What Is Computer Modeling and How Does It Work?
Recent news headlines are awash in references to “modeling the spread” and “flattening the curve.” You may have wondered what exactly this means and how it applies to the COVID-19 pandemic. Infectious disease modeling is part of the larger field of computer modeling. This type of research uses computers to simulate and study the behavior of complex systems using mathematics, physics, and computer science. Each model contains many variables that characterize the system being studied. Simulation is done by adjusting each of the variables, alone or in combination, to see how the changes affect the outcomes. Computer modeling is used in a wide array of applications, from weather forecasting, airplane flight simulation, and drug development to infectious disease spread and containment.
Continue reading “The Science of Infectious Disease Modeling”
Sohini Ramachandran, Brown University.
Credit: Danish Saroee/Swedish Collegium for Advanced Study.
Recent advances in computing enable researchers to explore the life sciences in ways that would have been impossible a few decades ago. One new tool is the ability to sequence genomes, revealing people’s full DNA blueprints. The collection of more and more genetic data allows researchers to compare the DNA of many people and observe variations, including those shared by people with a common ancestry.
Sohini Ramachandran , Ph.D., is director of the Center for Computational Molecular Biology and associate professor of biology and computer science at Brown University in Providence, Rhode Island. She is also a recent recipient of the Presidential Early Career Award for Scientists and Engineers (PECASE). Dr. Ramachandran researches the causes and consequences of human genetic variations using computer models. Starting with genomic data from living people, her lab applies statistical methods, mathematical modeling, and computer simulations to discover how human populations moved and changed genetically over time.
Continue reading “PECASE Honoree Sohini Ramachandran Studies the Genetic Foundations of Traits in Diverse Populations”
Historically, crowdsourcing has played an important role in certain fields of scientific research. Wildlife biologists often rely on members of the public to monitor animal populations. Using backyard telescopes, amateur astronomers provide images and measurements that lead to important discoveries about the universe. And many meteorologists use data collected by citizen scientists to study weather conditions and patterns.
Now, thanks largely to advances in computing, researchers in computational biology and data science are harnessing the power of the masses and making discoveries that provide valuable insights into human health.
Continue reading “Crowdsourcing Science: Using Competition to Drive Creativity”
Vern Schramm, professor of biochemistry at Albert Einstein College of Medicine, Bronx, New York. Credit: Albert Einstein College of Medicine.
Enzymes drive life. Without them, we couldn’t properly digest food, make brain chemicals, move—or complete myriad other vital tasks. Unfortunately, in certain cases, enzymes also can trigger a host of health problems, including cancer, bacterial infections, and hypertension (high blood pressure).
Understanding how enzymes work has been the research focus of Vern Schramm for more than 4 decades.
“When we started our work, we were driven not by the desire to find drugs, but to understand the nature of enzymes, which are critical to human life,” Schramm says. But his research already led to one drug, and promises many more.
Continue reading “Block an Enzyme, Save a Life”
A network of capillaries supplies brain cells with nutrients. Tight seals in their walls keep blood toxins—and many beneficial drugs—out of the brain. Credit: Dan Ferber, PLOS Biol 2007 Jun; (5)6:E169. CC by 2.5
The blood-brain barrier—the ultra-tight seal in the walls of the brain’s capillaries—is an important part of the body’s defense system. It keeps invaders and other toxins from entering the human brain by screening out dangerous molecules. But the intricate workings of this extremely effective barrier also make it challenging to design therapeutics that would help us. And as it turns out, getting a drug across the blood-brain barrier is only half the battle. Once it’s across, the drug needs to effectively target the right cells in the brain tissue. With this in mind, it’s no surprise that challenges this complex are solved through collaboration among scientists from several different specialties.
Elizabeth Nance , an assistant professor of chemical engineering at the University of Washington in Seattle and a recent recipient of the Presidential Early Career Award for Scientists and Engineers (PECASE), focuses her research on understanding the barriers in the brain and other cell- and tissue-based barriers in the body to see how nanoparticles interact with them. Her lab uses nanoparticles to package therapies that will treat newborn brain injury, which can occur when the brain loses oxygen and blood flow, often during or immediately prior to delivery. This damage can lead to cerebral palsy, developmental delays, or sometimes death. Early interventions for newborn brain injury can be valuable, but they need to target specific, injured cells without harming healthy ones.
Continue reading “PECASE Honoree Elizabeth Nance Highlights the Importance of Collaboration in Nanotechnology”
What do you have in common with rodents, birds, and reptiles? A lot more than you might think. These creatures have organs and body systems very similar to our own: a skeleton, digestive tract, brain, nervous system, heart, network of blood vessels, and more. Even so-called “simple” organisms such as insects and worms use essentially the same genetic and molecular pathways we do. Studying these organisms provides a deeper understanding of human biology in health and disease, and makes possible new ways to prevent, diagnose, and treat a wide range of conditions.
Historically, scientists have relied on a few key organisms, including bacteria, fruit flies, rats, and mice, to study the basic life processes that run bodily functions. In recent years, scientists have begun to add other organisms to their toolkits. Many of these newer research organisms are particularly well suited for a specific type of investigation. For example, the small, freshwater zebrafish grows quickly and has transparent embryos and see-through eggs, making it ideal for examining how organs develop. Organisms such as flatworms, salamanders, and sea urchins can regrow whole limbs, suggesting they hold clues about how to improve wound healing and tissue regeneration in humans.
Continue reading “Amazing Organisms and the Lessons They Can Teach Us”
Charmaine N. Nganje, PREP scholar at Tufts University in Boston.
Credit: Katherine Suarez.
Charmaine N. Nganje
Hometown: Montgomery Village, Maryland
Influential book : The Harry Potter series (not exactly influential, but they’re my favorite)
Favorite movie/TV show: The Pursuit of Happyness/The Flash
Languages: English (and a bit of Patois)
Unusual fact: I’m the biggest Philadelphia Eagles fan from Maryland that you’ll ever meet
Hobbies: Off-peak traveling
Q. Which NIGMS program are you involved with?
A. The Postbaccalaureate Research Education Program (PREP) at the Sackler School of Graduate Biomedical Sciences at Tufts University in Boston.
Continue reading “PREP Scholar’s Passion for Understanding Body’s Defenses”
Happy Fat Tuesday!
On this day, celebrated in many countries with lavish parties and high-fat foods, we’re recognizing the importance of fats in the body.
You’ve probably heard about different types of fat, such as saturated, trans, monounsaturated, omega-3, and omega-6. But fats aren’t just ingredients in food. Along with similar molecules, they fall under the broad term lipids and serve critical roles in the body. Lipids protect your vital organs. They help cells communicate. They launch chemical reactions needed for growth, immune function, and reproduction. They serve as the building blocks of your sex hormones (estrogen and testosterone).
Here we feature five of the hundreds of lipids that are essential to health.
Continue reading “Five Fabulous Fats”
Credit: Rommie Amaro, Jacob Durrant, Adam Gardner, and colleagues.
Ah, December—a month suffused with light-filled holidays, presents, parties . . . and the spread of colds and flu. This playful image uses a festive approach to the serious science of understanding and finding ways to combat the flu virus.
Continue reading “Festive Flu Virus Structure”
About 10 years ago, University of Utah geneticist Mark Yandell developed a software platform called VAAST (Variant Annotation, Analysis & Search Tool) to identify rare genes. VAAST, which was funded by NHGRI, was instrumental in pinpointing the genetic cause of a mystery disease that killed four boys across two generations in an Ogden, UT family.
NIGMS has been supporting Yandell’s creation of the next generation of his software, called VAAST 2, for the past few years. The new version incorporates models of how genetic sequences are conserved among different species to improve accuracy with which benign genetic sequences can be differentiated from disease-causing variations. These improvements can help identify novel disease-causing genes responsible for both rare and common diseases.
Yandell and his colleagues in the Utah Genome Project recently took part in a panel at the Sundance Film Festival called the “Genetics of Storytelling” to discuss film’s ability to convey the power of science and medicine. Yandell told the audience his story about his efforts to use VAAST to trace the Ogden boys’ genetic variation back to their great-great-great-great-great grandmother.
Continue reading “Computational Geneticist Discusses Genetics of Storytelling at Sundance Film Festival”