Tales from the Microbial Laboratory

Surprises, frustrations and a few things to do...

What a week.

Good thing.  I had forgotten that the bearded iris that I planted last spring was a rebloomer.  How fun!  Here it is, the last day in November, the last day of the 2006 Hurricane Season, and my garden is graced by a bearded iris in bloom.  Ends up there are alot of rebloomers - and although we're in the southeast but not southeast Michigan, their Iris Club has a pretty informative description of growing and caring for reblooming irises.  I recommend them.   

Sorta-maybe good thing.  My grant proposal got submitted a FULL three hours and fifteen minutes before the 4 pm deadline today.  That may not sound like much to you, but to have three hours and fifteen minutes of breathing time is huge.  I also snagged a letter of support from the US Navy Marine Mammal Program at the last minute - we'll incorporate their archived bacterial samples from Pacific Coast dolphins into our microbial molecular comparisons.  That was nice.  As I worked on this proposal - one thing that amazed me (and it always does) is how very little we know about the diversity on our planet - including microbial diversity.  Our preliminary data suggests that dolphin respiratory tract microbes are either unique at the Genus but definitely the species level, suggesting that there are probably novel strains specific to bottlenose dolphins - potentially novel pathogenic strains.  Anyway...I'm now in the 24 h post-grant submission coma that always requires wine, no meaningful conversation, and trashy television. 

Really crappy.  One really important thing about conducting research is what you're going to work on - you read, you learn, you collect a little detail, you go for it and write a grant proposal.  You cross your fingers (and toes).  The proposal submitted today is a new project for the lab - we've spent available time (and resources) obtaining a bit of interesting preliminary data (all sequence data - which can add up quickly) and isolating organisms from available dolphin respiratory fluids and archiving microorganisms and their DNA.  In other words, we bootleg the work the best we can.  That's a decision I made - but another equally big decision is who I collaborate with on projects - collaborators are pretty key today to environmental research that is often multi-disciplinary in nature.  I have some great collaborators - folks that I really respect and admire - but I have one collaborator that I perhaps need more than respect - for reasons that I can't go into here.  Anyway, this person let us down in a pretty big (and expensive) way this week - retrieving coral samples from San Salvador that were not taken in a careful, methodical way - and not being prepared so not getting almost half of the required samples needed for comparison.  The lab was geared up for these samples - excited, anxious - but prepared.  So what a letdown (an understatement) to find that our collaborator was so careless.  But he holds the permit that we need to collect the samples - and a historical relationship with the field station associated with the reefs.  We'll do it differently next time around - but it's a hard lesson to learn and I should have known better.

Kinda fun. Even though it might be a chilly, drizzly night, I'm looking forward to tomorrow night's French Quarter Artwalk.  I got this festive invite from Lime Blue (62 B Queen St) - artwalk is an open-to-all event, so consider yourself invited.  Since I'm not bartending for Jeff - I'll be able to wander around and I'm looking forward to that.  Tomorrow is also World AIDS Day - and there will be a march at 5:45 pm starting at Marion Square (with a rally at 5:30 pm) and ending at the College of Charleston Cistern at St. Phillip with a candlelight vigil.  Might be a good thing for folks to do, don't you think?

Another One

Popcorn Trees

More about popcorn trees later - for now, I've got a 4 pm grant deadline looming.

I need sleep.

Blurry

I know, this image isn't very focused - but it suites the day, one in which not enough (not nearly enough) sleep was obtained - an image taken in the early morning light after having already worked for a few hours...the continued writing saga of everything-you-always-wanted-to-know-about-the-bottlenose-dolphin-respiratory-tract....but were afraid to ask, learn, submit, then risk professional humiliation.  I love the colors in the image though - it's autumn in the south (can it still be called autumn when December is knocking on the door?). 

Through The Looking Glass

It's misleading, how quiet and calm the laboratory can look through the glass door.  I joke sometimes that the way the lab is designed, it often looks like no one is actually working - at least turn the lights on you guys, we all look like a bunch of cave dwellers (me, the one who has never turned her office overhead light on...).  But the emptiness is misleading - as you walk in, to the right, Ben spent much of the week picking colonies - mutants of a Burkholderia sp.  He has almost 1,000 of them - 'pilgrims' - our fingers (and toes) are crossed that one or two of them will have the mutation that we need.  Further into the lab, Maria was tossing old agar plates of microorganisms - anti-microbial assays and previous isolations - lots of effort, tossed into a biohazard bag in preparation for autoclaving.  Katherine has been pretty much everywhere - making glycerol artificial seawater agar plates in preparation for tomorrow's samples from San Salvador - sleeve after sleeve of plates in anticipation of the onslaught - and organizing in preparation for tomorrow.  Further into the lab Nikole is at the computer, on-line, doing whatever, but stopping to ask questions about the co-culture experiments for the proteomics study, saying that she'd handle the seawater filtrations tomorrow if needed - 2 liters of seawater from each coral reef sampled.  I just stand in the laboratory, enjoying the activity and their presence far more than the details that still need to be added to my grant proposal.  I put a few things away, help in a trivial way, ask Ben if he'd take all the cardboard boxes out to the recycle bin (he agrees), and then I realize that I really need to be in my office, incorporating the new preliminary data, doublechecking the budget, seeing if the letter of support for providing captive bottlenose dolphin respiratory tract samples has been faxed.   

Rosebud, with Edge

Okay, so this is sort of cheating - taking an old image and striking a key - and there you have it, a different image.  But it's quick and it's all I can do after waking up at 4 in the morning outlining a list in my head of everything that I still have to do for my grant.  It's a list that grows...and grows...but hopefully (well, definitely) must stop growing soon.  The old deadline thing and all.

Edges

Another view of a toad lily - using the 'edge' function in Microsoft Photo Editor...and yes, I have the CD to install Adobe Photoshop CS2, but I've  yet to get around to it - there was a problem with the ID and I need to get my office to look into it...it's on the list.  But for now, I'm enjoying what the edge funtion does (and does not) pick up when it transforms an image.

Yes, I'm procrastinating -- working on my grant.  I was up late last night, drafting letters of support, letters of collaborations, editing short-form CVs and budgets, facilities and permits -- it's a wonder that we ever get around to the science at all!  So a grant to submit, two of my doctoral students are submitting fellowship applications tomorrow, we've got ~500 mutants of PR1 hopefully starting to grow today (after a chilly Thanksgiving for them - nicknamed the 'Pilgrims' by our administrative assistant), and on Wednesday coral tissue and coral surface mucopolysaccharide layer samples and seawater samples arrive from San Salvador.  I have a prospective postdoc to interview today - who might start as soon as 15 December (at least I hope so!).  The lab is abuzz.

Another View

This bud, just another view.  Now, if it were only so easy to transform my grant proposal into something different, unique - something that will make reviewers go 'funding this one is a must!' - if only it were so easy.

Well, it most certainly won't happen while I'm posting this...submission date, 4 pm, Thursday 28 November.  There's still much to be done. 

Creeks, 'Butt Pie' and Special Thanksgiving Guests

Yesterday, while heading down Bohicket Creek towards the mud flats that change yearly, redefining the beginning of Church Creek (something that the bridge no longer defines) - I thought about why I like Thanksgiving perhaps best of all the 'holidays'.  Maybe it's because of the long weekend (but I'm not sure that's it this year - I have a grant due in less than a week!) or maybe it's because it's a long weekend not spent shopping (even once).  Or maybe it's because my parents never made a big fuss about it - there was always food and often guests - but there wasn't ever craziness or a big build-up or those oh-so-annoying expectations.  As an adult I've lived pretty far from home - and since my parents love the Christmas holiday best - they've never pressured me to come home for Thanksgiving, so for years now I've had quiet, easy days of thanks that are generally not very well-planned and are definitely not scripted.  This Thanksgiving, with my brother present, as well as the lab's Poet Laureate (Katherine) and her spouse, the poet Richard Garica, in between removing a three-legged cat from a heavy chair, discussing the myth of the Parker House Rolls, and declaring how we think that dogs most definitely need to stay indoors - inbetween listening to stories about Richard's father and Thanksgiving and special dinner guests, and how pumpkin pie to some should be renamed 'butt pie' -- in between easy conversation over turkey and even easier conversation over 'butt pie' loaded with homemade whipped cream, Richard read us this poem:

The Peaceable Kingdom by Richard Garcia

From The Persistence of Objects (2006, Boa Editions)

I wish I could write a poem about Squanto-
Squanto at our house for Thanksgiving
back in the fifties when I was a child, and all
of the family was still alive, younger, and together.
In the poem I'd introduce Squanto to my father,
John Garcia, former chef for the Matson Lines.
Thanksgiving was the one day of the year
he would cook at home.  He'd adjust his chef's hat
at a cocky angle, cinch his apron, and while sharpening
his knives, ban my mother and sisters from the kitchen.
Only men allowed, just me, my brothers and cousins,
and in this poem, Squanto too.  After all, hadn't they
both sailed the world's oceans? My father had seen things,
he always said, that a man should not see.  What things,
I wondered? The child prostitutes of Manila? The public
sexual dance called "Toro?"  Beheadings in Sumatra
or the slow Chinese execution by dismemberment
called "The Torture of the One Hundred Pieces?"
Squanto had seen a lot too-kidnapped twice,
taken, like Pocahontas, to London, but unlike her
he made it back somehow.  Later, tricked into boarding
a ship in the harbor, he was shanghaied to Spain,
escaped, and managed to come home from that too,
only to find his entire tribe had died from the plague.
In the poem, Squanto and my father get along;
after all, both men spoke English and Spanish.
Squanto would make the pumpkin pies.
Maybe, if he comes into the poem a couple of days
early, I can take him to school and he can be
in the Thanksgiving play we have to put on.
Take that, Miss Kapelhaus!-my third grade teacher
who thought I was a complete idiot.  Who didn't
believe I could read.  Who couldn't tell me and Juan
and Carlos apart.  Maybe she'll think Squanto
is the fourth Mexican at Dudly Stone Elementary.
At dinner we'll put three long tables together.
My cousins will be swinging from the lamps, sliding
down the banisters, and bouncing off the couch.
"Just like the first Thanksgiving," Squanto will say,
"those Puritan kids were pretty wild too."
In this poem I want to write, Squanto tells stories
about the Puritans.  How surprised they were
to be greeted by an Indian in the Queen's English.
Maybe he'll joke and tell us his first words to them
were "How" or "Kemo Sabi." Maybe he will tell us
he waved in the Mayflower like a parking attendant
saying "Easy now, watch out for that rock." We'll laugh,
careful not to ask him about the second Thanksgiving
That'll be something he does not want to talk about
in this poem-blood seeping into the snow, crows
dipping deep into the hole that a blunderbuss makes
in a man's back.  No, in this poem we'll just talk about
that first Thanksgiving that began a future
that never was.  We'll even have our picture taken,
all of us around the table, our dogs, my Cousin Bob
down on one knee, me reading this poem out loud
like a proclamation.  I'll add a lion, a tiger, some oxen
and cows, and I'll put my baby niece and nephew
sitting in front-The Peaceable Kingdom.  We'll praise
and be thankful that time doesn't exist in this poem.
After dessert my father and Squanto will sit, smoking
big Indian cigars, swapping tales-abductions,
imprisonment, bloody mayhem, escapes, and
thankfulness for safe returns from the high seas.

Lucky

There are days, simply perfect days, when I think 'Just how lucky am I that I live here?' - and today was one of those days, a day spent on the waters that surround Wadmalaw Island, a day spent in the sun and salt air.