Amazing Science

With ever-lowering sequencing costs, genomic sequencing projects have been initiated for a wide range of organisms, but the vast majority of genomes currently exist in the form of draft assemblies. Considering that an important driving force behind sequencing projects is the acquisition of a complete catalogue of genes, an important task lies in assessing the integrity and completeness of the assembled genome or transcriptome.

Researchers from the SIB Swiss Institute of Bioinformatics have developed an assessment tool that quantifies genomic data completeness in terms of expected gene content. The method (BUSCO) is published in Molecular Biology and Evolution.

The oxygenation of Earth’s atmosphere was thanks, in part, to iron and silica particles in ancient seawater, according to a new study by geomicrobiologists at the University of Alberta. But these results solve only part of this ancient mystery.

Early organisms called cyanobacteria produced oxygen through oxygenic photosynthesis, resulting in the oxygenation of Earth’s atmosphere. But cyanobacteria needed protection from the sun’s UV radiation in order to evolve. That’s where iron and silica particles in ancient seawater come in, according to Aleksandra Mloszewska, a former PhD student who conducted this research under the supervision of Kurt Konhauser, professor in the Department of Earth and Atmospheric Sciences, and George Owttrim, professor in the Department of Biological Sciences.

The research team characterized the effect of UV stress on cyanobacteria and the degree of radiation through the seawater medium through a combination of microbiological, spectroscopic, geochemical and modeling techniques. Their results show that the presence of high silica and iron concentrations in early sea water allowed for the formation of iron-silica precipitates that remained suspended in the ocean for extended periods of time.

“In effect, the iron-silica particles acted as an ancient ‘sunscreen’ for the cyanobacteria, protecting them from the lethal effects of direct UV exposure,” said Konhauser, the senior author from UAlberta. “This was critical on the early Earth before a sufficiently thick ozone layer was established that could enable marine plankton to spread across the globe, as is the case today.”

New approach for fabricating soft materials at the millimeter scale paves the way to a new generation of flexible microrobots for medical and environmental tasks

Roboticists are envisioning a future in which soft, animal-inspired robots could be safely deployed in difficult-to-access natural and human-made environments, such as in delicate surgical procedures in the human body, or in spaces too small and unpredictable to be conquered with rigid robots or too dangerous for humans to work with rigid robots in. Centimeter-sized soft robots have been created, but thus far it has not been possible to fabricate multifunctional flexible robots that can move and operate at smaller size scales.

A team of researchers at Harvard's Wyss Institute for Biologically Inspired Engineering, Harvard John A. Paulson School of Engineering and Applied Sciences (SEAS), and Boston University now has overcome this challenge by developing an integrated fabrication process that enables the design of soft robots on the millimeter scale with micrometer-scale features. To demonstrate the capabilities of their new technology, they created a robotic soft spider -- inspired by the millimeter-sized colorful Australian peacock spider -- from a single elastic material with body-shaping, motion, and color features. The study is published in Advanced Materials.

"The smallest soft robotic systems still tend to be very simple, with usually only one degree of freedom, which means that they can only actuate one particular change in shape or type of movement," said Sheila Russo, Ph.D., co-author of the study. Russo helped initiate the project as a Postdoctoral Fellow in Robert Wood's group at the Wyss Institute and SEAS and now is Assistant Professor at Boston University. "By developing a new hybrid technology that merges three different fabrication techniques, we created a soft robotic spider made only of silicone rubber with 18 degrees of freedom, encompassing changes in structure, motion, and color, and with tiny features in the micrometer range."

Wood, Ph.D., is a Core Faculty member and co-leader of the Bioinspired Soft Robotics platform at the Wyss Institute and the Charles River Professor of Engineering and Applied Sciences at SEAS. "In the realm of soft robotic devices, this new fabrication approach can pave the way towards achieving similar levels of complexity and functionality on this small scale as those exhibited by their rigid counterparts. In the future, it can also help us emulate and understand structure-function relationships in small animals much better than rigid robots can," he said.

In their Microfluidic Origami for Reconfigurable Pneumatic/ Hydrolic (MORPH) devices, the team first used a soft lithography technique to generate 12 layers of an elastic silicone that together constitute the soft spider's material basis. Each layer is precisely cut out of a mold with a laser micromachining technique, and then bonded to the one below to create the rough 3D structure of the soft spider.

Radio waves reveal person’s presence in a room, even beyond the sensor’s line of sight

Relief may be on the horizon for anyone who has ever jumped around a room like a jack-in-the-box to get motion-sensing lights to turn back on. A new motion sensor based on metamaterials is sensitive enough to monitor a person’s breathing. In a pair of new studies, researchers from Duke University and Institut Langevin, France, have shown that patterns made by radio waves can detect a person’s presence and location anywhere inside a room. The findings appeared recently in Scientific Reports and Aug. 6 in the Physics Review Letters.

This new motion-sensing technology could lead to new smart home devices for energy savings, security, healthcare and gaming.

“Energy companies don’t love infrared motion detectors because they have lots of problems,” said David R. Smith, the James B. Duke Professor of Electrical and Computer Engineering at Duke. “The amount of space they can cover is limited, a person has to be within their line of sight to be detected, and probably everyone has had the experience where the lights have gone off because they’ve sat still for too long. Radio waves can get around all of these limitations.”

In their initial paper published earlier this year, the researchers took advantage of patterns created by radio waves bouncing around a room and interfering with themselves. These unique patterns change with the slightest perturbation of the room’s objects, allowing a sensitive antenna to detect when something moves in or enters the room. And by comparing how these patterns change over time, they can also be used to detect cyclical movements like a fan blade turning—or even a person breathing.

In the latest paper, the team shows that with a bit of training, the system can also extract information necessary to locate objects or people in a space. The demonstration system was taught the pattern of radio waves scattered by a triangular block placed in 23 different positions on a floor. That calibration is enough not only to distinguish between the learned 23 scenarios, but to also distinguish the positions of three identical blocks placed in any one of 1,771 possible configurations.

The technology works by taking advantage of the way radio waves behave in an enclosed room. Their ability to continuously reflect off multiple surfaces creates complex interference patterns throughout a room. In the past, this complexity has been an obstacle for systems trying to locate the origin of a signal. But Smith and his colleagues have now shown that this same complexity can be tapped to detect movement and locate objects within a room.

Key aspects of the aging of human cells can be reversed by new compounds developed at the University of Exeter, research shows. In a laboratory study of endothelial cells – which line the inside of blood vessels – researchers tested compounds designed to target mitochondria (the “power stations” of cells). In the samples used in the study, the number of senescent cells (older cells that have deteriorated and stopped dividing) was reduced by up to 50%.

The Exeter team also identified two splicing factors (a component of cells) that play a key role in when and how endothelial cells become senescent. The findings raise the possibility of future treatments not only for blood vessels – which become stiffer as they age, raising the risk of problems including heart attacks and strokes – but also for other cells.

“As human bodies age, they accumulate old (senescent) cells that do not function as well as younger cells,” said Professor Lorna Harries, of the University of Exeter Medical School. “This is not just an effect of ageing – it’s a reason why we age. “The compounds developed at Exeter have the potential to tweak the mechanisms by which this ageing of cells happens. We used to think age-related diseases like cancer, dementia and diabetes each had a unique cause, but they actually track back to one or two common mechanisms. This research focuses on one of these mechanisms, and the findings with our compounds have potentially opened up the way for new therapeutic approaches in the future.

“This may well be the basis for a new generation of anti-degenerative drugs.” Professor Harries said the goal was to help people stay healthier for longer. She added: “This is about health span and quality of life, rather than merely extending lifespan.”

The Baltic Sea is home to some of the world’s largest dead zones, areas of oxygen-starved waters where most marine animals can’t survive. But while parts of this sea have long suffered from low oxygen levels, a new study by a team in Finland and Germany shows that oxygen loss in coastal areas over the past century is unprecedented in the last 1500 years. The research is published today in the European Geosciences Union journal Biogeosciences.

According to the researchers, human-induced pollution, from fertilizers and sewage running off the countries surrounding the Baltic into the sea, is the main driver of recent oxygen loss in the region’s coastal waters. The spread of low-oxygen areas can have dire consequences for the environment and for local populations as it can reduce fish yields and even lead to massive mortality of marine animals.

“The Baltic was strongly impacted by human nutrient inputs in the 20th century and is still experiencing the legacy of those inputs today,” says Tom Jilbert, an assistant professor at the University of Helsinki, Finland, who took part in the research. But despite recent measures to reduce the release of polluting nutrients, the researchers write in the new study that they found “no evidence of recovery” from oxygen depletion in the Archipelago Sea, a coastal area between mainland Finland and Sweden that is part of the Baltic.

A reason, they say, may be climate change. Since warm waters are less effective at holding oxygen, “global warming is likely to exacerbate oxygen depletion,” says Sami Jokinen, a researcher at the University of Turku, Finland, and lead-author of the Biogeosciences study. Jilbert adds: “Climate change was not the main cause of the current dead zone, but it is an important factor delaying the recovery.”

To find out what fueled oxygen loss in the past and what role climate played, the team drilled and studied a 4-meter-long sediment core from the seafloor in the Archipelago Sea. This allowed them to see, for the first time, how oxygen levels changed in this area over the past 1500 years. This period includes the Medieval Climate Anomaly, a time of warmer climate but low nutrient pollution from 900 to around 1350, as well as modern times.

Professor Ishikawa Komuro's Tokyo lab is better known for robot hands that can dribble and catch balls and spin pencils between their fingers. Now, two researchers have taken this speedy sensing tech and applied it to the ripping of paper books.

Books are different from other kinds of media, like music and movies – it's very hard to get them into a computer. There is no equivalent of CD or DVD rippers like iTunes or Handbrake. This not only makes piracy laborious, it also stops you from turning your own books into e-books.

This high-speed scanner changes that, at least if you have the room and tech skills to build one. By using a high-speed camera that shoots at 500 frames per second, lab workers Takashi Nakashima and Yoshihiro Watanabe can scan a 200-page book in under a minute. You just hold the book under the camera and flip through the pages as if shuffling a deck of cards. The camera records the images and uses processing power to turn the odd-shaped pictures into flat, rectangular pages on which regular OCR (optical character recognition) can be performed.

The technique is unlikely to be coming to the home anytime soon (although ripping a book by flipping it in front of your notebook's webcam would be pretty awesome), but it could certainly speed up large scanning efforts like Google's book project.

Focused ultrasound from outside the body can safely and reversibly open the blood–brain barrier in patients with Alzheimer’s disease, researchers in Canada have shown for the first time. The technique could offer a way to bypass the barrier and deliver therapeutic compounds to the brain that can treat Alzheimer’s and other neurologic disorders.

The blood–brain barrier separates the brain’s blood vessels from brain tissue. It regulates what can and can’t enter the brain, protecting it from toxins and pathogens in the blood. But it also presents a problem for the treatment of neurological diseases, because it blocks therapeutic drugs.

“A typical monoclonal antibody is several thousands of times larger than a compound that can readily get across the blood–brain barrier,” explains Nir Lipsman, a neurosurgeon and scientist at Sunnybrook Health Sciences Centre in Toronto. “This size restriction may limit the effectiveness of otherwise useful compounds.”

In a phase 1 safety trial, described in Nature Communications, Lipsman and his colleagues first gave five patients with mild-to-moderate Alzheimer’s an intravenous injection of microbubbles, and then focused low-frequency ultrasound on a region in the right frontal lobe of their brains. Real-time imaging in combination with medical dye showed that the blood–brain barrier opened in all patients, and had closed again within 24 hours.

A month later, four of the patients received the treatment again – with the same results. (The fifth patient developed a respiratory illness between the two procedures, which the researchers say was unrelated to the study.) None of patients showed any signs of brain hemorrhaging or swelling, or cogitative decline, on the days of the procedures or during follow-up examinations.

The ultrasound is delivered by a helmet-like device consisting of 1024 transducers, with a frequency of 220 kHz, and is guided by an MRI scan to the target area of the brain. The ultrasound causes the microbubbles to vibrate and rapidly increase and decrease in size, which physically separates the cells of the blood–brain barrier.

“The blood–brain barrier is a complex structure comprised of, among other things, a thin layer of cells held together by tight junctions,” explains Lipsman. “Opening the blood–brain barrier with ultrasound is a physical pulling apart of those tight junctions, and creating space between the cells provides compounds circulating in the blood with better access to the brain across the blood–brain barrier.”

What are neural networks?

Artificial neural networks are a form of machine-learning algorithm with a structure roughly based on that of the human brain. Like other kinds of machine-­learning algorithms, they can solve problems through trial and error without being explicitly programmed with rules to follow. They’re often called “artificial intelligence” (AI), and although they are are much less advanced than science-fiction AIs, they can control self-driving cars, deliver ads,recognize faces, translate texts and even help artists design new paintings – or createbizarre new paint colours with names like “sudden pine” and “sting grey”.

How do neural networks work?

Neural networks were first developed in the 1950s to test theories about the way that interconnected neurons in the human brain store information and react to input data. As in the brain, the output of an artificial neural network depends on the strength of the connections between its virtual neurons – except in this case, the “neurons” are not actual cells, but connected modules of a computer program. When the virtual neurons are connected in several layers, this is known as deep learning.

A learning process tunes these connection strengths via trial and error, attempting to maximize the neural network’s performance at solving some problem. The goal might be to match input data and make predictions about new data the network hasn’t seen before (supervised learning), or maximizing a “reward” function to discover new solutions to a problem (reinforcement learning). The architecture of a neural network, including the number and arrangement of its neurons, or the division of labour between specialized sub-modules, is usually tailored to each problem.

Why have I heard so much about them?

The growing availability of cheap cloud computing and graphics processing units (GPUs) are key factors behind the rise of neural networks, making them both more powerful and more accessible. The availability of large amounts of new training data, such as databases of labelled medical images, satellite images or customer browsing histories, has also helped boost the power of neural networks. In addition, the proliferation of new open-source tools such as Tensorflow, Keras and Torch has helped make neural networks accessible to programmers and non-programmers from a variety of fields. Finally, success begets success: as the value of neural networks in commercial applications becomes more apparent, developers have sought new ways of exploiting their capabilities – including using them to aid scientific research.

What are neural networks good at?

They’re great at matching patterns and finding subtle trends in highly multivariate data. Crucially, they make progress towards their goal even if the programmer doesn’t know how to solve the problem ahead of time. This is useful for problems with solutions that are complex or poorly understood. In image recognition, for example, the programmer may not be able to write down all the rules for determining whether a given image contains a cat, but given enough examples, a neural network can determine for itself what the important features are. Similarly, a neural network can learn to identify the signature of a planetary transit without being told which features are important. All it needs is a set of sample starlight curves that correspond to planetary transits, and another set of light curves that do not. This makes neural networks an unusually flexible tool, and the fact that neural network frameworks come in “flavours” specialized for tasks such as classifying data, making predictions, and designing devices and systems only adds to their flexibility.

However, Mars does not retain enough carbon dioxide that could practically be put back into the atmosphere to warm Mars, according to a new NASA-sponsored study. Transforming the inhospitable Martian environment into a place astronauts could explore without life support is not possible without technology well beyond today's capabilities.

Although the current Martian atmosphere itself consists mostly of carbon dioxide, it is far too thin and cold to support liquid water, an essential ingredient for life. On Mars, the pressure of the atmosphere is less than one percent of the pressure of Earth's atmosphere. Any liquid water on the surface would very quickly evaporate or freeze.

Proponents of terraforming Mars propose releasing gases from a variety of sources on the Red Planet to thicken the atmosphere and increase the temperature to the point where liquid water is stable on the surface. These gases are called "greenhouse gases" for their ability to trap heat and warm the climate.

"Carbon dioxide (CO2) and water vapor (H2O) are the only greenhouse gases that are likely to be present on Mars in sufficient abundance to provide any significant greenhouse warming," said Bruce Jakosky of the University of Colorado, Boulder, lead author of the study appearing in Nature Astronomy July 30.

Although studies investigating the possibility of terraforming Mars have been made before, the new result takes advantage of about 20 years of additional spacecraft observations of Mars. "These data have provided substantial new information on the history of easily vaporized (volatile) materials like CO2 and H2O on the planet, the abundance of volatiles locked up on and below the surface, and the loss of gas from the atmosphere to space," said co-author Christopher Edwards of Northern Arizona University, Flagstaff, Arizona.

The researchers analyzed the abundance of carbon-bearing minerals and the occurrence of CO2 in polar ice using data from NASA's Mars Reconnaissance Orbiter and Mars Odyssey spacecraft, and used data on the loss of the Martian atmosphere to space by NASA's MAVEN (Mars Atmosphere and Volatile Evolution) spacecraft.

"Our results suggest that there is not enough CO2 remaining on Mars to provide significant greenhouse warming were the gas to be put into the atmosphere; in addition, most of the CO2 gas is not accessible and could not be readily mobilized. As a result, terraforming Mars is not possible using present-day technology," said Jakosky.

Carbon materials (CMs) exhibit great application potentials in diverse fields due to their high electric conductivity, good chemical stability, and unique microstructure. Traditionally, CMs were prepared by the carbonization of low-vapor-pressure natural products or synthetic polymers. But they suffer from some distinct disadvantages, such as difficulty in tailoring the microstructures and chemical compositions of the obtained products, or complicated and slow polymerization processes. Up to now, it is still a significant challenge to develop a facile, low-cost, and highly controllable method for preparing CM with desired constituents and structures in a large scale.

A research team led by Prof. YU Shuhong and Prof. LIANG Haiwei from the University of Science and Technology of China (USTC) proposes a simple, effective, and versatile method to prepare a series of functional CMs from small organic molecules (SOMs) by a transition metal assisted carbonization process. This work was published on Science Advances entitled as "Transition metal-assisted carbonization of small organic molecules toward functional carbon materials" on July 27th (Science Advances 2018, 4, eaat0788).

Preparation of CMs. (A) Schematic illustration of the preparation process of CMs. (B) Structures of the investigated SOMs for the CM preparation. Small organic molecules (SOMs) as precursors for preparing CMs have some distinct advantages, such as common availability, relatively low cost, and diverse element species with various contents. Previous efforts on the transformation of SOMs into CMs almost relied on harsh synthesis conditions, e.g. pyrolysis in sealed reactors, chemical vapor deposition, or salt-melt-based ionothermal carbonization, due to the high volatility of SOMs at evaluated temperatures. To address this, the research group led by Prof. YU Shuhong and Prof. LIANG Haiwei develops a method of transition metal assisted carbonization of SOMs.

The transition metals can catalyze the preferential formation of thermally stable intermediate polymeric structures and thus avoid the direct sublimation of SOMs during the heating process, which guarantees the successful preparation of CMs with high carbon yield. Researchers have found that totally fifteen SOMs and nine TMSs can be employed as carbon precursors and catalysts respectively for preparing CMs. Besides, two hard templates can used in the method to enhance the porosity of obtained CMS. All of research results indicate that the method is a simple, effective, and versatile method to prepare CMs.

The prepared CM exhibited three different prominent microstructures (including bamboo-like multi-walled carbon nanotube, micrometer-sized nanosheets and irregular particles) that were highly dependent on the molecular structures of SOMs. Besides, the CMs possessed high specific surface areas, large pore volumes, abundant heteroatoms as well as highly graphitic structures. As a results, the CM showed great application potentials for heterogeneous catalysis, e.g. selective oxidization of ethylbenzene and hydrogenation of nitrobenzene, and electrocatalysis, e.g. hydrogen evolution reaction and oxygen reduction reaction. This work opens a new window for the synthesis of CMs with desired constituents and structures.

Animals often rely on their sense of smell to locate food. It's a law of nature: the first one to reach a food source has a better chance of surviving than those who do not. But how exactly does their brain translate scent and then navigate towards it?

In new research published this week in Nature Communications, Hebrew University of Jerusalem neurogeneticist Dr. Alon Zaslaver and his team reveal the complex mathematical calculations that animals -- even those as simple as worms -- do to find their next meal.

Think of the game "Hot or Cold?," says Zaslaver. "Imagine you're in a huge dark house and a chocolate cake has just been taken out of the oven. To find the cake, you'll probably sniff around to see what direction the cake scent is coming from and begin walking in that direction."

Turns out, worms employ this "Hot or Cold" computation in their search for food -- but with an added twist. First, a neural cell picks up the scent of food and set the worm on a course. As long as the scent intensity keeps getting stronger, this neural cell will remain active and direct the worm to keep moving forward. Otherwise, it will instruct the worm to stop and look for a better path.

But how does it calculate that better path? Enter a second neural cell which acts like Waze's "recalculating route" function. This second cell senses "derivatives," meaning it calculates whether the odor intensity is positive, and getting "hotter," or negative, and getting "colder." If the cell detects a negative derivative, it understands that it's getting further from the chocolate cake and needs to recalculate its route. This cell constantly computes new scent data to detect whether the current odor intensity is getting stronger or weaker and charts a path based on these new differential measurements. With a negative reading, the second cell will tell the worm to chart a new path whereas a positive one will tell it to stay the course.

This combination is a winning one, according to Zaslaver and Hebrew University graduate students Eyal Itskovits and Rotem Ruach. The two-part system of charting a course based on an initial scent measurement and then conducting follow up checks (all the time comparing them to the original measurement) to compute whether scent intensity numbers are going up or down is not only an impressive feat for a worm but a very smart and effective method in the search for food.

"These worms teach us an important lesson," shares Zaslaver. When looking to solve a problem, a quick solution is often attractive. "However, we need a backup system in place that monitors whether we are indeed moving in the 'right' direction, even if that new path differs from the one we originally set out on," concluded Dr. Zaslaver.

A team of Columbia researchers show that a widely used chemical tracer, combined with a cutting-edge microscope, can track metabolic changes within the living cells of animals.

Imaging tools like X-rays and MRI have revolutionized medicine by giving doctors a close up view of the brain and other vital organs in living, breathing people. Now, Columbia University researchers report a new way to zoom in at the tiniest scales to track changes within individual cells.

Described in the latest issue of Nature Communications, the tool combines a widely used chemical tracer, D2O, or heavy water, with a relatively new laser-imaging method called stimulated Raman scattering (SRS). The technique's potential applications include helping surgeons quickly and precisely remove tumors, to helping to detect head injuries and developmental and metabolic disorders.

"We can use this technology to visualize metabolic activities in a wide range of animals," said the study's senior author Wei Min, a chemistry professor at Columbia University. "By tracking where and when new proteins, lipids and DNA molecules are made, we can learn more about how animals develop and age, and what goes wrong in the case of injury and disease."

The breakthrough involves the use of heavy water as a chemical tracer. Made by swapping water's hydrogen atoms with their heavier relative, deuterium, heavy water looks and tastes like regular water and in small doses (no more than five tablespoons for humans) is safe to drink. Once metabolized by cells in the body, heavy water is incorporated into newly made proteins, lipids and DNA, where the deuterium forms chemical bonds with carbon.

When these carbon-deuterium bonds are hit with light, they vibrate at varying frequencies, the researchers discovered, allowing each macromolecule to be identified as a protein, lipid or DNA. From these frequency signatures, they could track the growth of new proteins, lipids and DNA in the animal's brain, skin, gut and other organs.

FOXP2, a gene implicated in affecting speech and language, is held up as a textbook example of positive selection on a human-specific trait. But in a new paper, researchers challenge this finding. Their analysis of genetic data from a diverse sample of modern people and Neanderthals saw no evidence for recent, human-specific selection of FOXP2 and revises the history of how we think humans acquired language.

"A paper published in 2002 (Enard et al., Nature 418, 869-872) claimed there was a selective sweep relatively recently in human evolutionary history that could largely account for our linguistic abilities and even help explain how modern humans were able to flourish so rapidly in Africa within the last 50-100,000 years," says senior author Brenna Henn, a population geneticist at Stony Brook University and UC Davis. "I was immediately interested in dating the selective sweep and re-analyzing FOXP2 with larger and more diverse datasets, especially in more African populations."

Henn says that when the original 2002 work was done, the researchers did not have access to the modern sequencing technology that now provides data on whole genomes, so they only analyzed a small fraction of the FOXP2 gene in about 20 individuals, most of whom were of Eurasian descent. "We wanted to test whether their hypothesis stood up against a larger, more diverse dataset that more explicitly controlled for human demography," she says.

FOXP2 is highly expressed during brain development and regulates some muscle movements, aiding in language production. When the gene isn't expressed, it causes a condition called specific language impairment in which people may perform normally on cognitive tests but cannot produce spoken language. FOXP2 has also been shown to regulate language-like behaviors in mice and songbirds.

"In the past five years, several archaic hominid genomes have been sequenced, and FOXP2 was among the first genes examined because it was so important and supposedly human specific," says first author Elizabeth Atkinson of Stony Brook University and the Broad Institute of Harvard and MIT. "But this new data threw a wrench in the 2002 paper's timeline, and it turns out that the FOXP2 mutations we thought to be human specific, aren't."

Effective therapeutics to counteract the formation of amyloid plaques in Alzheimer's disease and type 2 diabetes are not yet available. Scientists have now come a little bit closer to a solution: They have described a new class of designed macrocyclic peptides that are highly potent inhibitors of amyloid formation.

Amyloid plaques, which are protein deposits, play a crucial role in the development of Alzheimer's disease and type 2 diabetes. Several teams of scientists around the world are working on finding ways to prevent amyloid plaque formation in the human brain.  

The research team of Aphrodite Kapurniotu, Professor for Peptide Biochemistry (TUM) has been working on an idea for some time now in collaboration with the teams of Professor Martin Zacharias (TUM), Professor Gerhard Rammes (TUM Rechts der Isar Hospital) and Professor Jürgen Bernhagen (Institute for Stroke and Dementia Research (ISD) at Ludwig Maximilian University (LMU)). The researchers present now macrocyclic peptides (MCIPs) as potent inhibitors of amyloid formation; they reported their results in the journal "Angewandte Chemie”.

In its new study, the team presents macrocyclic peptides, developed as a new class of amyloid inhibitors.  "We have discovered an MCIP that is stable in human blood plasma and can also overcome the human blood-brain barrier in an in vitro cell culture model," explains Professor Kapurniotu. She adds: "So far we were 'only' able to demonstrate these properties in the test tube - thus further research is necessary. But these are two highly desirable properties for inhibitors of Alzheimer's amyloid." 

TUM has already applied for a patent for the newly developed macrocyclic peptides. "They could be a good alternative to the currently pursued antibody-based approaches as therapeutics against Alzheimer's amyloid plaque formation because they are easy to produce, have promising properties and, due to their peptidic nature, they will be significantly cheaper than antibodies," says Professor Kapurniotu. 

"Therefore, further investigations are now planned to verify whether the MCIPs are also effective in in vivo models.  Furthermore, the MCIPs could also be suitable as templates for the development of small molecule peptidomimetics (molecules mimicking peptide chains), which might also find application as anti-amyloid drugs in Alzheimer's and type 2 diabetes.

Trees are talking and sharing resources right under your feet, using a fungal network nicknamed the Wood Wide Web. CrowdScience presenter Marnie Chesterton reveals how plants use the system to support their offspring, while others hijack the network to sabotage their rivals.

In a dramatic restructuring, two teams have created versions with vastly reduced chromosome counts.

For millions of years, brewer’s yeast and its close relatives have packed their DNA into 16 distinct chromosomes. Now, two teams have used CRISPR gene-editing to stuff all of yeast’s genetic material — save a few non-essential pieces — into just one or two chromosomes. The feat represents the most dramatic restructuring yet of a complex genome and could help scientists understand why organisms split their DNA over many chromosomes. And, to the researchers’ surprise, the changes had little effect on most functions of the yeast (Saccharomyces cerevisiae). “That was the biggest shocker — that you can just get away with this and yeast seem to shrug its shoulders,” says Jef Boeke, a geneticist at New York University whose team jammed the yeast genome onto a pair of chromosomes1. A China-based group used a different technique to make yeast with one ‘super-chromosome’2. Both teams report their findings in Nature on 1 August, 2018.

Genetics 101

Yeast belongs to the eukaryotes, the branch of life that includes humans, plants and animals and whose cells store genetic material in a membrane-bound nucleus. But the number of chromosomes that eukaryotes have varies wildly and seems to have no correlation with the amount of genetic information they possess. In humans, genetic material is spread over 46 chromosomes, whereas male jack jumper ants (Myrmecia pilosula) have just 1. Single-celled brewer’s yeast — whose genome, at 12 million DNA letters long, is hundreds of times shorter than that of humans — boasts 16 chromosomes. “We don’t know why they have such different numbers,” says Zhongjun Qin, a molecular biologist at the Chinese Academy of Sciences’ Shanghai Institute of Plant Physiology and Ecology, whose team created the lone-chromosome yeast strain. “I thought it was probably random.”

Qin and his colleagues reasoned that if an organism’s chromosome count were down to chance rather than an underlying rule of nature, there should be no reason that a yeast cell shouldn’t be viable with 1 chromosome instead of 16. Researchers in the past had fused two3 — even four4 — yeast chromosomes together, and another team split the 16 chromosomes into 33. All products had viable cells5. But no one had ever performed such extreme genetic surgery as Qin and his colleagues set out to do several years ago. Their initial attempts ended in failure — until they turned to the genome-editing tool CRISPR–Cas9, which is adept at excising specific DNA sequences. Qin and his colleagues used CRISPR to remove DNA at telomeres, the ends of chromosomes that protect them from degrading. They also snipped out centromeres, sequences in the middle that are important to DNA replication.

These changes paved the way for a fit of tidying that would make home-organization guru Marie Kondo proud. The researchers first fused two chromosomes, then joined this product to another one, and in successive rounds, to another and another — until they were left with a lone-chromosome yeast strain.

30,000 years ago, a ground squirrel burrowed out a spot for itself, about 10 inches in diameter at its widest, where it brought back seeds and other grassy and fruited plants to nibble on. The place where the squirrel chose to make its burrow is now known as Siberia, and the burrow is close to 100 feet below the surface and in a layer of permafrost.

The squirrel, of course, is long gone. But tiny roundworms, a type of nematode, that also made their home there have lasted those tens of thousands of years, frozen and immobile. Now, though, scientists in Russia have revived them, making these worms—all of them female worms—the first multicellular organisms to have survived being frozen in Arctic permafrost.

The permafrost layer of the polar parts of the world contains all sorts of tiny creatures, including bacteria, algae, yeasts, and amoebas, as well as moss spores and seeds. After spending thousands of years in deep freeze, these bits of life are thawing out, as the poles heat up and the permafrost softens. Previously, scientists found that a giant virus that they named Pithovirus was still viable after 30,000 years.

In a new paper, published in Doklody Biological Sciences, the scientists describe how they analyzed 300 samples of permafrost. Of those, only two samples had viable nematodes in them. One came from the squirrel burrow; another came from a different permafrost deposit, part of a core drilling near the Alazeya River. That sample was about 42,000 years old.

The samples contained two different types of roundworms, Panagrolaimus detritophagus and Plectus parvus. The scientists let them thaw out, and once they had, the worms seemed ready to go on with their lives, eating and moving, which is about the extent of what ringworms do with themselves.

A team of physicists from the University of Nebraska-Lincoln, Stanford University and Europe has captured the clearest glimpse yet of a photochemical reaction—the type of light-fueled molecular transformations responsible for photosynthesis, vision and the ozone layer. The researchers precisely recorded how the atomic nuclei and chemical bonds of a five-atom molecule responded when being struck by a laser. Appearing in the June 6 edition of the journal Science, the team's study marks the culmination of a years-long effort to advance the quality of "molecular movies" from that of a rudimentary stop-motion animation to a high-definition motion picture.

"People have been modeling these things for a long time, but there was really no good way to test if these models were correct," said Nebraska's Martin Centurion, a Susan J. Rosowski Associate Professor of physics and astronomy. "There is now a way to compare, in detail, what is happening experimentally with what our models would predict. "The reason that's very important is because there are many, many different molecules, and you can excite them with many, many different wavelengths (of light). There's no way you could ever do experiments on everything, so at some point, you need some sort of model that's reliable."

Though refining those models will demand years of work and many studies, Centurion said, the Science study has established a new benchmark for using experimental data to better understand photochemical reactions on the atomic scale. That comprehension could eventually yield important applications, he said, whether in the form of solar cells that can store the energy they collect or custom molecules better at catalyzing the reactions that can produce renewable fuels.

This newborn black hole belched a fleeting yet astonishingly intense flash of gamma rays known as a gamma-ray burst (GRB) toward Earth, where it was detected by NASA's Neil Gehrels Swift Observatory on 19 December 2016.

While the gamma rays from the burst disappeared from view a scant seven seconds later, longer wavelengths of light from the explosion—including X-ray, visible light, and radio—continued to shine for weeks. This allowed astronomers to study the aftermath of this fantastically energetic event, known as GRB 161219B, with many ground-based observatories, including the National Science Foundation's Very Large Array.

The unique capabilities of the Atacama Large Millimeter/ submillimeter Array (ALMA), however, enabled a team of astronomers to make an extended study of this explosion at millimeter wavelengths, gaining new insights into this particular GRB and the size and composition of its powerful jets.

"Since ALMA sees in millimeter-wavelength light, which carries information on how the jets interact with the surrounding dust and gas, it is a powerful probe of these violent cosmic explosions," said Tanmoy Laskar, an astronomer at the University of California, Berkeley, and a Jansky Postdoctoral Fellow of the National Radio Astronomy Observatory. Laskar is lead author of the study, which appears in the Astrophysical Journal.

These observations enabled the astronomers to produce ALMA's first-ever time-lapse movie of a cosmic explosion, which revealed a surprisingly long-lasting reverse shockwave from the explosion echoing back through the jets. "With our current understanding of GRBs, we would normally expect a reverse shock to last only a few seconds. This one lasted a good portion of an entire day," Laskar said.

A reverse shock occurs when material blasted away from a GRB by its jets runs into the surrounding gas. This encounter slows down the escaping material, sending a shockwave back down the jet. Since jets are expected to last no more than a few seconds, a reverse shock should be an equally short-lived event. But that now appears not to be the case.

"For decades, astronomers thought this reverse shock would produce a bright flash of visible light, which has so far been really hard to find despite careful searches. Our ALMA observations show that we may have been looking in the wrong place, and that millimeter observations are our best hope of catching these cosmic fireworks," said Carole Mundell of the University of Bath, and co-author of the study.

Its new open-source software will help developers experiment with the machines, including Google’s own super-powerful quantum processor.

Quantum computers are still in their infancy, but builders of the exotic machines want to encourage software developers to experiment with them. Programming the circuits on quantum machines is a real challenge . Instead of standard digital bits, which represent either 1 or 0, quantum computers use “qubits,” which can be in both states at once thanks to a phenomenon known as superposition. Qubits can also influence one another even if they’re not physically connected. Moreover, they stay in their delicate quantum state for no longer than the blink of an eye. Exploiting them requires completely different software, and only a small band of developers currently has the highly specialized knowledge to write such programs.

Google wants to help change that. It has just released Cirq, a software toolkit that lets developers create algorithms without needing a background in quantum physics. Cirq is an open-source initiative, which means anyone can access and modify the software. Google likens it to its popular TensorFlow open source toolkit that has made it easier to build machine-learning software. For now, developers can use Cirq to create quantum algorithms that run on simulators. But the goal is to have it help build software that will run on a wide range of real machines in the future.

The tech giant has also released Open Fermion-Cirq, a toolkit for creating algorithms that simulate molecules and properties of materials. Indeed, chemistry is among the applications in which quantum computers are likely to be of most use in the short term. One of the companies that worked with Google on Cirq’s development is Zapata Computing, whose early focus is on software for chemistry and materials ("The world’s first quantum superstore—or so it hopes—is here”).

Another Google partner is Quantum Benchmark, which helps people assess the performance of different kinds of quantum hardware for various applications. “Cirq gives us an accessible platform for providing our tools to users,” says Joseph Emerson, the firm’s CEO and founder.

There are other open-source initiatives already under way that let developers build code for some existing quantum machines, but Google’s move is significant because the company has been at the forefront of developing powerful quantum processors like the Bristlecone chip in the image above, which holds the record for number of qubits (see the qubit counter here). 

Researchers working in the quantum field say that sharing code openly will help foster a more vibrant developer community, just as it has in other areas of software. “We’re at such an early stage in the development of quantum computing that it’s to everyone’s advantage that things are done out in the open,” says Andrew Childs, who is co-director of the Joint Center for Quantum Information and Computer Science at the University of Maryland.