The Yuck Factor

A glowing frog sounds like something one might find in a toy store bargain bin but for the first time, researchers have discovered that a species of frog—the South American polka dot tree frog—glows blue-green under ultraviolet light.

From the Nature.com Article:

The ability to absorb light at short wavelengths and re-emit it at longer wavelengths is called fluorescence, and is rare in terrestrial animals. Until now, it was unheard of in amphibians. Researchers also report that the polka dot tree frog uses fluorescent molecules totally unlike those found in other animals. The team published the find on 13 March in Proceedings of the National Academy of Sciences.

Unlike bioluminescence, in which organisms give off light even in total darkness, in fluorescence, light has to be absorbed by the organism before it can glow. Fluorescence is fairly common in the oceans but is rare on land—only parrots and some scorpions were previously known to fluoresce. Interestingly, the molecules responsible for fluorescence in these frogs are more closely related to fluorescent molecules found in plants than in other known fluorescing animals.

There is also the question of why the polka dot tree frog evolved the ability to fluoresce in the first place. One key to answering this is to determine whether the frogs can see their own fluorescence.

The newly described fluorescent molecules emit a surprising amount of light, providing about 18% as much visible light as a full Moon — enough for a related species of frog to see by. Almost nothing is known about the polka dot tree frog’s visual system or photoreceptors, so Taboada plans to study these to determine whether the frogs can see their own fluorescence.

This discovery raises the possibility of more species exhibiting similar traits. Dr. Julián Faivovich, the co-author of the study, believes other tree frogs with translucent skin like the polka dot tree frog’s might be good candidates for future research on fluorescence.  

Tardigrades– the micro-animals whose electron micrographs (like the one above) have done the rounds on social media for its adorable, bear-like appearance – is a famously hardly organism and is the first animal known to survive in space. Be it extreme heat, heavy radiation, high pressures and even desiccation, the “water bear” can shrug it off.

From The New York Times:

They can remain like that in a dry state for years, even decades, and when you put them back in water, they revive within hours,” said Thomas Boothby, a postdoctoral researcher from University of North Carolina at Chapel Hill. “They are running around again, they are eating, they are reproducing like nothing happened.”

To determine what allowed tardigrades to survive this kind of extreme dryness, Dr. Boothby and his colleagues designed a test in which the microscopic animals were put into a humidity chamber and slowly dried out as in an evaporating pond– the tardigrade’s native habitat. They discovered that the tardigrades have special genes that create glass-like proteins that can preserve their cells during desiccation.

“The glass is coating the molecules inside of the tardigrade cells, keeping them intact,” said Dr. Boothby said. This slows down the tardigrade’s metabolism, allowing it to remain in a suspended state until it is rehydrated. When they add water, the proteins melt into the liquid, and the molecules within the tardigrade are free to carry out their functions again.

In a recent report, researchers at Harvard Medical School brought up a promising yet eerie prospect in stem cell research– the development of synthetic embryos. Scientists are now able to assemble stem cells that can organize into embryo-like structures, and the day may not be far off when these cells lead to the development of complex human tissues and organs that can resemble those found in adult humans.  

Sheefs, which stands for “synthetic human entities with embryo-like features”, exist even today but only as simple assemblies of cells. 

From The New York Times’ article:

But in the future, they may develop into far more complex forms, the researchers said, such as a beating human heart connected to a rudimentary brain, all created from stem cells. Such a Sheef might reveal important clues about how nerves control heartbeats. Scientists might be able to use other Sheefs to test out drugs for diseases such as cancer or diabetes.

However, the full potential of this avenue of research may soon push the boundaries of what is currently legally acceptable. A rule that has been in existence since 1979 prohibits lab-raised embryos from being allowed to grow for more than 14 days. Scientists have largely found this to be a reasonable restriction because of how easy it has been to follow—until recently, scientists couldn’t even come close to keeping human embryos alive for even 1 week. But this may soon change.

Last year, two teams of scientists determined how to grow human embryos for 13 days. Those advances hinted that it might be possible to allow scientists to tack on a few days more, by changing the 14-day rule to, say, a 20-day rule.

With as much terror as rogue AI often inspires in movies, in the real world, computers haven’t yet been able to compete with the human brain when it comes to its plasticity and ability to learn.

A group of scientists seek to change that by creating a super-fast computer that “grows”. In order to achieve this, they have to look beyond silicon for its building material. Professor Ross D King and his team of scientists at The University of Manchester have come up with a model for what is known as a “nondeterministic universal Turing machine” (NUTM)—a type of computer that has yet to exist outside of the theoretical realm. The secret ingredient that makes this attempt more feasible than in the past is the new use of DNA in place of silicon.

"Imagine a computer is searching a maze and comes to a choice point, one path leading left, the other right," explained Professor King, from Manchester's School of Computer Science.

"Electronic computers need to choose which path to follow first.

"But our new computer doesn't need to choose, for it can replicate itself and follow both paths at the same time, thus finding the answer faster.

"This 'magical' property is possible because the computer's processors are made of DNA rather than silicon chips. All electronic computers have a fixed number of chips.”

By using the genetic alphabet of nucleobases, ATCG (adenine, thymine, cytosine and guanine) instead of 1s and 0s, scientists can make a computer that can not only be as small as a desktop computer but also outperform the fastest supercomputers in existence today.

Finding life on Mars has captured the imagination of generations, but experts still aren’t sure what exactly we’re looking for. The Danakil Depression in Ethiopia, with a landscape of boiling pools of water and mounds of salt and sulfur that itself seems extraterrestrial, might offer some clues. Despite being one of the lowest, hottest and driest places on Earth, the region is host to extremophiles–– microbes that thrive in these inhospitable conditions.

Dr. Felipe Gómez Gómez of the Centro de Astrobiología in Madrid, who is working on isolating and studying these bacteria, believes learning to identify life in extreme environments here on Earth is the key to identifying any alien life that might be out there.

“What is life? What are the limits of life? Scientists don’t agree on what is life,” Dr. Gómez said. “If we find life on Mars, would we be able to recognize it? We don’t know.”

These organisms might also provide insight into how potential life-forms might survive in the sparse environment of Mars. From the article:

These simple organisms can survive with a “very small battery,” and were probably among the first bacteria on Earth, Dr. Gómez said. “That is what makes them so interesting from an astrobiological point of view.”

Organisms such as chemolithotrophs don’t require traditional means of sustenance like light and organic compounds and instead use inorganic compounds such as sulfide, hydrogen and ammonia as energy sources. Though they might be a far cry from little green men with antennae, they could offer us a more realistic idea of what to expect if and when we finally make “first contact”.

“If you’re making resolutions for a healthier new year, consider a gut makeover.”

This is the starting sentence of a recent article in the New York Times, “A Gut Makeover for the New Year.” Given the recent uptick in research on the many effects the intestinal microbiota may have on human health–– our nutritional intake, our immune systems, and even diseases ranging from allergies to diabetes to depression–– a ‘makeover’ of these microbes could have a huge effect. 

Much of the composition of the microbiome is established early in life, shaped by forces like your genetics and whether you were breast-fed or bottle-fed. Microbial diversity may be further undermined by the typical high-calorie American diet, rich in sugar, meats and processed foods. But a new study in mice and people adds to evidence that suggests you can take steps to enrich your gut microbiota. Changing your diet to one containing a variety of plant-based foods, the new research suggests, may be crucial to achieving a healthier microbiome.

Achieving this healthier microbiome, the article admits, will probably not be an easy feat, and will take an as-yet unspecified amount of time.

“The nutritional value of food is influenced in part by the microbial community that encounters that food,” said Dr. Jeffrey Gordon, the senior author of the new paper and director of the Center for Genome Science and Systems Biology at the Washington University School of Medicine in St. Louis. Nutritional components of a healthy diet have to be viewed from “the inside out,” he said, “not just the outside in.”

Dr. Gordon’s study, published in Cell Host & Microbe recently, looked into how diet affects this microbial community. Human gut bacteria was placed into sterile mice, who were fed various diets and analyzed. Among the most interesting findings were that a ‘calorie restricted’ group of mice (eating less than 1,800 calories a day of plant-based foods for two years) had a richer microbial community and more strains of “good” bacteria. Mice fed a ‘typical American diet” (3,000 calories a day featuring processed cheese, lunch meats, and few fruits and vegetables) did not fare quite as well.

A recent episode of Science Friday explores the rhythm of the gut microbiome. Just as humans have a daily schedule, it seems that the microbiomes of our gut do too, influenced by our diet, movements, and health.

In the segment, Microbiologist Lawrence David of Duke University speaks of a yearly diary that he kept, which recorded the makeup of the biomes in his gut and mouth. Then, we learn more about a new study out in Cell titled, Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations. In it, “Immunologist Eran Elinav and his team looked at the circadian rhythm of gut microbes in mice. They found that those microbes changed locations and metabolic output throughout the day.”

Do you ever think about where you leave your DNA? Here’s one place you may not have considered: an ATM. NYU researchers took swabs from 66 ATMs around Manhattan, Queens, and Brooklyn, and found that the keypads on automated teller machines reveal traces of microbes from human skin as well as from food and household surfaces like kitchens, pillows, and yes, bathrooms. This means that ATMs are a great source for mapping the city’s DNA.

From Science Daily:

“Our results suggest that ATM keypads integrate microbes from different sources, including the human microbiome, foods, and potentially novel environmental organisms adapted to air or surfaces," explains senior study author Jane Carlton, director of the Center for Genomics and Systems Biology and professor of biology at NYU. "DNA obtained from ATM keypads may therefore provide a record of both human behavior and environmental sources of microbes."

In addition, researchers found that certain biomarkers were more common depending on where the ATM was located, such as more Lactobacillales (lactic acid bacteria) found in laundromat ATMs, while Xeromyces bisporus, found in spoiled baked goods, appeared most often in Manhattan. Because so many people use these ATMs daily, scientists are confident that these keypads represent an “average” microbial community, one that reflects both environmental and urban contact.

It also means you might want to wash your hands the next time you take out some cash. 

Scientists are studying a connection between the parasite Toxoplasma gondii (one of our personal favorites!) and its effect on behavior, most specifically, how it seemingly makes rats less afraid of cats. This isn’t mind control—if when a rat sees a cat, it’s still going to run away in fear. But while rats typically avoid cat urine, those infected with toxoplasma gondii do not.  

According to Ars Technica:

“When trying to explain how Toxo produces this effect, [researcher Ajai Vyas] initially focused on the obvious: the parasite’s presence in the brain. When Toxo infects, it barricades itself in thick-walled cysts to evade the immune system, and these cysts can remain for decades in a few sites, including the brain. If Toxo forms cysts in specific parts of the brain, it could do something there to affect behavior. But so far, different studies have found cysts in many different locations with no obvious pattern to their distribution, so it’s unclear if cyst location can influence behavior.”

Toxo, as the parasite is sometimes called, is not only interesting because of its curious influence on the predatory relationship between cats and rats, but also because it can infect many kinds of animals, including a third of humans worldwide. To the average person, Toxo is about as dangerous as the flu, but it is also associated with disorders like schizophrenia. However, scientists warn that these associations should be taken with a grain of salt. While connections between Toxo and behavior are present, researchers disagree on exactly what its effects are, on rats, cats, and humans alike.

“The reality is that human behavior and mental illness are complex, and many of the Toxo studies are not standardized and have yet to be replicated. Toxo certainly doesn’t make it easy to do this work—there’s no good way to detect Toxo cysts in a living person, and the studies rely on correlations with Toxo antibody levels. But antibodies are a crude measure that don’t tell you about a number of things that could affect behavior, such as when the infection occurred or which strain of the parasite you’re infected with.”

Smartphone and 3D printing technology are merging to create a microscope that students can use to interact with single-celled organisms. Introduced in the scientific journal PLOS ONE this month, the “LudusScope” could be utilized by classrooms for all grade levels.

From Reuters:

“It’s a microscope that you can 3D print and build yourself,” Ingmar Riedel-Kruse, an assistant professor of bioengineering at Stanford, told Reuters.

After it is assembled, tiny, light-responsive organisms called Euglena swim on a microscope slide surrounded by four LED lights. The lights are controlled by a joystick, allowing users to control the direction in which the microbes move.

By attaching a smartphone dock, students can connect their phones to the microscope, essentially using gaming technology as a form of education and research. Instead of simply observing micro-organisms, they can now interact with and study them on a whole new level.

“The scientists at the Palo Alto-based university have developed software programs that overlay on top of the image of cells. By selecting specific cells, users can influence their movement and guide them through a maze that resembles the 1980s video game Pac-Man. Kids can also play soccer by steering their microbes through goal posts.”

University of California researcher Bruce German has a lot to say on the subject of milk - specifically, human breast milk. While all mammals produce milk, the makeup of the substance differs from species to species, as one  might expect, to cater to that species' needs. But in researching the composition of human milk, German found a surprise.

From the New Yorker:

Every mammal mother produces complex sugars called oligosaccharides, but human moth­ers, for some reason, churn out an exceptional variety: so far, scientists have identified more than two hundred human milk oligosaccharides, or H.M.O.s. They are the third-most plentiful ingredient in human milk, after lactose and fats, and their structure ought to make them a rich source of energy for growing babies—but babies cannot digest them. When German first learned this, he was gobsmacked. Why would a mother expend so much energy manufacturing these complicated chemicals if they were apparently useless to her child?

The answer, researchers found, is that these H.M.O.s travel into the large intestine, where they are fed upon by a microbe called Bifidobacterium longum infantis, ​which will cause them to grow faster and more efficiently than any other gut bacteria. This process is motivated by evolution, and is beneficial to both the bacteria and the child.  

As [B. infantis] digests H.M.O.s, it releases short-chain fatty acids, which feed an infant’s gut cells. Through direct contact, B. infantis also encourages gut cells to make adhesive proteins that seal the gaps between them, keeping microbes out of the bloodstream, and anti-inflam­matory molecules that calibrate the immune system. These changes only happen when B. infantis feeds on H.M.O.s; if it gets lactose instead, it survives but doesn’t engage in any repartee with the baby’s cells. In other words, the microbe’s full beneficial potential is unlocked only when it feeds on breast milk.

There are a number of other ideas as to why such a vast and diverse number of H.M.O.s exist in humans over other mammals. Some scientists suggest that feeding B. infantis ​helps to stimulate brain growth; others note that it serves as a defense against pathogens. At a pediatric hospital in California, these microbes might be a solution to help nourish premature infants.

Case Western Reserve University School of Medicine has identified a fungus that is a key factor in Crohn’s disease. There is hope that this discovery, along with their finding of a new bacterium that is linked to the previous bacteria associated with the disease, will lead to new treatments and a cure.

From Science Daily: 

"We already know that bacteria, in addition to genetic and dietary factors, play a major role in causing Crohn's disease," said the study's senior and corresponding author, Mahmoud A Ghannoum, PhD, professor and director of the Center for Medical Mycology at Case Western Reserve and University Hospitals Cleveland Medical Center "Essentially, patients with Crohn's have abnormal immune responses to these bacteria, which inhabit the intestines of all people. While most researchers focus their investigations on these bacteria, few have examined the role of fungi, which are also present in everyone's intestines. Our study adds significant new information to understanding why some people develop Crohn's disease.

The research found that the combined presence of the two bacteria, Escherichia coli and Serratia marcescens, and the fungi Candida tropicalis was much higher in fecal samples of people with Crohn’s compared to those without the disease. 

Test-tube research by the Ghannoum-led team found that the three work together (with the E. coli cells fusing to the fungal cells and S. marcescens forming a bridge connecting the microbes) to produce a biofilm -- a thin, slimy layer of microorganisms found in the body that adheres to, among other sites, a portion of the intestines -- which can prompt inflammation that results in the symptoms of Crohn's disease.

A recent outbreak of hand foot and mouth disease on the campus of Florida State University has students and administrators taking extra precautions. Over a dozen cases of the illness, normally seen in children younger than 5, have been reported on the campus. 

Via CNN: 

The outbreak began as "a trickle" on Monday, Sacher said, noting that the infection is more common in day care centers than on college campuses. However, cases occur with regularity on college campuses, according to the American College Health Association.

Pediatricians have also noted a rise in cases of the disease among children this year. 

Dr. Christopher Houts of Powell Pediatric Care in Ohio said he's seen more cases this year than anytime in his 21 years as a pediatrician. While patients usually begin to come in during the summer, this year, they've arrived at his community practice early, beginning in the spring.

Signs and symptoms of the disease include fever, sore throat, and painful sores. The sores most often appear in the mouth and on palms and soles of the feet, though they can also show up on knees, elbows, buttocks or genitals, and can become ulcers. Adults often show now symptoms but can still be carriers and disburse the virus. The virus is spread the same way a cold might, through the air (sneezing or coughing) or direct contact with saliva, mucus, blister fluid, or feces. 

Besides the obvious discomfort the disease can cause, most cases resolve themselves within a week.

The Jefferson Memorial, originally built from smooth marble, has become pitted due to rain water over its 73 years. A biofilm has grown in those pits and taken over the outside of the building, leaving it black and dingy. Scientists are still figuring out the composition of the microbial invasion. It’s unclear at this point whether the microbes are eating the stone, though it is clearly growing at alarming rates. The Park Service says that the film also appears to be on the memorial amphitheater at Arlington National Cemetery, the Washington Monument and the Lincoln Memorial.

From The Washington Post: 

The film is actually a “multicultural” community of organisms living in the relatively harsh environment of the sun-blasted stone, said Federica Villa, a Milan-based microbiologist who has been studying the memorial’s surface. The black pigment is produced by the organisms to protect themselves from solar radiation, she said in an interview Tuesday.

But does the biofilm damage stone?

“We don’t know,” Villa said from Montana State University’s Center for Biofilm Engineering. “If you read the scientific literature, most of the scientists correlate the presence of a biofilm with deterioration.” But she said her experiments have shown that biofilm may have a protective impact on stone.

“To be honest, we have a lot of work to do,” she said.