“Currently, there’s a big push within the food industry to replace synthetic ingredients with natural alternatives, and this is being driven by consumers,” said Andrew S. Elder, doctoral candidate in food science. “Consumers want clean labels — they want synthetic chemical-sounding ingredients removed because of the fact that they don’t recognize them, and that some of them (the ingredients) have purported toxicity.”

The Penn State researchers studied a class of compounds called alkylresorcinols (AR). Plants such as wheat, rye and barley produce ARs naturally to prevent mold, bacteria and other organisms from growing on the grain kernels. The researchers wondered if ARs could also preserve food in the same way from a chemical standpoint.

Along with using more natural ingredients, the food industry is also supplementing more foods with healthy oils rich in omega-3 fatty acids. Adding these healthy oils to foods that normally would not contain them could boost the health benefits of these foods to consumers. However, omega-3 rich oils have a shorter shelf life, which could cause these foods to spoil more rapidly.

“Most people consume omega-3s from marine sources,” said Elder. “As they break down, they can make the product smell and taste fishy. Consumers then throw these products out and don’t buy them again, and this results in an economic loss.”

Antioxidants are compounds that slow the rate at which omega-3 fatty acids degrade, preserving their health benefits and preventing food from spoiling as quickly. While consumers demand more natural ingredients, the food industry has struggled to find natural antioxidants that are as effective as synthetic ones.

“There are not many natural alternatives for synthetic antioxidants,” said Elder. “Our work is focused on identifying new natural antioxidants to extend the shelf life of food and meet consumer demands.”

ARs have health benefits for humans as well and can help protect against cancer, according to a review published in European Food Research and Technology, making them ideal natural additives. ARs also come from the bran layer of cereal plants, which the food industry usually discards or uses for animal feed.

“Bran is often a waste stream,” said Elder. “We’re taking something that’s usually discarded in a waste stream and turning it into something useful.”

The team developed a technique to extract and purify ARs from rye bran, then studied how well ARs were able to preserve omega-3-rich oils in emulsions, where two fluids do not fully mix — for example, vinegar and oil. The researchers chose to study AR action in emulsions because most people consume oils as emulsions, such as salad dressings. The researchers reported their findings online in Food Chemistry, and the study will be published in the January print edition.

The researchers found that ARs did act as antioxidants in an emulsion, preventing omega-3 oils from spoiling as rapidly as they did in emulsions with no antioxidants added. Then, they compared ARs to two antioxidants widely used by the food industry — alpha-tocopherol or Vitamin E, a natural antioxidant; and butylated hydroxytoluene, a synthetic antioxidant. However, ARs were not as effective as either the natural or the synthetic antioxidant.

Although the ARs did not work as well as other antioxidants in this round of experiments, the researchers noted that their AR extracts were not completely pure, which could have reduced the effectiveness of the ARs. Also, the researchers used a blend of different ARs that had different molecular structures. Future work looking at different types of ARs will reveal whether an individual AR type is more or less effective than conventionally-used antioxidants.

“We’re trying to identify natural antioxidants that are consumer-friendly, safe and effective,” said Elder. “We hope that one day this work will lead to ARs being available on the market and provide more options for the food industry to use.”

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Researchers from a laboratory affiliated with the CNRS, l’ENS de Lyon, and l’Université Claude Bernard Lyon 1 have provided a first equation of this type, deduced from a measurement campaign conducted on crowds numbering tens of thousands of individuals. The physicists focused on cohorts of runners at the beginning of a marathon, as they are guided to the starting line by a row of organizers in successive sequences of walking and halting. This protocol creates a periodic and controlled disturbance similar to the stimulations that are typically used to probe the mechanical response of fluids.

Remarkably, group behavior varies very little from one assembly of runners to another, one race to another, and one country to another, with speed information propagating constantly at a little over 1 m/s. The researchers established a generic description that can precisely predict crowd flows, as flows observed in a road-race in Chicago in 2016 helped predict those of thousands of runners at the start of the Paris marathon in 2017.

By using technical standards from fluid mechanics to analyze images from the starting corrals of five races, researchers successfully measured crowd speed at each instant, subsequently describing it as a liquid flow. Their results show that information regarding the speed to adopt spreads to the back of the group in the form of waves measuring hundreds of meters, with no loss of intensity. In contrast, any change to the crowd’s movement trajectory dissipates quickly, spreading just a few meters through the crowd. In short, speed information spreads easily through this fluid, while orientational information does not.

The physicists now want to study the response of groups to extreme disturbances, in order to test the limits of their hydrodynamic description of crowds.

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“We could feed up to 200 million additional people with the calories lost to photorespiration in the Midwestern U.S. each year,” said principal investigator Donald Ort, the Robert Emerson Professor of Plant Science and Crop Sciences at Illinois’ Carl R. Woese Institute for Genomic Biology. “Reclaiming even a portion of these calories across the world would go a long way to meeting the 21st Century’s rapidly expanding food demands — driven by population growth and more affluent high-calorie diets.”

This landmark study is part of Realizing Increased Photosynthetic Efficiency (RIPE), an international research project that is engineering crops to photosynthesize more efficiently to sustainably increase worldwide food productivity with support from the Bill & Melinda Gates Foundation, the Foundation for Food and Agriculture Research (FFAR), and the U.K. Government’s Department for International Development (DFID).

Photosynthesis uses the enzyme Rubisco — the planet’s most abundant protein — and sunlight energy to turn carbon dioxide and water into sugars that fuel plant growth and yield. Over millennia, Rubisco has become a victim of its own success, creating an oxygen-rich atmosphere. Unable to reliably distinguish between the two molecules, Rubisco grabs oxygen instead of carbon dioxide about 20 percent of the time, resulting in a plant-toxic compound that must be recycled through the process of photorespiration.

“Photorespiration is anti-photosynthesis,” said lead author Paul South, a research molecular biologist with the Agricultural Research Service, who works on the RIPE project at Illinois. “It costs the plant precious energy and resources that it could have invested in photosynthesis to produce more growth and yield.”

Photorespiration normally takes a complicated route through three compartments in the plant cell. Scientists engineered alternate pathways to reroute the process, drastically shortening the trip and saving enough resources to boost plant growth by 40 percent. This is the first time that an engineered photorespiration fix has been tested in real-world agronomic conditions.

“Much like the Panama Canal was a feat of engineering that increased the efficiency of trade, these photorespiratory shortcuts are a feat of plant engineering that prove a unique means to greatly increase the efficiency of photosynthesis,” said RIPE Director Stephen Long, the Ikenberry Endowed University Chair of Crop Sciences and Plant Biology at Illinois.

The team engineered three alternate routes to replace the circuitous native pathway. To optimize the new routes, they designed genetic constructs using different sets of promoters and genes, essentially creating a suite of unique roadmaps. They stress tested these roadmaps in 1,700 plants to winnow down the top performers.

Over two years of replicated field studies, they found that these engineered plants developed faster, grew taller, and produced about 40 percent more biomass, most of which was found in 50-percent-larger stems.

The team tested their hypotheses in tobacco: an ideal model plant for crop research because it is easier to modify and test than food crops, yet unlike alternative plant models, it develops a leaf canopy and can be tested in the field. Now, the team is translating these findings to boost the yield of soybean, cowpea, rice, potato, tomato, and eggplant.

“Rubisco has even more trouble picking out carbon dioxide from oxygen as it gets hotter, causing more photorespiration,” said co-author Amanda Cavanagh, an Illinois postdoctoral researcher working on the RIPE project. “Our goal is to build better plants that can take the heat today and in the future, to help equip farmers with the technology they need to feed the world.”

While it will likely take more than a decade for this technology to be translated into food crops and achieve regulatory approval, RIPE and its sponsors are committed to ensuring that smallholder farmers, particularly in Sub-Saharan Africa and Southeast Asia, will have royalty-free access to all of the project’s breakthroughs.

Until now, it was unclear how this DNA packing affected development in early embryos. In a paper published this week in Science, researchers from the Perelman School of Medicine at the University of Pennsylvania found that in mouse embryos — only eight days after fertilization — compacted regions along the genome increase at protein-coding genes. Days later in the cell differentiation phase, these domains open to allow certain genes to be read and made into their corresponding proteins.

“This is a fundamental change in our understanding of how genes are controlled in the early embryo, even if we can’t yet see all the potential clinical impacts,” said Ken Zaret, PhD, director of the Penn Institute of Regenerative Medicine and a professor of Cell and Developmental Biology. “This study demonstrates the importance of the ‘off position’ for gene activity in early animal development.”

First author Dario Nicetto, PhD, a postdoctoral fellow in Zaret’s lab, explains that he and coauthors think that during the earliest stages of development, more compacted gene-coding regions arise so that a cell can make rapid “decisions” about which genes should be made into proteins. However, if genes are not open at the correct regions to be read and made into appropriate proteins, cells lose their proper identity and give rise to damaged tissue, and eventually death.

The team also found that compacted regions were marked by three methyl molecules, which occur at specific sites of protein binding along the genome. Basically, more trimethylation leads to more compaction, which means less of the genome is available to mRNA to eventually make full-length proteins. On the other hand, less trimethylation means less compaction, so more of the genome is available for transcribing into working proteins.

The team showed that if they deactivated the enzymes that add the methyl groups onto chromosomes, it causes out-of-place expression of cell-inappropriate genes leading to the eventual death of tissue. For example, they found that genes that are not normally “on” in liver cells are activated, which led to cell death and ultimately inadequate liver function.

Future studies will look at how the three enzymes “learn” which parts of the genome to silence.

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Until now, designing such structures has required technical expertise that puts the process out of reach of most people. Using the new program, anyone can create a DNA nanostructure of any shape, for applications in cell biology, photonics, and quantum sensing and computing, among many others.

“What this work does is allow anyone to draw literally any 2-D shape and convert it into DNA origami automatically,” says Mark Bathe, an associate professor of biological engineering at MIT and the senior author of the study.

The researchers published their findings in the Jan. 4 issue of Science Advances, and the program, called PERDIX, is available online. The lead authors of the paper are Hyungmin Jun, an MIT postdoc, and Fei Zhang, an assistant research professor at Arizona State University. Other authors are MIT research associate Tyson Shepherd, recent MIT PhD recipient Sakul Ratanalert, ASU assistant research scientist Xiaodong Qi, and ASU professor Hao Yan.

Automated design

DNA origami, the science of folding DNA into tiny structures, originated in the early 1980s, when Ned Seeman of New York University proposed taking advantage of DNA’s base-pairing abilities to create arbitrary molecular arrangements. In 2006, Paul Rothemund of Caltech created the first scaffolded, two-dimensional DNA structures, by weaving a long single strand of DNA (the scaffold) through the shape such that DNA strands known as “staples” would hybridize to it to help the overall structure maintain its shape.

Others later used a similar approach to create complex three-dimensional DNA structures. However, all of these efforts required complicated manual design to route the scaffold through the entire structure and to generate the sequences of the staple strands. In 2016, Bathe and his colleagues developed a way to automate the process of generating a 3-D polyhedral DNA structure, and in this new study, they set out to automate the design of arbitrary 2-D DNA structures.

To achieve that, they developed a new mathematical approach to the process of routing the single-stranded scaffold through the entire structure to form the correct shape. The resulting computer program can take any free-form drawing and translate it into the DNA sequence to create that shape and into the sequences for the staple strands.

The shape can be sketched in any computer drawing program and then converted into a computer-aided design (CAD) file, which is fed into the DNA design program. “Once you have that file, everything’s automatic, much like printing, but here the ink is DNA,” Bathe says.

After the sequences are generated, the user can order them to easily fabricate the specified shape. In this paper, the researchers created shapes in which all of the edges consist of two duplexes of DNA, but they also have a working program that can utilize six duplexes per edge, which are more rigid. The corresponding software tool for 3-D polyhedra, called TALOS, is available online and will be published soon in the journal ACS Nano. The shapes, which range from 10 to 100 nanometers in size, can remain stable for weeks or months, suspended in a buffer solution.

“The fact that we can design and fabricate these in a very simple way helps to solve a major bottleneck in our field,” Bathe says. “Now the field can transition toward much broader groups of people in industry and academia being able to functionalize DNA structures and deploy them for diverse applications.”

Nanoscale patterns

Because the researchers have such precise control over the structure of the synthetic DNA particles, they can attach a variety of other molecules at specific locations. This could be useful for templating antigens in nanoscale patterns to shed light on how immune cells recognize and are activated by specific arrangements of antigens found on viruses and bacteria.

“How nanoscale patterns of antigens are recognized by immune cells is a very poorly understood area of immunology,” Bathe says. “Attaching antigens to structured DNA surfaces to display them in organized patterns is a powerful way to probe that biology.”

Another key application is designing light-harvesting circuits that mimic the photosynthetic complexes found in plants. To achieve that, the researchers are attaching light-sensitive dyes known as chromophores to DNA scaffolds. In addition to harvesting light, such circuits could also be used to perform quantum sensing and rudimentary computations. If successful, these would be the first quantum computing circuits that can operate at room temperature, Bathe says.

• Initial data analysis has found no evidence of rings or satellites larger than one mile in diameter orbiting Ultima Thule.
• Data analysis has also not yet found any evidence of an atmosphere.
• The color of Ultima Thule matches the color of similar worlds in the Kuiper Belt, as determined by telescopic measurements.
• The two lobes of Ultima Thule — the first Kuiper Belt contact binary visited — are nearly identical in color. This matches what we know about binary systems which haven’t come into contact with each other, but rather orbit around a shared point of gravity.

“The first exploration of a small Kuiper Belt object and the most distant exploration of any world in history is now history, but almost all of the data analysis lies in the future,” said Alan Stern of the Southwest Research Institute in Boulder, Colorado.

Data transmission from New Horizons will pause for about a week while the spacecraft passes behind the sun as seen from here on Earth. Data transmission resumes Jan. 10, starting a 20-month download of the spacecraft’s remaining scientific treasures.

“Those of us on the science team can’t wait to begin to start digging into that treasure trove,” said Stern. New Horizons completed the farthest flyby in history when it came within about 2,200 miles (3,500 kilometers) of Ultima Thule at 12:33 a.m. EST on Jan. 1, zooming past the object at more than 32,000 miles (51,000 kilometers) per hour.

The Johns Hopkins Applied Physics Laboratory in Laurel, Maryland, designed, built and operates the New Horizons spacecraft, and manages the mission for NASA’s Science Mission Directorate. The Southwest Research Institute, based in San Antonio, leads the science team, payload operations and encounter science planning. New Horizons is part of the New Frontiers Program managed by NASA’s Marshall Space Flight Center in Huntsville, Alabama.

Follow the New Horizons mission on Twitter and use the hashtags #UltimaThule, #UltimaFlyby and #askNewHorizons to join the conversation. Live updates and links to mission information are also available on http://pluto.jhuapl.edu and www.nasa.gov.

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