Science-- there's something for everyone

Wednesday, March 31, 2010

Oxygen without photosynthesis

Margaret Butler of University of Queensland and her colleagues have identified an unusual mechanism of oxygen synthesis. It’s produced by the nonphotosynthetic bacteria Candidatus Methylomirabilis oxyfera.

M. oxyfera, a member of a group of anaerobic bacteria called NC10 first found in caves in Australia, was isolated from some ditches in the Netherlands. The bacteria were believed to be capable of converting methane to carbon dioxide, and the researchers wanted to test this. They placed the bacteria into a chamber that would allow them to carefully measure any oxygen or nitrogen either entering or leaving the chamber.

The bacteria were metabolizing methane, but that's not all. To their surprise, the scientists found that oxygen was being produced by a hitherto unknown mechanism. There is no known enzyme that will convert nitric oxide to oxygen and nitrogen gas, yet these bacteria have apparently invented such an enzyme.

Because these bacteria may predate photosynthetic bacteria on the early Earth, they could have been major contributors to oxygenating the atmosphere. In that case, aerobic organisms that utilize oxygen may have arisen before photosynthetic organisms.

One caveat is that the researchers were unable to grow pure cultures of M. oxyfera. Instead, they grew mixes of bacteria and then used DNA sequencing to reconstruct the M. oxyfera genome as well as to pick out some likely candidates for the oxygen-producing enzyme. In other words, the scientists haven’t proved that it is M. oxyfera making the oxygen. I’m sure that’s next.

Tuesday, March 30, 2010

Glow-in-the-dark sperm

Scott Pitnick and his colleagues from Syracuse University have created fruit flies (Drosophila melanogaster) that have red or green glowing sperm. The researchers were able to follow the sperm of competing males through the females’ reproductive tracts.

Photo credit: Scott Pitnick, Syracuse University

Reproductive tract of female D. melanogaster initially mated to green sperm male then remated to red sperm male. Green sperm heads have left the storage organs and can be seen mixing with red sperm heads in the bursa.

Among their findings: the sperm from both males traveled through the storage organs and reached the eggs at rates unrelated to the time of copulation. It was abundance, rather than timing that mattered.

Monday, March 29, 2010

Regenerative mice

Knocking out a single gene in mice greatly increases their regenerative capabilities. The gene in question is called p21 (a description of the molecular weight of the resulting protein).

Lead scientist Ellen Heber-Katz at the Wistar Institute first noticed that mice lacking a functional p21 gene had increased healing abilities over ten years ago. In 1996, she and her team were working with a particular type of mouse called MRL. They had pierced the mice’s ears for ID markers, but the holes closed up and healed completely. I too have pierced ears, and even though I sometimes do not wear earrings for months at a time, my holes have never healed. Not only did the mice heal holes in their ears, but they were also able to regrow cartilage and skin with no scarring. Rather than forming a scar at the wound site, the MRL mice formed a blastema, a structure normally seen only in developing embryos or in regenerative species such as salamanders.

What was up with these mice? It turned out that the MRL mice did not have active p21. When researchers examined other strains of mice that had had their p21 genes specifically knocked out, they saw the same results.

P21 is cell cycle regulator. In conjunction with other factors, it controls cell division. Under normal conditions, it is turned on in cells after DNA damage, preventing those cells from possibly running amok and becoming cancerous. Although the researchers did not see increased cancer in the MRL mice, they did notice an increase in apoptosis (programmed cell death), another cellular mechanism for removing damaged cells.

To be clear, the MRL mice were not regrowing limbs. Also, the researchers did not take normal adult mice and knock out their p21 genes, the mice were born without p21. On the other hand, humans too have p21 genes (though in our case they’re called CDKN1A). Perhaps we will one day be able to selectively knock out p21 at wound sites, and then, who knows?

Sunday, March 28, 2010

Just for fun: Ion Micrograph

Every year, the 'International Conference on Electron, Ion and Photon Beam Technology and Nanofabrication' (EIPBN) includes a 'Bizarre/Beautiful Micrograph' contest.

Here's an example. This specimen won the 2005 Most Bizarre Prize.

Nano Toilet

Title: Chisai Benjo
Description: An effective method of dealing with defects is to find a collection site.
Magnification: ~15,000X
: SII NanoTechnology Inc. / SMI2050MS2
Submitted by: Takahashi Kaito (SII Nanotechnology Inc.)

And for you Star Trek fans, here's the Best Ion Micrograph from 2003:

Title: Nano Trek
Description: Nano Space - The final frontier. The space ship Enterprise NCC-1701D of Star Trek was fabricated in one-billionth scale by 30 kV Ga+ focused-ion- beam CVD using phenanthrene gas. Length 8.8 µm.
Magnification (3"x4" image): 5,000X
Instrument: Seiko Instruments,Inc. SMI9200
Submitted by: Takayuki Hoshino & Shinji Matsui, Himeji Institute of Technology

Hat tip: Bad Astronomy

Saturday, March 27, 2010

Forget about check-out lines with new RFID

Researchers from Sunchon National University are hoping their method of making radio-frequency identification (RFID) tags will make check-out lines a thing of the past.

RFID tags are not new. The technology dates back to the World War II era and the devices themselves have been used for several decades. Today, RFID tags are found in lifestock, library books, toll road transponders, foot race timing chips and uncountable other places. One entomologist even glued tiny RFID tags to ants.

Gyoujin Cho and his colleagues from Sunchon National University, South Korea have invented a way to print out the tags in larger quantities. Rather than ink jet printers, Cho and his team have been using a rotogravure process. This ‘roll-to-roll’ technique adds the tags onto plastic foil. Instead of ink, the lab is using single-walled carbon nanotubes provided by James Tour (from Rice University), who is also advising Cho’s lab.

Credit: Gyou-Jin Cho/Sunchon National University

So far, the new tags work only at very short range and are too large for many applications. The researchers are working on reducing the size as well as increasing the range and the amount of information the tags can contain. Their ultimate goal is to allow shoppers to push their carts past scanners which will read all the tags at once and charge their credit cards.

Friday, March 26, 2010

The X-woman: a new species?

Johannes Krause and Svante Pääbo from the Max Planck Institute in Germany and their colleagues have sequenced the mitochondrial DNA (mtDNA) from a 40,000 year-old hominid finger bone. To their surprise, the DNA did not match either modern human or Neanderthal mtDNA, the only two hominid species known to be in the area at that time, but may be from a third species, representing a hitherto unknown migration out of Africa. The scientists dubbed this specimen the ‘X-woman’.

The bone fragment was originally found in the Siberian Denisova Cave in 2008 by Russian paleontologists, but only recently subjected to mtDNA sequencing. The researchers were extremely thorough, rereading the sequences well over a 100 times. That mtDNA was compared with mtDNA from 54 modern humans, from a 30,000 year-old modern human found in Russia and from 6 Neanderthals. Neanderthal mtDNA usually differs from that of Homo sapiens in about 200 spots, but the mtDNA from the X-woman differed from modern humans in about 400 positions.

The implication is that the bone fragment is from a new species of hominid, one which diverged from modern humans and Neanderthals about a million years ago.

simple xwoman tree

Credit: Nature

An alternate possibility will require a brief primer on mtDNA. Mitochondria are the energy factories within our cells. Although like all parts of the cell, they rely on information stored in the cell’s nucleus (nuclear DNA), mitochondria also have DNA of their own. Upon fertilization, the much larger egg cell contains maternal nuclear DNA as well as a cell’s worth of mitochondria, each containing its own DNA. The sperm contributes only nuclear DNA to the fusion. As a result, mtDNA is passed exclusively down the female line, whereas the nuclear DNA is a mixture from both parents.

Therefore, the X- woman might represent a new species, or she might be a fully modern human or Neanderthal who had a female ancestor who was a different species, say Homo erectus. That tryst might have occurred so long ago that the X-woman’s nuclear DNA, having been diluted with human (or Neanderthal) DNA over many subsequent generations, shows no more signs of that ancestor. The mtDNA was not diluted out, and thus does differ considerably from either humans or Neanderthals.

The scientists intend to sequence the X-woman's nuclear DNA in order to put this question to rest. No matter what they find, this will be the first time DNA sequencing was used to identify an extinct species.

Thursday, March 25, 2010

New, bigger type Ia supernovae

Type Ia supernovae occur when white dwarf stars explode. Until recently, it was understood that the stars undergoing this type of explosion had an upper size limit, known as the Chandrasekhar limit after the Indian astrophysicist Subrahmanyan Chandrasekhar. It was thought that larger white dwarf stars would collapse under their own weight rather than becoming type Ia supernovae. This limit, of about 1.4 times the mass of our Sun, was important because it allowed cosmologists to measure distances to the galaxies containing those resulting surpernovae.

Brighter white dwarf supernovae are occasionally discovered, but scientists weren’t sure whether they were also larger than the Chandrasekhar limit. That changed when a French and American collaboration called the Nearby Supernova Factory (SNfactory) measured the mass of one such anomaly, dubbed SN 2007if (no, the ‘if’ doesn’t imply that anyone was wishing on a star). At about two times the mass of the sun, SN2007if is indeed above the limit.

It’s not clear how these “super-Chandrasekhar” supernovae form. Richard Scalzo of Yale, suggested that 2N2007if was actually two white dwarfs that had merged together. In any case, astronomers will have to rethink using type Ia supernovae as cosmic rulers.

As Scalzo said:

Supernovae are being used to make statements about the fate of the universe and our theory of gravity. If our understanding of supernovae changes, it could significantly impact our theories and predictions.

Wednesday, March 24, 2010

The taste of fat

When I was a kid, people were thought to detect four different tastes: sweet, salty, bitter and sour. Thanks to the work of Russell Keast and his colleagues, we now know that humans can actually detect six different types of tastes.

It was also once thought that taste buds in distinct regions of the tongue were responsible for those tastes. For example, sweet was supposed to be detected by the tip of the tongue. For some reason, all the experiments my friends and I conducted to see if we only tasted sweet with the tips of our tongues never worked. Of course, we now know those experiments didn’t work because all parts of the tongue can detect all the different tastes. In addition, a fifth taste was discovered called ‘umami’ or ‘savoriness’.

Keast and his team have now added a sixth type of taste to the list. It turns out that people can taste ‘fat’. The researchers tested 31 people to see what their threshold of sensitivity was to a variety of common fats, such as oleic acid. Although most people could detect the taste of fat, there was considerable variability.

The scientists took a second group of 54 volunteers and, as with the first group, screened them for oleic acid sensitivity. This time, they also compiled diet and body mass index (BMI) records for each subject, and asked the subjects to rank how much fat they thought were in custard samples containing either 0, 2, 6 or 10% fat. It turned out that the people who were most sensitive to the taste of fat were best able to correctly rank the custard samples by fat content, and also had the lowest fat intakes and BMI.

In other words, insensitivity to the taste of fat correlated with higher BMI. To be clear, this finding does not necessarily imply causation. People who are less sensitive to the taste of fat may eat more fat to compensate, or people who eat more fat may have become desensitized to the taste of fat. Either way, the finding has interesting implications for the weight loss industry.

Tuesday, March 23, 2010

ID'd by our bacteria

Human beings are literally covered with bacteria, both inside and out. It’s estimated that we have about 150 different species of bacteria on our hands alone. Interestingly, we each possess a unique personal flora. Only about 13% of the bacteria on my hands will also be on yours. Noah Fierer and his University of Colorado team used that information to see if they could identify the owner of certain objects from the bacteria on those objects.

By some estimates, the microbes in and on our bodies outnumber the cells containing our chromosomes by ten to one. Every time we touch something, we leave a trail of bacteria from our hands on the surface we touched. Fierer and his colleagues swabbed computer keyboards and computer mice, as well as the fingers and hands of volunteers who may or may not have touched those devices. Using a rapid DNA sequencing technique called ‘metagenomic survey’, the types of bacteria from the various samples were identified and compared.

The scientists had a 70-90% accuracy rate in matching the right keyboard or mouse to the right user. In addition, they found that the bacterial colonies on the tested objects remained virtually unchanged for up to two weeks.

Although this could one day be a promising addition to the forensic science arsenal, allowing detectives to identify who touched objects even without fingerprints, the accuracy would have to be drastically improved first. Fierer himself admits that his experiments were simply proof-of-concept tests.

As Fierer explains:

If the technique were perfected, it would be amazingly compelling. After all, not even identical twins share the same skin flora.

Monday, March 22, 2010

Just for fun: Skull animations

Larry Witmer and his students at Ohio University study vertebrate heads. They now have a Youtube channel with almost a hundred animations of animal skulls, both living and extinct.

This one is an animation of the skull, brain endocast, and inner ear of the Oligocene creodont Hyaenodon (a carnivorous mammal which lived about 30 million years ago).

Hat tip: Laelaps.

Sunday, March 21, 2010

Golden bullets for cancer

Killing tumor cells without harming normal tissue is the great challenge of cancer treatment. Carl Batt and his team from Cornell University are working on a way to do just that.

The researchers used a two step process to ambush tumor cells from the inside. They first attached an antibody specific to colorectal cancer cells to nanoparticles made of gold and iron oxide. The antibodies bound the tiny constructs to the surfaces of the cancer cells, which promptly engulfed the nanoparticles. The next step was to use a near-infrared laser on the cells. This low-powered laser has no effect on normal cells, but the gold inside the cancerous cells absorbs the radiation, heating and killing those cells. Tissue culture tests of this treatment have been promising.

Another team led by Younan Xia from Washington University used gold nanocages to achieve a similar effect. In their case, the targeting and killing of tumor cells in mice was successfully tested.

Infrared images made while tumors were irradiated with a laser show that in nanocage-injected mice (left), the surface of the tumor quickly became hot enough to kill cells. In buffer-injected mice (right), the temperature barely budged.
Photo credit: WUSTL

Xia and his colleagues are working to increase the specific uptake of the gold particles by tumor cells. In addition, they are considering filling the hollow nanocages with anti-cancer medicines.

Saturday, March 20, 2010

Human cells take a random walk

Single celled organisms such as bacteria or amoebas must move around in their environments. What is perhaps less obvious is that the individual cells within a multi-cellular organism also migrate throughout the body. This movement can be benign or even necessary, as during development or immune responses. On the other hand, cell movement is a staple of metastatic cancer. How exactly do cells move around within a body? Peter Cummings and his team from Vanderbilt University set out to answer that question.

The researchers observed animal movement patterns. As animals ranging from marine predators to monkeys search for food, they move in a pattern called ‘Lévy motion’. This is a variation of a ‘random walk’ (successive random steps) in which longer flights of motion are separated by shorter jumps. Because individual cells must find food and oxygen as they travel through tissue, the scientists expected to find the same pattern of movement internally.

To test this, Alka Potdar, a co-author on the study, cultured human mammary epithelial cells and closely observed their movement across plastic plates. These cells move only a micron (one millionth) of an inch per minute, and Potdar was interested not in the total distance moved, but in plotting every change of direction along the way. Luckily, she could use time-lapse video-microscopy, otherwise I’m not sure whether she’d have gone mad or blind first.

In any case, Potdar found that the cells did not use a Lévy random walk, but the closely related 'bimodal correlated random walk' (BCRW). In this movement pattern, the cells travel in one direction, then pause briefly as if to reorient themselves before moving again.

Other cell types also seem to follow the BCRW search pattern when migrating through bodies. This knowledge could have an impact on cancer study and treatment.

Computer generated two-dimensional random walk

Friday, March 19, 2010

Following DNA repair proteins with quantum dots

DNA is subject to damage from UV light, toxins, and misreading during replication. These errors are repaired by a variety of specialized proteins that check and fix the DNA strands. Researchers led by Bennett Van Houten of the University of Pittsburgh have been able to directly observe this process in E. coli.

They labeled two exinuclease repair proteins, UvrA and UvrB with different colored quantum dots (semi-conductor nanocrystals). They combined the tagged proteins with untangled stretches of DNA they called ‘tightropes’ and watched what happened.

Cadmium selenium Quantum Dots (metal nanoparticles that fluoresce in a variety of colors determined by their size)

UvrA alone would bind to a spot on a DNA molecule, remain in place for about seven seconds, then hop to a different DNA molecule. UvrB alone did not bind DNA at all. When UvrA was combined with UvrB, this new complex was capable of sliding along the DNA strand for up to forty seconds. About a third of the UvrAB complexes exhibited what the scientists called ‘paused motion’, in which the repair proteins seemed to hesitate at specific sites.

Co-author David Warshaw of the University of Vermont suggested:

Paused motion could represent UvrAB complexes checking for structural abnormalities associated with DNA damage.

I dealt with the issue of proteins moving along DNA strands in a previous post, though at that time, the interaction was not directly observed.

Thursday, March 18, 2010

Candy-cane plants avoid gall flies

Over the eons, plants have developed a variety of tactics for dealing with herbivores, ranging from impenetrable bark, sharp thorns, to the production of toxins. Michael Wise, Warren Abrahamson and Julia Cole have discovered a novel mechanism employed by some plants for fending off insect attacks.

The team examined goldenrods, a common prey of the gall-inducing fly Eurosta solidaginis. This fly lays its eggs in apical leaf buds (the growing tip of a leaf), preventing the plants from flowering.

Some members of one species of goldenrod (Solidago altissima) bend their apices downward into a candy-cane shape. This dip occurs slowly, beginning in early spring. This corresponds with the reproductive cycle of the flies, so that during the peak egg-laying times, the plants are at their most downward-angled. By late summer, the plants have straightened out and are flowering.

A gall fly sits on a leaf near the top of the plant, seemingly oblivious to the nodding apical-leaf bud just centimeters below.

Photo credit: Courtesy of Michael Wise

Wise and his colleagues wondered whether the candy-cane shape offered any protection from the flies. They noticed that the same S. altissima plants that normally bent their stems would keep their stems straight if grown in the shade. Thus, the researchers set up a greenhouse experiment comparing bending goldenrods grown in sun (where they bent over) and in shade (where they stayed straight), with non-bending goldenrods grown in sun and in shade.

They found that the flies laid their eggs equally in all straight-stemmed plants, but not at all in the candy-cane shaped plants. This indicates that it is indeed the shape of the plant that is preventing egg-laying, rather than a distaste for the type of plants that can sometimes duck their stems or for growth conditions.

Surprisingly, bending specimens make up a minority within goldenrod populations. Clearly, there are advantages to staying upright that supercede the disadvantage of greater predation.

Wednesday, March 17, 2010

Just for fun: 50 years of space exploration

This stunning graphic depicting all the craft and satellites sent into space over the past 50 years was created by Sean McNaughton and Samuel Velasco, of National Geographic and 5W Infographics, respectively.

The images are from NASA/JPL.

Planet - Space exploration - Timeline of Solar System exploration - Fotopedia

To zoom around and explore, go to the National Geographic site here.
The easiest way to use it is to orient yourself first on the small insert in the top right corner, then once you have the size and position you want, use your mouse to move around the larger picture.

On the very bottom is a linear size scale. Look how far out the Voyager and Pioneer spacecraft are!

Tuesday, March 16, 2010

Nitric Oxide wound wrap

Kenneth Balkus and Harvey Liu of the University of Texas have invented a nitric oxide (NO) releasing bandage. Their wrap consists of three components: NO, Zeolite A, and a polyactic acid (PLA) polymer.

NO is well known to promote wound healing and to preserve organs prior to donation. Although too much NO can be toxic, too little can cause problems such as ischemia, in which blood flow to organs is reduced or eliminated. Therefore, additional NO can help diabetics, who have notoriously poor blood flow in their extremities, as well as preserving organs slated for transplant.

Zeolites are porous crystals made of aluminum and silicate. Known as molecular sieves, synthetic zeolites can be used to sift molecules by size. Although zeolites do occur in nature, they are rarely pure enough for laboratory use. Zeolite A is cubic, forming a cage within which NO can be held for transport and delivery.

The final part of the triad is the bandage itself, which is made of PLA. PLA is a water-repellent polymer and is both biocompatible and biodegradable. It is made via a process called ‘electrospinning’, in which a droplet of polymer is stretched using high voltage.

The researchers combined the PLA fiber with NO-infused Zeolite A. So far, the scientists have shown that their novel bandages can release controlled amounts of NO, and that the wraps successfully increased blood flow in rat hearts. If further studies are also positive, the new wrap could be used to protect organs prior to donation, as well as to make socks for diabetic patients.

A scrap of the therapeutic NO-releasing bandage

Monday, March 15, 2010

Shorter days after earthquakes

As I’m sure you all know, Chile suffered a devastating 8.8 magnitude earthquake on Feb. 27th. This was during the Vancouver Winter Olympics, leading to a failed attempt by one Chilean skier to return home early. Some 500 people were killed, with many more missing or homeless.

By comparison, the recent Haitian earthquake registered only 7.0, but was responsible for several hundred thousand deaths. Remember, earthquakes are rated on a logarithmic scale. In other words, the Chilean earthquake was almost a hundred times stronger than the Haitian quake. The proximity to populated centers and the lack of infrastructure led to the staggering death toll.

What you may not have known is that the February earthquake apparently shifted Earth’s figure axis (the axis about which Earth’s mass is balanced) by about 8 centimeters, or 3 inches. In consequence, the temblor shortened the length of our days by about 1.26 milliseconds. That’s millionths of a second for those of you resetting your alarm clocks.

How did this happen? The Chilean earthquake was what is known as a ‘thrust’ earthquake, in which one tectonic plate dives beneath another. The slightly reduced surface area caused the Earth to speed up like an ice skater drawing in her arms, in an analogy drawn by Keith Sverdrup, a seismologist at the University of Wisconsin-Milwaukee.

Only extremely powerful thrust earthquakes can alter the Earth’s figure axis in this manner, which is why the Earth’s rotation is not constantly changing. The position of the earthquake along the globe also determines the severity of the effect, with equatorial quakes being less effective.

Sunday, March 14, 2010

Precursor molecules of life found in space

Artist's impression of the Herschel Space Observatory

Astronomers have found evidence that the Orion nebula (a nearby stellar nursery) contains chemicals consistent with early life. The researchers used the Heterodyne Instrument for the Far Infrared (HIFI) on board the Herschel Space Observatory (launched in 2009) to detect infrared light coming from the Orion nebula. The light in turn was subjected to spectrum analysis, which told the scientists what kinds of molecules were present in the nebula.

Among the chemicals found were several molecules that are necessary precursors of life, including water, carbon monoxide, methanol and sulfur dioxide.


Spectrograph of data collected by Herschel. Peaks indicate the presence of the labeled molecules.
Image credit: ESA, HEXOS, HIFI Consortium.

To be clear, this does not indicate whether or not life exists in the far-flung reaches of space. It simply shows that it is not impossible for life to exist there. Actually finding life, if it exists, will be much trickier. Still, it’s nice to know that it could be out there.

Saturday, March 13, 2010

Sequencing family genomes

Hundreds of species, including Homo sapiens, have had their genomes sequenced, and more are being added to the list all the time. You can peruse a list of sequenced genomes here. In general, one or a few specimens of each species are used for genomic studies. Notoriously, John Craig Venter used his own DNA during his time at Celera Genomics.

David Galas and his team from the Institute for Systems Biology in Seattle have added a new twist by performing the first whole genome sequence of four members of a single family. The researchers sequenced the genes of both parents and two children within a single family. The siblings both suffer from a recessive genetic disorder known as Miller syndrome. After sequencing all four family members, the scientists were able to narrow down the list of possible genes responsible for this rare craniofacial disorder to just four. As more families have their genomes sequenced, associating disorders with specific mutations will be much easier.

In addition, by comparing the kids’ DNA to that of their parents, the geneticists found that the intergenerational mutation rate was actually about half the previously expected rate. This finding could have implications for estimates of genetic diversity and human dispersal rates.

Friday, March 12, 2010

Blocking mosquito pee to save lives

Aedes aegypti mosquitoes are major carriers of disease. They can transmit Dengue and yellow fevers, among other illnesses. They do this by picking up the viral pathogens from an infected person during a blood meal, and transferring the viruses to the next person at a subsequent blood meal. OK, I knew all that.

Here’s what I did not know: apparently, the mosquitoes have to urinate as they feed in order to balance both their salt and fluid levels, and their flight ballast. That just makes the thought of getting mosquito bites so much more pleasant.

There’s some good news though. Researchers from Cornell University have found a protein in the skeeter’s renal tubes that is critical for urination. When this protein is blocked, the insects’ ability to pee is adversely affected. The scientists hope that this will also prevent the mosquitoes from leaving infected patients and transmitting diseases.

Thursday, March 11, 2010

Wednesday, March 10, 2010

Using plants as models for disease

Some proteins are remarkably well conserved in both plants and animals. Not only does this demonstrate how closely related all living things on Earth are, but it also opens up new avenues of research. Proving that point, Wendy Peer of Purdue University successfully rescued plants deficient in one class of enzymes by giving them a mammalian equivalent.

She and her team knocked out the APM1 protein in the small flowering plant Arabidopsis thaliana. APM1 is one of a class of M1 aminopeptidases that, in humans, are responsible for trimming specific amino acids off of peptide chains, thereby either activating or deactivating those proteins. In addition, the M1 enzymes are thought to rid cells of excess proteins that may be responsible for Alzheimer's disease. Although not as well understood in plants, APM1 is essential for normal plant growth and reproduction.

Peer and her colleagues treated Arabidopsis plants with an APM1 inhibitor, destroying the plants’ natural enzyme. The researchers then genetically altered the plants to produce mammalian M1 proteins. The mammalian proteins effectively rescued the plants. In other words, the mammalian proteins were similar enough to the plant proteins to do the exact same job in the plant cells.

The ability to choose plant models rather than animal models would be a welcome addition for researchers. Not only are plants relatively easy to maintain, but working with them would also bypass many ethical questions faced by both scientists and the public.

Tuesday, March 9, 2010

Red snow of Antarctica

Blood Falls, an aptly named saltwater overflow from a subglacial lake in Antarctica, has been marveled at for almost a hundred years. The lake became trapped under Taylor Glacier between 1.5 and 2 million years ago. Occasional overflows allow scientists to study the trapped waters without digging through the glacier. Originally, explorers assumed that the red color came from algae. Subsequent research showed that it was the high amounts of iron in the water that was responsible for the color.

Recently, Jill Mikucki of Dartmouth College discovered that the water samples were teeming with 17 kinds of microorganisms. These organisms had survived 400 meters under a glacier with no light, heat or oxygen. How?

Mikucki and her team found that the Antarctic microbes were genetically related to microorganisms known to use sulfate rather than oxygen for respiration. They hypothesized that the newly found microbes use sulfate and iron, both present in the water, to metabolize organic matter trapped in the subglacial lake. Although never before observed, such a mechanism is theoretically possible. If confirmed, this could allow life to thrive on such icy, inhospitable places as Jupiter’s moon Europa.

Picture of Blood Falls

Photo credit: Benjamin Urmston

You can see more photos here.

Monday, March 8, 2010

A step toward quantum computing

Mark Saffman and other physicists at the University of Wisconsin-Madison have taken an important step in creating a quantum computer.

As computer components continue to shrink, they approach atomic size. At that level, quantum mechanics is required to understand and manipulate those components. In the past, ions, or charged particles, have been trapped and used to run small computing programs. However, you need a certain number of quantum bits, or qubits, to get decent computing power. Ions, by their very nature, tend to interact with each other and with their environment. For this reason, it’s difficult to scale up the computing power when relying on ions.

In contrast, the University of Wisconsin physicists used two neutral (uncharged) rubidium atoms. They first trapped the atoms, and then used a laser to create a controlled-NOT (CNOT) gate between the atoms and to entangle the two atoms with each other. The CNOT gate is essential circuitry for quantum computers. Saffman’s team produced the first CNOT gate between neutral atoms.

Although this work was done with only two atoms, the scientists are hopeful that they will be able to scale up considerably. As a start, they are now working with 50 uncharged atoms to see if similar results can be achieved.

Meanwhile, researchers at the University of Paris also generated entanglement of two neutral rubidium atoms. They did not create a CNOT gate.

Sunday, March 7, 2010

Underwater fly glue

Scientists from the University of Utah
have identified the caddisfly’s secret to underwater stickiness.

Caddisflies comprise thousands of species of insects in the order Trichoptera. They lay their eggs in water, where the larvae grow and develop. Many species use their silk to construct underwater tubes of sand or leaf debris. The larva lives protected in the tube, and eventually seals the tube off to pupate within it.

Caddisfly larva with underwater mobile home made of sand, rock grains and glass beads.

Credit: Fred Hayes

Russell Stewart and his lab used the caddisfly Brachycentrus echo as a study subject. This species drags its case of silk and rock around with it as it forages for food, ready to dive into the safety of the tube at any moment. The researchers found that the B. echo larvae were able to attach their ribbons of silk to all manner of organic and inorganic materials, all underwater.

A mesh of wet adhesive silk ribbon produced by a caddisfly larva to stitch together the inside of its shelter case, made with glass beads it was given in a laboratory aquarium.

Credit: University of Utah

Apparently, the silk ribbons are laid along the inside of the tube shelters like tape. Upon further study, including electron microscopy, the scientists found that the caddisfly silk protein was largely made of phosphorylated serine. The negatively charged phosphate groups line up across from other positively charged amino acids creating the silk ribbons.

Although the exact mechanism for allowing the silks to stick to things when wet is not yet understood, the researchers have observed that dry silks made from moths and butterflies do not contain phosphorylated serine. In fact, phosphates have been used to increase the adhesion of paints or dental fixtures.

As Stewart says:
The association of those plus or minus charges makes them water-insoluble. This is how you make a silk fiber under water.
Adhesive tape that retains its stickiness when wet could be a boon to surgeons, who could tape internal wounds rather than stitching them.