Life in a Virology Lab...

Hmm, this depends on the perspective on which you see it. Is a virus even considered life? This is debatable. Imagining the virus to be a conscious 'thinking, feeling, thing'... and taking the concept of 'life' even further... Life in a virology lab must be quite terrifying if you ask me. Short. Constantly being probed by scientists. Destroyed. Confined to the space within a flask. For the scientist though, it is interesting. Learning to work modified DNA into bacteria for replication is very alluring to say the least.

New Year's Resolution of a Labster

Ok so last semester was definitely not my best.  I could outline my frustrations here but that would take too long and you have probably heard me say something to that effect at one point or another recently.

I know it's a little cliché to talk about new beginnings and blah, blah, blah at the first of the new year but I'm gonna do it anyway.  I have a very simple goal and it is this: I may not be the subject matter expert now, but I will get one step closer.  Although I think this will be my motto for the next several years, I wanted to share it here.  So if you feel like you've been in a rut or that things aren't going exactly the way you envisioned them going, just get one step closer.  Even if that one step is a baby step, you'll eventually get there.

requested by david

http://www.youtube.com/watch?v=lGjEEXSASlQ

idk why david wanted this, I just told him I would leave it here

A look inside the hood...

What's it like beyond the locked doors of tissue culture? Here's a look inside inside the hood...

https://www.youtube.com/watch?v=RuN5YAoRGjw

Lab members at their finest...

"Gru/Charlie" coming to the lab every night thinking that he's going to conquer the world

 The minions reaction when they know that's not what's really going to happen

The minions going to their PI, Dr. Nafario for coffee

Gru/Charlie grumpy when his minions are having too much fun because they are hyped up on coffee

Dr. Nafario and his right hand man

Late nights at the lab with Papi Flu

Modern Frankenstein

Ok, so for some reason, the hood seems to have some sort of mystical power over me, especially late at night when I sit alone splitting my cell lines.  So far I have A549s and FT's, but I want to maintain a flask of everything, so if anyone has some, please, if you let me know it would be much appreciated.  Anyway...  So, I was sitting there alone last night splitting my cells and it got me thinking about life, which some how, through the powers of the hood, grew into something much more...

Plans for a "living" mechanical-cell:

Before I start, I'd like to point out that there is no solid definition of what life really is.  It's more descriptive and evolves over time.  The current biological "definition" has various characteristics of life, but can't tell us for sure, yes or no, is this life or not... (as is the case with viruses). So, anyway..

Creation of a large man-made cell using computer systems. Suppose a robotic self-sustaining system is developed, designed in such a way that it would need to harvest or synthesize a lubricant, metal, and a fuel source/materials for a solar panel. At first this system would be huge, it would need several different areas for carrying out it's various functions for self-sustainability.  Sensors would be put into place as a means of creating a signaling/mock immune/nervous system.

As means of a sort of homeostasis, the machine would be able to lubricate itself. Response to external and internal stimuli are done through sensors. Metabolism is done through the generation of energy whether it is powered by steam, fossil fuel, solar power, nuclear, etc.

The computer/brain would be capable of harvesting parts/raw materials to carry out the instructions of its onboard schematics(DNA). 

All of these machines would be connected in a sense, via something like the internet for the purpose of transmitting information needed to promote the survival of their species. For example, the onboard sensors would be able to recognize different elements; in the case that a one of these "cells" becomes damaged in anyway, it would be recorded in the onboard memory and beamed to other cells as a sort of warning. Other "cells" could then be able to develop ways to protect themselves of threats. In the case of acid rain or other corrosive materials, for example, "cells" would be able to add a new material capable of withstanding such threats to their list of items they are seeking (lubricant, metal, energy).

Metabolism would be the use of energy, as mentioned before.

Through the response to its environment and it's addition of different components based on its chemical knowledge, I could make the argument that this is a growing, evolving, dynamic machine.  

It seems to meet all of the biological requirements for life (I'm probably missing something or another), yet in all honesty I would consider this to be far from living. So, I'm curious as to what all of you think.  Is this technically life?

Immortalized Cell Lines

At first glance immortalized cell lines and maintaining them seem to be a sort of necessary evil of lab.  More of a tool to get work done than anything.  A protocol which until recently I haven't honestly put too much thought into.  I've known what goes into them and the purpose of different substances, but my thought on them plateaued in a sense.  However I've found that the more time I spent splitting the cell lines I've been maintaining, the more I think about what goes on beyond the normal routine of the protocol of splitting them.

At times I've wondered how these cell lines were produced. Why are they not cancerous? Could they be cancerous because they are indefinitely proliferating?

Is immortalization possible with other cell lines? Can stem cells be give rise to other stems? Can you clone pluripotent stem cells?

Is it possible that cells in vitro could evolve differently than in vivo cells?

Last but not least, my most "out there" idea. Would it be possible to reassemble life in space? Is the fusion of sex cells on an unmanned spacecraft possible to extend the length of interstellar voyages. How do cells react in zero gravity.

So many questions...

Beware...

Some of you might hear the myth about a little girl running around the lab at night...  but that is just a myth.

On the other hand, I encounter paranormal activity in our own lab. We called it THE centrifuge. It is a mentally deranged scientist from the 1920's who had an obsession for the power of a centrifuge. The story tells that he likes to grab as many tubes as possible and walk the halls of the lab trying to mix the solution until he forms a pellet. 

And, I happen to record him in action... take a look, but BEWARE! you might be scared...

I survived my first week in lab :)

Coming into a new laboratory is a very scary experience. Especially when you want to clean up and organize everything and you have a german lady as a lab technician that is about 6' 1'' feet tall! I found out that she was not very fond of my cleaning habits since she asked me "You are not one of those neat freaks are you?" But after seeing what I had done with the place, I think she actually liked it. Now I know where everything is and this place is now starting to feel more like home.  

Also, I was given a set of samples by another postdoc in the lab. He wanted me to analyze them by immunoblot in order to test my working abilities... I guess. Along the process everybody kept trying to tell me how to make my buffers, run the gel, treat the membranes and under what conditions I should transfer it, but I was very stubborn and stuck to the way I did my 10,000 previous immunoblots. All of this time I kept thinking, if surgeons are not told by every hospital how to perform a surgery, why should researchers be told how to run their immunoblots! hahaha (Yes, for researchers doing immunoblots and making them look perfect is as much of an art as surgery!) In the end, my immunoblot looked very good and it even got some people asking me under what conditions was the gel ran and transferred. So, I really hope that next time people will look at me as trustworthy and I am allowed to do things the way I know how to do them.     

Embarking on this journey called doctoral studies

Well with the start of a new semester, I start a new phase in my academic life: being a doctoral student.  I thought it wise to be conservative with my schedule since I did not know what would be expected of me and how I would need to perform.  This is new territory for me and I do feel a bit lost.  So here are the questions have been on my mind:

What do I need to accomplish this semester?
What is my plan for research?
Who should I do a rotation with?
Who should be on my committee And what the hell is a committee anyway?

I consider myself lucky to have other graduate students who can guide me. Granted I always have the program advisors and our illustrious P.I. but it is nice to have a student's perspective.  They understand better than anyone else because they were in my shoes at one time.  They will keep it real and tell me what is important for my survival.

With that, I will wish my fellow new students the best of luck and continued success as we do this thing we call science.

Labsick :S

Everybody who wants to pursue a career in research has to find a laboratory as a graduate student and jump through the hoops and loops this new environment imposes on you. At beginning, your mentor will quiz your intellectual abilities during lab meetings, and since you have never done any research in the past you will feel overwhelmed with all the new methodologies, signaling pathways, cellular mechanisms, viral life cycle events, etcetera that you are not even remotely familiarized with. Well, this is only the beginning of a long path to become someone in whom your PI will rely on completely for writing his next grants. And don't worry! As matter of fact enjoy those frustrating moments when you don't know the answer to questions, because those moments will be over sooner than you expect. Time will fly and you will start sitting down at those terrifying lab meetings thinking that all of those questions your mentor uses to quiz people are not really that hard, and in fact they will start to sound just like simple "bioLOGIC." When you reach this stage in you PhD, you will start noticing that all of the sudden you are not the new guy at lab. As a matter of fact, this place filled with flasks, buffers, chemicals, cells, bacteria, and many other weird looking things has already grown on you and is now the place you call “second home." Unfortunately, just about the time when you start to feel this way, it means that your PhD is coming to an end and that soon it will be time to move on and continue pursuing other long term goals you had in mind when you first started this journey... So, what I am saying is that you will be at some point in the same position that I am today. Once again in a new lab, as the new guy who needs to prove himself to become someone reliable and an essential component of this place that you will eventually call your second home.    

       

That girl is on fire!

This is what happens when your hair catches on fire. your fellow lab mates photoshop your hair on fire.

FIRE!

OK, I've been wondering if I should post anything related to this. And I have decided that I simply can't resist. Afterall, the idea of this blog is to tell people about "Life in a virology lab", right?
Well, about two days ago, I walked into our tissue culture area to check the progress on the egg innoculations. My group was amplifying some of our viral stocks and they were using eggs to that end. Since I have not handled that many eggs in my life (no double interpretations please, read it literally!), I wanted to see it one more time. When I was half way to our lab's cubicule, I smelled the characteristic and typical stench of burning human hair. This triggered an immediate subconscious tingle up my spine. Was my lab area in fire? I walked quickly down the corridor and reached our cubicle, only to discover a room full of smoke and a bunch of relatively silent and shocked students who were still trying to know how to react to what had just happened. Some were giggly, some were blowing air with sheets of paper, some were simply still in shock.
Apparently, one of my undergraduates got a bit too close to the candle we use to supply the wax that is used to seal the eggs after they are innoculated. She has a particularly long and luscious hair. But its length is perhaps a bit longer than recommended for lab work. So, as she relaxed against the counter where the candle had been strategically placed, her hair caught fire. Fortunately, one of our undergrads had the good sense of immediately grab her hair, pull it with his hands, and deprive it from the air it needed to continue burning. I didn't witness any of  this. But by the smoke that had been left in the room (the door had already been open for a few minutes and my students were venting air in hopes of making it less smoky inside), I'd say they probably saw flames going up her head.
On the down side, I'll have to file a report about this incident and I hope this won't have negative consequences for our lab. On the up side, .....well, perhaps there's no much to claim on that end, other that at least she was not hurt (although she may need to change her hairstyle for a while). Bottom line, ....life in a virology lab is full of surprises (some of which you wish never to experience!).

Being a PI is so much more....

So, I'm at the annual meeting of the American Society for Virology with two of my doctoral students and yesterday I had one of those moments that force you to log in and blog.
In the morning, my crew disappeared. They didn't come to some of the morning sessions and this raised a bit of anxiety in my heart. My two students were presenting back to back talks in the first session of the afternoon workshops and we had been preparing the talks already for a while. In fact, we had skept some of the sessions the day before to work on them. I felt that they both were ready, they had rehearsed their talks to a good extent and I thought that all they needed to do was to polish aa bit more the specific wording they were going to use in a couple of slides. But it was already really good the way it was. So, I felt confident and fairly relaxed about their presentations because I knew they were going to do OK. But when I noticed them missing in action, my heart all of the sudden skept a beat. I just felt a wave of adrenaline go through my veins, produce a chill in my back, and bring back emotions I had felt the first time I had one of my graduate students presenting our work. It was that sudden realization that I was not in control that produced a chill in my brain. When you are in control, you know that nothing bad is going to happen because you will make sure that nothing bad is going to happen. But when you are NOT in control, when somebody else is at the stearing weel, you know that you are not the one who defines the direction that the moving vehicle that your life turns into is going to take. Suddenly, you realize that nothing is in your hands, you know that anything that happens at that moment, the reputation of your scientific enterprise, the boldness of your research, the perceived strenght of your own science, is in someone else's hands. 1985 was the year I started my "scientific" career. That's when I commited myself to become a scientist (well, I had always known what I wanted to be, but that's the year I started my undergrad education, at age 16). More than 25 years of truly demanding work were in someone else's hands...well, perhaps not totally, but to some degree. The chill in my back turned into a memory. When I was a child, back in Colombia, I remember climbing this relatively tall mountain right next to the city where I was born. At some point on my way to the top, I remember turning around just to realize how high I was and how easy it would be to fall down. All the effort I had put getting to that point would be lost in just one second. That memory came to me like a flash. Fear. The most basic of the emotions. The one we share with all other vertebrates. It consumed me, even if for only a few seconds. Then, a soothing thought came to me, to rescue me, to save me: "If they are not here, it is not because they are not ready, it is not because they are insecure and overwhelmed by fear, it is because they want to make it perfect, because they know they can make it perfect, it is because they will make it great."
I decided that they didn't need me. No more criticism. No more coaching. It was all in their hands. They had each other to help each other. And I trusted them. I knew at that moment that this was not really anything new. I realized something that should've been obvious all this time: I've been doing exactly that for more than a while. I've been trusting my doctoral students, my master students, my undergraduate students, with everything I've been fighting for. And I've been doing that every day since I became a professor.
I was joined by them at lunch. They came my way and we made it to the auditorium where they were going to present their work. They seemed confident. And I felt confident. Then, they presented their work. First Jason. Then Katie. They both did great. Every word, every statement, every movement appeared to be perfectly orchestrated to deliver the right message. After each one of them, multiple hands were raised. People were anxious and willing to ask questions. Questions are the indirect way to indicate that your work matters, that you intrigued your audience, that they paid attention, that your message was heard. And there were plenty of hands asking for a chance to ask a question.
I felt proud. I felt safe. I felt thrilled. But more than anything else, I felt that the road I had taken up to that point had been worth it. Life is a nothing but a second. And everyone's life is easily forgotten in the infinite array of lives that converge in our world. But I felt that I had changed, at least to some degree, Jason and Katie's lives. And that gave a deeper meaning to my own existence.
Being a PI is so much more than just writing grants, trying to be scientifically creative, staying on top of the newest research, keeping up with the newest methods, trying your best to write decent papers, looking at your data with no attachment and no bias, trying to keep an open mind about what matters and what seems to be just noise....being a PI is so much more. It is about trust, about guidance, about developing life-long interactions, about making sure everyone gets the best, ....being a PI is so awesome in so many ways, I can't see myself doing anything else at any point in life.

Time is on my side, yes it is.

Time has to be on your side.  They say the force laughs at our plans on a regular basis. I was up real early and got to the lab at 8:15 am in order to prepare to run my protein gel as soon as the lab meeting was over. What could go wrong? All I needed to do was polymerize the stacking gel. It is midnight now and I am finally home.  There were plenty of breaks and I got to eat lunch with colleagues at our weekly lunch break.  Until I gain enough experience to know the ins and outs of the business, I must be diligent. What if that spot ruins my experiment? What if those extra 5 minutes of blocking a membrane ruin my results? A Bubble! Oh noooooo, my day can't be ruined, there has got to be a way. Ask Dr. Rosas.  A Tare! Oh Shoot, no way this can be fixed, do it over again.  Read the instructions over and over again. Don't miss anything, don't add anything. Overdoing it? Under doing it?  Listen to the girl next door or the guy down a bench? Ask Dr. Rosas.

At least I can bring Mateo into the lab still. Soon enough he will no longer be allowed and my precious time spent in lab is likely to be diminished.

Nonetheless, I get to come home and I know I did every step as carefully as I could without any rush because time is on my side. It has to be. All for the love of a good figure.

Lab isn't always fun and games...

Life in a virology lab isn't always fun and games. A lot of the time, things need to get done so they don't pile up in the future. 

Simple to Complex

Today we had lab meeting to discuss each lab member's projects (experiments) that have been completed, are in progress, or at a stand still. It was interesting to see all the different aspects of research that one can explore associated to SUMOylation and Influenza. Throughout the meeting the boss would add an explanation as to why a certain project was at a stand still or why the experiment was not working. He would draw diagrams of how the experiment would theoretically work. As he drew and explained, it seemed like a fairly logical and simple experiment that would not be a problem to execute. Then, he would say "but..." and "a factor we must consider"and so on. At this point it hit me. Research is a world full of millions of questions. You hypothesize that your experiment will proceed a certain path "but" then "you must consider many different factors."Your experiment may work the way you hypothesized and it certainly may take a path you would have never imagined. When you answer one question, you then open 10 more doors of questions. And this is when research turns from "simple" to complex.

Don't you love it when...

a gel runs properly?!

It has a tiny dent, but look at that straight line!

Hopefully the rest of my gels come out this good...

It's nice when experiment work, isn't it?

The 'Root' of the Situation

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It’s great to say that research, (for me; not sure about the chemist grad students next door), is a vivacious journey, rather than the culmination of specific accomplishments such as the production of noteworthy data and a fancy degree. From degreed professionals to newborn babies, we’re all curious little scientists, uncovering the various trends spotted in

Learning all the Way

I still remember my first time in a circus. As five years old, looking at elephants doing tricks, tigers jumping through fire, and people walking on a rope suspended three meters from the ground blew my mind. Being that young, the circus seemed to me like a completely different world. Three months ago when I first started in Dr. Rosas Acosta’s virology lab, I had the same feeling again. Every day that I shadowed somebody I learned something completely different. Just by opening the door of the lab I felt like entering to a whole different world with its own language where instead of talking English people talk in a vast variety of acronyms and scientific terms.  It was nice that after sixteen years, I was still able to discover small new worlds as when I first was exposed to a circus. Instead of seeing elephants, tigers, and acrobats; I learned about bacterial transformations, cell immortalizations, and designing DNA sequences. Three months in this lab have been a constant learning experience. This is why I like science. One never stops exploring different worlds.