University of Delaware professor wins top bio-innovation prize

Aditja Kunjapur PHOTO: AAAS.org

Biomolecular engineer Aditya Kunjapur, assistant professor at the University of Delaware, Newark, Delaware, recently won the 2024 BioInnovation Institute & Science Prize for Innovation,

Kunjapur and his colleagues have found a way to create bacteria that build and incorporate a key amino acid into their own proteins, making it easier to fight infections.

For this work toward building a better platform for possible ifuture bacterial vaccines, Kunjapur is the winner of the 2024 BioInnovation Institute & SciencePrize for Innovation, the American Association for the Advancement of Science announced April 5, in a news item on aaas.org.

“The prize seeks to reward scientists who deliver research at the intersection of the life sciences and entrepreneurship,” it noted.

“Dr. Kunjapur’s outstanding research demonstrates the potential to engineer live bacterial cells to produce and incorporate nitrated amino acids into antigenic proteins, thus shining a spotlight on these proteins for the human immune system,” Michael Funk, senior editor at Science is quoted saying in the new release. “This work provides a platform for antigen engineering that is adaptable, specific, and amenable to safety controls.”

Vaccines against bacterial infections would likely decrease the need for antibiotic medicines, which in turn could stem the development of antibiotic resistance in some key drugs, AAAS noted.

Kunjapur estimates that bacterial vaccines will have an estimated global market size of $39.6 billion by 2030.

In his winning essay published April 5 in Science, Kunjapur writes — “our primary hypothesis is that engineering cells to access a broader chemical repertoire of building blocks can improve live bacterial vaccine efficacy.”

According to the news report, Kunjapur saw potential in a building block from earlier research in which a bacterial protein was modified with a non-standard amino acid called para-nitro-L-phenylalanine (nitro-Phe). The combination “triggered sustained production of antibodies in mice, suggesting that the altered amino acid was making it easier for the immune system to access or recognize the bacterial protein,” the news report noted.

Kunjapur and colleagues programmed E. coli bacterial cells to produce their own nitro-Phe and incorporate it into target proteins. The altered proteins hold the potential of becoming the basis for a live bacterial vaccine, the researchers suggest.

“In principle, the nitro-Phe modified protein produced by the engineered bacteria within a patient would lead to a targeted, sustained, and protective immune response towards bacterial pathogens,” even versions of the protein that haven’t been nitrated, Kunjapur is quoted saying.

Kunjapur also indicated that his team’s bioengineering strategy could work with other bacteria as well, not just E coli.

“We could also continue to use E. coli as a platform vector that makes recombinant proteins that belong to other bacteria,” he said. “So you can pick your chassis or your protein delivery vehicle, but the proteins you choose to nitrate should determine what immune cells respond to.”

Kunjapur hopes to work toward a vaccine for staph infections. The Covid pandemic came in the way of procuring funding for expanding his work, so Kunjapur used his own funds for the patent application.

“At the time I had cautious optimism in investing in new potential vaccine modalities during the height of a pandemic, but a lot of it was also a bet on the people behind the idea and our collaborators,” he said.

Kunjapur co-founded Nitro Biosciences, Inc. with his postdoc, Neil Butler, to pursue the nitro-Phe technology. He said starting the company has made him think more about who is going to use the technology, and what kind of criteria and metrics they need to know so that it can be used successfully.

The BioInnovation Institute & Science Prize for Innovation, the editors of Science “seek to recognize bold researchers who are asking fundamental questions at the intersection of the life sciences and entrepreneurship. We seek scientists who can show that they have reached across field boundaries with an enthusiasm that combines outstanding basic science with an eye toward application in the marketplace,” Science.org says on its website.

Located in Copenhagen, Denmark, the BioInnovation Institute foundation (BII) is an international commercial foundation with a nonprofit objective supported by the Novo Nordisk Foundation. “BII operates an incubator to accelerate world-class life science innovation that drives the development of new solutions by early life science start-ups for the benefit of people and society,” the Science.org website said. University of Delaware professor wins top bio-innovation prize

Read More........→April 23, 2024

In World First, Scientists Share What Was Almost Certainly a Conversation with a Humpback Whale

Photo by Christopher Michel, CC license

In a world first, marine biologists were able to have a discourse with a humpback whale, pushing out the boundaries of cooperation and understanding that could be possible between our two species.

An adult female humpback whale, known as Twain, in Southeast Alaska, was located along with a group of whales and called with a recording of another humpback’s “whup/throp” call.

The recording was made by whales of the same group the day before, but the team didn’t know if the calls recorded were made by the same whale or were part of an exchange between two or more whales. To find out, the researchers conducted the trial on two days, with the first to find out if the whup calls they had recorded would be socially acceptable.

It turned out that whatever the whale(s) had been saying the day before was appropriate as far as Twain was concerned, and after the team broadcast the playback, she drifted away from her group and participated both physically and acoustically in three phases of interaction with the crew and their boat including periods of engagement, agitation, and disengagement.

First she called back, then she circled the boat three times, surfaced, and dived again. After this interaction, she gradually left.

Twain’s whup calls on day 2 and the whup calls recorded on day 1 were acoustically analyzed for both spectral and temporal features, specifically the inter-call interval, or latency between calls as measured by the time difference between the preceding call’s offset and the subsequent call’s onset.

The scientists determined that this metric would be able to determine both arousal and valence, thereby allowing them to get some idea of the emotional content of the exchange. The results indicated that substantial variation was found among the latencies in Twain’s calling behavior, which they took to mean excitement or arousal.

“After playing the contact call three times, we got this huge response,” said Brenda McCowan told the BBC. “Then, to keep the animal engaged, I started trying to match the latency of her calls to our calls. So, if she waited 10 seconds, I waited 10 seconds. We ended up matching each other. We did this 36 times over a 20-minute period.”

Twain’s calls were significantly shorter during engagement than either during the period defined as agitation, when she was circling the boat ejecting air through her blowhole, or as she was leaving.

The BBC reports that the songs of the humpback whale are thought to be among the most complex in the animal kingdom.A strong point of the whole experiment was that the results were determined with a degree of blinding—via independent, uninformed observers reporting on surface behavior and respiratory activity of the interacting whale.In World First, Scientists Share What Was Almost Certainly a Conversation with a Humpback Whale

Read More........→April 16, 2024

Scientists Discover Potential HIV Cure that Eliminates Disease from Cells Using CRISPR-Cas Gene Editing

HIV-1 virus particles under electron micrograph with H9 T-cells (in blue) – Credit: National Institute of Allergy and Infectious Diseases

A new study has unveiled a likely future cure for HIV which uses molecular scissors to ‘cut out’ HIV DNA from infected cells. To cut out this virus, the team used CRISPR-Cas gene editing technology—a groundbreaking method that allows for precise alterations to a patient’s genome, for which its inventors won the Nobel Prize in Chemistry in 2020. One of the significant challenges in HIV treatment is the virus’s ability to integrate its genome into the host’s DNA, making it extremely difficult to eliminate—but the CRISPR-Cas tool provides a new means to isolate and target HIV DNA. Because HIV can infect different types of cells and tissues in the body, each with its own unique environment and characteristics, the researchers are searching for a way to target HIV in all of these situations. In this study, which is to be presented ahead of this year’s European Congress of Clinical Microbiology and Infectious Diseases, the authors used CRISPR-Cas and two guide RNAs against “conserved” HIV sequences. They focused on parts of the virus genome that stay the same across all known HIV strains and infected T cells. Their experiments showed outstanding antiviral performance, managing to completely inactivate HIV with a single guide RNA and cut out the viral DNA with two guide RNAs. “We have developed an efficient combinatorial CRISPR-attack on the HIV virus in various cells and the locations where it can be hidden in reservoirs, and demonstrated that therapeutics can be specifically delivered to the cells of interest,” said Associate professor Elena Herrera Carrillo from the University of Amsterdam AMC. “These findings

HIV AIDS virus (in yellow) infecting a human cell – Credit: National Cancer Institute

represent a pivotal advancement towards designing a cure strategy.” The team has a long way to go before their cure will be available to patients, but said, “These preliminary findings are very encouraging’. Currently, HIV can be kept in check with anti-retroviral medication, but no one has actually been cured—although three patients receiving stem cell transplants for blood cancer were subsequently declared free of the disease when their HIV became undetectable. “We hope to achieve the right balance between efficacy and safety of this CURE strategy,” said Dr. Carrillo. “Only then can we consider clinical trials of ‘cure’ in humans to disable the HIV reservoir.“Our aim is to develop a robust and safe combinatorial CRISPR-Cas regimen, striving for an inclusive ‘HIV cure for all’ that can inactivate diverse HIV strains across various cellular contexts. Scientists Discover Potential HIV Cure that Eliminates Disease from Cells Using CRISPR-Cas Gene Editing

Read More........→March 26, 2024

Scientists Have 3D-Scanned Thousands of Creatures Creating Incredibly Intricate Images Anyone Can Access for Free

3D scanned creatures by oVert – Released by Florida Museum of Natural History / SWNS

An incredible new project has scanned thousands of creatures to advance scientific research and provide colorful images to the world. Natural history museums have entered a new stage of scientific discovery and accessibility with the completion of openVertebrate (oVert), a five-year collaborative project among 18 institutions to create 3D reconstructions of vertebrate specimens and make them freely available online. Now, researchers have published a summary of the project in the journal BioScience reviewing the specimens they’ve scanned to date, offering a glimpse of how the data might be  used to ask newquestions and spur the development of innovative technology. “When people first collected these specimens, they had no idea what the future would hold for them,” said Edward Stanley, co-principal investigator of the oVert project and associate scientist at the Florida Museum of Natural History. Such museums got their start in the 16th century as cabinets of curiosity, in which a few wealthy individuals amassed rare and exotic specimens, which they kept mostly to themselves. Since then, museums have become a resource for the public to learn about biodiversity. But, the majority of museum collections remain behind closed doors—accessible only to scientists who must either travel to see them or ask that a small number of specimens be mailed on loan—and oVert wants to change that. “Now we have scientists, teachers, students and artists around the world using these data remotely,” said David Blackburn, lead principal investigator of the oVert project and curator of herpetology at the Florida Museum. Beginning in 2017, the oVert team members took CT scans of more than 13,000 specimens, with vertebrate species across the tree of life, including over half the genera of all amphibians, reptiles, fishes, and mammals.

A collage of scanned fish from oVert – Released by Florida Museum of Natural History / SWNS

CT scanners use high-energy X-rays to peer past an organism’s exterior and view the dense bone structure beneath. Some specimens were also stained with a contrast-enhancing solution for visualizing soft tissues, like skin, muscle, and other organs. The models give an intimate look at internal portions of a specimen that could previously only be observed through destructive dissection and tissue sampling. “You want to protect specimens, but you also want to have people use them,” Blackburn said. “oVert is a way of reducing the wear and tear on samples while also increasing access, and it’s the next logical step in the

Hedgehog CT scan from oVert – Florida Museum of Natural History / SWNS

mission of museum collections.” Skeletons too large to fit into a CT scanner, like a humpback whale, were painstakingly taken apart so that 3D models of each individual bone could be scanned and reassembled. “These are not things you put in boxes and loan,” Blackburn pointed out. A set of iconic Galapagos tortoises at the California Academy of Sciences were each photographed in a 360-degree rotation. Photographing their undersides was problematic, as their curved shells made it impossible to keep them upright. After a few trial-and-error runs, they settled on placing the specimens on top of inflatable swimming tubes. Scientists have already used data from the project to gain astonishing insights into the natural world. Watch the incredible video below, and learn more at the bottom…In 2023, Edward Stanley was conducting routine CT scans of spiny mice and was surprised to find their tails were covered with an internal coat of bony plates, called osteoderms. Before this discovery, armadillos were considered to be the only living mammals with these structures. “All kinds of things jump out at you when you’re when you’re scanning,” Stanley said. “I study osteoderms, and through kismet or fate, I happened to be the one scanning those particular specimens on that particular day and noticed something strange about their tails on the X-ray. “That happens all the time. We’ve found all sorts of strange, unexpected things.”oVert scans were used to determine what killed a rim rock crown snake, considered to be the rarest snake species in North America. Another study showed that a group of frogs called pumpkin toadlets had become so small that the fluid-filled canals in their ears that confer balance no longer functioned properly, causing them to crash-land when jumping. One study of 500 oVert specimens revealed that frogs have lost and regained teeth more than 20 times throughout their evolutionary history. Other researchers concluded that Spinosaurus, a massive dinosaur that was larger than Tyrannosaurus rex and thought to be aquatic, would have actually been a poor swimmer, and thus likely stayed on land. And the list goes on, full of insights and ideas that would have been impossible or impractical before the project’s outset. “Now that we’ve been working on this for so long, we have a broad scaffold that allows us to take a broader view of

Fish CT scan from oVert – Florida Museum of Natural History / SWNS

evolutionary questions,” Stanley said. Artists and teachers are benefitting too Funded in part by the National Science Foundation, the value of the oVert project extends beyond science. Artists have used the 3D models to create realistic animal replicas, photographs of oVert specimens have been displayed as museum exhibits, and specimens have been incorporated into virtual reality headsets that give users the chance to interact with and manipulate them. A high school teacher in Cincinnati says it’s been a game-changer for her studies on evolution. “I teach juniors and seniors, and I absolutely love them, but they can be a tough audience,” said Jennifer Broo. “They know when things are fake, which makes them less engaged. Using the oVert models, my class has gotten so much better because I have had the opportunities to work with and expose my students to real data.”Visit Sketchfab to view a sample of 3D interactive models. At MorphoSource you can access the full openVertebrate repository.Scientists Have 3D-Scanned Thousands of Creatures Creating Incredibly Intricate Images Anyone Can Access for Free

Read More........→March 18, 2024

Scientists studied twins’ diets. Those who ate vegan saw fast results.

A member of staff works inside ‘Rudy’s Vegan Butcher’ shop, amid the coronavirus (COVID-19) outbreak, in London, Britain, October 30, 2020. Picture taken October 30, 2020. REUTERS/Henry Nicholls

Aleksandra Shai Chai needed a moment to process the idea that she would be stuck eating a vegan diet for eight weeks.

Shai Chai, who typically eats meat, was participating in a study to examine the effects of different diets on twins’ health. When Stanford University researchers randomly distributed slips of papers to the twins last year to indicate which diet they would follow, Shai Chai hoped hers would say “omnivore.”

Instead, it said “vegan.” Her twin sister, Mariya Foster, would eat a diet of meat and vegetables.

Shai Chai replaced her favorite foods – bacon, sushi and steak – with tofu, beans and vegetables. She didn’t love the diet, but when Shai Chai recently learned the study’s results, she felt thankful that she had briefly changed her eating habits.

After examining 22 pairs of identical twins, researchers found that vegan eaters had lower cholesterol, insulin and body weight than participants who followed a meat diet, according to the results published last week in the JAMA Network Open journal.

Vegan eaters’ low-density lipoprotein – bad cholesterol – dropped on average by 15.2 milligrams over eight weeks; omnivore dieters’ fell by 2.4. Vegan eaters on average shed 4.2 more pounds than omnivores, and their insulin – which regulates blood sugar – dropped by roughly 20 percent more.

“That made it all worth it, for sure,” Shai Chai, 43, told The Washington Post. “I was like, ‘All right, at least I have a little bit of payback; a little benefit for the trouble.”

Christopher Gardner, a Stanford University professor of medicine, said participants’ genetics have sometimes muddied researchers’ understanding of how different diets affect people’s health. He wanted to find a clear answer on the effects of eating or avoiding meat and animal products on cardiovascular health, and he thought the best subjects would be people with nearly identical genes and upbringings.

Near the start of 2022, Gardner found participants through Stanford’s twin research registry. Shai Chai and Foster had signed up a few years earlier, thinking the studies would be a fun way to contribute to scientific discoveries. They were exactly the type of twins Gardner was looking for.

Foster was born about five minutes before Shai Chai in December of 1979 in Kyiv before they immigrated to San Francisco in 1995. They like the same food (fish and chicken), the same music (pop and techno) and sometimes unknowingly buy the same clothes. The sisters, who are 5-foot-5 and live a few blocks from each other, said they often finish each other’s sentences and know what the other is thinking.

In May of 2022, participants in the study received 21 weekly prepackaged meals from Trifecta, a meal-delivery service, featuring food from their assigned diets. The vegan meals consisted of oatmeal, tofu, broccoli, spinach, beans, lentils and brown rice. The omnivore meals were still healthy, but featured eggs, chicken, turkey bacon, vegetables and jasmine rice. Participants logged their meals on Cronometer, an app that tracks diet and health data.

Shai Chai said the vegan meals were tastier than she had expected, though she disliked some dishes. Foster sacrificed her favorite snacks – M&Ms and granola bars – for healthy meats and fruits. After seeing examples of meals following their diets, participants purchased their own groceries during the second half of the eight-week study.

Dietitians called participants a few times to discuss how they were faring. Participants also gave blood and stool samples and underwent physical and cognitive tests to assess how the diets affected their balance and memories.

Shai Chai said that after four weeks of a vegan diet, she had more energy and slept better. Still, she missed her favorite foods. Once, she went out to a sushi restaurant with friends but forced herself to eat vegan sushi.

While some participants continued to follow a vegan diet after the study concluded in July 2022, Shai Chai said she immediately started eating sushi again – which she said tasted better than ever. Foster said she has become more mindful of eating healthy and has developed meal ideas from Trifecta.

Gardner, who’s a vegetarian, hopes nutritionists use the study’s results to persuade clients to eat more vegan products. He said that vegan food contributes to the three most crucial ways to improve cardiovascular health: by increasing fiber and decreasing saturated fat and body weight.

He added that eating a vegan diet offers health benefits that could prolong someone’s life – a discovery that Foster said has prompted sibling teasing.“I was already five minutes older,” Foster said, “and now I’m [figuratively] even older because she got the vegan diet.” Scientists studied twins’ diets. Those who ate vegan saw fast results.

Read More........→March 01, 2024