Culture

A Princeton team has developed a class of light-switchable, highly adaptable molecular tools with new capabilities to control cellular activities. The antibody-like proteins, called OptoBinders, allow researchers to rapidly control processes inside and outside of cells by directing their localization, with potential applications including protein purification, the improved production of biofuels, and new types of targeted cancer therapies.

In a pair of papers published Aug. 13 in Nature Communications, the researchers describe the creation of OptoBinders that can specifically latch onto a variety of proteins both inside and outside of cells. OptoBinders can bind or release their targets in response to blue light. The team reported that one type of OptoBinder changed its affinity for its target molecules up to 330-fold when shifted from dark to blue light conditions, while others showed a five-fold difference in binding affinity -- all of which could be useful to researchers seeking to understand and engineer the behaviors of cells.

Crucially, OptoBinders can target proteins that are naturally present in cells, and their binding is easily reversible by changing light conditions -- "a new capability that is not available to normal antibodies," said co-author José Avalos, an assistant professor of chemical and biological engineering and the Andlinger Center for Energy and the Environment. "The ability to let go [of a target protein] is actually very valuable for many applications," said Avalos, including engineering cells' metabolisms, purifying proteins or potentially making biotherapeutics.

The new technique is the latest in a collaboration between Avalos and Jared Toettcher, an assistant professor of molecular biology. Both joined the Princeton faculty in 2015, and soon began working together on new ways to apply optogenetics -- a set of techniques that introduce genes encoding light-responsive proteins to control cells' behaviors.

"We hope that this is going to be the beginning of the next era of optogenetics, opening the door to light-sensitive proteins that can interface with virtually any protein in biology, either inside or outside of cells," said Toettcher, the James A. Elkins, Jr. '41 Preceptor in Molecular Biology.

Avalos and his team hope to use OptoBinders to control the metabolisms of yeast and bacteria to improve the production of biofuels and other renewable chemicals, while Toettcher's lab is interested in the molecules' potential to control signaling pathways involved in cancer.

The two papers describe different types of light-switchable binders: opto-nanobodies and opto-monobodies. Nanobodies are derived from the antibodies of camelids, the family of animals that includes camels, llamas and alpacas, which produce some antibodies that are smaller (hence the name nanobody) and simpler in structure than those of humans or other animals.

Nanobodies' small size makes them more adaptable and easier to work with than traditional antibodies; they recently received attention for their potential as a COVID-19 therapy. Monobodies, on the other hand, are engineered pieces of human fibronectin, a large protein that forms part of the matrix between cells.

"These papers go hand in hand," said Avalos. "The opto-nanobodies take advantage of the immune systems of these animals, and the monobodies have the advantage of being synthetic, which gives us opportunities to further engineer them in different ways."

The two types of OptoBinders both incorporate a light-sensitive domain from a protein found in oat plants.

"When you turn the light on and off, these tools bind and release their target almost immediately, so that brings another level of control" that was not previously possible, said co-author César Carrasco-López, an associate research scholar in Avalos' lab. "Whenever you are analyzing things as complex as metabolism, you need tools that allow you to control these processes in a complex way in order to understand what is happening."

In principle, OptoBinders could be engineered to target any protein found in a cell. With most existing optogenetic systems, "you always had to genetically manipulate your target protein in a cell for each particular application," said co-author Agnieszka Gil, a postdoctoral research fellow in Toettcher's lab. "We wanted to develop an optogenetic binder that did not depend on additional genetic manipulation of the target protein."

In a proof of principle, the researchers created an opto-nanobody that binds to actin, a major component of the cytoskeleton that allows cells to move, divide and respond to their environment. The opto-nanobody strongly bound to actin in the dark, but released its hold within two minutes in the presence of blue light. Actin proteins normally join together to form filaments just inside the cell membrane and networks of stress fibers that traverse the cell. In the dark, the opto-nanobody against actin binds to these fibers; in the light, these binding interactions are disrupted, causing the opto-nanobody to scatter throughout the cell. The researchers could even manipulate binding interactions on just one side of a cell -- a level of localized control that opens new possibilities for cell biology research.

OptoBinders stand to unlock scores of innovative, previously inaccessible uses in cell biology and biotechnology, said Andreas Möglich, a professor of biochemistry at the University of Bayreuth in Germany who was not involved in the studies. But, Möglich said, "there is much more to the research" because the design strategy can be readily translated to other molecules, paving the way to an even wider repertoire of customized, light-sensitive binders.

"The impressive results mark a significant advance," he said.

"Future applications will depend on being able to generate more OptoBinders" against a variety of target proteins, said Carrasco-López. "We are going to try to generate a platform so we can select OptoBinders against different targets" using a standardized, high-throughput protocol, he said, adding that this is among the first priorities for the team as they resume their experiments after lab research was halted this spring due to COVID-19.

Beyond applications that involve manipulating cell metabolism for microbial chemical production, Avalos said, OptoBinders could someday be used to design biomaterials whose properties can be changed by light.

The technology also holds promise as way to reduce side effects of drugs by focusing their action to a specific site in the body or adjusting dosages in real time, said Toettcher, who noted that applying light inside the body would require a device such as an implant. "There aren't many ways to do spatial targeting with normal pharmacology or other techniques, so having that kind of capability for antibodies and therapeutic binders would be a really cool thing," he said. "We think of this as a sea change in what sorts of processes can be placed under optogenetic control."

WASHINGTON (August 13, 2020)-- An online COVID-19 symptom tracking tool developed by researchers at Georgetown University Medical Center ensures a person's confidentiality while being able to actively monitor their symptoms. The tool is not proprietary and can be used by entities that are not able to develop their own tracking systems.

Identifying and monitoring people infected with COVID-19, or exposed to people with infection, is critical to preventing widespread transmission of the disease. Details of the COVID19 Symptom Tracker and a pilot study were published August 13, 2020, in the Journal of Medical Information Research (JMIR).

"One of the major impediments to tracking people with, or at risk of, COVID-19 has been an assurance of privacy and confidentiality," says infectious disease expert Seble G. Kassaye, MD, MS, lead author and associate professor of medicine at Georgetown University Medical Center. "Our online system provides a method for efficient, active monitoring of large numbers of individuals under quarantine or home isolation, while maintaining privacy."

The Georgetown internet tool assigns a unique identifier as people enter their symptoms and other relevant demographic data. One function in the system allows institutions to generate reports about items on which people can act, such as symptoms that might require medical attention. Additionally, people using the system are provided with information and links to Centers for Disease Control and Prevention COVID-19 recommendations and instructions for how people with symptoms should seek care.

Development of the system was rapid -- it took five days to design. The joint project included Georgetown University's J.C. Smart, PhD, chief scientist of AvesTerra, a knowledge management environment that supports data integration and synthesis to identify actionable events and maintain privacy, and Georgetown's vice president for research and chief technology officer, Spiros Dimolitsas, PhD.

"We knew that time was of the essence and the challenges of traditional contact tracing became very clear to us based on one of our first patients who had over 500 exposures," says Kassaye. "This was what motivated us to work on this, essentially day and night."

The tool launched on March 20, followed by initial testing of the system with the voluntary participation of 48 Georgetown University School of Medicine students or their social contacts. Participants were asked to enter data twice daily for three days between March 31 and April 5, 2020.

"The lack of identifying data being collected in the system should reassure individual users and alleviate personal inhibitions that appear to be the Achille's heel of other digital contact tracing apps that require identifying information," says Kassaye. She also noted that this system could be used by health-related organizations during the re-opening of business to provide reassurance to their users that the enterprise is actively, rather than passively, monitoring its staff.

Feedback from healthcare groups using the platform led to the release of a Spanish language version. As the data currently needs to be entered through the website, development of an app for cellphone use could greatly enhance the usability of the tool, said the investigators. For places where internet access is problematic, the researchers are also pursuing development of a voice activated version.

The tracker can be view at http://www.covidgu.org.

WASHINGTON -- Researchers have designed an off-grid, low-cost modular energy source that can efficiently produce power at night. The system uses commercially available technology and could eventually help meet the need for nighttime lighting in urban areas or provide lighting in developing countries.

Although solar power brings many benefits, its use depends heavily on the distribution of sunlight, which can be limited in many locations and is completely unavailable at night. Systems that store energy produced during the day are typically expensive, thus driving up the cost of using solar power.

To find a less-expensive alternative, researchers led by Shanhui Fan from Stanford University looked to radiative cooling. This approach uses the temperature difference resulting from heat absorbed from the surrounding air and the radiant cooling effect of cold space to generate electricity.

In The Optical Society (OSA) journal Optics Express, the researchers theoretically demonstrate an optimized radiative cooling approach that can generate 2.2 Watts per square meter with a rooftop device that doesn't require a battery or any external energy. This is about 120 times the amount of energy that has been experimentally demonstrated and enough to power modular sensors such as ones used in security or environmental applications.

"We are working to develop high-performance, sustainable lighting generation that can provide everyone - including those in developing and rural areas - access to reliable and sustainable low cost lighting energy sources," said Lingling Fan, first author of the paper. "A modular energy source could also power off-grid sensors used in a variety of applications and be used to convert waste heat from automobiles into usable power."

Maximizing power generation

One of the most efficient ways to generate electricity using radiative cooling is to use a thermoelectric power generator. These devices use thermoelectric materials to generate power by converting the temperature differences between a heat source and the device's cool side, or radiative cooler, into an electric voltage.

In the new work, the researchers optimized each step of thermoelectric power generation to maximize nighttime power generation from a device that would be used on a rooftop. They improved the energy harvesting so that more heat flows into the system from the surrounding air and incorporate new commercially available thermoelectric materials that enhance how well that energy is used by the device. They also calculated that a thermoelectric power generator covering one square meter of a rooftop could achieve the best trade-off between heat loss and thermoelectric conversion.

"One of the most important innovations was designing a selective emitter that is attached to the cool side of the device," said Wei Li, a member of the research team. "This optimizes the radiative cooling process so that the power generator can more efficiently get rid of excessive heat."

The researchers demonstrated the new approach by using computer modeling to simulate a system with realistic physical parameters. The models reproduced previous experimental results faithfully and revealed that the optimized system designed by the researchers could come close to what has been calculated as the maximum efficiency using thermoelectric conversion.

In addition to carrying out experiments, the researchers are also examining optimal designs for operating the system during the day, in addition to nighttime, which could expand the practical applications of the system.

University of Toronto Engineering researchers have developed a new method of injecting healthy cells into damaged eyes. The technique could point the way toward new treatments with the potential to reverse forms of vision loss that are currently incurable.

Around the world, millions of people live with vision loss due to conditions such as age-related macular degeneration (AMD) or retinitis pigmentosa. Both are caused by the death of cells in the retina, at the back of the eye.

"The cells that are responsible for vision are the photoreceptors, which have an intimate relationship with another type of cell known as retinal pigmented epithelium (RPE) cells," says Professor Molly Shoichet.

"In AMD, the RPE die first, and this then causes the photoreceptors to die."

Many researchers have experimented with treatments based on injecting healthy photoreceptors or RPE cells into the eye to replace the dead cells. But integrating the new cells into the existing tissue is a major challenge, and most injected cells end up dying as well.

Shoichet and her team are experts in using engineered biomaterials known as hydrogels to promote the survival of newly injected cells after transplantation. The hydrogels ensure an even distribution of cells, reduce inflammation and promote tissue healing in the critical early days post-injection. Eventually, they degrade naturally, leaving the healthy cells behind.

In 2015, the team used hydrogels to inject healthy photoreceptor cells into damaged retinas in a mouse model. While the team observed some vision repair, the benefits were limited, so they began to think more carefully about the relationships between RPE cells and photoreceptors.

"RPE and photoreceptors are considered as one functional unit -- if one cell type dies, then the other one will too," says Shoichet. "We wondered if co-delivery of both cell types would have a bigger impact on vision restoration."

As with photoreceptors, many groups had tried implanting RPE cells on their own, but nobody had ever integrated both cell types into a single treatment. Once again, the hydrogels pointed to a solution.

"What other groups have typically done is either inject photoreceptors in a saline solution, which often results in cells clustering together, or surgically implant a layer of RPE cells usually grown on a polymer film," says Shoichet.

"Our hydrogel is viscous enough to ensure a good distribution of both cell types in the syringe, yet it also has important shear-thinning properties to facilitate injection through the very fine needle required for this operation," adds Shoichet. "The combination of these properties opened up a new strategy for successful delivery of multiple cells."

The team tested co-injection in a degenerative mouse model resembling AMD. In a paper recently published in the journal Biomaterials, they report that mice who received the co-injection regained about 10 percent of their normal visual acuity. Those who received either cell type on its own showed little to no improvement.

Co-injected mice were also more active in dark chambers than light ones, showing that these nocturnal animals could once again distinguish light and shadow.

"I still remember the long days of behavioural testing," says Nick Mitrousis, Shoichet's former PhD student and lead author of the paper, now a postdoctoral fellow at the University of Chicago.

"We designed the experiment so that I wouldn't know which mice had received the treatment and which received a placebo. When some of the mice started responding, I kept vacillating between optimism that the experiment might have actually worked, and worry that the recovering mice might just be split between the different treatment groups."

The worries were unfounded: it turned out that the co-injection treatment really had an effect. But both Mitrousis and Shoichet caution that there is a very long road between these preliminary results and a trial that could eventually find its way into the clinic.

"First, we need to demonstrate the benefit of this strategy in multiple animal models," says Shoichet. "We'll also need a source of human photoreceptor cells and a way to further improve cell survival, both of which we're working on. Still, we are very excited by these data and always open to collaboration to take the research further."

PROVIDENCE, R.I. [Brown University] -- As levels of atmospheric carbon dioxide continue to climb, scientists are looking for new ways of breaking down CO2 molecules to make useful carbon-based fuels, chemicals and other products. Now, a team of Brown University researchers has found a way to fine-tune a copper catalyst to produce complex hydrocarbons -- known as C2-plus products -- from CO2 with remarkable efficiency.

In a study published in Nature Communications, the researchers report a catalyst that can produce C2-plus compounds with up to 72% faradaic efficiency (a measure of how efficiently electrical energy is used to convert carbon dioxide into chemical reaction products). That's far better than the reported efficiencies of other catalysts for C2-plus reactions, the researchers say. And the preparation process can be scaled up to an industrial level fairly easily, which gives the new catalyst potential for use in large-scale CO2 recycling efforts.

"There had been reports in the literature of all kinds of different treatments for copper that could produce these C2-plus with a range of different efficiencies," said Tayhas Palmore, the a professor of engineering at Brown who co-authored the paper with Ph.D. student Taehee Kim. "What Taehee did was a set of experiments to unravel what each of these treatment steps was actually doing to the catalyst in terms of reactivity, which pointed the way to optimizing a catalyst for these multi-carbon compounds."

There have been great strides in recent years in developing copper catalysts that could make single-carbon molecules, Palmore says. For example, Palmore and her team at Brown recently developed a copper foam catalyst that can produce formic acid efficiently, an important single-carbon commodity chemical. But interest is increasing in reactions that can produce C2-plus products.

"Ultimately, everyone seeks to increase the number of carbons in the product to the point of producing higher carbon fuels and chemicals," Palmore said.

There had been evidence from prior research that halogenation of copper -- a reaction that coats a copper surface with atoms of chlorine, bromine or iodine in the presence of an electrical potential -- could increase a catalyst's selectivity of C2-plus products. Kim experimented with a variety of different halogenation methods, zeroing in on which halogen elements and which electrical potentials yielded catalysts with the best performance in CO2-to-C2-plus reactions. He found that the optimal preparations could yield faradaic efficiencies of between 70.7% and 72.6%, far higher than any other copper catalyst.

The research helps to reveal the attributes that make a copper catalyst good for C2-plus products. The preparations with the highest efficiencies had a large number of surface defects -- tiny cracks and crevices in the halogenated surface -- that are critical for carbon-carbon coupling reactions. These defect sites appear to be key to the catalysts' high selectivity toward ethylene, a C2-plus product that can be polymerized and used to make plastics.

Ultimately, such a catalyst will aid in large-scale recycling of CO2. The idea is to capture CO2 produced by industrial facilities like power plants, cement manufacturing or directly from air, and convert it into other useful carbon compounds. That requires an efficient catalyst that is easy to produce and regenerate, and inexpensive enough to operate on an industrial scale. This new catalyst is a promising candidate, the researchers say.

"We were working with lab-scale catalysts for our experiments, but you could produce a catalyst of virtually any size using the method developed," Palmore said.

Sugars and fats are the primary fuels that power every cell, tissue and organ. For most cells, sugar is the energy source of choice, but when nutrients are scarce, such as during starvation or extreme exertion, cells will switch to breaking down fats instead.

The mechanisms for how cells rewire their metabolism in response to changes in resource availability are not yet fully understood, but new research reveals a surprising consequence when one such mechanism is turned off: an increased capacity for endurance exercise.

In a study published in the Aug. 4 issue of Cell Metabolism, Harvard Medical School researchers identified a critical role of the enzyme, prolyl hydroxylase 3 (PHD3), in sensing nutrient availability and regulating the ability of muscle cells to break down fats. When nutrients are abundant, PHD3 acts as a brake that inhibits unnecessary fat metabolism. This brake is released when fuel is low and more energy is needed, such as during exercise.

Remarkably, blocking PHD3 production in mice leads to dramatic improvements in certain measures of fitness, the research showed. Compared with their normal littermates, mice lacking the PHD3 enzyme ran 40 percent longer and 50 percent farther on treadmills and had higher VO2 max, a marker of aerobic endurance that measures the maximum oxygen uptake during exercise.

The findings shed light on a key mechanism for how cells metabolize fuels and offer clues toward a better understanding of muscle function and fitness, the authors said.

"Our results suggest that PHD3 inhibition in whole body or skeletal muscle is beneficial for fitness in terms of endurance exercise capacity, running time and running distance," said senior study author Marcia Haigis, professor of cell biology in the Blavatnik Institute at HMS. "Understanding this pathway and how our cells metabolize energy and fuels potentially has broad applications in biology, ranging from cancer control to exercise physiology."

However, further studies are needed to elucidate whether this pathway can be manipulated in humans to improve muscle function in disease settings, the authors said.

Haigis and colleagues set out to investigate the function of PHD3, an enzyme that they had found to play a role regulating fat metabolism in certain cancers in previous studies. Their work showed that, under normal conditions, PHD3 chemically modifies another enzyme, ACC2, which in turn prevents fatty acids from entering mitochondria to be broken down into energy.

In the current study, the researchers' experiments revealed that PHD3 and another enzyme called AMPK simultaneously control the activity of ACC2 to regulate fat metabolism, depending on energy availability.

In isolated mouse cells grown in sugar-rich conditions, the team found that PHD3 chemically modifies ACC2 to inhibit fat metabolism. Under low-sugar conditions, however, AMPK activates and places a different, opposing chemical modification on ACC2, which represses PHD3 activity and allows fatty acids to enter the mitochondria to be broken down for energy.

These observations were confirmed in live mice that were fasted to induce energy-deficient conditions. In fasted mice, the PHD3-dependent chemical modification to ACC2 was significantly reduced in skeletal and heart muscle, compared to fed mice. By contrast, the AMPK-dependent modification to ACC2 increased.

Longer and further

Next, the researchers explored the consequences when PHD3 activity was inhibited, using genetically modified mice that do not express PHD3. Because PHD3 is most highly expressed in skeletal muscle cells and AMPK has previously been shown to increase energy expenditure and exercise tolerance, the team carried out a series of endurance exercise experiments.

"The question we asked was if we knock out PHD3," Haigis said, "would that increase fat burning capacity and energy production and have a beneficial effect in skeletal muscle, which relies on energy for muscle function and exercise capacity?"

To investigate, the team trained young, PHD3-deficient mice to run on an inclined treadmill. They found that these mice ran significantly longer and further before reaching the point of exhaustion, compared to mice with normal PHD3. These PHD3-deficient mice also had higher oxygen consumption rates, as reflected by increased VO2 and VO2 max.

After the endurance exercise, the muscles of PHD3-deficient mice had increased rates of fat metabolism and an altered fatty acid composition and metabolic profile. The PHD3-dependent modification to ACC2 was nearly undetectable, but the AMPK-dependent modification increased, suggesting that changes to fat metabolism play a role in improving exercise capacity.

These observations held true in mice genetically modified to specifically prevent PHD3 production in skeletal muscle, demonstrating that PHD3 loss in muscle tissues is sufficient to boost exercise capacity, according to the authors.

"It was exciting to see this big, dramatic effect on exercise capacity, which could be recapitulated with a muscle-specific PHD3 knockout," Haigis said. "The effect of PHD3 loss was very robust and reproducible."

The research team also performed a series of molecular analyses to detail the precise molecular interactions that allow PHD3 to modify ACC2, as well as how its activity is repressed by AMPK.

The study results suggest a new potential approach for enhancing exercise performance by inhibiting PHD3. While the findings are intriguing, the authors note that further studies are needed to better understand precisely how blocking PHD3 causes a beneficial effect on exercise capacity.

In addition, Haigis and colleagues found in previous studies that in certain cancers, such as some forms of leukemia, mutated cells express significantly lower levels of PHD3 and consume fats to fuel aberrant growth and proliferation. Efforts to control this pathway as a potential strategy for treating such cancers may help inform research in other areas, such as muscle disorders.

It remains unclear whether there are any negative effects of PHD3 loss. To know whether PHD3 can be manipulated in humans--for performance enhancement in athletic activities or as a treatment for certain diseases --will require additional studies in a variety of contexts, the authors said.

It also remains unclear if PHD3 loss triggers other changes, such as weight loss, blood sugar and other metabolic markers, which are now being explored by the team.

"A better understanding of these processes and the mechanisms underlying PHD3 function could someday help unlock new applications in humans, such as novel strategies for treating muscle disorders," Haigis said.

Additional authors on the study include Haejin Yoon, Jessica Spinelli, Elma Zaganjor, Samantha Wong, Natalie German, Elizabeth Randall, Afsah Dean, Allen Clermont, Joao Paulo, Daniel Garcia, Hao Li, Olivia Rombold, Nathalie Agar, Laurie Goodyear, Reuben Shaw, Steven Gygi and Johan Auwerx.

New Rochelle, NY, August 13, 2020--A rational design approach created novel variants of adeno-associated viral (AAV) capsids. These have improved transduction properties in the mouse retina and cornea. as reported in the peer-reviewed journal Human Gene Therapy. Click here to read the full-text article free on the Human Gene Therapy website through September 13, 2020.

The efficient gene delivery of these variants was confirmed in non-human primate tissue.

"The capsid modified AAV2 and AAV5 variants described here have novel attributes that will add to the efficacy and specificity of their potential use in gene therapy for a range of human ocular diseases," said Catherine O'Riordan and coauthors from Sanofi.

"The structural domains of the AAV capsid have become fundamental building blocks of many gene therapy vectors. The work by Dr. O'Riordan and her colleagues takes advantage of the new age of structural biology to intelligently redesign these building blocks rather than relying on empiric screening of variants. This rational design approach holds great promise for the field," according to Editor-in-Chief of Human Gene Therapy Terence R. Flotte, MD, Celia and Isaac Haidak Professor of Medical Education and Dean, Provost, and Executive Deputy Chancellor, University of Massachusetts Medical School.

"I'm fascinated with life, and that's why I want to break it."

This is how Betül Kaçar, an assistant professor at the University of Arizona with appointments in the Department of Molecular and Cellular Biology, Department of Astronomy and the Lunar and Planetary Laboratory, describes her research. What may sound callous is a legitimate scientific approach in astrobiology. Known as ancestral sequencing, the idea is to "resurrect" genetic sequences from the dawn of life, put them to work in the cellular pathways of modern microbes - think Jurassic Park but with extinct genes in place of dinosaurs, and study how the organism copes.

In a recent paper published in the Proceedings of the National Academy of Sciences, Kaçar's research team reports an unexpected discovery: Evolution, it seems, is not very good at multitasking.

Kaçar uses ancestral sequencing to find out what makes life tick and how organisms are shaped by evolutionary selection pressure. The insights gained may, in turn, offer clues as to what it takes for organic precursor molecules to give rise to life - be it on Earth or faraway worlds. In her lab, Kaçar specializes in designing molecules that act like tiny invisible wrenches, wreaking havoc with the delicate cellular machinery that allows organisms to eat, move and multiply - in short, to live.

Kaçar has focused her attention on the translation machinery, a labyrinthine molecular clockwork that translates the information encoded in the bacteria's DNA into proteins. All organisms - from microbes to algae to trees to humans - possess this piece of machinery in their cells.

"We approximate everything about the past based on what we have today," Kaçar said. "All life needs a coding system - something that takes information and turns it into molecules that can perform tasks - and the translational machinery does just that. It creates life's alphabet. That's why we think of it as a fossil that has remained largely unchanged, at least at its core. If we ever find life elsewhere, you bet that the first thing we'll look at is its information processing systems, and the translational machinery is just that."

So critical is the translational machinery to life on Earth that even over the course of more than 3.5 billion years of evolution, its parts have undergone little substantial change. Scientists have referred to it as "an evolutionary accident frozen in time."

"I guess I tend to mess with things I'm not supposed to," Kaçar said. "Locked in time? Let's unlock it. Breaking it would lead the cell to destruction? Let's break it."

The researchers took six different strains of Escherichia coli bacteria and genetically engineered the cells with mutated components of their translational machinery. They targeted the step that feeds the unit with genetic information by swapping the shuttle protein with evolutionary cousins taken from other microbes, including a reconstructed ancestor from about 700 million years ago.

"We get into the heart of the heart of what we think is one of the earliest machineries of life," Kaçar said. "We purposely break it a little, and a lot, to see how the cells deal with this problem. In doing this, we think we create an urgent problem for the cell, and it will fix that."

Next, the team mimicked evolution by having the manipulated bacterial strains compete with each other - like a microbial version of "The Hunger Games." A thousand generations later, some strains fared better than others, as was expected. But when Kaçar's team analyzed exactly how the bacteria responded to perturbations in their translational components, they discovered something unexpected: Initially, natural selection improved the compromised translational machinery, but its focus shifted away to other cellular modules before the machinery's performance was fully restored.

To find out why, Kaçar enlisted Sandeep Venkataram, a population genetics expert at the University of California, San Diego.

Venkataram likens the process to a game of whack-a-mole, with each mole representing a cellular module. Whenever a module experiences a mutation, it pops up. The hammer smashing it back down is the action of natural selection. Mutations are randomly spread across all modules, so that all moles pop up randomly.

"We expected that the hammer of natural selection also comes down randomly, but that is not what we found," he said. "Rather, it does not act randomly but has a strong bias, favoring those mutations that provide the largest fitness advantage while it smashes down other less beneficial mutations, even though they also provide a benefit to the organism."

In other words, evolution is not a multitasker when it comes to fixing problems.

"It seems that evolution is myopic," Venkataram said. "It focuses on the most immediate problem, puts a Band-Aid on and then it moves on to the next problem, without thoroughly finishing the problem it was working on before."

"It turns out the cells do fix their problems but not in the way we might fix them," Kaçar added. "In a way, it's a bit like organizing a delivery truck as it drives down a bumpy road. You can stack and organize only so many boxes at a time before they inevitably get jumbled around. You never really get the chance to make any large, orderly arrangement."

Why natural selection acts in this way remains to be studied, but what the research showed is that, overall, the process results in what the authors call "evolutionary stalling" - while evolution is busy fixing one problem, it does at the expense of all other issues that need fixing. They conclude that at least in rapidly evolving populations, such as bacteria, adaptation in some modules would stall despite the availability of beneficial mutations. This results in a situation in which organisms can never reach a fully optimized state.

"The system has to be capable of being less than optimal so that evolution has something to act on in the face of disturbance - in other words, there needs to be room for improvement," Kaçar said.

Kaçar believes this feature of evolution may be a signature of any self-organizing system, and she suspects that this principle has counterparts at all levels of biological hierarchy, going back to life's beginnings, possibly even to prebiotic times when life had not yet materialized.

With continued funding from the John Templeton Foundation and NASA, the research group is now working on using ancestral sequencing to go back even further in time, Kaçar said.

"We want to strip things down even more and create systems that start out as what we would consider pre-life and then transition into what we consider life."

Heavier mixed-breed dogs have higher health risks if neutered or spayed early, according to a new study from researchers at the University of California, Davis. The study found mixed-breed dogs weighing more than 44 pounds as adults are at higher risk for one or more joint disorders if neutered before 1 year of age. Dogs weighing up to 43 pounds had no increased risk for joint problems. The study was published in the journal Frontiers in Veterinary Science.

It's standard practice in the U.S. and much of Europe to neuter dogs by 6 months of age. This study, which analyzed 15 years of data from thousands of dogs at UC Davis Veterinary Medical Teaching Hospital, suggests dog owners should consider their options carefully.

"Most dogs are mixed breeds," said lead author Benjamin Hart, distinguished professor emeritus at the UC Davis School of Veterinary Medicine. "We hope this study will influence the spay or neuter process in order to give people wishing to adopt a puppy the time to make an informed decision on when to spay or neuter."

Researchers examined common joint disorders including hip dysplasia, elbow dysplasia and cranial cruciate ligament tears, a knee injury, in five weight categories. They also looked at risks of mixed-breed dogs developing cancers based on weight but found no increased risk in any weight category compared to intact dogs.

The risk of joint disorders for heavier dogs can be up to a few times higher compared to dogs left intact. This was true for large mixed-breed dogs. For example, for female dogs over 43 pounds, the risk jumped from 4 percent for intact dogs to 10-12 percent if spayed before a year of age.

NEUTERING POLICIES SHOULD BE REVIEWED

"The study raises unique challenges," noted co-author Lynette Hart, professor at the UC Davis School of Veterinary Medicine. "People like to adopt puppies from shelters, but with mixed breeds it may be difficult to determine just how big the dog will become if you don't know anything about the dog's parents."

Neutering prior to adoption is a common requirement or policy of humane societies, animal shelters and breeders. The authors suggested the policy be reviewed and modified appropriately. Shelters, breeders and humane societies should consider adopting a standard of neutering at over a year of age for dogs that will grow into large sizes.

Lynette Hart said the study is especially relevant for people and organizations raising service dogs.

"They need to take a serious look at this," said Hart. "Joint disorders can shorten a dog's useful working life and impact its role as a family member."

A previous study conducted by the UC Davis researchers found health risks based on neuter age varied greatly depending on the breed of the dog.

While there are many pests affecting cotton, the reniform nematode is one the most damaging, with the ability to cause annual losses of approximately $33 million within the Mid-Southern United States. Farmers struggle to manage this pest as commercially available resistance is not widespread and a limited number of products are commercially available for use in suppressing the reniform nematode.

The reniform nematode is prevalent in Mississippi, especially in fields with silt loam soil classes, where current management plans involve a carousel of strategies, including rotation, seed-applied nematicides, in-furrow nematicides that are difficult to obtain, or the costly application of an in-furrow fumigant. Cotton farmers who rely on income from farming may find themselves in a situation where reniform nematode management costs outweigh the money earned from cotton sales.

In a recent study, researchers based at Mississippi State University set out to determine the most effective management approach that would maintain economical cotton yield and reduce losses that result from the reniform nematode. Their research made comparisons between either seed-applied nematicides, in-furrow nematicides, or a soil fumigant application. The research also explored integrated forms of management and considered how seed-applied nematicides and in-furrow nematicides worked together.

"We determined that seed-applied nematicides were better than the base fungicide seed treatment package without nematicide, but that one seed applied nematicide in particular coupled with an in-furrow nematicide produced yield that was almost equal to the in-furrow soil fumigant," explained Tom Allen, who works out of the Delta Research and Extension Center in Stoneville, Mississippi. "We also determined that even when adding multiple nematode-related treatments together that cotton yield could be improved and still remain economically advantageous."

However, in situations where the in-furrow fumigant was used, production costs were deemed too expensive and risk-averse. According to Allen, "The biggest takeaway is that, in situations with reniform nematode pressure above the economic threshold, cotton farmers can economically manage the nematode with an in-furrow nematicide to reduce early-season threats from the nematode."

One-third of the people who could benefit from a special type of savings account to cushion the blow of their health plan deductible aren't doing so, according to a new study.

And even among people who do open a health savings account (HSA), half haven't put any money into it in the past year. This means they may be missing a chance to avoid taxes on money that they can use to pay for their health insurance deductible and other health costs.

The study also finds that those who buy their health insurance themselves, and select a high-deductible plan on an exchange such as http://www.healthcare.gov, are less likely to open an HSA than those who get their insurance from employers who offer only a high-deductible option.

HSAs are different from the flexible spending accounts that some employers offer. HSAs can only be opened by people in health plans that require them to pay a deductible of $1,400 for an individual or $2,800 for a family before their insurance benefits kick in.

In a new paper in JAMA Network Open, a team led by researchers at the University of Michigan and VA Ann Arbor Healthcare System reports results from a national survey of more than 1,600 participants in high-deductible health plans.

Key findings

They note that half of those who had an HSA and put money into their account in the past year had socked away $2,000 or more. And among those who hadn't put money in, 40% said it was because they already had enough savings to cover their costs.

But those with lower levels of education were much less likely to have opened an HSA, and to have contributed to it even if they did open one. Those with lower levels of understanding of health insurance concepts, called health insurance literacy, were also less likely to put money in their HSA if they had one.

And one-third of those who didn't put money into their HSA said it was because they couldn't afford to save up for health costs.

"These findings are concerning, given that nearly half of Americans with private insurance now have high-deductible plans," says Jeffrey Kullgren, M.D., M.S., MPH, who led the study and has done other research on HDHPs and health care consumerism. "While policymakers have focused on expanding availability and permitted uses of HSAs, and increasing how much money they can hold, work is needed to help eligible enrollees open them and use them to get the care they need at a price they can afford."

Change needed

In the new paper and in a report from the U-M Institute for Healthcare Policy and Innovation, Kullgren and his colleagues call for more efforts to increase uptake of HSAs, and contributions to HSAs, by employers, health insurers and the health systems that provide care and bill insurers for that care.

Targeted interventions, especially those aimed at people with lower levels of education or health insurance literacy, should be developed.

The researchers note that as federal and state exchanges prepare to open for 2021 enrollment, expanding the types of exchange plans that are eligible to be linked to an HSA will be important. Currently, just 7% of the plans bought on exchanges are eligible for an HSA, even though many exchange plans come with a high deductible.

The study data come from an online survey of English-speaking adults under age 65; the study population was weighted to include a higher proportion of people with chronic health conditions than the national population.

For the survey, the researchers asked respondents about HSAs using the National Health Interview Survey definition of an HSA as "a special account or fund that can be used to pay for medical expenses" that are "sometimes referred to as Health Savings Accounts (HSAs), Health Reimbursement Accounts (HRAs), Personal Care accounts, Personal Medical funds, or Choice funds, and are different from Flexible Spending Accounts."

Obesity as assessed by body mass index is associated with an increased risk of heart disease and progression of kidney disease in those with chronic kidney disease (CKD). In this cohort of patients with CKD, Sankar D. Navaneethan et al studied whether different obesity measures such as intra-abdominal fat, liver fat, and subcutaneous fat (obtained using an MRI scan) were associated with known cardiometabolic risk factors. The authors further assessed whether physical function (measured using a 400m walk test) was independently associated with the same cardiometabolic risk factors. Their analysis suggests that all measures of higher fat content were associated with an increased level of cardiometabolic risk factors. While slower walk time were associated with an increased level of cardiometabolic risk factors, it did not modify the associations between fat measures and these risk factors. In summary, these data highlight that various abdominal fat measures and lower physical fitness levels are associated with a higher cardiovascular risk in those with CKD

Bottom Line: Adult survivors of childhood abdominal and pelvic cancers who had been treated with radiation therapy experienced abnormalities in body composition and had worse cardiometabolic health compared with the general population.

Journal in Which the Study was Published: Cancer Epidemiology, Biomarkers & Prevention, a journal of the American Association for Cancer Research

Author: Carmen Wilson, PhD, assistant member in the Epidemiology and Cancer Control department at St. Jude Children's Research Hospital

Background: "Body composition abnormalities and cardiometabolic impairments are of concern among survivors given that in the general population, these conditions increase the risk of developing life-threatening diseases including cardiovascular disease and type 2 diabetes," said Wilson. The impacts of radiation therapy on metabolic health have been previously reported for survivors of pediatric leukemia, brain tumors, and hematopoietic stem cell transplants, but the impacts on survivors of pediatric abdominal and pelvic tumors remained unclear, she said.

How the Study was Conducted: In this study, Wilson and colleagues assessed 431 adult survivors of pediatric abdominal or pelvic solid tumors who had been previously treated at St. Jude Children's Research Hospital. The median age of participants during the study was 29.9 years. The most frequent childhood diagnoses were neuroblastoma, Wilms tumor, and germ cell tumor, and the median age of participants at diagnosis was 3.6 years. Approximately 37 and 36 percent of participants had received abdominal and pelvic radiation therapy, respectively, as part of their treatment.

To assess the impacts of radiation therapy, the authors compared the participants' body composition, metabolic abnormalities, and physical function to those of the general population, using age-, sex-, and ethnicity-matched data from the 2013 to 2014 National Health and Nutrition Examination Survey (NHANES).

Results: Wilson and colleagues found that compared with data from NHANES, the survivors in their study were significantly more likely to have insulin resistance (33.8 percent vs. 40.6 percent), high triglycerides (10.02 percent vs. 18.4 percent), and low levels of high-density lipoproteins, commonly referred to as "good cholesterol" (28.9 percent vs. 33.5 percent). There were no significant differences in the levels of low-density lipoproteins ("bad cholesterol") between survivors and the general population.

The analyses also demonstrated that survivors of abdominal and pelvic solid tumors had lower relative lean body mass than the general population and that the lower relative lean body mass was associated with the dose of prior abdominal or pelvic radiation. Lean body mass, which measures the non-fat content of the body, is related to basal metabolic rate; therefore, an individual with lower lean body mass burns fewer calories while resting than someone with higher lean body mass, Wilson explained.

There was no significant difference in relative fat body mass between survivors and the general population; however, survivors who had high relative fat mass had reduced quadricep strength and poor physical performance (as measured by a sit-and-reach test and distance covered during a six-minute walk) compared with survivors who had low relative fat mass.

Author's Comments: "It is possible that abdominal and pelvic-directed radiation therapy damages postural muscles or subtly impairs sex hormone production, ultimately affecting muscle mass," said Wilson. She explained that radiation therapy has been shown to cause muscle injury, resulting in muscle fiber loss and loss of muscle regenerative cells, in animal studies. Wilson added that lifestyle choices may also impact relative lean mass and cardiometabolic health among survivors.

Wilson suggested that future research could examine the impact of radiation therapy and other cancer treatments on fat distribution across the body since increased abdominal obesity has been shown to be a better predictor of adverse health effects than measures of overall obesity.

In addition, Wilson is interested in exploring how interventions directed at lifestyle behaviors could improve lean mass and decrease fat mass among survivors of pediatric cancers. "While it may not be possible to avoid radiation therapy as a key treatment for many solid tumors, early research suggests that resistance training interventions in survivors increase lean mass," said Wilson. "Further work is needed to see if training would also impact cardiometabolic impairments in this population."

Study Limitations: A limitation of the study is that cardiometabolic outcomes may have been measured differently in the study cohort compared with those surveyed by NHANES.

To enhance the number of beneficial insect species in agricultural land, preserving semi-natural habitats and promoting crop diversity are both needed, according to new research published in the British Ecological Society's Journal of Applied of Ecology.

The study, by researchers in Sweden, the UK, Italy, Germany, Spain and France, found that increasing the diversity of crops in agricultural landscapes increased the diversity of beneficial insects such as pollinators. However, this benefit was only seen in landscapes with high proportions of semi-natural habitats such as forests and grassland.

In landscapes with both high crop diversity and semi-natural habitat cover, the researchers observed an increased diversity of ground beetle species as well as pollinators like bees and hoverflies. These insects have the potential to benefit crops through predating pests or pollinating flowering crop plants, both important for crop yields.

The same effects were not found for spiders, which surprised the researchers. "We expected pollinators to benefit because they are a highly mobile species, but the difference between ground beetles and spiders is harder to explain since both share similar adaptations to inhabit local crops." said Guillermo Aguilera of the Swedish University of Agricultural Sciences and lead author of the study.

Many beneficial insects and invertebrates are in decline, partly due to intensive crop management practices and a loss of semi-natural habitats from agriculture land, meaning the results have important implications. Guillermo Aguilera said: "We show that increasing local insect communities is possible in landscapes with semi-natural habitats by increasing crop diversity. Therefore, reducing the arable land and increasing semi-natural habitats is not always the only way for obtaining benefits from insects."

Insects and other invertebrates provide important ecosystem services. "Ground beetles and spiders are predators of species that can become pests. Wild pollinators have one of the most important roles in flowering crops. Both services, pest control and pollination, are important for the final crop yield." explains Guillermo Aguilera.

A greater diversity of crops may benefit pollinators through giving them a more varied and continuous food source. Oilseed rape, the most abundant flowering crop in the study area, provides massive resources for pollinators. However, its flowers are only open for a short period of time. Growing other crops that flower throughout the year could help support pollinators.

Semi-natural habitats provide nesting sites and additional food for both pollinators and predators. They're likely to be particularly beneficial to mobile species of ground beetles which often colonise crop fields from these habitats.

The researchers compiled data from seven previous studies that looked at invertebrate abundances in crop fields. The data spanned 154 crop fields in southern Sweden, an area consisting of arable land and semi-natural habitats, like grassland and woodland, between 2007 and 2017.

"The ultimate goal was to investigate the effect of crop diversity in the landscape with local communities of invertebrates" said Guillermo Aguilera. "After obtaining the invertebrate information and the coordinates of the fields where they were collected, we analysed the diversity of crops present in the landscape at the time of the sampling as well as the amount of semi-natural habitats such as grasslands."

The research focussed on southern Sweden, the most agriculturally important region in the country in terms of crop production. While this gave the researchers a large study area, they acknowledge that it's hard to generalise the results to a more global landscape.

Guillermo Aguilera said "It would be interesting to see what happens in other landscapes with a higher crop diversity by default than Sweden. It would also be interesting to look at how invertebrate communities respond to other forms of diversification in agriculture landscapes. For instance, the management of certain crops is something that can vary a lot between countries or regions."

A plant breeder's goal is to release cultivars that are commercially economical and environmentally sustainable. Breeders never know how well new cultivars will perform under commercial production until they are released and grown across different environments.

In an article recently published in the Journal of Plant Registrations, a journal of the Crop Science Society of America, researchers examined the impact the cultivar 'Madsen' on Pacific Northwest wheat, as well as other national and international breeding programs. Madsen has been grown in the Pacific Northwest for over 30 years--it was the most widely grown wheat cultivar from 1991 until 2004. It was found that of the new cultivars that were replacing Madsen in production, many of them had Madsen as a parent of the cultivar.

Madsen was released because of its resistance to strawbreaker foot rot and stripe rust, both of which are fungal diseases. Through subsequent research, Madsen was also found to be resistant to nematodes and Wheat yellow mosaic virus, and moderately resistant to common bunt and powdery mildew. Although not fully resistant, it was also less susceptible than other commercially available cultivars to stresses like low pH soils and Cephalosporium stripe.

The excellent resistance to biotic and abiotic stress of Madsen contributed to its widespread success in the Pacific Northwest, and has also allowed it to be used in breeding programs across the globe to protect the wheat crop against many diseases which threaten global food security.