Culture

A new tool that simultaneously compares 1.4 million genetic sequences can classify how species are related to each other at far larger scales than previously possible. Described today in Nature Biotechnology by researchers from the Centre for Genomic Regulation in Barcelona, the technology can reconstruct how life has evolved over hundreds of millions of years and makes important inroads for the ambition to understand the code of life for every living species on Earth.

Protecting Earth's biodiversity is one of the most urgent global challenges of our times. To steward the planet for all life forms, humanity must understand the way animals, fungi, bacteria and other organisms have evolved and how they interact amongst millions of other species. Sequencing the genome of life on Earth can unlock previously unknown secrets that yield fresh insights into the evolution of life, while bringing new foods, drugs and materials that pinpoint strategies for saving species at risk of extinction.

The most common way scientists study these relationships is by using Multiple Sequence Alignments (MSA), a tool that can be used to describe the evolutionary relationships of living organisms by looking for similarities and differences in their biological sequences, finding matches among seemingly unrelated sequences and predicting how a change at a specific point in a gene or protein might affect its function. The technology underpins so much biological research that the original study describing it is one of the most cited papers in history.

"We currently use multiple sequence alignments to understand the family tree of species evolution," says Cédric Notredame, a researcher at the Centre for Genomic Regulation in Barcelona and lead author of the study. "The bigger your MSA, the bigger the tree and the deeper we dig into the past and find how species appeared and separated from each other.

"What we've made lets us dig ten times deeper than what we've been able to do before, helping us to see hundreds of millions of years into the past. Our technology is essentially a time machine that tells us how ancient constraints influenced genes in a way that resulted in life as we know today, much like how the Hubble Space Telescope observes things that happened millions of years ago to help us understand the Universe we live in today."

Researchers can use MSA to understand how certain species of plants have evolved to be more resistant to climate change, or how particular genetic mutations in one species makes them vulnerable to extinction. By studying a living organism's evolutionary history, scientists may come up with and test new ideas to stave off the collapse of entire ecosystems.

Technological advances have made sequencing cheaper than ever before, resulting in increasingly large datasets with more than a million sequences for scientists to analyse. Some ambitious endeavours, like the Earth BioGenome Project, may run to the tens of millions. Researchers have not been able to take full advantage of these enormous datasets because current MSAs cannot analyse more than 100,000 sequences with accuracy.

To evaluate the scale-up potential of MSA, the authors of the paper used Nextflow, a cloud-computing software developed in-house at the Centre for Genomic Regulation. "We spent hundreds of thousands of hours of computation to test our algorithm's effectiveness," says Evan Floden, a researcher at the CRG who also led on developing the tool. "My hope is that in combining high-throughput instrumentation readouts with high-throughput computation, science will usher in an era of vastly improved biological understanding, ultimately leading to better outcomes for consumers, patients and our planet as a whole."

"There is a vast amount of 'dark matter' in biology, code we have yet to identify in the unexplored parts of the genome that is untapped potential for new medicines and other benefits we can't fathom," concludes Cédric. "Even seemingly inconsequential organisms may play a pivotal role in furthering human health and that of our planet, such as the discovery of CRISPR in archaea. What we have built is a new way of finding the needles in the haystack of life's genomes."

Researchers from the University of Barcelona (UB) and the August Pi i Sunyer Biomedical Research Institute (IDIBAPS) found a new molecular mechanism involved in the regulation of the cholesterol movement in cells, an essential process for a proper cell functioning.

The study, published in the journal Cellular and Molecular Life Sciences, also identifies the protein Annexin A6 (AnxA6) as a key factor in this regulation and as a potential therapeutical target against diseases that are caused by the accumulation of cholesterol and other lipids in endosomes, such as the Niemann-Pick disease type C1, a minority genetic disease with no cure that causes hepatic damage and a type of dementia.

The study is led by Carles Enrich and Carles Rentero, lecturers at the unit of Cell Biology in the Department of Biomedicine of the Faculty of Medicine and Health Sciences at the UB and the CELLEX Biomedical Research Center (IDIBAPS-UB). This is the result of six years of research and a collaboration with Thomas Grewal, from the University of Sydney; Elina Ikonen, from the University of Helsinki, and the research group on Lipids and Cardiovascular Pathology of the Biomedical Research Institute at Hospital Sant Pau.

Study with the CRISPR/Cas9 editing technology

Cholesterol is essential in the organization of membranes and it also modulates the vesicular trafficking, basic mechanisms for the cell functioning. To coordinate and regulate the balance, or homeostasis in cholesterol, cells have developed a molecular machinery, which is not fully understood yet. "The understanding of these mechanisms is very important to treat diseases in which there is an accumulation of cholesterol and other lipids which cause serious physiological alterations in the liver, spleen and especially the nervous system", note Carles Enrich and Carles Rentero.

One of such diseases is Niemann-Pick type C1, caused by a mutation in the NPC1 gene, which causes the accumulation of cholesterol in the cell interior of the endosome. In order to study this mechanism, researchers used the CRISPR/Cas9 genetic editing technique to block a molecule -AnxA6 protein- in cells with the phenotype of the disease. The effect of such block resulted in the release of the endosome cholesterol, showing the essential role of this protein in the regulation of cholesterol transfer.

Increasing membrane contact sites

The results of the study also show this release occurred thanks to a significant increase of membrane contact sites (MCS), nanometric structures that can be seen through electronic microscopy. According to the authors, these membrane contact sites are just a few inside the cells of the affected patients, therefore, silencing AnxA6 induces the creation of MCS, stops the effect of the NPC1 gene mutation and redirects cholesterol towards other cell compartments, returning to cell normality.

"Results could help treating the clinical impact of the accumulation of cholesterol in Niemann-Pick and about twelve more diseases, among which are different types of cancer (pancreas, prostate, breast), in which the lipidic metabolism plays a fundamental role", note the researchers.

A new paradigm in the study of the cholesterol cell transport

The membrane contact sites being involved in the cholesterol transport is a pioneering result in this field, since researchers thought -so far- that lipid transport was carried out through vesicles and a type of specialized proteins. "We do not know much about the functioning and dynamics of membrane contact sites, but this study goes together with recent ones and shows MCS are a new paradigm for the understanding of the regulation, transport and homeostasis of lipids, cholesterol and calcium", conclude the researchers.

Cooperation - working together or exchanging services for the benefit of everyone involved - is a vital part of human life and contributes to our success as a species. Often, rather than helping specific others, we work for the good of the community, because this helps our friends and family who are part of the group, or because we share in the benefits with everyone else. However, even though the whole group can benefit when people work together, not everyone might be willing to contribute equally. One way for humans to cooperate is by exchanging information: from gossiping and storytelling to teaching and news reporting, we rely on some individuals possessing knowledge and sharing this knowledge for the greater good.

Like humans, many non-human primates live in close-knit social groups where individuals cooperate to their mutual benefit. As in our own species, information can be an important commodity for them: primates use a variety of calls to let each other know where they are going and whether they have found food. One of the most important messages to transmit is the presence of a threat: whenever a leopard or eagle has been spotted, calling for backup can help confuse predators or fight them off. While these calls help others in the group, they also clearly benefit the caller. This is different when the threat remains in one spot: many snakes, especially vipers, do not seem to actively hunt monkeys, but if stepped on, they can still bite and kill. However, once a monkey knows where the snake is, she herself is usually safe; giving a loud call to tell everyone about the snake costs time, and potentially exposes her to other dangers. Hence not all monkeys in a group will call out. So, why do some individuals call when they detect a threat that is not dangerous to themselves anymore?

Researchers from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, made use of the reaction of sooty mangabeys to snakes to understand how this monkey species cooperates by sharing information. Mangabeys live in the tropical Taï National Park, Côte d'Ivoire, in large groups (often consisting of more than 100 members), where individuals often cannot see everything that is happening to other group members, including their kin and friends. While mangabeys often find venomous snakes in the forest, it is hard to predict and film these encounters, so the researchers created realistic snake models out of mesh and paper-mâché and hid them where the mangabeys would pass. By filming the reaction of all the monkeys that would see the snake, the team could identify who called, when, and how often. This way, they hoped to understand whether monkeys called simply because they were scared of the snake, to show off how fearless they are, to warn their friends and family, or whether they share information widely across the group when it was likely that others who followed them did not know about the threat.

Over the course of a year, the researchers worked with a wild mangabey community within the context of the Taï Chimpanzee Project, conducting two to four experiments per month. Using snake models and up to five different camera angles, they were able to get detailed recordings of the behavior of each mangabey that came close enough to see the snake. All group members are used to human observers and cameras, and their family ties, friendships, and dominance relations are known, enabling the researchers to analyze in detail whether the presence and arrival of specific group members would prompt alarm calls. Typically, after monkeys find a snake, they will stick around and observe it for a time, while other individuals follow them and also inspect the snake. Between the first and last individual to encounter the threat, there is a line of monkeys that could call; however, not all of them do, and the question is whether the ones that call differ from the ones that do not.

"What surprised us, in both natural snake encounters and in our experiments, was how different individuals reacted to the threat: most individuals did not show strong reactions unless they almost stepped on the snake, and they would usually just call once or twice and then move on. On the other hand, we had a small number of individuals who called almost every time they saw a snake", says Alex Mielke, lead author of the study. "When we look at all experiments, though, a clear pattern emerges: mangabeys did not call specifically for their kin or friends, or ignorant group members. Individuals called when few others were around the snake or nobody had called in a while, effectively broadcasting the location of the snake to the general public when there is a chance that the information gets lost. This creates a system where no individual has to invest too much - one or two calls are enough before moving on - but because the threat is regularly re-advertised, the danger for following individuals is removed."

These results showcase how the social system an animal lives in changes how information needs to be transmitted: In mangabeys, groups are large but all group members travel together, so an individual in the front of the group who spots a snake and calls out can probably assume that their sister in the back of the group will also get the message. The information gets re-iterated by those between them. In chimpanzees, where the community splits into subgroups while moving around, the same research group in Leipzig could show that individuals wait close to the snake and inform arriving group members who are potentially ignorant of the danger.

The behavior of the mangabeys also illuminates how cooperation could have evolved in a group-setting. Even though the monkeys do not individually warn their kin and allies, if they find a snake and pass this information on to the rest of the group they can rely on others to contribute the same way, so that all group members (including family) are informed and hence less likely to get injured or killed by the snake. Similar mechanisms can be important in other situations where primates work together to achieve a goal, when defending their territory or acquiring food together. This study thus further illuminates the extent to which cooperation shapes social behavior in our primate cousins.

A team led by Brazilian researcher Elis Eleutherio, professor at the Federal University of Rio de Janeiro, in partnership with Tiago Outeiro, at University of Goettingen, Germany, made important progress in understanding the conformation and accumulation of certain proteins involved in lateral amyotrophic sclerosis (ALS).

"We believe protein accumulation is an important hallmark of ALS, and we still do not understand why the protein misbehaves and aggregates during the disease", explains Prof. Elis Eleutherio.

Amyotrophic lateral sclerosis (ALS) is a progressive and devastating neurodegenerative disorder affecting 1 to 3 individuals in 100.000, and is more prevalent in people between 55-75 years of age. The disease affects, primarily, a population of neurons known as 'motor neurons'. Patients suffer from irreversible motor paralysis, and become incapable of speaking, swallowing, or breathing as the disease progress.

Most ALS cases are sporadic, with no defined genetic origin, and only the minority is familial, with known associated genetic alterations. Certain familial forms of ALS (fALS) are associated with genetic alterations in the gene encoding for a protein known as superoxide dismutase 1 (Sod1), that cause alterations in the folding and function of the protein.

The study, published in the journal Proceedings of the National Academy of Sciences (PNAS), allowed scientists to understand the interaction between normal and mutant protein, which causes alteration of protein accumulation in the cell, but also impairs the function of Sod1 protein, thus contributing to the development of the disease. For the group, this discovery opens new perspectives for the treatment of ALS.

Sod1 is a protein that plays a role, among others, in the protection against oxidative damage in our cells. In some ALS cases, altered Sod1 protein accumulates inside neuronal cells and, researchers believe, cause damage to the neurons, leading to their death. Importantly, normal Sod1 protein, present in sporadic cases of ALS, can also misfold and accumulate, suggesting this is a central problem in ALS.

In the study, the researchers used simple experimental models, such as bakery yeast, used to make beer, wine and bread, and human cells, in order to better understand the context of protein aggregation in the disease. They also used a strategy that mimics the genetic context of fALS, where most patients carry one copy of the normal Sod1 protein, and one copy carrying a genetic alteration. "In patients, we think that the presence of a mutant copy of Sod1 alters the behavior of the normal copy", explains Dr. Aline Brasil, the first author of the study.

"By taking advantage of novel genetic manipulation tools, and powerful molecular imaging approaches, that enable the direct visualization of protein complexes in the cell (a technique known as BiFC), we were able to detect 'hetero-complexes' formed by normal and abnormal (mutant) Sod1 protein", said Prof. Tiago Outeiro, leader of the German team that participated in the study.

The research opens novel perspectives for therapeutic intervention, that the authors hope to continue to explore in the near future, such as the specific removal of mutant Sod1 protein.

"In a time when the scientific and education system in Brazil suffers from uncertainty, it is important to demonstrate that we can be competitive and conduct research that will contribute to society and may, ultimately, help change the lives of those affected by such devastating diseases", Prof. Elis Eleutherio concludes.

Hunger and undernutrition are still widespread problems in Africa. At the same time, overweight, obesity, and related chronic diseases are also on the rise. Recent research suggested that the growth of supermarkets contributes to obesity in Africa, because supermarkets tend to sell more processed foods than traditional markets. However, previous studies only looked at data from adults. New research shows that supermarkets are not linked to obesity in children, but that they instead contribute to reducing child undernutrition. The results were recently published in the journal Global Food Security.

For the research, agricultural and food economists from the University of Göttingen in Germany collected data from over 500 randomly selected children in Kenya over a period of three years. The data show that children from households with access to a supermarket are significantly better nourished than children in the reference group. Purchase of food in a supermarket has particularly positive effects on child growth and height, even after controlling for age, income, and other relevant factors. The most widely used indicator of chronic child undernutrition is child "stunting" which means impaired growth and development as shown by low height for their age.

"At first, we were surprised about the results, because it is often assumed that supermarkets in Africa primarily sell unhealthy snacks and convenience foods", says Dr Bethelhem Legesse Debela, the study's first author. "But our data show that households using supermarkets also consume healthy foods such as fruits and animal products more regularly." Professor Matin Qaim, the leader of the research project adds: "Not all processed foods are automatically unhealthy. Processing can improve the hygiene and shelf-life of foods. Poor households in Africa in particular often have no regular access to perishable fresh produce."

The findings clarify that modernization of the food retail sector can have multilayered effects on nutrition, which need to be analyzed in the local context. The United Nations pursues the goal of eradicating global hunger in all its forms by 2030. According to the study authors, "this can only be achieved when we better understand the complex relations between economic growth, nutrition, and health and identify and implement locally-adapted policies".

UNIVERSITY PARK, Pa. -- People who eat wildebeests, wart hogs and other wild African animals may be at risk for contracting potentially life-threatening diseases, according to an international team of researchers. The team analyzed samples of bushmeat -- meat derived from wildlife -- in the Western Serengeti in Tanzania and identified several groups of bacteria, many of which contain the species that cause diseases such as anthrax, brucellosis and Q fever.

"Many people in Sub-Saharan Africa regularly consume bushmeat, up to two-to-five times per week, which means that millions of people could be exposing themselves to these dangerous pathogens," said Robab Katani, assistant research professor of global health, Huck Institutes of the Life Sciences, Penn State. "And the number is growing. Bushmeat consumption and trade has been increasing because of growing food insecurity, low cost compared to other meat products, and perceived medicinal value, among other things."

The problem is not confined to Africa either, she added.

"Bushmeat is smuggled illegally into the U.S. and Western Europe on a daily basis," she said. "For example, Charles de Gaulle airport in France intercepts five tons per week. This practice puts even more people at risk for contracting dangerous bacterial diseases."

To quantify the risk associated with eating and handling bushmeat, the researchers first needed identify the bacteria present in the meat. They obtained 56 fresh and processed bushmeat tissue samples from the predominant large herbivores -- including buffalo, zebra and giraffe -- of the Serengeti National Park and surrounding areas. They collected these samples within three ecologically distinct regions, called Bunda, Serengeti and Tarime, within the Serengeti ecosystem. Using a broad genetic sequencing technique, called 16S rRNA sequencing, they analyzed the microbiomes -- all of the microorganisms -- present in each sample.

The team found 27 different groups -- called phyla -- of bacteria in the samples, with Firmicutes, Proteobacteria, Cyanobacteria and Bacteroidetes being the most abundant. All of these groups contain both pathogenic species. Within those phyla the researchers detected DNA signatures of bacteria within the genera Bacillus, Brucella and Coxiella, which contain the species that cause anthrax, brucellosis and Q fever, respectively. The team's findings on the microbiome analysis of the samples appear today (Dec. 2) in Scientific Reports.

"Anthrax, brucellosis and Q fever can be deadly if left untreated," said Vivek Kapur, professor of microbiology and infectious diseases, Huck Distinguished Chair in Global Health and associate director of the Huck Institutes of Life Sciences, Penn State. "Antibiotics work, but most people don't have access to them. We've encountered many people who've tragically lost a family member to these otherwise preventable diseases."

The researchers also found a particularly high prevalence of bacteria in the genus Clostridium, whose species cause diseases like botulism and tetanus. In fact, the microbiomes of wildebeest collected during the dry season comprised more than 78 percent Clostridial species.

"Understanding which bacteria are present in bushmeat is necessary to establishing a plan to help curb outbreaks of these dangerous diseases," said Kapur. "Our data suggest the presence of certain disease-causing species, and our objective now is to use species-level analyses to fine-tune our focus on specific pathogens and accurately assess and mitigate the associated risk of disease outbreaks. Ultimately, our goal is also to help build capabilities for rapid diagnosis and risk mitigation in the countries of origin to address these risks before they become a problem globally."

Particularly in the film industry, the rapid development of display technologies has created an urgent need to develop fast, automatic gamut mapping algorithms. An article published on 14 November in the advanced online edition of the IEEE Transactions on Pattern Analysis and Machine Intelligence presents significant progress in this area.

A screen's colour range is the set of colours it can reproduce. Wider screen formats can present more vivid and intense colours. The mapping of gamut or range is the process of adapting colours to the range of the screen to fully exploit the colour palette of the display device on which the content is shown, while preserving the artistic intent of the creator of the original content.

The goal of gamut mapping for film is to develop algorithms (gamut mapping algorithms, GMA) that reproduce the original content of the film insofar as possible respecting the artist's vision, because this is an important feature that all GMA should have in order to be adopted by the film industry. "Therefore, for this study we performed psychophysical experiments to compare the performance of the proposed GMA with other methods in film conditions using a digital film projector (Barco-DP-1200 [75]) and a large projection screen", the authors point out in their article.

Software that mimics the neural processes of the human visual system

"In this paper, we propose a new framework based on biological visual models. Our method both reduces and extends the gamut, is of low computational complexity, produces results that are free from artefacts, and outperforms the most advanced methods according to psychophysical tests", explain the authors Syed Waqas Zamir, researcher at the Inception Institute of Artificial Intelligence, Abu Dhabi (UAE) and PhD from UPF (2017), and Javier Vázquez-Corral and Marcelo Bertalmío, researchers at the Department of Information and Communication Technologies (DTIC) at UPF..

In this paper, the authors present the details of a new method based on neural models that come from scientific knowledge about human vision. As Bertalmío, coordinator of the Image Processing for Enhanced Cinematography (IP4EC) research group explains, "instead of working on the hardware, improving lenses and sensors, we resort to the latest knowledge of neuroscience and the existing models of visual perception to develop software methods that mimic the neural processes of the visual system applying these methods to the images harnessed by a regular camera".

"Our experiments also highlight the limitations of existing objective metrics to the problem of gamut mapping and provides solutions", they add.

A research team from the Universities of Manchester, Nottingham, and UCL evaluating a service delivered by pharmacists since 2011 have calculated it will save the English NHS around £651 million.

They also show it will allow patients to enjoy around 278,700 more quality adjusted life years, a long term measure of disease burden used by health economists.

Since the inception of the New Medicine Service (NMS), the team say community pharmacists in over 12,000 pharmacies have delivered 5.7 million consultations between 2011 and 2018.

NMS works with patients who are prescribed medicines for asthma and COPD, high blood pressure, Type 2 diabetes or are taking anticoagulant therapies such as warfarin.

The NMS, in which pharmacists follow up patients with a telephone call after 7 to 14 days, and then again 2-3 weeks later, aims to support people taking a new medicine prescribed by their doctor.

The NMS came about after the discovery by psychologists working with the research team that the decision to adhere to a medicine is often made in the first 2 weeks of it being prescribed.

The team developed the ideas behind the NMS in the late 1990s, and were influential in the decision by the Department of Health to start the scheme.

The team of pharmacists, GPs, patients, policymakers, health economists and health services researchers, ran a trial of the NMS, with 504 people in 46 pharmacies.

Their paper in 2016 showed that 11% more patients adhered to their medication regimen after 10 weeks when they used the NMS.

The present study, published in BMJ Quality and Safety, also followed up the same patients after 26 weeks, and showed that an extra 9% still stick their regimen, when they used the NMS.

However, because 66 people dropped out of the study after 10 weeks, the figures were not statistically significant. The cost to the NHS of paying community pharmacists to deliver NMS (£25) was absorbed by small reductions in other NHS contact-related costs.

The economic evaluation concluded that in the long-term, this improvement in adherence would still lead to reduced overall costs to the NHS and improved long-term health for patients.

Lead researcher from The University of Manchester Professor Rachel Elliott said: "The New Medicine Service has proved to be a simple, deliverable intervention which helps patients and saves the NHS money.

"The NMS workload had been absorbed into busy community pharmacists' daily routines alongside existing responsibilities with no extra resources or evidence of reduction in other responsibilities.

"It's not always easy for doctors to determine if their patients are sticking to their drugs regimen.

"As health care professionals, we sometimes underestimate the problems patients face around their medicines. Patients often decide to stop taking their pills when they see no difference in their symptoms, experience side effects, have found information from other sources such as the internet, or can't afford prescription charges.

Professor Elliott added: "The results of this longer-term follow-up suggests NMS helps people when the medicine is started, and some effect lasts for quite a long time. However, reviewing medicines-taking, for example every six months, is probably needed to continue the support patients need around taking medicines.

"And we think clinical pharmacists, now often based in primary care doctor's practices may be able to integrate NMS, and follow-up support, into their role.

"In addition to that, there are other medicines which we know patients are less likely to adhere to: for example, from talking to patient groups we know that mental health medicines, eyedrops and statins could also be candidates for the NMS."

Dr Boyd, Co-project lead from the University of Nottingham said "The way patients access healthcare is changing. This work highlights the valuable contribution pharmacists make in protecting valuable NHS budget and improving outcomes for patients."

Researchers have produced the first physics-based quantifiable evidence that thinning ice shelves in Antarctica are causing more ice to flow from the land into the ocean.

Their findings have been published in Geophysical Research Letters.

Satellite measurements taken between 1994 and 2017 have detected significant changes in the thickness of the floating ice shelves that surround the Antarctic Ice Sheet. These shelves buttress against the land-based ice, holding them in place like a safety band.

While it has been suggested that the thinning ice shelves were responsible for a direct loss of ice from the land-based ice sheet into the ocean, there was no actual evidence linking data and physics that could demonstrate this, until now.

Researchers in the UK and US have now undertaken the first continent-wide assessment of the impact the thinning ice shelves are having on the flow of ice in Antarctica.

They were particularly interested in seeing how much ice flowed across the 'grounding line'. This is the point where the land-based ice sheet meets the sea-based ice shelves.

They used a state-of-the-art ice-flow model developed at Northumbria University, UK, and newly available measurements of changes in the geometry of ice shelves to calculate the changes in grounded ice flow.

When the modelled results were compared with those obtained by satellites over the last 25 years, the researchers found what they described as 'striking and robust' similarities in the pattern of ice flowing from the ice sheet into the ocean.

The largest impact was found in West Antarctica, which already makes a significant contribution to sea level change. The largest changes are taking place around the Pine Island and Thwaites glaciers. On Pine Island Glacier, evidence of these changes could be seen almost 100 miles (150km) inland, upstream of the grounding line.

Hilmar Gudmundsson, Professor of Glaciology and Extreme Environments at Northumbria University led the study. He said there has been a long-standing question as to what was causing the changes we have observed in land-based ice over the last 25 years, and that while the thinning of the floating ice-shelves had been suggested as a reason, the idea had never been put to the test before now.

"I found it striking how well our modelled changes agree with the pattern of observed mass loss," he said.

"There are other processes in play as well, but we can now state firmly that the observed changes in ice-shelves do cause significant changes over the grounded ice, speeding up its flow into the ocean."

A critical element of the findings was the speed at which the ice flowed from the sheet into the ocean as a result of the thinning ice shelves.

"One of the most important lessons from this study is that the impact is felt without any delay," said Professor Gudmundsson.

"Generally, we distinguish between an instantaneous response or a delayed, transient response. Our study shows the thinning of the ice shelves results in a significant instantaneous response to ice flow and ongoing mass loss. This means that we are not protected against the impact of the Antarctic Ice Sheet on global sea levels by a long response time."

He added: "This study closes an important hole in our understanding. Lack of data and limitations in modelling previously made it challenging to quantify the importance of ocean-induced changes as a driver for ongoing mass loss, but we have now shown that the observed ice shelf changes do indeed impact on upstream flow significantly."

The research was led by Northumbria University, Newcastle in the UK, with the NASA Jet Propulsion Laboratory and the Scripps Institution of Oceanography at the University of California San Diego.

Helen Amanda Fricker, Professor at Scripps Institution of Oceanography, said: "Ice shelves are the most vulnerable parts of Antarctica's ice sheet system and we know that they are shrinking, but what we didn't know before this work was how that was impacting the grounded ice behind them."

Fernando Paolo, postdoctoral scholar at Jet Propulsion Laboratory/California Institute of Technology, added: "It is striking how far inland the changes in ice shelves can impact the ice sheet flow. Since we now know that shrinking ice shelves are directly responsible for increases in ice discharge to the ocean, it is important that we keep monitoring them to watch how they evolve."

It is believed that the ice shelves may be thinning due to changes in ocean heat content, either by ocean warming or from changes in how the ocean circulates around and below the shelves, but further research is needed to establish the specific reasons.

Small woodlands in farmland have more benefits for humans per area, compared to large forests according to a new study. The small woodlands, sometimes even smaller than a football field, can easily go unnoticed in agricultural landscapes. Yet, these small forest remnants can store more carbon in the topsoil layer, are more suitable for hunting activities and host fewer ticks than large forests.

"The value of these tiny forests has never been unraveled before, although the occurrence of small woodlands in agricultural landscapes has increased due to forest fragmentation", says Alicia Valdés, one of the authors of the study.

The reason why these tiny woodlands may provide us with more services is because they naturally have more edges exposed to the influence of the surrounding environment.

"For example, there is more food supply for roe deer, such as blueberries and seedlings of birch and oak, because edges receive more sunlight and nutrients from the surrounding farmlands. This in turn, is predicted to attract more roe deer that can be hunted by humans", says Alicia Valdés.

These tiny forests can also store more carbon per area in the topsoil layer than older big woodlands, because they have an increased soil biological activity, which makes them faster at absorbing organic matter. Potentially these can act as better carbon sinks and help counterbalance the effects of global warming.

Another benefit of the tiny forests is that they represent a lower risk of contracting a tick borne disease. This is because less tick larvae can survive in the dry and hot environments characterizing woodland edges.

"This is just a prediction of all the potential benefits. How people would use these is something that needs to be looked into", says Alicia Valdés.

Now that the authors found out that the smaller woodlands are of greater value than previously thought, they argue that more conservation efforts are needed to maintain their important role and value in agricultural landscapes.

"Preserving the large forests is important because of their higher biodiversity, but conserving smaller woodlands, especially the older ones, will help to increase human well being in agricultural landscapes. These small woodlands need specific policy instruments ensuring their future conservation", says Alicia Valdés.

A Queen's University Belfast scientist has led an international team to the ground-breaking discovery of why the Sun's magnetic waves strengthen and grow as they emerge from its surface, which could help to solve the mystery of how the corona of the Sun maintains its multi-million degree temperatures.

For more than 60 years observations of the Sun have shown that as the magnetic waves leave the interior of the Sun they grow in strength but until now there has been no solid observational evidence as to why this was the case.

The corona's high temperatures have also always been a mystery. Usually the closer we are to a heat source, the warmer we feel. However, this is the opposite of what seems to happen on the Sun - its outer layers are warmer than the heat source at its surface.

Scientists have accepted for a long time that magnetic waves channel energy from the Sun's vast interior energy reservoir, which is powered by nuclear fusion, up into the outer regions of its atmosphere. Therefore, understanding how the wave motion is generated and spread throughout the Sun is of huge importance to researchers.

The team, which was led by Queen's, included 13 scientists, spanning five countries and 11 research institutes including University of Exeter; Northumbria University; the European Space Agency; Instituto de Astrofísica de Canarias, Spain; University of Oslo, Norway; the Italian Space Agency and California State University Northridge, USA.

The experts formed a consortium called "Waves in the Lower Solar Atmosphere (WaLSA)" to carry out the research and used advanced high-resolution observations from the National Science Foundation's Dunn Solar Telescope, New Mexico, to study the waves.

Dr David Jess from the School of Mathematics and Physics at Queen's led the team of experts. He explains: "This new understanding of wave motion may help scientists uncover the missing piece in the puzzle of why the outer layers of the Sun are hotter than its surface, despite being further from the heat source.

"By breaking the Sun's light up into its basic colours, we were able to examine the behaviour of certain elements from the periodic table within its atmosphere, including silicon (formed close to the Sun's surface), calcium and helium (formed in the chromosphere where the wave amplification is most apparent).

"The variations in the elements allowed the speeds of the Sun's plasma to be uncovered. The timescales over which they evolve were benchmarked, which allowed the wave frequencies of the Sun to be recorded. This is similar to how a complex musical ensemble is deconstructed into basic notes and frequencies by visualising its musical score."

The team then used super computers to analyse the data through simulations. They found that the wave amplification process can be attributed to the formation of an 'acoustic resonator', where significant changes in temperature between the surface of the Sun and its outer corona create boundaries that are partially reflective and act to trap the waves, allowing them to intensify and dramatically grow in strength.

The experts also found that the thickness of the resonance cavity -the distance between the significant temperature changes - is one of the main factors governing the characteristics of the detected wave motion.

Dr Jess comments: "The effect that we have found through the research is similar to how an acoustic guitar changes the sound it emits through the shape of its hollow body. If we think of this analogy we can see how the waves captured in the Sun can grow and change as they exit its surface and move towards the outer layers and exterior."

Dr Ben Snow, from the University of Exeter and a co-author of the study, said: "This new research opens the door to providing a new understanding of the mystery surrounding the Sun's magnetic waves. This is a crucial step towards explaining the coronal heating problem - where the temperature a few thousand km from the surface - is hotter than the heat source itself."

On a daily basis, multitudes of molecules enter each cell in our body. These can be nutrients or signal molecules or pathogenic microorganisms. An organelle in the cell directs these molecules to other stations for further processing. This organelle is called the endosome. If the pathways by which this sorting occurs fails at any stage, several diseases such as neurodegenerative diseases and certain cancers can occur. Thus, a better understanding of the steps in these pathways is of utmost importance.

In a recent study published in Communications Biology, a group of scientists from Japan and Austria, led by Prof Jiro Toshima from the Tokyo University of Science, reports a new finding regarding the maintenance and functioning of the endosome.

Conventional knowledge is that two processes are necessary for the upkeep of endosomes: a) sacs of molecules constantly form at the cell membrane, are transported to the endosome, and fuse into it; b) protein-containing vesicles transported from the Golgi (another cell organelle) fuse with the endosome.

The researchers of this study claim that this is not the case.

They introduce genetic mutations and drugs into yeast cells to inhibit each of these transport processes at a time. When transport from the Golgi does not occur, a protein essential to the upkeep of the endosome, Rab5, is not activated, and endosome formation is affected. When cell transport from the membrane is inhibited, there is no effect on the endosome. Thus, essentially, transport from the Golgi is necessary and that from the cell membrane is dispensable, or not as crucial. "Our results provide a different view of endosome formation and identify the Golgi as critical for the optimal maintenance and functioning of endosomes," Prof Toshima says.
This study clarifies only a fraction of the molecule-sorting pathway in cells. But, this is certainly one giant step in the research in this field. Perhaps, the insights from this study will soon appear on the pages of cell biology textbooks.

Differences in cultural values have led some countries to tackle the spectre of cyber-attacks with increased internet regulation, whilst others have taken a 'hands-off' approach to online security - a new study shows.

Internet users gravitate towards one of two 'poles' of social values. Risk-taking users are found in 'competitive' national cultures prompting heavy regulation, whilst web users in 'co-operative' nations exhibit less risky behaviour requiring lighter regulation.

Researchers at the University of Birmingham used cultural value measurements from 74 countries to predict the Global Cybersecurity Index (GCI), which measures state commitments of countries to cybersecurity regulation.

Dr. Alex Kharlamov, from Birmingham Law School, and Professor Ganna Pogrebna, from Birmingham Business School, published their findings in Regulation & Governance.

They demonstrated that differences in cybersecurity regulation, measured by GCI, stem from cross-cultural differences in human values between countries. They also showed how cultural values mapped onto national commitments to regulate and govern cyber-security.

In China, where people are more risk taking than American and British web users across five categories of risk behaviours, regulation is far stricter than in the USA, which in turn is tighter than the UK.

Dr. Kharlamov and Professor Pogrebna showed that this corresponded to the countries' relative positions on the cultural value scale, with China closer to 'competitive' than the USA, which in turn is closer to this 'pole' than the UK.

Dr. Kharlamov commented: "We spend most of our lives in the digital domain and cyber-attacks not only lead to a significant financial damage, but also cause prolonged psychological harm - using social engineering techniques to trick people into doing something they otherwise would not want to do.

"Irresponsible use of digital technologies, such as the Cambridge Analytica case, cause harm to many citizens and tell us that Internet regulation is imminent. It is vital to understand the origins of human behaviour online, as well as values and behavioural patterns."

The five categories of risk behaviour - cyber-security, personal data, privacy, cyber-crime and negligence - each consisted of six behavioural examples such as:

Not using anti-virus or antimalware protection (cyber-security)

Providing private information, such as your email address, to obtain free WiFi in public places such as coffee shops, airports and train stations (personal data)

Linking multiple social media accounts such as Twitter, Facebook and Instagram (Privacy)

Using insecure connections or free WiFi (Cyber-crime)

Letting web browsers remember passwords (Negligence)

Professor Ganna Pogrebna said: "Culture shapes the way we govern cyber spaces. Human values lie at the core of the human risk?taking behaviour in the digital space, which, in turn has a direct impact on the way in which digital domain is regulated.

"We talk about establishing overarching international online regulation, such as a new International Convention of Human Digital Rights. Yet, it seems the main reason why the international community fails to agree on such regulation has deep cultural underpinning."

GCI is produced by the International Telecommunications Union and assesses each country's engagement with cybersecurity regulatory processes in five areas: Legal, Technical, Organizational, Capacity Building, and Co-operation.

Without hardly noticing, we make countless decisions: to turn left or right on the bus? To wait or to accelerate? To look or to ignore? In the run-up to these decisions the brain evaluates sensory information and only then does it generate a behavior. For the first time, scientists at the Max Planck Institute of Neurobiology were able to follow such a decision-making process throughout an entire vertebrate brain. Their new approach shows how and where the zebrafish brain transforms the movement of the environment into a decision that causes the fish to swim in a specific direction.

Young zebrafish are tiny. Their brain is not much bigger than that of a fly and almost transparent. "We can therefore look into the entire brain and see what happens, for example, when a decision is made," explains Elena Dragomir, who has done exactly this. "The first step was to find a behavioral paradigm that we could use to study decision making," says Elena Dragomir. Other animal species, for example, are shown dots that move more or less in one direction. The animals can be trained to indicate their decision on the direction of the dots' movement, and if it is correct, they receive a reward. The neurobiologists from Ruben Portugues' group have now adapted this experimental setup for zebrafish. "The trick is that we use a reliable behavior called the optomotor response as a readout of the fish's decision".

If a fish drifts in a current, an image of the environment moves past its eyes. Fish will swim in the direction of the perceived optic flow to prevent drifting. Moving dots can trigger this optomotor response in the lab, and fish will turn either to the left or to right, depending on the direction of the moving dots. "We can also vary the difficulty of the decision, by changing the strength of the visual stimulus," explains Ruben Portugues. "If a higher percentage of dots move in one direction, the fish will turn faster and more reliably to the correct direction."

Through the microscope, the researchers could observe that the fish brain registers the moving dots and integrates this directional motion in time. After enough evidence has been accumulated, it then triggers a decision to swim in the perceived direction of the moving dots.

Where do the dots move to?

The decision as to when and in which direction the fish will turn correlates with the motion pattern of the dots. "This could take up to several seconds and is definitely not a reflex, which is an immediate response to a sensory stimulus," explains Vilim Stih, co-author of the study. "This accumulation of sensory information over time is also part of decision making models in other animal species." In contrast to these species, the researchers are able to map almost all contributing brain regions underlying this decision process in the larval zebrafish.

Neuronal clusters in the pretectum/thalamus region, for example, are likely to process the visual input. The neurons in the hindbrain probably trigger the turning and swimming movements. In the "interpeduncular nucleus" (IPN), the researchers found activity patterns that strongly correlated to the turning rate of the fish. With their integrated behavior, neurophysiology and modeling approach, the Martinsried-based researchers have created completely new possibilities for investigating the flow of information during decision-making in the vertebrate brain.

Nitrogen is an essential component of life. For example, it is required for the production of proteins. Boran Kartal, head of the Microbial Physiology group at the Max Planck Institute for Marine Microbiology in Bremen, studies nitrogen-cycling microorganisms, which control the bioavailability of this vital resource. A particularly interesting part of the nitrogen cycle is the anammox process, short for anaerobic ammonium oxidation. Here, nitrite or nitric oxide and ammonium are converted directly into dinitrogen gas. Now Kartal and his colleagues discovered a protein involved in the anammox process that might have some surprises. Their results are published in the November issue of Journal of Biological Chemistry.

Too unusual to be noticed up to now

This protein, a heme-containing cytochrome, is involved in the conversion of ammonium and nitric oxide to hydrazine. "Heme proteins have profound functions in life, like hemoglobin in our blood that carries oxygen. Heme structures in general resemble a spider web with an iron atom sitting in its center. Throughout the tree of life, we can recognize where this spider web binds to the rest of a protein from a pattern typically formed by five amino acids," Kartal explains. "Surprisingly, the protein we discovered has a very unusual and unexpected structure. It forms this pattern with only four amino acids, and was therefore overlooked in studies up to now."

Reduction of climate-active gases

The new protein is in the center of a very exciting and relevant process. Anammox bacteria produce only atmospheric nitrogen (N2) from nitrite or nitric oxide (NO) and ammonium, as Kartal previously showed. Unlike many microorganisms, they do not convert nitric oxide to the greenhouse gas nitrous oxide (N2O). Consequently, each molecule of NO that is transformed into N2 instead of N2O is one less molecule adding to climate change. Anammox bacteria reduce the amount of NO available for N2O production, and therefore, the amount of released greenhouse gas.

A surprisingly common pattern

This relevance in mind, Kartal and his colleagues carried out a database search to investigate how widespread proteins with the newly discovered pattern are in nature. "Remarkably, this pattern is very common," says Kartal. Proteins with the four-amino-acid pattern are present in a large variety of microorganisms throughout the bacterial and archaeal domains. "It is found in many different groups of microorganisms such as methanotrophs, that live on methane, and metal degraders," Kartal continues.

The full potential of proteins with the four-amino-acid pattern is completely unexplored. "In the anammox bacteria, it is found in a protein that shuttles electrons." Kartal says, "In other organisms this pattern might confer special properties to the proteins it is in. This is definitely something to investigate further."