Amazing Science

Whether you have a huge honker, a puny proboscis, or a snubbed schnoz, the shape of your nose is in your genes. Now, researchers have sniffed out five of those stretches of DNA that control nose and chin shape. The team sequenced the genomes of more than 6000 men and women in Central and South America and used photographs of the participants to categorize 14 of their facial features—from cheekbone protrusion to lip shape. Then, the scientists analyzed whether any of the features were associated with certain genes. GLI3 and PAX1, both known to be involved in cartilage growth, were linked to the breadth of a person’s nostrils;DCHS2, also related to cartilage, controlled nose pointiness; RUNX2, which drives bone development, was associated with the width of the nose bridge, the upper area of the nose; and EDAR, which has previously been linked to ear and tooth shape and hair texture, affected chin protrusion. The results, published online today in Nature Communications, may help shed light on how the human face evolved and why different ethnicities have distinct facial features. Moreover, the research could help forensic scientists reconstruct faces based on genetic samples.

Ed Hawkins, a climate scientist at the National Center for Atmospheric Science at the University of Reading, devised the spiral animation to show how global average surface temperatures are increasing relative to the average temperature during preindustrial times.

Clutter is a special challenge for robots, but new Carnegie Mellon University software is helping robots cope, whether they're beating a path across the Moon or grabbing a milk jug from the back of the refrigerator.

The software not only helped a robot deal efficiently with clutter, it surprisingly revealed the robot's creativity in solving problems.

An international team of scientists, including two professors and three graduate students from UCLA, has detected and confirmed the faintest early-universe galaxy ever. Using the W. M. Keck Observatory on the summit on Mauna Kea in Hawaii, the researchers detected the galaxy as it was 13 billion years ago. The results were published in the Astrophysical Journal Letters.

Tommaso Treu, a professor of physics and astronomy in the UCLA College and a co-author of the research, said the discovery could be a step toward unraveling one of the biggest mysteries in astronomy: how a period known as the "cosmic dark ages" ended.

The researchers made the discovery using an effect called gravitational lensing to see the incredibly faint object, which was born just after the Big Bang. Gravitational lensing was first predicted by Albert Einstein almost a century ago; the effect is similar to that of an image behind a glass lens appearing distorted because of how the lens bends light. The detected galaxy was behind a galaxy cluster known as MACS2129.4-0741, which is massive enough to create three different images of the galaxy.

According to the Big Bang theory, the universe cooled as it expanded. As that happened, Treu said, protons captured electrons to form hydrogen atoms, which in turn made the universe opaque to radiation -- giving rise to the cosmic dark ages.

"At some point, a few hundred million years later, the first stars formed and they started to produce ultraviolet light capable of ionizing hydrogen," Treu said. "Eventually, when there were enough stars, they might have been able to ionize all of the intergalactic hydrogen and create the universe as we see it now."

That process, called cosmic reionization, happened about 13 billion years ago, but scientists have so far been unable to determine whether there were enough stars to do it or whether more exotic sources, like gas falling onto supermassive black holes, might have been responsible.

"Currently, the most likely suspect is stars within faint galaxies that are too faint to see with our telescopes without gravitational lensing magnification," Treu said. "This study exploits gravitational lensing to demonstrate that such galaxies exist, and is thus an important step toward solving this mystery."

The research team was led by Marusa Bradac, a professor at UC Davis. Co-authors include Matthew Malkan, a UCLA professor of physics and astronomy, and UCLA graduate students Charlotte Mason, Takahiro Morishita and Xin Wang.

The CRISPR/Cas9 system is currently the technique in genome editing. Thanks to recent developments in the CRISPR genome editing system, we are able to alter DNA with unprecedented precision and accuracy. Ultimately, this revolutionary genome editing technique allows us to modify any region of the genome of any species—without harming other genes. But more than that, we are able to edit these genes at just a fraction of the cost of previous methods.

It has utterly revolutionized gene editing. However, a team of researchers has just developed a new approach that just might prove to be as efficient and effective as the current standard.

In a study published in Nature Biotechnology, researchers from Chunyu Han’s lab have developed a novel genome editing technique basically just like CRISPR.

According to the report, the method is based on the Natronobacterium gregoryi Argonaute (NgAgo), a DNA-guided endonuclease that’s similar to Cas9, the endonuclease of CRISPR. These are a specific type of protein, otherwise known as restriction enzymes, that are responsible for cutting DNA at specific locations. Remarkably, the study shows that NgAgo is suitable for genome editing in human cells.

The team asserts that their study has a number of key differences between NgAgo and Cas9, where the former is at the advantage. They claim that that the method appears to have a low tolerance to guide-target mismatches, leading to a high efficiency in editing:

• One of these is that NgAgo does not need to be followed by a protospacer-adjacent motif (PAM), a DNA sequence seen in Cas9. Notably, Cas9 will not successfully bind or cleave a target DNA sequence if this is not followed by the PAM (as it is responsible for the protein to differentiate CRISPR DNA from target DNA).
• Another benefit is that the loading temperature of NgAgo is found to be at 55°C and not at Cas9’s 37°C. This shows that this could be another option for genome editing at conditions such as this. Also, at this temperature, the method follows a “one-guide-faithful” rule, that is, NgAgo cannot swap target DNA with other free DNA, minimizing off-target effects.

Though there has yet to be an extensive side-by-side comparison of the two enzymes, NgAgo and Cas9 appear to have similar efficiencies. The authors report that their tests with 47 guides targeting 8 human genes, the results showed a 21% to 41% efficiency.

A team of scientists from the Moscow Institute of Physics and Technology (MIPT), the National Research University of Electronic Technology (MIET), and the Prokhorov General Physics Institute have proposed a theoretical model that explains the unexpectedly high values of the linear magnetoelectric effect in BiFeO3 (bismuth ferrite) that have been observed in a number of experiments. The team also suggested a way of further enhancing the effect. The results of the study have been published in the journal Physical Review B.

One particular feature of bismuth ferrite is that in bulk samples, spins of Fe3+ iron ions are arranged in the form of a cycloid. This spin structure can be destroyed by a strong magnetic field or mechanical stress. Without a spin cycloid, bismuth ferrite exhibits a large linear magnetoelectric effect, and this effect was the focal point of the study.

"The theoretical description presented in the paper may be applicable to other multiferroics similar to BiFeO3. This will help in predicting the value of their magnetoelectric effect, which, in turn, will make it easier to find new and promising materials for industrial applications," says the head of MIPT's Laboratory of physics of magnetic heterostructures and spintronics for energy-saving information technologies, Prof. Anatoly Zvezdin.

Icy objects in our solar system have large oceans under their surfaces and here life could evolve and flourish. So says a new thesis by Jesper Lindkvist, PhD student at the Swedish Institute of Space Physics and Umeå University. The thesis will be defended on Tuesday 31 May at the Swedish Institute of Space Physics in Kiruna, Sweden.

There has long been speculation as to whether Jupiter's large, icy moon Callisto has an ocean beneath its surface. Observations of Callisto's near-space environment by instruments on board the spacecraft Galileo, which is orbiting Jupiter, lead us to believe that there is such a sub-surface ocean. Computer simulations of the space plasma interactions support this belief. "If you find an ocean beneath the surface of one moon, perhaps the same is true of other icy objects in space," says Jesper Lindkvist.

Outflow of water vapor has been detected from the surface of the dwarf planet Ceres, which is in the asteroid belt between Mars and Jupiter. This could indicate a reservoir of water, also related to a large sea beneath the surface. The spacecraft Dawn is at Ceres right now, trying to answer this question. "If someone was planning to build a future space base on one of these Solar System objects, for example to seek after signs of life, I would suggest they take an extra long ice bore and their fishing equipment," jokes Jesper Lindkvist.

The outflow of water vapor from moons and dwarf planets is similar to that we see from comets. The icy comet 67/Churyumov-Gerasimenko which rounded the sun in the summer of 2015 has been followed closely by the European spacecraft Rosetta. Measurements of the space environment round it show that the water flowing out from the comet's nucleus forms a prominent atmosphere which interacts with the constant flow of ionized particles from the sun, the so-called solar wind.

A team of scientists working at the U.S. Department of Energy's (DOE) Argonne National Laboratory and led by Northern Illinois University physicist and Argonne materials scientist Zhili Xiao has created a new material, called "rewritable magnetic charge ice," that permits an unprecedented degree of control over local magnetic fields and could pave the way for new computing technologies.

The scientists' research report on development of magnetic charge ice is published in the May 20, 2016 issue of the journal Science. With potential applications involving data storage, memory and logic devices, magnetic charge ice could someday lead to smaller and more powerful computers or even play a role in quantum computing, Xiao said. Current magnetic storage and recording devices, such as computer hard disks, contain nanomagnets with two polarities, each of which is used to represent either 0 or 1 -- the binary digits, or bits, used in computers. A magnetic charge ice system could have eight possible configurations instead of two, resulting in denser storage capabilities or added functionality unavailable in current technologies.

"Our work is the first success achieving an artificial ice of magnetic charges with controllable energy states," said Xiao, who holds a joint appointment between Argonne and NIU. "Our realization of tunable artificial magnetic charge ices is similar to the synthesis of a dreamed material. It provides versatile platforms to advance our knowledge about artificial spin ices, to discover new physics phenomena and to achieve desired functionalities for applications."

Over the past decade, scientists have been highly interested in creating, investigating and attempting to manipulate the unusual properties of "artificial spin ices," so-called because the spins have a lattice structure that follows the proton positioning ordering found in water ice.

Scientists consider artificial spin ices to be scientific playgrounds, where the mysteries of magnetism might be explored and revealed. However, in the past, researchers have been frustrated in their attempts to achieve global and local control of spin-ice magnetic charges.

To overcome this challenge, Xiao and his colleagues decoupled the lattice structure of magnetic spins and the magnetic charges. The scientists used a bi-axis vector magnet to precisely and conveniently tune the magnetic charge ice to any of eight possible charge configurations. They then used a magnetic force microscope to demonstrate the material's local write-read-erase multi-functionality at room temperature. For example, using a specially developed patterning technique, they wrote the word, "ICE," on the material in a physical space 10 times smaller than the diameter of a human hair.

Magnetic charge ice is two-dimensional, meaning it consists of a very thin layer of atoms, and could be applied to other thin materials, such as graphene. Xiao said the material also is environmentally friendly and relatively inexpensive to produce.

Although the technique presently works on just one virus, scientists say it could be adapted to detect a range of viruses that plague humans including Ebola, Zika and HIV.

"The ultimate goal is to build a cheap, easy-to-use device to take into the field and measure the presence of a virus like Ebola in people on the spot," says Jeffrey Dick, a chemistry graduate student and co-lead author of the study. "While we are still pretty far from this, this work is a leap in the right direction."

The new method is highly specific, meaning it is only sensitive to one type of virus, filtering out possible false negatives caused by other viruses or contaminants. There are two other commonly used methods for detecting viruses in biological samples, but they have drawbacks. One requires a much higher concentration of viruses, and the other requires samples to be purified to remove contaminants. The new method, however, can be used with urine straight from a person or animal.

The researchers demonstrated their new technique on a virus that belongs to the herpesvirus family, called murine cytomegalovirus (MCMV). To detect individual viruses, the team places an electrode — a wire that conducts electricity, in this case, one that is thinner than a human cell — in a sample of mouse urine. They then add to the urine some special molecules made up of enzymes and antibodies that naturally stick to the virus of interest. When all three stick together and then bump into the electrode, there's a spike in electric current that can be easily detected.

The researchers say their new method still needs refinement. For example, the electrodes become less sensitive over time because a host of other naturally occurring compounds stick to them, leaving less surface area for viruses to interact with them. To be practical, the process will also need to be engineered into a compact and rugged device that can operate in a range of real-world environments.

A key biochemical enables bacteria to repair otherwise fatal damage to their DNA, including that caused by antibiotics. That is the finding of a study.

Adjusting the action of a molecule called ppGpp (guanosine-3',5'-(bis)pyrophosphate), with future treatments may disable DNA repair in microbes to make them many times more vulnerable to existing antibiotics, say the study authors. Bacteria repeatedly exposed to the same drugs become resistant to treatment, according to the Centers for Disease Control and Prevention, with related infections linked to 23,000 deaths and 2 million illnesses each year in the United States.

"Most antibiotics have their effect, directly or indirectly, by causing damage to bacterial DNA, so finding ways to cripple DNA repair would represent a significant advance in the treatment of resistant infections," says senior study author Evgeny Nudler, PhD, the Julie Wilson Anderson Professor of Biochemistry, Department of Biochemistry and Molecular Pharmacology, NYU Langone.

"While reducing DNA repair in bacteria could help to overcome antibiotic resistance, we're also excited about the prospect of boosting DNA repair in human cells," says Nudler, also an investigator with the Howard Hughes Medical Institute. "DNA damage accumulates with age and creates risk for degenerative diseases from Alzheimer's to cancer."

The study results revolve around the delicacy of DNA molecules, the letters making up the genetic code. Experts estimate that DNA is damaged thousands of times an hour in each bacterial cell, and perhaps a million times a day in a human cell with larger, more complicated DNA chains. Sunlight and toxins do much of the damage, but the biggest culprit may be highly reactive byproducts created as cells use oxygen to turn sugar into energy.

Given that damaged DNA can result in lethal mistakes in the building of proteins that comprise vital structures and messages, cells evolved early on to have overlapping, split-second DNA repair mechanisms.

In both humans and the bacteria, a key protein complex called RNA polymerase clamps onto and ticks down the DNA chain, reading the code of DNA "letters" as it translates genetic instructions into intermediary RNA molecules on the way to building proteins. Studies in recent years have revealed that the RNA polymerase in bacteria also inspects the DNA chain for damage as it reads.

In 1997, Nudler and colleagues published a paper in Cell that found bacterial RNA polymerase, which moves down the DNA chain in one direction during normal reading, instead stops and slips backward in some instances - a process Nudler called backtracking. If RNA polymerase encounters a lesion in DNA, the theory went, backtracking could make room for repair enzymes to fly in, cut out the damaged section, and rebuild a normal chain in a process called nucleotide excision DNA repair (NER).

Indeed, in 2014, Nudler's team published work in Nature that found the NER enzyme UvrD causes RNA polymerase to backtrack in the bacterial species E. coli. The newly published paper identifies ppGpp (guanosine-3',5'-(bis)pyrophosphate), a compound related in structure to the guanine building block of DNA, as the central controller of UvrD-driven backtracking in the NER pathway. Levels of ppGpp rise rapidly as bacterial RNA polymerase encounters damage and backtracks, then drop as soon as the chain is repaired to return RNA polymerase to normal transcription. The study authors conclude that ppGpp is the sensor that enables RNA polymerase to shift back and forth between DNA transcription and repair, coupling the two processes in bacteria.

Bacteria must be able to repair DNA and preserve their genomic integrity to survive, so targeting this ability is sound strategy for drug development, says Nudler. In seeking to translate this work into new treatments that defeat antibiotic resistance, he says, the field needs to determine whether or not RNA polymerase directly communicates with enzymes that produce ppGpp, and if they do, to design specific inhibitors against them.

Researchers also hope to soon confirm that RNA polymerase backtracking enables related forms of DNA repair in human cells as theorized, an important step toward boosting human DNA repair in the future.

Scientists spot mutations that could explain how giraffes became the world’s tallest living mammals.

Call it a tall task: researchers have decoded the genomes of the giraffe and its closest relative, the okapi. The sequences, published on May 17 in Nature Communications, reveal clues to the age-old mystery of how the giraffe evolved its unusually long neck and legs.

Researchers in the United States and Tanzania analyzed the genetic material of two Masai giraffes (Giraffa camelopardalis tippelskirchi) from the Masai Mara National Reserve in Kenya, one at the Nashville Zoo in Tennessee and an okapi fetus (Okapia johnstoni) from the White Oak Conservation Center in Yulee, Florida.

“This is one more wonderful demonstration of the power of comparative genomics to connect the evolution of animal species on this planet to molecular events that we know must underpin the extraordinary diversity of life on this planet,” says David Haussler, director of the Genomics Institute at the University of California, Santa Cruz.