Tales from the Microbial Laboratory

Halloween 2009, a Recap

~The Deadbodys, at church on Halloween evening~

~~~~~

Shouldn't one sit back and reflect on such an important holiday?  Perhaps review a bit, take some notes, write a poem, plan for next year?  Such reflection sounds better than obsessing over one's worries:  a looming grant deadline, a looming birthday, a whole batch of looming decisions [about one's father and one's career and one's home and one's family (who is still finding their footing after it's matriarch passed away)], a head cold from hell and ...see?  You are bored already.

So - Halloween 2009 recapping it will be!  
  
~~~~~

~Airstream kitchen window shrunken heads~

~~~~~

The Airstream was decorated minimally this year - two heads hanging in the kitchen window (it's amazing how two $1.50 heads from CVS Pharmacy can entertain me).  Yes, once again, heads (or the lack thereof) was a continuing theme...

~~~~~

 

~Lily the Pencil~

~~~~~

Is this not the sweetest, scariest, most realistic pencil in the whole wide world?

That most certainly is not Lily, but I'm told that it is.

(Lily is a budding biologist, fellow lover of Halloween, and forever in my heart because of a lovely little prayer).

~~~~~

~Vincent Van Gogh~

~John Stewart~

~Jack Nicholson in 'The Shining'~

~~~~~

 The eclair-baking postdoc (yes, the one who hasn't brought us eclairs in a long, long time) is one of those fancy pumpkins carvers.  A skilled one in fact.  He sent me these images of his three selections this year (and forgive me, but doesn't 'John Stewart' look an awful lot like Vladimir Putin?).

~~~~~

~the lab's senior graduate student (newly appointed) in her Halloween socks~

~~~~~

A few years ago, a friend came to the lab one morning when I wasn't there, and placed a brain in the lab's 'deli box' - he was like a Halloween 'easter bunny, hiding Halloween-themed socks all over the place.  Every now and then a pair still surfaces, as demonstrated by the feet of the lab's senior graduate student.

My lab is very patient with my Halloween silliness, in fact - perhaps it's been a subconscious screening tool that I've been using all these years?

Now that's a thought.   

~~~~~

~Mr Sperman and SuperSperm~

~~~~~

Now how does one transition from Halloween-themed socks to Mr Sperman and SuperSperm?

I'll just leave this one alone (and no - I wasn't at the party).

However the lab's newly minted Ph.D., Mr Sperman, was.

(I hope that Mr Sperman is wrapping up his dissertation edits as I'm typing this.)

~~~~~

 

~Mr. and Mrs. Deadbody~

~~~~~

Each Halloween, Mr. and Mrs. Deadbody are spotted roaming the streets of Charleston, on their way to church on Halloween night.  They're a delightful pair, aren't they?  Rumor has it that they were both poets in the day - he a writer of magical tales, she a teller of family stories and famed observor of the Day of the Dead.

Did you happen to see them too?  I hope so.

~~~~~

~Jeff the dead...lumberjack or something or other~

~~~~~

So what does a Halloween sock Easter Bunny look like?  Does he have floppy ears?  No, no, no.  Does he hop?  Heavens no!

A Halloween sock Easter Bunny looks dead, no he is dead - more like undead - so watch out for him next Halloween.  If you are lucky, he might bring you a pair of socks too.

~~~~~ 

  

The Headless Marine Laboratory Presents...

“Being Headless in the Post-Cranial Era”

An Invited Seminar by

a seminar by

Dr. M. Vesicles

 

Head of the

Institute for the Promotion of Hideous Headless Research

Fort Johnson Campus, Charleston, South Carolina

 

~~~~~

 

At first, it was like any other HML seminar (except perhaps a bit better attended)...there were people with questions every few seconds, the token sleepyhead, the token airhead, others sitting back, taking it all in - there was even a pathetic cry for attention due to some unresolved 'mommy' issues....

 

 

~~~~~

 

There were annoying interruptions by headstrong members of the community (now, who is s/he really talking her/his head off to??)...and of course that stereotypic dopehead blatantly reading a silly romance novel titled 'Love in the Magnolia Garden Greenheaded Coneflowers'...

 

 

~~~~~

 

...and the usual finger-pointing by the omnipresent front row chuckleheads!!!

 

 

~~~~~

 

A heady Dr. Vesicles discussed several controversial trends in her data...sending shivers down the backs of the audience. raising the frightening question:

 

Will there ever be a headless recovery???

 

 

~~~~~

 

There were moments when Dr. Vesicles was riveting, leaving the audience on the edge of their seats...their hands clutched to their foreheads together...

 

 

~~~~~

 

...and moments when her words were met with outbursts of pure hardheaded disdain!

 

 

~~~~~

 

No one could ignore the ocassional be-heading, uuhh...choking,..the zombiesque lapses in appendage control... 

 

 

~~~~~

 

And of course there is always a bonehead in the crowd, raising his long-ago-severed head just so he could see it...while another shows complete disrespect, with their hands behind their head former head and feet propped up on the table in front of them.

 

 

~~~~~

 

At one point, Dr. Vesicles stops discussing trends in her data, and briefly reviews the history of headlessness in the Headless Marine Laboratory, recalling the reluctant members in '06 (rarely venturing out of the lab), the growing bullheadness in '07 (as evidenced by the restlessness at the lab's door, while growing increasingly anxious to escape the lab's confines and spread the word), and finally their growing numbers, proudly documented in this '08 archived image.

  

 

 

~~~~~

 

But the end of the seminar looms, and the audience quickly grows eager (well, at least some of them do...) as they anticipate Dr. Vesicles always illuminating concluding remarks... 

 

 

~~~~~

 

"You really can get a head in a headless laboratory

without while losing your own head!"

 

and

 

A Happiest of Halloweens from the Headless Among us!

 

 

 

 

 

~~~~~

 

~an Airstream party~

~a table filled with wild flowers~

~~~~~

Last night there was a gathering at my place - a time to celebrate the lab's new Ph.D.  Each time that a student finishes up in my lab, I throw a party in their honor:  there are few tried and true traditions involved, except that the student gets to choose their beverage of choice.  Usually this is a beer of some kind - and Ben chose a Sonoma County micro-brew - Racer 5.  Here's what they say about it on the Bear Republic Brewing Co. website:

This is a hoppy IPA. Did I say hops? Your brewer is a hop head! This is a full bodied beer using American grains. The goal was to create a base for showing off the unique floral qualities of two Pacific Northwest hops, Columbus and Cascade. Columbus is a new hybrid High Alpha Acid hop used mostly for bittering, but used heavily as an aromatic in this bold brew. Cascade is the balance that ties the malt and bittering hops together. It is a true specialty ale and is our brewer's statement on this style. 2004 L.A. Commercial Brewing Competition, Silver Medal Winner; 2004 World Beer Cup, Silver Medal Winner; 2001 Real Ale Festival, San Diego, Gold Medal Winner; 2001 Real Ale Festival, Chicago, Gold Medal Winner; 1999 Great Amercian Beer Festival, Gold Medal Winner - og 1.070, ABV 7.0%, IBU 69. California State Fair Bronze Medal, 1997 Beerfest Invitational. - og 1.070, ABV 7.0%, IBU 69.

It's a good beer, if you're in to beer.

Now this was the first 'Airstream' party - and so the plan was for it to be outdoors (in the front garden), with a small fire.  Unfortunately it rained - poured - the hour or so before guests were due to arrive, so I was still scrambling a bit to set up tables for food, etc once the rain stopped.  So it was damp, humid - and still air, and a fire was built anyway (because it is October, dammit, and there should be a fire!) and better yet, guests tended the fire with intense dedication - as we all ate chili and jalapeno cornbread and corn chowder and sourdough bread and homemade pumpkin cheesecake and a lemon meringue pie (made from meyer lemons from a friend's front yard) and chocolate angel food cake and a kahlua cake and homemade brownies and freshly boiled cayenne peanuts...and good conversation.

And then late into the night, at half past midnight, just the lab remained (and a few close lab friends) and the new Ph.D. received a few gifts and it was all quite sweet.  At a bit after 1 am everyone had left, the dogs had been freed - and I cleaned up a bit as they ran around.  The Pointer Sisters and Stanley then celebrated in their own special way, sniffing out boiled peanut shells - their late night reward for being so patient.

Now, more to the point...the flowers!  I was obsessed with having vases of flowers, and since my job situation (rather, lack of paycheck situation - since I most definitely have a 'job') has me trying hard to be frugal, I thought 'what could be better than late summer wildflowers?' - so early yesterday morning I traveled a few miles north of my place and collected wild sunflower and ageratum and aster and others, and filled several glass jars and a fired pot with the flowers (shown above, before they were moved around).  But it rained, the flowers got set out late - and then it was dark (except for the fire, a few tiki torches and a few candles).  Silly me - obsessing over those flowers.  But I thought they were beautiful...and doesn't an Airstream party need flowers?

~~~~~

~the Airstream, with flowers~

~~~~~

This afternoon I finished cleaning up - and moved the flowers to the front of the Airstream. With the awning up, a few chairs added - my small table of 'propagatees' put back on their table - well, it almost looks like home.

(Wait, it is home, isn't it?)

A home with a few yummy leftovers and wildflowers and propagatees and brownies!

~~~~~

I am still determined to be cheerful and happy, in whatever situation I may be; for I have also learned from experience that the greater part of our happiness or misery depends upon our dispositions, and not upon our circumstances.

Martha Washington

~natural cycles~

~the Microbial Lab and Friends, 'blebbing' in honor of Ben's newly minted doctorate (Ben is the one holding the bottle of champagne)~

~~~~~

What is 'blebbing' you ask?  You can see an image of our model organisms here, a Gram-negative organism (the rod shape in the middle of the image) - surrounded by smaller, spherical 'blebs' or membrane vesicles.  What does a group of geeky scientists do in such a festive photo opportunity?  In honor of Ben, they form their own silly blebs...since much of his work focused on these fascinating exosomic structures.

Silly scientists...

It was fun.  An hour seminar - followed by a three hour defense.  Then a fun lunch with pitchers of margaritas.

Another student successfully makes its way through the Microbial Lab...

~~~~~

So what did members of the lab do next?  Well, I left with my colleague who was in for the defense (we went downtown to a rooftop bar to further discuss science and life...) while other members of the lab went and painted the 'boat' on Folly Rd in honor of the new Ph.D.  The lab's 'new' senior graduate student sent me the image below of the boat - I love it!  The 'terminal masters' was related to an earlier incident when a member of Ben's committee suggested that he go for a 'terminal masters' if he couldn't get something to work.  It was one of those 'you have to be there' kind of dry jokes, but one that has obviously stuck...but what I love is the smiling rod-shaped microorganism on the boat - surrounded by blebs!  Yes, geekdom at it's very best.

~the boat on Folly Road~

~~~~~

And what did I do today?  First, it was a simply spectacular day.  Low humidity, crazy-blue sky - a breeze that reminded you that the Atlantic Ocean was just over there.  After a mid-day seminar I decided to go and see the Folly boat for myself - but when I got there, it had already been painted over (and by the way, Happy Birthday to Allison, whoever you are!).  Then - since I was already at the boat - and the day was just too too nice - I went onto Folly Beach, and sat and ate shrimp by myself at the Crab Shack (I've never been there - and basically stopped (because I wanted to eat outside and there was an easy parking spot).  After I was done - and walking to my car - I couldn't resist a shot of Planet Follywood.  It always makes me laugh.

~Planet Follywood, Folly Beach, South Carolina~

~~~~~

I made it back to the lab in time for another seminar - and then I left for home.  I've been enamored of late by the roadside 'ditch' flowers blooming - the ageratums and goldenrod and helianthus - and couldn't resist pulling over and taking a photo or two.  I want to go back, maybe over the next few days, to get some more shots - to drive home slowly and admire how beautiful a low spot and the right amount of neglect can be.

Sometimes, perhaps we work too hard.

As for work, and working too hard - I've got an invited review to work on.  The lab's Poet Laureate (from a distance) and I are writing it together.  She's gotten together the craziest, most impressive table that I've seen in a long time - as for me, I've got some writing to contribute - and the one reality of the Microbial Lab (and most labs, for that matter) is that there are natural cycles and a student's defense is one of them.  Another bottle of champagne is on my shelf, signed and dated by a new PhD.

Today I took a breather, and tomorrow the cycle begins again.

~roadside ageratums~

~~~~~

~tomorrow is a BIG day~

~Camellia sasanqua 'Apple Blossom'~

~~~~~

I was surprised today to see that one of my sasanquas was in bloom - it was one that I got in Virginia last December, no - actually my father got it to neighbors as a gift, who a few days before he was going to give it to them said that they hadn't had any luck with camellias...and had given up.  Lucky me!  I read somewhere that this one could bloom in late summer/early fall - but I guess I was thinking late October/early November.  What a treat to find a sasanqua in bloom in September!

~~~~~

Tomorrow is a big day around the Microbial Lab.  It's senior graduate student, Ben, defends his dissertation.  His seminar is at 10 am - it is open to anyone who wants to attend, and the defense will begin at 11 am - it is a closed defense, with only members of his doctoral committee present.  Last week we worked on his talk - the difficult thing about a defense seminar is that suddenly the student has to condense all of that work into a 50 minute or so presentation.  It isn't easy.  But it's also the time when a student can say 'Hey!  Look at this!  Do you realize how HARD this was to do??  Do you know how interesting this is?'.  A good seminar is usually a passionate one - organized passion.

They grow up - scientifically-speaking - so fast. 

~three hundred plus pages~

~Microbial Lab doctoral student, Ben, surrounded by copies of his dissertation~

~~~~~

I don't often post images here of members of my lab group, and when I do I generally try to remember to ask them first.  Earlier in the week I asked Ben, the Microbial Lab's senior doctoral student, if he would take a photograph of himself with copies of his dissertation before he distributed them to his committee - and he kindly humored me and sent me this image.  It was taken in the middle of the night, after a few days with little or no sleep -- after months of writing and analyzing and re-analyzing and editing and reading and re-reading and pulling one's hair out.  These are silly requests of mine, photographs such as these - but to me they're wonderful documentation of the real work, the behind the scenes reality of the dedication and perserverance required to see such a thing as a dissertation through to the end.  Ben, in the middle of the night, surrounded by three hundred plus pages of blood, sweat and tears.  Corny I know - but true.

~~~~~

It's a funny thing, this whole dissertation process.  Today Ben said that he almost wished he could start over again, knowing what he knows now - because he would design better experiments - experiments more focused and directed and, well, just better.  Ultimately, the process of learning is (hopefully) almost always a humbling process, and reminds one of how much there is yet to learn.  The hope is that we can contribute, even a baby's step worth of data, and expand what is known.  That is what we try to do.

~~~~~

When I think of Ben and his time in the lab, I'm sure that he will be remembered as the 'hypothesis generator'.  It's a gift, truly.  Lorenz would definitely approve.

It is a good morning exercise for a research scientist to discard a pet hypothesis every day before breakfast. It keeps him young.

 

Konrad Lorenz, German (Austrian-born) ethologist (1903 - 1989)

 ~~~~~

Ben has spent much of his time in the lab studying very small things.  Yes, a microorganism is small - but he has been studying nanoparticles and nano-sized bacterial structures, or vesicles, that 'bleb' off of his favorite microorganism, a strain of Burkholderia.  Take a look at the image below.  Fascinating, isn't it?  The larger (oblong) structures are the bacteria - and the narrow 'tubes' (connecting different bacteria) are pili (which facilitate exchange of genetic material between bacteria).  The clump of small (very small) spheres are membrane vesicles.  They do all sorts of interesting things.  Ben has taught us much about the membrane vesicle...and he's shared hypotheses galore.   

~Ben's much beloved Burkholderia~

 

~~~~~

 

Ben sent me a link to the Terry Beveridge Memorial Lecture late this afternoon, which on the last slide has this poem about 'the microbe' that I hadn't seen before.  I thought I'd end this post by sharing it with you.

The microbe is so very small
You cannot make him out at all.
But many sanguine people hope
To see him down a microscope.
His jointed tongue that lies beneath
A hundred curious rows of teeth;
His seven tufted tail with lots
Of lovely pink and purple spots
On each of which a pattern stands,
Composed of forty seperate bands;
His eyebrows of a tender green;
All these have never yet been seen -
But Scientists, who ought to know,
Assure us they must be so ...
Oh! let us never, never doubt
What nobody is sure about!

--  Hilaire Belloc in More Beasts for Worse Children (1897)

~chicken guilt~

 

~a Belfield rose, petals curling at the end of a warm day~

~~~~~

The roses are beginning to wake up again, new growth emerging and buds forming - a definite celebration in response to the end of the dog-days of August.  Much has been going on around the lab:  my senior doctoral student (on the far left in these images and the Jolly Green Giant here) got copies of his dissertation into his committee today (for a scheduled 28 September defense), another student is having success with a new software program to help further analyze her proteomic data, there is writing and samples being run, and I even, for the first time in 15 years, applied for a new position.  I sent off my application materials at 2:53 am this morning, after a long night of obsessing over details - finally deciding that the details were probably not all that important at the end of the day.  I also desperately wanted to get back to 'the lab mission' - writing and submitting to the 'new streamlined' peer-review process an exhausting number of publications in one years time.

~from Nearing-Zero by Nick D. Kim~

~~~~~

The Microbial Lab is fortunate that Katherine is still sending poems our way, even in her absence.  Not only is she still sending poems, but she's also still working on two important manuscripts.  How nice is that?

And what is it about chickens?  Bird dogs and chickens.  A collection of poems titled Chickenhead.  And now a wonderful poem from one chicken's perspective.  Perhaps we are a nation with collective chicken guilt?  

The White Chicken Gives a First Hand Account
- taken from an Associated Press story

by Ceci Peri

I love the red
wheelbarrow
rusting
by the barn---
my sturdy
nesting place,
my refuge
the night
raccoons
laid waste
the coop,
killed all
the laying hens
but me.

Farmer
buried them
in the far yard,
and Laslo,
the brown dog,
dug them
back up,
nuzzled each
gray bundle
against the long
hen house
and, there,
all morning
stood guard.

Laslo,
brother of my heart.

~~~~~ 

~a goofy dog~

~the relatively new old dog, Annabelle Lee, eating a pear~

~~~~~

She's a bit of a nut, isn't she?  I've decided this is her 'eating fruit' position - since I see her like this each time a stray pear or apple from a neighbor's yard makes it our way.  She LOVES fruit.  Today Stanley got a mole, buried it, the Dan dug it back up - and then she and Annabelle stood next to each other, growling:  the Dan protecting her freshly dug-up mole, Annabelle protecting her treasured pear.  I've said it before - but I think it's worth repeating:  the Pointer Sisters are NUTS.

~~~~~

Well, it's late - very early Monday morning in fact - and I just finished sending off edits of another chapter of my student's dissertation via email.  One more day and the dissertation needs to be in shape enough so that the committee will say it's 'defendable' - in one week a copy goes to each of the committee members for a 28 September defense date.  It'll happen.

For now, it's time to sleep.

~surprises~

~Lycoris radiata, Surprise Lily~

~~~~~

I love these lilies.  Each year I completely forget about them - and then one day in late August there they are, simply stunning, a pleasant surprise while in the midst of the late summer doldrums.  I think I need to plant more of them - in order to have more surprises at a time of year when the heat has beaten me down.

~~~~~

It's that time of year when we watch for storms along our coast - but so far this year we've watched them off our shore, racing north.  Yesterday was a beautiful day - because even though 'Danny' didn't come all that close to our shore, it's winds nonetheless cleared our skies and left them blue and breezy. 

~~~~~

Well, the Microbial Lab lost another member this week - a lover of all things zombie and data-driven.  He often sends me random emails late in the evening - like one that said how bummed he was that his dream doctoral project had been taken already.  The lab gathered Friday evening to wish him well before he heads to a job in the upstate at Clemson University - he packed up this morning and left this afternoon.  His new position is a good one - and with someone that I enjoy working with - and thankfully he plans to still work with us our much anticipated website, CoralMicrobes.org.  Sometimes I think I'm not meant for this transient type of work - essentially when my job is done, it means that a person is meant to move on.  I suppose the upside of this is folks scattered all around the country - I have to keep reminding myself of this.

~~~~~

 I'll end with an update of the Microbial Lab's mission (first mentioned here) - updates to 'the list' are in bold:

1. work describing a coral pathogen and the role of motility (led by our collaborators from Israel): Published (read abstract here).
2. work describing metabolites produced by a coral pathogen (led by local collaborators): In press. Yay!!! 
3. work describing genes involved in nutrient cycling in coral microbial communities: In review.
4. work describing the toxicity of Zn-containing nanoparticles to a much-loved bacterium: In review.
5. work describing the upper respiratory tract bacterial communities of bottlenose dolphins. In press.
6. work describing the presence of a certain coral pathogen in the Caribbean:  In review.
7. work describing the proteome of a certain coral pathogen at two different temperatures:  In internal review.

~~~~~

~wild dolphins~

~the new South Carolina 'Protect Wild Dolphins' specialty license plate~

~~~~~

I've never been someone who thought about their license plate - or the license plates of the cars on the road around me.  In fact, it's always baffled me a bit that anyone would care enough about their license plate to pay extra for one...until now.

According to the Protect Dolphin website:

 ...the funds generated from the sale of the plate will be used by EarthEcho International, Inc. for scientific and educational programs that serve to restore and protect the ocean environment and freshwater systems that sustain life on earth and to protect the sentinel species – wild dolphins. Some of the funds will be utilized for continuing promotion and marketing of the license plate. The remainder of the funds will be used to collect, analyze, and archive scientific data regarding the wild dolphin population in South Carolina waters when providing care and assistance to stranded wild dolphins; distribute information to the local scientific community, federal, state, and local government agencies, educational institutions, and all South Carolinians for the purpose of protecting and preserving wild dolphins.

~~~~~

The Microbial Lab, which is quite obsessed at the present time with dolphins and the microbiota in their upper respiratory tracts, oh, lets face it - their microbiota all over - is quite delighted about anyone or thing that promotes funding for research to protect and preserve us wild dolphins.

As part of this new license plate's 'coming out' party, there's a special showing of the documentary 'The Cove' - see below.  I'm planning on attending the 5:30 show.   

~~~~~

~~~~~