New Technology May Help Reduce Serious and Costly Post-Surgical Infections—Using Nothing but Air

According to a recent estimate, implant infections following hip and knee replacement surgeries in the U.S. may number 65,000 by 2020, with the associated healthcare costs exceeding $1 billion. A new small, high-tech device could have a significant impact on improving health outcomes and reducing cost for these types of surgeries. The device, Air Barrier System (ABS), attaches on top of the surgical drape and gently emits HEPA-filtered air over the incision site. By creating a “cocoon” of clean air, the device prevents airborne particles—including the bacteria that can cause healthcare-associated infections—from entering the wound.

Air Barrier System
The Air Barrier System creates a “cocoon” of clean air (gray area with size indicated) over a surgical site to remove airborne contaminants and reduce the risk of infection in patients who are receiving an artificial hip, a blood vessel graft, a titanium plate in the spine or other implants.

Scientists recently analyzed the effectiveness of the ABS device in a clinical study Exit icon—funded by NIGMS—involving nearly 300 patients. Each patient needed an implant, such as an artificial hip, a blood vessel graft in the leg or a titanium plate in the spine. Because implant operations involve inserting foreign materials permanently into the body, they present an even higher risk of infection than many other surgeries, and implant infections can cause life-long problems.

The researchers focused on one of the most common causes of implant infections—the air in the operating room. Although operating rooms are much cleaner than almost any other non-hospital setting, it’s nearly impossible to sterilize the entire room. Instead, the scientists focused on reducing contaminants directly over the surgical site. They theorized that if the air around the wound was cleaner, the number of implant infections might go down. Continue reading

Six Things to Know About DNA and DNA Repair

Deoxyribonucleic acid, better known as DNA, was first identified on a discarded surgical bandage almost 150 years ago. Increasingly sophisticated tools and techniques have allowed scientists to learn more about this chemical compound that includes all the instructions necessary for building a living organism. From among the dozens of fascinating things known about DNA, here are six items touching on the make up of DNA’s double helix, the vast amounts of DNA packed into every human’s cells, common DNA errors and a few ways DNA can repair itself.

1. DNA is in every living thing.

Nucleotide
DNA consists of two long, twisted chains made of nucleotides. Each nucleotide contains one base, one phosphate molecule and the sugar molecule deoxyribose. The bases in DNA nucleotides are adenine, cytosine, guanine and thymine. Credit: NIGMS.

The chemical instructions for building a person—and every other creature on Earth—are contained in DNA. DNA is shaped like a corkscrew-twisted ladder, called a double helix. The two ladder rails are referred to as backbones, made of alternating groups of sugar and phosphate. The ladder’s rungs are made from four different building blocks called bases, arranged in pairs: adenine (A) paired with thymine (T), and cytosine (C) paired with guanine (G). Humans have about 3 billion base pairs in each cell. The order of the base pairs determines the exact instructions encoded in that part of the DNA molecule. Also, the sequence of DNA base pairs in one person is about 99.9 percent identical to that of everyone else.

2. Humans have a lot of DNA.

Humans begin as a single fertilized cell containing (with some rare exceptions) the full complement of DNA—the genome—arranged into 46 discrete chromosomes (23 pairs, with mom and dad each contributing half of each pair) in the cell’s nucleus. There are about 5 feet of DNA coiled up tightly in that first cell. All the information in the DNA is replicated each time the cell divides. The amount of DNA packed into all of an adult’s cells is on the order of 100 trillion feet (about 19 billion miles)—so that if the DNA chain was stretched out, it would be long enough to reach back and forth between the Earth and the Sun more than 200 times. Continue reading

Birthdays, Nobel Prizes and Basic Research

James D. Watson
James D. Watson. Credit: Wikimedia Commons, Cold Spring Harbor Laboratory.

April 6 is the birthday of two Nobel Prize winners in physiology or medicine—James Watson and Edmond H. Fischer. They have also both been NIGMS-supported researchers.

Double helix model
In 1953, Watson and Crick created their historic model of the shape of DNA: the double helix. Credit: Cold Spring Harbor Laboratory archives.

James D. Watson, born on this day in 1928, was honored with the Nobel Prize in 1962. He shared it with Francis H. Compton Crick and Maurice Wilkins “for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material.” This laid the groundwork for future discoveries. In the early 1950s, Wilkins and another scientist, Rosalind Franklin, worked to determine DNA’s structure. In 1953, Watson and Crick discovered its shape as a double helix. This twisted ladder structure enabled other researchers to unlock the secret of how genetic information is stored, transferred and copied. Franklin is widely recognized as having played a significant role in revealing the physical structure of DNA; due to her death at age 37 in 1958, Franklin did not earn a share of the prize. Read more about DNA. Continue reading

Bit by the Research Bug: Priscilla’s Growth as a Scientist

This is the third post in a new series highlighting NIGMS’ efforts toward developing a robust, diverse and well-trained scientific workforce.

Priscilla Del Valle
Credit: Christa Reynolds.
Priscilla Del Valle
Academic Institution: The University of Texas at El Paso
Major: Microbiology
Minors: Sociology and Biomedical Engineering
Mentor: Charles Spencer
Favorite Book: The Immortal Life of Henrietta Lacks, by Rebecca Skloot
Favorite Food: Tacos
Favorite music: Pop
Hobbies: Reading and drinking coffee

It’s not every day that you’ll hear someone say, “I learned more about parasites, and I thought, ‘This is so cool!’” But it’s also not every day that you’ll meet an undergraduate researcher like 21-year-old Priscilla Del Valle.

BUILD and the Diversity Program Consortium

The Diversity Program Consortium (DPC) aims to enhance diversity in the biomedical research workforce through improved recruitment, training and mentoring nationwide. It comprises three integrated programs—Building Infrastructure Leading to Diversity (BUILD), which implements activities at student, faculty and institutional levels; the National Research Mentoring Network (NRMN), which provides mentoring and career development opportunities for scientists at all levels; and the Coordination and Evaluation Center (CEC), which is responsible for evaluating and coordinating DPC activities.

Ten undergraduate institutions across the United States have received BUILD grants, and together, they serve a diverse population. Each BUILD site has developed a unique program intended to engage and prepare students for success in the biomedical sciences and maximize opportunities for research training and faculty development. BUILD programs include everything from curricular redesign, lab renovations, faculty training and research grants, to student career development, mentoring and research-intensive summer programs.

Del Valle’s interest in studying infectious diseases and parasites is motivating her to pursue an M.D./Ph.D. focusing on immunology and pathogenic microorganisms. Currently, Del Valle is a junior at The University of Texas at El Paso (UTEP)’s BUILDing SCHOLARS Center Exit icon. BUILDing SCHOLARS, which stands for “Building Infrastructure Leading to Diversity Southwest Consortium of Health-Oriented Education Leaders and Research Scholars,” focuses on providing undergraduate students interested in the biomedical sciences with academic, financial and professional development opportunities. Del Valle is one of the first cohort of students selected to take part in this training opportunity.

BUILD scholars receive individual support through this training model, and Del Valle says she likes “the way that they [BUILDing SCHOLARS] take care of us and the workshops and opportunities that we have.”

Born in El Paso, Texas, Del Valle moved to Saltillo, Mexico, where she spent most of her childhood. Shortly after graduating from high school, she returned to El Paso to start undergraduate courses at El Paso Community College (EPCC), to pursue an M.D. Del Valle explains that in Mexico, unlike in the United States, careers in medical research are not really emphasized in the student community or in society, so she did not have firsthand experience with research.

Del Valle discovered her passion for research when she was assigned a project on malaria as part of an EPCC course. She was fascinated by the parasite that causes malaria. “It impressed me how something so little could infect a person so harshly,” she says. Continue reading

Actin’s Many Roles

Skin cancer cells

Skin cancer cells from a mouse. Credit: Catherine and James Galbraith, Oregon Health and Science University, Center for Spatial Systems Biomedicine, Knight Cancer Institute.

This heart-shaped image shows two mouse skin cancer cells connected to each other with actin, a protein that is part of the cellular skeleton. Researchers use mouse cells like these to tease out the molecular methods that cancer uses to invade new tissues in the body. It turns out that actin plays an essential role.

Cells can move as a collective, or independently. Movement of an individual cell requires a series of carefully controlled steps. Among them, a cell must break contacts with its neighbor cells and change its connections to the proteins and fibers around it. In addition, it must sense and follow a chemical path through the tissue it lies in. To do this, a cell changes shape, molding its membrane into flaps or feet called protrusions reaching in the direction it is traveling. Actin, among a variety of other molecules, is involved in all of these steps, but especially the shape change, when it gathers inside the cell membrane to help form the protrusions. Continue reading

On Pi Day, Computational Biologists Share What They Love About Math

Another cool fact about Pi: The mirror reflection of the numbers 3 1 4 spells out P I E.

Why do math lovers around the world call March 14 “Pi Day”? Because Pi, the ratio of a circle’s circumference to its diameter, is 3.14. Pi is a Greek letter (π) that represents a constant in math: All circles have the same Pi, regardless of their size. Pi has been calculated out to as many as 1 trillion digits past the decimal, and it can continue forever without repetition or pattern.

In honor of Pi Day, we asked several biomedical researchers in the field of computational biology to tell us why they love math and how they use it in their research. Continue reading

Online Virus Tracking Tool Nextstrain Wins Inaugural Open Science Prize

Credit: Trevor Bedford and Richard Neher, nextstrain.org.

Over the past decade, scientists and clinicians have eagerly deposited their burgeoning biomedical data into publicly accessible databases. However, a lack of computational tools for sharing and synthesizing the data has prevented this wealth of information from being fully utilized.

In an attempt to unleash the power of open-access data, the National Institutes of Health, in collaboration with the Howard Hughes Medical Institute and Britain’s Wellcome Trust, launched the Open Science Prize Exit icon. Last week, after a multi-stage public voting process, the inaugural award was announced. The winner of the grand prize—and $230,000—is a prototype computational tool called nextstrain Exit icon that tracks the spread of emerging viruses such as Ebola and Zika. This tool could be especially valuable in revealing the transmission patterns and geographic spread of new outbreaks before vaccines are available, such as during the 2013-2016 Ebola epidemic and the current Zika epidemic.

An international team of scientists—led by NIGMS grantee Trevor Bedford Exit icon of the Fred Hutchinson Cancer Research Center, Seattle, and Richard Neher Exit icon of Biozentrum at the University of Basel, Switzerland—developed nextstrain as an open-access system capable of sharing and analyzing viral genomes. The system mines viral genome sequence data that researchers have made publicly available online. nextstrain then rapidly determines the evolutionary relationships among all the viruses in its database and displays the results of its analyses on an interactive public website.

The image here shows nextstrain’s analysis of the genomes from Zika virus obtained in 25 countries over the past few years. Plotting the relatedness of these viral strains on a timeline provides investigators a sense of how the virus has spread and evolved, and which strains are genetically similar. Researchers can upload genome sequences of newly discovered viral strains—in this case Zika—and find out in short order how their new strain relates to previously discovered strains, which could potentially impact treatment decisions.

Nearly 100 interdisciplinary teams comprising 450 innovators from 45 nations competed for the Open Science Prize. More than 3,500 people from six continents voted online for the winner. Other finalists for the prize focused on brain maps Exit icon, gene discovery Exit icon, air-quality monitoring Exit icon, neuroimaging Exit icon and drug discovery Exit icon.

nextstrain was funded in part by NIH under grant U54GM111274.

Field Focus: High-Quality Genome Sequences Inform the Study of Human Evolution

Leafing through my favorite biology textbook from a handful of years ago, I was struck by the relative brevity of the chapter on human evolution. While other fields of biological research have enjoyed a steady gallop of productivity over the last few decades due in part to advances in computing power, imaging technology and experimental methods, the study of human evolution can be seen as having lagged behind until recently due to an almost complete dependence on fossil evidence.

Fortunately, contemporary biology textbook chapters on human evolution are being primed for a serious upgrade thanks to the recent availability of high-quality genome sequences from diverse modern human populations as well as from ancient humans and other non-human hominids, including the Neanderthals and Denisovans (but, for purposes of this story, not the Great Apes).

Modern human skull (left) and Neanderthal skull (right), shown to scale. There are not enough Denisovan bone fragments to reconstruct its skull. Credit: Wikimedia Commons, hairymuseummatt.

What are the new resources for studying human evolution?

The cost of DNA sequencing has dropped precipitously in the last decade. As a result, more complete human genome sequences become available for analysis with each passing year.

For example, the 1000 Genomes Project Exit icon includes more than 1,000 full human genome sequences of individuals from European, Asian, American and Sub-Saharan African populations. Earlier this year, the Simons Genome Diversity Project Exit icon further increased the number of available human genomes by adding 300 individuals representing 142 populations around the globe. Continue reading

Student Researcher Finds New Clues About Flu with Old Data

Do you like to find new uses for old things? Like weaving old shirts into a rug, repurposing bottles into candle holders or turning packing crates into tables? Katie Gostic, a University of California, Los Angeles (UCLA) graduate student, likes finding new uses for old data. She channeled this interest when she analyzed existing data to study whether childhood exposure to flu affects a person’s future immunity to the disease.

Katie Gostic
Gostic conducted research for the flu project during the summer of 2015 when she was visiting her boyfriend, a tropical biologist, in Alamos, Sonora, Mexico. Credit: Charlie de la Rosa.

As an undergraduate student at Princeton University, Gostic was originally pursuing a degree in engineering. Her focus shifted to biology after taking an infectious disease modeling class. Gostic’s background in math and programming allows her to take large, complex pre-existing data sets and reanalyze them using new tools and methods. The result: Information that wasn’t accessible when the data were first collected.

Now a graduate researcher in the ecology and evolutionary biology lab of James Lloyd-Smith Exit icon, Gostic studies infectious diseases. The lab builds mathematical models to investigate zoonotic diseases—diseases that animals can transmit to humans but that humans don’t frequently spread between each other. Examples include diseases caused by Leptospira, a type of bacteria that infects household pets and many other animals, and monkeypox, a virus whose transmission to humans is increasing since the eradication of smallpox. The lab also studies bird flus, a category of flu viruses that infect birds and other animals and only occasionally jump to people. A very small number of cases of human-to-human transmission of bird flus have been recorded. However, if a bird flu virus mutated in a way that allowed it to spread among humans, it could cause a pandemic. Continue reading

On this Darwin Day, Evolutionary Geneticist Dr. Dan Janes Discusses the Scientific Contributions of Charles Darwin

This Sunday, February 12, is Darwin Day—an occasion to recognize the scientific contributions of 19th-century naturalist Charles Darwin. In this video (originally posted on Darwin Day 2016), our own evolutionary geneticist, Dan Janes, answers questions about Darwin and the role of evolution in health and biomedicine.

Continue reading