Microbiology

Your “breathprint,” the chemical composition of each exhale, may hold potential as a new medical diagnostic tool, according to research recently published in PLOS ONE.

In the small study, Swiss researchers used a technique known as mass spectrometry to analyze the molecules in participants’ breath samples. As reported in the New Scientist:

The team was interested in metabolites, compounds produced by the body’s metabolism. The molecules are volatile and small enough to pass from the blood into airways via the alveoli in our lungs, so are present in our breath – albeit in miniscule amounts, sometimes less than one molecule per billion molecules of air.

The team found that metabolites in individuals’ breath remained “constant and clear”, says Swiss Federal Institute of Technology professor [Renato Zenobi, PhD].

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Zenobi’s team can identify compounds in breath immediately, so our breathprint could be used to detect signature metabolites associated with disease, giving an instant diagnosis. In a preliminary study, Zenobi has shown that breath samples can reveal whether people have chronic obstructive pulmonary disease.

While more research is needed to understand how breathprints might be used in a clinical setting, the research is noteworthy in light of the growing body of scientific showing a variety of unique biological identifiers, including microscopic ecosystems that exist in the human body, could offer insights into our personal health.

Photo by Sean Friend

You’ve heard of Sputnik, that little tiny antenna-clad chunk of metal heaved into low orbit on October 4, 1957, effectively kicking off the Space Age?

Well, make way for Gutnik. A news release issued by NASA’s Ames Research Center foretells the launch into space of a satellite inhabited by a bunch of nano-mariners who, left to their own devices, would no doubt rather curl up inside a bowel.

Sometime in the next one to three years, according to the release, a so-called “nanosatellite” weighing about 30 pounds and peopled by the intestinal bug E. coli will streak into the sky, with the mission of amassing data on whether the zero-gravity environment that cloaks our planet might increase microbes’ resistance to antibiotics. That’s important, because, as the release states:

Bacterial antibiotic resistance may pose a danger to astronauts in microgravity, where the immune response is weakened. Scientist believe that the results of this experiment could help design effective countermeasures to protect astronauts’ health during long-duration human space missions.

E. coli is probably the most-studied micro-organism in all of science. While most strains are harmless and actually quite friendly (producing vitamin K for us, just to name one of the nice things they do), some of them can cause food poisoning, urinary-tract infections and more.

Gutnik (whose real name is EcAMSat) is the brainchild of Stanford microbiologist A.C. Matin, PhD, the principal investigator for the joint NASA/Stanford University School of Medicine project. Matin’s previous inventions include microbes capable of gobbling up environmental toxins like uranium and chromium, as well as magnetic-field-seeking bacteria that can increase the contrast of magnetic-resonance imaging. So this new satellite caper is just one more in a series of wild but potentially very useful feats of imagination.

The thing that really knocks me out, though, is how all these scientists and engineers will manage to get those billions of little tiny bugs to sit still while the chin straps on their little tiny space helmets are being fastened.

Previously: Space: A new frontier for doctors and patients and Outer-space ultrasound technologies land on Earth
Photo by Per Olof Forsberg

Scientific illustrator Dee Breger specializes in creating images using a scanning electron microscope (SEM), which has an incredible level of magnification. In this recently posted TEDEducation video, Breger takes viewers on a tour of the hidden world inside the human body and offers close-up shots of a blood clot, the thyroid gland and neurons involved in memory. It’s worth taking a moment to watch. (The dental plaque image alone will motivate you to take better care of your teeth.)

Previously: Cool video of the intestinal immune system, Exploring the microbes that inhabit our bodies and Video of innate immune reaction in the lymph node

DNA may be the main building blocks of the body, but researches are starting to discover that RNA, which transports genetic information within a specific cell, could hold greater potential in understanding a wide range of diseases and developing novel therapeutics.

This recently posted National Institutes of Health video offers a great primer explaining how some RNA, known as extracellular RNAs (exRNA), can travel through bodily fluids and alter cells at a distance. The NIH Common Fund’s Extracellular RNA Communication program is currently investigating how exRNAs control cell behavior. By doing so, researchers hope to develop methods for detecting disease earlier and to create new treatment options, such as harnessing exRNAs’ communication power to turn a diseased cell into a healthy one.

Previously: Slicing and dicing small RNA molecules can better combat viruses, enhance gene therapies, say Stanford researchers and The RNA insurrection: Genes’ “humble servant” rules from behind the scenes

Here’s something to contemplate post lunch: In addition to delivering carbohydrates, fats and proteins to your body, the food you gobbled down midday contains nutrients and chemicals that may communicate instructions to your cells. A piece published today in Scientific American offers insights into how our diets may affect overall health:

Cells talk to each other in a complex language of chemical messages. They instruct each other to grow, to move and to respond to threats. Problems in cell communication lead to diseases such as diabetes and cancer. The messages take many forms, including hormones and charged molecules called ions. Cells also listen to signals that come from outside the body.

Recent findings show that molecules found in food can change cell chatter. For example, in 2010 a team of researchers in California and Japan found that omega-3 fatty acids from food bind to a specialized protein studding cell surfaces. That protein, called GPR120, is found in adipose and muscle tissues. When omega-3 fatty acid attaches to the protein, fitting like a key in a lock, GPR120 sets off a chain reaction of cellular events that ultimately protect against weight gain and inflammation.

Understanding the influence of food on cells could offer a better way to design diets, says Randy J. Seeley, the director of the Cincinnati Diabetes Center at the University of Cincinnati. A special diet to tone down inflammation might also combat weight gain or protect against diabetes.

Previously: Nature/nurture study of type 2 diabetes risk unearths carrots as potential risk reducers
Photo by Jeremy Keith

Today, President Barack Obama presented 23 innovators and researchers, including Stanford developmental biologist Lucy Shapiro, PhD, with national medals for their contributions to science, technology and innovation.

As reported by my colleague, Shapiro arrived in the nation’s capitol on Wednesday to attend a whirlwind of events commemorating her accomplishment. At a press conference this afternoon in the East Room at the White House, she and eleven other researchers were awarded the National Medal of Science alongside eleven inventors who received the National Medal of Technology and Innovation.

During the event, Obama joked that “this is the most collection of brainpower we’ve had under this roof in a long time” and lauded honorees for their hard work and commitment to their field. He said:

Thanks to the sacrifices they’ve made, the chances they’ve taken, the gallons of coffee they’ve consumed, we now have batteries that power everything from cell phones to electric cars. We have a map of the human genome and new ways to produce renewable energy. We’re learning to grow organs in the lab and better understand what’s happening in our deepest oceans. And if that’s not enough, the people on this stage are also going to be responsible for devising a formula to tame frizzy hair as well as inspiring the game Tetris.

But what also makes these individuals unique is how they’ve gotten here - the obstacles they’ve overcome and the commitments they’ve made to push the boundaries of our understanding.

Shapiro was honored for “the pioneering discovery that the bacterial cell is controlled by an integrated genetic circuit functioning in time and space that serves as a systems engineering paradigm underlying cell differentiation and ultimately the generation of diversity in all organisms.”

In addition to Shapiro, Sidney Drell, PhD, a senior fellow at the Hoover Institution, was also named a recipient of the National Medal of Science. He received the award for his contributions “to quantum field theory and quantum chromodynamics, application of science to inform national policies in security and intelligence, and distinguished contributions as an advisor to the United States government.”

Previously: Stanford’s Lucy Shapiro receives National Medal of Science

It’s a big week for developmental biologist Lucy Shapiro, PhD.

On Friday, she will be awarded the National Medal of Science - an honor often referred to as “America’s Nobel Prize.” Shapiro is being recognized not only for her research, but also for her active involvement in national policy. As I wrote in a story in today’s Inside Stanford Medicine:

In the past few years, [Shapiro has] garnered an impressive list of national and international awards for her work on understanding how the genetic circuitry of the bacterial cell functions in time and space to orchestrate a cell division that yields two unique cells — the fundamental basis of stem cell function and the generation of diversity in the living world. Her insights helped launch the field of systems biology and have led to the development of novel antibacterial and antifungal drugs.

I had the privilege of interviewing Shapiro and hearing first hand about her research and her unique journey from an undergraduate studying the fine arts (and Dante!) to the lab bench and even the White House:

Along the way, Shapiro has become an outspoken resource for politicians and policymakers struggling with the growing threat of emerging infectious diseases and the reality of bioterrorism in an age when scientific information — and people — flow much more quickly and freely across international borders than ever before. She served in an advisory role in the Clinton administration and second Bush administration, and is now a member of the Center for International Security and Cooperation at the Freeman Spogli Institute for International Studies at Stanford University.

“As my research progressed, I felt that I was in a position where I could, in fact, influence policy,” said Shapiro. “I had done the basic science that would allow me to understand how bacteria work, and I felt the responsibility to educate and inform the public about what I began to perceive as a growing threat. Our legislators and our government leaders have to know what’s really going on. So I’ve kind of been thrust into a position as a spokesperson for these issues.”

Congratulations Dr. Shapiro!

Previously: New method may speed identification of antibiotic targets
Photo by Justin Lewis

We’ve written previously about how researchers at Stanford and elsewhere are working to determine how microscopic ecosystems that exist in and on the human body may impact personal health. A video posted today on the TEDEducation YouTube channel offers a good primer on how the various species of bacteria populating our skin, mouths, digestive tracks and other areas make us intrinsically unique and influence our well-being.

Previously: Naval gazing: Belly Button Biodiversity project identifies thousands of bacteria species, Cultivating the human microbiome and Contemplating how our human microbiome influences personal health

For many of us, questions about our belly buttons rarely go beyond: Innie or outie? But a team of North Carolina-based researchers is looking past what the shape of our navel may indicate and examining the species of bacteria residing in it. Their work may help us better understand the biodiversity present on the human body and if these bacterial communities are helpful or harmful.

As part of the Belly Button Biodiversity (BBB) project, researchers recruited a group of individuals, swabbed their navels and analyzed all the various bacterial species of each sample. Findings published recently in PLoS One show that the team identified 2,368 bacterial species, 1,458 of which may be new to science. According to a post in the Atlantic:

the BBB project could make important progress in understanding how the bacteria that colonize us actually affect our health. Analogous to the parasite Toxoplasmosis gondii - which we only recently found out is present in 20-50 percent of our brains, subtly shaping our personalities and maybe even making us try to hurt ourselves — some of these little bacteria that go unnoticed are probably affecting us in ways unknown, good and bad. Ways that we’re currently just chalking up to chance or genetics or God or gluten.

As previously reported on Scope, researchers at Stanford and elsewhere are also engaged in ongoing efforts to determine how microscopic ecosystems that exist in the human body may impact personal health.

Previously: Diverse microbes discovered in healthy lungs shed new light on cystic fibrosis, Cultivating the human microbiome, Contemplating how our human microbiome influences personal health and New York Times explores our amazing microbes
Photo by dualdflipflop

Scientists have used powerful X-rays at the SLAC National Accelerator Laboratory at Stanford to reveal a potential way to combat the common stomach bacterium Helicobacter pylori. About half the people in the world carry the bacteria, which can cause ulcers and significantly increase the odds of developing stomach cancer.

In the study, researchers focused in on tiny channels that H. pylori uses to allow in urea from gastric juice in the stomach; it then breaks this compound into ammonia, which neutralizes stomach acid. Blocking the channels would disable this protective system and could lead to a new treatment for those with the infection. More from a recent Stanford Report article:

Using X-rays from SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL), “we have deciphered the three-dimensional molecular structure of a very promising drug target,” said Hartmut “Hudel” Luecke, a researcher at the University of California-Irvine and principal investigator on the paper. …

Solving the structure of the protein to find the specific area to target wasn’t easy. It is notoriously difficult to crystallize membrane proteins, which is a prerequisite step for using protein crystallography, the primary technique for visualizing protein structures. This technique bounces X-rays off of the electrons in the crystallized protein, which generates the experimental data used to build a 3-D map of the protein’s atoms.

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“This is the hardest structure I’ve ever deciphered, and I’ve been doing this since 1984,” Luecke said. “You have to try all kinds of tricks, and these crystals fought us every step of the way. But now that we have the structure, we’ve reached the exciting part – the prospect of creating specific, safe and effective ways to target this pathogen and wipe it out.”

Scientists, including those at Stanford, are still working to determine how the bacteria colonies that exist in our bodies influence our well being. And, as a past story in the New Yorker pointed out, there could be health consequences from eradicating the body of H. pylori or other microbes.