“This is fundamentally important, in particular from a topology-focused perspective, since framed knots provide a platform for topological quantum computations,” explained senior author, Professor Ebrahim Karimi, Canada Research Chair in Structured Light at the University of Ottawa.

“In addition, we used these non-trivial optical structures as information carriers and developed a security protocol for classical communication where information is encoded within these framed knots.”

The concept

The researchers suggest a simple do-it-yourself lesson to help us better understand framed knots, those three-dimensional objects that can also be described as a surface.

“Take a narrow strip of a paper and try to make a knot,” said first author Hugo Larocque, uOttawa alumnus and current PhD student at MIT.

“The resulting object is referred to as a framed knot and has very interesting and important mathematical features.”

The group tried to achieve the same result but within an optical beam, which presents a higher level of difficulty. After a few tries (and knots that looked more like knotted strings), the group came up with what they were looking for: a knotted ribbon structure that is quintessential to framed knots.

“In order to add this ribbon, our group relied on beam-shaping techniques manipulating the vectorial nature of light,” explained Hugo Larocque. “By modifying the oscillation direction of the light field along an “unframed” optical knot, we were able to assign a frame to the latter by “gluing” together the lines traced out by these oscillating fields.”

According to the researchers, structured light beams are being widely exploited for encoding and distributing information.

“So far, these applications have been limited to physical quantities which can be recognized by observing the beam at a given position,” said uOttawa Postdoctoral Fellow and co-author of this study, Dr. Alessio D’Errico.

“Our work shows that the number of twists in the ribbon orientation in conjunction with prime number factorization can be used to extract a so-called “braid representation” of the knot.”

“The structural features of these objects can be used to specify quantum information processing programs,” added Hugo Larocque. “In a situation where this program would want to be kept secret while disseminating it between various parties, one would need a means of encrypting this “braid” and later deciphering it. Our work addresses this issue by proposing to use our optical framed knot as an encryption object for these programs which can later be recovered by the braid extraction method that we also introduced.”

“For the first time, these complicated 3D structures have been exploited to develop new methods for the distribution of secret cryptographic keys. Moreover, there is a wide and strong interest in exploiting topological concepts in quantum computation, communication and dissipation-free electronics. Knots are described by specific topological properties too, which were not considered so far for cryptographic protocols.”

The origins

The idea behind the project emerged in 2018, during a discussion with Israeli researchers at a scientific meeting in Crete, Greece.

Scientists from Ben-Gurion University of the Negev and Bar-Ilan University, in Israel, developed the prime number encoding protocol.

The project then crossed the Mediterranean Sea and the Atlantic Ocean before ending up in Dr. Karimi’s lab located in the Advanced Research Complex at the University of Ottawa. That’s where the experimental procedure was developed and conducted. The resulting data were then analyzed, and the braid structure extracted through a specially devised program.

The applications

“Current technologies give us the possibility to manipulate, with high accuracy, the different features characterizing a light beam, such as intensity, phase, wavelength and polarization,” said Hugo Larocque. “This allows to encode and decode information with all-optical methods. Quantum and classical cryptographic protocols have been devised exploiting these different degrees of freedom.”

“Our work opens the way to the use of more complex topological structures hidden in the propagation of a laser beam for distributing secret cryptographic keys.”

“Moreover, the experimental and theoretical techniques we developed may help find new experimental approaches to topological quantum computation, which promises to surpass noise-related issues in current quantum computing technologies,” added Dr. Ebrahim Karimi.

The discovery, published in Environmental Microbiology, also provides a model for the understanding and modification of other economically and clinically important microbiomes, such as in soil or the gastrointestinal tract.

“Humans have appreciated the diverse aromas of cheeses for hundreds of years, but how these aromas impact the biology of the cheese microbiome had not been studied,” said Benjamin Wolfe, professor of biology in the School of Arts and Science at Tufts University and corresponding author of the study. “Our latest findings show that cheese microbes can use these aromas to dramatically change their biology, and the findings’ importance extends beyond cheese making to other fields as well.”

Many microbes produce airborne chemical compounds called volatile organic compounds, or VOCs, as they interact with their environment. A widely recognized microbial VOC is geosmin, which is emitted by soil microbes and can often be smelled after a heavy rain in forests. As bacteria and fungi grow on ripening cheeses, they secrete enzymes that break down amino acids to produce acids, alcohols, aldehydes, amines, and various sulfur compounds, while other enzymes break down fatty acids to produce esters, methyl ketones, and secondary alcohols. All of those biological products contribute to the flavor and aroma of cheese and they are the reason why Camembert, Blue cheese and Limburger have their signature smells.

The Tufts researchers found that VOCs don’t just contribute to the sensory experience of cheese, but also provide a way for fungi to communicate with and “feed” bacteria in the cheese microbiome. By pairing 16 different common cheese bacteria with 5 common cheese rind fungi, the researchers found that the fungi caused responses in the bacteria ranging from strong stimulation to strong inhibition. One bacteria species, Vibrio casei, responded by growing rapidly in the presence of VOCs emitted by all five of the fungi. Other bacteria, such as Psychrobacter, only grew in response to one of the fungi (Galactomyces), and two common cheese bacteria decreased significantly in number when exposed to VOCs produced by Galactomyces.

The researchers found that the VOCs altered the expression of many genes in the bacteria, including genes that affect the way they metabolize nutrients. One metabolic mechanism that was enhanced, called the glyoxylate shunt, allows the bacteria to utilize more simple compounds as “food” when more complex sources such as glucose are unavailable. In effect, they enabled the bacteria to better “eat” some of the VOCs and use them as sources for energy and growth.

“The bacteria are able to actually eat what we perceive as smells,” said Casey Cosetta, post-doctoral scholar in the department of biology at Tufts University and first author of the study. “That’s important because the cheese itself provides little in the way of easily metabolized sugars such as glucose. With VOCs, the fungi are really providing a useful assist to the bacteria to help them thrive.”

There are direct implications of this research for cheese producers around the world. When you walk into a cheese cave there are many VOCs released into the air as the cheeses age. These VOCs may impact how neighboring cheeses develop by promoting or inhibiting the growth of specific microbes, or by changing how the bacteria produce other biological products that add to the flavor. A better understanding of this process could enable cheese producers to manipulate the VOC environment to improve the quality and variety of flavors.

The implications of the research can even extend much further. “Now that we know that airborne chemicals can control the composition of microbiomes, we can start to think about how to control the composition of other microbiomes, for example in agriculture to improve soil quality and crop production and in medicine to help manage diseases affected by the hundreds of species of bacteria in the body,” said Wolfe.

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“For the last few decades, cell or tissue sheets have been increasingly used to treat injured or diseased tissues. A crucial aspect of tissue transplantation surgery, such as corneal tissue transplantation surgery, is surgical gripping and safe transplantation of soft tissues. However, handling these living substances remains a grand challenge because they are fragile and easily crumple when picking them up from the culture media,” said study leader Hyunjoon Kong, a professor of chemical and biomolecular engineering at Illinois.

Kong’s group, along with collaborators at Purdue University, the University of Illinois at Chicago, Chung-Ang University in South Korea, and the Korea Advanced Institute for Science and Technology, published their work in the journal Science Advances.

Current methods of transferring the sheets involve growing them on a temperature-sensitive soft polymer that, once transferred, shrinks and releases the thin film. However, this process takes 30-60 minutes to transfer a single sheet, requires skilled technicians and runs the risk of tearing or wrinkling, Kong said.

“During surgery, surgeons must minimize the risk of damage to soft tissues and transplant quickly, without contamination. Also, transfer of ultrathin materials without wrinkle or damage is another crucial aspect,” Kong said.

Seeking a way to quickly pick up and release the thin, delicate sheets of cells or electronics without damaging them, the researchers turned to the animal kingdom for inspiration. Seeing the way an octopus or squid can pick up both wet and dry objects of all shapes with small pressure changes in their muscle-powered suction cups, rather than a sticky chemical adhesive, gave the researchers an idea.

They designed a manipulator made of a temperature-responsive layer of soft hydrogel attached to an electric heater. To pick up a thin sheet, the researchers gently heat the hydrogel to shrink it, then press it to the sheet and turn off the heat. The hydrogel expands slightly, creating suction with the soft tissue or flexible electronic film so it can be lifted and transferred. Then they gently place the thin film on the target and turn the heater back on, shrinking the hydrogel and releasing the sheet.

The entire process takes about 10 seconds. Video: https://www.youtube.com/watch?v=EhMySEk-lRw&feature=emb_logo

Next, the researchers hope to integrate sensors into the manipulator, to further take advantage of their soft, bio-inspired design.

“For example, by integrating pressure sensors with the manipulator, it would be possible to monitor the deformation of target objects during contact and, in turn, adjust the suction force to a level at which materials retain their structural integrity and functionality,” Kong said. “By doing so, we can improve the safety and accuracy of handling these materials. In addition, we aim to examine therapeutic efficacy of cells and tissues transferred by the soft manipulator.”

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Materials provided by University of Illinois at Urbana-Champaign, News Bureau. Original written by Liz Ahlberg Touchstone. Note: Content may be edited for style and length.

The researchers are from The University of Texas Health Science Center at San Antonio (UT Health San Antonio) and the Wroclaw University of Science and Technology. Information gleaned by the American team helped Polish chemists to develop two molecules that inhibit the cutter, an enzyme called SARS-CoV-2-PLpro.

SARS-CoV-2-PLpro promotes infection by sensing and processing both viral and human proteins, said senior author Shaun K. Olsen, PhD, associate professor of biochemistry and structural biology in the Joe R. and Teresa Lozano Long School of Medicine at UT Health San Antonio.

“This enzyme executes a double-whammy,” Dr. Olsen said. “It stimulates the release of proteins that are essential for the virus to replicate, and it also inhibits molecules called cytokines and chemokines that signal the immune system to attack the infection,” Dr. Olsen said.

SARS-CoV-2-PLpro cuts human proteins ubiquitin and ISG15, which help maintain protein integrity. “The enzyme acts like a molecular scissor,” Dr. Olsen said. “It cleaves ubiquitin and ISG15 away from other proteins, which reverses their normal effects.”

Dr. Olsen’s team, which recently moved to the Long School of Medicine at UT Health San Antonio from the Medical University of South Carolina, solved the three-dimensional structures of SARS-CoV-2-PLpro and the two inhibitor molecules, which are called VIR250 and VIR251. X-ray crystallography was performed at the Argonne National Laboratory near Chicago.

“Our collaborator, Dr. Marcin Drag, and his team developed the inhibitors, which are very efficient at blocking the activity of SARS-CoV-2-PLpro, yet do not recognize other similar enzymes in human cells,” Dr. Olsen said. “This is a critical point: The inhibitor is specific for this one viral enzyme and doesn’t cross-react with human enzymes with a similar function.”

Specificity will be a key determinant of therapeutic value down the road, he said.

The American team also compared SARS-CoV-2-PLpro against similar enzymes from coronaviruses of recent decades, SARS-CoV-1 and MERS. They learned that SARS-CoV-2-PLpro processes ubiquitin and ISG15 much differently than its SARS-1 counterpart.

“One of the key questions is whether that accounts for some of the differences we see in how those viruses affect humans, if at all,” Dr. Olsen said.

By understanding similarities and differences of these enzymes in various coronaviruses, it may be possible to develop inhibitors that are effective against multiple viruses, and these inhibitors potentially could be modified when other coronavirus variants emerge in the future, he said.

The study, published today by The Lancet in the journal EClinicalMedicine, was commissioned by the World Health Organization (WHO) as part of a planned update to its guidelines for HIV antiretroviral treatment (ART). The study found that dolutegravir is the optimal medication for first-line treatment for people newly diagnosed with HIV, a choice that has not been clear over the past several years.

“Research supporting the 2016 WHO guidelines suggested that dolutegravir was effective and well tolerated, but its efficacy and safety among key populations, such as pregnant women and people living with both HIV and tuberculosis (TB), remained unclear,” said the study’s lead author, Dr. Steve Kanters, who completed the research as a PhD candidate in UBC’s School of Population and Public Health (SPPH). “In 2018, new research warned of a potentially serious increase in risk of neural tube defects in the children of women who became pregnant while taking this treatment.”

The risk of adverse reaction meant that, although dolutegravir was found to be favourable compared to other options, it was only recommended as an alternative, with an antiretroviral called efavirenz recommended as the primary treatment.

The study team, which included Dr. Nick Bansback, associate professor at SPPH, Dr. Aslam Anis, professor at SPPH and director of the Centre for Health Evaluation and Outcome Sciences (CHÉOS), and Dr. Ehsan Karim, assistant professor at SPPH, completed a network meta-analysis of research stemming from 68 available antiretroviral therapy (ART) clinical trials.

They found dolutegravir was superior to efavirenz in most outcomes, including viral suppression, tolerability, and safety. According to Kanters, the increased odds of viral suppression with dolutegravir could have a significant impact on achieving international goals for HIV treatment.

“We found about a five per cent increase in the probability of viral suppression, which means that more people who start treatment will be able to successfully control their HIV,” he said.

Another key attribute of dolutegravir is that it is effective in people who are resistant to NNRTI-class antiretrovirals, like efavirenz, a problem that is becoming increasingly common.

The analysis also showed that dolutegravir and efavirenz had similar rates of adverse events for pregnant women — the increased risk of neural tube defects for dolutegravir was estimated to be less than 0.3 per cent.

“The new evidence on neural tube defects show that the risk with dolutegravir is much more tolerable than previously thought and should quell the initial worry about this drug,” said Kanters.

“Dolutegravir appears to be here to stay as the preferred treatment for people newly diagnosed with HIV,” he said. “However, it is important to recognize the good that efavirenz has done over the past two decades, as it helped lead the ART scale-up around the world.”

Despite the many benefits of dolutegravir, dolutegravir use was associated with increased weight gain, a side effect that could increase the risk of aging-associated comorbidities, like heart attack or stroke.

“In many places, well-treated HIV has become a chronic condition and we are now seeing people living long lives with HIV,” said Kanters. “The research community will continue to monitor the effects dolutegravir may have on the healthy aging process.”

While this study is specifically focused on the optimal treatment for people newly diagnosed with HIV, an upcoming publication will review the evidence in support of switching to dolutegravir for people whose first treatment choice has been unsuccessful in controlling their infection. This recommendation could mean improved treatment for the many people living with HIV around the world who are unable to achieve viral suppression despite being on treatment.

Rising CO₂ levels helped end the last ice age, but the cause of this CO₂ rise has puzzled scientists for decades. Using geochemical fingerprinting of fossil corals, an international team of scientists has found new evidence that this CO₂ rise was linked to extremely rapid changes in ocean circulation around Antarctica.

The team collected fossil remains of deep-sea corals that lived thousands of metres beneath the waves. By studying the radioactive decay of the tiny amounts of uranium found in these skeletons, they identified corals that grew at the end of the ice age around 15,000 years ago.

Further geochemical fingerprinting of these specimens — including measurements of radiocarbon — allowed the team to reconstruct changes in ocean circulation and compare them to changes in global climate at an unprecedented time resolution.

Professor Laura Robinson, Professor of Geochemistry at Bristol’s School of Earth Sciences who led the research team, said: “The data show that deep ocean circulation can change surprisingly rapidly, and that this can rapidly release CO₂ to the atmosphere.”

Dr James Rae at St Andrew’s School of Earth and Environmental Sciences, added: “The corals act as a time machine, allowing us to see changes in ocean circulation that happened thousands of years ago.

“They show that the ocean round Antarctica can suddenly switch its circulation to deliver burps of CO₂ to the atmosphere.”

Scientists have suspected that the Southern Ocean played an important role in ending the last ice age and the team’s findings add weight to this idea.

Dr Tao Li of Nanjing University, lead author of the new study, said: “There is no doubt that Southern Ocean processes must have played a critical role in these rapid climate shifts and the fossil corals provide the only possible way to examine Southern Ocean processes on these timescales.”

In another study published in Nature Geoscience this week the same team ruled out recent speculation that the global increase in CO₂ at the end of the ice age may have been related to release of geological carbon from deep sea sediments.

Andrea Burke at St Andrew’s School of Earth and Environmental Sciences, added: “There have been some suggestions that reservoirs of carbon deep in marine mud might bubble up and add CO₂ to the ocean and the atmosphere, but we found no evidence of this in our coral samples.”

Dr Tianyu Chen of Nanjing University said: “Our robust reconstructions of radiocarbon at intermediate depths yields powerful constraints on mixing between the deep and upper ocean, which is important for modelling changes in circulation and carbon cycle during the last ice age termination.

Dr James Rae added: “Although the rise in CO₂ at the end of the ice age was dramatic in geological terms, the recent rise in CO₂ due to human activity is much bigger and faster. What the climate system will do in response is pretty scary.”

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Materials provided by University of Bristol. Note: Content may be edited for style and length.