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2011 (4)
February (2)

PSA: It's cold, buy a Carbon Monoxide Detector.
Thursday, February 10, 2011

Cold Fusion
Tuesday, February 1, 2011
January (2)

Going back
Thursday, January 27, 2011

Fun with Jackass
Wednesday, January 26, 2011
2010 (33)
December (4)

The 12 days of (Lab) Christmas
Friday, December 24, 2010

I really hope there isn't a number 3
Thursday, December 9, 2010

So why don't you have more papers?
Tuesday, December 7, 2010

Picking a project
Thursday, December 2, 2010
November (2)October (7)

As promised: Geeka and A Cow
Saturday, October 23, 2010

Finishing something
Saturday, October 23, 2010

A cartwheeling Geeka
Monday, October 18, 2010

Some Classroom got funded, I get embarrassed.
Wednesday, October 13, 2010

Bounty for Donor's Choose
Wednesday, October 6, 2010

If I couldn't be a scientist
Tuesday, October 5, 2010

That's not the shape of his head.
Friday, October 1, 2010
September (6)

Glutton for Punishment
Saturday, September 25, 2010

I talk to machines.
Friday, September 24, 2010

World's worst Journal Club.
Monday, September 20, 2010

The IACUC Chair
Thursday, September 16, 2010

Hell, I did know then, I just didn't know it until it hit me.
Tuesday, September 7, 2010

Stuff Geeka Likes: The Toys Edition
Wednesday, September 1, 2010
August (9)

How I ended up a scientist.
Saturday, August 28, 2010

Monday morning crapped on my head.
Monday, August 23, 2010

Naming your equipment
Thursday, August 19, 2010

Stuff Geeka Likes: Inaugural edition
Thursday, August 12, 2010

Silent Squee
Wednesday, August 11, 2010

In which I come clean
Tuesday, August 10, 2010

Having a bad day
Monday, August 9, 2010

My blogging philosophy
Friday, August 6, 2010

Balance? We don't need no stinking balance.
Tuesday, August 3, 2010
July (5)
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Hi! I'm Geeka. I've been a scientist for, I don't know, it seems like forever, I guess since I started college, so, like 15 years? Anyhow, this is where I'm going to give my take on a bunch of stuff. I'm usually a little bit out there (that is, I don't see the obvious at the outset), which means that you are probably going to have to deal with reading such topics as: Interpersonal relationship training for scientists, my lab pet peeves, how to get along in business when you just came straight out of academia, trying to deal with having a life and being a scientist, really odd topics for a paper, random stuff I found on the internet that made me shoot coffee out of my nose, you know, (ab)normal Geeka. Why the title? Because at the very heart of me, I'm a virologist, and while I don't necessarily do that now, it's how I view the scientific world.

My posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, my employer, or my educational institution.

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Saturday, July 31, 2010

One of the most important things that you can do when you discover a new virus is to figure out how it gets into the cell. Viruses need a specific receptor to get in, think of it as a key and lock method (and yes, there are some ways to pick a lock, and yes, there are also some skeleton keys lying around), you may not know exactly what the key on the virus looks like, or what the lock on the cell looks like, but, if you can block this interaction, the virus won’t infect the cell. Fun (and profit) for everyone.

A classic experiment (once you have a hyphothesis of what receptor the virus is using to enter the cell) is to transfect a cell line that doesn’t naturally express the receptor with the receptor and let the virus infect it. If you are lucky, 293Ts don’t express your receptor (cause you can transfect them by looking at them wrong). If you are very unlucky, you have to do the reverse experiment, and knock out the receptor in the permissive cells with something like siRNA (to prove that this is in fact, the real receptor).

Here’s what bugs the hell out of me: there are a lot of people out there that use viral transduction for their work, and they have worked out all these fancy things to get these viruses in the cells that they are working on, and people have applied these to receptor mediated fusion experiments. What? Why could I possibly be annoyed about this? Someone has figured out all the bullshit that I need to do to get my virus in my cell, I should be jumping for joy.

Not quite.

See, if you are studying the most critical interaction of virus and cell, you need this to be the most native interaction. You don’t want to screw with things too much. For instance, my back door key fits my front door too, and if I put my back door key in the front door lock, and then bust the door open, I still got into my house. So, if I let a cell interact with a virus, but, I introduce a chemical to mediate this interaction, am I still studying binding and receptor mediated interaction? I’m going to have to say no.

If you do any lentiviral work, you are probably familiar with ‘spinfection’ (cells in supernatant spun with virus in a centrifuge to maximize virus cell interaction) and something called polybrene. Polybrene is a chemical that when added to the cell media, coats the cell surface and shields negative charges. This charge negation allows the cell and virus to come into closer contact due to opposite attraction.

I’m one of those people that think that if you are going to study the interaction of virus with receptor you shouldn’t be using something that changes the cell surface. What happens if the virus depends on a certain charge for interaction, or binding, or fusion? If you get substantially better results with polybrene rather than without, what does that say? Is there some biological situation that’s being replicated by polybrene, or is it just something to make our lives a little easier.

So, dear scientists, if you were reading a paper that was touting finding a receptor for a virus, and in the materials and methods, they detailed a chemical modification (such as polybrene) to the cell, how valid would you think this was?

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Genomic Repairman
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Never gave to much thought to this before Geeka, great point!

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So true.. An interaction that is possible may not necessarily happen.. But this could be helpful with regulation actually.. Just a thought..
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