Author Archives: Steve Murray

About Steve Murray

I'm a freelance writer, former scientist, and part-time engineering professor. I'm interested in how science and technology change us as a society, a focus I try to bring to my blog, "Ripple Effect".

Valuable Viruses – ancient infections essential to human development

Pluripotent, embryonic stem cells originate as inner mass cells within a blastocyst. (Credit: Mike Jones for Wikipedia)

Pluripotent, embryonic stem cells originate as inner mass cells within a blastocyst. (Credit: Mike Jones for Wikipedia)

We may owe much of what we are as humans to the actions of old viruses. According to a new study from the Stanford University School of Medicine, human cellular development appears to depend on the actions of genetic material left over from ancient viral infections.

The researchers have identified several noncoding RNA molecules that enable a fertilized human egg to become all of the different cell types in the body. All of these molecules have viral origins and all are essential to growth; blocking their action stops cell development.


Viral remnants

Many cells, including fertilized eggs, are pluripotent. That is, they can develop into any cell or tissue type in the body. Scientists can even induce fully-developed human cells to become pluripotent by exposing them to the kinds of proteins found in early human embryos, although the molecular details of this process are not well understood.

The Stanford team was interested in how pluripotency begins. Their work extends previous Stanford research showing that early human embryos contain what appear to be significant amounts of viral particles in the cells from ancient genetic material.

“We’re starting to accumulate evidence that these viral sequences, which originally may have threatened the survival of our species, were co-opted by our genomes for their own benefit,” said Vittorio Sebastiano, PhD, assistant professor of obstetrics and gynecology.

Their study focused on long-intergenic noncoding RNA molecules. Among other biological processes, lincRNAs are known to be involved in enabling cells to acquire pluripotency. Although they’re made from DNA, noncoding molecules don’t make proteins directly but influence the protein expression of other genes.

The team employed RNA sequencing to identify which lincRNAs were most expressed in human embryonic stem cells. Most of these molecules contain highly similar and repetitive regions, however, which make them difficult to sequence accurately. The new study was aided by recently-developed and improved sequencing techniques.

The Stanford researchers identified more than 2,000 previously unknown RNA sequences, and found that 146 were specifically expressed in embryonic stem cells. They then focused on the 23 most highly expressed sequences (HPAT1-23) and found that 13 of these were made up almost entirely of genetic material left behind after an ancient infection by the HER-V retrovirus.

A retrovirus spreads by inserting its genetic material into the genome of an infected cell. The cell generates more viral proteins as part of its normal production processes which can then be assembled into a new viral particle that infects other cells.

If the infected cell is a sperm or an egg, these retroviral sequences can be passed to future generations. Our genomes are littered, therefore, with sequences of age-old retroviral infections. Over time, however, evolutionary changes and mutations have depleted their capacity to produce functional proteins and these sequences are considered to be relatively inert.

Blastocyst - day 5. (Credit: Ekem at English Wikipedia. Transferred from en.wikipedia to Commons.)

Blastocyst – day 5. (Credit: Ekem at English Wikipedia. Transferred from en.wikipedia to Commons.)

The team examined the expression of HPAT 1-23 sequences in the human blastocyst – the hollow cluster of cells that grow from the fertilized egg. They found that HPAT2, HPAT3 and HPAT5 were expressed only in the inner cell mass of the blastocyst, the part that becomes the developing fetus. They found that blocking this expression in one cell of a two-celled embryo stopped the affected cell from contributing to that inner mass. Subsequent work also showed that these three genes are also required for changing adult cells into pluripotent stem cells.


Only in primates

“This is the first time that these virally derived RNA molecules have been shown to be directly involved with and necessary for vital steps of human development,” said Sebastiano. “What’s really interesting is that these sequences are found only in primates, raising the possibility that their function may have contributed to unique characteristics that distinguish humans from other animals.”

“Previously retroviral elements were considered to be a class that all functioned in basically the same way,” added Jens Durruthy-Durruthy, PhD and postdoctoral scholar. “Now we’re learning that they function as individual elements with very specific and important roles in our cells. It’s fascinating to imagine how, during the course of evolution, primates began to recycle these viral leftovers into something that’s beneficial and necessary to our development.”

So viral material isn’t just tolerated in our cells – it’s vital to how we become people.


Lead authors for the research paper, published online this month in Nature Genetics, were Sebastiano, Durruthy-Durruthy, and Renee Reijo Pera, PhD, former professor of obstetrics and gynecology at Stanford and now on the faculty at Montana State University. Other Stanford authors were postdoctoral scholars Mark Wossidlo, PhD, Jonathan Davila, PhD, and Moritz Mall, PhD; research associate Diana Cepeda, PhD; former postdoctoral scholar Jun Cui, PhD; graduate student Edward Grow; Wing Wong, PhD, professor of statistics and health research; and Joanna Wysocka, PhD, professor of chemical and systems biology and of developmental biology.
Source: Ancient viral molecules essential for human development, Stanford researchers say


Rocks Traveled Far in Ancient Martian Rivers

The presence of rounded pebbles on Mars was evidence of a prior history of water on the planet. (Credit: NASA/JPL-Caltech/MSSS)

The presence of rounded pebbles on Mars was evidence of a prior history of water on the planet. (Credit: NASA/JPL-Caltech/MSSS)

How do you understand the natural history of rocks and water on another planet when all you have are pictures? You do the math.

Scientists have discovered how to use images of pebble shapes to estimate to estimate how far water may have moved them in ancient Martian riverbeds. These estimates enhance geographic information about the planet to provide even more evidence that Mars once had an extensive river system, and possible life.


Martian rivers

Although Mars looks cold and dry today, conditions could have been very different in its early history. In 2012, the Mars Curiosity rover sent images to earth that showed evidence of ancient water on the planet (and more recent data indicate that water may still flow there). These surface images showed smooth, rounded pebbles that usually result from abrasion as they’re carried along by flowing water.

Douglas Jerolmack, a geophysicist at the University of Pennsylvania, and Gábor Domokos, a mathematician at Budapest University of Technology and Economics, wanted to extract more information from the images, if possible. Could the pebble characteristics (specifically, their round shapes) be used to reveal something about the water that had transported them?

The answer appears to be “yes.” In a new report published in Nature Communications, Jerolmack, Domokos and colleagues describe an original method to quantitatively estimate the transport distance of river pebbles based only on their shapes. Measures of water flow on Mars would be valuable information to planetary geophysicists.

Pebbles lose mass in riverbeds as they get knocked against other pebbles, and current geophysical theory links a pebble’s transport history to the mass it loses from such collisions. How do you determine a transport history, however, if your pebbles are on Mars and you can’t measure mass? Fortunately, pebbles also change shape, becoming smoother and more rounded as they travel.

“An object’s shape can itself tell you a lot,” said Domokos. “If you go to the beach, natural history is written underneath your feet. We started to understand that there is a code that you can read to begin to understand that history.”

From the lab to the field

Project work began with Domokos and was inspired by the Gömböc, a three-dimensional object with just two static balance points. A Gömböc shape rights itself on a horizontal surface like a Weeble toy. Unlike the egg-shaped toy, however, a Gömböc has no added bottom weight; the self-righting property is the result of the shape alone. The water abrasion process tends to reduce the number of static balance points on an object, evolving it toward a Gömböc shape. Therefore, information about the natural history of a pebble could be reflected in its shape changes during the transport process.

Domokos was also aware of a recent mathematical proof for the Poincaré conjecture (which described topological identities between a variety of three-dimensional shapes and spheres) and adapted it to describe changes to structures like rocks. The Domokos model showed that when two particles of similar size collide with each other, their mutual influence can be reduced to a purely geometric problem. Shape changes could be determined mathematically, regardless of the rock material or the environment in which they are moving.

The research team first tested their new model by rolling limestone fragments in a drum and periodically pausing to record the changes to the shape and mass of each piece. The researchers then traveled to a mountain river in Puerto Rico and measured the shapes and weight of rocks every few hundred meters as they traveled down the river from their points of origin.

Their final test took place in the sediment deposits of an alluvial fan at the mouth of a New Mexico canyon, an environment chosen because it matched the location of the pebbles imaged on Mars. Their data closely agreed with prediction of their model in all cases. The team could estimate the distance a pebble traveled from its source using only its shape.

Curiosity rover image of Link outcrop on Mars, showing rounded gravel fragments, compared with similar rocks seen on Earth. (Credit: NASA/JPL-Caltech/MSSS and PSI)

Curiosity rover image of Link outcrop on Mars, showing rounded gravel fragments, compared with similar rocks seen on Earth. (Credit: NASA/JPL-Caltech/MSSS and PSI)

Back to Mars

The next challenge was extraterrestrial. Tímea Szabó, lead author of the paper (who worked with Domokos as a graduate student and later as a postdoctoral researcher in Jerolmack’s lab), analyzed publicly available images of rounded pebbles from the Mars Curiosity mission. Szabó traced their contours and applied the team’s geometric model to show that that the pebbles had lost approximately 20 percent of their volume.

The researchers then used their earlier lab and field data to help convert the calculated change in mass into distance traveled. The team based their work on the kind of basalt material found on Mars and corrected for reduced Martian gravity. The results showed that the pebbles had traveled an estimated 50 kilometers (30 miles) from their source.

John Grotzinger, of the California Institute of Technology and, until recently, lead scientist for NASA’s Curiosity mission, collaborated with the research team. His earlier NASA estimate for the pebble movement had been 30 kilometers (19 miles), beginning at a crater rim, which meshed nicely with the new calculations.

Although Jerolmack is pleased with the performance of their model, he’s also excited about what the advance represents to a range of current science problems.

“Now we have a new tool we can use to help reconstruct ancient environments on Earth, Mars and other planetary bodies where rivers are found such as Titan,” he said.

The work also shows how a seemingly esoteric piece of mathematics can find real world application.

“Once math enters the subject,” said Domokos, “the subject changes forever.”



Source: Pebbles on Mars likely traveled tens of miles down a riverbed, Penn study finds

Your microbial cloud is your “signature”

New research focused on the personal microbial cloud. (Credit: Viputheshwar Sitaraman, of Draw Science)

New research focused on the personal microbial cloud. (Credit: Viputheshwar Sitaraman, of Draw Science)

Humans are walking ecosystems. Each of us carries around about 100 trillion microbes in and on our bodies, which make up our microbiome. The quality of this bacterial community has a lot to say about our health and well-being. The blend of microbes is also surprisingly unique, which says a lot about who we are as individuals.

New research published in the September 22 issue of PeerJ has found that people can be identified by the nature of the microbial cloud that they release in the air around them. We each have our own microbial “signature.”

A not-so-empty room

Scientists have already amassed plenty of information about the human microbiome and they already know that people disperse some of those bacteria to their environments. These microbes come primarily from dust, our clothing, and our bodies.

Two new experiments, conducted at the University of Oregon, investigated the individual nature of these bacterial clouds.

The first experiment was designed to test whether researchers could confirm the presence of a person based only on bacterial traces. The researchers asked study participants to sit alone in a sanitized chamber that was filled with filtered air. A second, unoccupied chamber was used as a sterile control.

Each participant was given a clean outfit to wear to reduce the number of particles coming from clothing. Participants also sat in a plastic chair that had been disinfected and were given a disinfected laptop to use for communication and for personal entertainment during the study.

The experiment involved three participants, each tested for a total of six hours. Air in the test chamber was compared to the air in the unoccupied chamber. Any particles that came from a participant were filtered out of the chamber air and genetically sequenced to identify the mix of bacteria. The analyses involved thousands of different bacteria types in over 300 air and dust samples.

The researchers were able to determine that a person was present in the chamber after two hours, based only at the presence of bacteria in the air samples. They also found, however, that they could distinguish one person from another based on the unique combinations of bacteria from each participant.

This result motivated a second, more precise experiment.

Eight new people were asked to sit alone in the chamber for two 90-minute sessions. Analyzing the bacteria in the air revealed several individual features of each participant, including whether the person was male or female.

“We expected that we would be able to detect the human microbiome in the air around a person,” said lead author James Meadow, who was a postdoctoral researcher at the University of Oregon from the Biology and the Built Environment Center at the University of the time of the study. “But we were surprised to find that we could identify most of the occupants just by sampling their microbial cloud.”

A few bacteria groups, such as Streptococcus (commonly found in the mouth), Propionibacterium and Corynebacterium

(found on the skin), were primary indicators in the study. While these microbes are common in humans, it was the different combinations of these bacteria populations that distinguished between individuals.

Subtle differences were also found in the microbial clouds. Some people, for example, gave off different amounts of bacteria to the air due to such personal habits as how much they scratched and how much they fidgeted.

Tracking individual biology

The demonstration that bacteria clouds can be traced to individuals could shed light on how infectious diseases spread in buildings.

The results could also have a forensic use. Bacterial residue in the air might, for example, be used to determine where a person has been, even after they’ve left a space. The contributions of other people – or even animals – in those spaces, however, could easily complicate any analysis, so forensic uses will likely require more research.

Many things are used to detect and identify us in modern life. Now we know that the bacteria on, in, and around each of us has a close connection to the places we occupy, can be detected even after we’re gone . . . . and can be traced back to us.



Primary Source: New research finds that people emit their own personal microbial cloud


Binary black hole discovery may hint at genesis of quasars

An international astronomy team has detected two supermassive black holes that appear to be orbiting each other in a nearby galaxy. The discovery of a likely binary black hole system suggests that supermassive black holes assemble their masses through violent unions.

OU astrophysicist and his Chinese collaborator used observations from NASA's Hubble Space Telescope to find two supermassive black holes in Markarian 231. Credit: Space Telescope Science Institute,  Baltimore, Maryland

OU astrophysicist and his Chinese collaborator used observations from NASA’s Hubble Space Telescope to find two supermassive black holes in Markarian 231. Credit: Space Telescope Science Institute,Baltimore, Maryland

A dynamic duo

The black holes are located in Markarian 231, (Mrk231) – 600 million light years away, but the nearest galaxy to Earth that hosts a quasar. The central black hole is estimated to be 150 million times the mass of our Sun, while its companion is estimated to be 4 million solar masses. They orbit around each other every 1.2 years.

The smaller black hole appears to be the remnant of a galaxy that merged with Mrk 231. The physical asymmetry of Mrk 231, and the long tidal tails of its young blue stars, indicate that the two galaxies merged fairly recently, at least in cosmological time scales.

Quasars are the brightest objects in the universe and are powered by incredible amounts of energy. Black holes at the centers of galaxies are surrounded by large, rotating clouds of gas. As the gas is drawn in by the gravity of the black hole, it is heated to millions of degrees and emits broad-spectrum radiation that drives quasar brightness.

Black holes can also eject material around them into outflows that penetrate and compress the surrounding galactic gases, driving star formation. Mrk 231 is an energetic galaxy with a star formation rate 100 times greater than our Milky Way galaxy.

Searching the spectrum

Xinyu Dai, professor in the Homer L. Dodge Department of Physics and Astronomy, University of Oklahoma College of Arts and Sciences, collaborated with Youjun Lu of the National Astronomical Observatories of China, Chinese Academy of Sciences for the study.

The astrophysicists examined archival observations from the Hubble Space Telescope looking for ultraviolet radiation emitted from the center of Mrk 231. They then fitted a dynamical model developed by Lu to the spectrum data to predict the existence of the binary black hole system.

The study suggests that two, not one, supermassive black holes may lie at the heart of many quasars, and that their pairing is the result of a galactic collision. The merger of two galaxies could lead to their central black holes falling into orbit around each other, generating the immense energies needed to power a quasar.

If only a single black hole were present, the surrounding hot gas of its entire accretion disk would glow in the ultraviolet range of the spectrum. The ultraviolet glow of the Mrk 231 disk, however, drops off suddenly towards the center, leaving a huge gap around the central supermassive black hole. The best explanation for this gap is the mutual orbit of the two black holes. The smaller black hole, with its own accretion disk, orbits the larger black hole at the inner edge of the larger accretion disk, cleaning out the region.

Collisions to quasars

The work demonstrates a new investigative approach, as well as a new science discovery.

“We are extremely excited about this finding because it not only shows the existence of a close binary black hole in Mrk 231, but also paves a new way to systematically search binary black holes via the nature of their ultraviolet light emission,” said Lu.

The binary black holes of Mrk 231 are predicted to spiral together and collide within a few hundred thousand years. That final, violent merger should form a quasar with a single supermassive black hole at its center. Although the lifespan of quasars isn’t certain, the process behind their formation may be a common feature of the universe.

“The structure of our universe, such as those giant galaxies and clusters of galaxies, grows by merging smaller systems into larger ones, and binary black holes are natural consequences of these mergers of galaxies,” said Dai.


Journal Reference
A Probable Milli-parsec Supermassive Binary Black Hole in the Nearest Quasar Mrk 231,” Chang-Shuo Yan, Youjun Lu, Xinyu Dai, Qingjuan Yu., 2015 August 20, Astrophysical Journal, Vol. 809, No. 2

A Second Look at the Iceman – New discoveries motivate new analyses

Ötzi Reconstruction (© South Tyrol Museum of Archaeology –

Ötzi Reconstruction (© South Tyrol Museum of Archaeology –

Hikers discovered Ötzi the Iceman in the Ötztal Alps of Tyrol, Austria in 1991. Forensic analysis showed that he died around 5,300 years ago, making his the oldest intact human body every found. Ötzi had been preserved by glacier ice and was found with his tools, clothes, and weapons – a time capsule of Copper Age life. While years of study have enhanced our knowledge of his world, recent work with the Iceman has shown that he still holds a few mysteries for science.

Ötzi’s ailments

The Iceman’s body was found with a rich set of tattoos, something that had never been seen from this period before. Early studies revealed about 50 markings, made by rubbing soot into small skin incisions. The body had been darkened by centuries in the snow, however, so the tattoos had little contrast. Finding them visually was difficult and researchers couldn’t be sure that they had discovered all of them.

Initially, scientists believed that this body art was for decoration, but further study yielded a more intriguing theory: Investigators noted that the tattoos were placed over areas of physical wear such as the wrist, knees, and ankles, which meant that their purpose might have been pain relief. A medical study later pointed out that the tattoo locations matched known acupuncture meridians. If this theory were correct, the practice would predate the earliest recorded use of acupuncture in China by 2,000 years.

Although the idea was exciting, the evidence wasn’t definitive, and some researchers had their doubts.Therefore, scientists recently took another at Ötzi, to create a complete map of his tattoos. This time, they came with technology.


Looking deeper . . .

Ötzi Wrist Tattoo (© South Tyrol Museum of Archaeology/Eurac/Samadelli/Staschitz)

Scientists from the South Tyrol Museum of Archaeology and the Institute for Mummies and the Iceman (at the European Academy of Bozen) recently surveyed Ötzi using multispectral photographic tools.

Multispectral imaging records the reflection responses of materials to different wavelengths of light and combines those results into a single, color-coded picture. Different reflectance properties make fine distinctions easier to see, exposing and highlighting fine contrasts. This imaging method has been used by art restorers to find evidence of earlier painting beneath a canvas, and archaeologists to recover writing on charred papyri.

The camera used for the Iceman survey was fitted with filters that captured wavelengths from ultraviolet (300 nanometers) to infrared (1,000 nanometers). Human visual response, for comparison, spans about 400 – 700 nanometers.




. . . yields new insights

After the survey, the tattoo count went up to 61, and the research team thinks that they’ve completed a full tally.

“It is an extraordinary result. Finally, we have been able to clarify many doubts on the existence of these tattoos,” said Marco Samadelli, of the South Tyrol Museum of Archaeology.

Ötzi Chest Tattoo (© South Tyrol Museum of Archaeology//Eurac/Samadelli/Staschitz)

Ötzi Chest Tattoo (© South Tyrol Museum of Archaeology//Eurac/Samadelli/Staschitz)

The survey produced a surprise, however, when it revealed a new group of tattoos on the right lower right side of Ötzi’s rib cage. Unlike the earlier tattoos, this group was in an area with no apparent physical ailment. So, did the markings represent medical treatments or not? Several possibilities still fit the pattern.

Ötzi might have suffered another condition that also resulted in chest pain, such as gallstones, colonic worms, or atherosclerosis (plaque in arteries). If this were the work of a Copper Age healer, then treating symptoms where they were reported would only be logical.

An unfinished story

Samadelli and his research team want to use the new mapping for fresh examinations into the purpose of the tattoos, including any relation to acupuncture points.

“Future comparative studies based on the known health problems of the Iceman as evidenced by radiological investigations and molecular studies, could help to find out whether the tattoos had a therapeutic, diagnostic or more symbolic background.”

The new imaging work has been published in the Journal of Cultural Heritage.

Analysis and interpretation of Ötzi’s tattoos will likely continue for a while, but at least the puzzle seems to have all its pieces now.

The Iceman has been teaching scientists about Copper Age life for almost 25 years, and new information is still coming to light.

Not bad for a chance discovery on a Tyrolean hike.

A New Class of Magnet Could Mean New Tech Capabilities

Researchers have discovered a new class of magnet that increases in volume when placed in a magnetic field and generates only negligible amounts of heat in the process. These properties could transform many existing technologies and enable a few new ones.

Harsh Deep Chopra, Professor and Chair of Mechanical Engineering at Temple University, and Manfred Wuttig, Professor of Materials Science and Engineering at the University of Maryland, published their findings in the May 21st issue of the journal Nature.

Important work
Magnets and magnet operation are central to a lot of modern technology. Magnets are used to:

  • Sense a mechanical input and convert it to an electrical signal (sensors)
  • Use an electrical signal to displace a mechanical structure (actuators)
  • Generate power from a mechanical input (generators)

It’s no surprise, then, that an advance in magnet performance could have a big impact on a wide range of activities.

Breaking an old rule
A conventional iron-based magnet will change shape, but not volume, when placed in a magnetic field. As a magnet grows longer, it also grows thinner so that its total volume remains unchanged. This principle – magnetostriction – was first described by physicist James Prescott Joule in the 1840s. Conventional magnets, therefore, can only exert force in the single direction of their shape change, which limits what they can do to as energy conversion tools. If a device must move in more than one direction, bulky stacks of magnets are required.

Chopra and Wuttig discovered that some thermally-treated iron-based alloys could be freed from Joulian magnetostriction. The researchers baked the alloy at 1400o F (760o C) for 30 minutes and then rapidly cooled it to room temperature. The treatment changed its molecular structure and introduced a microscopic cell-like organization into the material that had never been seen before. The structural change was also accompanied by an important change in behavior.

The altered alloy significantly increased its volume in all directions when exposed to a magnetic field, and returned to its original volume when the field was removed. A non-Joulian material, showing non-Joulian magnetostriction (NJM), had been created.

Magnified image of a non-Joulian iron-gallium alloy, showing the periodic magnetic “cells” (Harsh Deep Chopra – Temple University)

Magnified image of a non-Joulian iron-gallium alloy, showing the periodic magnetic “cells”
(Harsh Deep Chopra – Temple University)

NJM alloys adapt to magnetic fields by reorienting their micro-cell structures. Magnetization within the cells isn’t uniform, however, but is modulated across cell boundaries in the material. The strain gradients between these cell regions relax in the presence of a magnetic field, allowing a uniform volume change.

“Our findings fundamentally change the way we think about a certain type of magnetism that has been in place since 1841,” said Chopra in a recent press release.

New technology tools
Non-Joulian magnets offer some major advantages over conventional magnets. Omnidirectional devices, for example, could be easily designed without the need for stacked magnet assemblies.

Movement of non-Joulian magnets generates very little heat, which makes them ideal candidates for low-thermal systems such as sonars. Non-Joulian alloys are also free of rare-earth elements which gives them improved mechanical properties, and lower cost, compared to conventional magnets.

The insights gained from this work will likely foster further advances in magnetic materials and processes.

“Knowing about this unique structure will enable researchers to develop new materials with similarly attractive properties,” said Wuttig.

Certainly, the Chopra and Wuttig work confirms the continued value of basic research, even involving processes that we thought we understood for 175 years.

As Wutting observed, “The response of these magnets differs fundamentally from that likely envisioned by Joule.”


Primary Source:
New class of swelling magnets to boost energy efficiency


This 3D printed system can turn your iPhone in a 1,000x microscope


Antonie van Leeuwenhoek, also referred to as the “father of microbiology”, was the first scientist to produce a truly functioning microscope, improving on earlier primitive designs. His efforts allowed him to observe for the first time a single celled organism, almost 300 years ago. Microscopes have gone a long way since, of course, but one thing for sure: after all this time, microscopes are still bulky and extremely difficult to use in the field. Physicists at the Pacific Northwest National Laboratory have set to change this. Using 3D printed materials and a simple glass bead, they’ve created a magnifying system that works with your smartphone’s or tablet’s built-in camera to magnify matter 100x, 350x or 1,000x. The whole system costs only 1$ to manufacture.

“We believe it can fill a need for professional first responders, and also for teachers and students in the classroom, health workers and anyone who just wants an inexpensive microscope readily available,” said Rebecca Erikson, an applied physicist at Pacific Northwest National Laboratory.


Of course, this isn’t the first time someone has tried to make a microscope for smartphones. This solution, however is elegant, cheap and available to anyone to make. You don’t have to buy it – just download the design which is up for free on the web and print the system at home or at a friend who owns a 3D printer. So, for less than one dollar worth of materials, you can print your very own microscope you can the use to study things like parasites in blood and water-contaminating microorganisms like protozoa (at 350x) or objects as small as tiny pathogens (at 1000x).

While citizen scientists can learn a lot by using the magnifying system, the PNNL scientists designed it for professionals working in the field in mind to enhance response time. A technician or specialist could take a quick snapshot of a sample, send it to the lab for expertise via email and get a response back while still being at the scene.


“An inexpensive, yet powerful microscope in the field could be used to quickly determine whether the material is a threat or a hoax,” Erikson said. “Combine the microscope with the picture sharing capability of a smartphone and now practically anyone can evaluate a sample at the source and have a trained microbiologist located in a lab elsewhere interpret the results within minutes.”

sing designer genes, researchers at UB and Harvard were able to 'turn on' specific neurons in the brainstem that result in deep sleep. Image: Dreamstime

Newly discovered ‘sleep node’ in the brain puts you to sleep without sedatives

sing designer genes, researchers at UB and Harvard were able to 'turn on' specific neurons in the brainstem that result in deep sleep.  Image: Dreamstime

sing designer genes, researchers at UB and Harvard were able to ‘turn on’ specific neurons in the brainstem that result in deep sleep. Image: Dreamstime

Neuroscientists at University of Buffalo have identified a sleep-promoting circuit inside the brainstem or the primitive part of the brain, whose activity appears to be both necessary and sufficient to produce deep sleep. This is only the second ‘sleep node’ in the mammalian brain that was identified to serve this function. To demonstrate the sleep node’s function, the researchers used molecular tools that activate neurons in this region of the brain and found the test animals quickly fell into deep sleep. Thus, the research highlights an alternate and novel therapy for treating sleep disorders like insomnia without using sedatives.

Where the Zzz comes from

The brain stem is the posterior area of the brain that attaches to the spinal cord. Here information is sent back and forth between the cerebrum or cerebellum and the body. It’s also called the primitive part of the brain because  it was the first brain structure to evolve, and is responsible for our basic vital functions like  breathing, blood pressure, heart rate and body temperature.

“The close association of a sleep center with other regions that are critical for life highlights the evolutionary importance of sleep in the brain,” says Caroline E. Bass, assistant professor of Pharmacology and Toxicology in the UB School of Medicine and Biomedical Sciences and a co-author on the paper.

The team found that nearly half of the brain’s sleep-promoting activity originates from the parafacial zone (PZ) in the brainstem. It is here that they identified a key type of neuron that produces a neurotransmitter called gamma-aminobutyric acid (GABA), which effectively puts your into a deep sleep state. To test their findings, the researchers introduced a ‘designer’ virus into the PZ that expressed a  receptor on GABA neurons only, without altering other brain functions. When the scientists turned on the GABA neurons in the PZ, the animals quickly fell into a deep sleep without the use of sedatives or sleep aids.

“These new molecular approaches allow unprecedented control over brain function at the cellular level,” says Christelle Ancelet, postdoctoral fellow at Harvard School of Medicine. “Before these tools were developed, we often used ‘electrical stimulation’ to activate a region, but the problem is that doing so stimulates everything the electrode touches and even surrounding areas it didn’t. It was a sledgehammer approach, when what we needed was a scalpel.”

It’s yet unclear how these newly identified neurons in the PZ region interact with other well known sleep and wake-promoting brain regions. The UB researchers plan on extensively studing this relationship and hope that their work might eventually render a novel type of medication for treating sleep disorders, as well as better and safer anesthetics.

“We are at a truly transformative point in neuroscience,” says Bass, “where the use of designer genes gives us unprecedented ability to control the brain. We can now answer fundamental questions of brain function, which have traditionally been beyond our reach, including the ‘why’ of sleep, one of the more enduring mysteries in the neurosciences.”

Findings were reported in the journal Nature Neuroscience.

Amazing fungus gnat larvae group together to form a ‘snake’ [VIDEO]

Fungus gnats (Bradysia species) – also known as dark-winged fungus gnats, are small, mosquito-like insects often found in homes and offices, usually in the vicinity of houseplants. The larvae that hatch are legless, with white or transparent bodies and shiny black heads. From the first glimpse you’ll notice they’re not the prettiest sight, but what they lack in looks, they make up in cleverness.

The fungus gnat larvae are incredibly vulnerable when alone; they’re puny, non-poisonous and practically at the mercy of predators – basically anything larger than them. To survive, the larvae have adapted a group behavior in which they join together by the hundreds to form a slimy, moving mass. The video embedded in this post illustrates this behavior. At first, you might be fooled to think you’re watching a snake (a two-headed snake?), but once the video zooms in all hell breaks loose.

While this instance of fungus gnat larvae behavior is very clever (or grouse), they’re consider serious pests and can cause severe damage to both houseplants and commercial crops. Some fungus gnat larvae are known for their propensity to feed on the roots and lower stem tissues of plants. These feeding habits stunt and might kill affected plants.

Social Media Sentinels and Early Disease Detection

Ebola virus

Ebola virus (Public Health Image Library via Wikimedia Commons

The fast-moving news about the West Africa Ebola outbreak – the largest and longest ever recorded for the disease – may have overshadowed news of an important technical advance. An online data tool signaled a “mystery hemorrhagic fever” in forested areas of southeastern nine days before the World Health Organization announced the epidemic. In disease control, that’s a life-saving edge.

The tool is HealthMap and it scoured thousands of social media sites, local news sources, government websites, and physicians’ social networks for indicators of emerging or spreading disease.

Early detection makes a big difference in how epidemics are contained. Health response teams have to know the disease they’re dealing with, how fast it’s moving, and where, if they’re going to position the right people and supplies to deal with it. Speed is even more essential in the developing world, where dangerous diseases are likely to emerge and where public health infrastructure may be weak.

The latest Ebola outbreak sprang up in Guinea in March. It then spread to Sierra Leone, Liberia, and Nigeria: places that weren’t familiar with its symptoms. The public and many under-prepared health care workers responded with confusion. By the time doctors realized that they were dealing with the Ebola virus, patients had already been to hospitals and clinics that lacked the equipment and trained personnel needed to contain the disease.

Ebola outbreak map

Ebola outbreak map as of August 2014 (Centers for Disease Control)

And so, it spread . . . along with eyewitness reports, social media threads, and blog posts from health care workers. By March 10, HealthMap began to pick up on these Internet nuggets and fit them together. On March 19, its algorithm triggered an alert, one of the earliest warnings of the Ebola threat.


Why social media?
Conventional case reporting is the foundation of modern disease surveillance, but collecting the right data can be time-consuming. Of all the methods used to track disease indicators, however, social media is one of the fastest, which is probably why it’s been tried before as an early harbinger of disease outbreaks.

Twitter was tried during the 2009 swine flu outbreak, but results were noisy because Twitter users generated too many different types of conversations. Google Flu Trends, launched in 2010, used aggregated Google search data and seemed to work better.

In 2012, Sickweather was launched as one of the first consumer-focused tools for tracking disease through social media chatter. The program scanned social networks for mentions of 24 different symptoms. That same year, the US Health and Human Services sponsored a contest to develop a Twitter-based disease detection system. Results are still being evaluated.

Social media have an important advantage as a data source. The WHO and similar organizations must maintain good relationships with the countries where they operate. Because some countries consider the release of any information concerning disease outbreaks as a state secret, public health programs can require a delicate balance of science and politics. Social media resources, however, are publicly available so the algorithms that use them can bypass many government roadblocks. And because most social media data sources are public, tools like HealthMap are available to users for free. Everyone can access HealthMap.


Detailed digging
So, what was the specific contribution of HealthMap? Yes – its algorithm.

The HealthMap edge was its ability to sift out small bits of information and fit them into patterns as soon as the first reports surfaced. HealthMap data processing includes filters that weed out irrelevant data and classify what remains until it converges on identification. In many ways, the algorithm functions like a semantic web, allowing fast, automatic searches for germane content from the large data sets.

In the eight years since the site was first introduced, HealthMap has evolved into an interactive tool used by millions of people worldwide. Variants of the algorithm are being used to monitor:

The 2014 Ebola outbreak will challenge health care systems internationally, and the human cost in deaths, fear, and disrupted communities won’t be known for months. The crisis has shown, however, that social media may offer a potent resource to detect and contain future outbreaks.

Losing ground in Greenland – New model shows faster glacial melting

News about glacial melting in Antarctica has been uniformly grim; the loss is likely unstoppable. News about melting of the Greenland Ice Sheet has been no better; Scientists had earlier believed that the losses in Greenland would eventually slow or stop, owing to the solid bedrock of the continent. Now, that view may also melt away by results of a new study that shows how the rocky topography of Greenland may actually contribute to glacier loss.

Why Greenland matters

Greenland is the world’s largest island. It’s ice sheet sits atop its rugged rock surface, often to a depth of three miles (five kilometers), and represents eight percent of the earth’s fresh water. That’s 680,000 cubic miles of frozen water which, if it all melted. would raise world sea levels by up to 18 feet (6 meters). Climate scientists pay close attention to the “health” of Greenland’s Ice Sheet (although that wasn’t always the case; back before the days of international ice patrols a Greenland glacier, Jakobshavn, is believed to have calved the iceberg that sank the Titanic).

Ice has historically been measured by ground surveys but, on a land mass that would cover over one quarter of the continental Unites States, systematic data are hard to come by. Ground-penetrating radar has been used since the 1970s to find the depth of bedrock beneath the Greenland ice but the technology doesn’t work well along the coasts because of rough surfaces and water pockets. Large portions of the island remained unexplored.

An IceBridge survey target in southwest Greenland. (Michael Studinger/NASA)

An IceBridge survey target in southwest Greenland.        (Michael Studinger/NASA)

When NASA began Project IceBridge – aircraft surveys with radar – in 2009, the number of measurements tripled and a clearer picture emerged of the rough rock valleys that lay underneath the enormous glacier cover.  When glaciologists from the University of California Irvine and NASA glaciologists analyzed the new data, they found previously unknown that extended for miles under the ice. And those valleys were much deeper than anyone had expected.

Different kinds of melting

Geology gives Greenland ice a different melting dynamic than that of Antarctica. Antarctic glaciers extend directly into the ocean where warm waters can melt them from below. Greenland glaciers sit on a landmass and ocean melting occurs only at the coasts.

Topography of Greenland – blue is below sea level          (Mathieu Morlighem/UC Irvine)

Topography of Greenland – blue is below sea level
(Mathieu Morlighem/UC Irvine)

Scientists had believed that glacier melting in Greenland would slow and stabilize after the ice moved back to where the underlying rock was higher than the sea. At that point, the land would presumably protect the ice from the surrounding ocean currents.  New data changed that presumption.

“That turns out to be incorrect,” said Mathieu Morlighern, UC Irvine associate project scientist and lead author of a new study published in the May 18 issue of Nature Geoscience. “The glaciers of Greenland are likely to retreat faster and farther inland than anticipated – and or much longer – according to this very different topography we’ve discovered beneath the ice.”

What they discovered was a valley under each outlet glacier around most of Greenland’s periphery. May of those valleys are miles deep – well below sea level – and extend inland an average of 41 miles (67 kilometers). This means that as glaciers retreat, they will sink into gorges where ocean waters can follow, continuing to warm and melt the low-lying ice.

“It will take much longer for these glaciers to lose contact with the ocean,” said Morlighem. “This has major implications, because the glacier melt will contribute much more to rising seas around the globe.”

Any good news?

The scientists are no strangers to bearing bad news. The UC Irvine / NASA team involved with the new Greenland analysis are the same researchers who reported that Antarctic ice melting was “unstoppable.” Such news has the power to reignite debates about the reality and pace of climate change but not enough power to resolve coherent action.

To the extent that climate debates drift into attacks on source data and theoretical models, however, any effort to improve data quality will clarify both issues and solutions. Each contribution brings the facts into better focus.

“Operation IceBridge vastly improved our knowledge of bad topography beneath the Greenland Ice Sheet,” said Eric Rignot of UC Irvine and the NASA Jet Propulsion Laboratory. “This new study take a quantum leap in filling the remaining, critical data gaps on the map.”

The latest findings on Greenland glacier dynamics have added new factors to climate models that, unfortunately, are still pointing in the same disturbing direction.


Something from nothing? Scientists find a way to turn light into matter

Three physicists involved with fusion research have found an elegant way to convert light to matter. And, it can be accomplished with current technology. Demonstrating the process would round out a critical set of theories about energy and matter, so a race may soon be on to test it.

The Einstein relationship, E= mc2, states that energy and matter are equivalent and, therefore, interchangeable. We see this in nuclear reactions, where small amounts of matter release enormous energies, but going the other way – energy to matter – is harder because those energies have to be put back into the system.

A model to do just this, however, was proposed by Gregory Breit and John Wheeler in 1934. The American physicists theorized that forcing two photons together should yield an electron and its antimatter equivalent, a positron. That is, two particles without mass could create two particles with mass.

Oliver Pike, who’s completing his PhD in Plasma Physics at Imperial College London, said the Breit-Wheeler process was “the simplest way matter can be made from light” and one of the most elegant demonstrations of Einstein’s famous relationship.

The flexible hohlraum
While the physics community accepted the model as sound, Breit and Wheeler never thought that the idea would be achieved in the laboratory. But Pike and his colleagues, Professor Steven Rose (of the Imperial College Faculty of Natural Sciences) and Felix Mackenroth (a visiting theoretical physicist from the Max Planck Institute of Nuclear Physics) realized that a tool they were using in their own work – a hohlraum (German for “empty room”) – could also be applied to a direct test of the Breit-Wheeler theory. “Within a few hours of looking for applications of hohlraums outside their traditional role in fusion energy research, we were astonished to find they provided the perfect conditions for creating a photon collider.”

Their proposed process involves three steps:

1. Electrons are first accelerated to just below the speed of light with a high-energy laser, and then fired into a slab of gold to create a beam of photons a billion times more energetic than visible light

2. Another laser is fired at the inner surface of a gold vacuum container (the hohlraum) which emits another set of photons as blackbody radiation.

3. Finally, the photon beam is directed through the center of the chamber where photons from the two sources collide. The collisions should generate electrons and positrons when they exit the hohlraum.

The scientists recently detailed their method in Nature Photonics.

“We have shown in principle how you can make matter from light,” said Professor Rose. “If you do this experiment, you will be taking light and turning it into matter.” Calculations by the team showed that the equipment could squeeze enough particles of light, with high enough energies, into a small enough volume to create about 100,000 electron-positron pairs.

Photon collider schematic (Nature Photonics)

Photon collider schematic (Nature Photonics)

A simpler way
The conversion of photons to electrons and positrons was actually demonstrated in earlier research using the incredibly high energies of the Stanford Linear Accelerator. Because that work required the use of electrons to boost the photons to the required energy states, however, mass was involved at the beginning of the energy-to-mass conversion. The newly-proposed process combines the photons within the hohlraum chamber so any electrons stay outside. Any electrons that make it through the gold slab are filtered out by a magnetic field so the entire generating process is mass-free.

“Such a collider could be used to study fundamental physics with a very clean experimental setup: pure light goes in, matter comes out. The experiment would be the first demonstration of this,” Pike said.

The Breit-Wheeler model complements a set of theories about light-matter interaction, such as the photoelectric effect , and the creation of and destruction of matter and antimatter, work that has involved or produced nine Nobel laureates.

Theories describing light-matter interactions (Oliver Pike, Imperial College London)

Theories describing light-matter interactions (Oliver Pike, Imperial College London)

This process of creating matter from energy was critical in the first 100 seconds of the universe, and is seen today in gamma ray bursts, where photons are energized by high-energy electrons to form gamma rays during stellar explosions

After 80 years of theory, a practical way to convert mass from energy was published only this month. Now, researchers are hoping to build a machine that can demonstrate it within a year.

Events are accelerating toward the speed of light.

Japanese Fishing Net (Credit: Shin-ichi Uye, Hiroshima University)

Inevitable Invasion? The Coming of the Jellyfish

Healthy wildlife populations aren’t always good news.

Global jellyfish populations are surging and marine scientists are sounding alarms – some of them dire. Biologist Lisa-ann Gershwin, author of Stung! On Jellyfish Blooms and the Future of the Ocean, states that jellyfish could displace Antarctic penguins, devastate world fisheries, and even starve whales to extinction.

Are things really that serious? There’s plenty of evidence that jellyfish invasions (or “blooms”) inflict significant damage on ecosystems and economies and that blooms are increasing. Unfortunately, science is finding that these problems are largely effects of . . . us.

Not on anyone’s endangered list

Jellyfish are well-designed for surviving changed conditions. Their bodies are more than 95 per cent water, so growing doesn’t increase metabolic demands as much as it does in more complicated creatures.

Jellies are also unique in their ability to reduce their body size when food is scarce and to grow again when food is plentiful. Their lower metabolic rate also means a low oxygen requirement, which can be very useful in polluted waters

And jellies can eat just about anything, including young fish, fish eggs, and plankton. Their diet that can decimate fish populations and, because plankton remove carbon dioxide from the water, their diet can contribute to climate change.

Japanese Fishing Net (Credit: Shin-ichi Uye, Hiroshima University)

Japanese Fishing Net (Credit: Shin-ichi Uye, Hiroshima University)

Such adaptability has paid off. Today, there are 1,000 – 1,500 known types of jellyfish. Jellies and their phylogenetic cousins represent up to one third of the world’s marine biomass and, in some regions, they exceed fish biomass more than three to one.

Jellyfish may be the tribbles of the ocean.

We’re here to help

While jellyfish come with all the right tools for success, humans make things a lot easier for them. Piers, oil platforms and floating trash, for example, serve as ideal jellyfish nurseries, providing the good anchoring surfaces that polyps need for growth.

Human activity also provides useful transportation. Jellies travel in the ballast water of ships and are dropped off in new ports when that water gets dumped. An even easier way to catch a ride is on the hulls of ships (known as “hull-fouling”). In fact, ships may be responsible for almost 70 percent of the transport of non-native marine species around the world.

Jellyfish Cluster (Wikimedia Commons

Jellyfish Cluster (Wikimedia Commons

Even land activities work to tilt the survival advantage in favor of jellies. Fertilizers and other runoff can strip oxygen from sea water (a process known as eutrophication) but, because jellyfish tolerate low oxygen better than other marine animals, they can thrive to the detriment of almost everything else.  Jellies can be found in some seas that are otherwise “dead zones” from fertilizer runoff.

The most direct effect of human activities is probably overfishing, which simply removes jellyfish predators and competitors from the environment. Jellyfish blooms seen in the Black Sea and off of South Africa, for example, were likely due to overfishing of anchovies, which would otherwise compete with jellies for food.

A lack of good data

The consequences of jellyfish blooms would seem to be increasingly easy to identify. The salmon killed by the 2008 jellyfish bloom near Northern Ireland, for example, were valued at $2 million. Jellyfish eventually caused the complete collapse of Black Sea anchovy and sardine fisheries by devouring the fish’s food, their eggs, and their young. Power plants in Scotland, Japan and Israel have also been temporarily shut down when jellyfish clogged their cooling-water intake systems.

The problems would seem to be growing increasingly urgent, too. Fears that jellyfish are taking over the oceans have escalated in the past decade with increasing numbers of bloom reports. The clearest stories may be the Nomura jellyfish blooms off Japan: While only three blooms were recorded between 1920 and 1995, six blooms were recorded between 2002 and 2010. Not an encouraging trend.

Despite anecdotes and field reports, however, not everyone is ready to predict calamity. Some scientists don’t believe that there’s yet enough solid data to characterize a problem or to design countermeasures. Consequently, they’re now trying to fill some of the holes in the data record with new programs and new technologies. Citizen scientists are also being recruited to aid in the effort to expand our knowledge of jellies.

Jellyfish are believed to be at least 500 million – 700 million years old. That they preceded most other creatures in the sea and are still thriving today is reason enough to respect the hazard that jellies present if they continue to move and displace other species. Science is concerned but not panicked.

It’s rare to see the effects of common human activities align so conveniently to “aid” a part of nature. While future activities may change things, jellies seem built to take advantage of all we have to offer them today.