Category: Being a Scientist

Posted on

Meet Jeff Shaman

by
0 comments
Jeff Shaman
Jeff Shaman
Field: Climatology
Works at: Columbia University’s Mailman School of Public Health, N.Y.
Favorite high school subject: Biology
First job: Guide at the Franklin Institute in Philadelphia, Pa.
Alternative career: Opera singer
Credit: Anne Foulke

Before he wrote any scientific papers, Jeff Shaman wrote operas. At the premiere of one of his operas, an 80-minute story about psychoanalysis, reviewers said the work “crackle[d] with invention.”

After 4 years of training to become an opera singer, Shaman realized that the work wouldn’t offer him career stability. He started thinking about his other interests. After college, where he majored in biology with a focus on ecology, he had volunteered to help with HIV clinical trials and developed a fascination with understanding infectious diseases. He wondered if the quantitative tools and methods used to study the physical sciences—another interest area—could inform how contagions spread and possibly even lead to systems for monitoring or predicting their transmission.

So Shaman returned to school—this time, for advanced degrees in earth and environmental sciences. He now studies the relationship between soil wetness and mosquito-borne diseases such as malaria in Africa and West Nile in Florida.

“I love science—probing questions, thinking about problems, finding solutions, pursuing my ideas,” says Shaman.

His Findings

A few years ago, Shaman took some of his scientific compositions in another direction by focusing on seasonal flu outbreaks. For more than 60 years, researchers have linked seasonal flu outbreaks with environmental data like humidity and temperature. Shaman analyzed this work and figured out that absolute humidity, rather than relative humidity, was the best predictor of outbreaks. Now he’s applied state-of-the-art mathematical modeling and real-time observational estimates of influenza incidence to predict when outbreaks will likely occur.

His forecasting technique mimics that used by meteorologists to predict weather conditions like temperatures, precipitation and even hurricane landfall. Shaman’s version incorporates variables like how transmissible a virus is, the number of days people are contagious and sick, and how much humidity is in the air.

The flu forecasts build on a series of studies in which Shaman and his colleagues used data from previous influenza seasons to test their predictions and improve reliability of their model. The work culminated with real-time predictions for 108 cities during the 2012-2013 influenza season. The forecasts could reliably estimate the peaks of flu outbreaks up to 9 weeks before they occurred.

For the 2013-2014 flu season, the researchers continued to make weekly predictions. But instead of first publishing the results in a scientific journal, they posted them on a newly launched influenza forecasts Web site Exit icon where the public could view the projections.

“People understand the limitations and capabilities of weather forecasts,” says Shaman. “Our hope is that people will develop a similar familiarity with the flu forecasts and use that information to make sensible decisions.” For instance, the prediction of high influenza activity may motivate them to get vaccinated and practice other flu-prevention measures.

As he waits for the start of the next flu season, Shaman continues to tweak his forecast system to improve its reliability. He’s also beginning to address other questions, such as how to predict multiple outbreaks of different influenza strains and how to predict the spread of other respiratory illnesses.

Learn more:
Influenza Forecasts Web Site Exit icon

Posted on

Meet Ravi Iyengar

by
0 comments
Ravi Iyengar
Ravi Iyengar
Fields: Systems pharmacology and systems biology
Works at: Mount Sinai School of Medicine, New York, NY
Favorite sports team: Yankees
Favorite subject in high school: Math
Recently read book: The Signal and the Noise by Nate Silver
Credit: Pedro Martinez, Systems Biology Center New York

Ravi Iyengar, a professor at Mount Sinai School of Medicine, stood in an empty lecture hall, primed to tell thousands of students about systems biology, a holistic approach to studying fundamental life processes. To prepare for this moment, he had spent 4 months reading hundreds of scientific papers and distilling the research into understandable nuggets. But that day, his only student was a videographer.

Together, they recorded 15 different lectures about systems biology—many related to Iyengar’s own research—that thousands of people would stream or download as part of a MOOC, or massive open online course.

Trained in biochemistry, Iyengar built his research career around studying molecules and developing a list of all the parts that help nerve, kidney and skin cells to function. As he obtained more information, he realized he needed to know how all the components worked together. To achieve this comprehensive understanding, Iyengar turned to computational techniques and mathematical analyses—cornerstones of systems biology.

For more than a decade, he has been using and developing systems biology approaches to explore a range of biomedical questions, from very basic to translational ones with immediate relevance to human health.

Iyengar’s Findings

In his earlier work, Iyengar used mathematical analyses to show that molecules within cells connect with one another to form switches that produce cellular memory. This may allow, for instance, an immune cell to remember a foreign object and secrete an antibody. In recent work, he and his team developed a mathematical model showing that the shape of a cell influences the flow of information across the membrane, possibly contributing to disease states and offering a way to study and identify them under the microscope. In another study, they analyzed a database of drug side effects to find combinations of medications that produce fewer adverse reactions and then created a cell biology interaction network that explains why a certain drug pair had this beneficial outcome. The approach could point to other combinations of FDA-approved drugs that reduce serious side effects and thereby guide clinical practice.

“Systems biology is a powerful way to explore important biological and medical questions, and it’s relevant to many fields of science,” said Iyengar. But he added that the majority of educational institutions, including liberal arts and community colleges, don’t have systems biology courses. So, Iyengar teamed with colleagues to create a series of MOOCs.

The first course, offered last summer and taught by Iyengar, presented all the facets of systems biology. The syllabus included lessons on genomics and bioinformatics, fields that have contributed to systems biology; gathering and integrating data; and the use of modeling in drug development.

“My goal was for the students to get the general gestalt of systems biology,” explained Iyengar, who directs an NIH-funded center focused on the systems-level study of medicine and therapeutics.

In total, more than 12,000 participants watched at least one video lecture, 3,000 submitted one or more of the weekly quizzes and 1,800 took a mid-term or final exam. The online discussions forum included nearly 400 topics with about 5,000 posts. The students, most enrolled in a graduate program or working full-time, had some training in the biological, biomedical, computer and information sciences.

“The stats tell me that many people are in fields adjacent to systems biology and don’t have access to more traditional systems biology courses,” concluded Iyengar. “Through the MOOC, we can reach them in a substantial way.”

The second course, which covers network analysis, wrapped up in early December, and the third course, which covers dynamical modeling methods, began in January. Iyengar plans to offer the intro course again in late March.

Learn more:
MOOC Systems Biology Courses Exit icon

Posted on

Meet Jasmine Johnson and Gabe Vela

by
0 comments
Jasmine Johnson and Gabriel 'Gabe' Vela
Jasmine Johnson and Gabriel “Gabe” Vela
Field: Genetics of sleep and obesity
Worked as researchers at: The Jackson Laboratory, Bar Harbor, Maine
Graduated from high school at: Rockdale Magnet School for Science and Technology in Conyers, Ga.
Now freshman at: Stanford University in Palo Alto, Calif. (Johnson) and Southern Polytechnic State University in Marietta, Ga. (Vela)
Fascinating fact: Johnson presented her research at the 2013 White House Science Fair
Credit: Joe Piergrossi

Jasmine Johnson and Gabe Vela might still be teenagers, but they are also seasoned scientists. It all started 3 years ago, when, as high school juniors, they took the research course Independent Studies in Computational Biology at The Jackson Laboratory in Bar Harbor, Maine. They were hooked. They continued to do research until they graduated, working part-time for 2 academic years and full-time for 2 summers.

They worked with statistical geneticist Gary Churchill, using computational biology to explore the relationship between sleep and obesity. They focused on finding genes that regulate sleep and understanding how sleep affects the body. One goal of the research is to tease out a genetic explanation for why sleep deprivation increases the risk of obesity.

Working in a lab “completely changed what I thought I was going to do with my life,” said Vela. “Now I’m going to focus more on research than anything else.”

For Johnson, the experience provided the opportunity to present her research at the 2013 White House Science Fair, where she hobnobbed with some political hot shots.

“It was an amazing experience,” she said. Having “important White House officials be interested in my project … inspired me.”

Johnson and Vela visited NIH a few months ago and talked with us about their research experiences, their lives and their future goals. Jasmine Johnson & Gabriel Vela on their experience as high school researchers at The Jackson Laboratory in Bar Harbor, Maine.

Learn More
Article Exit icon about Johnson and Vela and other young researchers, from The Jackson Laboratory’s magazine The Search.
Article about the work of Gary Churchill, from NIH’s Findings magazine.

Posted on

Meet Dave Cummings

by
0 comments
Dave Cummings. Credit: Marcus Emerson, PLNU.
Dave Cummings
Field: Environmental microbiology
Works at: Point Loma Nazarene University, San Diego, Calif.
Hobbies: Hiking, backpacking, fly-fishing
Dream home: One that doesn’t need a lot of work
Credit: Marcus Emerson, PLNU

In college, as a pre-med student majoring in biology and chemistry, Dave Cummings grew frustrated with the traditional “cookbook” approach to doing labs in his science classes. Turned off by having to follow step-by-step lab procedures that had little to do with scientific discovery, Cummings changed his major to English literature. Studying literature, he says, “helped me find myself” and taught him to think critically.

Ultimately, Cummings says, “I came to realize that it wasn’t the practice of medicine that got me excited, but the science behind it all.” He decided to pursue a graduate degree in biology and—after “knocking on a lot of doors”—was accepted at the University of Idaho, where he earned his master’s and doctoral degrees and discovered his passion for microbiology.

Today, Cummings applies his critical thinking skills to his work as professor of biology back at his alma mater, Point Loma Nazarene University (PLNU), a small university focused on undergraduate education. There he studies the role of urban storm water in spreading genes for antibiotic resistance in natural environments, and pursues his enthusiasm for training the next generation of scientists. He enlists his students in his research, giving them what he calls “real, live, on-the-ground” research experience that relatively few undergraduate students at larger universities receive.

Cummings’ Findings

Antibiotic resistance, which can transform once-tractable bacterial infections into diseases that are difficult or impossible to treat, is a major public health challenge of the 21st century. The most common way that bacteria become drug resistant is by acquiring genes that confer antibiotic resistance from other bacteria. Often, such drug resistance genes are found on small, circular pieces of DNA called plasmids that are readily passed from one species of bacteria to another.

Urban wetlands provide ideal conditions for bacteria to mingle, swap genes and spread antibiotic resistance, notes Cummings. He focuses on the wetlands around San Diego, which act as a giant mixing bowl for storm runoff, human sewage, animal waste, naturally occurring plant and soil microorganisms, and plasmids indigenous to the wetlands.

Cummings and his students examine sediment samples from these wetlands in search of plasmids that carry resistance genes. They’ve found that during winter rains, the San Diego wetlands receive runoff containing antibiotic-resistant bacteria and plasmids, which can persist at low, but detectable, levels into the dry summer months.

“We know that urban storm water carries with it a lot of antibiotic-resistant bacteria, and along with that the DNA instructions [or genes] that code for the resistance,” says Cummings. “We have solid evidence of genes encoding resistance to clinically important antibiotics washing … into coastal wetlands in San Diego.”

“We’re trying to understand the scope of the problem, and ultimately what threat that poses to human health,” he says. His concern is that the drug-defying bacterial genes will accumulate in the wetlands, and then “[find] their way back to us, where they will augment and amplify the problem of resistance.”

Precisely how resistance genes might move from the environment into people is not yet known. One way this could occur is through direct contact with contaminated water or sediment by anglers, swimmers, surfers and other recreational users. Fish, birds and insects could also transmit resistance genes from contaminated wetlands to humans.

“There is good evidence elsewhere that birds are important vectors of drug-resistant pathogens, and this is my favorite possibility,” says Cummings. “Hopefully someday we can test that hypothesis.”

Cummings’ studies, done in collaboration with Ryan Botts at PLNU and Eva Top at the University of Idaho, could reveal antibiotic resistance genes with the potential to move into new species of disease-causing bacteria and back into human populations. By identifying these genes and raising awareness of the problem, he hopes to aid future efforts to mitigate the spread of antibiotic resistance.

Posted on

Meet Shanta Dhar

by
1 comment
Shanta Dhar
Shanta Dhar
Fields: Chemistry and cancer immunotherapy
Works at: University of Georgia, Athens
Born and raised in: Northern India
Studied at: Indian Institute of Science, Bangalore; Johns Hopkins University, Baltimore, Md.; and Massachusetts Institute of Technology, Cambridge, Mass.
To unwind: She hits the gym
Credit: Frankie Wylie, Stylized Portraiture

The human body is, at its most basic level, a giant collection of chemicals. Finding ways to direct the actions of those chemicals can lead to new treatments for human diseases.

Shanta Dhar, an assistant professor of chemistry at the University of Georgia, Athens (UGA), saw this potential when she was exposed to the field of cancer immunotherapy as a postdoctoral researcher at the Massachusetts Institute of Technology. (Broadly, cancer immunotherapy aims to direct the body’s natural immune response to kill cancer cells.) Dhar was fascinated by the idea and has pursued research in this area ever since. “I always wanted to use my chemistry for something that could be useful [in the clinic] down the line,” she said.

A major challenge in the field has been training the body’s immune system—specifically the T cells—to recognize and attack cancer cells. The process of training T cells to go after cancer is rather like training a rescue dog to find a lost person: First, you present the scent, then you command pursuit.

The type of immune cell chiefly responsible for training T cells to search for and destroy cancer is a called a dendritic cell. First, dendritic cells present T cells with the “scent” of cancer (proteins from a cancer cell). Then they activate the T cells using signaling molecules.

Dhar’s Findings

Dhar’s work focuses on creating the perfect trigger for cancer immunotherapy—one that would provide both the scent of cancer for T cells to recognize and a burst of immune signaling to activate the cells.

Using cells grown in the lab, Dhar’s team recently showed that they could kill most breast cancer cells using a new nanotechnology technique, then train T cells to eradicate the remaining cancer cells.

For the initial attack, the researchers used light-activated nanoparticles that target mitochondria in cancer cells. Mitochondria are the organelles that provide cellular energy. Their destruction sets off a signaling cascade that triggers dendritic cells to produce one of the proteins needed to activate T cells.

Because the strategy worked in laboratory cells, Dhar and her colleague Donald Harn of the UGA infectious diseases department are now testing it in a mouse model of breast cancer to see if it is similarly effective in a living organism.

For some reason, the approach works against breast cancer cells but not against cervical cancer cells. So the team is examining the nanoparticle technique to see if they can make it broadly applicable against other cancer types.

Someday, Dhar hopes to translate this work into a personalized cancer vaccine. To create such a vaccine, scientists would remove cancer cells from a patient’s body during surgery. Next, in a laboratory dish, they would train immune cells from the patient to kill the cancer cells, then inject the trained immune cells back into the patient’s body. If the strategy worked, the trained cells would alert and activate T cells to eliminate the cancer.

Posted on

Meet Emily Scott

by
0 comments
Emily Scott
Emily Scott
Field: Biochemistry
Works at: University of Kansas in Lawrence
Favorite hobby: Scuba diving
Likes watching: “Law & Order”
Likes reading: True-life survival stories
Credit: Chuck France, University of Kansas

With an air tank strapped to her back, college student Emily Scott dove to the bottom of the Gulf of Mexico to examine life in an oxygen-starved area called the Dead Zone. The bottom waters had once teemed with red snapper, croaker and shrimp, but to Scott, the region appeared virtually devoid of life. Then, from out of the mud, appeared the long, undulating arms of a brittle star.

As Scott learned, that particular species of brittle star survived in the Dead Zone because it has something many other marine creatures don’t: an oxygen-carrying protein called hemoglobin. This same protein makes our blood red. Key to hemoglobin’s special oxygen-related properties is a small molecular disk called a heme (pronounced HEEM).

Once she saw what it meant to brittle stars, Scott was hooked on heme and proteins that contain it.

Scott’s Findings

Now an associate professor, Scott studies a family of heme proteins called cytochromes P450 (CYP450s). These proteins are enzymes that facilitate many important reactions: They break down cholesterol, help process vitamins and play an important role in flushing foreign chemicals out of our systems.

To better understand CYP450s, Scott uses a combination of two techniques–X-ray crystallography and nuclear magnetic resonance spectroscopy—for capturing the enzymes’ structural and reactive properties.

She hopes to apply her work to design drugs that block certain CYP450 reactions linked with cancer. One target reaction, carried out by CYP2A13, converts a substance in tobacco into two cancer-causing molecules. Another target reaction is carried out by CYP17A1, an enzyme that helps the body produce steroid sex hormones but that, later in life, can fuel the uncontrolled growth of prostate or breast cancer cells.

“I’m fascinated by these proteins and figuring out how they work,” Scott says. “It’s like trying to put together a puzzle—a very addictive puzzle.” Her drive to uncover the unknown and her willingness to apply new techniques have inspired the students in her lab to do the same.

Content adapted from Hooked on Heme, an article in the September 2013 issue of Findings magazine.

Posted on

Meet Brad Duerstock

by
0 comments
Brad Duerstock
Brad Duerstock
Fields: Neuroscience, assistive technology design
Works at: Purdue University, West Lafayette, IN
Hobbies: Gadgetry, architectural design
Bizarre collectible: Ecuadorian shrunken head (not a real one—it’s a replica made from goatskin)
Credit: Andrew Hancock, Purdue University

At the age of 18, Brad Duerstock had a devastating accident. A star member of his high school swim team, Duerstock hit his head during practice in a way that broke his neck and paralyzed all of his limbs. Today, he studies spinal cord injuries much like his own, investigating how the damage occurs and how it could possibly be repaired.

Duerstock has worked to make science accessible to people with disabilities, whether they use wheelchairs, as he does, or have visual or other impairments. For example, he has redesigned laboratory space to make it easier for people with disabilities to navigate and perform tasks.

“I like knowing that what I do can ultimately impact others,” Duerstock says.

Duerstock’s Findings

Much of Duerstock’s research deals with what occurs immediately following a nerve injury. In a spinal cord injury, nerve tissue becomes severed or dies. The immune response and bleeding in the injured area can cause extra damage to nerves in the spinal cord. Duerstock and his team have found that a molecule called acrolein is produced in spinal cord injuries and that it kills the nerves it encounters as it spreads around the injury site. They have been investigating a compound called polyethylene glycol (PEG), a polymer that could seal ruptured nerve cell membranes, possibly protecting nerve tissue from further damage immediately following a spinal cord injury.

Duerstock also founded and leads the Institute for Accessible Science (IAS), a community of scientists, students, parents and teachers whose goal is to promote better accommodations for people with disabilities who are studying or working in the sciences. The IAS looks into how to redesign lab spaces and equipment to increase accessibility for people with disabilities, particularly those with limited mobility or vision.

Although Duerstock originally wanted to be a doctor, he believes his true calling is in research. “The sense of discovery and the impact on others are big motivations for me,” says Duerstock. “Being a researcher, you might have a broader impact on society than you would as a practicing physician.”

Content adapted from the NIGMS Findings magazine article Opening Up the Lab.

Posted on

Meet Galina Lepesheva

by
2 comments
Galina Lepesheva
Galina Lepesheva
Field: Biochemistry
Works at: Vanderbilt University, Nashville, TN
Born, raised and studied in: Belarus
To unwind, she: Reads, travels, spends time with her family

Galina Lepesheva knows that kissing bugs are anything but romantic. When the lights get low, these blood-sucking insects begin feasting—and defecating—on the faces of their sleeping victims. Their feces are often infected with a protozoan (a single-celled, eukaryotic parasite) called Trypanosoma cruzi that causes Chagas disease. Lepesheva has developed a compound that might be an effective treatment for Chagas. She has also tested the substance, called VNI, as a treatment for two related diseases—African sleeping sickness and leishmaniasis.

“This particular research is mainly driven by one notion: Why should people suffer from these terrible illnesses if there could be a relatively easy solution?” she says.

Lepesheva’s Findings

Currently, most cases of Chagas disease occur in rural parts of Mexico, Central America and South America. According to some estimates, up to 1 million people in the U.S. could have Chagas disease, and most of them don’t realize it. If left untreated, the infection is lifelong and can be deadly.

The initial, acute stage of the disease is usually mild and lasts 4 to 8 weeks. Then the disease goes dormant for a decade or two. In about one in three people, Chagas re-emerges in its life-threatening, chronic stage, which can affect the heart, digestive system or both. Once chronic Chagas disease develops, about 60 percent of people die from it within 2 years.

The Centers for Disease Control and Prevention (CDC) has targeted Chagas disease as one of five “neglected parasitic infections,” indicating that it warrants special public health action.

“Chagas disease does not attract much attention from pharmaceutical companies,” Lepesheva says. Right now, there are only two medicines to treat it. They are only available by special request from the CDC, aren’t always effective and can cause severe side effects.

Lepesheva’s research focuses on a particular enzyme, CYP51, that is the target of some anti-fungal medicines. If CYP51 can also act as an effective drug target for the parasites that cause Chagas, her work might help meet an important public health need.

CYP51 is found in all kingdoms of life. It helps produce molecules called sterols, which are essential for the development and viability of eukaryotic cells. Lepesheva and her colleagues are studying VNI and related compounds to examine whether they can block the activity of CYP51 in human pathogens such as protozoa, but do no harm to the enzyme in mammals. In other words, her goal is to cripple disease-causing organisms without creating side effects in infected humans or other mammals.

Lepesheva has tested the effectiveness of VNI on Chagas-infected mice. Remarkably, it has worked 100 percent of the time, curing both the acute and chronic stages of the disease. It acts by preventing the protozoan from establishing itself in the host’s body. If it is similarly effective in humans, VNI could become the first reliable treatment for Chagas disease.

Posted on

Meet David Patterson

by
2 comments
David Patterson
David Patterson
Field: Psychology
Works at: University of Washington, Seattle
Alternative career: Full-time rock ‘n’ roll drummer
Hobbies: Part-time rock ‘n’ roll drummer (with his band, the Shrinking Heads)
Credit: Clare McLean, UW Medicine Strategic Marketing & Communications

The pain stemming from second- and third-degree burns is among the worst known. Throughout recovery, the intense, disabling pain patients feel can lead to sleeplessness, anxiety and depression.

David Patterson first entered a burn ward as a psychologist hoping to help patients cope with these issues. He saw patients refuse wound cleaning because of how painful it could be.

“I’ve learned how horribly difficult it is to control burn and trauma pain with medications alone,” he says. “The amount of pain people feel affects how well they adjust in the long term.” Pain and the mental, social and emotional problems it causes also hinder the body’s ability to heal physically.

Today, Patterson is committed to helping burn patients overcome pain, allowing their bodies—as well as their minds—to heal more efficiently. Using virtual reality (VR) technology, Patterson has found an effective complement to pain-relieving drugs such as morphine and other opioid analgesics.

Patterson’s Findings

“To be honest, for acute pain, you give someone a shot or a pill and it’s instant relief,” Patterson says. But opioid analgesics carry problems.  Sometimes patients don’t respond well to morphine or require high dosages that carry strong side effects.

When burn patients undergo routine wound care, the pain can be excruciating—as bad as or worse than the original burn incident. Realizing the brain can take only so many stimuli, Patterson collaborated with fellow UW psychologist Hunter Hoffman to experiment with VR in pain relief. When combined with minimal pain medications, VR is a powerful solution to acute pain. By providing a computer-generated reality—for example, an icy canyon filled with snowmen and Paul Simon’s music, as in the case of their creation SnowWorld—the patient’s eyes, ears and mind are so occupied that he or she can effectively ignore the pain.

Patterson and his team found that VR pain reduction strategies are as powerful as opioid analgesics, without the negative side effects. The technology doesn’t require specialized expertise and is getting progressively less expensive, making it economically attractive.  At least eight hospitals have adopted the methods as part of their clinical program, allowing Patterson an opportunity to conduct further studies on the long-term effects of using these complementary methods and the efficacy of the techniques on other kinds of pain.

Learn more:
Burns and Physical Trauma Fact Sheets
SnowWorld News Segment Featured on NBC’s Rock Center Exit icon