Molecular Awards

  The DNA foundation model Evo 2 has been published in the journal  Nature . Trained on the DNA of over 100,000 species across the entire tree of life, Evo 2 can identify patterns in gene sequences across disparate organisms that experimental researchers would need years to uncover. The machine learning model can accurately identify disease-causing mutations in human genes and is capable of designing new genomes that are as long as the genomes of simple bacteria. Evo 2 was developed by scientists from Arc Institute and NVIDIA, convening collaborators across Stanford University, UC Berkeley, and UC San Francisco. The model's code is publicly accessible from Arc's GitHub, and is also integrated into the NVIDIA BioNeMo framework, as part of a collaboration between Arc Institute and NVIDIA to accelerate scientific research. Arc Institute also worked with AI research lab Goodfire to develop a mechanistic interpretability visualizer that uncovers the key biologic...

  One stem cell generates 14 million tumor-killing natural killer (NK) cells in major cancer breakthrough. Scientists in China have unveiled a breakthrough way to mass-produce powerful cancer-fighting immune cells in the lab. By engineering early-stage stem cells from cord blood—rather than trying to modify mature natural killer (NK) cells—they created a streamlined process that generates enormous numbers of highly potent NK cells, including CAR-equipped versions designed to hunt specific cancers. NK cells play a critical role in the body’s early defense against viruses and cancer, along with other immune functions. Because of their natural ability to detect and destroy abnormal cells, they are an attractive tool for cancer treatment. In chimeric antigen receptor (CAR)-NK therapy, scientists equip NK cells with a lab-designed receptor (a CAR) so they can recognize a specific marker on cancer cells and attack them more precisely. Traditional CAR-NK approaches usually depend on matur...

  Viral infectious diseases have caused millions of deaths worldwide. Antiviral agents are critical for controlling these infections; however, an open-access database dedicated specifically to antiviral agents remains unavailable. Here, we present AntiviralDB  an expert-curated resource that compiles both approved and experimental antiviral agents with laboratory-confirmed   in vitro   activity against a broad spectrum of human viruses. These include the human immunodeficiency virus, coronaviruses, hepatitis viruses, influenza virus, respiratory syncytial virus, herpes simplex virus, varicella-zoster virus, human cytomegalovirus, human papillomavirus, dengue virus, Zika virus, Ebola virus, mpox virus, norovirus, chikungunya virus, and 16 other common or life-threatening pathogens. Each antiviral agent in the database is annotated with key information, including its molecular target,   in vitro   antiviral activity (IC 50 , EC 50 , and CC 50   across sp...

  Chromothripsis is also surprisingly common. Studies suggest that about one in four cancers shows signs of this type of chromosome damage, and in some cancers the rate is even higher. Nearly all osteosarcomas, an aggressive bone cancer, display evidence of chromothripsis, and many brain cancers show especially elevated levels. "This discovery finally reveals the molecular 'spark' that ignites one of the most aggressive forms of genome rearrangement in cancer," said senior author Don Cleveland, Ph.D., professor of cellular and molecular medicine at UC San Diego School of Medicine and member of UC San Diego Moores Cancer Center. "By finding what breaks the chromosome in the first place, we now have a new and actionable point of intervention for slowing cancer evolution." Chromothripsis begins when errors during cell division trap individual chromosomes inside small, fragile compartments known as micronuclei. When a micronucleus ruptures, the chromosome inside...

  Three years ago, Portnoy cofounded a startup, Laguna Biotherapeutics, that worked with scientists in his University of California, Berkeley lab to eliminate the bacteria's ability to cause disease while retaining its ability to rev up production of a type of immune system cell associated with increased survival in cancer patients. These so-called  gamma delta T cells  are general-purpose killers of cancer cells or any cell infected by a pathogen—bacteria, virus, or fungus. Laguna Bio will soon ask the FDA for clearance to evaluate the therapy in children with leukemia who have received unmatched bone marrow transplants. Stanford University Medical Center doctors hope that the engineered Listeria will boost gamma delta T cells in pediatric patients and help them stave off graft-versus-host disease, fight potentially deadly infections that take advantage of a transplant patient's compromised immune system, and prevent the cancer from returning. Portnoy and his colleagues ...

  Scientists have uncovered new DNA-binding proteins from some of the most extreme environments on Earth and shown that they can improve rapid medical tests for infectious diseases. The work has been published in  Nucleic Acids Research . The international research team, led by Durham University and working with partners in Iceland, Norway and Poland, analyzed genetic material from Icelandic volcanic lakes and deep-sea vents more than two kilometers below the surface of the North Atlantic Ocean. Nature is the world's largest source of useful enzymes, but many remain undiscovered. By using next-generation DNA sequencing, the researchers were able to search huge databases containing millions of potential proteins. This approach allowed them to identify previously unknown proteins that bind to single-stranded DNA and remain stable under harsh conditions such as high temperatures, extreme pH or high salt levels. The newly discovered proteins were carefully studied using a range of...