How to get a single cell

The key to my summer research is isolating a single bacterial cell.  There are a variety of ways to do this.  The primary way my lab does this is by micromanipulation -- that is, physically picking up a single bacterial cell and moving it away from everything else.  Micromanipulation is done using a manipulator attached to a microscope.  Here's one of the micromanipulators in lab:

If you look carefully just slightly above and to the left of the microscope stage, there's something that looks like a metal rod.

micromanipulator with capillary tube

That is the micromanipulator.  At the end of the rod is a very small glass tube called a capillary tube.  The tube is attached to a hollow rod that filled with first air and then further up oil.  The rod then continues as tubing that comes over to the left side of the microscope.  On that side, you can see a much bigger tube, a pump, with a knob on the end.

the pump

That pump allows you to change the pressure inside the capillary tube.  What this means is that if you turn the knob one direction, you can pull liquid into the capillary tube.  If you turn the knob the opposite way, liquid is expelled.  Basically, that thing is a very carefully controlled straw.

So the micromanipulator can suck up things.  But only very small things since the capillary tube is so small.

Next, how do you select what to suck up?  The manipulator can be moved around the stage of the microscope using a joystick.

the joystick

Yes, its just like any video game joystick.  With the joystick, you can move the micromanipulator in three dimensions. 

Let's put this all together.  On the microscope stage, you put a small puddle of liquid with the broken up termite gut.  Then you move the micromanipulator so that the capillary tube is positioned just next to the cell you like.  Next, you turn the knob on the pump and suck up your cell.  Finally, you move the micromanipulator to a clean puddle and drop your cell down.  Repeating this process a few times with the same cell washes it clean.

Your cell is then ready to have its DNA played with! 


The big and small of Tokyo!

Tokyo Tower

Sky Tree from Tokyo Tower

performer monkey

lake in my neighborhood

Imperial Palace grounds

Meeting my termites and their microbes

Straight from Okinawa:

Nasutitermes takasagoensis

 This is, of course, the wood eating termite.

At the very top of the plate, there's the termite!

Unfortunately, the soil eating termite, Percapritermes nitobei could not be caught.  So my work this summer will be restricted to analyzing the gut bacteria of N. takasagoensis.

To get at the gut microbes, the first thing I learned in lab was how to dissect out their gut.  Here's the procedure:

1) Hold termite with tweezers by the section between the head and body.

2) With a second tweezers, pull off the head.

Removing the head is a quick way to kill the termite and keep it from moving around...

3) Turn the termite over and hold it by the butt end.

4) With the other tweezers, carefully and very slowly pull on the outer cuticle. 

5) If all goes well, the gut will remain whole and the outer cuticle will come off.

Here's my first dissected gut!

The dark spot at the top is the biggest section of the gut, the P3 region.

To look at the microbes, all you do next is rip apart the gut and look under the microscope!

Next up, micromanipulation!



Photo shoot of four different districts of Tokyo:

Shinjuku

Shibuya

Akihabara

Ueno

Week 1 Slide Show!

I have finished the orientation for my program in Japan.  Last week I had 11 hours of Japanese language class and now I can speak a little Japanese! 

My orientation included lectures about Japanese science and culture.  My two favorite lectures where on traditional Japanese music and on the history of genetics in Japan.

instruments from left to right: koto, shamisen (or sangen), shakuhachi

 I tried to play the koto... and failed.  It is very hard!

During the lecture, we heard pieces that ranged from very traditional to more modern.  The most modern piece was in the western style of variation on a theme.  To my western ear, it was definitely the most enjoyable (as well as the most complex!). 

During the lecture on history of genetics in Japan, we learned that genetics in Japan grew out of wheat genetics.  Science in Japan is marked with feeling extreme pressure to "catch up" with the western world.  Language as well as politics have been barriers in this regard.  Today, Japan is well recognized in science and many international meetings are held there.  Later this summer in Kyoto, I will attend an international meeting for evolutionary biology.

Over the weekend, I had a home stay with a family living in Yokohama.  We visited a variety of sites in Kamakura and Tokyo.  Here are a few of my favorite shots!

Meigestsu-in Temple, Kamakura

Zeniarai Benten Shrine, Kamakura

Kamakura

Daibutsu, Kamakura

Meiji Shrine, Tokyo

Meji Shrine, Tokyo

Yoyogi Park, Tokyo

Yoyogi Park, Tokyo

Yoyogi Park, Tokyo

Okinawa! Mix it up!

I arrived in Japan yesterday and today my host researcher is off to Okinawa to collect termites for my experiment.

Okinawa is composed a set of islands located in the south most part of Japan.

(http://kittiehoward.blogspot.com/2011/04/welcome-to-okinawa-blogfest.html)

Okinawa is a tropical area and grows pineapple and papaya.  The culture of Okinawa is completely different from that of the rest of the country.  It is a very laid back environment and a very popular vacation destination.  You can kind of think of it like the Mexico of Japan.  In fact, the best mexican food in all of Japan is said to be in Okinawa.

Okinawa is known for its chanpuru culture.  Chanpuru means mixed up and is the name of stir fry in Okinawa.

Random facts:
If you've watched or heard of the anime Samurai Champloo, it takes place in Okinawa.
   
The highest proportion of centenarians is found in Okinawa.  Their diet low salt, low cholestrol, high soy and fish diet are thought to be result for the longevity in Okinawa.

Termites from Okinawa!

To study the microbiome, human samples are not always very convenient.  There are many laws to protect human rights and those laws extend to samples used for science, even in cases where the samples are non-invasively taken (like a poop sample).  But since every organism and environment has a microbiome, there are no shortage of fantastic microbiomes to study.

One of the microbiomes of choice is that of termites.  Why termites?

Termites are horrible pests doing millions of dollars worth of damage... sometimes directly on money itself! 

Termites are unusual in their capacity to digest really tough plant material like cellulose and xylan.  If people could create reactors to turn plants into energy (without burning them), we'd have a truly "green" source of energy.

Termites are key to the nitrogen cycle.  The more we know about the nitrogen cycle, the better chance we have improving everything like crop production and waste production and removal.

For my work, I'll be working with two types of termites, one that eats wood and one that eats soil:

The wood-eating one: Nasutitermes takasagoensis (http://hodotermopsis.seesaa.net/article/67842051.html)

 

 

 

The soil-eating one: Pericapritermes nitobei (http://www.sinfonia.or.jp/~isoptera/myhtm/genus.htm)

Both of these termites come from the tropical part of Japan called Okinawa.

http://www.wallcoo.net/human/SZ_154_OKINAWA_Japan_02/html/wallpaper44.html

Next time, more on Okinawa!

My Microbiome

Each part of the human body is completely different in the microbial world view.  Temperature varies, the surface can be dry, moist, or oily, and air exposure varies dramatically.  So different microbes grow on different parts of your body.

I made some plates of my microbiome.  They weren't very interesting at first, but after growing up for weeks sitting out at room temperature, some interesting things grew!

Face: forehead (top), cheek (left), chin (right)

Mouth: cheek (top), tongue (bottom)

Hand: fingers (top), thumb (bottom)

Foot: toes (top), heel (bottom)

 
The hand plate looks crazy, I know.  I believe those two colonies that overgrew the whole plate are not my microbiome!  They look like the stuff we call contamination in the lab.  Look how invasive it is.  If it were really part of my microbiome, it would completely kill off everything else.

In general, moist areas have more microbes in total.  My feet and mouth are the most moist of the areas I sampled so it makes sense that I got the most stuff growing on the plates from those areas.

The biggest shock for me from these plates is how different my cheek and tongue are.  I would have thought the same stuff is growing on both of them.

PS. these plates smell awful... bacteria stink.

A quadrillion cells on your body... that aren't human!

The human body is made of about 100 trillion human cells. 
The human body also contains about a quadrillion non-human cells. 

That's right.  You are 90% microbe.

You might not change much over the course of your life, but each day, those microbes keep growing and changing according to how you live your life.  What you eat, what kind of life you lead, how often you bathe, everything affects your microbes.

You need your microbes to stay healthy.  They protect you against harmful microbes and help you get the most out of your food.  They might even affect the way you think.  So respect your microbiome!

Let's start by trying to learn something about how we affect our microbes through our diet.