Culture

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."

This release has been removed upon request of the submitter. For more information please contact George Hunka, Communications Manager, American Friends of Tel Aviv University, ghunka@aftau.org

Journal

OncoTargets and Therapy

DOI

10.18632/oncotarget.27268

HOUSTON - (Dec. 2, 2019) - A tiny termite might see an elephant's foot as its biggest threat. But when elephants and other large herbivores are lost to hunting, the termite's troubles are just beginning.

Rice University scientists were surprised to learn the extent to which declines of large mammals like elephants, buffaloes and gorillas in hunted areas of an African forest were linked to changes in the population of the tiny-but-important insects.

A study by Rice ecologist Amy Dunham and graduate student Therese Lamperty, published in Biological Conservation, reported that in African rainforests where large animals are hunted, the abundance of termites falls by 170 times.

Even in an environment that is home to an estimated 10,400 termites per square meter, that's a significant drop, according to the researchers. Termites, they reported, are important ecosystem engineers responsible for plant decomposition, carbon flux and the physical properties of the soil, and serve as a key food resource for other denizens.

And while they're not the only organisms affected by the winnowing of the elephant herd, they serve as a worthy bellwether of how any change in an ecosystem might influence the whole.

Lamperty, who led the study as part of her Ph.D. research, was aware that earlier studies found termites are sensitive to habitat change. "I was kind of thinking we might find something there," she said. "But when we looked at herbivore dung from elephants and other animals, the difference between the heavily hunted areas and the protected areas was pretty stark. That's a food source for termites, so it makes sense."

When megafauna like elephants are removed from the environment, termites lose both deadwood from trampled brush and their dung as nutrients, Lamperty said.

The study also found that where elephants and other megafauna disappear, the forest floor becomes dense with vegetation, providing a platform for increased numbers of web-building spiders. These in turn eat such flying insects as pollinators and are themselves a food source for insectivorous birds. That may also have consequences for the ecosystem that require further scientific study, she said.

Lamperty spent three months in 2016 in the inland rainforests of the central African nation of Gabon. There, she set up experiments in established study plots in preserved and hunted regions of the forest to see how the presence or absence of large herbivores influenced the ecosystem.

Gabon was a good site for the survey because of the juxtaposition of protected forests with areas near settlements that are hunted. "It's one of the few countries that has a sizable amount of continuous forest left that can support megafauna like forest elephants," Dunham said. "When you have large animals like elephants that have disappeared from a forest, you're likely to have some cascading impacts, and these small things that run the world, the insects, are likely to be affected.

"If you go into a forest that's been hunted, you can see differences right in the understory because you don't have these big things trampling and eating all the vegetation," she said. "So we expected we'd see differences in the vegetation, but didn't know what was likely to happen to the invertebrate populations. The termites caught us off guard."

Lamperty set her experiments in 11 regions of forest in northeastern Gabon at least 1.8 kilometers apart, five of them in protected and six in hunted forest. At each site, she established three plots and collected invertebrate samples in pitfall traps, cups placed with their lips at ground level and filled with ethanol to preserve whatever creatures fell in.

A bit of positive news was that the level of rainforest defaunation -- the disappearance of large vertebrates -- could not be used to predict the potential decline of several measured ecosystem processes, suggesting such systems have functional redundancy and mechanisms in place to prolong their survival. "I guess it's comforting in a way that there seems to be some compensation," Dunham said.

She said further studies should be conducted to quantify the effect of termite decline on animals that depend on them for food, and the roles that termites provide for a healthy ecosystem. Such studies could also reveal a tipping point beyond which those buffer mechanisms are no longer effective.

"It's really important to try to understand the consequences of hunting beyond the direct loss of hunted animals," Dunham said.

BOSTON (December 2, 2019) - Collecting rigorous public health data through large survey-based studies is a slow, expensive process. New research from Boston Children's Hospital shows that mining people's alcohol-related tweets and online searches offers a more immediate, localized information source to complement traditional methods, offering public health professionals the opportunity to spot emerging trends and measure the effects of alcohol-related interventions. Findings appear December 2 in the American Journal of Preventive Medicine.

"Online user-generated data are fluid and nimble - and have the potential to be really rich sources of information in specific geographic areas and during tight time intervals," says Elissa Weitzman, ScD, MSc, of the Division of Adolescent/Young Adult Medicine and the Computational Health Informatics Program at Boston Children's and the study's first author and principal investigator. "We set out to draw a relationship between these novel data and established, curated, nationally representative survey data."

Alcohol use in particular is difficult to track accurately at the local level, where drinking patterns may vary according to local culture, policy changes, and awareness campaigns. And large-scale surveillance systems aren't fine-grained enough to detect the effects of anti-alcohol campaigns.

"These systems are constructed to create a population-representative picture - they don't usually reflect local patterns or shed light on the effects of local or regional interventions," says Weitzman. "By examining online interactions, there's the potential to rapidly evaluate health activity and translate what you've learned into public policy and programming -- you can get out in front of things."

Weitzman and her colleagues used Google Trends data to estimated search volumes for seven alcohol-related keywords (alcohol, alcoholic, alcoholism, drinking, beer, liquor, wine) relative to all Google searches. To complement that, they also estimated the proportion of Twitter posts broadcasting personal alcohol use, using natural language processing to classify tweets and eliminate "false positives" (like tweets referencing "drinking" in a non-alcohol context).

The team then took these estimates state by state and compared them to survey responses in the same state to questions about alcohol use, from the national Behavioral Risk Factor Surveillance System (BRFSS). Among its many questions, the survey asked: "During the past 30 days, how many days per week or per month did you have at least one drink of any alcoholic beverage such as beer, wine, a malt beverage, or liquor?"

Of the BRFSS survey's nearly 1.3 million respondents in 2014-16, 53 percent reported recent alcohol use. Weitzman and colleagues found clear associations between a survey respondent's use of alcohol and the relative volume of alcohol-related searches and tweets in that respondent's state for the year and month they were surveyed. The relationships held in sub-analyses that looked at reported frequency and amount of drinking.

"It was astonishing to me that we could see this, because drinking behaviors are subtle and personal," says Weitzman, "On the other hand, it was exactly as expected, because the online world represents a powerful source of influence on behavior and can be a fairly accurate mirror of reality."

The team further showed that in states with strong alcohol policies, such as increasing the price of alcohol, limiting happy hours, and regulating public consumption, individuals' likelihood of drinking was reduced, even in areas with high levels of alcohol-related searching and tweeting. This suggested that the prevailing "alcohol environment," as captured by online behavior, had less of an influence on an individual's drinking.

"This is sound evidence of alcohol policies working as intended," says Tim Naimi, MD, MPH, of Boston Medical Center, a coauthor and leading expert on alcohol policy.

The study lays a groundwork for tracking emerging alcohol-related public health concerns.

"Informal social media and search data may be really important for detecting and responding to things that we don't anticipate - or that occur naturally," says senior author Lauren Wisk, PhD, formerly of Boston Children's Hospital and now at the University of California Los Angeles.

"Our results give confidence in our public health tools and in using novel data approaches to measure health behaviors and policy effects -- a real win," Weitzman adds.

Young cancer survivors face unique medical and psychosocial challenges that can hinder their ability to move on mentally and socially, even years after their final treatment. Lingering feelings of isolation and loss can contribute to a lack of confidence and self-efficacy, or the sense that they will be able to handle whatever arises in the future. But new research suggests survivors who retell their story through photography can significantly increase their self-esteem and self-efficacy.

Two years after receiving their final treatments, 18 leukemia survivors -- diagnosed as teenagers -- participated in the Framed Portrait Experience, an intervention which integrates therapeutic photography and re-enactment therapy. In the study by researchers at the University of Houston and the Catholic University of the Sacred Heart in Milan, Italy, where the intervention was developed, participants were empowered to express emotions connected to their illness in order to make meaning of their experience.

Working with a portrait photographer who was also a licensed social worker, the survivors chose three settings to take portraits that integrated meaningful objects and memories to represent their past, present and future.

Study co-author Chiara Acquati, assistant professor at the UH Graduate College of Social Work, recalled a young survivor who took her "past" portrait alongside her father fixing cars. "Her father was the one who stood by her side during her cancer treatment, so he was an important part of her cancer journey," said Acquati. That survivor's "present" portrait was one of reflection -- taken deep in thought along a serene riverbank. She dressed as a street performer who makes people laugh for her "future" photo.

"The goal is to retell their stories in contexts meaningful to them. It can be very emotional and challenging, but we hope that by looking back from a distance now that their cancer treatments are over, they can move forward with their lives," Acquati said.

Following the photo shoot, the pictures are printed and used during a clinical interview to guide the survivors' reflection about the changes they experienced as a result of cancer, and how those changes relate and integrate into their narrative of past, present, and future.

Young cancer survivors often feel isolated and distant from the experience of their healthy-peers, according to the researchers. This easy-to-implement and low-cost intervention allows them a safe space to retell their story and promote self-efficacy. "The objective is to reorganize their cancer narrative, or the story they tell themselves about their experience and better accept cancer as part of their life story," said study co-author Emanuela Saita, associate professor of psychology at the Catholic University of the Sacred Heart.

While the researchers acknowledge the small sample size, they said they are encouraged that participants now perceive themselves as better able to manage problems and more equipped to face obstacles.

BIRMINGHAM, Ala. - Extremely premature infants are at risk for life-threatening infections that spread into their bodies from the intestine. Infections after the first three days of life are called late-onset sepsis, or LOS.

University of Alabama at Birmingham researchers now report a new model for LOS in an article in Nature Medicine, and they show that disrupting the normal maturation of microbes in the intestine can make newborn mouse pups highly susceptible to LOS. Furthermore, they found they could prevent the deadly infection by giving the pups specific protective bacteria before a challenge with invasive Klebsiella pneumoniae bacteria.

"Our findings offer the possibility for rational design and testing of effective probiotic therapies to protect at-risk premature infants," said corresponding authors Jeffrey Singer, Ph.D., and Casey Weaver, M.D. "These studies substantiate clinical research suggesting that overgrowth of a single bacterial species, called neonatal dysbiosis, often precedes the development of LOS. Our model should help define mechanisms by which pioneer species of the developing microbiome of neonates prevent -- or fail to prevent -- dysbiosis that predisposes to LOS."

Their model is aided by the fact that the intestine of the newborn pup is still developing after birth, similar to the still-developing intestine of extremely premature infants.

At UAB, Singer is a student in the M.D./Ph.D. Medical Scientist Training Program, and Weaver is the Wyatt and Susan Haskell Professor of Medical Excellence in Pathology.

Bioluminescence

The UAB researchers placed a virulent K. pneumoniae strain, Kp-43816, into the stomachs of pups. The bacteria carried a bioluminescent marker that allowed researchers to use an imaging system to see where in the intestinal tract the bacteria were growing in live animals, and then measure the microbes' invasive spread out of the intestine and into the rest of the body. Bioluminescent bacteria in living animals can be seen through nearly an inch of tissue.

Using a dose that caused 50 percent mortality by 10 days, the researchers saw that translocation out of the intestine occurred where Klebsiella colonization was most dense in the intestine. However, not all pups with dysbiosis developed sepsis, just as not all premature human infants with dysbiosis develop LOS.

When the UAB team placed the same dose of an avirulent K. pneumoniae strain, Kp-39, into the stomach, an intriguing result followed. Kp-39 caused no mortality in the pups, yet it also translocated from the intestine into the abdomen, and like Kp-43816, it also infected the liver and mesentery. The Kp-39 infection was cleared over the next nine days.

This suggested that both strains of K. pneumoniae were capable of spreading out of the gut, but differences in host clearance by the immune defense system after translocation contributed to the differential virulence of these related strains. Indeed, when either strain was injected directly into the peritoneum -- bypassing the need for translocation from the intestine -- Kp-43816 caused 100 percent mortality in one day, but the Kp-39 caused no mortality in pups and was cleared in a week. The researchers found differences in the capsule surrounding the bacteria that allowed Kp-43816 to resist infection-clearing phagocytosis by immune cells more strongly than Kp-39.

"Notably, therefore, while the Kp-43816 infection models LOS," Singer and Weaver said, "Kp-39 enables tracking of dysbiosis without the confounding effects of sepsis and mortality."

The researchers then found that altering the microbiome of the pups changed susceptibility to dysbiosis and LOS. The normal intestinal microbiome is known to have a critical role in restricting the colonization and spread of a pathogen. Pups without a microbiome, raised in germ-free conditions, were uniformly susceptible to Kp-43816 LOS.

To look further, researchers treated dams with two antibiotics starting one day before delivery and several days thereafter, prior to infecting with Klebsiella. Both antibiotics are poorly absorbed and unlikely to be transmitted to pups; but they would alter the mother's intestinal microbiomes in different ways, which in turn should alter the microbiome that the pups acquire after birth from the dams. The UAB team found that pups of mothers given gentamicin were markedly more susceptible to sepsis, while pups of mothers given vancomycin were less susceptible to sepsis, compared with controls.

When the antibiotic experiment was repeated using the avirulent Kp-39, there was no mortality. However, pups whose mothers had been given vancomycin had fewer Kp-39, or less dysbiosis, compared to controls; pups whose mothers had been given gentamicin showed more Kp-39, or more dysbiosis, compared to controls.

Protective bacteria

The difference? Researchers found that pups of the vancomycin-dams had greater abundance of Lactobacillus bacteria in their intestinal microbiome, and the pups of gentamicin-dams had lesser amounts of Lactobacillus. Thus, presence or absence of lactobacilli appeared to correlate with resistance or susceptibility, respectively, to neonatal dysbiosis and LOS.

DNA analysis showed that the vancomycin-pups were dominated by the species Lactobacillus murinus, while the gentamycin pups were largely devoid of L. murinus. They also found that L. murinus was sensitive to gentamicin and resistant to vancomycin, suggesting that gentamycin treatment killed this protective species in dams, thus preventing its passage to pups through vertical transmission.

When the L. murinus species was given prophylactically to gentamycin-pups before a Klebsiella challenge, it dramatically reduced overgrowth of Kp-39 compared with controls. Through a different series of experiments, the researchers found that a strain of probiotic E. coli also was able to confer protection in gentamycin-pups. This protection was not seen for several other commonly utilized Lactobacillus probiotic species.

The researchers also found that younger pups, like extremely premature infants, have microbiomes dominated by bacteria called facultative anaerobes that can grow in either the presence or the absence of oxygen. As pups grew older, their microbiomes become more like term infants because they are dominated by bacteria called obligate anaerobes, which grow well in the absence of oxygen but die if oxygen is present. The older pups, with a mature microbiome dominated by obligate anaerobes, were resistant to neonatal dysbiosis. It appeared that presence of oxygen in the intestinal lumens of neonate pups prevented colonization by obligate anaerobes. The UAB researchers hypothesized that this might explain why dysbiosis is more prevalent in very-low-birthweight infants.

"Our findings establish that normal constituents of the microbiome are both necessary and sufficient to buffer pathobiont expansion in the neonatal gut to prevent LOS," Singer and Weaver said. "They further provide a basis for understanding why some probiotics are protective, whereas others are not. This may have important implications for clinical practice, where both maternal and neonatal antibiotic use can alter the neonatal microbiome, and where very-low-birthweight infants are given probiotics without clear evidence as to preferred probiotic species."

Cambridge, Mass. -- Microbes can be engineered to produce a variety of useful compounds, including plastics, biofuels, and pharmaceuticals. However, in many cases, these products compete with the metabolic pathways that the cells need to fuel themselves and grow.

To help optimize cells' ability to produce desired compounds but also maintain their own growth, MIT chemical engineers have devised a way to induce bacteria to switch between different metabolic pathways at different times. These switches are programmed into the cells and are triggered by changes in population density, with no need for human intervention.

"What we're hoping is that this would allow more precise regulation of metabolism, to allow us to get higher productivity, but in a way where we minimize the number of interventions," says Kristala Prather, the Arthur D. Little Professor of Chemical Engineering and the senior author of the study.

This kind of switching allowed the researchers to boost the microbial yields of two different products by up to tenfold.

MIT graduate student Christina Dinh is the lead author of the paper, which appears in the Proceedings of the National Academy of Sciences this week.

Double switch

To make microbes synthesize useful compounds that they don't normally produce, engineers insert genes for enzymes involved in the metabolic pathway -- a chain of reactions that generate a specific product. This approach is now used to produce many complex products, such as pharmaceuticals and biofuels.

In some cases, intermediates produced during these reactions are also part of metabolic pathways that already exist in the cells. When cells divert these intermediates out of the engineered pathway, it lowers the overall yield of the end product.

Using a concept called dynamic metabolic engineering, Prather has previously built switches that help cells maintain the balance between their own metabolic needs and the pathway that produces the desired product. Her idea was to program the cells to autonomously switch between pathways, without the need for any intervention by the person operating the fermenter where the reactions take place.

In a study published in 2017, Prather's lab used this approach to program E. coli to produce glucaric acid, a precursor to products such as nylons and detergents. The researchers' strategy was based on quorum sensing, a phenomenon that bacterial cells normally use to communicate with each other. Each species of bacteria secretes particular molecules that help them sense nearby microbes and influence each other's behavior.

The MIT team engineered their E. coli cells to secrete a quorum sensing molecule called AHL. When AHL concentrations reach a certain level, the cells shut off an enzyme that diverts a glucaric acid precursor into one of the cells' own metabolic pathways. This allows the cells to grow and divide normally until the population is large enough to start producing large quantities of the desired product.

"That paper was the first to demonstrate that we could do autonomous control," Prather says. "We could start the cultures going, and the cells would then sense when the time was right to make a change."

In the new PNAS paper, Prather and Dinh set out to engineer multiple switching points into their cells, giving them a greater degree of control over the production process. To achieve that, they used two quorum sensing systems from two different species of bacteria. They incorporated these systems into E. coli that were engineered to produce a compound called naringenin, a flavonoid that is naturally found in citrus fruits and has a variety of beneficial health effects.

Using these quorum sensing systems, the researchers engineered two switching points into the cells. One switch was designed to prevent bacteria from diverting a naringenin precursor called malonyl-CoA into the cells' own metabolic pathways. At the other switching point, the researchers delayed production of an enzyme in their engineered pathway, to avoid accumulating a precursor that normally inhibits the naringenin pathway if too much of the precursor accumulates.

"Since we took components from two different quorum sensing systems, and the regulator proteins are unique between the two systems, we can shift the switching time of each of the circuits independently," Dinh says.

The researchers created hundreds of E. coli variants that perform these two switches at different population densities, allowing them to identify which one was the most productive. The best-performing strain showed a tenfold increase in naringenin yield over strains that didn't have these control switches built in.

More complex pathways

The researchers also demonstrated that the multiple-switch approach could be used to double E. coli production of salicylic acid, a building block of many drugs. This process could also help improve yields for any other type of product where the cells have to balance between using intermediates for product formation or their own growth, Prather says. The researchers have not yet demonstrated that their method works on an industrial scale, but they are working on expanding the approach to more complex pathways and hope to test it at a larger scale in the future.

"We think it certainly has broader applicability," Prather says. "The process is very robust because it doesn't require someone to be present at a particular point in time to add something or make any sort of adjustment to the process, but rather allows the cells to be keeping track internally of when it's time to make a shift."

New Rochelle, NY, December 2, 2019--A new study has shown that more than half (53.1%) of office-based physicians in the U.S., across specialty areas, recommended at least one complementary health approach (CHA) to their patients during the previous 12 months, with female physicians (63.2%) more likely to recommend a CHA than male physicians (49.3%). This unique study, which found physician's sex, race, specialty, and U.S. region to be significant predictors of CHA recommendation, is published in JACM, The Journal of Alternative and Complementary Medicine, a peer-reviewed publication from Mary Ann Liebert, Inc., publishers, dedicated to paradigm, practice, and policy advancing integrative health. Click here to read the article free on the JACM website through January 2, 2020.

The article entitled "U.S. Physician Recommendations to Their Patients About the Use of Complementary Health Approaches" was coauthored by Barbara Stussman and Richard Nahin, PhD, MPH, National Center for Complementary and Integrative Health, National Institutes of Health, Bethesda, MD, and Patricia Barnes and Brian Ward, PhD, National Center for Health Statistics, Hyattsville, MD. The data are based on the 2012 Physician Induction Interview of the National Ambulatory Medical Care Survey (NAMCS PII).

The researchers analyzed recommendations by physicians to their patients for any CHA and for individual approaches, including massage therapy, herbs/nonvitamin supplements, chiropractic/osteopathic manipulation, yoga, acupuncture, and mind-body therapies. Overall, massage therapy was the most commonly recommended CHA, followed by chiropractic/osteopathic manipulation, herbs/nonvitamin supplements, yoga, and acupuncture. The analysis also looked at physician specialty area, including general/family practice physicians, psychiatrists, OB/GYNs, and pediatricians, and their likelihood of recommending any or a specific CHA. The authors anticipate that their findings will "enable consumers, physicians, and medical schools to better understand potential differences in use of CHAs with patients."

JACM Editor-in-Chief John Weeks, johnweeks-integrator.com, Seattle, WA, states: "It is remarkable that these 2012 data pre-date the systematic inclusion of complementary and integrative approaches in pain and opioid-related guidelines and reports from the Joint Commission, National Academy of Medicine, American College of Physicians, Food and Drug Administration, and others in the 7 years since. The data likely significantly understate present level of recommendations of complementary health practices by physicians."

An international group of researchers led by Brazilian scientists has assembled the most complete genome sequence of commercial sugarcane. They mapped 373,869 genes or 99.1% of the total genome.

This feat is the result of almost 20 years of research supported by São Paulo Research Foundation - FAPESP and will serve as a basis for the genetic improvement of the world's largest crop in tonnage according to the UN Food & Agriculture Organization (FAO).

An article describing the study is published in GigaScience. Its lead authors are (Glaucia Mendes Souza, a full professor at the University of São Paulo's Chemistry Institute (IQ-USP) and a member of the steering committee for the FAPESP Bioenergy Research Program (BIOEN- FAPESP), and Marie-Anne Van Sluys, a full professor at the same university's Bioscience Institute (IB-USP) and a member of FAPESP's Life Sciences Adjunct Panel.

"It's the first time all the genes of the sugarcane plant, or the vast majority, have been seen. In previous projects by various research groups, the sequences had to be collapsed for lack of a proper assembly tool, so they were only an approximation," said Souza, who is the principal investigator for the Thematic Project "Signaling and regulatory networks associated with 'energy sugarcane'.

"This knowledge opens up many possibilities, from applications in biotechnology to genetic improvement and gene editing [substitution or elimination of genes with specific functions]," said Van Sluys, principal investigator for the Thematic Project "Contribution of genes, genomes and transposable elements to plant-microbe interaction: a sugarcane study case".

Challenges

As the researchers explained, today's commercial sugarcane hybrids have been bred over thousands of years by crossing different varieties of two species (Saccharum officinarum and S. spontaneum) and have a highly complex genome comprising 10 billion base pairs in 100-130 chromosomes. Sequencing the genome is no easy task, requiring substantial computing power to assemble the DNA fragments while keeping homologous chromosomes separate.

For comparison, the wheat genome contains 17 billion base pairs but only 46 chromosomes, while the human genome has a mere 3.2 billion base pairs, also organized into 46 chromosomes.

Although the technology available at the start of the project was capable of producing long sequences, these long sequences had to be built from smaller fragments. Assembling the genome with these sequences required significant computing power, which was supplied by Microsoft.

The idea for the whole-genome sequencing of sugarcane dates to the onset of the BIOEN Program in 2008. A presentation by Souza at a conference held by Microsoft and FAPESP in 2014 left David Hackerman, a researcher at Microsoft Research Institute in Los Angeles, fascinated with the computational challenges posed by the initiative. He proposed a collaboration with FAPESP, which took the form of the project "Development of an algorithm for the assembly of the sugarcane polyploid genome", with Souza as the principal investigator funded by FAPESP's program Research Partnership for Technological Innovation (PITE). The project was a collaboration with other partners, such as Bob Davidson, then a researcher with Microsoft at its Seattle unit and now with Amazon.

The sequence published has made it possible for the first time to identify the diversity in genome segments called gene promoters - DNA regions that control gene expression.

"Although in some cases the genes are 99.9% identical, we can detect differences in their promoters, and these help us determine which ancestor the copies derive from, S. officinarum or S. spontaneum," Souza said.
The achievement permits studies, for example, of how different copies contribute to increased sugar and fiber yields and which copies may be advantageous to the different genotypes selected by programs to breed sugarcane varieties for sugar and for energy.

"The result confirms Brazil's and São Paulo state's leadership in research on sugarcane which is such an important plant for our country. It also reflects foresight on the part of the São Paulo research community and of FAPESP, regarding the challenge of learning about the sugarcane genome to extract knowledge leading to increased efficiency and productivity. We should always recall that research on sugarcane is one of the factors that enabled Brazil to achieve something no other country of a similar size has achieved to date, namely, producing 40% of its total energy from renewables and with low carbon emissions," said Carlos Henrique de Brito Cruz, FAPESP's Scientific Director.

Background

The variety chosen for sequencing was SP80-3280 because more data are available about this variety in scientific literature than about any other variety. During Project Sugarcane Genome (known as FAPESP SucEST, 1999-2002), 238,000 functional gene fragments from this variety were partially sequenced (read more at: https://revistapesquisa.fapesp.br/en/2012/08/22/mapping-sugarcanes/).

Today, SP80-3280 ranks among the top 20 sugarcane varieties grown in São Paulo state. It is also part of the genealogy of several commercial varieties, since it is used in new crossings. Its agricultural yield is high, and it is easily regrown by the sett method (setts are stem cuttings taken from old plants containing one or more buds), thus making it an option for late harvesting at the end of the crop year in São Paulo state.

"The knowledge obtained for this variety can be applied in studies of other genotypes, particularly for the discovery of genes that control biomass accumulation," explained Augusto Lima Diniz, a coauthor of the study and currently on a research internship abroad at Cold Spring Harbor Laboratory (CSHL) in the United States as part of his postdoctoral research for IQ-USP.

Souza and Van Sluys recently participated in an international team that sequenced the genome of S. spontaneum, the ancestor species corresponding to 10-15% of the commercial sugarcane genome. S. officinarum contributes 80-85%, and 5% is recombinant chromosomes of these two progenitor species. The study is published in Nature Genetics.

In 2018, Van Sluys was one of the authors of an article on the results of a study that mapped about half of the sugarcane monoploid genome (only one chromosome in each pair).

Based on the information obtained from this latest whole-genome sequencing effort, researchers at the University of São Paulo (USP) are developing tools for the genetic improvement of sugarcane and testing several candidate genes in Genetically Modified (GM) plants. They are also conducting comparative genomics studies on large gene families with the aim of understanding their contributions to the sugarcane varieties used in Brazilian genetic improvement programs. They hope to find genes that can increase yields, enhance drought resistance and contribute to the development of novel compounds from sugarcane.

"We're also offering the community a Genome Browser that can be used to search for specific genes and analyze sequences in comparison with previous sequencing exercises. This will be valuable to biotech projects not just relating to sugarcane but also to other crops and plants," Souza said.