03 December 2019

Old Norse plunder tactic inspires Oslo team to call android flaw StrandHogg


An Android bug can steal bank credentials, namely bank logins. The flaw is called StrandHogg and security investigators at an Oslo, Norway-based security company say it has been targeting 60 financial institutions at least.

StrandHogg takes its name from the old Norse for a Viking tactic of coastal raids in order to plunder and hold people for ransom.

In Silicon UK, Matthew Broersma on Monday said that the flaw affects Android's multitasking system, and it "allows malicious apps to overlay fake login screens on legitimate apps," and that was according to the security firm that studied the vulnerability, Promon.

What does that really mean multitasking system? Dark Reading referred to "its ability to run several apps at the same time and switch from app to app on the screen."

"This exploit," said the Promon site, is based on an Android control setting called 'taskAffinity' which allows any app including malicious ones to freely assume any identity in the multitasking system they desire.

Silicon UK showed a photo of a fake permissions pop-up appearing while an app was in use. "Allow to access photos, media and files on your device." Below that is a box for clicking "Don't ask again" and two boxes for "Deny" and "Allow."

You would be unaware that something is out there to harvest your data. The Promon researchers consider the bug as "dangerous." They said the vulnerability was such that all versions of Android were affected, and that would include Android 10.

The security company Lookout similarly wrote in a blog that StrandHogg attackers could mount an attack even against current versions of Android.

How did Promon discover this? The BBC said Promon, working along with US security firm Lookout, set out to scan apps in Android's Play store just to see if any were being abused via the StrandHogg bug. That is how Lookout came up with the number 60 the sum of financial institutions that were being targeted via apps that sought to exploit the loophole, said the BBC.

Dark Reading went further in the discovery story: Promon researchers found StrandHogg when its customer, an Eastern European security firm, noticed a trend of money being siphoned from accounts at some banks. They traced the root of the problem to StrandHogg.

Results of the Promon search of malware under study found all of the top 500 most popular apps (as ranked by app intelligence company 42 Matters) were at risk.

Welcome to a nefarious world of "permission harvesting."

Dark Reading said that "malicious apps can request any permission while pretending to be legitimate. An attack could be designed to ask for permissions that seem natural for the targeted apps. By doing this, adversaries could lower the chance of victims realizing something is wrong. Users have no indication they're granting permission to a malicious app and not the authentic one."

A discomforting side note is that in spite of Google's Play Protect security suite, dropper apps continue to be published and frequently slip under the radar, with some being downloaded millions of times before being spotted and deleted, found Promon's researchers.

"The potential impact of this could be unprecedented in terms of scale and the amount of damage caused," said Promon CTO Tom Hansen.

What has been the damage thus far? Hansen, in the BBC News report, said It targeted several banks in several countries. The malware "successfully exploited end users to steal money." The Lookout blog said that "Screen overlay attacks on financial institutions have increased significantly in the past 18 months."

Promon said they submitted their report to Google earlier this year.

BBC News reported on Monday that "Google said it had taken action to close the loophole and was keen to find out more about its origin." They referred to a Google statement that voiced appreciation of the research. Google said they suspended the potentially harmful apps that were identified.

Google is now to look at how they can improve Google Play Protect's ability to protect users against similar issues.

This is what Promon had to say about Google's response, which it did welcome, as other apps were potentially exploitable via the bug. At the same time, however, Promon's chief technology officer noted that it still remained possible to create fake overlay screens in Android 10 and earlier versions of the operating system.

Meanwhile, the Promon partner called Lookout, which is in the business of cybersecurity, went to recognized some variants of the BankBot banking trojan observed as early as 2017. BankBot was called one of the most widespread banking trojans around by Promon, "with dozens of variants and close relatives springing up all the time."

The above video is a presentation by the Promon researchers John Høegh-Omdal and Lars Lunde Birkeland about the victim experience. At least you can know the type of behavior that ensues if you are hacked.

"I will now demonstrate how hackers can read your SMS, steal your private photos, and hijack your social media accounts." The video showed one of the two researchers sitting on a park bench with a Samsung Galaxy S10 running the latest Android version. On this weather app you see the fake permission pop-up asking if it is ok to send SMS messages.

The StrandHogg vulnerability makes it possible for a malicious app to replace a legitimate permission pop-up with its own fake version that asks for access to any permission, including SMS, photos, microphone, and GPS, allowing them to read messages, view photos, eavesdrop, and track the victim's movements.

Two noteworthy messages appeared in the reader comments section of the Dec. 2 video. One asked if this was only an Android headache would iOS devices be vulnerable to this as well? The Promon reply was that the research only applied to Android, not iOS. The second interesting message from the researchers said that although Google removed the affected apps, "to the best of our knowledge, the vulnerability has not yet been fixed for any version of Android (incl. Android 10)."


Latest science behind cryogenically freezing your body and coming back to life

Cryogenically Freezing Human Body

Credit: The American Chemical Society

Will cryogenically freezing yourself and coming back to life ever be reality?

When you die, there are a lot of things you can do with your dead body embalm it, cremate it, donate it to science (the list goes on…), but some people will choose to have their dead bodies, or body parts, frozen until the technology of the future has (hopefully) advanced enough to bring them back to life. This video breaks down the chemistry of cryogenic freezing and if it’s realistic to think we could ever reanimate a frozen corpse.


Cryonics is the low-temperature freezing (usually at −196 °C or −320.8 °F or 77.1 K) and storage of a human corpse or severed head, with the speculative hope that resurrection may be possible in the future.

Cryopreservation (cryo-preservation or cryo-conservation) is a process where organelles, cells, tissues, extracellular matrix, organs, or any other biological constructs susceptible to damage caused by unregulated chemical kinetics are preserved by cooling to very low temperatures (typically −80 °C using solid carbon dioxide or −196 °C using liquid nitrogen). At low enough temperatures, any enzymatic or chemical activity which might cause damage to the biological material in question is effectively stopped.

Cryoprotectants are substances used to protect biological tissue from freezing damage (i.e. that due to ice formation).


01 December 2019

Researchers evolve bacteria that consume CO2 for energy.


Over the course of several months, researchers in Israel created Escherichia coli strains that consume CO2 for energy instead of organic compounds. This achievement in synthetic biology highlights the incredible plasticity of bacterial metabolism and could provide the framework for future carbon-neutral bioproduction. The work appears November 27, 2019, in the journal Cell.

“Our main aim was to create a convenient scientific platform that could enhance CO2 fixation, which can help address challenges related to sustainable production of food and fuels and global warming caused by CO2 emissions,” says senior author Ron Milo, at systems biologist at the Weizmann Institute of Science. “Converting the carbon source of E. coli, the workhorse of biotechnology, from organic carbon into CO2 is a major step towards establishing such a platform.”

The living world is divided into autotrophs that convert inorganic CO2 into biomass and heterotrophs that consume organic compounds. Autotrophic organisms dominate the biomass on Earth and supply much of our food and fuels. A better understanding of the principles of autotrophic growth and methods to enhance it is critical for the path to sustainability.

This diagram shows how researchers converted a common laboratory sugar eating (heterotrophic) E. coli bacterium (left) to produce all of its biomass from CO2 (autotrophic) by metabolic engineering combined with laboratory evolution. The new bacterium (center) uses the compound formate as a form of chemical energy to drive CO2 fixation by a synthetic metabolic pathway. The bacterium may provide the infrastructure for future industrial renewable production of food and green fuels (right). Credit: Gleizer et al.

A grand challenge in synthetic biology has been to generate synthetic autotrophy within a model heterotrophic organism. Despite widespread interest in renewable energy storage and more sustainable food production, past efforts to engineer industrially relevant heterotrophic model organisms to use CO2 as the sole carbon source have failed. Previous attempts to establish autocatalytic CO2 fixation cycles in model heterotrophs always required the addition of multi-carbon organic compounds to achieve stable growth.

“From a basic scientific perspective, we wanted to see if such a major transformation in the diet of bacteria from dependence on sugar to the synthesis of all their biomass from CO2 is possible,” says first author Shmuel Gleizer, a Weizmann Institute of Science postdoctoral fellow. “Beyond testing the feasibility of such a transformation in the lab, we wanted to know how extreme an adaptation is needed in terms of the changes to the bacterial DNA blueprint.”

In the Cell study, the researchers used metabolic rewiring and lab evolution to convert E. coli into autotrophs. The engineered strain harvests energy from formate, which can be produced electrochemically from renewable sources. Because formate is an organic one-carbon compound that does not serve as a carbon source for E. coli growth, it does not support heterotrophic pathways. The researchers also engineered the strain to produce non-native enzymes for carbon fixation and reduction and for harvesting energy from formate. But these changes alone were not enough to support autotrophy because E. coli‘s metabolism is adapted to heterotrophic growth.

To overcome this challenge, the researchers turned to adaptive laboratory evolution as a metabolic optimization tool. They inactivated central enzymes involved in heterotrophic growth, rendering the bacteria more dependent on autotrophic pathways for growth. They also grew the cells in chemostats with a limited supply of the sugar xylose a source of organic carbon to inhibit heterotrophic pathways. The initial supply of xylose for approximately 300 days was necessary to support enough cell proliferation to kick start evolution. The chemostat also contained plenty of formate and a 10% CO2 atmosphere.

In this environment, there is a large selective advantage for autotrophs that produce biomass from CO2 as the sole carbon source compared with heterotrophs that depend on xylose as a carbon source for growth. Using isotopic labeling, the researchers confirmed that the evolved isolated bacteria were truly autotrophic, i.e., CO2 and not xylose or any other organic compound supported cell growth.

“In order for the general approach of lab evolution to succeed, we had to find a way to couple the desired change in cell behavior to a fitness advantage,” Milo says. “That was tough and required a lot of thinking and smart design.”

By sequencing the genome and plasmids of the evolved autotrophic cells, the researchers discovered that as few as 11 mutations were acquired through the evolutionary process in the chemostat. One set of mutations affected genes encoding enzymes linked to the carbon fixation cycle. The second category consisted of mutations found in genes commonly observed to be mutated in previous adaptive laboratory evolution experiments, suggesting that they are not necessarily specific to autotrophic pathways. The third category consisted of mutations in genes with no known role.

“The study describes, for the first time, a successful transformation of a bacterium’s mode of growth. Teaching a gut bacterium to do tricks that plants are renowned for was a real long shot,” Gleizer says. “When we started the directed evolutionary process, we had no clue as to our chances of success, and there were no precedents in the literature to guide or suggest the feasibility of such an extreme transformation. In addition, seeing in the end the relatively small number of genetic changes required to make this transition was surprising.”

The authors say that one major study limitation is that the consumption of formate by bacteria releases more CO2 than is consumed through carbon fixation. In addition, more research is needed before it’s possible to discuss the scalability of the approach for industrial use.

In future work, the researchers will aim to supply energy through renewable electricity to address the problem of CO2 release, determine whether ambient atmospheric conditions could support autotrophy, and try to narrow down the most relevant mutations for autotrophic growth.

“This feat is a powerful proof of concept that opens up a new exciting prospect of using engineered bacteria to transform products we regard as waste into fuel, food or other compounds of interest,” Milo says. “It can also serve as a platform to better understand and improve the molecular machines that are the basis of food production for humanity and thus help in the future to increase yields in agriculture.”

Reference: “Conversion of Escherichia coli to Generate All Biomass Carbon from CO2” by Shmuel Gleizer, Roee Ben-Nissan, Yinon M. Bar-On, Melina Shamshoum, Arren Bar-Even and Ron Milo, 27 November 2019, Cell.
DOI: 10.1016/j.cell.2019.11.009

This work was supported by the European Research Council, the Israel Science Foundation, the Beck-Canadian Center for Alternative Energy Research, Dana and Yossie Hollander, the Helmsley Charitable Foundation, the Larson Charitable Foundation, the Estate of David Arthur Barton, the Anthony Stalbow Charitable Trust, and Stella Gelerman, Canada. The authors declare a provisional patent related to the manuscript.


28 November 2019

New skin-like device could bring touch to virtual reality

Layers of VR Skin

The layers of the lightweight device designed to add touch to virtual reality experiences.

The lightweight sheets could combine hundreds of vibrating components to create tactile sensations.

Imagine a virtual reality system in which you don’t just see and hear, but also feel experiences such as a grandmother's embrace or the strikes in a combat video game.

"Adding touch to audio and video experiences could really help expand the immersive, personal quality of virtual reality," said John Rogers, a materials scientist and director of Northwestern University's Center for Bio-Integrated Electronics in Evanston, Illinois. Rogers and his colleagues have taken an important step toward more widespread tactile virtual reality by designing soft, thin, skin-like wearable interfaces that generate sensations of touch using wirelessly powered and controlled miniature vibrating devices. They detail their findings in the Nov. 21 issue of the journal Nature.

The new inventions are lightweight sheets that eschew the wires and batteries that made previous devices bulky and awkward.

At the core of each interface is an array of vibrating components called actuators made of copper wire coils mounted above magnetic disks.  When electric currents run through the coils, the magnets vibrate at the same frequencies as the currents. Each actuator is only 12 to 18 millimeters wide, 2.5 millimeters thick and 1.4 grams in weight one 15 centimeter by 15-centimeter prototype held 32 actuators.

Above the actuators are electronics that receive and transmit radio signals to wirelessly control the vibrating devices. These electronics also include antennas to convert energy from incoming radio signals into electricity to power the interface. All these components are embedded in soft, thin, flexible silicone materials that stick to the body without tape or straps.

In contrast with the limit of a dozen or so actuators in previous VR garments, the researchers suggest they could readily scale up to hundreds. "By analogy, imagine going from a collection of LED lights to an LED display," Rogers said.

In the future, the researchers plan to incorporate heating and cooling into the device and find ways to generate mechanical forces not just directly at the skin, but along it as well for shearing or twisting sensations. In addition, the level of force the actuators currently generate "feels like a light fingertip touch it would be nice to extend our work to higher levels of pressure, and to make the entire system thinner and more lightweight," Rogers said.


27 November 2019

New hybrid device efficiently captures and stores solar energy.


The hybrid device consists of a molecular storage material (MSM) and a localized phase-change material (L-PCM), separated by a silica aerogel to maintain the necessary temperature difference. Credit: University of Houston

Device offers a new avenue for capitalizing on abundant solar energy.

Researchers from the University of Houston have reported a new device that can both efficiently capture solar energy and store it until it is needed, offering promise for applications ranging from power generation to distillation and desalination.

Unlike solar panels and solar cells, which rely on photovoltaic technology for the direct generation of electricity, the hybrid device captures heat from the sun and stores it as thermal energy. It addresses some of the issues that have stalled wider-scale adoption of solar power, suggesting an avenue for using solar energy around-the-clock, despite limited sunlight hours, cloudy days and other constraints.

The work, described in a paper published today (November 20, 2019) in Joule, combines molecular energy storage and latent heat storage to produce an integrated harvesting and storage device for potential 24/7 operation. The researchers report a harvesting efficiency of 73% at small-scale operation and as high as 90% at large-scale operation.

Up to 80% of stored energy was recovered at night, and the researchers said daytime recovery was even higher.

Hadi Ghasemi, Bill D. Cook Associate Professor of Mechanical Engineering at UH and a corresponding author for the paper, said the high-efficiency harvest is due, in part, to the ability of the device to capture the full spectrum of sunlight, harvesting it for immediate use and converting the excess into molecular energy storage.

The device was synthesized using norbornadiene-quadricyclane as the molecular storage material, an organic compound that the researchers said demonstrates high specific energy and exceptional heat release while remaining stable over extended storage times. Ghasemi said the same concept could be applied using different materials, allowing performance – including operating temperatures and efficiency – to be optimized.

T. Randall Lee, Cullen Distinguished University Chair professor of chemistry and a corresponding author, said the device offers improved efficiency in several ways: The solar energy is stored in molecular form rather than as heat, which dissipates over time, and the integrated system also reduces thermal losses because there is no need to transport the stored energy through piping lines.

“During the day, the solar thermal energy can be harvested at temperatures as high as 120 degrees centigrade (about 248 Fahrenheit),” said Lee, who also is a principle investigator for the Texas Center for Superconductivity at UH. “At night, when there is low or no solar irradiation, the stored energy is harvested by the molecular storage material, which can convert it from a lower energy molecule to a higher energy molecule.”

That allows the stored energy to produce thermal energy at a higher temperature at night than during the day – boosting the amount of energy available even when the sun is not shining, he said.

Reference: “Full Spectrum Solar Thermal Energy Harvesting and Storage by a Molecular and Phase-Change Hybrid Material” by Varun Kashyap, Siwakorn Sakunkaewkasem, Parham Jafari, Masoumeh Nazari, Bahareh Eslami, Sina Nazifi, Peyman Irajizad, Maria D. Marquez, T. Randall Lee and Hadi Ghasemi, 20 November 2019, Joule.
DOI: 10.1016/j.joule.2019.11.001

In addition to Ghasemi and Lee, researchers involved with the work include first author Varun Kashyap, Siwakorn Sakunkaewkasem, Parham Jafari, Masoumeh Nazari, Bahareh Eslami, Sina Nazifi, Peyman Irajizad and Maria D. Marquez, all with UH.


26 November 2019

Seeds coated with fertilizer-generating microbes may enable agriculture on marginal land

Seeds coated with fertilizer
Researchers have used silk derived from ordinary silkworm cocoons, like those seen here, mixed with bacteria and nutrients, to make a coating for seeds that can help them germinate and grow even in salty soil. Credit: Courtesy of the researchers

A specialized silk covering could protect seeds from salinity while also providing fertilizer-generating microbes.

Providing seeds with a protective coating that also supplies essential nutrients to the germinating plant could make it possible to grow crops in otherwise unproductive soils, according to new research at MIT.

A team of engineers has coated seeds with silk that has been treated with a kind of bacteria that naturally produce a nitrogen fertilizer, to help the germinating plants develop. Tests have shown that these seeds can grow successfully in soils that are too salty to allow untreated seeds to develop normally. The researchers hope this process, which can be applied inexpensively and without the need for specialized equipment, could open up areas of land to farming that are now considered unsuitable for agriculture.

The findings are being published this week in the journal PNAS, in a paper by graduate students Augustine Zvinavashe ’16 and Hui Sun, postdoc Eugen Lim, and professor of civil and environmental engineering Benedetto Marelli.

The work grew out of Marelli’s previous research on using silk coatings as a way to extend the shelf life of seeds used as food crops. “When I was doing some research on that, I stumbled on biofertilizers that can be used to increase the amount of nutrients in the soil,” he says. These fertilizers use microbes that live symbiotically with certain plants and convert nitrogen from the air into a form that can be readily taken up by the plants.

fertilizer-generating mcrobes

Planted in identical pots of salty soil, untreated seeds (left) mostly fail to germinate, while the coated seeds (right) develop normally. Credit: Courtesy of the researchers

Not only does this provide a natural fertilizer to the plant crops, but it avoids problems associated with other fertilizing approaches, he says: “One of the big problems with nitrogen fertilizers is they have a big environmental impact, because they are very energetically demanding to produce.” These artificial fertilizers may also have a negative impact on soil quality, according to Marelli.

Although these nitrogen-fixing bacteria occur naturally in soils around the world, with different local varieties found in different regions, they are very hard to preserve outside of their natural soil environment. But silk can preserve biological material, so Marelli and his team decided to try it out on these nitrogen-fixing bacteria, known as rhizobacteria.

“We came up with the idea to use them in our seed coating, and once the seed was in the soil, they would resuscitate,” he says. Preliminary tests did not turn out well, however; the bacteria weren’t preserved as well as expected.

That’s when Zvinavashe came up with the idea of adding a particular nutrient to the mix, a kind of sugar known as trehalose, which some organisms use to survive under low-water conditions. The silk, bacteria, and trehalose were all suspended in water, and the researchers simply soaked the seeds in the solution for a few seconds to produce an even coating. Then the seeds were tested at both MIT and a research facility operated by the Mohammed VI Polytechnic University in Ben Guerir, Morocco. “It showed the technique works very well,” Zvinavashe says.

The resulting plants, helped by ongoing fertilizer production by the bacteria, developed in better health than those from untreated seeds and grew successfully in soil from fields that are presently not productive for agriculture, Marelli says.

In practice, such coatings could be applied to the seeds by either dipping or spray coating, the researchers say. Either process can be done at ordinary ambient temperature and pressure. “The process is fast, easy, and it might be scalable” to allow for larger farms and unskilled growers to make use of it, Zvinavashe says. “The seeds can be simply dip-coated for a few seconds,” producing a coating that is just a few micrometers thick.

The ordinary silk they use “is water soluble, so as soon as it’s exposed to the soil, the bacteria are released,” Marelli says. But the coating nevertheless provides enough protection and nutrients to allow the seeds to germinate in soil with a salinity level that would ordinarily prevent their normal growth. “We do see plants that grow in soil where otherwise nothing grows,” he says.

These rhizobacteria normally provide fertilizer to legume crops such as common beans and chickpeas, and those have been the focus of the research so far, but it may be possible to adapt them to work with other kinds of crops as well, and that is part of the team’s ongoing research. “There is a big push to extend the use of rhizobacteria to nonlegume crops,” he says. One way to accomplish that might be to modify the DNA of the bacteria, plants, or both, he says, but that may not be necessary.

“Our approach is almost agnostic to the kind of plant and bacteria,” he says, and it may be feasible “to stabilize, encapsulate and deliver [the bacteria] to the soil, so it becomes more benign for germination” of other kinds of plants as well.

Even if limited to legume crops, the method could still make a significant difference to regions with large areas of saline soil. “Based on the excitement we saw with our collaboration in Morocco,” Marelli says, “this could be very impactful.”

As a next step, the researchers are working on developing new coatings that could not only protect seeds from saline soil, but also make them more resistant to drought, using coatings that absorb water from the soil. Meanwhile, next year they will begin test plantings out in open experimental fields in Morocco; their previous plantings have been done indoors under more controlled conditions.

The research was partly supported by the Université Mohammed VI Polytechnique-MIT Research Program, the Office of Naval Research, and the Office of the Dean for Graduate Fellowship and Research.


21 November 2019

Milky Way’s supermassive black hole exploded 3.5 million years ago: Study

An artist's impression of the massive bursts of ionizing radiation exploding from the center of the Milky Way and impacting the Magellanic Stream. Photo: James Josephides/ASTRO 3D
A supermassive black hole in the centre of the Milky Way galaxy exploded 3.5 million years ago, according to a study.

The black hole, known as Sagittarius A, or Sgr A* (pronounced Sagittarius A-sta about 4.2 million times more massive than the Sun - exploded due to nuclear activity, according to a team of scientists at Australia's ARC Centre of Excellence for All Sky Astrophysics in 3 Dimensions (ASTRO 3-D).

The burst, known as a Seyfert flare, created two huge ‘ionisation cones’ of radiation, which flared to both poles of the galaxy and out into deep space.

The impact was felt at Magellanic Stream a long trail of gas extending from nearby dwarf galaxies called the Large and Small Magellanic Clouds which lies at an average 200,000 light years from the Milky Way, said the Australian-US research team.

“The flare must have been a bit like a lighthouse beam,” said Joss Bland-Hawthorn, professor at ASTRO 3-D.

“Imagine darkness, and then someone switches on a lighthouse beacon for a brief period of time,” Bland-Hawthorn added.

The blast took place just 3.5 million years ago 63 million years after an asteroid wiped out the dinosaurs.

Moreover, during the time of the explosion, our earliest ancestors the Australopithecines were roaming in Africa, revealed the study, to be published in The Astrophysical Journal. 

While Milky Way was always thought “as an inactive galaxy, with a not so bright centre”, the new study “instead opens the possibility of a complete reinterpretation of its evolution and nature”, said co-author Magda Guglielmo from the University of Sydney.

“A massive blast of energy and radiation came right out of the galactic centre and into the surrounding material. This shows that the centre of the Milky Way is a much more dynamic place than we had previously thought. It is lucky we're not residing there!” said Lisa Kewley, director of ASTRO 3-D.

The study follows a 2013 research, also led by Bland-Hawthorn, which ruled out a nuclear starburst as the cause of the massive explosive event. It had linked the event to activity in SgrA*.

Although the new study, which used data gathered by the Hubble Space Telescope, asserts SgrA* as the prime suspect more research needs to be done on how black holes evolve, influence and interact with galaxies, the researchers noted.


16 November 2019

Researchers Find More Than 1 Million Alternatives to DNA

Life on Earth uses DNA and RNA to store and utilize genetic information, but what if there’s another way? A new analysis from researchers at Emory University and the Tokyo Institute of Technology suggests a plethora of molecules could serve the same basic task of organizing and storing genetic information. They estimate more than a million possible stand-ins for DNA, some of which could help us fight disease or help us know what to expect as we search for alien life.

DNA (and RNA) consist of several components that make up the familiar double helix. There are the base pairs like adenine and guanine, a sugar (deoxyribose for DNA and ribose for RNA), and a phosphate group. The sugar and phosphate give nucleic acid an alternating sugar-phosphate backbone. We already know there are many alternatives to the five bases at work in DNA and RNA on Earth, but the new study looks at how the scaffolding of nucleic acid could vary.

The team used a computer simulation to explore a so-called “chemical space” within certain constraints. To choose the constraints, the team had to distill what makes nucleic acid molecules distinct. They settled on organic molecules that can assemble into a linear polymer with at least two attachment points, plus a place for nitrogen bases to connect. The substructure of the molecule also needs to be stable in a polymer configuration. Since these molecules don’t contain the traditional sugars and phosphorus, you can’t call them DNA — they’re some other kind of nucleic acid with potentially similar properties.

The analysis points to more than 1,160,000 potential nucleic acid molecules. That number exceeded even the most extreme estimates beforehand, but researchers can now start looking at these molecules in a laboratory setting to see if they can work as a DNA alternative. The team says this shows evolution on Earth may have experimented with several different molecular designs for storing genetic information before DNA ultimately won out.

Researchers around the world are working on therapeutic drugs that resemble nucleic acid, some of which could help combat viruses and cancer. A better understanding of these DNA alternatives could make those treatments more effective. And then there’s the importance to exobiology research. If we’re looking for evidence of extraterrestrial life, it might help to remember they could have genetic material using one of the other million possible molecules.


Young people are growing horns, thanks to phones + tablets

horns for youngs
CC BY 4.0 Example radiograph of 28-years-old male presenting with large enthesophytes emanating from the occipital squama. (Scientific Reports)

You thought 'text neck' was bad? Kids these days are growing 'enlarged external occipital protuberances.'

I used to joke that soon enough humans would evolve to have unusually large thumbs and be generally myopic because of our attachment to smartphones. But my silly sense of humor could have never imagined what is really happening, and happening surprisingly quickly: We are growing horns.

Or at least that's what scientists are suggesting after research on the emergence of "enlarged external occipital protuberances" (EEOP) amongst young people. Could this be true?

As Isaac Stanley-Becker reports for The Washington Post:
New research in biomechanics suggests that young people are developing hornlike spikes at the back of their skulls bone spurs caused by the forward tilt of the head, which shifts weight from the spine to the muscles at the back of the head, causing bone growth in the connecting tendons and ligaments. The weight transfer that causes the buildup can be compared to the way the skin thickens into a callus as a response to pressure or abrasion.

So far, the odd new bits of anatomy have garnered all kinds of names, including head horns, phone bones, spikes, or weird bumps. All are accurate, says David Shahar, a chiropractor with a PhD in biomechanics and first author of the paper.

“That is up to anyone’s imagination,” Shahar told The Post. “You may say it looks like a bird’s beak, a horn, a hook.”

The new skeletal accessory extends out from the skull, just above the neck. And its appearance has come as a surprise to the pair of scientists who conducted the study at the University of the Sunshine Coast in Queensland, Australia.

In a previous study, the team reported the development of prominent exostosis (which the dictionary defines as a "benign outgrowth of cartilaginous tissue on a bone") jutting out from the external occipital protuberance (EOP) in 41 percent of young adults. Since this isn't usually seen in young people, they decided to do more research.

For the more recent study, they compared the EOPs in 1,200 X-rays of subjects between the ages 18 to 86. They found that a combination of sex, the degree of forward head protraction, and age predicted the presence of enlarged EOPs. Males with increased forward head protraction had more prominent exostosis; and these were for the younger males. Surprisingly, for the older subjects, the size decreased. From the study:

"Our latter findings provide a conundrum, as the frequency and severity of degenerative skeletal features in humans are associated typically with aging. Our findings and the literature provide evidence that mechanical load plays a vital role in the development and maintenance of the enthesis (insertion) and draws a direct link between aberrant loading of the enthesis and related pathologies."

They conclude that EEOPs may be linked to postures that have developed with the extensive use of hand-held devices like smartphones and tablets. "Our findings raise a concern about the future musculoskeletal health of the young adult population and reinforce the need for prevention intervention through posture improvement education," the authors write.

The horn itself may not be much of a problem, says co-author Mark Sayers. (Because, who doesn't like horns?) However, the formation is a “portent of something nasty going on elsewhere, a sign that the head and neck are not in the proper configuration,” he told The Post.

That we are contorting ourselves in service to our gadget obsessions – to the point that we are growing horn-beak-hook things in the back of our heads – just doesn't seem like something that ends well. As the authors conclude in their paper:

"An important question is what the future holds for the young adult populations in our study, when development of a degenerative process is evident in such an early stage of their lives?"

Read more at The Washington Post, and see the whole study and illustrations in Scientific Reports.

And for another take on this – as in, is this really possible? – see what our sister site MNN has to say: Will children really grow horns from too much phone use? (Though I'm sticking with horns!)


24 April 2018

An alternative to antibiotics - weakening superbugs' grip

alternative to antibiotics weakening superbugs grip

An illustration showing the beginning of a bacterial infection. At the bottom, human proteins coat the surface of a medical implant. The colorful rods are bacteria initiating the infection. The transparent structure below the center bacteria is the protein that anchors bacteria to the implant surface. (Image: NIH Center for Macromolecular Modeling and Bioinformatics)

There is a growing medical emergency in our society caused by the constant growth in the number of people affected by untreatable bacterial infections. The discovery of antibiotics in the early 20th century gave us decades of relative safety, a period that is coming to an end the antibiotics that saved millions of lives in the last century are increasingly powerless against a growing number of antibiotic-resistant bacteria.

According to the U.S. Centers for Disease Control (CDC), more than 23,000 Americans die each year from infections caused by germs resistant to antibiotics. While this number in itself is alarming, the scary thing is that unusually resistant germs bacteria that are resistant to all or most antibiotics tested and are uncommon or carry special resistance genes are constantly developing and spreading. The scientists at the CDC, who are not prone to panic easily, call this type of bug nightmare bacteria. Lab tests in the U.S. uncovered unusual resistance more than 200 times in 2017 in these nightmare bacteria alone.

This problem is not new. Already in 2012, the then Director General of the World Health Organization (WHO), Dr Margaret Chan, has warned vividly that the growing threat of antibiotic-resistant bacterial strains may pose grave risks for society: "A post-antibiotic era means, in effect, an end to modern medicine as we know it. Things as common as strep throat or a child's scratched knee could once again kill."

Chan pointed out that there is a global crisis in antibiotics caused by rapidly evolving resistance among microbes responsible for common infections that threaten to turn them into untreatable diseases. Every antibiotic ever developed was at risk of becoming useless.

A work recently published in Science ("Molecular mechanism of extreme mechanostability in a pathogen adhesin") may offer some hope. Using a combination of laboratory experiments and GPU-accelerated supercomputer simulations, researchers discovered why staph bacteria the leading cause of healthcare-related infections can be so tough to beat.

This work could point the way to new treatments for now-invincible bacterial foes, not by developing a new antibiotic that would kill these bacteria, but by making them weaker so that they get more easily attacked by our immune system.

Staph infections are caused by staphylococcus bacteria, types of germs commonly found on the skin of healthy individuals. Most of the time, these bacteria cause no problems or result in relatively minor skin infections.

The research team showed that methicillin-resistant Staphylococcus aureus (MRSA) adhere to their hosts us humans with exceptional mechanical resilience. That's what makes pathogenic bacteria so persistent.

"Understanding the physical mechanisms that underlie this persistent stickiness at the molecular level is instrumental to combat these invaders," Rafael Bernardi, a research scientist in the Theoretical and Computational Biophysics group at the Beckman Institute, tells Nanowerk.

Combining experimental and sophisticated computer simulations, Bernardi and the late Klaus Schulten from the Beckman Institute teamed up with Lukas Milles and Hermann Gaub from the Physics Department at Ludwig-Maximilian-University Munich to decipher the mechanism responsible for staph adhesion.

Using an Atomic Force Microscope (AFM), the University of Munich team was able to measure the forces that govern the interaction between an individual adhesin (a staph protein) and its human target molecule. Independently, the Illinois team investigated the same protein complex by performing computationally-intensive steered molecular dynamics (SMD) simulations, carried out using the NCSA’s Blue Waters supercomputer, deconstructing the mechanism of the interaction between staph adhesion factors and human proteins.

The scientists were surprised by the shear forces that were necessary to rupture the interaction between the bacterial and human proteins: they are much stronger than any other non-covalent interaction known. They discovered that the mechanism that makes staph bacteria cling so tightly to its human host is a series of hydrogen bonds arranged in a corkscrew shape that works like superglue to clamp bacteria protein molecules to human ones.

"It’s easy to break one hydrogen bond," says Bernardi. "What makes this attachment so strong is that you have to break all the bonds at once in order to detach the protein molecules."

"The unbinding force of a single adhesin-human protein complex measured was exceptional, about an order of magnitude stronger than any other protein-protein interaction known," he continues. "The rupture forces reached over two nanonewtons, a regime generally associated with the strength of covalent bonds, and nearly an order of magnitude stronger than most other protein-protein interactions known."

A summary of the molecular mechanism responsible for extreme mechanostability in the complex between bacterial adhesion proteins and human fibronectin proteins. (Video produced by Rafael Bernardi (University of Illinois), based on simulations results taking advantage of GPU-accelerated software NAMD and VMD)

The combination of innovative simulation methods and experimental confirmations showed that the extreme physical strength of the staph adhesion is largely independent of protein sequence and biochemical properties, but rather a built-in physical property an invasive advantage for these staphylococci.

The whole description of this unexpected mechanism is new and shows how bacteria evolved to take advantage of simple hydrogen-bonds in an remarkable way. These findings expand our understanding of why pathogen adhesion is so resilient and may open new ways to inhibit staphylococcal invasion.

Understanding the mechanism of staph infection at the molecular and now atomic level may open new avenues for an intelligent design of antimicrobial therapies. The development of anti-adhesion therapy could promote the detachment of staph bacteria, facilitating bacterial clearance by our own immune system.

"The main challenge now is to design a drug that targets this bacterial adhesion mechanism and either blocks or at least weakens it," Bernardi concludes. "As a more general aspect, the combined use of AFM experiments and SMD simulations should greatly contribute to the identification of new binding mechanisms in bacterial adhesins, thus helping to show how they regulate biofilm formation. In diagnosis and therapy, this combined approach could represent a powerful platform for the treatment of microbial infections"

Source: nanowerk
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