WIRWed: 12-19-12

This past week has been hectic and emotional.  In addition to packing up a lab, moving, and unpacking into new lab space, I’ve been distraught, as many of you were, over the tragedy in Newtown, CT last Friday.  As a result, I haven’t had much of a chance to do actual scientific reading, at least pertaining to the field of Virology.  What I have been reading about is various commentary on gun policy and mental health support.  One particular white paper has been on my desktop that I would like to share.

There are so many levels of discussion that need to happen in the wake of this horrific tragedy, not the least of which is long term support for the families and the community as a whole.  As bystanders, we are all too quick to move on and get back to normal, understandibly so, given how terrible and emotionally wracking this has been.  But for the people directly affected, they will never know normal again.  They will forever be plagued with visions of what those children and educators faced in three short minutes.  They will forever feel the emptiness of losing a loved one. They will need to know that those heroic people are not forgotten, ever.

In the honor of the 20 children and 6 educators, and even the mother of the assailant, we need to have an honest and open discussion about how to move forward as a country and do whatever it takes to prevent this type of horror again.  I think that discussion includes, among other topics, gun control reform.  The white paper above was recently put out by the Johns Hopkins Center for Gun Policy and Research.

“The higher prevalence of gun ownership and much less restrictive gun laws are important reasons why violent crime in the U.S. is so much more lethal than in countries of similar income levels.”

 

“Using various statistical methods, estimates range from a one to nine percent increase in aggravated assaults as a result of [Right-To-Carry] laws.”

 

“… the Australian government developed a process for the government to buy banned weapons from citizens when that country banned semi-automatic and pump-action rifles and shotguns in response to a mass shooting. In the decade following enactment of the policy, there was not a single mass shooting, and declines in homicide rates accelerated.”

 

The holidays are coming. I’ll be hugging my girls a little tighter this year, but I’ll get back to perusing the scientific literature and finding inspiring work out there.

 In the meantime, happy holidays to all, Merry Christmas, and Happy New Year!

 

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.

What I’m Reading Wednesday (WIRWed): 11-21-12

“What I’m Reading Wednesday” or WIRWed is a weekly post where I’ll share some of the interesting articles that I’ve come across.  As a student, I became far too focused on only those publications that directly related to my thesis work all the while missing the amazing science that was going on around me.  What I failed to understand as a student is that there is insight and inspiration to be gained by reading publications outside of your specific family of viruses, field of virology or immunology, or even field of study altogether.

So, to keep me accountable, I plan to blog once a week about the articles that I find fascinating.  They may or may not be relevant to my specific field of study.  I’ll try to vary it a bit, although, don’t be surprised to see some influenza in there (Hey!, it’s a really interesting virus!).  I’d love to hear from you as well!  Comment with links to articles that you would like to share and tell us why they captured your attention.

I’ll be enjoying these articles on a 6+ hour car ride up to New England to spend the holiday with family.  Wish me luck.  T-day traffic and two girls under 3 years old don’t mix well!

Just like her Mummy

Without further ado…

1. 

Love when an article challenges the currently accepted model and makes us all stop and think.

 

2. 

So fascinated by non-coding RNA.  It was ignored for so long as a contributing factor, overshadowed by coding RNA.

OK, here comes some influenza…

3. 

So important to recognize differences in responses amongst the various animal models we employ and carefully assign the value we place on the information we glean from them.

 

4. 

Something about the ability of viruses to thwart our every countermeasure, infecting the very cells that should be able to gobble, gobble them up and clear them.  Gets me every time.  (BTW, that gobble reference was in honor of the looming holiday!)

 

Now, its your turn.  What are you finding interesting this week?  Something new and cutting edge?  A classic?  Doing a bit of catching up in a particular field?  Let’s hear it!  Post a link to the article and your thoughts so we can all share.

 

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.

Read Cube

Look familiar?

As a grad student, I probably destroyed acres and acres of trees with printouts of scientific articles.  I love to organize with binders and I had a 4″ binder for each aspect of my thesis research: TLR2, Arenaviruses, innate antiviral responses, etc.  The day I cleaned out my desk/bench space, I filled several boxes with paper to be recycled.

Read moreRead Cube

Wax On, Wax Off

We make sacred pact. I promise teach (science) to you, you promise learn. I say, you do, no questions.

Much like Daniel-san, I had a thesis mentor whose practices were less than traditional.  We didn’t have many conversations regarding science, career ambitions, or research strategies.  It was a much more “Here’s some rope, don’t hang yourself” kind of deal.

Not getting anywhere with the project handed to me? It was up to me to find a new one (learned how to search current literature, find an open question, figure out how to answer it and write a proposal).

Bad experience presenting data at department forum? I learned from my mistakes, modified my presentation style and cues, and sought out ways to practice presenting.

Read moreWax On, Wax Off

Busy, busy

Daily To-Do List
Only 3/4 might actually get done

Just as I used to think I was busy pre-kids, I used to think I was busy when I was a grad student.  However, as a grad student, I had plenty of time to check my pinterest boards (melissawhayes, if you’re interested!), catch up on my shows (usually The Walking Dead and a couple others), heck, even sit down for an hour to eat lunch with friends.

Now my lunches are more like drive-by casualties.  Walking from one lab to the next, I grab as many bites as I can before the 15 steps between doors is up.  This is how I’ve been starting my day, every day, for the last two weeks (the actual items change daily, this is a rather short list):

Read moreBusy, busy

Selecting a Mentor

Plan B, in case grad school didn't work out
Plan B, in case grad school didn't work out

When I started graduate school, I had been working for 6 years in the biotech industry.  Having had a handful of bosses during that time, I thought I knew how to choose a mentor.  In fact, I put much more weight on choosing the project than on the mentor itself.  I had it all wrong.

I’ve mentioned how my thesis mentor was less than traditional.  When I joined his lab, I hadn’t even rotated with him previously.  But I was infatuated with the project and the science and thought that would carry me through.

Read moreSelecting a Mentor