Top Secret Mission

 

agentcat

Within this packet of papers is your mission, should you choose to accept.  Read the enclosed materials, find the necessary resources, and then report back to me.  The experiment is top secret.  This message is scheduled to self-destruct in 3… 2… 1- BOOM!

While I was a student, my mentor often gave my lab mate little side projects here and there.  He never bothered me with these little projects and at the time, I was so thankful for that.  I was able to focus my energies on my thesis and get things done.  I graduated with one first author paper and one review article.  My lab mate graduated with one first author paper and was included on several others because of all those side projects.

The other day, my postdoc mentor handed me a stack of papers and gave me my first side project – for sh–s and giggles, he said.  I am beyond excited!  First, it’s a project for which there is relatively little published material, making the project idea seem novel and exciting – “no one else is even thinking of doing this!” are the thoughts going around in my little head.  Sure, it may be a total fail, but if its not…

This kind of excitement, while not rare, it not necessarily common.  I love my work, I love what I do, but most days, I come in, I get things done, I check off the list and move closer to completing the aims set forth for my project.  But this,… I have been thinking about this project day in and day out for the last three days.  I leave work and I take papers home with me to read!  I do lit searches on my iPhone while rocking the baby to sleep.  I wake up in the morning with new inspiration.

I do hope it turns out to be a great little project with new interesting information discovered at the end of it.  But even if it doesn’t, its a great reminder of how exciting science and research can and should be.  The feeling that you and your mentor had an idea that no one else had, that you are about to discover something completely new, that you could change the way your colleagues think about a protein, system, etc. is why we enter into research in the first place.  I wish I could tell you more about it, but I’m sworn to secrecy!

top secret

 

Sick baby and lost work (worth?)

I’ll post the final conclusion to my tribute to Edith Schoenrich (Pt. 1 and Pt. 2) soon, but I wanted to talk about my obvious absence lately.

Maybe you’ve noticed I haven’t blogged in a couple of weeks.  Maybe you’ve given up on “The Experience”.  Maybe you thought, “Well, that had potential, she just didn’t follow through.”  I worry about how many of you thought that, and I worry whether my boss thinks that.

In addition to having some jam-packed days in the lab (absence from blogging excuse), I’ve also had some sick baby days where I’ve been home taking care of my little ones.  Unfortunately, the baby just doesn’t want to take a bottle at home, and so it makes no sense for my husband to stay home with her, hungry and sick and miserable.  That means that whatever I’m planning in lab has to take a back seat.  Experiments are put off, ongoing assays are ruined, cells and materials get thrown away, materials wasted.  After being out, I come back to lab exhausted, frustrated, apologetic, and feeling like I’m on probation.

When I chose my postdoc, I was very aware of the fact that my boss was a family man, had young-ish kids, and would understand the occasional sick day.  And to his credit, any time I email him that one of the kids are sick and I need to stay home with them, he always replies positively.  I worry though.  Is he really okay with the time off?  He offers to take care of whatever is critical, but I certainly can’t ask him to do the 18 plates of TCID50 assays that would take me 6 hours to complete.  And, then, all of those resources are wasted, plates, cells, media, etc.

TCID50
TCID50 plates to determine virus titer

Our companies and institutions are all very clear in that sick days are part of our benefits package.  They all want to be seen at family friendly, striving to help achieve work/life balance for their employees.  It all looks great on paper.  But when you start to cash in and use those benefits (not abusing them at all), there seems to be some unspoken repuercussions.  Certainly my output and achievements will be affected and this will be reflected negatively upon review.

And so, back in lab now, I’m trying to make up for lost work days while still leaving in time to pick up the girls from daycare.  It makes for some stressful, hectic days.  It makes for long days for the girls too.  I’m looking forward to warmer weather, less sick time, and in general feeling more accomplished in all areas of life.

Power trips of the powerless

As part of being a post-doc in a new institution, I need to undergo training for equipment, procedures, etc. that I am already quite familiar with.  But, because of historical issues, my new department has put in place training modules that require assessment and approval before I can use their facilities.

One such area that I’ve had to address recently is the use of the microscope facilities.  Having limited experience, I welcomed the idea of actual microscope training by a qualified instructor.  Instead, the “training course” was a series of videos that identified each part of a microscope and the general turning on/off of each instrument.  That’s all acceptable, if unsatisfactory.

EarlyMicroscopeMammoth

The problem began when the assessment course was administered by the “Department Engineer”, essentially a glorified technician. (I went to an engineering college, and you sir, are no engineer.)  This “engineer” feels the need to exert his unfounded power on helpless post-docs and students to make himself feel better, all the while holding us captive because we can’t move on with our research until he says so.  The assessment course was written in broken English by him, of course, and he feels the need to lecture you on the questions you got wrong before allowing you to use the facilities.

Let me be perfectly honest, there is nothing that makes me twitch and shake with anger faster than being condescended to.

phd-frustration-072707s-crop

It is impossible to relate here the manner in which he corrected me on the room number (seriously, I know where the room is, why do I need to know the room number?), the fact that he is the department engineer responsible (with illustration of his “title” on his email signature), and that I underestimated the magnification required to see bacteria on a tape strip.  I doubt he could tell me the difference between bacteria and viruses, but that’s beside the point. Unfortunately, I did not meet his criteria for passing, he categorized my performance along with a specific racial group (so not cool, dude. way to be racist.), and I had to take the test again.

Luckily, this time, I did pass, but still with a few answers wrong, including, again, the room number. Ha!  Take that! He didn’t miss the opportunity to be condescending again, even in an email (highlighted):

microscope results

At least today, I can respond to this email with laughter instead of angry eye twitches.  My boss offered up a bottle of champagne to celebrate, or to use as a weapon, my choice.  At least my boss gets it.  I was this close to making Mr. Engineer address me as Dr.!

WIRWed 12-12-12

Week Three of What I’m Reading Wednesday! (#WIRWed, if you follow on twitter)

You may have noticed I didn’t post last week.  Well, I was elbow deep in ethics training, bloodborne pathogen training, and microscope training.  Sharing that information may have had this effect:

Not wanting to lose any of my new readers to sleep-induced workplace injuries, I decided to take a week off, but I’m back!

 

Uncanny how Jorge Cham can illustrate our lives as researchers so well (substituting thesis with proposal in the above cartoon, of course)!  As I was sharing about miRNA’s two weeks ago, I was formulating how these might be developed as an antiviral for acute infections and then I found this paper:

Great work Guo et al.!  Let me know if you want to do a collaboration!

 

Okay, so moving on, here are a couple more articles I’m reading this 12-cubed week of WIRWed:

 

I’m spending some time learning about ciliogenesis – or the development of ciliated cells.  Were you aware that every cell in our body has at least one cilia, used for motion, sensing, etc.  Cells that are multiciliated are terminally differentiated and are of importance to my research with influenza in a primary epithelial cell culture model.

 

This next article speaks to one of my first loves in virology – Hemorrhagic Fever viruses (HFV).  Okay, I’ll admit it, when I read The Hot Zone in high school, I was hooked and I forever wanted to wear a space suit and hunt for life saving monkey serum alongside Dustin Hoffman.  My dreams have matured (those suits get HOTTT inside!), but I still love HFV and studied one for my graduate thesis work.  The following article combines a new favorite topic of mine, viral immune evasion strategies.  The crystallized structure of the Marburg IFN inhibitory domain of VP35 with dsRNA is amazing!

 

That’s it for this week.  Let me know what you think of this week’s readings.  I’d love to get a conversation going!  Are you reading anything that you’d like to share?  Send a link!

WIRWed: 11-28-12

Welcome to week 2 of “What I’m Reading Wednesday” (WIRWed)!

I’ve noticed in these first couple of months of my post doc fellowship that my readings tend to take on a topical nature.  One week, I’m reading about inflammasomes.  The next week, I’m reading about interferon lambda.  This week, my focus is turned to microRNAs.  I missed some of the hype while suffering from tunnel vision during my graduate student days, so I’m doing some catch up with some reviews and then a great paper looking as small viral RNA (svRNA) produced during influenza infection.

 

First, a bit light reading, a news feature from 2007 on researchers building their case for RNAi causing increased gene expression instead of the negative regulation associated with small RNAs.  Hmm, worth following up on to see if they were able to elucidate a mechanism.

Ok, now for the real reviews:

Focus on biogenesis of small RNAs, from generation of the guide strand to complex formation.

 

miRNAs specifically encoded by viruses, with particular attention to Herpesviruses, and their targets.

Now that we are all caught up to speed and are experts on miRNAs (ha!), here are some interesting articles I found involving miRNAs and influenza.

 

This was a fascinating article!  The authors set out to determine if small viral RNAs (svRNA), similar in length to miRNA but not necessarily derived in the same manner, could help explain the mechanistic switch from production of viral mRNA to genomic vRNA.  Accumulation of svRNA coincided temporally with this switch, and treatment with complementary sequences to the svRNA demonstrated decreased genomic vRNA production and decreased virion progeny.  This opens up a possibility for broad spectrum anti-viral therapeutics that would be specific to influenza (or another virus).  Great work!

 

OK, that’s it for me today.  What are your thoughts?  I’d love to hear what you think about this last paper, using anti-svRNA as a therapeutic.  Currently, these types of treatments are being evaulated for as cancer therapeutics and against chronic viral infections (i.e. HCV).  Could it be done for an acute infection?

 

Blunder

I had my first big blunder as a post doc a couple of weeks ago.  Very humbling.

The blunder? Forgetting the Ethanol precipitation step in my RNA isolation (with a kit).

The true blunder? Thinking that I’m infallible and perfect now that I have a few more letters after my name.

I’d only been in my new position for a couple of months.  It was my first big experiment, a long infection with multiple time points for growth curves (I really detest 12 hour timepoints).  Along side that, I piggybacked another experiment.  A high multiplicity of infection in primary cells for RNA isolation and analysis.  In my new lab, they use kits to isolate RNA, making it even easier than how I used to do them as a graduate student.  I’ve “grown up” as a researcher on nucleic acid isolation and kits.  Every single benchtop job I’ve ever had prior to grad school was grounded in molecular biology.  I can do kit isolation in my sleep.

Well, I must have been sleeping because I skipped the most important step.  I didn’t even realize it until I was quantitating what turned out to be nothing but RNAse free water.  Those were some interesting absorbance curves.  Having realized my mistake, I now had to face my boss, my relatively new boss, and confess.  In preparation, I came with explanation of the mistake (EtOH), and how to prevent it in the future (printed out protocol instead of flipping through pages of the provided protocol). To his credit, my boss reacted exactly the way he should, disappointed, but moving forward.

For me, it was a lesson learned.  Just because I’m a post doc (or any stage in my career, truly), doesn’t mean that I won’t make mistakes, especially when I think I am above them or not giving a task the required amount of focus.  So, I’ve stepped off my pedestal and am eating humble pie for a few more day until I can repeat the experiment and get beautiful RNA.  But, this time, I will give my RNA the attention it deserves.