Thursday
Jan102013

Science Highlights

by Brooke Napier

A wrinkle in your finger

C'mon buddy, why so wrinkely?It never really made sense to me that you would get wrinkled fingers from being in water, even when people would say that it was just your skin taking up water from the environment and swelling… Which is why it was particularly interesting to find out that the wrinkles in our fingers come directly from an involuntary nerve response.  Specifically a reaction by the body’s autonomic nervous system, the system that also takes care of heart rate, digestion, respiratory rate, salivation, perspiration, papillary dilation, urination, and sexual arousal (I’m sure there are other functions too).

Well, turns out we’ve known that information for over 80 years, apparently we knew all along that if the nerve to the finger has been cut wrinkles cannot occur. Mark Changizi and colleagues thought perhaps this was an evolutionary mechanism, which allows your figures to morph into water drainage systems. While the water drains out of the fingers, it allows grip of surfaces and objects more efficiently in wet situations (like a tire!).

In fact, this past week an article published by Kareklas, et al. expanded on this evolutionary mechanism. They found that submerged objects are handled more quickly with wrinkled fingers than with unwrinkled fingers… supporting the idea that water-induced wrinkling of fingers and toes may be an adaptation for handling objects in wet conditions.

For more information on this topic read:

Becky Summers’ article at Nature News

…and the primary articles:

Changizi, M., Weber, R., Kotecha, R., & Palazzo, J. (2011). Are Wet-Induced Wrinkled Fingers Primate Rain Treads? Brain, Behavior and Evolution, 77 (4), 286-290 DOI: 10.1159/000328223 Kareklas, K., Nettle, D., & Smulders, T. (2013). Water-induced finger wrinkles improve handling of wet objects Biology Letters, 9 (2), 20120999-20120999 DOI: 10.1098/rsbl.2012.0999

Trust in age

While perusing through the new weekly additions of journal articles I found a very interesting title, “Neural and behavioral bases of age differences in perceptions of trust”.

This paper, written by Elizabeth Castle and friends, shows that older adults, who are notably vulnerable to fraud, have a diminished “gut” response to cues of untrustworthiness. They showed older and younger adults faces and asked them to rate them on a scale of “untrustworthiness”. What they found was that older adults significantly found more trustworthy and approachable faces, and these data mimicked in neural activation.

Here's your anterior insula, yo!The area of the brain devoted to the sense of “trustworthiness” is the anterior insula, which is more active while judging “untrustworthiness”, and is said to be the area of the brain devoted to “gut feelings”, which represent expected risk and predict risk-avoidant behavior. Essentially, the younger adults showed more neural activation in the anterior insula more frequently than the older adults.

TL;DR – there is science behind your Grandfather believing everything he hears on Fox News.

C'mon, really?

Primary literature found here:

Castle E, Eisenberger NI, Seeman TE, Moons WG, Boggero IA, Grinblatt MS, & Taylor SE (2012). Neural and behavioral bases of age differences in perceptions of trust. Proceedings of the National Academy of Sciences of the United States of America, 109 (51), 20848-52 PMID: 23213232

Friday
Jan042013

Star Formation Formed the Fermi Bubbles

by Sarah Scoles

 

You may recall the Fermi Bubbles: Those 20,000-light-year-tall Cadbury eggs of gamma radiation blowing upUh, you've got a little something, um, on your, yeah. Right there (Credit: NASA/Fermi). from the center of our galaxy. But, like you do when gigantic, high-energy monsters appear in nightmares, you have to ask yourself, "What causes these?"

In the case of your monsters, the answer is likely the temperature of your bedroom or your consumption of Doritos before sleep. But in the case of the Fermi Bubbles, there are two possibilities:

 

  1. The supermassive black hole in the middle of the Milky Way (Sagittarius A*) is not dormant, and its activity could, and could have in the past, powered outflows like this.
  2. Star formation is intense in the center of the galaxy. There's a lot of stuff in a small space, and the closer together stuff is, the more often "stuff" changes into "stars." These processes could be energizing the outflows, releasing high-energy cosmic rays and causing plasma to shoot up and down from the Milky Way's disk.

 

Evidence from a new paper titled "Giant magnetized outflows from the center of the Milky Way" suggests that #2 is the winner. The research team, led by Ettore Carretti of Australia's CSIRO, looked at the the regions where the Fermi Bubbles are, but instead of looking for gamma rays, they looked for radio waves.

Why would radio waves help clarify?

Just try to tell me that doesn't look like fun (Credit: daviddarling.com)

All non-neutral particles will interact with magnetic fields. When the charged particles encounter a magnetic field, they spiral around the field lines. The curving of their path causes them to emit radio waves called "snychrotron radiation."

In areas where supernovae are going off and stars are forming, electrons are sometimes accelerated to very high speeds (making them "cosmic rays"), and then they make these loops and emit all those identifiable radio waves.

The Parkes Radio Telescope mapped the radio waves above and below the galactic center.

And guess what? The map lined up nearly perfectly with the gamma rays of the Fermi Bubbles, suggesting that whatever is causing one is also causing the other. And the qualities of the photons suggested that they were not just any old radio waves, but synchrotron radiation.

It's a match! You win! The gamma rays are the colors, and the dotted lines represent the extent of the radio emission (Credit: Carretti).

So the question then is: 

So why do they think it's star formation?

The Bubbles have a "narrow waist," as the Nature paper says--a waist whose diameter happens to correspond to the size of the star-forming gas ring around the center of the galaxy and also approximately a size 4 at J. Crew.

That star-forming area is also "missing" a bunch of radio and gamma-ray emission. Based on the amount of infrared light that busts out of there, scientists expected to see a lot more radio and gamma right in that region. But it's not there. They think that it might instead be jetted up and down into these Bubbles, hiding right under their noses. In fact, if they take the Bubble radiation pretend to put it back into the star-forming region, the level is almost precisely what they expected to see.

For the cosmic rays to get to out that far before losing their energy and to make the shape we see, they need to be going about 1,000-1,100 km/s. For that to happen, and for the magnetic field to be as strong as we observe it to be, 10^39 erg/s of magnetic energy needs to be "injected" into the system every few million years (what a prescription, huh?). That's about as much as 10,000,000,000,000,000,000,000,000,000,000 refrigerators. Not that that means anything to you. Anyway, that's how many refrigerators' worth of energy the star formation (simulations say) would put out.

But that's not a totally constant number, and the Fermi Bubbles, symmetric as they are, are not homogeneous. They do have structure.

On StructureThose curves are not just the outflow: They also trace out the magnetic field lines the outflow was following (Credit: Carretti, et al.).

The structures--called "ridges" in the paper--must have formed at a time that is not now, when the energy injection was different and the magnetic field was different. They show us (if we use some careful backtrack-extrapolation) what star formation was like as many as 10 million years ago. 

Fast fact

If you could see these lobes, they would span 2/3 of the sky from horizon to horizon. But you can't see them. And that's why it's important to have telescopes that see the universe differently from the way our eyes do. Our eyes are great at seeing oncoming cars and what kind of saber-toothed tiger is lurking outside the cave, but they are not great at keeping their shutters open for long periods of time and detecting the rays and radiation that would kill us if we were close-by. Happy New Year, telescopes.

 

ResearchBlogging.org Carretti, E., Crocker, R., Staveley-Smith, L., Haverkorn, M., Purcell, C., Gaensler, B., Bernardi, G., Kesteven, M., & Poppi, S. (2013). Giant magnetized outflows from the centre of the Milky Way Nature, 493 (7430), 66-69 DOI: 10.1038/nature11734

Monday
Dec312012

Thinking outside of the box: How do complex organisms clear infections? 

by Brooke Napier

Sometimes when you have a big, hard, involved question you have to think outside of the box in order to answer it. Stepping outside of the box can be uncomfortable and brings a lot of uncertainty, but it can also be extremely interesting. 

Which brings me to my big, hard, involved question…This picture comes up when you google "Hard questions". I have a lot of questions about this picture, I'm not sure if they're "hard".

How do complex organisms, like us, clear infections?

Scientists generally go about this question by looking at very specific mechanisms used by the immune system and asking, how does such and such mechanism contribute to clearing infections?

An example of what I’m talking about would be:

Question: Does Peptide B contribute to clearance of a Listeria monocytogenes (causative agent of listeriosis) infection?

Method: Delete the peptide B gene in the mouse genome and infect that mouse with Listeria monocytogenes, conjointly infect a normal, non-mutated (wild-type) mouse with Listeria monocytogenes.

Results: Twenty-four hours post-infection the wild-type mouse has no detectable bacteria throughout its organs, however the Peptide B gene mutant mouse has large quantities of L. monocytogenes in its lung, spleen, and liver. Therefore, Peptide B is important in the clearance of L. monocytogenes in the lung, spleen, and liver.

This is a good way to start answering questions about clearing infections, and we are light-years ahead of what we knew only 10 years ago about this question… but perhaps we should step away from picking apart the specific immune system mechanisms, considering our immune system is an intricate network of mechanisms all striving to clear the infection together. Essentially, “each [immune] response does not exist in a vacuum”.

So what’s a different way? Well, you have to step outside of the box.I know, I feel it too.

David Schneider and his group at Stanford have done just that.

Moria Chambers, from this group, writes: “While it may be simplest to examine the effect of immune components individually, in order to effectively control immunity clinically we need a better understanding of the full immune network… [and that] patients normally do not have a single pathway or gene responsible for their entire pathology, and we need to develop the tools to deal with these levels of complexity.” 

How do you look at how complex immunological networks interact to contribute to clearance of pathogens?

It’s a similar technique, but instead of studying one immune function you study one multi-factorial immune component in the presence of a variety of pathogens.

Also, mutant flies aren't like mutant mice - something about hairless mice that makes me question if there is a God.David Schneider’s group decided they wanted to look at two specific immune system components within the model they study, Drosophila. As they elegantly put it, “Infected fruit flies get sick in ways that human patients would recognize; bacterial infections in Drosophila induce changes in feeding, metabolism and circadian rhythm…” – or as I like to put it: flies get sick too and it’s easier to manipulate their genetics than humans genetics.

They asked how do phagocytosis and melanization, two components of the Drosophila immune system, contribute to clearance of the infection and subsequent survival of the Drosophila?

First, wtf are phagocytosis and melanization?

They are the first-line response team during infection of Drosophila, equivalent to an innate immune response in humans, if they had that. Both of these immune components happen within seconds/minutes of infection.

Phagocytosis, from the view of a bacteria (dark purple).Phagocytosis – this comes from the Ancient Greek work phagein, meaning “to devour”, cytos (or kytos), meaning “cell”, and -osis, meaning “process”. OR… it’s the process by which a cell engulfs particles (FIGURE). This process was first revealed by one of my favorite microbiologists, Ilya Mechnikov in 1882. Basically, this mechanism is used to engulf foreign entities, like bacteria or viruses, and digest them. When you inhibit phagocytosis USUALLY this helps bacteria thrive and cause disease.

Melanization of a cuticle due to tramatization. Bring in the color (melanin), bring in the pain (ROS production).Melanization – this immune response is specific to invertebrates. The production of melanin, a derivative of tryosine, is triggered by the immune system and within minutes microbes (especially bacteria) can be encapsulated within the melanin – the really cool part is that the act of encapsulation of the microbe by melanin triggers the production of reactive oxygen species which can destroy the microbe. Again, when you inhibit melanization USUALLY this helps bacteria thrive and cause disease. 

Ok, so they have two immune components, and eureka! They have two Drosophila mutants that correspond to two different immune systems. Introducing: Mutant #1, which has increased phagocytosis and decreased melanization and Mutant #2, which has increased phagocytosis and increased melanization. Using these mutants they will try to understand the relationship of these two immune components in clearance of bacterial pathogens.

One more layer, they now have two bacterial pathogens. Bacterial pathogen #1: Listeria monocytogenes, which replicates within cells. Bacterial pathogen #2: Streptococcus pneumoniae, which replicates outside of cells. The differences in pathogen lifecycle will reveal the importance of each immune component during these two very different infections.

What they found was:

By using Mutant #1 they found the immune contribution of phagocytosis was dependent on the type of bacteria that was used for the infection.

If they infected flies with S. pneumoniae, or the bacteria that replicates outside of the cells, they found phagocytosis was the “death knell” for these bacteria. Therefore, if they amped up phagocytosis, they saw increased clearance of S. pneumoniae, or basically NO sick flies.

HOWEVER, if they infected flies with L. monocytogenes, or the bacteria that replicates within cells, phagocytosis HELPED this pathogen replicate and cause disease. This makes sense because L. monocytogenes can only replicate within cells, therefore it needs phagocytosis to be picked up from the environment so it has access to the intracellular environment.  In fact, they found that in both fly mutants (both have increased phagocytosis) you could increase the frequency of L. monocytogenes infection, tricky little bugs.

Let’s think about this in context. What’s the point of having a robust immune system if sneaky bugs like L. monocytogenes are just going to use it against you? There must be a very special amount of phagocytosis that is just enough to clear extracellular bacteria but not enough to help intracellular bacteria, but what is this amount?

They say thinking of it this way is a trap, and that it’s more complex than the perfect amount of phagocytosis…  by using their second mutant that has increased phagocytosis and increased melanization they found that little melanization (Mutant #1) increased killing flies by infection with L. monocytogenes (no environmental stress party!), and that increased melanization (Mutant #2) showed decreased amounts of killing flies by infection with L. monocytogenes – independent of level of phagocytosis. So things are more complicated than they seem!

I would love to tidy this post up with a nice bow, but the truth is this type of data opens more doors than it is closing… so the research continues…

Keep on fighting the fight.

How do all of our complex multi-factorial immune components combine to clear bacterial infections? How do they all relate, and what is the perfect balance of just enough immune function, but not too much?

Onward microbiologists and immunologists alike! 

 

Chambers MC, Lightfield KL, & Schneider DS (2012). How the fly balances its ability to combat different pathogens. PLoS pathogens, 8 (12) PMID: 23271964

Thursday
Dec272012

News Highlights of the Holidays

Glitchiness

Indeed (NBC).

Pulsars: Those crazy-dense, fast-spinning leftovers of supernova explosions. Their spin rates are very stable over time, rivaling and often besting atomic clocks in their precision. Their rotation times decrease as the pulsars lose energy and grow old(er than they already are), but they decrease predictably—most of the time. Scientists have observed “glitches,” spin-ups that occur all of a sudden. The prevailing idea behind glitches is that the strange stars—which are believed to have a “crust” (of sorts) with a superfluid under the surface. The superfluid can transfer some of its rotational energy (it’s sloshingly spinning too) to the crust. When that happens, the spin as a whole (which we measure from the crust) is faster. Or so scientists thought. Dr. Nils Andersson and Dr. Wynn Ho from the University of Southampton say, “We don’t think so, and we’ve got some math.” The math says that the volume of superfluid inside a pulsar is not large enough to produce the observed effects. Isn’t it great to be wrong? University of Southampton.

 

The Universe’s Baby Picture

This will be so embarrassing when it's a teenager (WMAP).

The Wilkinson Microwave Anisotropy Probe (WMAP) was launched in 2001 and took observations for nine years. It was looking at the cosmic microwave background, remnant radiation from the early universe that did not come from stars, galaxies, and the like but suffuses the entire universe with a (mostly) uniform “glow.” It’s the earliest picture we have, and it can tell us a lot about how that baby universe became this mature, grown-up thing we see today. Just like babies have uniform skin, skin, skin and then the “anomalies” of eyes, nose, mouth, the early universe was the same all over, except where it wasn’t. These anomalies—or anisotropies as they are called in cosmology-speak—are the seeds of structures to come later. Scientists have finally finished analyzing WMAP’s massive dataset and have some things to tell you:

  1. The universe is only 4.6% atoms.
  2. 24% of it is dark matter.
  3. 71% of it is dark energy.
  4. This place is weird; take me home.
  5. Stars first shone 400 million years after the Big Bang.
  6. Inflation—when the universe grew 1,000,000,000,000,000,000,000,000 times in 1/1,000,000,000,000th of a second—happened. Anisotropies formed during this mind-blowing epoch.
  7. Surprise, the Big Bang happened. In case you were wondering.

Johns Hopkins University.

 

Germany Jumps on It

That's a whole lot of countries that have "our place in the universe" and "technological innovation" as a high priority. Notably absent: US. Click to enlarge this political and scientific mistake (SKA).

The Square Kilometer Array (SKA) is the largest, most sensitive, most expensive telescope every conceived, is an international collaboration by economic and space-based necessity (read more about this project’s background and purpose). It, if completed, will truly be one of the wonders of the twenty-first century world. And Germany has put forth the weapons (money) in the fight for scientific relevance. It joins Australia, Canada, China, Italy, the Netherlands, New Zealand, South Africa, Sweden, and the UK—aka, everybody besides us, the US—in the SKA Organization. SKA Telescope.

 

 

 

World Still Here

Don't run, John. It's not the end of the world (2012: The Movie).

In other news, the world did not end on December 21, 2012. You are still here. I am still here. John Cusack is still here. Let us move on to the next apocalyptic scenario. 

Monday
Dec172012

Black hole jets: Same-same* no matter what

As we all know, it doesn't matter if you're black or white. Now we also know that it doesn't matter if you're as massive as billions of stars and stuck in the middle of a galaxy or only 10 times the mass of the Sun and hanging out in a spiral arm--if you're a black hole, your jets apparently work the same way.

In a December 14 Science paper entitled "A Universal Scaling for the Energetics of Relativistic Jets from Black Hole Systems," Nemmen (et al.) showed that a black hole--regardless of its size--uses the same fraction of its jet's kinetic energy to produce the gamma rays that we observe on Earth.

First, this statement:"It's a bit like a poor man and a billionaire spending the same percentage of their incomes on their heating bills," said team member Markos Georganopoulos, an associate professor of physics at the University of Maryland. (Which, of course, they might, depending on the size of the billionaire's house.)

Second, let's look at this topic by going backwards through the title of the paper:

"Black hole systems"

As it fuses heavier and heavier elements, a massive star comes closer to the end of its life. As it collapses, these jets form and, in their extreme energy that could kill all of us from light-years away, send out gamma rays. RIP this star. I never knew thee. (Credit: NSF)

The astronomers studied two different types of black holes: the kind that are known affectionately as "supermassive" and form the cores of galaxies, and the kind that are just the dead-ends of massive stars.

The astronomers who wrote this paper studied both kinds, because they wanted to see if the same rules that applied to small ones applied to big ones.

 

 

"Relativistic jets"

Massive stars, when they are about to die, are running out of fuel. The balance between the forces of hydrostatic pressure from their interiors (outward) and gravity (inward) begins to be off--pressure decreases as the star runs out of fuel, and gravity starts to win. In the cases of black holes, gravity wins big-time; the star collapses in on itself, rips a "hole" in spacetime, and all that other stuff you've heard. It doesn't collapse instantaneously, though; the layers cascade inward like ... like ... well, like nothing within our everyday experience. Somehow (and don't let the astronomers fool you; they're not sure how), this collapse leads to a disk of material that has two jets shooting out of its center. When the jet pierces the collapsing star's surface--BOOM. Where "BOOM" is interpreted as "GAMMA RAYS." In your face. 

Maybe. If the jet is pointed toward Earth. And we're looking at the right time, as it lasts from a few milliseconds to a few minutes. In those few seconds, though, the black hole will shoot out as much energy in gamma rays as the Sun puts out total in 3 billion years.

That tiny red dot in the middle is M87. The insane things extending out of it are its relativistic jets. Note how much bigger they are than the galaxy, and note how big galaxies are. (Credit: VLA).

Active black holes in the centers of galaxies--quasars and blazars--also have disks and jets of accelerated material. But as long as there is gas in the middle of the galaxy, those disks and jets remain, so we can see their gamma rays for much longer than a few minutes. Some have been around for so long and are shooting out material at such high speeds that their jets extend much farther than the galaxy itself. 

"Relativistic" just means "traveling at a significant fraction of the speed of light, such that Einstein's theory of relativity must be taken into account."

"The Energetics"

Or, how much of its total energy does each type of black hole put into its jet? Astronomers asked two questions about the 54 stellar-mass black holes and the 274 quasars/blazars in the study:

  1. How bright are the gamma rays?
  2. How much power goes into accelerating the particles in the jets?

Proportional to energy in the same way 4eva (Credit: Zazzle).

Of course, the scientists, like the stereotypes they are, wanted to examine the relationship between the two quantities--brightness and power. And they wanted to examine the relationship between the relationships between brightness and power in supermassive and semi-massive black holes.

Which brings us to

 

"Universal Scaling"

Scientists hypothesize that power in a black hole's jet is proportional to the gamma-ray energy in a meaningful way. Here, "meaningful" implies that the power-energy connection is the result of some specific physical process (or processes). It has a cause. 

But that is pretty straightforward.

A more interesting question, and the question the paper asks is, "Is the power-energy connection the same whether a black hole is 10 times the mass of the Sun or 10,000,000,000 times the mass of the Sun?" The answer, while it may sound obvious, is not. You would think that a black hole is a black hole is a black hole. But stellar-mass black holes form from massive stars and supermassive black holes form from ... well, we don't know, really, but definitely not from the deaths of 10,000,000,000 solar-mass stars. Since their origins are different, it seems possible that other properties could be different too. 

But the activity of black holes both large and small "is governed by the same set of rules -- whatever they happen to be," says the NASA/Goddard press release. 

To make gamma rays of the observed brightness, black holes use 3-15% of the total power in their jets. It doesn't matter if they're old or newborn. It doesn't matter if they're huge or puny. It doesn't matter if they only put 10^42 ergs/second into their gamma rays or 10^42 ergs/second into their jet power--independent of all that, the relationship remains.

Sigh. (Credit: NASA/GSFC).It's kind of romantic.

But what does it mean?

It means either that

  1. Whatever causes these jets is the same no matter what.
  2. There are two different mechanisms that cause jets, and both produce exactly the same results.

It's kind of an inconclusive conclusion, and the paper does not definitively say what that mechanism (or those mechanisms) is, but it brings us one step closer.

In a more human and political conclusion, Neil Gehrels, an author on the paper and the principal investigator of NASA's gamma-ray-detecting Swift, said, "One especially useful outcome of this research will be to foster greater communication between astronomers studying GRBs and those working on active galaxies, which in the past we've tended to regard as separate areas of study." 

 

ResearchBlogging.org Nemmen, R., Georganopoulos, M., Guiriec, S., Meyer, E., Gehrels, N., & Sambruna, R. (2012). A Universal Scaling for the Energetics of Relativistic Jets from Black Hole Systems Science, 338 (6113), 1445-1448 DOI: 10.1126/science.1227416

 

 

 *According to Wikipedia, "Same Same was a pop band consisting of identical twinsBob and Clint Moffatt, originally members of the Canadian boyband The Moffatts. Same Same was based in Thailand, and they sold albums and perform mainly in Thailand,IndonesiaMalaysia and the Philippines." Why? Who knows.

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