Tales from the Microbial Laboratory

~a native, minor edits, and a tomato-eating pointer~

~Coralberry, Symphoricarpos orbiculatus~

~~~~~

Last October I added this US native to my garden - it's called coralberry, I've also seen it called Indian currant.  The leaves and berries are small, much smaller than beautyberry - but it's still quite pretty.  I might move where I have mine - I think it would look better in another part of my yard (where I have some yellow anise, native azaleas, and camellias), and not in a perennial border.  Yes, I'll definitely move it this fall.

~~~~~

It was another beautiful day along this part of the coastline - the kind of day that makes you want to just stand in the middle of the garden, arms spread out, feeling the breeze.  It was a good day around the Microbial Lab too - reviews came back on a student's manuscript, and the edits were extremely minor.  It's a manuscript that I'll be excited to have published - it's a solid contribution to what we know about nutrient cycling by coral-associated microbial communities.  And minor edits are always a relief!

~~~~~

I also learned something very important today.

The new old dog, Annabelle Lee, has been eating my cherry and paste tomatoes.  Right off the vines.  I have one 'Big Mama' and one 'Sungold' in pots - and I just had a second flush of Sungold cherries on the vine.  They were just starting to get ripe...and then they were gone.  I was blaming just about every animal I could think of but my dogs.  Damn those squirrels!  And the racoons...OUT!!  Yet this afternoon, there she was, carefully biting each tomato from a cluster right off the vine.  Damn that Annabelle Lee!  Not my tomatoes!!!!

~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. 

~a thank you to Annie~

~Thunbergia grandiflora, blue sky vine~

~~~~~

The late September garden is filled with flower vines - the perennial morning glory has finally decided to bloom again (and again and again...) - the cypress vine (Ipomoea quamoclit) is starting to reach up to the first branch of the nearby live oak tree - and the blue sky vine is starting to bloom on the front fence (and climb the nearby ash tree, climbing the trunk almost to the top).  I love Autumn in the southern garden, it's as if all of the garden's occupants do one big exhale, and start to grow once again.

~~~~~

I need to say a big thank you tonight to Annie in Austin of The Transplantable Rose fame.  She kindly suggested my name to Associate Editor Michelle Gervais at Fine Gardening - which resulted in my writing a small piece for their Regional Reports on 'Three Garden Wishes' for my own southeastern garden (November/December 2009, Issue Number 130).  It was alot of fun to write - and so, thank you Annie, and thank you Michelle for letting a microbiologist-by-day rant about florida betony in Fine Gardening magazine.  It was a thrill.  

~late evening distractions~

~a palm~

~~~~~

Last November I visited Sunken Gardens in St Pete - a wonderful garden hidden in the middle of a busy part of the city - and tonight while wandering outside with the dogs I suddenly thought about the images of the tree trunks that I took there.  I loved the images - the colors and the texture and the diversity - the one above, of a palm tree, was one of my favorites.  I couldn't resist digging it out tonight.

Isn't nature amazing?

~~~~~

Science Photo Blog

Science Photo Library

The Science Photo of the Day

And look at this from the Smithsonian photography blog The Bigger Picture...a post on Conservation and Chrysanthemums.

~~~~~

Fun distractions, these sites.  Especially after a busy day - meetings, abstracts to edit, one (unfinished) manuscript entering internal review, reviews back on another, and yet another one with a looming deadline.  A practice run through of a seminar for a student's big day - his doctoral dissertation defense.  Dogs that need to run, a garden that begs for attention...I love life's distractions.  Amidst all the rest. 

~self-explanatory~

~weeds, weeds, and more weeds~

~a song from down the street~

~Ipomoea indica, oceanblue morning glory~ 

I spoke too soon about this morning glory a week or so ago - it's on my front fence, attracting a county's worth of cotton aphids (and not looking so good in the process) - and so what does it decide to do?  Bloom like a crazy thing.  What a pleasant surprise.

~~~~~

I enjoyed hearing today that someone from my very own neck of the woods won 1st place in the Coastal Conservation League's 'Music with a Message' contest.  Very cool.  Corey Webb will be playing this Saturday during the SC Green Fair at Marion Square.  Here's his winning song, titled 'Coastal Conservation Coconut'.

~~~~~

~a mood~

~moss on a clay pot, in grayscale~

You've had those days, those funky-wish-it-would-rain all day days, when your battery on the cell goes low and you let it die for awhile, because your mood is even boring to yourself so why would you want to bore someone else?  One of those moods where you feel the opposite of 'light' and would hate to have your mood infect an otherwise beautiful late September day.  What ashame that would be!  So instead of washing your hands a million times (for fear of transferring this mood to others) you choose not to attend a festive gathering that included a pinata and a trip to watch a roller derby match (are they called matches?  does anyone know this?).

The Microbial Lab's Poet Laureate emailed me that a line in the play she saw last night - 'A Year of Magical Thinking' - reminded her of me:  "getting nibbled to death by ducks" and I thought 'Wow!  She's right' and then... 'How horrible is that?'  My dysfunctional work situation is now beyond bizarre and if I could explain it to you I would - but then I'd bore you...and there's no point in that tonight.  Luckily a few others have decided to carry the torch for awhile - and with much gratitude I will let them.  I'm exhausted and crave quiet and happy dogs and a growing vegetable garden and no storms out in the Atlantic.  I want to sit and listen to Bebel Gilberto sing - a voice that a good friend recommended to me earlier today and by God he's right, she's good - really good.  So instead of infecting you with my boring nonsense, I'll share a bit of Gilberto with you.

~~~~~   

~finally, some time spent in the garden~

In my self-imposed, poorly orchestrated attempt at reducing my plant budget (you know, the whole life during wartime thing), I've been on a propagating rampage.

My latest round of propagatees - lovely little cuttings - have been remarkably successful.

I would share with you what they are - that is, if I had a clue.  All I know is that I snipped them from lovely plants that were new to me - either because of interesting flowers or foliage, and I suppose my hope is that most of them are perennials.

I enjoy propagating plants - it's quite rewarding.  I think I had forgotten that.  Silly me.

~~~~~

Finally, this afternoon, I forced myself into one of my vegetable beds - after promising myself that I was going to have a productive fall vegetable garden...come hell or high water.

(It's hurricane season - so the whole 'high water' thing isn't one of those long-range possibilities).

There were weeds, more weeds - and still more weeds.  I'm a 'no-till' fan, so I was out there with my pitch fork, turning over the soil - picking out the weeds as I went.  Long strings of white dollar weed roots, secret stashes of Florida betony, and wild morning glory winding around stalks of grass.  The bed was quite a mess.

Anyway, my plan is to plant alot from seed - but I did purchase a pot filled with cilantro - that today I divided into three and planted.  Then I mulched around them with a bale of hay that I had sitting around for a long while (all the better!).

What else did I plant?  Six beautiful little chinese cabbages (aka bok choy) - also from one pot and divided.  Then asian greens and brocolli and brussel sprouts (mostly from seed) - other lettuces too.  I want to also get onions in too - and garlic in a few weeks.

I feel good, knowing that my fall vegetable garden is started.

~~~~~ 

I also put my foxglove in the ground - grown from seed, started by a colleague and given to me in a few small soil plugs.  I separated them - and placed them into individual small pots - and had good success with them. 

I still need to mulch them - but I did get them in the ground and watered.  I'll try and remember to mulch them tomorrow.

I wish I had planned ahead, and started more seedlings - but this little patch of them will have to do - at least this year.   

We've been having rain in the forecast for several days now - but no rain is falling on my garden.  We're having a dry late summer.

~~~~~

Bergenia cordifolia 'Autumn Glory'

Planted right into an area of grass - more weeds than grass - and tomorrow I'll mulch them (back to the whole no-till thing).  It was one pot and I divided them into three small clumps, and planted them at the edge of a larger bed, adjacent to a mulched path surrounding a vegetable bed.

I've not grown Bergenia before -- and must admit I'm a bit confused.  According to the 'Proven Winners' tag that came with the plant, it's a zone 4-11 perennial.  However if you go to the Proven Winners page for this plant, it's zone 4-9.  The Dave's Garden page for 'Autumn Glory' says it's zone 4a-7b.   

Huh?

My garden is definitely an 8b warming to a 9 - so 7b isn't gonna work.

So please allow me to end with the lyrics from a song perfect for the ocassion:

Does anybody really know what zone it is?
Does anybody really care??
If so, I can't imagine why...

La, la, lalalalaaaaaaaaaaa...

~~~~~

~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)