Tiny Topics

Quorum call, without voices

2010-01-26T15:37:00.003-06:00

Is there anybody out there?
When it comes to political intrigue, it’s important to know whether you stand united or alone. Are you surrounded by friends or enemies? Is it time to lead the charge or wait for reinforcements? Tallying how many supporters you have—or how many enemies are waiting in your midst—can be critical to your success.

For bacteria, things aren’t much different. Bacteria survey their surroundings for others of their kind, and others NOT of their kind. They may wait until they have sufficient numbers to launch an attack on your body, or to coordinate effective mining of a nutrient source. But bacteria don’t have eyes, ears, or a mouth; they cannot see, hear, or speak. So how do they tell who is out there?

The peril of the tennis ball
Time to use your imagination, folks. Imagine you are in a windowless room. The door is closed. You are wearing a blindfold and earplugs. You cannot speak. In your hand is a fuzzy tennis ball. When you throw the tennis ball, it bounces off the walls until, eventually, it stops. Think about the chances of the ball ricocheting off a wall and hitting you in the head.

Now remember: you cannot speak, you cannot hear, you cannot see. But, if I put another person in the room with a tennis ball to throw, do you think you’d be able to tell you were not alone in the room? Maybe. How about if I dropped in TEN people, each with one tennis ball? How often do you think you’d be smacked square in head?

It probably seems strange to imagine all this blindfolded tennis ball throwing, and I’m pretty sure it won’t give you a better understanding of human politics. But if you understand how you’d be able to sense the presence of more people in the room based on how often you got a tennis ball concussion, you understand the microbial behavior called quorum sensing.

Bacteria don’t throw tennis balls, they “throw” chemical signals
The tennis ball in our thought-experiment represents a quorum-sensing signal. These are chemical compounds that bacteria can “throw” out into the environment, and “catch” if they hit the cell. In this way, bacteria can sense if they are relatively alone, or if they are surrounded by thousands of others.

If you play around with the tennis ball room scenario, you can start to envision more complex issues with quorum sensing. Can you imagine ways to trick the bacteria into thinking they were not alone? Or trick a crowd of bacteria into thinking they were all alone?

Microbial Grappling Hooks

2010-01-25T13:45:00.000-06:00

It's a common theme for my view of microbes: for many real-world problems, microbes have already developed a solution.

Want to turn biomass into fuel? Microbes can do it!
Want to seed clouds for rain? Microbes can do it!
Want to move around using a grappling hook? Microbes can do it!

I've had the honor of contributing a blog entry to the delightful blog "Small Things Considered" on the topic of microbial grappling hooks, known more technically as "Type IV pili." It's basically a rope or filament that is sticky at the end. The bacteria can extend this filament out of the cell, and if the sticky end catches on something the microbe can pull itself along by reeling the filament back in. This is just one of many fascinating structures bacteria can use to interact with the world around them.

If you want a little more technical detail on how Type IV pili work, check out my "Small Things Considered" blog entry on the subject!

Nature wins by a hair

2009-12-31T14:06:00.000-06:00

When I first started doing lab work, I found all the specialized equipment quite glamorous. Especially the cold room—basically a walk-in fridge—which always billowed out fog when you opened the door and reminded me very much of the embryo storage room in Jurassic Park. In my lab, we’ve got centrifuges large and small, precision pipettors for measuring out droplets of chemicals, and lots of vials and beakers. In fact, there are whole companies focused on providing labs like ours with expensive, specialized equipment.

But if you look closely in every lab, you’ll find very normal items pressed into scientific service. After all, we scientists are in the business of innovation. In fact, some tools are actually the result of Mother Nature’s innovation, not ours. My favorite examples of nature-made scientific tools are cat whiskers and human eyelashes.

Some scientists study proteins by crystallizing them. One of the challenges of this approach can be getting BIG crystals to form. So sometimes big crystals are formed by micro-seeding a solution with smaller crystals. This requires a very small implement to pick up that small crystal (seed crystal). To this day, scientists sometimes use cat whiskers for the task. They are fine enough to grab a small crystal as you drag the whisker through the solution.

Another set of researchers works on the tiny nematode (worm-like creature) Caenorhabditis elegans. When your research subject is the about the size and length of an eyelash, how do you poke, prod, and transfer such a creature? With a human eyelash, that’s how.

It is a bit humbling that, despite all the sophisticated lab equipment available, sometimes the best tool for the job is something nature created!

Our bodies, ourselves, our microbial ecosystems

2009-12-17T12:23:00.004-06:00

Winter has finally and unquestionably hit Madison, hard. Staring out at the wintry landscapes I’ve been reminded of how harsh and ever-changing a smaller set of landscapes—our bodies—can be.

Just as we live on a planet with different terrains and environments, microbes live on, and in, the human body. As you can imagine, some areas of your body are more forgiving than others. Your mouth is a great place to get food, but with all that saliva it can be hard for a microbe to STAY there. Your skin can be welcoming where it is moist (like your armpits or between your toes) but challenging where it becomes a dry, cragged desert around your elbows. And of course, there is your digestive tract, a warm, nutrient-rich home for millions of microbes.

Though all this probably sounds a bit creepy and makes you want to take a shower, please remember that living with microbes is the healthy norm. They were here long before we arrived on the scene: my friend Dr. Mark O. Martin has a saying about this: “First to evolve, last extinct” I believe. But I digress!

When it comes down to sheer numbers, scientists have estimated that in your body there are ten times as many bacterial cells as human cells. Another motto comes to mind: “You are born 100% human and will die 90% bacteria.”

So, who are all these microbes are and what are they doing with our bodies?

A new National Institute of Health (NIH) “roadmap initiative” aims to answer this question, or at least BEGIN to answer this question, with The Human Microbiome Project. Scientists across the country will be sampling various sites on the bodies of healthy and diseased individuals to ask “who’s there?” and “what are they doing?” Along the way, we may get some interesting insight into how much our microbes very from body site to body site, person to person, week to week, state to state . . . you get the picture!

It always comes back to Jurassic Park, doesn't it?

2009-11-19T17:07:00.001-06:00

I just got back from a seminar by George Weinstock of Washington University, St. Louis about the human microbiome project. I was planning on doing a blog entry on the human microbiome project--and still will write one--but during the talk I was struck by the amount of data the Wash. U. genome sequencing center was producing, and how a huge percentage of the talk centered on the challenges of storing and processing all that data.

For example, the center needs an additional 4 terabytes of storage each day. They've built an entire storage facility which is in great part air conditioners and electrical equipment to maintain the data storage. It uses the same amount of electrical power it takes to light a New York Skyscraper.

It made me think back to all those Cray supercomputers used to process the ancient dinosaur DNA sequences in that most-influential novel "Jurassic Park" by the late Michael Crichton. The speed of current DNA sequencing technology is blinding in comparison to what those ol' Cray computers would have been capable of. But though the speed of the sequencing has gotten faster, all that data requires a huge space to house the technology to store it.

In a world overrun by antibiotics, what are we selecting for?

2009-11-11T15:55:00.006-06:00

As a graduate student, I read a lot of self-help books. One of my favorite concepts is from Marcus Buckingham’s “Find Your Strongest Life”:

What does working look like?

It’s a very goal-oriented approach to life. Envision what you want your life to look like, and work backwards from there.

The concept of selection is very similar to the “what does working look like” approach. In my college microbiology class, I was tasked with isolating a microbe—from the environment—that could eat milk (casein proteolysis). So I left an open container of milk out in my dorm room for a week and waited to see what grew. To select for a milk-eating microbe, provide an environment where a milk-eating microbe would do well.

But what does this have to do with the zombie apocalypse that I was rambling on about in an earlier blog entry?

Well, if you want to get humans who are good at surviving zombie attacks, one way to do it would be to flood the world with zombies and see who’s left. If you did that, you’d be selecting for zombie survivors.

But while you would nearly guarantee the remaining humans were zombie-resistant, you would have little control over HOW they were zombie-resistant, or any number of other traits they would possess. You might end up with an excellent marksman, a swift runner, or a violent sociopath. You might find the survivor was just very good at hiding.

So what do antibiotics select for?
When you take antibiotics, you’re basically flooding your microbial world with something deadly. Unless you kill every single microbe, you will select for microbes that survived the antibiotics onslaught. They will survive and multiply in a land empty of competing microbes that used to keep them in check.

I could go on for several more paragraphs about antibiotics, but I’ll try to wrap this up: when you use antibiotics, anything that survives is antibiotic-resistant, but both “good” and “bad” microbes can have that ability. High dosages of antibiotics will kill off more microbes, leaving less to prosper. Using a combination of antibiotics would be like unleashing zombies on the world and then following it up with vampires: while there are citizens uniquely skilled at surviving either monster, there are far fewer individuals who can survive both.

So what happens if the world is full of violent criminals and suddenly zombies kill off a huge portion of civilized society, including law enforcement? Do you think a bad guy or two would survive? Would anyone left standing be able to keep them in check?

Tales from Home Economics UPDATE

2009-11-06T11:26:00.003-06:00

After I posted my "Tales from Home Economics" entry, I received an e-mail from my mother-in-law Ellen (her description of yeast producing gas was the feature of that post). Thankfully she was happy about me putting her words on my blog (I have to admit I didn't check beforehand. I am a poor journalist!).

Now, I've never been in her class when she gives the description, so I was excited to get more specific information on what she tells her students about yeast:

When I tell the kids about the yeast they are about to use, I tell them they will first give the yeast a bath and then give the yeast a snack and then the burps come . . . Then I tell them to look very closely after they pour the yeast into the water and maybe they can see the yeasts smiling back at them!!! These poor kids will have a twisted science education by the time they leave my class!

Actually, I think a twisted science education may be just what students need to get excited about science. I think sometimes we get the impression that science only happens in laboratories, and that we need advanced degrees to understand it. But science happens everywhere, and with a little imagination we can understand even the things we can't see with the naked eye.

Although hopefully I won't see the yeast smile before I put them in the oven!

Tales from Home Economics

2009-10-29T14:39:00.000-05:00

I come from a family of teachers. The newest addition to my teaching family is my mother-in-law Ellen, who teaches Home Economics to middle school students. As you can imagine, she sometimes has to get REALLY creative to hold the attention of that age group!

Now, cooking often involves a bit of microbiology, like using yeast to make bread dough rise. Many of Ellen's students are indeed surprised to learn that they are adding LIVE MICROBES to the dough. Some even feel bad about killing so many microbes to make a loaf of bread. But how do yeast make the dough rise? The explanation Ellen gives is this:

The yeast eat sugars in the dough and 'burp' or 'fart' out gas.

Can you imagine the expressions on her students' faces? Her statement is accurate, in the same way good soil is really made up of worm poop. For better or for worse, when microbes are used in food products you will end up eating something that has been excreted from a microbe. Thank goodness it is all so delicious!

What can the zombie apocolypse teach us about microbiology? Part 1

2009-10-25T13:35:00.001-05:00

You may not have known it, but Madison is both an epicenter of top-notch microbiology research AND zombie rights. The latest zombie lurch organized by COLD (Coalition of the Living Dead) inspired me to talk a little about what zombies can teach us about microbiology. What's on my BRAAAAIIIIN today are the concepts of fitness and selection.

In the latest zombie flick "Zombieland" the protagonist is a neurotic introvert, and he credits his success in a world overrun by zombies to his obsessive adherence to a set of survival rules and a lack of friends who could turn into zombies and devour him. His traits did not make him very popular or successful in the pre-zombie world.

A simple way to think of fitness is the capability to persist and continue your species. Based on this definition, our nerdy protagonist was not very fit, was he? He didn't have many resources and he certainly wasn't a hit with the ladies.

But then the world changes, and zombies kill off a huge portion of what was once considered a normal, healthy population. Under this different set of demands--under different selection--he is left to prosper.

In summary, different environments can select for different traits. As long the selection doesn't kill off ALL individuals, then those that possess the traits endure the selection and subsequently reproduce would be considered the most fit.

I think you'll find cinematic history is full heroes and heroines that had traits that helped them survive very unusual situations!

COMING SOON IN PART 2: In a world overrun by antibiotics, what are we selecting for?

The Sweet Sound of Microbiology

2009-10-23T11:50:00.001-05:00

As a fiddle enthusiast, I felt compelled to link you to an inspiring story: fungi are being used to age modern wood into Stradavarius-quality wood, and create an award-winning bioviolin:

Fiddling with Fungi

Not only can microbes perform simple chemical reactions efficiently, they can also perform complex, almost mysterious aging processes to give soy sauce its flavor and violins their timbre. How sweet the sound of microbiology can be!

Why use microbes to make biofuels?

2009-10-20T14:32:00.000-05:00

Some fuels are easier to access than others. Biomass, for instance, represents a great deal of potential energy that’s tied up in very strong chains of molecules, such as cellulose. To get access to that energy, what you need is a molecular wood chipper: something that can break down tough chains into molecules we CAN use, like ethanol.

The problem: breaking down tough, energy-containing compounds into useable fuel sources.

The solution: microbes (bacteria, yeast, algae, etc.)

You may be asking yourself: why use microbes to break these things down? Don’t we have chemicals that can do the same thing?

I’d answer your question with another question:

Why do we use microbes for making beer, or cheese? Why didn’t your grandma wheel in a tank of gas to bubble into the bread dough and make it rise? You’d probably say “because it’s easier” and you’d be right. She’d sprinkle in some yeast (microbes) to get the dough to rise. Humans and microbes have a rich, delicious history together when it comes to food, but the idea of using microbes to process biomass into biofuels is, by comparison, quite new.

Microbes are tiny toolkits that can break down molecules or build new ones—often more efficiently than a chemist in a lab can. A microbe’s toolkit has developed over endless generations to be as cheap and effective as it can be. So why reinvent the wheel? Just as silk worms were harnessed by humans to create raw silk for fabrics, we can use microbes to perform complicated processes under simple conditions.

Just getting started!

2009-10-14T11:34:00.001-05:00

It's a brave new adventure for a rogue graduate student: a science blog!

I came up with all sorts of clever names for the blog, like "The Sound of Science" and "Simply Science" but amazingly, the internet is chock-full of cleverly-named science blogs and podcasts. In the end, I found that "Tiny Topics" was not YET taken.

Undoubtedly, "Tiny Topics" will not be the most creative, most in-depth, or most up-to-speed science blog/podcast. My goal is to craft small morsels of science that don't take up much of your day to absorb, but might change the way you view the world around you (especially the parts you can't see).

"Tiny Topics" is all about small science for a great big world. Enjoy!