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Bacterial Fingerprinting: A Microbial Future on CSI?

Posted on August 25th, 2010

In 1915, detectives dusted for physical fingerprints. In 1990, they started using PCR (polymerase chain reaction) to determine DNA fingerprints from bits of hair and skin. In 2020, scientists might be identifying culprits with a whole new type of fingerprint: a bacterial fingerprint.

fingerprintA bacterial fingerprint is a unique mix of microbes by which an individual person can be identified. Recently, Rob Knight, Noah Fierer, and their colleagues at University of Colorado in Bounder swabbed bacteria off of computer mice and used the DNA of that bacteria to identify individual subjects.1 The scientists also showed that these bacterial fingerprints are durable: even after bacteria were left on the exposed surface for two weeks, the scientists could still swab, extract, and match the bacterial DNA to its correct human origin.

Bacterial fingerprints can also be used to “catch” people in ways other than just linking them to the scene of a crime. Molecular epidemiology (the use of molecular biology to trace outbreaks of microbial diseases) already helps to identify cases such as:

  • medical negligence resulting in patient infection, or
  • negligent or intentional contamination of food, resulting in disease.

To make bacterial fingerprints useful, a repository of microbial DNA with which samples can be matched is necessary. Such initiatives are already underway, such as Pulsenet, run by the U.S. Centers for Disease Control, which collects the DNA identities of disease-causing bacteria such as E. coli, Salmonella, and Listeria. Additionally, the NIH-funded Human Microbiome Project aims to analyze and record 1000 bacterial genomes.

Read “The four faces of microbial forensics,” an article describing potential uses for microbial forensics in the context of law enforcement and national security.2

Read “Microbial Forensics: A Scientific Assessment,” a report by the American Academy of Microbiology concerning the future of microbial forensics.

Watch a slideshow to learn more about molecular epidemiology.


1. Fierer, N., Lauber, C., Zhou, N., McDonald, D., Costello, E., & Knight, R. (2010). From the Cover: Forensic identification using skin bacterial communities Proceedings of the National Academy of Sciences, 107 (14), 6477-6481 DOI: 10.1073/pnas.1000162107

2. Tucker JB, & Koblentz GD (2009). The four faces of microbial forensics. Biosecurity and bioterrorism : biodefense strategy, practice, and science, 7 (4), 389-97 PMID: 20028247

Posted in Genetics, Nifty Research | No Comments »

Is Seaweed the New Diet Food?

Posted on August 18th, 2010

Diet medications may damage your liver, low-carbohydrate diets can cause kidney failure, and gastric bypass carries with it all the risks and complications of any body-altering surgery. However, recent research has suggested a slightly less risky fat-fighting alternative: seaweed.

Giant Kelp Photo ©Patricia McQuadeA team of scientists at Newcastle University have demonstrated that a natural fiber found in seaweed— specifically in kelp—can reduce fat absorption by close to 75%. By using an artificial gut to test more than 60 natural fibers, they found this fiber (called alginate) to be the most effective preventing fat absorption.

Alginate works by inhibiting the fat-digesting enzyme lipase. While popular diet pills also inhibit this enzyme, they divert the undigested fat to the colon, which causes unpleasant side effects like bloating and diarrhea. As an indigestible fiber, alginate helps the fat to pass through the colon without producing these same side effects.

With its high content of antioxidants, vitamins, and minerals, seaweed is actually eaten more regularly than one might imagine. For instance, laver—also known as nori (in Japan), gim (in Korea), or “slake”—is used to make the traditional Welsh dish laverbread, and also as a wrap for sushi and onigiri (rice balls). Another variety of seaweed, dulse, grows in the North Atlantic and is commonly consumed in Ireland and on the Atlantic coast of Canada.

The fiber alginate is found in giant kelp (Macrocystis pyrifera) and various types of brown algae (Ascophyllum nodosum and Laminaria). While powdered alginate is already used in a number of foods as a thickener, Brownlee and Pearson (the two scientists leading the Newcastle team) baked alginate powder into bread. After receiving positive results from their initial taste tests, they have recently begun human trials to determine the effects of alginate when it is consumed as part of a regular diet.

Watch an interview with lead researcher Jeffrey Pearson.

Read other research on the nutritional value of alginate:

Posted in Uncategorized | No Comments »

The Search for Earth-Like Planets

Posted on August 4th, 2010

“Are we alone in the universe?”

From Copernicus to Galileo to Tombaugh, scientists have spent lifetimes attempting to answer this question. Planetary size, distance, and relation to the stars they orbit have presented continuous obstacles. In recent years, however, astronomers, physicists, and engineers have developed increasingly sophisticated methods and instruments that are enabling progress on the hunt for planets that might—or might not—be capable of sustaining life.

Doppler Shift: light spectrumThe orbits of planets and stars are determined by the bodies’ common center of mass: the point at which both bodies’ gravitational pulls balance one another. Therefore, scientists can estimate a planet’s gravitational force—and therefore, mass—without even being able to see it; they just use the star’s orbit. To do this, they study the Doppler shift: the phenomenon by which light waves emitted by a star moving toward a viewer appear move toward the blue end of the light spectrum, while light waves emitted by a star moving away shift toward the red end. This is because the waves compress as the star moves closer to the viewer and decompress as the star recedes.

kepler telescopeTransit Method: Using extremely strong wide-diameter telescopes like the Kepler (launched in March 2009), scientists measure the change in apparent brightness of a star when a planet passes in front of it (sort of like a mini-eclipse). This change in brightness allows them to detect a planet’s existence and to estimate its size.

Nulling Interferometry: By observing a planet in infrared light, scientists use four telescopes capture the light waves from a star and arrange them so that they cancel each other out—thus making the orbiting planet(s) visible. This method was first conceived in the late 1970s. Recent improvements by engineer Stefan Martin and his collaborator A.J. Booth1 have improved its effectiveness so much that this method can now be used in the hunt for earth-sized planets.

Watch a lecture by astronomer Dimitar Sasselov about the discovery of earth-like planets.

Find out more about planet discovery on the NASA Jet Propulsion Laboratory website.

1 S. R. Martin, ., & A. J. Booth, . (2010). Demonstration of exoplanet detection using an infrared telescope array Astronomy & Astrophysics DOI: 10.1051/0004-6361/201014942

Posted in Nifty Research, Planets/Galaxy/Universe | No Comments »

Running Improves Memory: Steps to a Better Brain

Posted on July 28th, 2010

Running is good for your heart, lungs, and legs. Now research shows that it might improve your brain, too.

Mouse RunningAccording to a study published in Proceedings of the National Academy of Sciences1, voluntary running can improve synaptic plasticity and, as a result, spatial memory. Neuroscientists at Cambridge University separated mice into two groups: one group was given unlimited access to a running wheel, and the other served as a control group. Then, the scientists trained the mice to discriminate between squares displayed on the right and left sides of a computer screen. If a mouse nudged the left square with its nose, it was rewarded with a sugar pellet; if it nudged the right square, it received nothing.

After training, the mice were given a memory test in which the squares were displayed side-by-side 30cm apart. The scientists then gradually decreased the space between the squares in order to see how close the squares could be situated before the mice could no longer discriminate. (The closer the squares, the “more similar” the memory of each square and, thus, the harder for the mice to discriminate between the two.)

The running mice scored nearly twice as high on the memory test as the control mice. Furthermore, when the scientists changed the task and began rewarding the mice for nudging the opposite (i.e. right hand) square, the running mice recognized the change more quickly.

Scientists hypothesize that these behavioral changes are due to running-induced neurogenesis. In their dentate gyrus—an area of the hippocampus (the memory center of the brain)—the running mice generated approximately 6,000 new brain cells per cubic millimeter.

Other research has revealed similar patterns of running-induced neural growth:

  • A study published already in 1999 in Nature Neuroscience2 showed that voluntary running doubled the number of cells born in rats’ dentate gyrus. (Yoked swimming and maze learning, comparatively, showed no significant effects.)
  • A study published in the journal Hippocampus3 showed that rats that engaged in long-term voluntary running showed an increase in dendritic spines and synapses in several regions of the hippocampus, as well as in the entorhinal cortex (the memory-related area of the medial temporal lobe).
  • A study published in the journal Neurobiology of Aging4 showed that voluntary running not only enhances hippocampal cell proliferation but also reduces stress.

So if you’re feeling a little stressed or forgetful, a pair of tennis shoes and some wide open pavement might be just the remedy.

1 Creer, D., Romberg, C., Saksida, L., van Praag, H., & Bussey, T. (2010). Running enhances spatial pattern separation in mice Proceedings of the National Academy of Sciences, 107 (5), 2367-2372 DOI: 10.1073/pnas.0911725107

2 Gage, F., van Praag, H., & Kempermann, G. (1999). Running increases cell proliferation and neurogenesis in the adult mouse dentate gyrus Nature Neuroscience, 2 (3), 266-270 DOI: 10.1038/6368

3 Stroth, S., Hille, K., Spitzer, M., & Reinhardt, R. (2008). Aerobic endurance exercise benefits memory and affect in young adults Neuropsychological Rehabilitation, 19 (2), 223-243 DOI: 10.1080/09602010802091183

3 Stranahan, A., Khalil, D., & Gould, E. (2007). Running induces widespread structural alterations in the hippocampus and entorhinal cortex Hippocampus, 17 (11), 1017-1022 DOI: 10.1002/hipo.20348

4 Kannangara, T., Lucero, M., Gil-Mohapel, J., Drapala, R., Simpson, J., Christie, B., & van Praag, H. (2010). Running reduces stress and enhances cell genesis in aged mice Neurobiology of Aging DOI: 10.1016/j.neurobiolaging.2009.12.025

Posted in Health, Neuroscience | 4 Comments »

Motivation: Extrinsic or Intrinsic?

Posted on July 20th, 2010

You run ten miles; you practice the guitar; you sweep the floor; you write a poem. Regardless of what it is, every task requires motivation. That motivation is driven by the promise of some sort of reward, whether it be a rush of endorphins or a $25,000 check. The question is: are the most powerful rewards extrinsic or intrinsic?

Reaching for CarrotArguing for the intrinsic rewards are advocates of self-determination theory (SDT). The theory, developed by University of Rochester psychologists Edward Deci and Richard Ryan, posits that motivation develops internally from our need for competency, autonomy, and relatedness. A person will do his best work if he believes he is acting of his own free will and that his goals are meaningful. In fact, Deci and Ryan have found that extrinsic rewards (e.g. money) can actually lessen people’s sense of motivation.

In 1969, Deci conducted a study by which he placed two groups of college students rooms with a Soma cube (a puzzle similar to a Rubik’s cube) and several magazines. One group was offered money for each design they could assemble with the cube, and the other group was merely asked to work on the puzzle. After some time, Deci told the students that their time was up. For the next ten minutes, he observed them (in secret) and found that paid participants were more likely to quit the puzzle and pick up the magazines, whereas unpaid participants continued to work on the puzzle. Thus, the focus of the paid participants had shifted to the compensation, whereas the unpaid participants were still motivated by the inherently engaging task.

However, other researchers present opposing evidence. In one brain-imaging experiment, Alison Adcock, a researcher at the Duke Institute for Brain Sciences, showed subjects cue symbols signifying whether the next scene they would see would be worth five dollars or ten cents if they could remember that scene the next day. Unsurprisingly, subjects were much better able to identify high-value scenes than low-value scenes the next day. However, Adcock also found that the high-value cues (not the scenes themselves) activated reward areas of the mesolimbic region as well as the learning-centric hippocampus. Cue-induced activation suggests that the brain physically prepares to filter incoming information based upon the promise of a reward. (Like Pavlov’s dogs, but on a neuronal level.)

Thus, the debate continues. In recent years, it has even extended into the sphere of politics and education, as researchers such as Harvard economist Roland Fryer Jr. investigate whether paying students will motivate them to learn.

To read more and determine your own stance, check out some of these resources:

Posted in Education, Psychology | No Comments »

Antibiotics, Agriculture, and Superbugs

Posted on July 14th, 2010

Antibiotics are typically thought to treat bacterial infections. However, around 1950, farmers discovered another use: as they treated sick animals with antibiotics, the animals not only became healthier, but they also grew faster. Thus began the practice of administering antibiotics to healthy animals . . . and the evolution of today’s superbugs.

Superbug Transmission ChartThe more often bacteria are exposed to antibiotics, the greater the likelihood that the bacteria will accidentally mutate and survive—thus creating an antibiotic-resistant strain, called a superbug. With 50 million pounds of antibiotics administered to U.S.-raised animals every year, today’s bacteria are receiving ample opportunity to perform genetic trial-and-error. (By comparison, animals were only given 2 million pounds of antibiotics per year back in the 1950s, offering bacteria much less opportunity.)

Once the disease-resistant bacteria are “born” in healthy animals, humans can contract them in one of three ways:

  1. by eating contaminated meat,
  2. by directly handling contaminated animals or their waste,
  3. or by drinking water or eating plants that have absorbed the bacteria from contaminated manure runoff.

In June of this year, the FDA finally addressed the issue, releasing guidelines for antibiotics usage in agriculture. Meanwhile, Congress is also looking into the matter. Currently, the government is looking at legislation that, if passed, will phase out non-health-related agricultural use of seven different classes of antibiotics.

While the U.S. continues to deliberate, other countries have taken definitive and successful steps to eliminate nontherapeutic use of antibiotics. In December 1999, Denmark announced a final ban on the use of antibiotics to promote animal growth. Similar bans have become law across the entire European Union and New Zealand, as well.

To find out more about the relationship between antibiotics, agriculture, and superbugs, check out a few of these articles:

  • Mechanisms of Antimicrobial Resistance in Bacteria Tenover, F. (2006). The American Journal of Medicine, 119 (6) DOI: 10.1016/j.amjmed.2006.03.011
  • Industrial Food Animal Production, Antimicrobial Resistance, and Human Health Silbergeld, E., Graham, J., & Price, L. (2008). Annual Review of Public Health, 29 (1), 151-169 DOI: 10.1146/annurev.publhealth.29.020907.090904
  • Antibiotic use in animals–prejudices, perceptions and realities. Turnidge J (2004). The Journal of antimicrobial chemotherapy, 53 (1), 26-7 PMID: 14657093
  • What Do We Feed to Food-Production Animals? A Review of Animal Feed Ingredients and Their Potential Impacts on Human Health Sapkota, A., Lefferts, L., McKenzie, S., & Walker, P. (2007). Environmental Health Perspectives, 115 (5), 663-670 DOI: 10.1289/ehp.9760
  • Public Health Consequences of Use of Antimicrobial Agents in Food Animals in the United States Anderson, A., Nelson, J., Rossiter, S., & Angulo, F. (2003). Microbial Drug Resistance, 9 (4), 373-379 DOI: 10.1089/107662903322762815
  • The Need to Improve Antimicrobial Use in Agriculture Guest Editors: Michael Barza, M.D., & Sherwood L. Gorbach, M.D (2002). Clinical Infectious Diseases, 34 (s3) DOI: 10.1086/512410
  • Epidemiology of resistance to antibiotics Links between animals and humans van den Bogaard, A. (2000). International Journal of Antimicrobial Agents, 14 (4), 327-335 DOI: 10.1016/S0924-8579(00)00145-X

Posted in Animals, Health | No Comments »

Body Image Distortion: As Nature Intended?

Posted on July 7th, 2010

What if you’re not as fat as your brain thinks you are?

According to research by Matthew Longo and other neuroscientists at the University College London, this is a definite possibility. In their study, Longo and his colleagues asked volunteers to place their left hand palm-side-down underneath a board and to then estimate the size of their hand by identifying landmarks such as fingertip and knuckle locations. As it turns out, volunteers consistently overestimated the width of their hand—sometimes by up to 80%.

cortical homunculusWhile Longo and his colleagues have discovered the “what,” however, they have not yet quite determined the “why.” After all, what advantage is there to representing the body as overly wide?

The brain naturally uses proprioception to create internal maps of the body, many of which are distorted for specific reasons. One such map is the cortical homunculus: a map that represents the amount of cortex devoted to:

1) processing stimuli and

2) controlling motor functions in each portion of the body.

When represented pictorially, this map shows body parts significantly out of proportion; this is because more cortex is required to oversee finer movements and greater concentrations of nerve endings in areas such as the fingertips or lips than in, say, the chest or leg.

Nevertheless, Longo and his colleagues’ findings could shed some insight into the neurological causes of eating disorders. If the mind implicitly believes the body to be wider than it really is, then that mental representation may be over exaggerated in individuals with conditions such as anorexia nervosa, where body image is distorted.

Read the research behind Longo’s findings. 1

Investigate body image distortion and how it affects disordered eating. 2

Find out more about cortical homunculi.

1. Longo, M., & Haggard, P. (2010). An implicit body representation underlying human position sense Proceedings of the National Academy of Sciences, 107 (26), 11727-11732 DOI: 10.1073/pnas.1003483107

2. Liechty, J. (2010). Body Image Distortion and Three Types of Weight Loss Behaviors Among Nonoverweight Girls in the United States Journal of Adolescent Health DOI: 10.1016/j.jadohealth.2010.01.004

Posted in Neuroscience, Psychology | No Comments »

Eclipse in The Odyssey: Science Meets Mythology

Posted on July 1st, 2010

“Poor men, what terror is this that overwhelms you so? Night shrouds your heads, your faces, down to your knees—cries of mourning are bursting into fire—cheeks rivering tears—the walls and the handsome crossbeams dripping dank with blood! Ghosts, look, thronging the entrance, thronging the court, go trooping down to the realm of death and darkness! The sun is blotted out of the sky—look there—a lethal mist spreads all across the earth!”—Homer (translation by Robert Fagles)

Solar EclipseIn The Odyssey, this passage, delivered by the oracle Theoclymenus, portends the suitors’ deaths at the hand of Odysseus. However, some scholars believe that Homer, the poem’s author, was also describing a total solar eclipse.

The first to make this suggestion was the Greek philosopher and intellectual Plutarch. Then, circa 1920, astronomers Carl Schoch and Paul Neugebauer determined that a total solar eclipse occurred over the Ionian islands (which include Ithaca) at about noon on April 16, 1178 B.C. This sparked a debate over whether Homer had referred to this specific eclipse in The Odyssey. However, the connection was ultimately deemed too improbable and the debate was dropped . . . until physicist Marcelo Magnasco and astronomist Constantino Baikouzis picked up the trail.

Together, Magnasco and Baikouzis investigated whether three separate celestial events, which were explicitly mentioned in The Odyssey, could set the story at the time of the 1178 B.C. eclipse1:

  1. Twenty-nine days before the suitors’ slaughter (and, consequently, the supposed eclipse), Odysseus sees both the Pleiades and Boötes constellations simultaneously at sunset. This double-sighting can only occur two times a year. Since Homer describes Odysseus as watching the Boötes setting late, the voyage must have taken place in the spring, since the sun approaches Pleiades first in that season (making the Boötes the “later-setting” constellation), while it approaches the Boötes first in the fall.
  2. Six days before the slaughter, Odysseus’ crew sees Venus rise before dawn, which further marks the season.
  3. The actual day of the slaughter is a New Moon. (Having nothing to do with the Stephanie Meyers novel, a New Moon is when the moon’s un-illuminated side faces almost directly toward Earth, rendering the moon nearly invisible.) This lunar phase is a prerequisite for a total solar eclipse.

In addition to these three clues, Magnasco and Baikouzis developed two more conjectures: they reinterpreted the east-westward journey of the god Hermes—known to the Romans as “Mercury”—as planetary movement, and they considered the return of the god Poseidon—also known as the “Earthshaker”—from the southern hemisphere as potentially referring to the Equinox. Using these five events as “conditions,” Magnasco and Baikouzis scanned 1,684 new moons between the years 1250 and 1115 B.C. for dates that fit their conditions. One date in the whole 135-year span matched all five criteria: April 16, 1178 B.C.—the very same date on which Schoch and Neugebauer calculated the solar eclipse over Ithaca.

In spite of this evidence, skepticism persists. For one thing, Homer certainly did not see the eclipse himself; he is believed to have lived in the 9th and 8th centuries B.C.—several hundred years after the events of the Odyssey. Thus, as there is next-to-no evidence that the ancient Greeks tracked detailed movements of the stars and planets, Homer’s ability to gain such detailed astrological knowledge remains a mystery.

Attend a talk by Dr. Magnasco discussing his and Dr. Baikouzis’ research. July 2, 2010

Chase the last total solar eclipse of the year! July 11, 2010

1 Baikouzis, C., & Magnasco, M. (2008). From the Cover: Is an eclipse described in the Odyssey? Proceedings of the National Academy of Sciences, 105 (26), 8823-8828 DOI: 10.1073/pnas.0803317105

Posted in Nifty Research | No Comments »

Recycling Plastic into Fabric: Re-Wear Your Bottles

Posted on June 23rd, 2010

You drink a soda. You throw out the bottle. Hopefully, you toss it into the blue recycling bin, not the trash can. But have you ever considered wearing that bottle?

Plastic BottleLiterally wearing a plastic bottle sounds ludicrous, but turning that bottle into soft, comfortable fabric is the newest recycling fad. This year’s Brazil and USA World Cup soccer teams are wearing 100% recycled polyester jerseys, manufactured by Nike, while Reebok plans to collect bottles at NFL and NHL games, which the company will then turn into shirts to sell back to fans.

Now, the process of recycling plastics is nothing new, but how do you turn a bottle into a T-shirt?

  1. At the recycling plant, the plastic bottle (made of polyethylene terephthalate, or PET) is separated from other materials (bottle caps, wrappers, etc.) and then sorted: colored plastic will be used to make darkly colored thread, while clear plastic can be made into any color.

  2. The plastic is chopped up and then crushed up into tiny flakes.
  3. The flakes are melted in large vats, and the resulting liquid is pushed through a showerhead-like strainer to create fibrous polyester strands.
  4. The strands are stretched to make them thinner and stronger.
  5. Finally, the strands are cut, bundled, and shipped to manufacturers.

The “green” benefit to recycling old plastic bottles is obvious: it keeps them out of landfills and, consequently, decreases the amount of trash accumulating on our planet. However, there is a secondary benefit as well: reusing old plastic instead of manufacturing new plastic actually conserves natural resources. Thirty percent less energy is required to make shirts from recycled PET than from virgin polyester. Furthermore, 500,000 barrels of oil are saved each year by turning bottles into fabric—enough to power a city the size of Atlanta for a year! 1

Watch a video about plastic-to-fabric recycling.

Read recently published research about challenges and opportunities in plastics recycling. 2

Buy recycled plastic clothing from these companies:

1. Eartheasy.com

2. Hopewell, J., Dvorak, R., & Kosior, E. (2009). Plastics recycling: challenges and opportunities Philosophical Transactions of the Royal Society B: Biological Sciences, 364 (1526), 2115-2126 DOI: 10.1098/rstb.2008.0311

Posted in Environment, Nifty Research | No Comments »

Immune Attack: Video Games as Teaching Tools

Posted on June 14th, 2010

Video games are usually a student’s self-reward for sitting through a day at school. But what if video games were actually part of a regular day at school?

Immune Attack dashboardImmune Attack is one such video game. Middle and high school students try to fix a teenager’s immunodeficiency by piloting a nanobot through his body and teaching his immune system how to fight off a bacterial infection. In the process, they gain knowledge of cell biology and molecular science.

The game started as the brainchild of Melanie Stegman and Michelle Fox, scientists at Federation of American Scientists’ Learning Technologies Program. Using grant money from the National Science Foundation (NSF), Stegman and Fox collaborated with immunologists from Brown University and graphic artists from University of Southern California to create the video game. They then collected a panel of scientists to peer review each “mission” in the game and have called for teachers’ help in evaluating Immune Attack in their classrooms. Five hundred teachers have signed up so far, and, moreover, 9,000 people have downloaded the video game.

Immune Attack GameImmune Attack is a more effective teaching tool than lecturing about immunology for several reasons. For one thing, because students are trying to beat the game, they actively engage in obtaining and retaining information that will help them accomplish that goal, as opposed to sitting passively through a lecture. Furthermore, having a goal (i.e. to beat the game) keeps students focused on the immunology information for longer than they would listen to it in a lecture.

Download the game and start fighting bacteria!

Read more about the effectiveness of Immune Attack in the ASCB 2009 Press Book.

Check out two other science-related educational video games, Re-Mission and Didget.

Posted in Education, Health, Uncategorized | No Comments »

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