September 10, 2013
Rising gas prices and a dangerously low world panda population–what if someone told you that we soon could have one solution to both these problems? If it seems too good to be true, think again; scientists at Mississippi State University are conducting research on the feasibility of using pandas to help solve our biofuel woes, a step that could lead to a bump in conservation efforts and a drop in fuel expense. The secret to the solution? It’s all in the panda’s poop.
When it comes to biofuels, the market is dominated by one word: ethanol, a biofuel made from corn. Though ethanol is the most widely used biofuel, it isn’t necessarily touted as a perfect replacement for fossil fuels–in fact, the benefit of ethanol is been hotly debated since its creation.
The debate goes a little something like this: in order to fill the tank of an SUV with ethanol fuel, you need to use enough corn to feed a single person for an entire year. A 2012 paper published by the New England Complex Systems Institute cites ethanol as a reason for the increasing price of crops since 2005. And even environmental groups steer clear of ethanol, citing the massive amounts of fossil fuel needed to render corn a useable biofuel product and the propensity of companies to buy land in developing countries to grow the lucrative biofuel rather than food for local consumption.
Ashli Brown, a researcher at Mississippi State University, thinks she’s found the answer to this alternative fuel conundrum. By taking corn byproducts–the husks, the stems and cobs–ethanol could be created without dipping into the edible parts of corn, reducing the chance of a food shortage and price spike. The issue is that to break down these materials, which are extremely high in lignocellulose, or dry plant matter, a special pretreatment process is required. The process is extremely costly and not very time-efficient, using high temperatures, high pressures and acid to break down the dry plant matter before it can become ethanol. To circumvent this problem, Brown and other researchers have been looking for a natural solution–bacteria, which could help with the breakdown of the lignocellulose material.
Biofuel companies have been seeking a natural method to break down plant material for a while; so far, termites have been a favorite for chewing through the woody material. But it turns out there might be a better–and cuter–animal that can help produce biofuel
. The intestines of pandas are remarkably short, a physical attribute which means their intestines have come to contain bacteria with unusually potent enzymes for breaking down their woody diet of bamboo in a short amount of time.
“The time from eating to defecation is comparatively short in the panda, so their microbes have to be very efficient to get nutritional value out of the bamboo,” Brown, the researcher heading the work, said. “And efficiency is key when it comes to biofuel production—that’s why we focused on the microbes in the giant panda.”
The study began more than two years ago, when Brown and a team of researchers began looking at panda feces. In 2011, they identified these super-digesting microbes are present in panda feces, but they had yet to specify the type and amount of microbes present until now. Using the poop from two giant pandas–Ya Ya and Le Le in the Memphis Zoo–Brown and her team performed DNA sequencing on microbes in their samples, identifying more than 40 microbes in the panda feces that could be useful to the breakdown and creation of biofuels.
To grow these microbes on an industrial scale
, Brown believes that scientists could put the genes that produce those enzymes into yeasts--these yeasts could then be mass-produced and harvested for biofuel production. The process would go something like this: Large pits of corn husks, corn cobs, wood chips, and other forms of discarded fibrous material are covered with the genetically altered yeasts. As the microbes digest woody substances, they quickly turn it into sugar, which would then be allowed to ferment. Over time and after filtering out solids and any excess water, you would have ethanol, distilled from woody waste products.
Pandas aren’t the only animal that subsists on a grassy diet, but their physiology makes them a unique candidate for breaking down plant byproducts in a hyper-efficient way. Pandas have the same digestive track as any other bear; unlike cows or other herbivores, pandas don’t have an extra stomach where hard lignocellulostic material is pretreated before being digested. Instead, they have the intestinal system of a carnivore, and yet manage to extract enough nutrients from their herbaceous diet to survive.
“Because their retention time is very short—they’re constantly eating and they’re constantly pooping—in order to get the material for nutrition, they have to be really quick at breaking it down and extracting the sugars,” Brown explained. “Many microbes produce celluloses that breakdown lignocellulostic biomass, but it’s about how efficiently or how effectively they do it.” When it comes to a panda, Brown notes, their microbes are some of the most efficient scientists have seen at breaking down the woody material of a plant.
And Brown thinks that using pandas for their poop could lead to more than a greener economy: it could also lead to increased conservation for the animals, who have seen their numbers in the wild drop to a dangerous 1,600 (though there has been recent luck with breeding pandas in captivity, like the new baby panda at the National Zoo). “These studies also help us learn more about this endangered animal’s digestive system and the microbes that live in it, which is important because most of the diseases pandas get affect their guts,” said Brown.
Brown notes that if the panda becomes valuable to the market for more reasons than its incredibly adorable demeanor, it might spark greater steps toward conservation–a move that could be mutually beneficial to pandas and humans alike.”It’s amazing that here we have an endangered species that’s almost gone from the planet, yet there’s still so much we have yet to learn from it. That underscores the importance of saving endangered and threatened animals,” she said. “It makes us think—perhaps these endangered animals have beneficial outputs that we haven’t even thought about.”
September 9, 2013
Mosquitoes are utterly, stupendously annoying. They can also carry diseases, such as malaria and West Nile virus. Some people—those with type O blood and robust colonies of bacteria on their skin, among other traits—are especially prone to getting bitten by them, and there’s growing evidence that many of the insects are evolving resistance to DEET, the main repellant we’ve relied upon for years.
All of which makes an ongoing project led by Ulrich Bernier, a chemist at the U.S. Department of Agriculture (USDA) Mosquito and Fly Research Unit, especially exciting. He’s taking a new approach to battling mosquitoes: Instead of developing chemicals that repel mosquitoes with unpleasant scents, he’s searching for substances that disrupt their ability to smell in the first place.
And as he announced today at the annual meeting of the American Chemical Society, his group has isolated a few chemicals that are naturally present on human skin in trace quantities and appear to inhibit mosquitoes’ capability to smell and locate humans. If one of these chemicals—mostly likely one called 1-methylpiperzine, which has been the most successful so far—holds up in future tests and can be produced synthetically on a bigger scale, wearing it could be a way of rendering yourself effectively invisible to mosquitoes.
Conventional insect repellants take advantage of the fact that the creatures rely mainly on their sense of smell to locate humans (they can smell us from as far as 100 feet away). DEET, which was developed during World War II, works mainly because it smells unpleasant to mosquitoes and other insects, so when you wear it, they prefer to fly elsewhere.
But DEET may be gradually growing less effective and has other drawbacks. Some people avoid using it because of evidence that it can, in rare cases, cause central nervous system problems—the EPA found (PDF) that it causes seizures in roughly one out 100 million users.
“We are exploring a different approach, with substances that impair the mosquito’s sense of smell,” Bernier explained in a press statement on his presentation. “If a mosquito can’t sense that dinner is ready, there will be no buzzing, no landing and no bite.”
To find these kinds of substances, he looked back at USDA research that started in the 1990s and was aimed at finding the natural compounds that attracted mosquitoes to human skin. As researchers isolated and analyzed 277 different substances that we naturally secrete in trace quantities, though, they found a handful that seemed to have the opposite effect, making mosquitoes less likely to come near.
Bernier and colleagues have since tested larger quantities of these chemicals to precisely measure their effect on the insects. In a lab, they built a cage divided in half by a screen. One half was filled with a swarm of mosquitoes; in the other half, they sprayed each of the chemicals to see how many of the mosquitoes would try to cross over.
Many of the compounds (most notably 1-methylpiperzine) seemed to inhibit the mosquitoes’ sense of smell, leaving them unable to detect other chemicals they normally find quite appealing. In trials, lactic acid—a substance that occurs in large amounts in sweat—pulled about 90 percent of the mosquitoes toward the screen, but when they mixed in a bit of 1-methylpiperzine, the mosquitoes stayed in place, seemingly unaware of the lactic acid nearby.
The group proceeded to tests with actual human skin and found the same results. “If you put your hand in a cage of mosquitoes where we have released some of these inhibitors, almost all just sit on the back wall and don’t even recognize that the hand is in there,” Bernier said.
He says that these inhibitors induce anosmia (the inability to detect odors) in the insects, making the secretor invisible. As it turns out, some people produce more of these inhibitors than others—which may account for part of why, for example, some people can emerge from an hour outside with bites on every inch of exposed skin, while a friend nearby can come back from the same place entirely unscathed.
The next step is figuring out how to incorporate these chemicals into commercial products. Bernier’s group isn’t the only one analyzing these natural inhibitors, and so far, others have run into a key problem: It’s hard to get the substances to stay on human skin instead of evaporating off, as they naturally do over time. But if they can figure that out and produce insect sprays that inhibit mosquitoes, rather than simply repelling them, all of us may someday be able to enjoy the same benefits as the lucky few who secrete these chemicals naturally.
September 8, 2013
For decades scientists have known that sudden cardiac death–a failure in the heart’s electrical system that leads people to, well, suddenly drop dead–occurs more often in the morning hours. Analysis of data from the ambitious Framingham Heart Study led to the scientific documentation of the curious link as early as 1987. But for just as long, scientists haven’t been able to do much with that knowledge. A flurry of papers in the late 1980s pointed to possible explanations: the assumption of an upright posture, for example, or problems with the process that typically prevents blood clots. Still, scientists have been unable to pin down a basic mechanism to explain the connection between the body’s circadian clock and the electrical mishap that causes sudden death.
Now an international team of researchers has stumbled upon a lead. Mukesh Jain of Case Western Reserve University in Cleveland and his colleagues recently identified a protein whose levels oscillate with the circadian clock and, in mice, cause the ion channels governing the heart’s electrical system to oscillate with the clock too. On September 8 in Indianapolis at a meeting of the American Chemical Society (ACS), Jain reported that these oscillations also occur in human heart cells. The results point to an era when doctors may be capable of preventing sudden cardiac death, which is the leading cause of natural death in the United States, killing more than 300,000 people each year.
the ins and outs of Jain’s finding, one first needs to understand how the heart works. Think: car engine, says James Fang, the chief of cardiovascular medicine at the University of Utah School of Medicine in Salt Lake City. There’s the circulating blood, which is the fuel. There are the muscles, which pump that fuel. And there is an electrical system, with charge separation created not by a battery but by ion pumps and ion channels. Without a working electrical system, the muscles won’t expand and contract and the blood won’t flow. In a heart attack, the flow of fuel to the heart is blocked. But in sudden cardiac death, there is an electrical malfunction that prevents the heart from properly pumping blood to the body and brain. The heart’s beating becomes erratic, often displaying a type of arrhythmia called ventricular fibrillation. Heart attacks can lead to the kind of arrhythmia that can lead to sudden cardiac death, but in other cases there is no obvious trigger. No matter how the heart’s plug is pulled, death typically occurs within minutes.
Though drugs for the heart do exist–think beta blockers, ACE inhibitors–there is no drug that acts specifically to prevent the onset of arrhythmia. The most common medical response is just that: a response. Doctors treat the electrical malfunction after it has happened with a defibrillator, a technology with a history stretching back to the end of the 19th century. In 1899, two physiologists found that electrical shocks could not only create but also stop rhythmic disturbances in the heart of a dog. By the end of the 1960s, cardiac defibrillation was being reliably used on people. And in 1985, a Johns Hopkins University doctor got FDA approval for an implantable defibrillator.
Defibrillation has been the primary solution for life-threatening arrhythmias since. These devices have shrunk from “the size of luggage to the size of a cigarette box,” says Fang, and automated external versions have become popular so bystanders can help a victim without the delay of an ambulance ride. But, “it’s a bit of a crude approach,” Fang says. “Defibrillators have really formed the cornerstone for the past two or three decades, but it is not really much of a management solution,” he adds. “It is not preventing the problem. It is letting it happen and then shocking you out of it.” It’s the equivalent of jump-starting a car after the battery has died.
What’s more, Fang says, because scientists don’t know what triggers the arrhythmia to begin with, it’s tough to predict who needs a defibrillator. Take, say, 100 patients who all have weak hearts. “Probably only 10 are going to die suddenly. We don’t know who those 10 are, so we give defibrillators to all 100 people,” Fang says. “It is overkill because 90 don’t even need it. But I can’t tell which 10 are going to die.”
Here’s where Jain’s work comes in. His team, which has long studied a protein known as KLF15, serendipitously discovered that the amount of the protein in a mouse’s heart tissue cycles–going from low to high and back again over a 24-hour period. Though Jain doesn’t study electrophysiology specifically, he was aware of the link between the clock and sudden cardiac death, and he wondered whether his protein (which had been previously connected to some heart diseases) might play a role. Jain’s team found that levels of KLF15 should be high during transitions from night to day, but instead are low in mice that experience sudden cardiac death–suggesting their hearts don’t have enough of the protein during a crucial window. KLF15 controls the levels of another protein that affects how ions flow into and out of the mouse’s heart, meaning the ion channels also follow a circadian rhythm. When the researchers eliminated the presence of KLF15, “the ion channel expression went down and didn’t oscillate,” Jain says. “And these animals had increased susceptibility to ventricular arrhythmias and sudden death.” The study was published last year in Nature.
Follow-up observations, presented at the ACS meeting, confirm that the oscillation of KLF15 and the ion channels occur in human heart cells. Those findings “start to build a case that this is potentially important to human biology and human disease,” Jain says.
Jain believes his molecular work and other similar studies on the horizon could lead to drugs that offer a solution better than defibrillation. “We need a fresh start,” he says. “What we are doing ain’t working.” But there is a long way still to go. Future studies will try to find molecules that could boost KLF15 levels, to look for other clock-related molecules at work in the heart and to seek out genetic variants associated with sudden cardiac death.
August 28, 2013
If the phenomena of Star Trek, Area 51, Ancient Aliens, or War of the Worlds can be taken as anthropological clues, humanity is consumed with curiosity about the possibility of life beyond Earth. Do any of the 4,437 newly discovered extrasolar planets contain traces of life? What would these life forms look like? How would they function? If they came to Earth, would we share ET-esque embraces or would the visit be more a Battle Los Angeles style throw down?
Life outside of Earth has spawned endless interest, but less public interest seems to be given to how life on Earth began 3 to 4 billion years ago. But the two topics, it turns out, might be more connected than one would believe–in fact, it’s possible that life on Earth really began outside of Earth, on Mars.
At this year’s Goldschmidt conference in Florence, Steve Benner, a molecular biophysicist and biochemist at the Foundation for Applied Molecular Evolution will present this idea to an audience of geologists. He’s well aware that half the room will be adamantly against his idea. “People will probably throw things,” he laughs, hinting at a consciousness of how out-of-this-world his ideas sound. But there’s scientific basis for his assertion (PDF), a logical reason for why life maybe truly did begin on Mars.
Science holds a number of paradoxes: If there are an infinite number of stars in the sky, why is the night sky dark? How can light act as both a particle and a wave? If the French eat so much cheese and butter, why is the incidence of coronary disease in their country so low? The origins of life are no different; they, too, are dictated by two paradoxes: the tar paradox, and the water paradox. Both, according to Benner, make it difficult to explain the creation of life on Earth. But both, he also notes, can be solved by placing the creation of life on Mars.
The first, the tar paradox, is simple enough to understand. “If you put energy into organic material it turns to asphalt, not to life,” Benner explains. Without access to Darwinian evolution–that is, without organic molecules having the opportunity to reproduce and create offspring who themselves, mutations and all, are reproducible–organic matter that is bathed in energy (from sunlight or from geothermal heat) will turn into tar. Early Earth was full of organic materials–chains of carbon, hydrogen and nitrogen that are believed to be the building blocks of life. Given the tar paradox, these organic materials should have devolved into asphalt. “The question is, how is it possible that the organic materials on early Earth managed to leap from their asphaltic fate to something that had access to Darwinian evolution? Because once that happens–presumably–you’re off to the races, and then you can manage whatever environment you want,” Benner explains.
The second paradox is the so-called water paradox. The water paradox states that even though life needs water, if organic material could escape its asphaltic fate and move toward Darwinian evolution, you can’t assemble the necessary building blocks in a flood of water. The building blocks of life start with genetic polymers–the well-known player DNA and its less-famous but still very smart friend RNA. Experts agree that RNA was likely the first genetic polymer, partly because in the modern world, RNA plays such an important role in the manufacturing other organic compounds. “RNA is the key to the ribosome, which is what makes proteins. There’s almost no question that RNA, which is a molecule involved in catalysis, arose before proteins arose,” Benner explains. The difficulty is that for RNA to assemble into long strands–which is needed for genetics–you can’t have the assembly taking place in water. “Most people think that water is essential for life. Very few people understand how corrosive water is,” Benner says. For RNA, water is extremely corrosive–bonds cannot be made within water, preventing long-strands from forming.
However, Benner says that these paradoxes can be resolved with the help of two very important groups of minerals
. The first are borate minerals. Borate minerals–which contain the element boron–prevent life’s building blocks from devolving into tar if incorporated into organic compounds. Boron, as an element, is seeking electrons to make itself stable. It finds these in oxygen, and together the oxygen and boron form the mineral borate. But if the oxygen boron finds is already bonded to carbohydrates, the carbohydrates linked with boron form a complex organic molecule dotted with borate that’s less resistant to decomposition.
The second group of minerals that come into play
involve those that contain molybdate, a compound that consists of molybdenum and oxygen. Molybdenum, more famous for its conspiratorial relation to the Douglas Adams classic A Hitchhiker’s Guide to the Galaxy than for its other properties, is crucial, because it takes the carbohydrates that borate stabilized, bonds to them and catalyzes a reaction which rearranges them into ribose: the R in RNA.
Which brings us–however circuitously–back to Mars. Both borate and molybdate are scarce and would have been especially scarce on early Earth. The molybdenum in molybdate is
highly oxidized, meaning that it needs electrons from oxygen or other readily available negatively charged ions to achieve stability. But early Earth was too oxygen-scarce to have readily created molybdate. Plus, returning to the water paradox, early Earth was quite literally a water world–with land making up only two to three percent of its surface. Borates are soluble in water–if early Earth was a flooded planet, as scientists believe, it would have been difficult for an already scarce element now diluted in a huge ocean to find ephemeral organic molecules to bond with. Moreover, Earth’s status as a water-logged planet makes it difficult for RNA to form, because that process can’t easily happen in water on its own.
These concepts become less of an issue on Mars, however. Though water was certainly present on Mars 3 to 4 billion years ago, it was never as abundant as it was on Earth, creating the possibility that Martian deserts–locations where borate and molybdate could concentrate–could have fostered the formation of long strands of RNA. Moreover, 4 billion years ago, Mars’ atmosphere contained much more oxygen than Earth’s. Further, recent analysis of a Martian meteorite confirms that boron was once present on Mars.
And, Benner believes, molybdate was there too. “It’s only when molybdenum becomes highly oxidized that it is able to influence how early life formed,”Benner explains. “Molybdate couldn’t have been available on Earth at the time life first began, because three billion years ago the surface of the Earth had very little oxygen, but Mars did.”
Benner believes that these factors imply that life originated on Mars, our closest neighbor in space equipped with all the right ingredients. But life wasn’t sustained there. “Of course Mars dried out. The process of drying was very important for life originating, but not sustaining,” Benner explains. Instead, a meteor would have to have hit Mars, projecting materials into space–and eventually those materials, including some building blocks of life, might have made it to Earth.
Would the sudden change in environment have been too harsh for the fledgling building blocks to survive
? Benner doesn’t think so. “Let’s say life starts on Mars, and becomes very happy in the Martian environment,” Benner explains. “A meteor comes to hit Mars, and the impact ejects rocks on which your predecessor is sitting. Then you land on Earth, and you discover that there is lots of water that you were treating as a scarce element. Will it find the environment adequate? It certainly appreciated the existence of enough water that it didn’t have to worry.”
So, sorry Lil Wayne, looks like it might be time to relinquish your claim to the fourth rock from the Sun. As Brenner notes, “The evidence seems to be building that we are actually all Martians.”
August 22, 2013
Modern archeologists, excavating ancient Egyptian tombs, have often found something unexpected amongst the tombs’ artifacts: pots of honey, thousands of years old, and yet still preserved. Through millennia, the archeologists discover, the food remains unspoiled, an unmistakable testament to the eternal shelf-life of honey.
There are a few other examples of foods that keep–indefinitely–in their raw state: salt, sugar, dried rice are a few. But there’s something about honey; it can remain preserved in a completely edible form, and while you wouldn’t want to chow down on raw rice or straight salt, one could ostensibly dip into a thousand year old jar of honey and enjoy it, without preparation, as if it were a day old. Moreover, honey’s longevity lends it other properties–mainly medicinal–that other resilient foods don’t have. Which raises the question–what exactly makes honey such a special food?
The answer is as complex as honey’s flavor–you don’t get a
food source with no expiration date without a whole slew of factors working in perfect harmony.
The first comes from the chemical make-up of honey itself. Honey is, first and foremost, a sugar. Sugars are
hygroscopic, a term that means they contain very little water in their natural state but can readily suck in moisture if left unsealed. As Amina Harris, executive director of the Honey and Pollination Center at the Robert Mondavi Institute at Univeristy of California, Davis explains, “Honey in its natural form is very low moisture. Very few bacteria or microorganisms can survive in an environment like that, they just die. They’re smothered by it, essentially.” What Harris points out represents an important feature of honey’s longevity: for honey to spoil, there needs to be something inside of it that can spoil. With such an inhospitable environment, organisms can’t survive long enough within the jar of honey to have the chance to spoil.
Honey is also naturally extremely acidic. “It has a pH that falls between 3 and 4.5, approximately, and that acid will kill off almost anything that wants to grow there,” Harris explains. So bacteria and spoil-ready organisms must look elsewhere for a home–the life expectancy inside of honey is just too low.
But honey isn’t the only hygroscopic food source out there. Molasses, for example, which comes from the byproduct of cane sugar, is extremely hygroscopic, and is acidic, though less so than honey (molasses has a pH of around 5.5). And yet–although
it may take a long time, as the sugar cane product has a longer shelf-life than fresh produce, eventually molasses will spoil.
So why does one sugar solution spoil, while another lasts indefinitely? Enter bees.
“Bees are magical,” Harris jokes. But there is certainly a special alchemy that goes into honey. Nectar, the first material collected by bees to make honey, is naturally very high in water–anywhere from 60-80 percent, by Harris’ estimate. But through the process of making honey, the bees play a large part in removing much of this moisture by flapping their wings to literally dry out the nectar. On top of behavior, the chemical makeup of a bees stomach also plays a large part in honey’s resilience. Bees have an enzyme in their stomachs called glucose oxidase (PDF). When the bees regurgitate the nectar from their mouths into the combs to make honey, this enzyme mixes with the nectar, breaking it down into two by-products: gluconic acid and hydrogen peroxide. “Then,” Harris explains, “hydrogen peroxide is the next thing that goes into work against all these other bad things that could possibly grow.”
For this reason, honey has been used for centuries as a medicinal remedy. Because it’s so thick, rejects any kind of growth and contains hydrogen peroxide, it creates the perfect barrier against infection for wounds. The earliest recorded use of honey for medicinal purposes comes from Sumerian clay tablets, which state that honey was used in 30 percent of prescriptions. The ancient Egyptians used medicinal honey regularly, making ointments to treat skin and eye diseases. “Honey was used to cover a wound or a burn or a slash, or something like that, because nothing could grow on it – so it was a natural bandage,” Harris explains.
What’s more, when honey isn’t sealed in a jar, it sucks in moisture. “While it’s drawing water out of the wound, which is how it might get infected, it’s letting off this very minute amount of hydrogen peroxide. The amount of hydrogen peroxide comes off of honey is exactly what we need–it’s so small and so minute that it actually promotes healing.” And honey for healing open gashes is no longer just folk medicine–in the past decade, Derma Sciences, a medical device company, has been marketing and selling MEDIHONEY, bandages covered in honey used in hospitals around the world.
If you buy your honey from the supermarket, that little plastic bottle of golden nectar has been heated, strained and processed so that it contains zero particulates, meaning that there’s nothing in the liquid for molecules to crystallize on, and your supermarket honey will look the same for almost forever. If you buy your honey from a small-scale vendor, however, certain particulates might remain, from pollen to enzymes. With these particulates, the honey might crystallize, but don’t worry–if it’s sealed, it’s not spoiled and won’t be for quite some time.
A jar of honey’s seal, it turns out, is the final factor that’s key to honey’s long shelf life, as exemplified by the storied millennia-old Egyptian specimens. While honey is certainly a super-food, it isn’t supernatural–if you leave it out, unsealed in a humid environment, it will spoil. As Harris explains, ” As long as the lid stays on it and no water is added to it, honey will not go bad. As soon as you add water to it, it may go bad. Or if you open the lid, it may get more water in it and it may go bad.”
So if you’re interested in keeping honey for hundreds of years,
do what the bees do and keep it sealed–a hard thing to do with this delicious treat!