Archive for the ‘microbiology’ Category

Have you ever been on the subway and seen something that you did not quite recognize, something mysteriously unidentifiable?

Well, there is a good chance scientists do not know what it is either.

Researchers at Weill Cornell Medical College released a study on Thursday that mapped DNA found in New York’s subway system — a crowded, largely subterranean behemoth that carries 5.5 million riders on an average weekday, and is filled with hundreds of species of bacteria (mostly harmless), the occasional spot of bubonic plague, and a universe of enigmas. Almost half of the DNA found on the system’s surfaces did not match any known organism and just 0.2 percent matched the human genome.

“People don’t look at a subway pole and think, ‘It’s teeming with life,’ ” said Dr. Christopher E. Mason, a geneticist at Weill Cornell Medical College and the lead author of the study. “After this study, they may. But I want them to think of it the same way you’d look at a rain forest, and be almost in awe and wonder, effectively, that there are all these species present — and that you’ve been healthy all along.”

Dr. Mason said the inspiration for the study struck about four years ago when he was dropping off his daughter at day care. He watched her explore her new surroundings by happily popping objects into her mouth. As is the custom among tiny children, friendships were made on the floor, by passing back and forth toys that made their way from one mouth to the next.

“I couldn’t help thinking, ‘How much is being transferred, and on which kinds of things?’ ” Dr. Mason said. So he considered a place where adults can get a little too close to each other, the subway.

Thus was the project, called PathoMap, born. Over the past 17 months, a team mainly composed of medical students, graduate students and volunteers fanned out across the city, using nylon swabs to collect DNA, in triplicate, from surfaces that included wooden benches, stairway handrails, seats, doors, poles and turnstiles.

In addition to the wealth of mystery DNA — which was not unexpected given that only a few thousand of the world’s genomes have been fully mapped — the study’s other findings reflected New York’s famed diversity, both human and microbial.

The Bronx was found to be the most diverse borough in terms of microbial species. Brooklyn claimed second place, followed by Manhattan, Queens and Staten Island, where researchers took samples on the Staten Island Railway.

On the human front, Dr. Mason said that, in some cases, the DNA that was found in some subway stations tended to match the neighborhood’s demographic profile. An area with a high concentration of Hispanic residents near Chinatown in Manhattan, for example, yielded a large amount of Hispanic and Asian genes.

In an area of Brooklyn to the south of Prospect Park that roughly encompassed the Kensington and Windsor Terrace neighborhoods, the DNA gathered frequently read as British, Tuscan, and Finnish, three groups not generally associated with the borough. Dr. Mason had an explanation for the finding: Scientists have not yet compiled a reliable database of Irish genes, so the many people of Irish descent who live in the area could be the source of DNA known to be shared with other European groups. The study produced some less appetizing news. Live, antibiotic-resistant bacteria were discovered in 27 percent of the collected samples, though among all the bacteria, only 12 percent could be associated with disease. Researchers also found three samples associated with bubonic plague and two with DNA fragments of anthrax, though they noted that none of those samples showed evidence of being alive, and that neither disease had been diagnosed in New York for some time. The presence of anthrax, Dr. Mason said, “is consistent with the many documented cases of anthrax in livestock in New York State and the East Coast broadly.”

The purpose of the study was not simply to satisfy scientific curiosity, the authors said. By cataloging species now, researchers can compare them against samples taken in the future to determine whether certain diseases, or even substances used as bioterrorism weapons, had spread.

City and transit officials did not sound grateful for the examination.

“As the study clearly indicates, microbes were found at levels that pose absolutely no danger to human life and health,” Kevin Ortiz, a spokesman for the Metropolitan Transportation Authority, said in an email. And the city’s health department called the study “deeply flawed” and misleading.

Dr. Mason responded by saying he and his team had simply presented their complete results.

“For us to not report the fragments of anthrax and plague in the context of a full analysis would have been irresponsible,” he said. “Our findings indicate a normal, healthy microbiome, and we welcome others to review the publicly available data and run the same analysis.”

http://www.nytimes.com/2015/02/06/nyregion/among-the-new-york-city-subways-millions-of-riders-a-study-finds-many-mystery-microbes.html?hp&action=click&pgtype=Homepage&module=mini-moth&region=top-stories-below&WT.nav=top-stories-below

Thanks to Kebmodee for bringing this to the attention of the It’s Interesting community.

By Susanna Capelouto, CNN
Since February 49 people have gotten sick and 29 have died from an unidentified illness characterized by fever, diarrhea and vomiting in Guinea, according to the West African nation’s minister of health, Remy Lamah.

Lamah said initial test results confirm the presence of a viral hemorrhagic fever, which according to the U.S. Centers for Disease Control and Prevention refers to a group of viruses that affect multiple organ systems in the body.

The Guinean health ministry warned in a statement that the disease is mainly spread from infected people, objects belonging to ill or dead people and by the consumption of meat from animals in the bush.

So far, most of the cases have been in the forest area of southern Guinea, and health officials say they are offering free treatment for all patients.

They’ve urged people to stay calm, wash their hands and report all cases to authorities.

http://www.cnn.com/2014/03/22/world/africa/fever-epidemic-guinea

Thanks to Da Brayn for bringing this to the attention of the It’s Interesting community.

When Manu Prakash, PhD, wants to impress lab visitors with the durability of his Origami-based paper microscope, he throws it off a three-story balcony, stomps on it with his foot and dunks it into a water-filled beaker. Miraculously, it still works.

Even more amazing is that this microscope — a bookmark-sized piece of layered cardstock with a micro-lens — only costs about 50 cents in materials to make.

Prakash’s dream is that this ultra-low-cost microscope will someday be distributed widely to detect dangerous blood-borne diseases like malaria, African sleeping sickness, schistosomiasis and Chagas.

“I wanted to make the best possible disease-detection instrument that we could almost distribute for free,” said Prakash. “What came out of this project is what we call use-and-throw microscopy.”

The Foldscope can be assembled in minutes, includes no mechanical moving parts, packs in a flat configuration, is extremely rugged and can be incinerated after use to safely dispose of infectious biological samples. With minor design modifications, it can be used for bright-field, multi-fluorescence or projection microscopy.

One of the unique design features of the microscope is the use of inexpensive spherical lenses rather than the precision-ground curved glass lenses used in traditional microscopes. These poppy-seed-sized lenses were originally mass produced in various sizes as an abrasive grit that was thrown into industrial tumblers to knock the rough edges off metal parts. In the simplest configuration of the Foldscope, one 17-cent lens is press-fit into a small hole in the center of the slide-mounting platform. Some of his more sophisticated versions use multiple lenses and filters.

To use a Foldscope, a sample is mounted on a microscope slide and wedged between the paper layers of the microscope. With a thumb and forefinger grasping each end of the layered paper strip, a user holds the micro-lens close enough to one eye that eyebrows touch the paper. Focusing and locating a target object are achieved by flexing and sliding the paper platform with the thumb and fingers.

Because of the unique optical physics of a spherical lens held close to the eye, samples can be magnified up to 2,000 times. (To the right are two disease-causing microbes, Giardia lamblia and Leishmania donovani, photographed through a Foldscope.)

The Foldscope can be customized for the detection of specific organisms by adding various combinations of colored LED lights powered by a watch battery, sample stains and fluorescent filters. It can also be configured to project images on the wall of a dark room.

In addition, Prakash is passionate about mass-producing the Foldscope for educational purposes, to inspire children — our future scientists — to explore and learn from the microscopic world.

In a recent Stanford bioengineering course, Prakash used the Foldscope to teach students about the physics of microscopy. He had the entire class build their own Foldscope. Then teams wrote reports on microscopic observations or designed Foldscope accessories, such a smartphone camera attachment.

http://scopeblog.stanford.edu/2014/03/10/stanford-bioengineer-develops-a-50-cent-paper-microscope/
Thanks to Kebmodee for bringing this to the attention of the It’s Interesting community.

heart infection

University of Iowa researchers have discovered what causes the lethal effects of staphylococcal infective endocarditis – a serious bacterial infection of heart valves that kills approximately 20,000 Americans each year. According to the UI study, the culprits are superantigens — toxins produced in large quantities by Staphylococcus aureus bacteria — which disrupt the immune system, turning it from friend to foe.

“The function of a superantigen is to ‘mess’ with the immune system,” says Patrick Schlievert, PhD, UI professor and chair of microbiology at the UI Carver College of Medicine. “Our study shows that in endocarditis, a superantigen is over-activating the immune system, and the excessive immune response is actually contributing very significantly to the destructive aspects of the disease, including capillary leakage, low blood pressure, shock, fever, destruction of the heart valves, and strokes that may occur in half of patients.”

Other superantigens include toxic shock syndrome toxin-1, which Schlievert identified in 1981 as the cause of toxic shock syndrome.

Staph bacteria is the most significant cause of serious infectious diseases in the United States, according to the Centers for Disease Control and Prevention (CDC), and infective endocarditis is the most serious complication of staph bloodstream infection. This dangerous condition affects approximately 40,000 people annually and has a death rate of about 50 percent. Among patients who survive the infection, approximately half will have a stroke due to the damage from the aggressive infection of the heart valves.

Despite the serious nature of this disease, little progress has been made over the past several decades in treating the deadly condition.

The new study, led Schlievert, and published Aug. 20 in the online open-access journal mBio, suggests that blocking the action of superantigens might provide a new approach for treating infective endocarditis.

“We have high affinity molecules that neutralize superantigens and we have previously shown in experimental animals that we can actually prevent strokes associated with endocarditis in animal models. Likewise, we have shown that we can vaccinate against the superantigens and prevent serious disease in animals,” Schlievert says.

“The idea is that either therapeutics or vaccination might be a strategy to block the harmful effects of the superantigens, which gives us the chance to do something about the most serious complications of staph infections.”

The UI scientists used a strain of methicillin resistant staph aureus (MRSA), which is a common cause of endocarditis in humans, in the study. They also tested versions of the bacteria that are unable to produce superantigens. By comparing the outcomes in the animal model of infection with these various bacteria, the team proved that the lethal effects of endocarditis and sepsis are caused by the large quantities of the superantigen staphylococcal enterotoxin C (SEC) produced by the staph bacteria.

The study found that SEC contributes to disease both through disruption of the immune system, causing excessive immune response to the infection and low blood pressure, and direct toxicity to the cells lining the heart.

Low blood flow at the infection site appears to be one of the consequences of the superantigen’s action. Increasing blood pressure by replacing fluids reduced the formation of so-called vegetations – plaque-like meshwork made up of cellular factors from the body and bacterial cells — on the heart valves and significantly protected the infected animals from endocarditis. The researchers speculate that increased blood flow may act to wash away the superantigen molecules or to prevent the bacteria from settling and accumulating on the heart valves.

In addition to Schlievert, the research team included Wilmara Salgado-Pabon, PhD, the first author on the study, Laura Breshears, Adam Spaulding, Joseph Merriman, Christopher Stach, Alexander Horswill, and Marnie Peterson.

The research was funded in part by grants from the National Institutes of Health (AI74283, AI57153, AI83211, and AI73366).

http://www.infectioncontroltoday.com/news/2013/08/bacterial-toxins-cause-deadly-heart-disease.aspx

sn-atmosphere

Each year, hundreds of millions of metric tons of dust, water, and humanmade pollutants make their way into the atmosphere, often traveling between continents on jet streams. Now a new study confirms that some microbes make the trip with them, seeding the skies with billions of bacteria and other organisms—and potentially affecting the weather. What’s more, some of these high-flying organisms may actually be able to feed while traveling through the clouds, forming an active ecosystem high above the surface of the Earth.

The discovery came about when a team of scientists based at the Georgia Institute of Technology in Atlanta hitched a ride on nine NASA airplane flights aimed at studying hurricanes. Previous studies carried out at the tops of mountains hinted that researchers were likely to find microorganisms at high altitudes, but no one had ever attempted to catalog the microscopic life floating above the oceans—let alone during raging tropical storms. After all, it isn’t easy to take air samples while your plane is flying through a hurricane.

Despite the technical challenges, the researchers managed to collect thousands upon thousands of airborne microorganisms floating in the troposphere about 10 kilometers over the Caribbean, as well as the continental United States and the coast of California. Studying their genes back on Earth, the scientists counted an average of 5100 bacterial cells per cubic meter of air, they report in the Proceedings of the National Academy of Sciences. Although the researchers also captured various types of fungal cells, the bacteria were over two orders of magnitude more abundant in their samples. Well over 60% of all the microbes collected were still alive.

The researchers cataloged a total of 314 different families of bacteria in their samples. Because the type of genetic analysis they used didn’t allow them to identify precise species, it’s not clear if any of the bugs they found are pathogens. Still, the scientists offer the somewhat reassuring news that bacteria associated with human and animal feces only showed up in the air samples taken after Hurricanes Karl and Earl. In fact, these storms seemed to kick up a wide variety of microbes, especially from populated areas, that don’t normally make it to the troposphere.

This uptick in aerial microbial diversity after hurricanes supports the idea that the storms “serve as an atmospheric escalator,” plucking dirt, dust, seawater, and, now, microbes off Earth’s surface and carrying them high into the sky, says Dale Griffin, an environmental and public health microbiologist with the U.S. Geological Survey in St. Petersburg, Florida, who was not involved in the study.

Although many of the organisms borne aloft are likely occasional visitors to the upper troposphere, 17 types of bacteria turned up in every sample. Researchers like environmental microbiologist and co-author Kostas Konstantinidis suspect that these microbes may have evolved to survive for weeks in the sky, perhaps as a way to travel from place to place and spread their genes across the globe. “Not everybody makes it up there,” he says. “It’s only a few that have something unique about their cells” that allows them survive the trip.

The scientists point out that two of the 17 most common families of bacteria in the upper troposphere feed on oxalic acid, one of the most abundant chemical compounds in the sky. This observation raises the question of whether the traveling bacteria might be eating, growing, and perhaps even reproducing 10 kilometers above the surface of Earth. “That’s a big question in the field right now,” Griffin says. “Can you view [the atmosphere] as an ecosystem?”

David Smith, a microbiologist at NASA’s Kennedy Space Center in Florida, warns against jumping to such dramatic conclusions. He also observed a wide variety of microbes in the air above Oregon’s Mount Bachelor in a separate study, but he believes they must hibernate for the duration of their long, cold trips between far-flung terrestrial ecosystems. “While it’s really exciting to think about microorganisms in the atmosphere that are potentially making a living, there’s no evidence of that so far.”

Even if microbes spend their atmospheric travels in dormancy, that doesn’t mean they don’t have a job to do up there. Many microbial cells are the perfect size and texture to cause water vapor to condense or even form ice around them, meaning that they may be able to seed clouds. If these microorganisms are causing clouds to form, they could be having a substantial impact on the weather. By continuing to study the sky’s microbiome, Konstantinidis and his team hope to soon be able to incorporate its effects into atmospheric models.

http://news.sciencemag.org/sciencenow/2013/01/microbes-survive-and-maybe-thriv.html