Culturing Science – biology as relevant to us earthly beings

Archive for December 2009

The Known Universe by the AMNH [Video]

I’m not going to pretend to know anything about astronomy.  But I know one thing:  this video will blow your mind.  I try to remind myself how small I am every day, and this video sure does the trick.

It’s vids like this that make me thankful for the internet.

Y’know, with that much unexplored space, maybe the Battlestar Galactica fleet is really out there somewhere, looking for us…

(A girl can dream.)

Written by Hanner

December 25, 2009 at 1:24 am

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How dirt affects global atmospheric carbon dioxide (Wingate et al. 2009, PNAS)

This post was chosen as an Editor's Selection for I have a tendency to root for the underdog.  I rooted for the Phillies throughout the 90s, when my heroes Lenny Dykstra and Darren Dalton could rarely lead them to a win.  It’s a mixture of a desire for upheaval, that the unexpected can happen, as well as pure sympathy for the ones who always lose.

Do you know who always loses in science?  Dirt.  No one cares about it.  I mean, it’s a mixture of poop and rotting plants and animals.  It harbors fungus and worms and bacteria.  And while it is generally accepted that it has an important role to play, it tends to be overlooked because it’s just not all that exciting on the surface.  Why study ground up brown stuff when you can study WHALES or CANCER?

That’s why I love it when dirt wins, as it does in this early-access article from PNAS entitled “The impact of soil microorganisms on the global budget of δ18O in atmospheric CO2” (doi:10.1073/pnas.0905210106).  The closest I’ve heard soil come to being included in the climate debate is the possibility of pumping liquid carbon dioxide deep beneath the earth’s surface to sequester it: not the most dignified of positions.  But this article provides evidence that it is more involved than that, and helps to mollify some discrepancies between prior models and observed measurements in carbon dioxide.

One of the most common ways to trace the origins of oxygen in the atmosphere is through isotope analysis.  Carbon dioxide cannot dissolve in water on its own, but needs to be made into the ions HCO3+ and H+ so that it can be transported in fluids.  An enzyme, carbonic anhydrase (CA), switches carbon dioxide between its dissoluble and soluble forms, and is found in both plants and animals.  It is an incredibly important enzyme for both respiration and photosynthesis.  If CO2 were ionizing on its own, without an enzyme, it would take far longer, and the systems would be far less efficient.  However, it leaves a mark: a heavy isotope of oxygen.  The new CO2 molecule, built by CA, adds 2 more neutrons to oxygen, creating a δ18O isotope which we can trace, thus tracing the activity of CA.

Since δ18O is a heavy isotope compared to oxygen-16, the normal form, it preferentially remains in leaf tissues during transpiration and evaporation.  Eventually these leaves die and fall to the soil, where they are broken down.  The amount of δ18O in the soil has traditionally been used as a measurement of plant photosynthesis.  The possibility of CA activity in soil has been disregarded bcause of the high levels of δ18O in just the top few centimeters of soil, indicating that it is due just from decomposing leaves.

The 18 authors of this paper decided that this assumption wasn’t good enough.  What if microorganisms are creating δ18O in the soil due to their own CA activity?  What would this mean for the overall oxygen budget?  First of all, it would mean that plant photosynthesis would have a lesser role.  It could also change the estimations of photosynthesis vs. respiration in our atmosphere, since the microbes could be either photosynthetic algae or cyanobacteria, or respiratory little buggers.

The authors took the measurements of δ18O at different soil depths from 7 different major earth ecosystems from the field, and also created the artificial conditions in chambers with to determine if δ18O levels differed between the two.  They also used this “chamber-flux” data to estimate different rates of δ18O creation under different CA catalyzation levels.  These data showed that naturally measured δ18O levels were greater than the control levels without CA: up to 300x in the more productive ecosystems!  This provided clear evidence that δ18O is being created by soil microorganisms through CA enzymatic activity on their own.

This information was consistent with  previously observed and modelled δ18O curves, shown in the figure above.  The top half shows the observed δ18O levels in dark blue dots, with the modelled line in black, with the frames increasing in CA activity from left to right.  In the right frame, with CA activity at 300x the left frame, the modeled and observed δ18O creation rates overlap.  (The curve is based on latitude — northern latitudes, with much vegetation and high photosynthesis on the left, decreasing in photosynthetic production as we move southwards.)  This provides more evidence that CA is present in soils, as in an ideal world, observations and models will match up.

The bottom half of the figure is based on the concept of isoflux.  This is a measurement of CO2 in the atmosphere, with positive values indicating photosynthesis, while negative values indicate greater respiration, which removes CO2.  The “soil invasion” line, in orange, goes from showing no-change in the no-catalyzation scenario, to absorbing nearly as much CO2 as respiration.

So, really, what is this paper saying?  First of all, don’t ignore the dirt!  Soil microbes may be small, but they are vast in number and can really have an impact on our element cycling.  More than anything, this paper helps to adjust previous models.  It suggests that the soil may be more of a carbon dioxide sink that we previously thought, because we now have evidence that respiration is taking place due to this increase in δ18O from CA use.

To me, what this paper really shows is how little we know.  We’re trying to model oxygen and carbon in the atmosphere and earth, and there’s so little way of knowing.  If it weren’t for this enzyme, carbonic anhydrase, that happens to incorporate a heavy oxygen isotope, where would we be?  Modelling is important, don’t get me wrong.  But it is also incredibly frustrating because we really don’t know enough to create very accurate models.  This paper is a little slice, sure; but we could be missing huge impacts just because they are untraceable.

Wingate, L., Ogee, J., Cuntz, M., Genty, B., Reiter, I., Seibt, U., Yakir, D., Maseyk, K., Pendall, E., Barbour, M., Mortazavi, B., Burlett, R., Peylin, P., Miller, J., Mencuccini, M., Shim, J., Hunt, J., & Grace, J. (2009). The impact of soil microorganisms on the global budget of 18O in atmospheric CO2 Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0905210106

Written by Hanner

December 24, 2009 at 11:31 am

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Corkscrew duck genitals — WITH VIDEO!

One of my fondest days of an undergrad ornithology course was the day we learned about duck genitals.  It was funny, clearly, because it’s about penises and we were in undergrad.  But equally fascinating evolutionarily: why would a male duck evolve a penis that twists like a screw?  And how could a female evolve a vagina that is shaped like a screwhole with opposite threading?  (Insert your favorite sexual screwing joke here.)

I cannot do the new research by Patricia Brennan more justice than Carl Zimmer does, so I recommend that you head over to his post on The Loom.  He includes video of a duck boner, as well as a duck penetrating glass tubes of different shapes.  If you have a duck fetish, I would stay away from these videos at work.

Written by Hanner

December 23, 2009 at 11:09 am

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How to convince students that “there is nothing in science that isn’t worth being excited about.”

From Bill Bryson’s interview in the New Scientist about his new book:

Science classes are almost always taught, in my experience, as if they are trying to produce the next generation of scientists. Of course, that is a vital function. But there is no recognition that a very large proportion of people are not going to become scientists.

What always disappointed me about science lessons was how the teacher would, almost as soon as they got through the door, turn around and start writing equations on the blackboard. This meant I was quickly out of my depth; I don’t have a brain that is comfortable dealing with mathematics and algebra.

In fact, there is nothing in science that isn’t worth being excited about. Unfortunately, the place you are least likely to find excitement, in my view, is in schools, when that is the precise place you should be handing it out to people.

Bryson’s treatment of science teachers is a little harsh, as oftentimes their material is prescribed and not up to them.  However — he is right about the fact that science is cool and exciting, and that oftentimes classes let those who aren’t already interested in science slip through.

I believe that the main obstacle in gaining student interest is the skill set required to study science.  All fields require a skill set — for English, you have to learn how to think critically, compare, and write; for art, it’s painting or drawing, photography, or even a certain eye for viewing the world aesthetically.  These skill sets perhaps seem more organic: a natural development that is part interest or inbred talent, that becomes more complex as you study more.

Science also requires reading comprehension and writing.  But, to study modern science, a great deal of fact-learning is also necessary, which is a deterrent in itself.  It makes science seem less artistic or creative; the required effort can seem like a drag or a waste of time.  As if science is for people who can’t think for themselves, just memorize facts.  P’shaw!

My roommate and I love to stare at the ceiling and ramble on about all the things that amaze us about the world.  And in a way, we speak slightly different languages: she studies philosophy and writing, while I study biology.  But we are actually asking the same questions.  We are simply trying to make sense of our worlds; we just go about it in a slightly different way.

And this is what I think is key.  We can’t get students interested in science by just telling them that it’s important to know, that being a geek is cool, that science teachers are more fun to be around (Filming them in simulated space to get their students’ attention?  Please, no.), or encouraging them to be on the “cutting edge.”

Science needs to be presented as another language used to put order to our world — just like literature or art.  It’s not a field that is better than any other, or worse.  It is a creative force that is constantly being reinvented, despite the common misconception that it is set in stone.  Scientists aren’t some sort of unsociable, labcoat-clad army, but just normal people trying learn as much as they can about the world in order to help each of us understand why we are the way we are.

Written by Hanner

December 22, 2009 at 1:07 am

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Epigenetics: A Primer in Sketches [Link]

Epigenetics.  So hot right now.

I study epigenetics in my lab.  (That’s right, I’m hot.)  When someone asks me what that means, I give the brief definition: “It’s the study of changes in gene expression without a change in the actual DNA sequence.” “Like, molecules or proteins can bind to the physical DNA and affect whether the DNA is transcribed.”  “Y’know?”

If you’re looking for a more technical, yet understandable, explanation, head over to the Sketch Overview of Epigenetics at Genes to Brains to Mind to Me.  The author is a great artist, as you can see above, and the primer gives a good overview of epigenetics basics to keep you hip to the scene.

[Thanks to Genomeweb Daily Scan for the tip]

Written by Hanner

December 17, 2009 at 10:42 pm

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Apoptosis, or programmed cell death, is regulated by the protein RanBPM (Atabakhsh et al. 2009, Molecular Cancer Research) I have been fearful of molecular biology for most of my life.  This is partially because I so clearly defined myself as an ecologist that I partitioned molecules into “little biology” and out of my range.  But mostly it was a fear of what I considered unnatural.  Scientists who play around with chemicals and little tubes of liquid DNA cannot be real biologists, as they are studying life in a tube and not as it truly exists.  These actions seemed so separate from what I considered “real biology,” these little details so far from actual application to learning about life as we know it.

And now look at me.  I spend my days playing with chemicals and little tubes of DNA.  I HAVE BECOME WHAT I FEAR MOST.

But I’ve been learning that molecular biology isn’t all boring.  Molecules can be COOL and some of the little processes really interesting and relevant on a larger scale.

One of my favorite small-scale processes is apoptosis, or programmed cell death.  For a long time, I never really thought about what the body does with old or sick cells.  When your cells get old, you just die, right?  Not exactly.  The body can destroy and reabsorb its sick cells — incredible!  That the body would kill off parts of itself!  Maybe this isn’t so amazing to most, but it was a pretty big revelation to me.  Apoptosis is also important in development.  We start off as one cell which becomes a ball of cells.  In order to create cavities, such as the digestive tract, the cells go through apoptosis and creates functional holes in itself.

Apoptosis is especially relevant to cancer regulation.  When a cell is dividing and, inevitably, accidentally mutating its DNA (see my DNA primer for basics), there are processes that essentially spellcheck the DNA to ensure that it is functional.  If there is a mutation that the cell cannot fix, it will send out DNA damage signals to neighboring cells, signaling that it’s time for this cell to die, or it could become cancerous.

Additionally, most cancers actually disable apoptosis.  That is, they disable the signals so that the body cannot recognize the cell as cancer and force it through apoptosis.  As you can imagine, the study of apoptosis has all kinds of implications for cancer treatments.  If we could find a way to induce apoptosis in cancerous cells, we could potentially force cancer cells to kill themselves.

Scientists from the University of Western Ontario just published a paper online on December 8th in Molecular Cancer Research identifying a protein that activates apoptotic pathways in DNA damaged cells (doi:10.1158/1541-7786.MCR-09-0098).  RanBPM, or Ran-binding protein M, had a previously unknown function.  They discovered it’s potential for apoptosis regulation in a large screen looking for proteins that bind with Oct-1, a transcription factor implicated in cell survival after DNA damage, and decided to look further.

The authors stained cells with DAPI, which is a fluorescent molecule that attaches to DNA and RNA to make it fluoresce under a microscope. The apoptotic cells are condensed and marked with arrows. The right panels show the same image stained with RanBPM-specific fluorescent staining. The apoptotic cells express RanBPM!

One problem in studying molecular biology is that living tissue doesn’t take well to being cultured in the lab, so biologists often have to use certain cells types that will grow under laboratory conditions.  Where I work, we use yeast, which is beneficial because it is easy to take care of and grow, cheap, and easy to manipulate because it is a simple, single-celled fungus; the downside is that it is not human.  The authors here used Hela cells, which are derived from human cervical cancer, and are essentially immortal.  These have the benefit of being actual human cells — but they have been described jokingly as their own species because of their immortality, ability to thrive under laboratory conditions, and their abnormal chromosome number (caused by contamination from an HPV virus).  However, they are still a good starting point for studying human biology because they are human derived, if a little mutated.

The first two steps in molecular biology are usuallyto overexpress the molecule, and underexpress the molecule.  The researchers inserted an extra copy of the RanBPM gene into the cells, causing them to make twice as much RanBPM protein.  These cells did not survive well compared to normal cells, indicating a potential link with apoptosis.  Now they had to double check that this was actually due to a cellular pathway, and not because too much RanBPM poisons cells and kills them, known as necrosis.  Caspase 3 is an enzyme commonly associated with apoptosis; the authors then looked at caspase 3 levels in RanBPM overexpressed cells compared to normal cells, and saw a dramatic increase in caspase 3 activation, showing that it is related to apoptosis and not necrosis.

So now we know what happens when we have too much RanBPM in a cell.  What happens when we have too little?  To downregulate RanBPM, the authors used siRNA, or small interfering RNAs.  (Read my Protein Synthesis Basics primer to learn about RNA.)  These siRNAs have a complementary sequence to the RNA used to produce RanBPM protein.  When they are released into the cell, these siRNAs bind with the RanBPM RNA, making it double-stranded and unable to be made into protein, blocking its production.  The authors did several experiments where they damaged cell DNA on purpose by radiating it and observed how the cells survived.  In the image to the right, you can see that cell survival in downregulated RanBPMcells is greater than controls (injected with a random shRNA, a kind of siRNA, to ensure that the shRNA process doesn’t affect the cells’ survival)  even with high radiation levels.  This demonstrates that a loss of RanBPM protein affects the ability of a cell to undergo apoptosis when it is affected by DNA damage, further implicating this molecule in being important to this pathway.

The next step, after over- and underexpressing a gene, is to work out it’s molecular function.  The authors looked at the expression of two proteins known to be involved in apoptosis, Bax and Bcl2.  When there is a DNA damage signal present, Bax relocates to the mitochondria to do its part in apoptosis.  The authors found that in the shRNA RanBPM cells, with reduced apoptosis, Bax never relocated to the mitochondria after radiation, showing that RanBPM affects the Bax pathway.  They then looked at another protein which regulates Bax, Bcl2, and also found increased expression in shRNA RanBPM cells.  Previous studies have shown that Blc2 overexpression blocks the apoptotic pathway, and can even lead to cancer.  When they reintroduced RanBPM to nearly wild-type levels, Bcl2 expression decreased.  These studies show that RanBPM is in fact affecting the expression of other proteins involved in apoptosis, and a known relevant apoptotic pathway at that.

This study, and many molecular biology studies, rely heavily on correlation.  That is, looking at changed levels without showing causation.  We know now that RanBPM is part of this pathway and affects other molecules, but it still isn’t clear how it affects these other molecules and how it functions in a wild-type cell.  If only we could simply use the methods the authors used to overexpress or underexpress these proteins in cancer cells, but regular human cells don’t accept these kinds of treatments.  While doing this sort of research is important to pinpoint particular molecules that regulate cell survival, until we have developed treatments to actually utilize proteins in human therapy, we won’t be able to cure cancer.

Atabakhsh, E., Bryce, D., Lefebvre, K., & Schild-Poulter, C. (2009). RanBPM Has Proapoptotic Activities That Regulate Cell Death Pathways in Response to DNA Damage Molecular Cancer Research DOI: 10.1158/1541-7786.MCR-09-0098

Written by Hanner

December 15, 2009 at 8:29 am

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Carl Safina speaks for me, as usual

From science writer and ocean activist Carl Safina’s blog:

Reality: The atmosphere is as thin as shellac on the globe. Where does all the exhaust go? Into that thin, thin layer. We measure carbon dioxide from the exhaust, and find it climbing every year. Physicists have learned that it traps heat. We measure the temperatures worldwide and find them warming. If we’re wrong about all of that, we can look at satellite photos of the polar seas and see how much ice has melted in recent years. Same with almost all the glaciers. In the tropics, reefs have started dying due to excess heat and due to water turning acid from carbon dioxide only since the 1980s. I’ve seen this all with my own eyes.

Stupidity: The idea that the climate scientists in the world are in a conspiracy to lie is just insane. People who think that are either nuts or are being manipulated by the greed of those whose ox will be gored. Even in the days of big tobacco, they never raised such a ridiculous claim against all of science.

Morality: Consider the last energy conversion: Slavery to oil. Slaves are much cheaper. They create a very nice life-style. The economy would collapse without our freedom to have slaves. Obviously, this moral rot is an absurd argument. And this absurdity was vehemently held, and viciously, bloodily defended. Pretty much like today.

Practicality: The world is warming and we’re warming it. That is indisputable. It will have great negative consequences; that’s also indisputable. Denying it won’t change it.

And–no one needs to give up energy. We only need to convert from caveman energy (burning something every time we need energy) to clean energy that powers the whole planet (sun, wind, the energy in the ground, with nuclear as a possible bridge). No one cares whether the energy comes from oil, coal, slaves, sunlight, or wind, as long as the light goes on when you flick the switch and the car goes when you step on the pedal. Except that, wait, we do care if it comes from slaves because that’s immoral. Well, wrecking the future is also immoral. Today’s slaves are our own children whose options are closing because we’re dictating the world they’ll be stuck with.

Patriotism: As China and Germany and Denmark know, far from wrecking the economy, building and exporting the high-tech technology for capturing clean, free-flowing energy and the grids for distributing it will involve tremendous investment and job opportunities.

The United States is falling farther behind in developing these technologies; other countries are positioning to leave us in the dust. The unpatriotic people are not the ones who want the U.S. to lead in developing clean energy. It’s the ones who don’t.

– Carl Safina

I have nothing to add.

Written by Hanner

December 10, 2009 at 2:32 pm

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