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?

 

Electronic Lab Notebooks

Ten years ago, when I was working as a research associate in the biotech industry, someone suggested we switch to a digital form of notebooks.  At the time, we all thought she was crazy.  And, at the time, we were right.  No one had smart phones, at least none of us actually working in the labs.  Very few even had MP3 players.  We weren’t constantly attached to our devices and so the idea of an electronic device replacing our trusty paper notebooks was simply unrealistic.

The original smartphone

Over the past decade, many of those early electronic lab notebooks (or ELNs) have come and gone.  Their software was too specific and too limited.  Those that offered more in the way of convenience or ease of use also came with price tags.  Now, software companies have gotten smarter.  They offer lighter versions for free, get you hooked on their software and then you can upgrade for a price.  They are the new corner dealers, some might say.  These newer versions have a lot of promise.  They purportedly make your projects more organized, streamlined, easier to search and share, and ultimately, make research better.

Not convinced?  Jim Giles wrote this news feature on the promise of ELNs.

When I started my new postdoc position a couple of months ago, my PI mentioned that I could choose my own format for my notebook, paper or digital.  I hadn’t even considered an ELN as a possibility, and so I got to work to find the format that would best suit my needs.  My requirements were that it be either free or very inexpensive, easy to use (I’m no computer wiz), support and import many different media formats, and have longevity.

That last requirement was a big one for me.  I didn’t want to invest time in an ELN, only to have it be obsolete in a couple years and unattainable.  These projects take years to complete and small details now may be hugely important later on.  I need to be able to access my data for years to come.

By searching “electronic lab notebook”, “ELN”, and “Digital Lab Notebook”, you can quickly become overwhelmed with what is available.  If you’re handy with software and HTML, you can even design your own.  I’m not that crafty and so I focused on the following options.  Each offered a free version.  Some even offered interfacing between software on your laptop and apps on your tablet or phone.  Most offer access to your notebooks even when you don’t have access to your laptop, either through cloud storage or linked accounts.

Lab Archives

eCAT

Evernote

In the end, I decided to go with Microsoft OneNote.  I’m in a PC lab and the software is supported by my university and the department.  It just made sense.  There’s a lot to know about this software, more than I’ve even touched on so far.  Here’s the basics that I have discovered so far.  You can have several “notebooks” and within each notebook, you have sections.  Within each section, you can have separate pages.  For instance, I have a project page in my primary cell culture section in my experiment notebook.  I also have a notebook for notes from meetings and seminars, and another for the lab management tasks such as ordering supplies, inventory, etc.  I can put links to protocols and databases right into each page, so the information retrieved is always up to date.

Example of page/section/notebook

 

There are some downsides.  Once I’ve planned a project, I generally have to print it out anyways so that it is handy when completing the experiment.  This results in more notes scribbled on the fly.  I can probably just enter these after the fact and somehow just make it traceable that these notes were added, perhaps using different font color.  I still feel the need to keep the original notes, though, and so I keep a binder to put these into.  One thing I would have liked, in this software, is the ability to scribble on a page.  I can get around that using the paint software, but it’s an extra step.  Perhaps if I did have an iPad to link to, this would be easier.

 

Using Paint to doodle ideas

 

I wouldn’t go into an ELN blindly without having some idea of how you want it organized.  If you’re not organized, it won’t magically sort and categorize for you.  Spend some time and think about how you want to structure your notebook before starting.  OneNote does offer an uncategorized page, but I try not to use this.  My desk is messy enough with random pieces of paper, I don’t need my ELN to look like that too.  However, it does solve the problem I always faced with a paper notebook in that my projects were always broken up and separated by other projects.  With this, all the information pertinent to a project is on the same page.

When I informed my PI that I was going to go the ELN route, he offered one piece of advice.  Make sure to print out a hard copy once in a while.  No matter what else happens, you can always read paper.  So while the ELN may finally become a reality in research labs and make us the most efficient scientists of all time (if you buy into the hype), we may never get away from the paper notebook.  Afterall, you can’t argue with its longevity and technical support.