Tales from the Microbial Laboratory

~crackling~

  

Last Monday evening in Virginia, the view of the sunset from my Father's backyard was spectacular:  streaks of pink raced across the sky, broken up by the blue sky of a cold winter's day.  Then on Tuesday morning I joined the masses on I-95, driving south to warming weather - today was in the 60s and tomorrow should top 70.  The warmth is nice.

The holiday was a challenging one.  Things I won't go into here; troubling family issues.  They mostly make me sad.  Returning to my little Airstream life seemed quite sane and manageable - as it is.  I applied for a job yesterday that I'm actually interested in, and that is actually interested in a more senior scientist.  That was optimistic.

I spent some of the day today putting together a mental 'wishlist' from Plant Delights Nursery and Select Seeds - only a mental list, mind you.  I picked up a scattering of small branches spread around the garden - looked to see how damaged the camellia buds are from the unusually cold December we've had.  I purchased a wedding gift (for a New Year's Day wedding that I am attending).  I laughed at the Pointer Sisters - running around like crazy things, digging their new sweaters (yes, for the first time in my life I have purchased clothing for dogs).  I examined the broccoli up-close - I'm not sure that it will do much.  December was just too cold. 

Yes, it's time to burn the old year - it's gone, up in flames, it's crackling.  I shouldn't be glad perhaps, but I am.

~~~~~~

Burning the Old Year by Naomi Shihab Nye (from The Poetry Foundation)

 

Letters swallow themselves in seconds.   

Notes friends tied to the doorknob,   

transparent scarlet paper,

sizzle like moth wings,

marry the air.

 

So much of any year is flammable,   

lists of vegetables, partial poems.   

Orange swirling flame of days,   

so little is a stone.

 

Where there was something and suddenly isn’t,   

an absence shouts, celebrates, leaves a space.   

I begin again with the smallest numbers.

 

Quick dance, shuffle of losses and leaves,   

only the things I didn’t do   

crackle after the blazing dies. 

~the ritual of living~

~pieces of greenspire cypress, flower heads of Hydrangea arborescens 'Annabelle', invasive chinese privet, popcorn tree seed pods, a few rose hips, and long shoots of an Elaeagnus species as the frame~

~~~~~

Another front gate wreath, thrown together at the last minute with what looked interesting around the garden... a  wreath that has become an unpredictable ritual of my holiday season.  I put it up the day evening before I left town - in the light of late evening.

I'm still in Virginia, after having spent the past two days here cooking and baking obsessively (when all else fails, cook - right?)... sweet potato biscuits, a fresh apple cake, yeast rolls, a turkey and a whole bunch of side dishes.  Almost all of the recipes chosen from my Mother's book of recipes.  On Christmas Eve my brother and I took a tour of an Assisted Living facility - in anticipation of our Father's future (and trust me, nothing says 'Merry Christmas Eve' like touring a dementia care ward).  I keep telling folks about my new favorite quote... "life is messy" and boy, that sums it up, doesn't it?   Messy and snowy - yes, snow is falling on this Christmas night.  A few inches expected.

Here is a wonderful poem by South Carolina Poet Kwama Dawes.  I find him getting more amazing with each poem -- and this one is rich in resonating phrases -- "...find the howl of the spirit", "...the warm healing of anger", and "...find the ritual of living".

Yes, finding the ritual of living - that's important, don't you think?

Happy Holidays All.

 

Talk
by Kwame Dawes

            For August Wilson

No one quarrels here, no one has learned
the yell of discontent—instead, here in Sumter
we learn to grow silent, build a stone
of resolve, learn to nod, learn to close
in the flame of shame and anger
in our hearts, learn to petrify it so,
and the more we quiet our ire,
the heavier the stone; this alchemy
of concrete in the vein, the sludge
of affront, until even that will calcify
and the heart, at last, will stop,
unassailable, unmovable, adamant.

Find me a man who will stand
on a blasted hill and shout,
find me a woman who will break
into shouts, who will let loose
a river of lament, find the howl
of the spirit, teach us the tongues
of the angry so that our blood,
my pulse—our hearts flow
with the warm healing of anger.

You, August, have carried in your belly
every song of affront your characters
have spoken, and maybe you waited
too long to howl against the night,
but each evening on some wooden
stage, these men and women,
learn to sing songs lost for centuries,
learn the healing of talk, the calming
of quarrel, the music of contention,
and in this cacophonic chorus,
we find the ritual of living.

 

...another champagne bottle signed!

 ~Nikole, The Microbial Lab's newly minted Ph.D.~

~~~~~

 Last Friday, a doctoral student in my lab defended her dissertation - always an exciting day - except that the morning of the defense I came down with the illness from hell.

Yep, sick as a dog.

(With nothing bad intended towards dogs, I mean, as you all know - I like dogs alot).

The defense wasn't until the afternoon (3 pm) - so in the morning, I was in denial that I wasn't up to standing for any length of time (much less was I up to getting dressed, looking acceptable for public viewing, driving, or sitting upright during an hour long seminar).  So during this period of denial, another committee member (who was conferencing in from Maryland) contacted me that she was unable to do so - and so I was a bit stressed, wondering if I should postpone the defense.

[But...I knew that postponing the defense would have been cruel.  Unusual and cruel.  And in my feverish state I kept thinking (rather hilariously) to myself:  "I can't postpone.  Nikole is a Virgo."]

Now, we all know that astrological signs don't generally come into play during defenses, but it had become something that Nikole often used to explain her pathological need to get things done not only on time, but early.  And she was into lists, and checking things off her lists.

So her list for Friday:

(1)  defend dissertation

How could I postpone that?

 I was in denial until early afternoon.

I also couldn't keep down water, couldn't sit upright for more than a few minutes, and was thinking an awful lot about astrology, which was a bit out of character for me.

So - I did what I didn't want to do (and had never done before):  I participated in the defense from the comfort of my 1973 Airstream home.  Fortunately we had already set up a web meeting program, and had a call-in number - one committee member was already conferencing in from Australia.  I got approval to have the Maryland committee member talk with Nikole the following Monday... and at a few minutes before 3 pm I called in - and introduced my graduate student to an audience of about 40 folks over the phone.  Now, I will say it was weird introducing her over the phone - but I also had to laugh at myself, because I think I did a better job than I normally do.  When I am present, I tend to downplay introductions - because I think 'they want to hear him/her, not me' - so I end up doing a lame job.  But because I felt a little strange doing it over the phone via distance, I put a bit more thought into it... and had to laugh when my student Maria said it was the better than most of my introductions.

So for a hour-long seminar, and a two-hour defense afterwards, I sat in the Airstream at my computer with phone in hand.  The end result:  I didn't have to rush out of the auditorium to vomit during her talk (I could do it in the privacy of my own Airstream) and Nikole got to check off the one thing that was on her list for last Friday.

The next evening I was feeling a bit better - and went to her home where she and a small gathering of friends toasted to her accomplishment.  Then, in a Microbial Lab ritual, she signed the ceremonial bottle of champagne with her name and the date of her defense.  The bottle will join the others in my office - a symbol of a successful day that represented years of hard work and dedication.

I always get teary eyed during my students' defenses.  Even in the Airstream, as I listened to her seminar - tears welled up.  Maria and Nikole have behaved with such integrity over the past year, during this wartime year, and the respect that I have for them is beyond words.  They are both good scientists, but they are even better human beings.

Gifts for that Special Microbiologist on your List, The 2010 Edition

 
~Carbon (top image) and phosphorus (bottom image) associated with a single cell of Burkholderia vietnamiensis PR1₃₀₁, obtained at the Advanced Photon Source by the Microbial Lab~

~~~~~ 
 
  Yes, it's that time again that you've all been looking forward to - the annual release of the 'Gifts for that Special Microbiologist on your List, The 2010 Edition'!  If you're catching up, please take a look a prior years to see what all of the fuss is about... I try not to overlap (or at least much) from previous years - so check out lists from the years below to get some additional ideas.

• 2009
• 2008
• 2007
• 2006

And before I go on - please remember that all microbiologists, well, at least most microbiologists, have been very good this year.  So now... let's jump right in!

~~~~~

 
~Coral Reefs in the Microbial Seas by F. Rohwer with Merry Youle (2010)~

From their website:

For millennia, coral reefs have flourished as not only one of the planet's most magnificent ecosystems, but also as its most biodiverse. However, since the 1980s the corals have been struggling. Both coral bleaching and disease have spread globally. During recent research expeditions to the remote Line Islands, microbial ecologist Forest Rohwer and his colleagues found that the large-scale changes to the reefs in recent decades are the work of the microbes as they respond to various human impacts. Coral Reefs in the Microbial Seas is the first book to recount this story, complete with introductions to the coral reef ecosystem, 21st century metagenomic research tools, and the coral's microbial and viral partners. An engaging book, its science is liberally spiced with artistic illustrations and playful stories from the research expeditions.

The perfect book for that adventuresome marine microbiologist in your life! 

 ~~~~~

 
~The Fatal Menace of MRSA Superbug by Maryn McKenna~

Is there someone on your list looking for a little microbial reading that will keep them up at night?  Then this book is just the thing.

~~~~~

What special man in your life doesn't dream of having a 'I love Microbiology' necktie?  (And if he doesn't dream of having one, then you might want to reconsider your relationship...).

 ~~~~~

What about a 'Trust me, I'm a Microbiologist' button?  The perfect stocking stuffer I'd say, or perhaps a festive addition to your holiday package wrapping paper and ribbon?

~~~~~

 
Who doesn't want a Gift Box of Mini Plush Microbes?  Now, the big decision is whether your Microbiologist would want the collection that includes Spermatozoon, Human Ovum, Epstein-Barr Virus, Amoeba proteus, and Penicillium chrysogenum (Set 1) or Herpes Simplex Virus 2, Treponema pallidum, Human papillomavirus, Chlamydia trachomatis, and Pennicillium chrysogenum (Set 2).  Or perhaps they want both?  The perfect microbial stocking stuffer I'd say.

~~~~~

 
~Cyanobacteria asymmetric necklace in green agate~

I've mentioned Arctida's work on Etsy before (her rabies virus garnet pendant necklace) - but this year I came across this lovely necklace.  Here is Arctida's description of the piece:

The pendant in this necklace is totally made from scratch using various gauges of sterling silver wire. The frames were meticulously coiled with micro-faceted Emerald Green Agate rondelles. The necklace fastens with a lobster clasp and extension chain, which I've finished off with a single Green Agate rondelle.

Also - go and take a look at Arctida's Streptococcus pneumoniae asymmetric necklace.  [And don't forget to check out her 'science talk' that accompanies it's description (charming, don't you think?)]:

Streptococcus pneumoniae is a normal inhabitant of the human upper respiratory tract. S. pneumoniae can cause pneumonia, as well as infections in other parts of the body such as in the bloodstream (bacteremia), lining of the brain and spinal cord (meningitis), bones (osteomyelitis), joints (arthritis), ears (otitis media) and sinuses (sinusitis). Usually, they are seen as pairs of cocci (spherical or spheroid shape), but they may also occur singly and in short chains. The primary virulence factor (or in other words the ability of a microbe to cause disease) of pneumococci is their polysaccharide capsule (which can be seen as a "halo" around the cells on the last pic). It is non-toxic but helps bacteria to evade the host immune cells.

~~~~~

 
~green and orange amoeba necklace~

What about this lovely amoeba necklace?  There's this one - and other lovely options - over at starvingartistbazaar's Etsy webpage.  Go check them out.

~~~~~

 
~microbial coin purse or gift card holder~

  Check out FruteJuce's coin purse over at Etsy.

~~~~~

 
~Louis Pasteur linocut~

Is there a Louis Pasteur fan on your gift list (and how could there not be)?  Check out Minouette's Etsy webpage - and this Louis Pasteur linocut.

And don't forget to take a look at these wonderful fused glass Louis Pasteur cufflinks by minijean3 or this original ink and watercolor drawing of Louis Pasteur by davidrcollier.

~~~~~

 
 ~Tuberculosis virus from Vintage French Medical book cufflinks~

What microbiologist doesn't need a pair of tuberculosis or tetanus cufflinks?  Or this incredible vintage microscope pendant?  spiffycool has a fascinating collection of cufflinks, pendants on etsy - all Scrabble tile creations.  Spiffy indeed...

~~~~~

 
~swine flu scarf~

Infectious Awareables has always been a favorite of mine.  So what about this swine flu scarf for her, and the matching swine flu necktie for him?  The perfect gift for that microbiologist-couple in your life (although, really, if they do wear them - at the same time - you might want to start worrying just a bit...).

~~~~~

 
~microbial Rita Hayworth~

Now go check this out:  FamousMicrobal's Microbial Rita Hayworth.  Pretty fun, huh?  There's also a Microbial Tim Leary, Microbial Klaus Nomi, Microbial James Dean... pretty unique gift I'd say.

~~~~~

     
~Microbes~   

 From carlacrafts - this wonderful acrylic and mixed media (sand) on vinyl piece (48"x48").  Also check out the piece titled 'Microbes Study" (watercolor and mixed media on watercolor paper).

~~~~~

 
~Under the Microscope 2 original watercolor~

Check out Articlogica's Etsy page - and gorgeous collection of microbial watercolors.  Under the Microscope 2 and more...

~~~~~

 
  ~image of bacteria growing on agar by Amy Chase Gulden~ 

   Now - for something really fun and different.  Head over to Growing Impressions, and take a look at their bacteria prints and cyanotypes.  Bacterial paint - pretty cool, eh?  I'm not exactly sure if these are for sale - but you can inquire using the email address at the bottom of their Welcome page.  They have a blog as well - so you might want to take a look there as well.

(And go take a look at this piece on Alexander Fleming's 'germ art'... on don't forget to browse the gallery over at Microbial Art.)

~~~~~

 
~Bacteriogram by Erno-Erik Raitanen~

      I've mentioned Erno-Erik Raitanen before - and his exquisite bacteriograms.  But since I last looked at his website, he's added some new pieces - so go and take a look.  (And read a little bit about his process here).

~~~~~

Now, maybe you have a microbiologist friend that you just want to infect with an addictive online game - so why not Microbe Kombat?

~~~~~

Now, your microbe-lovin' friend may just want some quality time with you... yes, that is possible you know.  So why not take a look at the Nikon's Small World Photomicrography competition website - and then plan a visit to one of places participating in the Nikon Small World Museum Tour?  I think that would be a lovely gift - and I can't imagine a microbiologist that isn't just dying to see one of the Small World exhibits.

~~~~~

As for this microbiologist, any of the vintage microscopes from this site will do...(hint, hint) - I've mentioned these before, and still think they're beauties for sure.  I hope this updated list for 2010 helps you shop for those difficult (and not-so-difficult) to shop-for microbiologists in your life - whom I'm sure have all been very, very good this year.

And finally - best wishes for a Happy Holiday Season from the Microbial Lab!    

(ps  As always - if you've come across anything else new and interesting that you think belongs on this list - please leave a comment or email me - I'll definitely include it.).       

~a book of family recipes~

 
~Mom's Book of Family Recipes~

~~~~~

Well, I finally finished it.

Shortly after my Mom passed away, I gathered all of her recipe boxes (yes, boxes) and I started talking with family members about their favorite recipes.  Mom was a wonderful cook - and a generous one - and our household was one in which it was the rare visit to not be offered a slice of homemade pound cake as you walked in the door, or given a glass of freshly brewed iced tea before you sat down - and almost everyone was asked if they wanted to stay for dinner - there was always enough to go around, and sometimes it felt like Mom waved a magic wand and an abundance of dishes appeared.  She was one of those effortless cooks, at least the effort wasn't something she made a big deal of.

I started working on a book of her recipes two years ago through the photobook website Shutterfly.  She passed away on 15 April 2008.  I started tossing in family photographs, especially photographs of her last year - our Mother's Day dinner at the Trapp Family Lodge in Stowe, Vermont, Mom at the stove with my brother demonstrating the correct way to make gravy from turkey drippings, a photograph that I took during Christmas of 2007 of the last fruit cake she made.  I included photographs of her and my Father's wedding, of her decorating Easter Eggs with my niece (her only grandchild) and of my Mom, my niece and I celebrating my niece's 16th birthday with a german chocolate cake my Mom made.  The recipes range from jello salads that my Mom used to make when we were young, the Christmas cookies of our childhood and the cakes of our adulthood, my Mom's favorite chicken-broccoli casserole and my Dad's favorite Whoopie Pies.  Each recipe represents a dozen or more family stories - memories tossed in with the ingredients, mixed thoroughly and baked until a cake tester comes out clean.

At the end of the book, I wrote about the compliment given my Mom by one of her sisters.  She said that if everyone my Mom had made a cake for over her 74 years of living came to her funeral, that the funeral would be filled to overflowing (and it was).  I can't tell you the number of times that my brother, father and I were told "Don't touch that!" as a hot pound cake, german chocolate cake or coconut cake came out of the oven.  "It's for someone else."  During the first Christmas after she was gone, I went to Virginia and all I did was bake cakes for all of the people that I knew Mom would want to have one - from early morning to late at night I obsessively baked cakes, trying to fill her absence by filling cake pans and plates.  To this day, I feel closest to her when I am baking a cake for someone other than myself.

When I returned home today from the lab, there at the gate was a box filled with 15 copies of my Mom's Book of Family Recipes.  It's 75 (front and back) pages and contains 50 family recipes.  It's bound in brown leather - and the 'cover' photo is of my parent's dining room table, partially ready for Thanksgiving dinner in November of 2007.  I like the simplicity of the table - only the china had been set, there were no glasses or flowers or food dishes placed on the table yet.  Outside the window you can see the late Autumn brown leaves of the English oaks that surround the house.  But soon after the china was placed on the table - flowers were added as a centerpiece, other family members arrived, and dishes magically and effortlessly appeared (even as cancer was metastasizing throughout Mom's body) - and dinner was served.  It was lovely.

~~~~~

 
~Mom's favorite Baked Praline Popcorn~

Store in an air-tight tin after preparing.  Mom would make it at Christmas - and often prepare bags of it for Trick-or-Treaters at Halloween.

~~~~~

Yellow Sulphur Springs

 
~Yellow Sulphur Springs Hotel, Montgomery County, Virginia~

From the Virginia Tech ImageBase:

Built in 1888 and torn down in 1944. Contained 60 rooms, with a ballroom, a dining room, a billiard room, a system of water works, hot and cold baths, and other facilities of the day for the comfort and pleasure of the guests.

~~~~~ 

When I was an undergraduate at Virginia Tech, in addition to the science courses I took each semester, I'd often take a class in the Art Department.  Drawing, watercolors - a photography class in the Architecture Department - I always took them with an incredibly talented friend who was majoring in Art.  One of my favorite memories from those days was when our watercolor instructor, Ray Kass, would take the class out to Yellow Sulphur Springs to paint.  I remember on one of the first days of class when Kass told us to paint and paint like crazy, and that we'd then throw away our first 100 or so paintings.  I remember how remarkably freeing that was - to just paint, fast or slow, it didn't matter - we were just told to paint.  After that, we start over, and begin painting again. 

~~~~~

But the reason for this post is only indirectly about watercolor class, and painting at Yellow Sulphur Springs.  It's really about friendship, rich friendships - and how when artist friends and music friends stay in your life, that it is a very wonderful thing.

~~~~~

On the Yellow Sulphur Springs property, there used to be a bowling alley, dating back to the 1870s, all in wood - the walls were braced and in decay, the lane warped, but at the end of the lane the wooden pins were perfectly placed - as if someone were expected to show up at any moment with a ball and try to knock them all down.  One could only imagine the games that were played on this tiny open-air bowling alley, tucked away in the folds of Montgomery County, Virginia. 

 

 But back to friends and friendship...

Last September when I was staying with my Father for a longer than usual visit, my artist friend began scanning in, and posting on Facebook, photographs from our undergraduate days at Virginia Tech.  As I struggled with the care of my father (and even more so, with my own impatience), periodically I'd get 'tagged' in another photograph - bringing back memories of a simply near-perfect time in my life.  Those photographs carried me through the visit - and I ended up joining in, finding photographs from those days that were stored safely in my father's home.     

 

One photograph that I scanned in and posted on Facebook was one of the bowling pins sitting at the end of the bowling alley at Yellow Sulphur Springs - as well as one of a longer view of the alley itself (above).  Shortly after this time, another friend - my music friend and occasional contributor to this blog (the "3D Sound" category) - also joined Facebook and saw this image.  It seems that he had taken a photograph of me taking a photograph of the bowling pins - and scanned in his image and posted it on Facebook.  He also wrote about this, in his own blog 3Dsound: Draggin' the Line - you can read his post here.

 I love this story, and I love my artist friend that led me to this place - and my music friend for joining me on an autumn day to capture these images of a special place.  My artist friend said that the bowling alley is long gone now (she's still in touch with  Ray Kass).  However, the Yellow Sulphur Spring website says that the spring is 'still flowing and mineral rich' and still surfaces in a gazebo in the middle of the property.  For me, this place will always symbolize an abundance of flowing riches - mineral and otherwise. 

Belfield Rose

 
~Belfield rose (considered the ancestor of modern red roses, obtained from Ruth Knopf)~

(color image and and information on Belfield Roses found at this 12 May 2006 post).

Mutabilis

 
~Mutabilis (Prior to 1894 China)~

(another view of Mutabilis in Black & White). 

Mermaid

 
~Mermaid (1918, Species)~

Persimmons

 

 

Persimmons by Li-Young Lee

In sixth grade Mrs. Walker

slapped the back of my head

and made me stand in the corner   

for not knowing the difference   

between persimmon and precision.   

How to choose

persimmons. This is precision.

Ripe ones are soft and brown-spotted.   

Sniff the bottoms. The sweet one

will be fragrant. How to eat:

put the knife away, lay down newspaper.   

Peel the skin tenderly, not to tear the meat.   

Chew the skin, suck it,

and swallow. Now, eat

the meat of the fruit,

so sweet,

all of it, to the heart.

Donna undresses, her stomach is white.   

In the yard, dewy and shivering

with crickets, we lie naked,

face-up, face-down.

I teach her Chinese.

Crickets: chiu chiu. Dew: I’ve forgotten.   

Naked:   I’ve forgotten.

Ni, wo:   you and me.

I part her legs,

remember to tell her

she is beautiful as the moon.

Other words

that got me into trouble were

fight and fright, wren and yarn.

Fight was what I did when I was frightened,   

Fright was what I felt when I was fighting.   

Wrens are small, plain birds,   

yarn is what one knits with.

Wrens are soft as yarn.

My mother made birds out of yarn.   

I loved to watch her tie the stuff;   

a bird, a rabbit, a wee man.

Mrs. Walker brought a persimmon to class   

and cut it up

so everyone could taste

a Chinese apple. Knowing

it wasn’t ripe or sweet, I didn’t eat

but watched the other faces.

My mother said every persimmon has a sun   

inside, something golden, glowing,   

warm as my face.

Once, in the cellar, I found two wrapped in newspaper,   

forgotten and not yet ripe.

I took them and set both on my bedroom windowsill,   

where each morning a cardinal

sang, The sun, the sun.

Finally understanding   

he was going blind,

my father sat up all one night   

waiting for a song, a ghost.   

I gave him the persimmons,   

swelled, heavy as sadness,   

and sweet as love.

This year, in the muddy lighting

of my parents’ cellar, I rummage, looking   

for something I lost.

My father sits on the tired, wooden stairs,   

black cane between his knees,

hand over hand, gripping the handle.

He’s so happy that I’ve come home.

I ask how his eyes are, a stupid question.   

All gone, he answers.

Under some blankets, I find a box.

Inside the box I find three scrolls.

I sit beside him and untie

three paintings by my father:

Hibiscus leaf and a white flower.

Two cats preening.

Two persimmons, so full they want to drop from the cloth.

He raises both hands to touch the cloth,   

asks, Which is this?

This is persimmons, Father.

Oh, the feel of the wolftail on the silk,   

the strength, the tense

precision in the wrist.

I painted them hundreds of times   

eyes closed. These I painted blind.   

Some things never leave a person:

scent of the hair of one you love,   

the texture of persimmons,

in your palm, the ripe weight.