To solve a problem, we have to see it clearly. Whether it’s an infection by a novel virus or memory-stealing plaques forming in the brains of Alzheimer’s patients, visualizing disease processes in the body is the first step toward alleviating human suffering. It’s also often the most difficult and costly.

But an artificial intelligence (AI) breakthrough by Virginia Tech computer scientists published in Cell Systems is bringing those fog-bound processes into focus.

The new ProRNA3D-single tool developed by Debswapna Bhattacharya, associate professor of computer science, and his research team offers a new and more accurate way to predict and visualize what’s going on inside us when novel viruses and devastating neurological diseases attack—offering a new pathway to treating them or preventing them altogether.

“The ultimate goal is to accelerate the drug discovery process to prevent the RNA viruses from interacting with host proteins, potentially stopping infections before they grow into pandemics or inhibiting altered function of RNA binding proteins in Alzheimer’s disease,” he said.

A bilingual ChatGPT for biology

For decades, scientists have struggled to understand how viral ribonucleic acid (RNA) binds to human proteins to form complex 3D molecular structures. That’s important because those forms control whether pathogens such as SARS-CoV-2 can spread or if diseases such as Alzheimer’s take hold.

AI systems are helping by creating an “alphabet” to represent DNA, RNA, and proteins, which researchers can then use to train large language models (LLMs) for biological sequences to analyze and simulate how these molecules interact in the body.

But ProRNA3D-single goes further than alphabets. It uses AI to generate finely detailed images of these molecules in 3D.

“The bio LLMs are basically like ChatGPT, but for biological sequences. And just like ChatGPT, we can ask our models questions and get answers,” Bhattacharya said.

The Virginia Tech team took two existing biological LLMs—one for proteins and another for RNA sequences—and created a third model that allows these LLMs to “talk” to each other. Out of those “conversations,” ProRNA3D-single can generate 3D structural models of viral RNA interacting with proteins in the body. It’s a big breakthrough.

“This is basically a neural pairing of two different large language models, leading to bilingual reasoning,” Bhattacharya said. “From a computer science standpoint, that’s a contribution in itself.”

Even recent breakthrough AI models developed by Google DeepMind and others have fallen far short of accurately predicting and modeling protein-RNA complex 3D structures, leaving researchers to rely primarily on costly trial-and-error experiments.

But the new ProRNA3D-single method has significantly increased accuracy and has opened a promising new road to AI-assisted scientific discovery.

Bringing disease into focus

Little is known about how novel viruses such as SARS-CoV-2 evolve or how conditions such as dementia develop at the molecular level, but ProRNA3D-single helps fill those gaps and generate more accurate maps of the inner landscape. Now, instead of guessing, drug developers can analyze where viruses attach to human proteins and design treatments to block them. That could dramatically cut the time and cost of interventions and speed up responses to outbreaks.

“If you remember the COVID-19 pandemic and the mRNA-based vaccine that actually helped a lot—that vaccine worked because it was an RNA-based therapeutic,” said Sumit Tarafder, a fourth-year Ph.D. student on the project. “Modeling of protein-RNA interactions in 3D is crucial, so that we know where the drug can actually target molecules that cause disease.”

Not only that, but by generating new data about RNA-protein interactions, the ProRNA3D-single model creates insights that could lead to groundbreaking treatments for a range of maladies.

While the Virginia Tech team used viruses as a case study, “the method is fully generic. It’s not specific to a single type of virus or a family of viruses,” Bhattacharya said. “This method can be applied to any use case.”

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Open science, global impact

Innovative methods like ProRNA3D-single don’t come easily. Two years of work have gone into this project.

Alumnus Rahmatullah Roche, Ph.D. ’24, did much of the coding, publishing more than a dozen papers on the subject during his doctoral work. He has since joined Columbus State University as a tenure-track assistant professor.

“The lead Ph.D. students did enormous work,” Bhattacharya said. “They did most of the heavy lifting.”

“We can’t overstate the importance of investing in science to benefit society. We believe that openness is the key to making science accessible to everybody,” Bhattacharya said. “Taxpayers fund us, so we have an obligation to give back, which is why we make our work open source and publicly available.”

The team hopes to continue development of the tool to improve its accuracy and get even more detailed models of various biological processes.

“We should constantly remind ourselves the problem is far from being solved,” Bhattacharya said. “We made progress, yes, but we’re mindful of the fact that these models have a long way to go.”

Three new technologies to detect and manage African Swine Fever have been unveiled in the Philippines amid ongoing concerns about a vaccine imported from Vietnam.

African Swine Fever, which causes hemorrhagic fever in pigs, has had a devastating effect on the country’s swine industry, with outbreaks occurring in 76 out of 82 provinces since 2019 and six provinces recording active cases last month.

Vietnam is also battling a serious outbreak, with thousands of pigs infected.

The Philippines’ Department of Science and Technology (DOST) and Filipino-owned life science company BioAssets Corporation have developed a rapid DNA extraction kit and real-time detection kit for farmers.

A mobile biocontainment laboratory, developed by BioAssets Corporation, is designed to support rapid response to potential outbreaks and improve disease surveillance, enabling farmers to diagnose the disease on-site.

DOST Secretary Renato U. Solidum, Jr. said the interventions demonstrated how science, technology and innovation can offer “holistic solutions to pressing animal health challenges” impacting food security.

However, Fermin Diaz, editor of the online magazine Livestock and Meat Business, told SciDev.Net: “The way I look at it, it seems that these new tools are just palliatives … so that the DOST can say that they are addressing the matter.

“Those kits have very minimal contribution to the overall diagnostic aspect of disease management.”

African Swine Fever is a highly contagious viral disease affecting domestic and wild pigs, with mortality rates as high as 100%. It has caused huge economic losses and disruption to the pork supply chain, threatening food security across the region.

If left unchecked, there is a risk that the virus could mutate, potentially making it more transmissible or virulent.

The Philippine government, with the assistance of the UN Food and Agriculture Organization (FAO), has adopted a three-pronged strategy to combat the virus in the last year, focused on prevention, control and vaccination.

Constante Palabrica, the Philippines’ agriculture undersecretary for livestock, said cases were going down thanks to “zoning and checkpoints” as part of the new program. He noted that no microbial mutations have been identified.

According to official figures, more than 495 cities and municipalities have been upgraded from “red” infected zones to “pink”, meaning they are no longer under quarantine.

Vaccine controversy

The Philippine government has imported large quantities of the Vietnam-made AVAC vaccine, despite concerns over trial data, it emerged at a House of Representatives committee meeting on trade, industry and agriculture in June.

The vaccine was distributed to local livestock raisers in a bid to prevent mass deaths of farmed pigs, a source of livelihood for thousands of people.

But the move alarmed some who fear a repeat of the experience in Vietnam with live attenuated vaccines—a live vaccine which has been weakened—where it affected the health of pigs.

“The nationwide implementation of Live Attenuated Vaccines in Vietnam for prophylaxis has likely influenced the viral genetic pool among the swine population,” said an article published in the journal Scientific Reports.

The Philippines’ Food and Drug Administration said in 2024 that field trials had been ongoing in the country for almost two years and claimed that the vaccine had a 100 efficacy with no side effects. However, no trial data has been made public.

“I would like to express grave concern over the vaccine trials,” said representative Ferjenel Biron, a doctor of medicine, during the 11 June Congressional hearing.

He questioned why a Certificate of Public Registration was issued despite two veterinarians who evaluated the AVAC vaccine deeming it to be unsafe.

According to Diaz, the vaccine has a low acceptance rate among farmers in the Philippines, with only about “5 to10%” using it.

“The product is being heavily and indiscriminately endorsed by the Department of Agriculture … with very inadequate orientation taken about the product’s risks and downside effects,” he added.

An association of swine raisers in Batangas province told SciDev.Net it was concerned about using the vaccine on swine herds.

“We won’t take the risk,” the group representative said on condition of anonymity. “It’s still experimental.”

The AVAC ASF LIVE vaccine, was created by AVAC Vietnam JSC and imported into the Philippines by KPP Powers Commodities Inc. It is derived from a virus strain called ASFV-G-MGF, or MGF.

In 2022, the US Department of Agriculture issued a public notice warning that MGF had “the potential to pose a severe threat to animal health or animal products”.

“It has also been determined that the virus strain is not safe for use in pigs because its genome is unstable, potentially leading to reversion of virulence,” the notice warned.

Low vaccination rate

Nguyen Van Diep, general director of AVAC Vietnam Joint Stock Company and project leader for the ASF vaccine, said the vaccine been in use since July 2022.

“The reason that outbreaks still occur is because of the low vaccination rate,” he told SciDev.Net. “According to our estimates, at any given time, it is at less than 5%.”

Disputing that the vaccines from AVAC sent to the Philippines were substandard, Diep said vaccine-makers adhered to strict standards on quality and highlighted the perishable nature of vaccines.

“Preserving a live-attenuated vaccine is also important. It should be kept at 2 to 8C. It has a shelf life of 24 months from the date of manufacture,” he said.

Since the first outbreak in China in 2018, 20 countries have reported African Swine Fever, according to the World Organisation for Animal Health.

Lionel Dabbadie, FAO representative in the Philippines, told SciDev.Net: “There is no cure as of today, so traditional control measures, such as culling infected and susceptible animals, enforcing stringent biosecurity protocols, and restricting the movement of pigs and pork products have been the main control method used so far,” Dabbadie told SciDev.Net.

He stressed that a multi-faceted approach was crucial to stem the disease. “Vaccines are promising, but they are not a panacea,” he said.

A joint research team from POSTECH and Inha University researchers has successfully developed a novel biomaterial that overcomes the limitations of natural elastin.

Our bodies contain a special protein called elastin, which has a remarkable ability to stretch like a rubber band and snap back to its original shape. This elasticity is crucial for the function of various organs, allowing the lungs to inhale and exhale, blood vessels to expand and contract with each heartbeat, and the skin to remain smooth and supple.

Despite its utility, using natural elastin for medical applications is challenging. It’s available in limited quantities naturally, the purification process is complex, and there’s a risk of an immune reaction when administered to humans in other individuals. To address these issues, scientists developed elastin-like polypeptides (ELPs), which could be produced in large quantities but could not fully replicate the complex, precise functions of natural elastin.

The joint research team from POSTECH and Inha University created a new protein by selecting and reassembling the most critical parts of tropoelastin, the precursor to human elastin. They precisely combined three distinct domains—a hydrophobic domain that influences the protein’s physical properties, a cross-linking domain that provides stability, and a cell-interaction domain that promotes interactions between cells. This new protein was named elastin domain-derived protein (EDDP).

EDDP offers several advantages. It can be mass-produced like conventional ELPs while retaining the elasticity and resilience comparable to natural elastin. More remarkably, EDDP promotes cell adhesion and growth by transmitting signals that were lacking in conventional ELPs. This enhanced cell-interaction function directly aids cell survival and growth, making it highly effective in regenerating damaged tissues.

Professor Hyung Joon Cha of POSTECH expressed optimism about the discovery, stating, “This newly developed EDDP could be used to regenerate tissues where elasticity is crucial, such as heart valves, blood vessels damaged by heart disease, or torn ligaments.”

The research, led by Professor Cha’s team at POSTECH with Seung Kyeum Cho and Professor Yun Jung Yang’s team at Inha University, is published online in Acta Biomaterialia.

Alexander Fleming’s accidental discovery of penicillin in 1928 changed the world: Once-common bacterial infections, sometimes deadly, were treatable, and a slew of antibiotics followed. But bacteria have proven a wily adversary, adapting to resist antibiotic treatment.

In a recent scientific advancement, a team led by James Fraser, chair and professor of Bioengineering and Therapeutic Sciences at the University of California, San Francisco, developed a compound that may restore the efficacy of a class of antibiotics known as streptogramins.

To do this, the researchers used bright X-rays at the Stanford Synchrotron Radiation Lightsource (SSRL) at the Department of Energy’s SLAC National Accelerator Laboratory and the Lawrence Berkeley National Laboratory’s Advanced Light Source (ALS) to study molecular structures and interactions between candidate drug compounds and bacteria. Their findings, published in Structure, point to a promising lead in designing new therapies.

“This discovery is an exciting step forward in the fight against antibiotic resistance,” said Aina Cohen, division director of Structural Molecular Biology at SSRL. “By harnessing the intense X-ray beams at synchrotrons, the Fraser group identified previously hidden binding sites that offer a promising path to inhibit a bacterial enzyme that makes antibiotics less effective. This could help bring back the power of certain antibiotics that no longer work against resistant infections.”

Narrowing the search with powerful X-rays

Antibiotics kill bacteria by disrupting structures and functions crucial for the bacteria’s survival. Over time, bacteria have evolved mechanisms to interfere with this process—with some particularly pesky bacteria able to resist multiple antibiotics. Streptogramins are naturally occurring antibiotics that can overcome these mechanisms in multidrug-resistant Gram-positive bacteria, which often cause blood or severe skin infections. Streptogramins bind to the bacteria’s ribosome to hinder critical protein synthesis processes.

In recent years, some multidrug-resistant Gram-positive bacteria strains evolved to produce a protein, Virginiamycin acetyl transferase D (VatD), that interferes with the binding of streptogramin to the ribosome. Fraser’s team aims to develop a drug that interrupts VatD’s ability to do that.

The first step is to find small molecule fragments that could bind to VatD. These fragments could serve as a foundation for creating drugs that inhibit VatD. Using special libraries that house chemical and structural information on hundreds of small molecules, Pooja Asthana, postdoctoral researcher in the Fraser lab and lead author of the paper, soaked each candidate into a VatD crystal to allow them to interact and hopefully bind.

To check if the binding was successful, she turned to X-ray crystallography at SSRL and ALS. The high-resolution structural information from this technique helped Asthana determine if the candidate bound to the protein target site. More than 30 fragments did bind. Next, she added other chemical groups to the fragments to enhance their binding with VatD.

After creating and testing approximately 70 such compounds, she found one showing moderate activity, indicating it could be further developed to enhance its properties. “I was both excited and a little surprised when we got the hit,” said Asthana. “After all the rounds of screening and optimization, seeing a compound that checked all the boxes felt rewarding.”

Next, the team will try to increase this compound’s inhibition by making small changes to its structure through adding or removing molecular groups.

“This work shows that we can use SSRL to rapidly generate starting points for inhibitors that could potentiate the streptogramin class of antibiotics,” said Fraser. “With further development, inhibitors based on these scaffolds might enable streptogramin antibiotics to be used in clinical and agricultural contexts where antibiotic resistance currently renders streptogramins and other classes of antibiotics ineffective.”