THE CRISPR revolution continues. The genome editing technique has now been tested in animals as a possible therapy for saving the sight of people with inherited eye diseases, and the results are looking good.
“We are certainly very excited by the potential,” says Alex Hewitt at the University of Tasmania, Australia, whose team has shown that it is possible to use CRISPR to disable genes in the eyes of mice.
The first trials of CRISPR treatments in people could start soon. In August, a group in China plans to treat lung cancer with the technique (see “First human trial“). But the team will simply remove immune cells from the body, edit their DNA to make them better at killing cancer cells, and put them back. For many other diseases, though, we need to find ways to use CRISPR to alter cells while they are still inside the body – a much greater challenge.
The appeal of using genome editing to treat eye diseases is that it is easier to get new DNA into the cells of the eye than other tissues. Several teams are exploring the possibility – the firm Editas Medicine in Cambridge, Massachusetts, has said it hopes to start testing a CRISPR treatment for a form of blindness in people next year.
It's one of the greatest mysteries of modern science: how did life begin exactly? While most scientists believe that all lifeforms evolved from a common, primitive ancestor microorganism, the details are blurry. What kinds of genes did this lifeform carry and where did it live? A new study, published in Nature Microbiology, now sheds some light on this early organism and the environment it evolved in.
Experimental scientists interested in the origins of life generally tackle the problem in two distinct ways. One is a bottom-up approach in which they try to imagine how early life might have emerged and then try to recreate the key steps in the laboratory. The alternative, a top-down approach, is to analyse or strip down modern cells to simplify them and deduce how the key stages in the evolution of complexity might have taken place.
Informaticians interested in this problem exploit the huge amounts of data emerging from the revolution in DNA sequencing. This has resulted in a sea of information about the genomes of organisms – from bacteria to humans. Hidden in this should be the echoes of DNA sequences from primitive cells – the first cells on the planet to use the modern genetic code – passed on through billions of generations.
Rice, or Oryza sativa as its scientifically known, feeds more than a third of the globe. Yet the majority of rice crops that supply 90 percent of the world come from just two domesticated varieties, japonica and indica.
Despite its importance on global palates and economies, the domestication and origins of rice have remained a mystery. The popular consensus is that japonica, the shorter stickier grain perfect for sushi, has been exclusively cultivated exclusively in northern part of East Asia. In northern parts of East Asia, consisting of Japan, Korea, and northern part of China, current rice production and consumption are japonica with very little exceptional use of indica.
Now, using new data collected samples of ancient, carbonized rice, a team of Japanese and Chinese scientists have successfully determined DNA sequences to make the first comparisons between modern and ancient rice. To do so, they used new techniques to carefully cull chloroplast DNA from ancient rice 900-2,800-years-old, which had been excavated from seven archaeological sites in Japan and Korea.
Graphene oxide has been hailed as a veritable wonder material; when incorporated into nanocellulose foam, the lab-created substance is light, strong and flexible, conducting heat and electricity quickly and efficiently.
Now, a team of engineers at Washington University in St. Louis has found a way to use graphene oxide sheets to transform dirty water into drinking water, and it could be a global game-changer.
"We hope that for countries where there is ample sunlight, such as India, you'll be able to take some dirty water, evaporate it using our material, and collect fresh water," said Srikanth Singamaneni, associate professor of mechanical engineering and materials science at the School of Engineering & Applied Science.
The new approach combines bacteria-produced cellulose and graphene oxide to form a bi-layered biofoam. A paper detailing the research is available online in Advanced Materials.
"The process is extremely simple," Singamaneni said. "The beauty is that the nanoscale cellulose fiber network produced by bacteria has excellent ability move the water from the bulk to the evaporative surface while minimizing the heat coming down, and the entire thing is produced in one shot.
Water plays a major role for our planet not only in its liquid form at the surface. In the atmosphere too, it considerably affects our lives as well as weather and climate. Clouds and rainfall are one example. Water vapor, the gaseous form of water, also plays a prominent role on Earth. It is the most important greenhouse gas in the atmosphere, without it the Earth would be a frozen planet. For climate variations, water vapor is particularly important in the stratosphere at altitudes between 15 and 50 kilometers. How much of the gas actually reaches the stratosphere mainly depends on the temperature at the transition between the lowest atmospheric layer, the troposphere, and the overlying stratosphere. This boundary layer is called the tropopause.
Now scientists of the GEOMAR Helmholtz Centre for Ocean Research Kiel, together with a colleague from Bergen (Norway), were able to demonstrate for the first time that natural fluctuations in water temperatures of the Pacific - which occur on decadal timescales - are directly related to the temperature of the tropical tropopause. "It has long been thought that human influences already affected the tropopause. However, it seems that natural variability is still the dominating factor," says Dr. Wuke Wang from GEOMAR, lead author of the study just published in the international journal Scientific Reports.
For their study, the researchers used observations for the period 1979-2013 and also climate models. "We were thus able to extend the study period to nearly 150 years. The model allows us to easily look at both human and natural influences and to separate their impacts from each other," explains Prof. Dr. Katja Matthes, climate researcher at GEOMAR and co-author of the study.
A well-known climatic phenomenon is the so-called Pacific Decadal Oscillation (PDO). "This natural variation with decadal timescale leads to anomalously high or low water temperatures of the Pacific," explained Dr. Wang. The PDO influences the climate and ecosystems in the Pacific region and also the global mean temperature of the Earth.
Conducting the first large-scale, genome-wide analyses of ancient human remains from the Near East, an international team led by Harvard Medical School has illuminated the genetic identities and population dynamics of the world's first farmers.
The concentric bubbles, which comprise what researchers call a triple-bubble, are actually three supernova remnants, shells of gas and dust that form following the explosion of a star. This is the first known case of three supernova remnants nesting one inside the other, said the researchers from the Institute of Astrophysics of the Canary Islands (IAC), who made the discovery. The above illustration shows what a cross section of the three rings might look like if scientists could get a closer look.
The shells provide a unique opportunity to study the remains of these stellar explosions, as well as the the interstellar medium, which is the gas and dust that lies between stars, John Beckman, co-author of the new study, said in a news release. Beckman is an astrophysicist with the Spanish National Resource Council and IAC. "We can measure how much matter there is in a shell, approximately a couple of hundred times the mass of the sun in each of the shells," he said. [Supernova Explosion Seen in Nearby Galaxy (Video)]
"Evidence from an ancient lunar rock suggests that the moon once harbored a long-lived dynamo — a molten, convecting core of liquid metal that generated a strong magnetic field 3.7 billion years ago. The findings point to a dynamo that lasted much longer than scientists previously thought, and suggest that an alternative energy source may have powered the dynamo. “The moon has this protracted history that’s surprising,” says co-author Benjamin Weiss, an associate professor of planetary science at MIT. “This provides evidence of a fundamentally new way of making a magnetic field in a planet a new power source.”
The paper is the latest piece in a puzzle that planetary scientists have been working out for decades. In 1969, the Apollo 11 mission brought the first lunar rocks back to Earth — souvenirs from Neil Armstrong and Buzz Aldrin’s historic moonwalk. Since then, scientists have probed the rocky remnants for clues to the moon’s history. They soon discovered that many rocks were magnetized, which suggested that the moon was more than a cold, undifferentiated pile of space rubble. Instead, it may have harbored a convecting metallic core that produced a large magnetic field, recorded in the moon’s rocks."
A team of Brazilian astronomers, led by Denilso Camargo of the Federal University of Rio Grande do Sul in Porto Alegre, has discovered seven new embedded clusters located unusually far away from the Milky Way's disc. The findings, presented in a paper published July 3 on arXiv.org, could provide new insights on star cluster formation.
Embedded clusters are stellar clusters encased in an interstellar dust or gas, consisting of extremely young stars. They are crucial for astronomers to better understand star formation and early stellar evolution. Studying these clusters could reveal the origin of stellar masses as well as the origin and evolution of protoplanetary disks, where planet formation processes take place.
In the Milky Way galaxy, most of embedded clusters lie within the thin disc less than 1,000 light years from the galactic midplane, especially in the spiral arms. However, Camargo and his team detected two young stellar clusters earlier this year, and now, after spotting seven more, suggest that they could be more common on the outskirts of the galaxy than previously thought.
People can detect flashes of light as feeble as a single photon, an experiment has demonstrated — a finding that seems to conclude a 70-year quest to test the limits of human vision.
The study, published in Nature Communications on 19 July1, “finally answers a long-standing question about whether humans can see single photons — they can!” says Paul Kwiat, a quantum optics researcher at the University of Illinois at Urbana–Champaign. The techniques used in the study also open up ways of testing how quantum properties — such as the ability of photons to be in two places at the same time — affect biology, he adds.
“The most amazing thing is that it’s not like seeing light. It’s almost a feeling, at the threshold of imagination,” says Alipasha Vaziri, a physicist at the Rockefeller University in New York City, who led the work and tried out the experience himself.
A highly sensitive chemical sensor based on Raman spectroscopy and using nitrogen-doped graphene as a substrate was developed by an international team of researchers working at Penn State. In this case, doping refers to introducing nitrogen atoms into the carbon structure of graphene. This technique can detect trace amounts of molecules in a solution at very low concentrations, some 10,000 times more diluted than can be seen by the naked eye.
Raman spectroscopy is a widely adopted identification technique used in chemistry, materials science and the pharmaceutical industry to detect the unique internal vibrations of various molecules. When a laser light irradiates crystals or molecules, it scatters and shifts colors. That scattered light can be detected in the form of a Raman spectrum, which serves almost as a fingerprint for every Raman-active irradiated system.
"Basically, different colors in the visible spectrum will be associated to different energies," said Mauricio Terrones, professor of physics, chemistry and materials science at Penn State, who led the research. "Imagine each molecule has a particular light color emission, sometimes yellow, sometimes green. That color is associated with a discrete energy."
The team chose three types of fluorescent dye molecules for their experiments. Fluorescent dyes, which are frequently used as markers in biological experiments, are particularly hard to detect in Raman spectroscopy because the fluorescence tends to wash out the signal. However, when the dye is added to the graphene or N-doped graphene substrate, the photoluminescence—fluorescence—is quenched.
"A combined team of researchers from Massachusetts General Hospital/Harvard Medical School in the U.S. and Xuanwu Hospital, Capital Medical University in China has found that when neurons in the mouse brain suffer mitochondrial damage astrocytes donate some of their own to help repair them. In their paper published in the journal Nature, the team describes how they conducted a series of tests designed to find out whether astrocytes donate mitochondria material and if so, whether it helps to restore health to damaged neurons.
Astrocytes are star-shaped glial cells that surround neurons, providing insulation and support—prior studies have shown that they are involved in carrying out removal of dead material. In this new effort, the researchers started with the results of experiments conducted by a team at Columbia University four years ago that showed that bone marrow stem cells provided mitochondria to damaged lung cells to help them recover—they wanted to know if the same might be true for astrocytes and neurons.
To find out, the researchers engineered mice to produce extra amounts of a signaling enzyme called CD38. They then found that when rodent astrocytes were mixed with them, they expelled some degree of mitochondrial material—neurons added to the mix were then found to absorb some of the mitochondrial material."
Researchers at NCMM, the Centre for Molecular Medicine Norway at University of Oslo, and Oslo University Hospital have shown exactly how sensitive the bacteria’s transport system is.
"We have identified a nano-sized magnesium pump," explains researcher Jens Preben Morth.
The researchers manipulated an E. coli bacterium so that it overproduced using its own magnesium pump.
"The pump was isolated in the bacterium’s cell membrane. There are different methods of achieving this type of isolation. We could either divide up the proteins according to size, or we could examine the positive or negative electric charges of the proteins on the surface of the pump."
"As soon as the pump was isolated, we were able to work with the pure protein without disruption from other proteins," Morth explains.
With the aid of enzyme kinetics, a special method of analysing chemical reactions, the researchers were able to obtain a calculation of the sensitivity to magnesium.
In addition to the pump itself, the researchers also discovered unique lipid components that assist the bacteria in this process.
Lipid components are building blocks for the cell membrane just as amino acids are for proteins. The cell membrane is the cell’s husk.
Polylactic acid, or PLA, is a biodegradable polymer commonly used to make a variety of products from disposable cups to medical implants to drug delivery systems. A team of Brown University researchers has shown that by treating PLA at various temperatures and pressures, they can induce a new polymer phase in the material -- one that could possibly decrease the rate at which it degrades.
"It's an exciting finding from the standpoint of basic science, in that we've found a new polymer phase and have identified a method for inducing it," said Edith Mathiowitz, a professor of medical science and engineering at Brown. "In terms of applications, the polymer we worked with in this study has many uses, and we believe the properties we have discovered now will allow us to make it better."
Tilted pillars, cracked steps, and sliding stone canopies in a number of 7th-century A.D. temples in northwest India are among the telltale signs that seismologists are using to reconstruct the extent of some of the region's larger historic earthquakes.
In their report published online July 27 in Seismological Research Letters, Mayank Joshi and V.C. Thakur of the Wadia Institute of Himalayan Geology show how the signs of destructive earthquakes are imprinted upon the ancient stone and wooden temples.
The temples in the Chamba district of Himachal Pradesh, India lie within the Kashmir "seismic gap" of the Northwest Himalaya range, an area that is thought to have the potential for earthquakes magnitude 7.5 or larger. The new analysis extends rupture zones for the 1905 Kangra earthquake (magnitude 7.8) and the 1555 Kashmir earthquake (possibly a magnitude 7.6 quake) within the Kashmir gap.
The type of damage sustained by temples clustered around two towns in the region—Chamba and Bharmour—suggests that the Chamba temples may have been affected by the 1555 earthquake, while the Bharmour temples were damaged by the 1905 quake, the seismologists conclude.
The epicenter of the 1555 earthquake is thought to be in the Srinagar Valley, about 200 kilometers northwest of Chamba. If the 1555 earthquake did extend all the way to Chamba, Joshi said, "this further implies that the eastern Kashmir Himalaya segment between Srinagar and Chamba has not been struck by a major earthquake for the last 451 years."
Washington State University researchers have mapped the damage of ultraviolet radiation on individual units of DNA, opening a new avenue in the search for how sunlight causes skin cancer and what might be done to prevent it.
"This technique gives you almost a satellite-view image of all the damage across the genome," said John Wyrick, a WSU geneticist specializing in DNA repair and corresponding author of a study out this week in the journal Proceedings of the National Academy of Sciences.
Wyrick and WSU colleagues Peng Mao, Michael Smerdon and Steven Roberts irradiated yeast cells and looked for patterns of damage at the level of individual base pairs, the DNA building blocks whose order serves as an organism's blueprint. Some parts of the genome were more damaged than others, said Wyrick, offering clues to how and why damage occurs.
Wyrick used a large DNA model made of interlocking pieces of plastic to explain. The model shows the classic double helix of DNA strands going in opposite directions with nucleotides linking to each other across the strands to form base pairs.
Inside the nucleus of a human cell, a single unit of DNA will stretch to some 6 billion nucleotides. Ostensibly to save space, they are spooled around structures called histones to form units called nucleosomes.
Someday, chemically protective suits made of fabric coated in self-healing, thin films may prevent farmers from exposure to organophosphate pesticides, soldiers from chemical or biological attacks in the field and factory workers from accidental releases of toxic materials, according to a team of researchers.
"Fashion designers use natural fibers made of proteins like wool or silk that are expensive and they are not self-healing," said Melik C. Demirel, professor of engineering science and mechanics. "We were looking for a way to make fabrics self-healing using conventional textiles. So we came up with this coating technology."
The procedure is simple. The material to be coated is dipped in a series of liquids to create layers of material to form a self-healing, polyelectrolyte layer-by-layer coating.
This coating is deposited "under ambient conditions in safe solvents, such as water, at low cost using simple equipment amenable to scale-up," the researchers report today (July 25) online in ACS Applied Materials & Interfaces.
A very unusual new species of zoantharian surprised Drs Takuma Fujii and James Davis Reimer, affiliated with Kagoshima University and University of the Ryukyus.
The scientists stumbled upon a solitary individual polyp while conducting SCUBA surveys around the southern Japanese island of Okinawa. They noticed that the creatures were buried almost completely in the soft sediment of the seafloor. It was only their oral disks and tentacles that were protruding above the surface.
Generally, most known zoantharians are colonial (hence their common name of 'colonial anemones'), and many dwell in shallow waters of subtropical and tropical regions, where their large colonies can be found on coral reefs.
Researchers at MIT and the University of California at San Diego (UCSD) have recruited some new soldiers in the fight against cancer — bacteria.
In a study appearing in the July 20 of Nature, the scientists programmed harmless strains of bacteria to deliver toxic payloads. When deployed together with a traditional cancer drug, the bacteria shrank aggressive liver tumors in mice much more effectively than either treatment alone.
The new approach exploits bacteria’s natural tendency to accumulate at disease sites. Certain strains of bacteria thrive in low-oxygen environments such as tumors, and suppression of the host’s immune system also creates favorable conditions for bacteria to flourish.
“Tumors can be friendly environments for bacteria to grow, and we’re taking advantage of that,” says Sangeeta Bhatia, who is the John and Dorothy Wilson Professor of Health Sciences and Electrical Engineering and Computer Science at MIT and a member of MIT’s Koch Institute for Integrative Cancer Research and its Institute for Medical Engineering and Science.
"Each year, Siberian rivers pump vast quantities of fresh water into the Arctic Ocean. And together with other sources of fresh water around the Arctic, they could disrupt vital ocean circulation that drive weather systems throughout Europe and North America.
(See side story)
While computer models can simulate these ocean circulation systems, they need observations to validate their results and to identify where the fresh water has come from--glaciers, sea ice, or rivers. And this is important if you want to understand how these various contributions of fresh water into the north Atlantic might change in the future."
Her computer, Karin Strauss says, contains her "digital attic"—a place where she stores that published math paper she wrote in high school, and computer science schoolwork from college.
She'd like to preserve the stuff "as long as I live, at least," says Strauss, 37. But computers must be replaced every few years, and each time she must copy the information over, "which is a little bit of a headache."
It would be much better, she says, if she could store it in DNA—the stuff our genes are made of.
Strauss, who works at Microsoft Research in Redmond, Washington, is working to make that sci-fi fantasy a reality.
She and other scientists are not focused in finding ways to stow high school projects or snapshots or other things an average person might accumulate, at least for now. Rather, they aim to help companies and institutions archive huge amounts of data for decades or centuries, at a time when the world is generating digital data faster than it can store it.
Solar wind forms the energy source for aurora explosions. How does the Earth's magnetosphere take in the energy of the solar wind? An international team led by Hiroshi Hasegawa and Naritoshi Kitamura (ISAS/JAXA) analyzed data taken by the US-Japan collaborative mission GEOTAIL and NASA's MMS satellites and revealed that the interaction between the magnetic fields of Earth and the Sun, or more precisely the phenomenon known as magnetic reconnection, can feed the aurora explosions.
Artist concept of the GEOTAIL and the MMS missions to study how does the Earth's magnetosphere take in the energy of the solar wind. (Credits: ISAS/JAXA)
The region of outer space near Earth, also called geospace, is not a peaceful region. For example, solar wind, a fast flow of charged particles driven by the Sun's magnetic field that blows against the Earth, is harmful for lives on the Earth. Fortunately, our planet has a shield. The Earth's magnetosphere provides an invisible protection from the solar wind.
The interaction between the solar wind and Earth's magnetosphere can cause various phenomena, such as aurora.
According to the prevailing theory, an aurora explosion involves four main processes:
(1) The energy of the solar wind enters the Earth's magnetosphere, (2) The tail of the magnetosphere stores the energy, (3) The stored energy is released quickly and transferred to the plasma particles, (4) These plasma particles move toward the Earth's polar region along magnetic field lines, and finally cause an aurora explosion.
Magnetic reconnection is believed to be the key mechanism involved in the entry (1) and release (3) of the energy of the solar wind.
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