Dec 16, 2017

Mapping the evolutionary history of a sugar gene

Beef cattle in pasture
Around two million years ago, a genetic change occurred that differentiated humans from most other primates that both protected humans from diseases, yet made red meat a health risk.

At this point in human evolution, a certain gene, known as CMAH, that allows for the synthesis of a sugar called Neu5Gc, went missing. This sugar is present in red meats, some fish and dairy products. When humans consume an animal that has that gene, the body has an immune reaction to the foreign sugar, which can cause inflammation, arthritis, and cancer.

University of Nevada, Reno researchers, led by College of Science Assistant Professor David Alvarez-Ponce, have analyzed 322 animal genome sequences from the National Center for Biotechnology Information looking for animals that show the presence of active CMAH genes. They placed the data from the 322 animal genomes into a "tree" to determine when in an animal's evolutionary history did the CMAH gene became inactive or "turned off." This is useful in explaining why certain species have an active CMAH gene and why similar species don't.

The Alvarez-Ponce lab specializes in studying the evolution of genes and genomes using bioinformatics. When it comes to the few fish investigated so far, there is an insignificant concentration of the Neu5Gc sugar to be a medical concern, but the concentrations of Neu5Gc are significantly higher in fish eggs, better known as caviar. As masters' student Sateesh Peri puts it, "one of the most expensive foods is among the ones with the highest amount of toxic Neu5Gc."

Birds also lack active CMAH genes, implying that consuming animals like chicken, turkey, and geese is not associated with the harmful side effects. Another class of animals that do not have the CMAH gene are reptiles, except for one species of lizard. The presence of the gene in this lizard challenges prior propositions that the gene may have been lost in an ancestor of reptiles and birds.

Aside from dietary issues, the CMAH gene also proves to be a major factor in whether or not a transplanted organ from an animal would be accepted by a human because of the gene. When an animal with a CMAH gene's organs are transplanted into a human who does not have the CMAH gene, the human body might reject the organ because of the presence of the Neu5Gc sugar.

"Inactivation of CMAH during human evolution might have freed humans from a number of pathogens," Alvarez-Ponce said. "For instance, there's this certain type of malaria that requires Neu5Gc for infection -- other primates are susceptible to it, but not humans."

The presence of the CMAH gene determines what animals humans should avoid eating (or should eat in moderation) and which animal bites humans should avoid. If the animal has the CMAH gene, then it shouldn't be eaten because it could cause inflammation, arthritis and cancer. However, consuming red meat in moderation is considered to be fine. If the animal doesn't have the CMAH gene, then those animals are more likely to contain pathogens that attach to Neu5Ac (the precursor of Neu5Gc) and that can affect humans.

Read more at Science Daily

Engineers program tiny robots to move, think like insects

RoboBees manufactured by the Harvard Microrobotics Lab have a 3 centimeter wingspan and weigh only 80 milligrams. Cornell engineers are developing new programming that will make them more autonomous and adaptable to complex environments.
While engineers have had success building tiny, insect-like robots, programming them to behave autonomously like real insects continues to present technical challenges. A group of Cornell engineers has been experimenting with a new type of programming that mimics the way an insect's brain works, which could soon have people wondering if that fly on the wall is actually a fly.

The amount of computer processing power needed for a robot to sense a gust of wind, using tiny hair-like metal probes imbedded on its wings, adjust its flight accordingly, and plan its path as it attempts to land on a swaying flower would require it to carry a desktop-size computer on its back. Silvia Ferrari, professor of mechanical and aerospace engineering and director of the Laboratory for Intelligent Systems and Controls, sees the emergence of neuromorphic computer chips as a way to shrink a robot's payload.

Unlike traditional chips that process combinations of 0s and 1s as binary code, neuromorphic chips process spikes of electrical current that fire in complex combinations, similar to how neurons fire inside a brain. Ferrari's lab is developing a new class of "event-based" sensing and control algorithms that mimic neural activity and can be implemented on neuromorphic chips. Because the chips require significantly less power than traditional processors, they allow engineers to pack more computation into the same payload.

Ferrari's lab has teamed up with the Harvard Microrobotics Laboratory, which has developed an 80-milligram flying RoboBee outfitted with a number of vision, optical flow and motion sensors. While the robot currently remains tethered to a power source, Harvard researchers are working on eliminating the restraint with the development of new power sources. The Cornell algorithms will help make RoboBee more autonomous and adaptable to complex environments without significantly increasing its weight.

"Getting hit by a wind gust or a swinging door would cause these small robots to lose control. We're developing sensors and algorithms to allow RoboBee to avoid the crash, or if crashing, survive and still fly," said Ferrari. "You can't really rely on prior modeling of the robot to do this, so we want to develop learning controllers that can adapt to any situation."

To speed development of the event-based algorithms, a virtual simulator was created by Taylor Clawson, a doctoral student in Ferrari's lab. The physics-based simulator models the RoboBee and the instantaneous aerodynamic forces it faces during each wing stroke. As a result, the model can accurately predict RoboBee's motions during flights through complex environments.

"The simulation is used both in testing the algorithms and in designing them," said Clawson, who helped has successfully developed an autonomous flight controller for the robot using biologically inspired programming that functions as a neural network. "This network is capable of learning in real time to account for irregularities in the robot introduced during manufacturing, which make the robot significantly more challenging to control."

Aside from greater autonomy and resiliency, Ferrari said her lab plans to help outfit RoboBee with new micro devices such as a camera, expanded antennae for tactile feedback, contact sensors on the robot's feet and airflow sensors that look like tiny hairs.

"We're using RoboBee as a benchmark robot because it's so challenging, but we think other robots that are already untethered would greatly benefit from this development because they have the same issues in terms of power," said Ferrari.

One robot that is already benefiting is the Harvard Ambulatory Microrobot, a four-legged machine just 17 millimeters long and weighing less than 3 grams. It can scamper at a speed of .44 meters-per-second, but Ferrari's lab is developing event-based algorithms that will help complement the robot's speed with agility.

Read more at Science Daily

Dec 15, 2017

To sleep or not: Researchers explore complex genetic network behind sleep duration

Fruit fly
Scientists have identified differences in a group of genes they say might help explain why some people need a lot more sleep -- and others less -- than most. The study, conducted using fruit fly populations bred to model natural variations in human sleep patterns, provides new clues to how genes for sleep duration are linked to a wide variety of biological processes.

Researchers say a better understanding of these processes could lead to new ways to treat sleep disorders such as insomnia and narcolepsy. Led by scientists with the National Heart, Lung, and Blood Institute (NHLBI), part of the National Institutes of Health (NIH), the study will be published on Dec. 14 in PLOS Genetics.

"This study is an important step toward solving one of the biggest mysteries in biology: the need to sleep," says study leader Susan Harbison, Ph.D., an investigator in the Laboratory of Systems Genetics at NHLBI. "The involvement of highly diverse biological processes in sleep duration may help explain why the purpose of sleep has been so elusive." Scientists have known for some time that, in addition to our biological clocks, genes play a key role in sleep and that sleep patterns can vary widely. But the exact genes controlling the duration of sleep and the biological processes that are linked to these genes have remained unclear.

To learn more, scientists artificially bred 13 generations of wild fruit flies to produce flies that were either long sleepers (sleeping 18 hours each day) or short sleepers (sleeping 3 hours each day). The scientists then compared genetic data between the long and short sleepers and identified 126 differences among 80 genes that appear to be associated with sleep duration. They found that these genetic differences were tied to several important developmental and cell signaling pathways. Some of the genes identified have known functions in brain development, as well as roles in learning and memory, the researchers said.

"What is particularly interesting about this study is that we created long- and short-sleeping flies using the genetic material present in nature, as opposed to the engineered mutations or transgenic flies that many researchers in this field are using," Harbison said. "Until now, whether sleep at such extreme long or short duration could exist in natural populations was unknown."

The researchers also found that the lifespan of the naturally long and short sleepers did not differ significantly from the flies with normal sleeping patterns. This suggests that there are little physiological consequences -- whether ill effects or benefits -- of being an extreme long or short sleeper, they said.

Read more at Science Daily

Engineers create plants that glow

Illumination of a book ('Paradise Lost,' by John Milton) with the nanobionic light-emitting plants (two 3.5-week-old watercress plants). The book and the light-emitting watercress plants were placed in front of a reflective paper to increase the influence from the light emitting plants to the book pages.
Imagine that instead of switching on a lamp when it gets dark, you could read by the light of a glowing plant on your desk.

MIT engineers have taken a critical first step toward making that vision a reality. By embedding specialized nanoparticles into the leaves of a watercress plant, they induced the plants to give off dim light for nearly four hours. They believe that, with further optimization, such plants will one day be bright enough to illuminate a workspace.

"The vision is to make a plant that will function as a desk lamp -- a lamp that you don't have to plug in. The light is ultimately powered by the energy metabolism of the plant itself," says Michael Strano, the Carbon P. Dubbs Professor of Chemical Engineering at MIT and the senior author of the study

This technology could also be used to provide low-intensity indoor lighting, or to transform trees into self-powered streetlights, the researchers say.

MIT postdoc Seon-Yeong Kwak is the lead author of the study, which appears in the journal Nano Letters.

Nanobionic plants


Plant nanobionics, a new research area pioneered by Strano's lab, aims to give plants novel features by embedding them with different types of nanoparticles. The group's goal is to engineer plants to take over many of the functions now performed by electrical devices. The researchers have previously designed plants that can detect explosives and communicate that information to a smartphone, as well as plants that can monitor drought conditions.

Lighting, which accounts for about 20 percent of worldwide energy consumption, seemed like a logical next target. "Plants can self-repair, they have their own energy, and they are already adapted to the outdoor environment," Strano says. "We think this is an idea whose time has come. It's a perfect problem for plant nanobionics."

To create their glowing plants, the MIT team turned to luciferase, the enzyme that gives fireflies their glow. Luciferase acts on a molecule called luciferin, causing it to emit light. Another molecule called co-enzyme A helps the process along by removing a reaction byproduct that can inhibit luciferase activity.

The MIT team packaged each of these three components into a different type of nanoparticle carrier. The nanoparticles, which are all made of materials that the U.S. Food and Drug Administration classifies as "generally regarded as safe," help each component get to the right part of the plant. They also prevent the components from reaching concentrations that could be toxic to the plants.

The researchers used silica nanoparticles about 10 nanometers in diameter to carry luciferase, and they used slightly larger particles of the polymers PLGA and chitosan to carry luciferin and coenzyme A, respectively. To get the particles into plant leaves, the researchers first suspended the particles in a solution. Plants were immersed in the solution and then exposed to high pressure, allowing the particles to enter the leaves through tiny pores called stomata.

Particles releasing luciferin and coenzyme A were designed to accumulate in the extracellular space of the mesophyll, an inner layer of the leaf, while the smaller particles carrying luciferase enter the cells that make up the mesophyll. The PLGA particles gradually release luciferin, which then enters the plant cells, where luciferase performs the chemical reaction that makes luciferin glow.

The researchers' early efforts at the start of the project yielded plants that could glow for about 45 minutes, which they have since improved to 3.5 hours. The light generated by one 10-centimeter watercress seedling is currently about one-thousandth of the amount needed to read by, but the researchers believe they can boost the light emitted, as well as the duration of light, by further optimizing the concentration and release rates of the components.

Plant transformation

Previous efforts to create light-emitting plants have relied on genetically engineering plants to express the gene for luciferase, but this is a laborious process that yields extremely dim light. Those studies were performed on tobacco plants and Arabidopsis thaliana, which are commonly used for plant genetic studies. However, the method developed by Strano's lab could be used on any type of plant. So far, they have demonstrated it with arugula, kale, and spinach, in addition to watercress.

For future versions of this technology, the researchers hope to develop a way to paint or spray the nanoparticles onto plant leaves, which could make it possible to transform trees and other large plants into light sources.

"Our target is to perform one treatment when the plant is a seedling or a mature plant, and have it last for the lifetime of the plant," Strano says. "Our work very seriously opens up the doorway to streetlamps that are nothing but treated trees, and to indirect lighting around homes."

Read more at Science Daily

Hope for one of the world's rarest primates: First census of Zanzibar Red Colobus monkey

A team of WCS scientists recently completed the first-ever range-wide population census of the Zanzibar red colobus monkey (Piliocolobus kirkii an endangered primate found only on the Zanzibar archipelago off the coast of East Africa.
A team of WCS scientists recently completed the first-ever range-wide population census of the Zanzibar red colobus monkey (Piliocolobus kirkii) an endangered primate found only on the Zanzibar archipelago off the coast of East Africa.

The good news: there are more than three times as many Zanzibar red colobus monkeys (more than 5,800 individual animals) than previously thought, and many more monkeys living within protected areas than outside of them. And the bad news: survivorship of young animals is very low, species now extinct in 4 areas, forest habitat on which the primates and others species depend are rapidly being cleared for agriculture and tourism development projects and hunting is common.

The paper titled "Zanzibar's endemic red colobus Piliocolobus kirkii: first systematic and total assessment of population, demography and distribution" has been published in the online version of the journal Oryx. The authors are: Tim R.B. Davenport; Said A. Fakih; Sylvanos P. Kimiti; Lydia U. Kleine; Lara S. Foley; and Daniela W. De Luca.

"Scientists have known about the Zanzibar red colobus monkey for 150 years, yet this is the first systematic study of this poorly understood species across its entire range," said Dr. Tim Davenport, Director of WCS's Tanzania Country Program and the lead author of the study. "The systematic assessment redefines almost everything we know about this amazing animal, and is now guiding effective management strategies for this species."

Seeking to gain a better understanding of the status and ecological needs of the Zanzibar red colobus monkey, the WCS team of researchers spent two years (4,725 hours spent in the field) searching for and observing the arboreal primates. The surveys occurred both within and outside of protected areas on the main Zanzibar island of Unguja, and the scientists employed a new sweep census technique to collect data on group sizes and structures, demographics, and locations with the help of GPS devices.

The results of the study provided researchers with proof that Zanzibar's protected areas are, to some extent, working. Some 69 percent of the population of Zanzibar red colobus monkeys live inside Unguja's protected area network, and monkey groups found within protected areas boasted both higher average group sizes and more females per group.

Conversely, the assessment also highlighted challenges for conservation. Especially for the more than 30 percent of the monkey's population that live outside of protected areas. The scientists discovered that four of the forests previously known to contain Zanzibar red colobus monkeys no longer do. Four other locations were found to contain only one family group, which are unlikely to survive in isolation.

One of the largest threats to the Zanzibar red colobus monkey is deforestation. Forests on Zanzibar's main island of Unguja are being lost at a rate of more than 19 square kilometers per year due to agricultural activities, residential development, and human population growth. The hunting of monkeys for food and retaliation for crop raiding is also a concern.

The authors recommend creating a new protected area to further safeguard the Zanzibar red colobus monkey as well as increasing primate and forest tourism operations. The team has also suggested making the primate the official national animal of Zanzibar.

"The Zanzibar red colobus monkey is unique to Zanzibar and could be a wonderful example of how conservation efforts can succeed in protecting both wildlife and habitat, which in turn benefits communities" added Davenport, who recently presented the study's results to the Zanzibar government. "The species could serve as a fitting symbol for both Zanzibar and the government's foresight in wildlife management."

Read more at Science Daily

Effects of climate change could accelerate by mid-century

Climate change effects are expected to become more apparent by the middle of the century.
Nature lovers beware, environmental models used by researchers at the University of New Hampshire are showing that the effects of climate change could be much stronger by the middle of the 21st century, and a number of ecosystem and weather conditions could consistently decline even more in the future. If carbon dioxide emissions continue at the current rate, they report that scenarios of future conditions could not only lead to a significant decrease in snow days, but also an increase in the number of summer days over 90 degrees and a drastic decline in stream habitat with 40 percent not suitable for cold water fish.

"While this research was applied to New Hampshire, the approach can be generally applied, and a number of things that people care about will worsen due to climate change," said Wilfred Wollheim, associate professor in the department of natural resources and the environment and one of the study's authors. "For example, right now the average number of snow days is 60 per year, but in 20 to 30 years the models show that the number of snow days could be as low as 18 days per year."

The research, published recently in the journal Ecology and Society, used models bench marked to field measurements to evaluate the Merrimack River watershed in New Hampshire. They found that along with a decrease in snow cover in the winter, other potential impacts could include up to 70 hot summer days per year with temperatures of 90 degrees or more by the end of century, a greater probability of flooding, a considerable loss of cold water fish habitat, and accelerated nitrogen inputs to coastal areas which could lead to eutrophication, an abnormal amount of nutrients which can pollute the water and deplete fish species. Researchers say that the biggest impact will be around urban areas, near where people live.

"Land use and population growth interacting with climate change are also important drivers," said Wollheim. "These models can help guide efforts to make plans to adapt to the changing climate. Alterations in land use policy could reduce these impacts. In particular, prevention of sprawl and investment in storm and waste water infrastructure would further maintain more ecosystem services. Implementing policies that reduce greenhouse gas emissions are essential to limit even further changes."

Read more at Science Daily

Dec 14, 2017

Ancient genetic mutation helps explain origin of some human organs

DNA
A neutral genetic mutation -- a fluke in the evolutionary process that had no apparent biological purpose -- that appeared over 700 million years ago in biological evolution could help explain the origin of complex organs and structures in human beings and other vertebrates, according to an article published in Nature Communications by a team led by CRG group leader Manuel Irimia, university professor Jordi García-Fernàndez, of the Faculty of Biology and the Institute of Biomedicine of the University of Barcelona (IBUB), and Maria Ina Arnone (Anton Dohrn Zoological Station, Italy).

Specifically, this mutation, which likely occurred very early in evolution after the separation of our group from that of sea anemones, affected a gene of the Fgfr (fibroblast growth factor receptors) family. Curiously, this genetic change triggered, millions of years later, the connection between two gene regulatory networks (those controlled by ESRP and by Fgfr), which became key for the origin of many vertebrate organs and structures (lungs, forelimbs and inner ear).

The Nature Communications article, whose lead author is Demian Burguera (CRG and UB-IBUB), took their approach from the field of evolutionary developmental biology (evo-devo). This is a relatively new paradigm in the study of evolution, which focuses on comparing the embryonic development of multiple living beings to understand how their adult forms have changed giving rise to new species.

From chance mutation to formation of organs in vertebrates

A gene can code for different proteins -- with diverse functionality -- through the genetic mechanism of alternative splicing (the cutting and rejoining of genes). In some human cell types, this process is controlled by a family of regulatory proteins called ESRP. They act as a molecular switch: when these regulatory proteins are present, a group of genes involved in morphogenesis and cell-cell interactions generate specific protein variants; when they are absent, different protein variants are produced. And this molecular switch controls how cells behave and interact with their neighbors during embryonic development. However, the evolutionary importance of this mechanism was unknown.

"We have studied the functions of ESRP genes during the embryogenesis of various animals. Our results suggest that these genes were part of an ancient genetic machinery, shared by animals as diverse as fish, sea urchins and ourselves, that controls the integration of certain cells into the linings of developing organs. This is a fundamental step in the formation of some organs, and it is the reverse of a process that is central to cancer metastasis, by which cells leave the tumor to colonize other parts of the body" explains Manuel Irimia, group leader at the Centre for Genomic Regulation (CRG).

The article published in Nature Communications shows how the same regulatory genes have been used to generate different organs and biological structures in living beings during the evolutionary process. In the same vein, the article describes how a chance "mistake" -- an apparently meaningless mutation that took place over 700 million years ago -- became the molecular driver for complex morphological developments in a number of vertebrates (including the human species).

"Clearly, the most exceptional result of the work is the proof of how important serendipity is for evolution. It is surprising to find that a single gene (ESRP), through its ancestral biological role (cell adherence and motility) has been used throughout the animal scale for very different purposes: from the immune system of an echinoderm to the lips, lungs or inner ears of humans," states professor Jordi Garcia-Fernàndez, of the University of Barcelona's Department of Genetics, Microbiology and Statistics and the IBUB.

Read more at Science Daily

Spaghetti-like, DNA 'noodle origami' the new shape of things to come for nanotechnology

A DNA origami with an emoji-like smiley face.
For the past few decades, scientists have been inspired by the blueprint of life, DNA, as the shape of things to come for nanotechnology.

This burgeoning field is called DNA origami. Scientist borrowed its moniker from the paper artists who conjure up birds, flowers and planes from imaginatively folding a single sheet of paper.

Similarly, DNA origami scientists are dreaming up a variety of shapes -- at a scale one thousand times smaller than a human hair -- that they hope will one day revolutionize computing, electronics and medicine.

Now, a team of Arizona State and Harvard scientists has invented a major new advance in DNA nanotechnology. Dubbed "single-stranded origami," their new strategy uses one long, thin noodle-like strand of DNA, or its chemical cousin RNA, that can self-fold -- -without even a single knot -- into the largest, most complex structures to date.

And, the strands forming these structures can be made inside living cells or using enzymes in a test tube, allowing scientists the potential to plug-and-play with new designs and functions for nanomedicine -- -like tiny, nanobots playing doctor and delivering drugs within cells to the site of injury.

"I think this is an exciting breakthrough, and a great opportunity for synthetic biology as well," said Hao Yan, a co-inventor of the technology, director of the ASU Biodesign Institute's Center for Molecular Design and Biomimetics, and the Milton Glick Professor in the School of Molecular Sciences.

"We are always inspired by nature's designs to make information-carrying molecules that can self-fold into the nanoscale shapes we want to make,"

As proof of concept, they've pushed the envelope to make Emoji-like smiley faces, hearts, triangle shapes -- 18 shapes in total -- that significantly expand the design studio space and material scalability for so-called, "bottom-up" nanotechnology.

Size matters

To date, DNA nanotechnology scientists have had to rely on two main methods for making spatially addressable structures with finite dimensions.

The first was molecular bricks, small, short pieces of DNA that can fold together to make a single structure. The second method was scaffolded DNA, where a single strand is shaped into a structure by using helper strands of DNA, that staple the structure into place.

"These two methods are not very scalable in terms of synthesis," said Fei Zhang, a senior co-author on the paper. "When you have so many short pieces of DNA, you can't replicate it using biological systems. One way around this is to engineer one long strand that could fold itself into any design or architecture."

Furthermore, each method has been limited because as the size of the structure increases, the ability to fold correctly becomes more challenging.

Now, there is a new third way.

For Yan and his team to make their breakthrough, they had to go back to the drawing board, which meant looking at nature again for inspiration. They found what they were looking for with a chemical cousin of DNA, in the form of complex, RNA structures.

The complex RNA structures discovered to date contain single-stranded RNA molecules that self-fold into structures without any topological knots. Could this trick work again for single-stranded DNA or RNA origami?

They were able to crack the code of how RNA makes structures to develop a fully programmable single-stranded origami architecture.

"The key innovation of our study is to use DNA and RNA to construct a structurally complex yet knot-free structure that can be folded smoothly from a single strand," Yan said. "This gave us a design strategy to allow us to fold one long strand into complex architecture."

"With help from a computer scientist in the team, we could also codify the design process as a mathematically rigorous formal algorithm and automate the design by developing a user-friendly software tool," said Yan.

The algorithm and software were validated by the automated design and experimental construction of six distinct DNA ssOrigami structures (four rhombuses and two heart shapes).

Form and function

It's one thing to make crafty patterns and smiley faces with DNA, but critics of DNA origami have been wondering when the practical applications would come about.

Now, these are possible. "I think we are much closer to real practical applications of the technology," said Yan. "We are actively looking at the first nanomedicine applications with our ssOrigami technology."

They were also able to demonstrate that a folded ssOrigami structure can be melted and used as a template for amplification by DNA copying enzymes in a test tube and that the ssOrigami strand can be replicated and amplified via clonal production in living cells.

"Single-stranded DNA nanostructures formed via self-folding offer greater potential of being amplifiable, replicable, and clonable, and hence the opportunity for cost-efficient, large-scale production using enzymatic and biological replication, as well as the possibility for using in vitro evolution to produce sophisticated phenotypes and functionalities," said Yan.

These same design rules could be used for DNA's chemical cousin, RNA.

A key design feature of single-stranded origami (ssOrigami) is that the strand can be made and copied in the lab and in living cells and subsequently folded into designer structures by heating and cooling the DNA.

To make it inside the lab, they used the photocopier of cloning sequences, called PCR, to replicate and produce ssDNA.

Inside living cells, they first placed it inside a mule of molecular cloning, called a plasmid, after it was placed into a common lab bacteria called E. coli cells. When they treated the bacteria with enzymes to free up the ssDNA, they could isolate it, and then fold it into its target structure.

"Because plasmid DNA can be easily replicated in E. coli, the production can be scaled up by growing a large volume of E. coli cells with low cost," said Yan. This gets around the constraint of having to synthesize all of the DNA in the lab from scratch, which is far more expensive.

It also moves them in a direction now, where they can potentially make the structures inside of cells.

"Here we show bacteria to make the strand, but still need to do thermal annealing outside the bacteria to form the structure," said Yan. "The ideal situation would be to design an RNA sequence that can get transcribed inside the bacteria, and fold inside the bacteria so we can use bacteria as a nanofactory to produce the material."

Here, they demonstrated a framework to design and synthesize a single DNA or RNA strand to efficiently self-fold into an unknotted compact ssOrigami structure that approximates any arbitrary user-prescribed target shape.

"Its single-strandedness enabled the demonstration of facile replication of the strand in vitro and in living cells, and its programmability allowed us to codify the design process and develop a simple web-based automated design tool."

A new design school

In the software, made through a collaboration with BioNano Research Group, Autodesk Research, first, the user selects a target shape, which is converted into pixelated representation. The user can upload a 2D image or draw a shape using a 2D pixel design editor.

The user can optionally add DNA hairpins or loops, which can serve as surface markers or handles for attaching external entities. The pixels are converted into DNA helical domains and locking domains to do the folding. The software will then generate ssOrigami structures and sequences, and the user can view the molecular structure via an embedded molecular viewer. Finally, the DNA sequence is assigned to the cycle strand, and the expected folded structure manufactured in the lab and visually confirmed by viewing it under a powerful microscope that are the eyes of nanotechnology, atomic force microscopy, or AFM.

Read more at Science Daily

Artificial intelligence, NASA data used to discover eighth planet circling distant star

´With the discovery of an eighth planet, the Kepler-90 system is the first to tie with our solar system in number of planets. Artist's concept.
Our solar system now is tied for most number of planets around a single star, with the recent discovery of an eighth planet circling Kepler-90, a Sun-like star 2,545 light years from Earth. The planet was discovered in data from NASA's Kepler Space Telescope.

The newly-discovered Kepler-90i -- a sizzling hot, rocky planet that orbits its star once every 14.4 days -- was found using machine learning from Google. Machine learning is an approach to artificial intelligence in which computers "learn." In this case, computers learned to identify planets by finding in Kepler data instances where the telescope recorded changes in starlight caused by planets beyond our solar system, known as exoplanets.

"Just as we expected, there are exciting discoveries lurking in our archived Kepler data, waiting for the right tool or technology to unearth them," said Paul Hertz, director of NASA's Astrophysics Division in Washington. "This finding shows that our data will be a treasure trove available to innovative researchers for years to come."

The discovery came about after researchers Christopher Shallue and Andrew Vanderburg trained a computer to learn how to identify exoplanets in the light readings recorded by Kepler -- the miniscule change in brightness captured when a planet passed in front of, or transited, a star. Inspired by the way neurons connect in the human brain, this artificial "neural network" sifted through Kepler data and found weak transit signals from a previously-missed eighth planet orbiting Kepler-90, in the constellation Draco.

Machine learning has previously been used in searches of the Kepler database, and this continuing research demonstrates that neural networks are a promising tool in finding some of the weakest signals of distant worlds.

Other planetary systems probably hold more promise for life than Kepler-90. About 30 percent larger than Earth, Kepler-90i is so close to its star that its average surface temperature is believed to exceed 800 degrees Fahrenheit, on par with Mercury. Its outermost planet, Kepler-90h, orbits at a similar distance to its star as Earth does to the Sun.

"The Kepler-90 star system is like a mini version of our solar system. You have small planets inside and big planets outside, but everything is scrunched in much closer," said Vanderburg, a NASA Sagan Postdoctoral Fellow and astronomer at the University of Texas at Austin.

Shallue, a senior software engineer with Google's research team Google AI, came up with the idea to apply a neural network to Kepler data. He became interested in exoplanet discovery after learning that astronomy, like other branches of science, is rapidly being inundated with data as the technology for data collection from space advances.

"In my spare time, I started Googling for 'finding exoplanets with large data sets' and found out about the Kepler mission and the huge data set available," said Shallue. "Machine learning really shines in situations where there is so much data that humans can't search it for themselves."

Kepler's four-year dataset consists of 35,000 possible planetary signals. Automated tests, and sometimes human eyes, are used to verify the most promising signals in the data. However, the weakest signals often are missed using these methods. Shallue and Vanderburg thought there could be more interesting exoplanet discoveries faintly lurking in the data.

First, they trained the neural network to identify transiting exoplanets using a set of 15,000 previously vetted signals from the Kepler exoplanet catalogue. In the test set, the neural network correctly identified true planets and false positives 96 percent of the time. Then, with the neural network having "learned" to detect the pattern of a transiting exoplanet, the researchers directed their model to search for weaker signals in 670 star systems that already had multiple known planets. Their assumption was that multiple-planet systems would be the best places to look for more exoplanets.

"We got lots of false positives of planets, but also potentially more real planets," said Vanderburg. "It's like sifting through rocks to find jewels. If you have a finer sieve then you will catch more rocks but you might catch more jewels, as well."

Kepler-90i wasn't the only jewel this neural network sifted out. In the Kepler-80 system, they found a sixth planet. This one, the Earth-sized Kepler-80g, and four of its neighboring planets form what is called a resonant chain -- where planets are locked by their mutual gravity in a rhythmic orbital dance. The result is an extremely stable system, similar to the seven planets in the TRAPPIST-1 system.

Their research paper reporting these findings has been accepted for publication in The Astronomical Journal. Shallue and Vanderburg plan to apply their neural network to Kepler's full set of more than 150,000 stars.

Kepler has produced an unprecedented data set for exoplanet hunting. After gazing at one patch of space for four years, the spacecraft now is operating on an extended mission and switches its field of view every 80 days.

"These results demonstrate the enduring value of Kepler's mission," said Jessie Dotson, Kepler's project scientist at NASA's Ames Research Center in California's Silicon Valley. "New ways of looking at the data -- such as this early-stage research to apply machine learning algorithms -- promise to continue to yield significant advances in our understanding of planetary systems around other stars. I'm sure there are more firsts in the data waiting for people to find them."

Read more at Science Daily

New Data From Mars Further Dampens Prospects for Life Around Red Dwarf Stars

The illustration depicts charged particles from a solar storm stripping away charged particles of Mars' atmosphere, one of the processes of Martian atmosphere loss studied by NASA's MAVEN mission, beginning in 2014.
Could a Mars-like planet be habitable if it was orbiting a red dwarf star that is cooler and less bright than our sun? New calculations — based on data from a NASA Mars orbiter — suggest the window for life would be short.

The activity on these red dwarf stars could shorten the time during which habitable conditions exist on a planet by a factor of about 5 to 20, the researchers said. In the worst case, extremely active stars could shorten habitability by at least a factor of 1,000 — barely any time for life to establish itself, let alone thrive.

The news comes in the wake of a separate study of Proxima Centauri b, a rocky planet that orbits a red dwarf star just four light-years from Earth. When the planet was discovered in 2016, researchers were initially excited by Proxima Centauri b, a planet orbiting in its star’s habitable zone. However, a new study concluded that habitability would be tough to come by because the red dwarf that Proxima Centauri b orbits likely stripped away the planet's atmosphere over time.

Together, the two studies indicate that the idea of habitability — usually defined as the zone around a star in which liquid water can exist on a rocky planet — needs revisiting, as this zone can be greatly altered by factors such as a planet's atmosphere or a star's activity.

"Habitability is one of the biggest topics in astronomy, and these estimates demonstrate one way to leverage what we know about Mars and the Sun to help determine the factors that control whether planets in other systems might be suitable for life," said Bruce Jakosky, the principal investigator of MAVEN, the Mars Atmosphere and Volatile Evolution mission.

MAVEN has been orbiting Mars since September 2014, studying the rate of atmospheric loss from the Red Planet. Mars doesn't have a global magnetic field. This means that over time charged particles from the sun can strip away lighter molecules in the atmosphere.

For Mars, that process might have had devastating consequences for life. Geological evidence shows that water used to flow on the Martian surface billions of years ago. Since water is a key ingredient of habitability, some researchers suggest that life could have flourished in the past, but only briefly until the atmosphere became too thin to support water and the surface permanently dried up.

A new study, presented Dec. 13 by MAVEN co-investigator David Brain at the fall meeting of the American Geophysical Union, uses data from MAVEN to better understand habitable rocky planets orbiting other stars.

Since MAVEN arrived at Mars, the sun's activity has varied — sometimes experiencing peaks such as solar storms, solar flares, and coronal mass ejections (ejections of solar particles into space). MAVEN monitored how quickly molecules from the Martian atmosphere escaped.

Brain and his colleagues then applied the data to a theoretical Martian-sized planet at the edge of the habitable zone of a red dwarf star, the most common type of star in our galaxy.

A planet orbiting a red dwarf star needs to huddle closer to that star (compared to our own sun) to get enough light and warmth for water to run on its surface, they found. But this comes at a price: The hypothetical planet would receive 5 to 10 times more ultraviolet radiation than Mars does. This radiation would in turn fuel atmospheric escape at a much greater rate than Mars experiences — 3 to 5 times as many charged particles, and 5 to 10 times more neutral particles.

The charged particles would also contribute to a separate atmospheric loss phenomenon called sputtering, which occurs when energetic particles crash into the atmosphere and disturb molecules, propelling some of them out into space.

But the planet would experience only about the same amount of thermal escape, which happens for lighter molecules like hydrogen. Thermal escape happens at the top of the atmosphere. On the theoretical Mars-like planet at a red dwarf star, the rate of thermal escape only increases if UV radiation moves more hydrogen to the top of the atmosphere, the researchers found.

The researchers added, however, that a planet might have other geological processes that could fight back against atmospheric loss. Perhaps it has a stronger magnetic field, unlike Mars, or active geology that could replenish the atmosphere. Also, planets larger than Mars could better maintain their atmospheres because of stronger gravity.

Read more at Seeker