Archive for: January, 2011

Help Wanted?

Jan 31 2011 Published by under Mentoring

Since I had such a positive experience last year with having Genomic RepairGirl as high school intern last summer, I think I'm going to mentor another student this summer.  And keeping with my belief that promoting in women in science should be a priority, I'd like to take another female applicant.  Genomic RepairGirl wanted to come back to my lab but I refused her on grounds that she should try out another lab this summer to broaden her experiences and skills.  Besides the mechanism that funds their stipends is centered around getting students access to science, letting them see how hypothesis driven research works.  So it would be nice to give a fresh face and opportunity to have this experience.  So here is the position description in case you were interested in being mentored by the Genomic Repairman.

Job Duties include:
-Actually giving a crap about what you do and are not just here for the paycheck.
-Attention to detail.
-Waking me up from my naps that I take in the dark room.
-Upon adequate training assuming all my responsibilities for cell culture. This is a time sink for me and its a testament to how much I trust you to let you manage my cells.
-Beer runs for me (if you are a college student above the age of 21).
-You must entertain me with stories of how difficult it is to choose between watching Jersey Shore or Teen Mom if they are on at the same time.
-Don't mind being laughed at by me when you ask to be my Facebook friend. It took me 5 years to friend my sister and you think 10 weeks of indentured servitude is going to get you into my exclusive circle of friends that includes the girl in high school who stood me up for a date and later got pregnant by some bucktooth motherfucker that worked in the Dairy Queen in my town? Puleez.
-Willing to learn how to run and optimize new techniques that I need for use in my project.
-Act as my security detail and keep vendors at bay by telling them I'm busy while I'm loading gels or just sitting in the corner of the lab reading ESPN magazine.
-Go outside and play catch with me when something in the lab pisses me off.
-Be the best intern I've ever had

On second thought I might rehire Genomic RepairGirl...

9 responses so far

Is this an inspection or an investigation?

Jan 28 2011 Published by under Uncategorized

So we just wrapped up our lab inspection with our safety department and what a relief it is to be done with it.  Now I can bring all my goodies that I had stashed away and put them back up on my shelves.  They generally frown on you keeping even the most minute amount of flammables at your station and my mini-bottles of chloroform (which I use for phenol:chloroform precipitations but BrooksPhD tells me its convenient tool in his bag of tricks to get a date), methanol, and ethanol would draw ridicule and scorn, so I put them away.

Unfortunately trailing our safety inspectors was an administrator who had no clue what we do in the lab.  He saw I was working with Proteinase K this morning and asked if I had a protocol for it and could I provide it to him.  I told him I sure did and showed him the vendor's specification sheet.  This apparently was not good enough for him and he asked did I have a specific protocol for what I was using it for, what exactly I did with it and that that was what he wanted.  At this point I'm staring at him, looking at him like really?

So dutifully I took out a sheet of paper and scribble down this:

"Proteinase K Protocol

-Take vial of Proteinase K from freezer.

-Let it thaw.

-Add to stuff.

-Heat at 55 degrees Celsius for 4 hours.


This now concludes the Proteinase K protocol"

Then said administrative bureaucrat asks if I have an IBC for the Proteinase K.  The Safety person and I both look at each other and say there is no requirement for that.  This is but part of the series of exchanges that I have with Adminitard during the inspections.  After the inspection is over, one of our safety inspector, a former technician who I get along with quite well, confides in me that Adminitard asked to tag along on these inspections along him and his supervisor, a zealous inspector who probably was a Marine Corp DI before doing this.  They also took it upon themselves to go through our fridges and freezers asking what each item was and what it was for.  By a certain point in time I had reached limit and told them that they had to close up the freezer, because the alarms were going off and the temperatures are rising.  I am not losing my samples to these fools.

I understand that safety is an on-going dialogue and even brought up some issues that I had to them, but rooting through my stuff like this is the Spanish Inquisition is not going to make the workplace safer.  Especially when you have no idea what we do or what our coded samples mean.  And no I can't tell you what they mean, some of our samples are blinded.

I'd like to chat more but I'm having to relabel my NaCl and PBS bottles as Sodium Chloride and Phosphate Buffered Saline.  Well at least we are good for another six months or so.  I hope.  Hell hath no fury like a safety inspector and a bureaucrat who have no lab experience or science training.

Fuck my life.

11 responses so far

New TV show: Lab Nightmares

Jan 27 2011 Published by under Uncategorized

So after watching many episodes of Gordon Ramsay's Kitchen Nightmares and the new Kitchen Impossible show on Food Network, I have come up with a great new show idea for science.  Lab Nightmares!  We take a faltering lab that is funded by the NIH or trying to obtain funding for them and send in Comrade Physioprof and Drugmonkey for a week to whip them into shape and show them how the big boys kids do it.  I can only imagine CPP pressing the finest Italian leather Danskos to the neck of some sad trainee who has offended him with their poor work ethic, while simultaneously swigging Jameson and shouting profanities at the poor fucker.  Drugmonkey, of course, would play good cop to CPP's bad beligerent cop.  And I'm keeping in mind branching out so, I could recruit PLS and Odyssey to do a version of the show for NSF funded labs.  What do you think?  Oh and Fox television, I'm waiting for my phone call.

16 responses so far

Band of Trainee Brothers: The lazy & crazy

Jan 20 2011 Published by under Uncategorized

So yesterday some of the blogs here took a little bit of a tangent onto the topic of trainees being possibly lazy.  This made me flash back to all the kinds of lazy and crazy trainees that I have interacted with in the past or are interacting with presently.  So lets review this cast of characters:


No not the crazy Russian mystic, although I know a few PI’s who were old enough to mentor this guy.  No Rasputin was a new postdoc in my previous lab that drove us up the wall and to consider concealed weapons permits for our own protection.  Rasputin and I used to share a cell culture hood would get pissed at me for switching the vacuum and burner set up because you see he was left handed and I right handed.  He would yell and scream at me to just use my left hand, I refused on the grounds that my left hand literally acts like its drunk all the time and is sort of clumsy, and who the fuck was he to tell me what to do.  I was always polite and set everything back up for him in the way he liked but something made him become angry to the point of physically shaking if he saw me pipeting in media to a flask right handed.  Rasputin, on his first day of work, also made the demand for me to switch desks with him because mine was in a more secluded part of the lab.  He was ill prepared for me to tell him tough shit.  Needless to say our time spent in the lab was terse and full of explosions.  Shortly after I left, my boss shitcanned Rasputin and he went back home to his country of origin.

7th Day Adventist:

No, this person was lazy or crazy because of their religious beliefs; they just got the nickname because this trainee in the lab next door showed up once a week, usually on the day of lab meetings.  The PI in the lab next door suffered with this fool for almost two years before firing them.

The Ayatollah of Terrible RockinRollah:

Ok, not a true trainee but a medical resident on loan to us for a year for them to do research.  This guy used to blast terrible music in the lab all day and spent more time on his playlists than his project.  Worse was that he would put songs on repeat, and folks it was bad music.  You must be shitting me, I have to hear Barenaked Ladies “One Week” for the eighth time in a row?  While he was a nice guy, it was nice to see the cleric of poor music choices get transferred to another diocese.


This wasn’t so much a lazy trainee in the truest sense.  SF, a trainee in a lab on another floor, showed up to work and did what she was supposed to do but she didn’t put much thought or planning into experiments.  This resulted in her not ordering supplies need for experiments and we could catch SF in our supply room taking stuff from us as she was scrambling mid-experiment.  Several of us always caught SF taking bottles of media or PBS from us.  Apparently, SF’s lab manager commented to our lab manager that SF had not ordered cell culture media for her experiments in over a year.  No shit, she was taking ours.

Creepy McFunster:

If you were a gal and he met you, Creepy McFunster couldn’t tell us what shoes you had on or even what hair color you had.  Dude was focused on the area above the navel and below the neck.  He was a weird motherfucker, but the guy had boobdar.  He would be locked away in cell culture but as soon as a cute vendor rep crossed the threshold into his lab, Creepy was like a shark that smelled blood in the water.  And he was on it.  He skeeved out all the girls on the floor who had to use a vital piece of common equipment in his lab so much so, that they would get other folks, including me, to use the plate reader for them.  Don’t ever know what became of Creepy McFunster, but I’m sure his HR file is thick with complaints.


Sadly this was my nickname given to me by the night cleaning crew.  I used to do a lot of qPCR for my MS research and had the luxury of having two machines in my lab.  I was cranking out tons of data, doing multiple runs a day and even coming in at night to start runs.  If I was there at night, it was a given fact I would be drinking beer waiting to pop a plate in the machine or crunching data at my computer.  I used to leave a lot of beer cans in the trash, so much so, that the cleaning crew put an aluminum-recycling bin right outside the door to the lab.  Everyone thought it was weird, but I got the gist, they were tired of picking my cans out of the trash and putting them into recycling.  Where is Cans now?  I’m doing a PhD and am a bit more civilized these days.  But even my Shiite Pentecostal boss turned a blind eye to my poor behavior because I turned out data at a faster clip than any of his other trainees.

So do you folks have any characters you crossed paths with?

12 responses so far

Tech tip of the day...Strategic Placement 101

Jan 19 2011 Published by under Uncategorized

Don't put one of the nifty vendor magnets (the kind that could hold a 2x4 to a filing cabinet) on the side of your computer right where your hard drive is located, and bitch to me that your files are fucked up.

Guess who is restoring a computer today?

Fuck my life.

10 responses so far

Virtual Peer Review?

Jan 18 2011 Published by under Uncategorized

Faithful readership, all four of you (it would be five, but mom's "google machine" has crashed) I wanted to survey your opinions on an interesting topic.  I read in the a recent issue of Science, that NSF is looking at virtual peer review of grant proposals through use of Second Life.  Seems like an interesting way to "get everyone in the same room" but not be in the same room to hash out these proposals in a virtual panel.  So I'm hoping PLS can chime in since he has been in on NSF grant evaluation panels.

The NIH is starting to take some interest in this since they are becoming more reliant on videoconferencing.  I can see that the infrastructure for videoconferencing could be somewhat expensive but this Second Life-based review system would be less expensive.  However I don't like this because the NSF is using someone else's infrastructure and you have to wonder about access issues, accounts getting hacked, DDoS attacks, etc.  Also, I think part of the review panel is getting folks out of the office, shoving them in a room together and plowing through these proposals.  Will reviewers be stay focused in this virtual review environment when their office phone is ringing, the damn trainees are beating on the door to get some form signed, and chair really wants you to show up at the faculty meeting this afternoon because after all, you are here are you not?

Those are some of the downsides, lets check out the positives.  You don't have to travel, which may be important to those with families or who hate sitting in airport lounges waiting for their delayed flights.  It would be a huge cost savings, NSF isn't having to lodge and feed all these folks.  This might increase the number of folks who would participate in an evaluation panel that would not normally?

If this ever makes its way to the NIH, I could see:
-CPP's avatar stumbling around drunk with a bottle of Jameson that he might chuck at a reviewer who gets off topic.
-Dr. Isis, changing her virtual footwear throughout the study section.
-Pascal avatar blogging on her iPad because she bored of some old graybeard rambling on about something off topic.
-Some torrid affair of tenure-tracked professors potentially involving cybersex on top of the conference table while a mortified Drugmonkey looks on.  Pascal would be capturing video but her Flip Mino is still busted.


20 responses so far

Its not going to be a good day...

Jan 18 2011 Published by under Uncategorized

When you are lined up to do 4-5 hours of cell culture work and there is a huge puddle in your hood and technicians working on the roof.

To quote PLS, dude, fuck.  Sigh.

3 responses so far

Hank Fenton, DNA damage, and why we store our DNA in EDTA

Jan 17 2011 Published by under Uncategorized

So chatting with a undergrad that was shadowing me last week before my surgery we got on the topic of DNA damage and that a primary endogenous source of DNA damage comes in the form of hydrolytic damage causing loss of bases, as well as base modification (18,000 events per cell per day).  Similarly another major cause of damage created in the cell is reactive oxygen species that arise as a result of mitochondrial leakage (3-4,000 events per cell per day).

What usually occurs is that as a result of mitochondrial metabolism molecular oxygen is converted to superoxide (·O2-).  This ROS species is not particularly dangerous to DNA because it is short-lived and gets rapidly converted to peroxide by superoxide dismutase (H2O2).  Peroxide is what poses a huge threat to DNA because when peroxide is in close proximity with our DNA it gets converted to hydroxyl radical (·OH) through what is called the Fenton Reaction.

Fe2+ +  H2O2 -->  Fe3+ +  ·OH  +  -OH

British chemist Hank Fenton discovered this reaction way way back in 1894 but I’m going to assume he had no appreciation for how potent a genotoxic insult this simple reaction would play in our bodies.   The key part of this reaction lies in ferrous iron (Fe2+) found in the DNA that plays a key role in the conversion of peroxide to hydroxyl radical.

A common form of oxidative DNA damage is the conversion of guanine to 8-oxo-guanine, which while in the syn conformation, can mispair with adenine.  The end game is that the damage has resulted in a mutation, but fear not there are specialized enzymes called DNA glycosylases that can remove this damage base and incorporate the proper nucleotide triphosphate.  If you are interested this pathway is called base excision repair and the particular DNA glycosylase that is predominantly responsible for the removal of 8-oxo-guanines from our genome is called OGG1.

So lets end this post on why you toss in some EDTA in addition to Tris when resuspending DNA.  Its because we use it to chelate these metal ions like iron so that it cannot participate in the Fenton reaction and cause damage to our precious DNA samples in addition to binding other metal ions required for enzymatic activity by nucleases, which can further degrade your sample.

Postscript:  One last note on DNA storage, which we debate back and forth endlessly with each other.  Most of us store DNA at 4 °C for short-term use, but keep most of our precious samples at -80 °C for long-term storage.  You can store DNA at -20 °C but you run the risk of it falling out of solution but vortexing will easily bring it back into solution.  Note this is fine for plasmids, but vortexing will rip the shit out of genomic DNA so be kind to it and store it at -80 °C.  And one last bit, don’t store DNA in a freezer model that automatically defrosts, this freeze thaw cycle will end up degrading your DNA.

Values of DNA damage come from:  PMID  12760027

21 responses so far

When Human Research Gets Inside Your Mind

Jan 16 2011 Published by under Uncategorized

Go read Dr. Isis's most recent post on "When Human Research Gets Inside Your Mind." This is one of the most insightful and beautifully written blog posts that I have ever read. I'll post something unique of my own soon but go read this great post in the meantime.

No responses yet

The embarrassing behavior of Dr. Feldman

Jan 13 2011 Published by under Uncategorized

I'm feeling like crap and might punch out a post later but skip over to Dr. Isis's blog if you haven to read about Shameful Gender Discrimination at UC Davis Veterinary School.

There's a storm a brewing...

2 responses so far

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