Tales from the Microbial Laboratory

The List, Updated.

~Annabelle Lee~

~~~~~

I doubt that Annabelle Lee has a list of any kind, unless it's a mental list of snakes that she hopes to wrangle in her lifetime.  I can see her 'bucket list' now:  (1)  catch black racer snake that has thus far proved elusive, (2)  if black racer snake is caught, obtain the courage to kill it (and not just bark and jump around, which will entice Handsome Stanley to saunter over and kill the snake without all of the silly Pointer Sister drama), and (3)  parade the black racer snake around the garden, and show it off in front of THE DAN.

I'm thinking that's a pretty nice bucket list for a Pointer Sister.

~~~~~

My list is a little different.  And even amidst the craziness of the past year, we've been slowing slogging through it, sometimes modifying it as we go, adding another paper as new data presents itself - a team effort for a lab that has had a challenging year.  We're smaller in number now (the eclair-baking postdoc has accepted a position at  non-profit in Maryland) but we're no less determined - our numbers will soon dwindle even more, with both of my doctoral students slated to defend their dissertations in December.  But new students will appear, new scientists will wander into the Microbial Lab and decide to stay.  The ebb and flow of the lab, something that I still haven't fully gotten used to, but recognize as the natural ryhthm of an academic life.

~~~~~

I haven't been spending much time here.  At the end of the day, when I often want to write, I simply haven't felt like doing so.  I suppose it's the ebb and flow of blog life, or perhaps it can be explained better by inertia brought on by a long, hot summer and a difficult year and a Nikon that is shedding it's last images.  Work has been a constant though, as has the garden - and through it all, some positive things are beginning to happen, and I'm slowly, but surely, washing myself of the dysfunctional situation that I was in.  A new wind is beginning to blow.

~~~~~ 

The List first emerged in August of 2009, just a few days after my termination from my job of 15 years - and more recently here, in April of 2010.  It's a nice list, considering the circumstances, and I'm proud of what my lab has accomplished (more or less since June of 2009).  The truth is that everyone has been working their asses off.  Posting The List helps to keep me focused, helps me to prioritize what I need to work on next.  There is still much to be done, much to write, edit, proofread and celebrate.

~~~~~   

THE LIST

1. work describing a coral pathogen and the role of motility (led by our collaborators in Israel): Published.
2. work describing metabolites produced by a coral pathogen (led by local collaborators): Published.
3. work describing genes involved in nutrient cycling in coral microbial communities: Published (and take a look at the journal cover photo).
4. work describing the bacterial communities in the upper respiratory tract of Atlantic bottlenose dolphins: Published.
5. work describing the phylogeny of a globally-distributed coral pathogen (collaborative with colleagues from Australia):  Published.  
6. work validating the presence of a coral pathogen in the Caribbean and the pathogen's antimicrobial characteristics: Published.
7. work describing a method to detect and quantify a coral pathogen in environmental samples: Published.
8. work describing culturable bacteria and fungi in gastric, upper respiratory tract and fecal samples of Atlantic bottlenose dolphins: In Press.  
9. work describing the genome and proteome of a coral pathogen, with a specific focus on temperature-dependent virulence: In Preparation.
10. work describing the genome (full description) of a coral pathogen at two different temperatures: In Preparation.
11. work describing the proteome (full description) of a coral pathogen at two different temperatures: In Preparation. 
12. work describing the antimicrobial resistance and susceptibility profiles of coral-associated bacteria: In Preparation.
13. work describing the anti-microbial activity/properties of coral-associated bacteria:  In Preparation. 
14. a review focused on the urgent need for coral diagnostic approaches:  In Preparation.
15. work describing the effect of pH on membrane vesicle production and composition in a Gram negative bacterium:  In Preparation. 
16. manuscripts 9-15 are all close to submission - in addition to these 7 manuscripts, we have ~10 additional manuscripts where the data is collected, some writing has been done, but they are not yet close to submission.

a picnic

~Sullivan's Island~

I joined friends for a picnic dinner on Sullivan's Island last night - it was a beautiful evening, and we were on the end of the island where all of the beginning kite boarders were practicing on the beach.  I thought I'd share this image.

Otherwise, not much to say.  It was a hard week, felt like paperwork-unemployment hell, and I'm glad that it's the weekend.  I'm guessing you're glad it's the weekend too.

 

a cedar

~Hobcaw Barony~

The marsh grasses are greening up...southern fields of spring grain.

Annabelle Lee and her 'Kong'

 

She's a crazy thing.

Runs like she's being timed, sleeps like she's never slept, dreams of being a snake wrangler, and curls up into a tiny ball when there's thunder.

She's wonderful. 

Airstream Note to Self No. 9

(Alternate Title:  "Another Day in my Glamorous Life")

~~~~~

I haven't posted in two weeks here, not sure why - since, as always, I have a million plus thoughts playing pinball in my head.  The ideas build up, but instead of writing I've been weeding the side perennial garden, thinking about preparing the vegetable beds for a fall garden (but only thinking thus far), dealing with unemployment (another rant is due soon), dealing with a recently awarded grant (yay!), transitioning to a new research home (which will occur over the next few months), working with the lab on a manuscript (to submit here, a journal with a humbling 8% acceptance rate), and...

...defrosting the Airstream refrigerator-freezer.

Airstream Note to Self No. 9:

I've been procrastinating defrosting the Airstream refrigerator-freezer for no reason other than it's not such a fun thing to do.  And I must confess this is the first time that I've defrosted it, since I moved in back in late July of 2009.  But the weekend after my 1-year Airstream Anniversary party seemed as good a time as any.  During the week prior, I tried to eat up the contents, and so only had to store condiments and some salad dressing in a color while the freezer was defrosting.  This is the original 1973 unit, and runs off of electricity or propane - and unfortunately doesn't have an automatic defrost mode.

Or an ice maker.

~~~~~ 

~freezer compartment~ 

I don't have any images prior to defrosting, but ice had built up badly in the freezer compartment, in fact, so badly (I'm embarrassed to say) that it had surrounded a container of chili placed in there months (and months?) ago.

~~~~~ 

~refrigerator compartment~

Ice had also built up in the back of the refrigerator, along the metal sheets that transfer cold air into the compartment.  I need to read up a bit about this, because I'd like to find out if a different setting (warmer or cooler) would prevent this.  It's now been clean for almost two weeks, and part of these metal sheets are already frozen over (perhaps this is due to the summer humidity?  and air condenses on the metal and freezes?).  Also, notice the wide-V-shaped part under the metal sheets - this is designed to catch the water dripping off the sheets, and has a tube that takes the water to the back of the refrigerator, so that the water runs 'outside' (more or less, see below).

(I'll read a bit up on this, and check back in and update this post soon - because I'm sure you are all dying to know why this is happening). 

~~~~~

~access to the rear of the refrigerator from the outer Airstream compartment~

So - there is a tube that should send the water to the rear of the refrigerator, an area that is accessible from the outside of the Airstream.  The top arrow, above, points to the tube - and the bottom arrow, above, points to an area where the tube was dripping water.  Now, call me crazy, but this didn't seem like a great place to be leaking, since the water was essentially dripping awfully close to the where the refrigerator-freezer is plugged in to an outlet.  I'm guessing that I need to orient the tube differently, so this is something that I need to look into before the next time I defrost the unit (which needs to be more frequently than once per year!). 

~~~~~

~The Pointer Sisters~

Yes, the Pointer Sisters were around while I was defrosting the refrigerator-freezer, and while they didn't get in the way, there weren't awhole lot of help either.  I think they were bummed that there wasn't random refrigerator contents lying around, like huge hunks of cheese, that they could devour.  All-in-all I think they thought that the whole process was a bit boring.  Imagine that.  

the names of trees

 
 ~live oaks, surrounding the Airstream~

~~~~~

When I was young, from about several months old to about age 12, my family lived in a neighborhood called Airport Acres.  Our brick ranch house was on two acres of land, and the expansive front yard was often the location of neighborhood football games, which usually consisted of my brother's older (and much bigger) friends and my two friends, Barbara and Glenn.  Barbara, Glenn and I are tiny in comparison to my brother's friends, but we held our own, even if it meant that on ocassion we were used as the football itself.  Our front yard was my 'school of hard knocks'.

There weren't many trees on the two acres.  In the front there were several dogwoods, including one gorgeous pink dogwood that was always my mother's favorite.  In second or third grade I remember getting a pine tree, I think it was an Eastern White Pine, on Arbor Day.  Each kid was given a tree, and instructed on how to plant and care for it.  I remember coming home and caring for that tree, and watering it for weeks afterward.

My parents sold that house when I was 12.  My Mom always would tell the story about how much I cried because I had to leave that tree.  I think now about ways that I've changed, but the thought of leaving trees behind still makes me sad.  However I'm grateful that of the things that I grow attached to, that trees are on the list.  I'm glad that I know their names.

I neglected, earlier in the summer, to mention that the U.S. has a new Poet Laureate, W.S. Merwin.  We all should know his name too.   

Native Trees by W. S. Merwin

Neither my father nor my mother knew   

the names of the trees   

where I was born

what is that

I asked and my

father and mother did not

hear they did not look where I pointed   

surfaces of furniture held   

the attention of their fingers   

and across the room they could watch

walls they had forgotten   

where there were no questions   

no voices and no shade

Were there trees

where they were children   

where I had not been   

I asked

were there trees in those places

where my father and my mother were born   

and in that time did

my father and my mother see them

and when they said yes it meant

they did not remember

What were they I asked what were they   

but both my father and my mother

said they never knew

I could get used to this.

I have to laugh at myself - and this situation that I'm in, and thankfully life in an Airstream brings with it many funny moments.  Like, for example, last Sunday - when I was cleaning up after my Airstream Anniversary celebration.  A table that I had used as a makeshift bar - well, I've discovered that I kinda like having a bar set up outside of the Airstream. 

So I left it there.  Complete with gin and tonic water.

Now, you are probably going 'red flag! she's got a problem!' or 'won't someone steal the stuff?' or 'wow, great idea' - so let me first assure you that I am (quite fortunately) not a stress drinker - in fact, even the ocassional glass of wine that I pour generally gets forgotten, so I've stopped pouring it altogether for the most part.  That said, it surprised even me that I liked having a bar outside of my Airstream front door, and it makes me laugh - there's an element of the absurd that fits the situation, and last evening, after working in the garden for a bit, I went inside the Airstream, filled a glass with ice, and came outside and made a gin and tonic.  Perfect.

Three Dog (and One Cat) Airstream

~Three Dog Airstream~

~~~~~

I often get asked 'how can you live in such a small space with three dogs' - to which I add 'there's also a cat, or at least most of a cat, since Haiku is missing on her back leg and her tail.'

 

Well, as crazy as it can be at times, it isn't that crazy - there is alot of musical chairs-style moving around, but it's all done rather calmly.  They all play well together, and respect each others space (as they should).

So here's some rare footage of my Airstream life...(okay, so it's not all that rare - I was just trying to add some drama to my little world).  All within the course of a few hours.

~~~~~

 

~Annabelle Lee and Haiku~

~~~~~