs to be watched. The three papers I linked to above talk about new suggested courses of action for patients with thalassemia, like frequent blood transfusions.

So, anonymous emailer, the answer is probably not. The biggest risk that thalassemia would give you is misrepresenting symptoms, which can lead to improper care. Yes, that can be really dangerous, especially with hemorrhagic fevers. But, luckily, if you have a high fever and other viral (standard) infection symptoms, your doctor will usually run other diagnostic tests (like an ELISA or PCR, etc.). That's why they always ask you questions about where you've been, what you've been in contact with, and other patient history questions.

This is definitely research that should be done, even if it starts with a retroactive epidemiology study.

Thanks for your question!

If any of you have other questions, feel free to email me at!

Wednesday, October 15, 2014

Shift, Not Drift

There have been a few reasons why I haven't been updating my blog lately.

1. I've been trying to get a side-blog up off the ground with a good friend. It has nothing to do with science, but if you are interested in reviews of vegan candies from around the world, you can check it out here.

2. My main project at work was coming to an end, and I was in a mad dash to collect some final data and write up a massive report, summarizing all of the work I did to support the project for the last 3 years. I'm sure you can imagine how time consuming that was.

3. I've been working on creating some content on antibacterial resistance for Khan Academy, but the editing and re-writing process has taken longer than I initially anticipated.

aaaaand, lastly:

4. Given the fact that my previous project with NASA was ending (now: has ended), I decided that it was time for me to take the plunge back into my original research field: virology. Tomorrow is my first day as a researcher for Stanford University's School of Medicine, specifically in the pediatric department and infectious disease division! Yes, that's right, I'm leaving the world of life support and heading into a world of dengue fever and chikungunya!

Side note: how wild is it that I had just posted about chikungunya? Totally weird coincidence.

So, as I transition into this new job, I hope you can wait patiently for my next entry. I actually have the topic already picked out, and am slowly working on creating the content. The next entry will actually be based off of a question that I received via email, and I'm really excited to dive in. (Hint: it's something about Ebola).

Thank you for bearing with me while I make this ridiculously exciting jump to Stanford! Woo!

Wednesday, August 27, 2014

Clearing the Mass Miasma

I’ve had a number of inquiries about the Ebola outbreak, whether for clarification (“what is Ebola?” or “should I be scared?”) or desperation (“I don’t know what to believe anymore!”). Let me start by saying that it’s OK to be confused or a little nervous. The media has done a great job at reporting on this terrible and unfortunate situation, but has done an even better job at making people nervous or question their ability to prepare for such a situation in their own town.

It’s always been a little aggravating to me that most science reporters or science writers don’t have a science background. There are a lot of benefits to that, such as their vernacular may not be jargon-heavy, or they might be able to cover a wide range of topics on a broad, elementary level. But, there are also a lot of writers that are feeding into the media-based hysteria to get more clicks. How do you get people to read your stuff? Scare the crap out of them.

You really can’t escape it. I’ve seen posts on Facebook to articles that detail inaccurate methods of Ebola transmission (thanks, “friends”…), and I even heard about it on the radio. Whenever I drive into work, I usually have the radio on so I can get traffic updates. A week ago, one of the personalities on a stupid morning show was talking about the isolated testing for Ebola that was happening in Sacramento (which actually happened for some missionaries, that much is true), and it really made me sad, because it solidified how little people feel they need to research the stuff they read online. Everything the deejay said was inaccurate, and all I could think about was the hundreds (thousands maybe?) of people listening at that moment...and believing everything.

But I’m not writing this to call people stupid, or make anyone feel bad about their news choices. Instead, I’m writing to give you the facts of what I’ve gathered so far. I’m not on the front lines, and I may not be a popular blogger or writer for Jezebel or Huffington Post, so I’ll it up to you whether I’m contributing to they nonsense or not.

So you want to understand Ebola. Where do you start?
If you want to understand the virus itself, you can read some of my previous entries on Ebola.

There are only a few places in the world that are allowed to research and work with any and all strains of the Ebola virus. For a long time, that list was limited to only major governmental agencies (CDC, etc.), especially research agencies that have the capability to work with biosafety level – 4 (BSL-4) pathogens. You can read more about BSLs here, but I’ll break it down for you:
  • BSL-1: all microorganisms used are not known to consistently cause disease in healthy adults and present minimal potential hazards to lab members and the environment. A good example of this is non-pathogenic E. coli, which is used in almost every lab that has ever existed. Think everything from entry level biology classes to, well, most other labs.
  • BSL-2: In addition to being able to work with BSL-1 organisms, BSL-2s can work with organisms that pose a moderate risk or hazard to lab members and the environment. A good example of this is Staphylococcus aureus.
  • BSL-3: This is a restricted environment, as the hazards are increased from BSL-1 and BSL-2. The pathogens or organisms researched in these labs can often cause lethal diseases via respiratory transmission, like Mycobacterium tuberculosis which causes tuberculosis.
  • BSL-4: Lab work involves microorganisms that are dangerous and exotic, and may or may not have a defined method of transmission yet. This is where Ebola is researcher. Researchers who work with BSL-4 organisms have to change their clothes before entering the clean room, and must shower and decontaminate all materials before leaving the research space. These researchers have to wear full body, pressurized, and air-supplied suits. This is the solitary confinement of pathogen research.
Image from Frankfurter Rundschau

Get it? It’s incredibly dangerous, and you should thank the researchers that risk their lives to perform the groundbreaking experiments that they do. If you want to read the follow-up report regarding a researcher accidentally becoming exposed to Ebola, you can download that here.

Am I at risk of becoming infected?
Unless you are a health care worker who is working with individuals who are infected and currently experiencing symptoms, your chances of contracting Ebola are slim to none.

With that being said, the only known method of transmission for Ebola is direct contact with the bodily fluids of an infected individual. If you have traveled to Africa recently, and have had contact with someone else’s bodily fluids, you may want to check in with your doctor. Once someone has recovered from the virus, they are typically no longer contagious, but the Ebola virus has been shown to be present in semen for up the 3 months post-infection.

This isn’t like our seasonal flu. Ebola is an incredibly debilitating infection that can have symptoms including high fever, headaches, muscle pain, vomiting and diarrhea, and unexpected bleeding or bruising. There have been some really sad stories about churches, mortuaries, and even entire towns banning traditional funeral and burial practices because it puts otherwise healthy people at risk.

Will the outbreak spread to the US?
The CDC has not indicated any potential risks for the outbreak to spread. Yes, there have been medical professionals and missionaries that have contracted Ebola during this outbreak, and yes, they have been brought back to the US for treatment.

BUT, there is a reason for that. Almost all the major research that has been done to figure out the Ebola virus has been conducted in the US (or in collaboration with the CDC). Experimental treatments are here, better medical facilities with isolated rooms and chambers are here. 

Let me put it this way: As of right now, there are 2,615 cases of Ebola between Guinea, Sierra Leone, Liberia, and Nigeria. There are more than 1 million individuals who are infected with HIV in the US, and 1 in 6 of them are unaware of their infection (typically due to negligence with regular testing). HIV is also spread through direct contact with bodily fluids. But, every time you go into a hospital, you don’t panic about HIV because medical facilities are prepared to handle and minimize these types of risks. Take a deep breath and don’t believe everything Donald Trump says.

What. an. ass.
OK, I believe you about the risk of getting Ebola in the US, but I’m still paranoid and want to track it every day.
That’s fine. Check out this amazing website that will give you a detailed update every time something happens with the outbreak. You can also watch an illustration of the spread of the outbreak since March 14, 2014.

What about treatments? Why aren’t there treatments?
There are currently 3 companies working on developing experimental treatments against the Ebola virus: Tekmira, Biocryst Pharmaceuticals, and Mapp Biopharmaceuticals. All of them are in very early stages of development, meaning none of them have been approved for use in humans. ZMapp is the product that is getting the most media because the experimental monoclonal antibody-based therapy was given to two US patients in Liberia.

Since this experimental therapy has not been approved, it requires each patient to consent, and understand the potential risks associated with experimental, non-approved therapies. Compared to some of the other funded research, Ebola isn't seen as a major threat. Maybe that's because we haven't seen an outbreak this large before, or that it hasn't been a threat to the US yet. Either way, it's getting the attention it needs now to really get some momentum in terms of pushing drug and vaccine development through to (hopefully) a reality.

It is possible for patients to recover and survive an Ebola infection. In order to do this, the patient needs constant monitoring for fluid balance, oxygen and blood pressure, and additional treatments for complicating infections.

This is a lot of information to digest, so I'm going to leave it at that. If you have any other questions that you'd like answered, feel free to let me know!

Sunday, June 15, 2014

That Which Bends Up

 Just before leaving for my trip to Costa Rica, I purchased a some Ultrathon insect repellent and an insect repellent bracelet. This trip was going to be my first time traveling in Central America, and I had heard that the mosquitoes were "no joke". This was also my first international trip with a group, and I had to give myself time to adjust to the fact that I would have no control over our itinerary at all (which is a big deal, because I enjoy planning everything about my trips).

I'm usually not a major target for mosquitoes here in the states. I honestly cannot remember ever really getting a mosquito bite in the past, but if you are a regular reader, you'll remember that I've had my fair share of ticks and other things. I'm sure it wont surprise you to hear that I did my research before going, and made sure I was aware of any infectious disease-related hazards. Giant spiders and venomous snakes don't really worry me, but I did my research for everything else. There's a giant list of illnesses that are prevalent in Central America, but you can research those on your own. The only real possibility of exposure was Dengue fever. I've traveled to areas that have had outbreaks of Dengue fever before, without any insect repellent, so I was already doing a better job of being prepared.

I was traveling with a group of field biologists, and I learned right away that most field biologists have absolutely no time or motivation to worry about infectious diseases. Yes, they were all prepared with their massive spray bottles of OFF! and some with their insect repellent shirts and hats. But, I've never seen so many people willingly jump after poisonous frogs, handle venomous snakes, catch bats, and handle potentially dangerous insects without a bit of hesitance. Most of it was traumatic for me (I'm more of a "let's be as unobtrusive as possible and observe from afar" type of biologist), but seeing their childlike excitement was kind of inspiring.

Speaking of excitement, here's me at a beautiful waterfall near La Fortuna.

We brought microscopes with us and stayed at the Texas A&M Soltis Research Center during a majority of our trip. The microscopes we were able to pack weren't anything fancy, just two Leica dissecting scopes and three Primostars for fluorescence work. Here are some of the images I took (the primostars didn't have cameras, so these are all taken through the oculars with my iphone):

Clockwise from the upper left:
 tree moss autofluorescing under a DAPI filter, the wing of a fly under a FITC filter, 
floral structure under FITC filter, plant structure under DAPI filter.

Anyway, the point of this blog post was not to showcase my vacation photos, but to talk about what I experienced afterward. Upon returning to work the very next day (mistaaaaake!), some interested colleagues asked if I had "brought anything back" from my trip. They weren't asking if I bought coffee or chocolate, but if I had contracted any diseases while gallivanting through the rainforest. Sure, I might have made some jokes about wanting to get myself a pet botfly larvae, but I wasn't serious. I mentioned that there was a chance I could be in an environment with mosquitoes carrying Dengue fever, and one of my colleagues said, "but there's a new one, right? It's like Dengue, but not?"

That, my friends, is Chikungunya. Chikungunya, which means "that which bends up", has been an issue since the 1950s, but reached epidemic proportions in 2004. Since 2004, Chikungunya has spread rapidly in Africa, Asia, the Indian subcontinent, Europe and the Americas. Recent spread of Chikungunya through the Caribbean islands has caused isolated incidents to show up in North America, thanks mainly to tourism.

Chikungunya is a mosquito-borne RNA virus that shares initial symptoms with Dengue fever, which often results in misdiagnosis. Most regions affected by Chikungunya don't have clinics or labs with the capability to test for both Chikungunya and Dengue fever. 

While Chikungunya doesn't have a high mortality rate, the symptoms can be excruciating. Much like Dengue fever, fever, muscle pain, headache, nausea, and fatigue are common, but joint pain and rashes are the distinguishing symptoms. Dengue has been called "bone breaking" fever for the muscle and bone pain associated with infection, but Chikungunya, or "that which bends up" was named for the contorted posture associated with the debilitating joint pain. 

Via El National

The emergence of the Chikungunya epidemic and the warnings against Dengue fever at the World Cup bring up an interesting question: in the age of synthetic biology, should we try to wipe out mosquitoes once and for all? We've been down this road with malaria and using insecticides to reduce mosquito populations, and...well, malaria is still a problem. But, if you are interested in what's being done to control mosquito populations in specific areas, I highly suggest you listen to the Kill 'Em All episode of Radiolab.

By the way, the CDC has a map tracking cases and local transmission of Chikungunya that is updated as reports of cases come in.

Check back soon for my next blog post on a disease that causes self-cannibalism!

Tuesday, March 18, 2014

New Beginnings: Spring Edition

My life has completely changed since my last post, seven months ago. I wanted to write, in fact, I had a list of topics going for a while, but I just couldn't find a spare hour or two to really iron out the details. In the time since my last post, I got married, traveled to Europe (specifically Paris and London) for my honeymoon, had a birthday, got some new science-specific tattoos, published some papers, was asked to teach a few classes in the fall, took some steps to better myself in my career and my personal life, and got a cat. I have a hard time fitting in time for the gym, or even really breathing!

Here's my husband, on our honeymoon, in a Medical History Museum in Paris (I'll blog about that later). 
I have ideas for new blog posts every day, and I'm going to do my best to start catching up. Be warned, though, my ability to write somewhat blog posts may have decreased, since I've been working on writing three papers simultaneously in the last few months. Maybe you're a distinguished scientist, maybe you're a student, or maybe science is just a hobby to you, but I don't think I need to explain that scientific writing is not the most flavorful of writing styles.

The weather is getting warmer, especially for those of us in California (It was 80 degrees this weekend!). This means gardening, hiking, a general increase in "outdoorsiness". There are two things that I want you to be aware of as you start enjoying the warm weather: Lyme Disease and soil-transmitted parasites! I'll cover soil-transmitted parasites in my next blog post.

One of my dear friends, Kristen, has been trying to dig her heels into some research on Lyme Disease, and I promised I'd post something about it. Since I am stupid, I forgot that I had already written about ticks! Not necessarily Lyme Disease, but a tick-borne virus. Actually, maybe I should try to convince her to write a little guest-blog post for us about what she's learned!? I can imagine myself asking her to do that, and can clearly picture the mixed emotion of extreme excitement and annoyance that would wash over her face. Kristen, if you are reading this, I won't make you do it!

The Tick, via PopGunChaos
Lyme Disease is a bacterial infection that is quite weird, in that you have the ability to be successfully treated with the use of antibiotics within the first few weeks, but it can become chronic if left untreated. Lyme disease has been reported in 80 countries worldwide, and is especially concentrated on the east and west coast of the United states in regions with wooded areas and areas with tall grasses.

Lyme Disease rash variations, via bayarealyme

The bacteria responsible for Lyme Disease is Borrelia burgdorferi, which is a spirochete that has a double membrane, instead of being gram positive or negative. B. burgdorferi is an obligate parasite that uses ticks (Ixodes pacificus) as a vector to infect their mammalian hosts, like rodents, deer and humans. Transmission of B. burgdorferi to smaller mammals doesn't typically result in Lyme Disease (although the rash has been seen in many domesticated dogs that live in rural areas), making that complication specific to human hosts. Ticks transmit B. burgdorferi to humans while taking a blood meal. A simple "bite" doesn't usually do the trick. Transmission is dependent on the length of time the tick has been present on the host (usually 36-48 hours minimum), and on the level of infection within the vector (is the bacteria just in the midgut? or is it present in many different organs, like on the mouth parts and throughout the digestive tract?).

Also, according to samples studied from the Pacific Northwest (California and Oregon), only about 1-1.5% of ticks are infected with B. burgdorferi. With increases in tick populations, the probability of transmission increases. This is one of the reasons warmer seasons lead to more infections.

Ixodes pacificus, via Riekes Nature Blog
Tick size comparison before and after a blood meal, via WA Department of Health
Many studies are trying to determine the proliferation and survival mechanisms of B. burgdorferi because it lacks common pathogenic factors, like lipopolysaccharide, toxins, and specialized secretion systems. Researchers think this may be because B. burgdorferi did not evolve to cause disease in mammals. Not only is there a wide range of variation between bacterial strains of B. burgdorferi, but the analysis of the DNA has shown that it is rapidly evolving.

So why don't you want Lyme Disease? If you are one of the lucky ones that has a resident tick for more than 36 hours, and doesn't identify the symptoms within the first few weeks of infection (meaning you probably wouldn't seek treatment either), then you could experience a wide range of chronic symptoms. Initial symptoms are classic "flu-like" symptoms, such as fever, chills, muscle aches, stiff neck, and just feeling like crap (clinical phrase). To be fair, unless you see a rash with these symptoms, I don't know why you would seek treatment. We've all been sick before, and usually flu-like symptoms aren't severe enough to run to the doctor. A lot of people miss the rash because it's on their scalp/under hair, or somewhere they can't see, like on the back of their neck and trunk areas.

Most people who have chronic Lyme Disease and are being actively treated still feel exhausted all the time. But, without treatment, B. burgdorferi can spread to your brain and heart, resulting in major organ damage and failure. The most common and alarming symptoms are numbness, paralysis, and muscle weakness. It's pretty awful, and you don't want it.

My family has many stories that involve ticks. As you probably know, I am a huge hypochondriac. My poor husband, Peter, has to put up with text messages from me saying things like "AM I HAVING A STROKE?" and "MAYBE ITS CANCER". (Whatever, he knew what he was getting himself into...). I'm also pretty outdoorsy. I'm a runner and love to hike. I hike year-round, but that doesn't stop me from asking Peter to check me for ticks every time I come home from a hike.

My first run in with a tick was in elementary school, on a class hike. My mom, a nurse, was one of the chaperones, and saw it crawling on the back of my neck. I don't remember it actually biting me, but every time we bring that story up, she gets very serious. She hates bugs.

After a hike with my mom, I had the fun opportunity of getting a tick to back out of her skin by using a hot matchstick. She thought it was a mole on her back that was being irritated by her running bra. Sorry mom. Luckily we caught it and she escaped sans Lyme Disease.

Another awesome tick story: my sister is an amazing athlete, and signed up to do her first triathlon a few years ago. She felt sluggish and terrible a few weeks before, was diagnosed with early Lyme Disease despite not seeing a rash (there are diagnostic tests that are done, too), and started treatment immediately. She still competed in the triathlon and finished with a great time. See what I have to live up to? Ugh.

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?