Molecular Awards

  A new multicenter study by researchers at the Icahn School of Medicine at Mount Sinai, in collaboration with the National Cancer Institute-funded Clinical Proteomic Tumor Analysis Consortium (CPTAC) and colleagues around the world, has discovered that the genes we are born with—known as germline genetic variants—play a powerful, underappreciated role in how cancer develops and behaves. The findings could have major implications for how doctors treat cancer in the future. While current treatments are largely guided by the genetic makeup of a patient’s tumor, this research suggests that looking at a patient’s inherited DNA could further refine diagnosis, risk prediction, and therapy selection. Until now, most cancer research has focused on somatic mutations—changes that occur in cells over a person’s lifetime. But inherited germline variants outnumber somatic mutations by a wide margin, and their impact on cancer has remained poorly understood, say the investigators. To conduct ...

  The groundbreaking study, published today in  Genomic Psychiatry , examines how different substances, such as alcohol, opioids, and stimulants, affect the brain’s aging process at the molecular level, potentially explaining why individuals with SUDs often experience early-onset age-related diseases . Accompanying the research article is an insightful editorial titled “The forgotten clockwork of the brain: Untangling accelerated aging in substance use disorders,” authored by Dr. Julio Licinio, Editor-in-Chief of  Genomic Psychiatry . Revolutionary Study Design and Methodology The research team, led by Drs. Bruno Kluwe-Schiavon, Gabriel Fries, and Consuelo Walss-Bass, analyzed brain tissue from 58 donors with SUDs to assess differential aging patterns using specialized epigenetic clocks designed specifically for brain tissues. Unlike previous studies that relied on more general epigenetic aging markers, this investigation employed brain-specific tools (DNAmClockCortical,...

  A new study from Oregon Health & Science University has uncovered how small molecules within bacteria interact with proteins, revealing a network of molecular connections that could improve drug discovery and cancer research . The multi-disciplinary research team, led by Andrew Emili, Ph.D., professor of systems biology and oncological sciences in the OHSU School of Medicine and OHSU Knight Cancer Institute, alongside Dima Kozakov, Ph.D., professor at Stony Brook University, studied Escherichia coli, or E. coli, a simple model organism, to map how metabolites—small molecules essential for life—interact with key proteins such as enzymes and transcription factors. These interactions control important processes such as cell growth , division and  gene expression, but how exactly they influence protein function is not always clear. The team used advanced tools like chemo-proteomics—developed in the Emili lab—and artificial intelligence-driven structural modeling...

  Bioengineering professor Michael C. Jewett shares how Stanford researchers are working with the building blocks of biology to produce greener chemicals, more climate-resilient agriculture, and new ways to repurpose food waste. Since the development of recombinant DNA technology 50 years ago – pioneered here at Stanford – we’ve seen the rise of breakthrough therapeutics that have transformed countless lives. What, then, could 50 more years of biotechnology do to support the health of our planet? “Synthetic biology advances our ability to engineer living systems to address some of the world’s biggest sustainability challenges, allowing us to rethink how we meet human needs on a planetary scale,” said Michael C. Jewett, professor of bioengineering in the Schools of Engineering and Medicine. In this Q&A, Jewett explains a bit of background about this field and exciting projects already in the works to enable new solutions for planetary health. Synthetic biolog...

  In a recent perspective article published in the journal  Nature Communications , over 30 scientists from around the world discussed the action plans and principles of the global scientific initiative designed to create detailed reference maps of human cells , known as the  Human Cell Atlas (HCA) , to establish the commitment of the HCA project to equity and ensure that the atlas is accessible and beneficial to all individuals. The HCA aims to map cells, the fundamental building blocks of life. It seeks to revolutionize the understanding of human biology by cataloging the diversity of cells, their functions, and interactions in healthy tissues. The goal of the project is to utilize this knowledge to enhance disease  diagnosis , treatment, and prevention across diverse populations. Furthermore, the HCA intends to bridge gaps in cellular biology by addressing questions of variation in cell types across individuals with different genetic backgrounds , environmental...

  Human cells , like the people they create, are dynamic and complex. And while researchers can create images and videos of how they move, organize and change their properties, it’s hard to efficiently and accurately describe all that’s happening. So a 75-person team at Seattle nonprofit Allen Institute is embarking on a 10-year project called  Cell Scapes to devise a new language using mathematics to capture these essential processes. “This is a new way of approaching very fundamental cell biology ,”  Ru Gunawardane , executive director and vice president of the Allen Institute for Cell Science , told GeekWire. “We want to combine math and biophysical modeling, which are things that people are doing right now, but in a siloed way in very different systems.” The Allen Institute was founded more than 20 years ago by the late Microsoft co-founder Paul Allen and his sister Jody Allen to dive into challenging problems in the biosciences. Previous efforts at multiple ins...

  In a recent study published in the journal  Scientific Reports , researchers investigated how a diet consisting exclusively of wild foods influences the composition, structure, and persistence of changes in the gut  microbiome  (GM) in modern humans. Background What happens when we stop eating anything cultivated or processed? Many urban populations consume mass-produced, high-sugar, and low-fiber diets that can disrupt GM balance. In contrast, “traditional” populations consuming fiber-rich, minimally processed foods tend to have greater microbial diversity linked to better immunity and lower inflammation. Prior research shows that diet changes can reshape the GM, but most studies remain within the boundaries of industrial diets based on domesticated foods. Since early humans relied on wild foods, studying this pattern could offer insights into our evolutionary biology . Further research is needed to validate these findings in diverse populations. The wild fo...

  Natural molecule reverses age- and dementia-related cognitive decline.  In a new study, researchers identified a molecule produced by a particular type of brain cell that reversed the cognitive decline seen in both healthy aging and dementia. It provides a deeper understanding of the aging process and a potential target for future treatments. In a new study, researchers identified a molecule produced by a particular type of brain cell that reversed the cognitive decline seen in both healthy aging and dementia. It provides a deeper understanding of the aging process and a potential target for future treatments. “Hevin is a well-known molecule involved in neural plasticity,” said the study’s co-corresponding author, Flávia Alcantara Gomes, PhD, head of the Cellular Neurobiology Laboratory in the Institute of Biomedical Sciences at UFRJ. “It’s naturally secreted by cells in the central nervous system that support the functioning of neurons and are known as astrocytes. W...

  Scientists have developed a powerful new method for selectively and reversibly breaking connections between brain cells —a leap forward that could transform how we study brain processes and, one day, how we treat neurological disorders such as epilepsy, addiction and post-traumatic stress disorder. The study, led by USC Dornsife College of Letters, Arts and Sciences neurobiologist Don Arnold and published in  eLife , introduces a suite of genetically engineered tools that allow researchers to eliminate either excitatory or inhibitory synapses—the specialized junctions where neurons communicate—with molecular precision. Crucially, the technique affects only the targeted synapses, leaving the rest of the neuron intact. This level of specificity, Arnold says, marks a first in neuroscience. "As far as I know, no one else has ever been able to ablate [knock out] specific synapses without affecting the whole neuron," he said. The ability to selectively dismantle parts of a n...

    As I wrote here yesterday, molecular biologist John Mattick’s new  Bio Essays  paper reviews many “anomalies” in the evidence that contradict the “junk DNA” paradigm that has reigned in biology over the past few decades. If there are so many problems with the paradigm, why do so many biologists still adhere to it? Mattick believes it’s because “many molecular biologists are invested in the current paradigm and a coherent alternative synthesis has not been offered.” His  BioEssays  paper thus turns to the task of offering a new paradigm that accepts the importance of non-coding DNA . But he notes that according to the famous historian of scientist Thomas Kuhn, a new paradigm won’t be accepted “unless it is both credible and consistent with the established body of knowledge.”  “Another Class of Genes That Produce RNAs” The main point of Mattick’s new paradigm is that in addition to protein-coding genes, there’s “another class of genes t...