Monday, November 29, 2010

It shall be done!

At the end of my last post I complained about having to work over the weekend...but it's over and done now.  Hopefully the effort will yield some good data.

And today I managed to do something so far yet undone:  Convince my PI that my new scheduling of several up-coming experiments works better!

You see, today my PI wanted me to start a 3-day process that I did not want to start. 
I just like that photo.  It is not a photo of the Spoiled Rotten Cat (SRC). 

After being hunched over my bench for ~7 hours on Sunday, the last thing I wanted to do was start another big process.  In fact, my back has been aching all day.  I'm not a spring chicken. (I'm what is called a "non-traditional student.")

Anyway, I managed to convince my PI that I'll actually get MORE work done if I shift it around like so.....
And it actually worked. 

I still managed to get a boat-load of stuff done today...

Most of it is to organize part of the extra stuff I'm doing.  You see, it has recently come to light that the DLM isn't just dumb, but pretty much completely incompetent.  About 1.5 weeks ago, this became painfully known to my PI.  This was much to the satisfaction of the other grad student and myself, as we were worried that PI would think we were training the kid horribly.  We weren't; we tried to make idiot-proof protocols, but there's only so much you can do.
So the PI now knows that somehow they were duped into taking on this kid.  Thankfully the MRU is funding his one-year masters program thing.  But now my PI is stuck with him, and he's working (well, kinda) on part of project that's funded by a grant that's under review soon.  Because I have done similar experiments, I can pitch in and help out. 

And this has pretty much turned into my PI and me doing all of DLM's work...because PI doesn't trust the kid anymore.  At.  All.  He's pretty much been demoted to making buffers and cleaning the lab. 
I honestly don't know what the PI is going to do.  The DLM certainly couldn't defend his thesis.  I asked him about one of the papers (our lab's own) which is the foundation for his thesis, and apparently he can't recall too much about it. 

I suppose the PI is going to let the system work its magic.  Come the late spring, he'll have to defend, and when he doesn't pass, it isn't necessary for the PI to take him back.  I don't know how all the money or administrative jumbo works, nor do I care.  I'll be grateful when I get done doing double duty for this kid. 

Until then...I'm trying to steam ahead to the end of this semester.  I have two papers and one project for classes, plus a ton of work for this grant review.  Hold onto something bolted down; it's going to be a bumpy ride! 

Wednesday, November 24, 2010


Over at Neurotic Physiology and other bloggers over at Scientopia have posted "what are you thankful for?"  This includes an item, a person, and an idea.

I really like this concept, and maybe if you had contacted me a week ago, I would have a thoughtful, meaningful answer to these questions.* (the reason for this is below)
Instead, you get my half-assed answers:

My item that I'm thankful for:  coffee and the old coffee maker given to me and the Mr. when we move to the town where the MRU is.
My parents bought us a super nice espresso maker as an actual wedding gift, but as we were packing up, my mom found an old drip coffee maker they never used.  This thing has a timer, and THAT is priceless.  A lot of times I have to get up at about 4am for some long experiments.  There's something entirely comforting about having the coffee ready as soon as I drag myself out of bed.

The person I'm thankful for:  easily this could go to the Mr., as he keeps everything sane in the household.  However, I think that as far as my academic career's one of my non-advisor mentors.

In confession, my PI is an amazing scientist, but is also one of the busiest.  I can't say my PI is the most encouraging person, and that's ok.  Some of my classmates have very enthusiastic and animated PI's, and they benefit from the overflow of that effervescent passion.  While I would have loved to have landed in such a situation, I'm ok with the reality I have.  My PI is often too busy, and they tend to run the lab like the business that it is.  When I have times of low morale, it's good when I have to go to another facility for some experiments.  At that location I get to see one of my committee members, who is also the enthusiastic and passionate type.  Our conversations give me inspiration, and they fire me up for my ideas and my research.  In that regard, I am very thankful. 

As for my idea...
A friend once joked, "If you don't feel like a complete fraud who's in over their head, you're not stretching your abilities enough."  
I think one of the bigger mental challenges that grad school has presented is the sense of being overwhelmed.  I feel like I have more contact with various specialists in many different fields, and while talking to them you have to know exactly what they're talking about.  And most of the time it feels like I have to wing it, and then later read up on it.  

I bought a chemistry model kit after a discussion with one of our collaborators, a biochemist who knows all sugars backwards and forwards.  I could follow the discussion, but I knew that I needed to be able to look at several different molecules, regardless of how they were presented on the page, and know what from what.  It's like having to learn to think like a microbiologist, a biochemist, and a geneticist all at the same time.  When I feel overwhelmed, and "in over my head," I remind myself that this probably happens to every grad student at some point.  Unfortunately, due to the unique structure of my program, I'm kinda isolated and don't have the constant camaraderie that my peers benefit from, so this is only a guess.  The alternative is that I'm just a complete idiot...

Unfortunately, after the explosion on Saturday things continued to all go downhill.  (By the way, my PI said she had never seen or heard of an anaerobic culture causing a glass 1L bottle to explode, but perhaps the bottle had been compromised in some way which lead to its demise.)
I had been harvesting cells for both some anaerobic cultures and some VERY slow growing aerobic cultures.  I was on my feet pretty much all of Saturday and Sunday, and I still hadn't started a paper that was due on Monday.  Monday rolls around, and I'm on track.  I think, I'll get this stuff sorted and that experiment started....and then I can get home and start on my paper.

And about halfway through the day, my PI and I were looking at the data, and slowly....but then very surely, we realized that all of that work was for naught.  Despite harvesting all the cells that I had, it wasn't enough.  There was no way of knowing this until we got there.  I think I saw genuine sympathy in my PI's face.  I was exhausted, and I understood that I was about to be cheated out of my Thanksgiving Day weekend.

Frustration and anger gripped me all day Monday, and I realized I had to snap back into it to churn out a paper by 10pm that evening.  Tuesday I woke in a zombie state and sat through another class.  More stuff surfaced that I have to get done.  The numbness helped in my resignation that there will be no rest until I board a plane for the UK in late December.  The project manager of our grant has requested a review of all data on the 16th, and due to the DLM, we are scrambling to get his data.  (There's more to that story, but that's another post.)

So sometime around 10pm tonight, the Mr, the Spoiled Rotten Cat and I will trek up to my parents for Thursday and Friday, and then we'll be back on Saturday for me to continue harvesting cells.  I'm ok with this now, but earlier I'm not sure I was.

Saturday, November 20, 2010

Things that explode and my new definition for "frisky."

This is not the explosion that occurred, but I would have preferred this:

I have some big experiments coming up, and I need a TON of culture to complete them.  By a ton, I mean 3-4 liters.  This includes my anaerobic cultures.

I spent the week cultivating some awesome dense and fast growing starter cultures of about ~80ml.  I call these "frisky" because if I take a syringe full of nitrogen, and push the needle into the bottle, the culture spurts into the syringe before I can plunge all the nitrogen gas in.  I tend to put personalities to my cultures, and for whatever reason, the first time I saw this happen I thought, "well that's frisky."

The culture is producing hydrogen gas, and it grows so fast that there's TONS of pressure in these small bottles.  I use a small amount to re-inoculate smaller starter cultures, and hope to relieve some of the pressure.

Then, under nitrogen gas, I open the bottles (they sound like champagne bottles popping), dump the culture into my large 1 liter jars, and seal it up.  These are then incubated at 85 degrees C.  Dumping ~80ml of culture into ~1 liter dilutes the culture, and I'm thinking that by ~24 hours, these bottles will be ready for harvest.  Easy peasy.

Today I'm well rested, well fed, and walking up the stairwell.  I should explain that our lab is in a bit of shambles, and we're in the process of moving soon, so the high temp incubators are in the hallway.  The moment I turn down the hallway....I smell it.

Instantly I know that something absolutely wrong has happened with the anaerobes.  
Basically, they ferment the sugars at a high isn't a good ferment like beer, it's an evil waft you get when you have food gone wrong in your fridge.  And it's still 25 feet from where I'm standing.  THAT is how horrid it is.

And in the back of my head, I knew something like this could happen.  I just thought that it would have taken more time.  
The leak of culture is so bad that it's triggered the sensors to go into error mode, and the heat has shut off.  I open the incubator, and thankfully only one of the four liter bottles have exploded.  I still have 3L left (which is sufficient for my experiments).  

But this wasn't a leak.  This was an all out explosion.  The rubber stopper is still lodged in the neck of the bottle, with the cap in place.  There are bits of shattered glass EVERYWHERE.  I think that must be a LOT of pressure.  

And I should've known better.  There should have been more head space in the bottles, but I'd been having problems with oxygen getting in the media, so I decided the less, the better.  
Fortunately, because the incubator shut off, the temperature dropped, the remaining culture quit growing, so they didn't go 'splody as well.  

But boy, are those cultures dense.  Here's a comparison of an un-inoculated culture (with some oxygen in it, hence the orange/pink tinge to it) next to one of the surviving bottles:

So yah....I'll be cleaning and cleaning....and cleaning again.  I've notified my PI, and I'm worried that I might have damaged the high temp incubator.  The sad thing is...I showed up ~17 hours after I inoculated the culture.  Had I been a little sooner, it might have been avoided.  And I'm curious as hell if it made a huge bang or anything.  Tiny shards of glass were stuck ALL over the incubator.

I'm also lucky.  If I had arrived earlier, I could have removed the bottles, and that one particular could have continued to grow and produce gas and pressure while sitting out on my bench.  In which case, it could have exploded near me, spraying glass and the bog of eternal stench onto me.

I also hope the smell dissipates a ton before Monday.  I'm about to become quite unpopular in my department.

Thursday, November 18, 2010

A good day

Today was one of those days that strangely turned out for the better.
There's a TON that needs to be done in the next month, and it almost feels overwhelming.  I was trying to get things going while working with the anaerobes when the nitrogen ran out.  Thankfully I was able to call someone up and get another for tomorrow morning. 

Then something strange happened.  With half of the work unable to be done, everything else got done!  I got just about everything I'd been meaning to do over the course of 6 hours...and then I didn't stop.  I organized my entire bench, updated the lab books, and managed to step out on campus for a cup of coffee. 

In the early evening, I had the option of going to a discussion panel, but I found that I wanted to continue the flow of things and set to task some things I had been putting off.  Today I truly did ALL the science!

If only everyday felt as easy and flowing as today.  I guess I get overwhelmed with the "so much to do" thought that sometimes I go into overload and my brain shuts down.  When things were automatically taken out of the to-do list by necessity, everything was so much easier. 

I even get to sleep in until 7:30am tomorrow!  THAT is awesome.  I'll probably be at the lab all weekend, but Thanksgiving is on the horizon.  The Mr. and I are looking forward to driving to my folks' house with the Spoiled Rotten Cat.  It feels good to be optimistic occasionally.  It's going to be awesome to walk into the lab to my clean bench.  And with the nitrogen tank delivered tomorrow, I can finish off the other half of all the science. 

Thursday, November 11, 2010

I try...

In the spirit of having consistent posts....

I'm waiting on the autoclave, so to kill time:
There's always one in every lab I think.  I've only been in two, so I don't really know. 
And I always try NOT to be that one.  You know, the dumb labmate (DLM).

This does not include the learning curve that new members have when they're integrated into the lab.  Everyone goes through it.  After a while, you find your groove, and you understand how things work.  As you continue to run experiments, you start to trust your instinct.  Unless being in the lab is your *first* non-class lab experience. 

The DLM was in chemistry as an undergrad.  He took some basic micro, so he's been introduced to the principles.  And I encourage asking questions.  I've told the undergrads to ask as many as they want, as that's what I did as an undergrad.  That goes with the territory.

But the DLM doesn't seem to be getting it.  At. All.

Exhibit A: The DLM is asking a ton of questions as usual about a certain protocol.  I didn't write it, so today he's asking the another labmate who did.  I'm not paying too much attention, but I hear this:
DLM:  So do I leave the lid on?
Labmate:  Yah.
DLM walks away.
Me:  Leave the lid on what?
Labmate:  The centrifuge.

*cue the confused look on my face*
When is it ever a good idea to leave the lid off a centrifuge when working with culture? 
I wouldn't care so much...but tomorrow I'm rolling into work early just to babysit the DLM through what is most certainly a straight-forward TCA extraction that should take 20 minutes to complete.  The sad thing is, I know there will be tons of commonsense questions, on a procedure he's already done. 

Part of me knows it isn't being dumb, but more lazy. 
Over the weekend, one of the keys to a room the lab uses was missing.  Often someone will accidentally leave the key in the room.  DLM called me to ask if I had it.  I didn't, but I suggested he simply call security and have them let him into the room. 

Without missing a beat, the first thing he said was:  Do you have the number for security?
That's laziness on a grand scale there.  The brain hurts from the laziness.  Security numbers are posted in every room and on the lab doors.  Everyone knows this.  And yet he though I would just have it handy on my laptop or something.  WTF?

Wednesday, November 10, 2010

The worst pun evar....

I just had the worst (or best) pun ever.  I was explaining to my labmate how my advisor suggested using the same media for two of my anaerobes.  This would theoretically simplify things.  Making the media is generally a pain in the neck as I don't have an anaerobic chamber.

Actually, we do have one at the lab, but my advisor is loathe to set it up, as we don't have the space.  Instead everything is made by boiling oxygen out while flushing with nitrogen gas.  Hence, working with boiling liquids while trying to pour it into bottles, which then bubble out at you as the nitrogen does its thing....all while trying to work as quickly as possible to prevent oxygen getting into the a pain in my @ss. 

Thankfully I've also become more comfortable working with syringes.  All inoculation and addition of any nutrients, etc. are done by syringe into the sealed bottles of media.  I admit at first, I had a lot of torn gloves and thanked my luck that I hadn't stabbed myself.  I'm naturally accident prone and clumsy, so getting the hang of working with needles took some time.

I really didn't want to relive the scene from Four Rooms.

But I digress....

For whatever reason, both organisms prefer* different media types, despite what is in the literature.
Continuing the discussion with my labmate...
Me:  Ya know, I think I would save a lot of time and frustration if I just abandon the thought of finding a happy medium and make two separate ones.

Immediately thereafter my labmate laughed a bit, and I groaned to myself.

(*By prefer, I mean grow quickly.)