Targeting Toxic RNA Molecules in Muscular Dystrophy

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Genetic defect that causes myotonic dystrophy type 2 and used that information to design drug candidates to counteract the disease. Credit: Ilyas Yildirim, Northwestern University.
Scientists revealed a detailed image of the genetic defect that causes myotonic dystrophy type 2 and used that information to design drug candidates to counteract the disease. Credit: Ilyas Yildirim, Northwestern University. View larger image

Myotonic dystrophy type 2 (DM2) is a relatively rare, inherited form of adult-onset muscular dystrophy that has no cure. It’s caused by a genetic defect in which a short series of nucleotides—the chemical units that spell out our genetic code—is repeated more times than normal. When the defective gene is transcribed, the resulting RNA repeat forms a hairpin-like structure that binds to and disables a protein called MBNL1.

Now, research led by Matthew Disney of The Scripps Research Institute (TSRI), Florida Campus, has revealed the detailed, three-dimensional structure of the RNA defect in DM2 and used this information to design small molecules that bind to the aberrant RNA. These designer molecules, even in small amounts, significantly improved disease-associated defects in a cellular model of DM2, and thus hold potential for reversing the disorder.

Drugs that target toxic RNA molecules associated with diseases such as DM2 are few and far between, as developing such compounds is technically challenging. The “bottom-up” approach that the scientists used to design potent new drug candidates, by first studying in detail how the RNA structure interacts with small molecules, is unconventional, noted Jessica Childs-Disney of TSRI, who was lead author of the paper with Ilyas Yildirim of Northwestern University. But it may serve as an effective strategy for pioneering the use of small molecules to manipulate disease-causing RNAs—a central focus of the Disney lab.

This work also was funded by NIH’s National Cancer Institute.

Learn more:
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Meet Dave Cummings

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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.

Local Flu Forecasts Posted on New Web Site

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Incidence of influenza during the week starting 12/29/2013 (top); influenza incidence forecasts for selected cities (bottom). Credit: Columbia Prediction of Infectious Diseases.
Incidence of influenza during the week starting 12/29/2013 (top); influenza incidence forecasts for selected cities (bottom). Credit: Columbia Prediction of Infectious Diseases Exit icon.

News articles this weekend reported an uptick in flu cases in many parts of the country. When will your area be hardest hit? Infectious disease experts at Columbia University have launched an influenza forecast Web site Exit icon that gives weekly predictions for rates of flu infection in 94 U.S. cities. The predictions indicate the number of cases in Chicago; Atlanta; Washington, D.C.; and Los Angeles will peak this week, with New York City, Boston, Miami and Providence peaking in following weeks. The forecasts are updated every Friday afternoon, so check back then for any changes.

The forecasting approach, which adapts techniques used in modern weather prediction, relies on real-time observational data of people with influenza-like illness, including those who actually tested positive for flu. The researchers have spent the last couple of years developing the forecasting system and testing it—first retrospectively predicting flu cases from 2003-2008 in New York City and then in real time during the 2012-2013 influenza season in 108 cities.

“People have become acclimated to understanding the capabilities and limitations of weather forecasts,” said Jeffrey Shaman Exit icon, who’s led the flu forecasting project. “Making our forecasts available on the Web site will help people develop a similar familiarity and comfort.” Shaman and his team are hoping that, just as rainy forecasts prompt more people to carry umbrellas, an outlook for high influenza activity may motivate them to get vaccinated and practice other flu-prevention measures.

This work also was funded by NIH’s National Institute of Environmental Health Sciences.

Learn more:

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Cool Images: Holiday Season Cells

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Yeast cells deficient in zinc and the Tsa1 protein have protein tangles. Credit: Colin MacDiarmid and David Eide, University of Wisconsin-Madison.

Yeast cells deficient in zinc and the Tsa1 protein have protein tangles. Credit: Colin MacDiarmid and David Eide, University of Wisconsin-Madison.

Just in time for the holidays, we’ve wrapped up a few red and green cellular images from basic research studies. In this snapshot, we see a group of yeast cells that are deficient in zinc, a metal that plays a key role in creating and maintaining protein shape. The cells also lack a protein called Tsa1, which normally keeps proteins from sticking together. Green areas highlight protein tangles caused by the double deficiency. Red outlines the cells. Protein clumping plays a role in many human diseases, including Parkinson’s and Alzheimer’s, so knowledge of why it happens—and what prevents it in healthy cells—could aid the development of treatments.

See more festive images!

One Mutation Leads to Another—At Least in Yeast

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DNA mutation. Credit: Stock image.
Newly discovered genetic effect in yeast could shed light on carcinogenesis. Credit: Stock image.

Cancer cells typically include many gene mutations, extra or missing genes, or even the wrong number of chromosomes. Scientists know that certain genetic changes lead to ones elsewhere. But they’ve had a chicken-and-egg problem trying to figure out which changes trigger which others—or whether mutations accumulate randomly in tumors.

New research led by J. Marie Hardwick Exit icon of Johns Hopkins University sheds light on the issue. She found that incapacitating a single gene in yeast cells—regardless of which gene it was—spurred mutations in one or two other genes. The process was anything but random: If, say, gene X was knocked out, yeast cells almost always developed a secondary mutation in gene Y. It’s as if knocking out one gene disrupts the genomic balance enough that the cell must alter a different gene to compensate.

Significantly, the secondary mutations—but not the original ones—caused altered yeast cell characteristics, including traits linked to cancer. Also, many of the secondary mutations occurred in genes associated with cancer in humans, further suggesting that these secondary changes might play a role in carcinogenesis.

This new information will help researchers better understand the chain of genetic events that lead to cancer. It might also prompt scientists to reevaluate years of research that attributed changes in cell behavior or appearance to a given gene knockout.

This work also was funded by NIH’s National Institute of Neurological Disorders and Stroke.

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Abnormal Mitochondria Might Cause Resistance to Radiation Therapy

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Mitochondria. Credit: Judith Stoffer.
Bean-shaped mitochondria are cells’ power plants. The highly folded inner membranes are the site of energy generation. Credit: Judith Stoffer. View larger image

Why some cancers are resistant to radiation therapy has baffled scientists, but research on abnormalities in mitochondria, often described as cells’ power plants, could offer new details. A research team led by Maxim Frolov Exit icon of the University of Illinois at Chicago learned that the E2F gene, which plays a role in the natural process of cell death, contributes to the function of mitochondria. Fruit flies with a mutant version of the E2F gene had misshapen mitochondria that produced less energy than normal ones. Flies with severely damaged mitochondria were more resistant to radiation-induced cell death. Studies using human cells revealed similar effects. The work could help explain why people with cancer respond differently to radiation therapy and might aid the development of drugs that enhance mitochondrial function, thereby improving the effectiveness of radiation therapy.

This work also was funded by NIH’s National Cancer Institute.

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New Models Predict Where E. coli Strains Will Thrive

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Illustration of E. coli. Credit: Janet Iwasa, University of Utah.
Illustration of E. coli. Credit: Janet Iwasa, University of Utah (image available under a Creative Commons Attribution-NonCommercial-ShareAlike license Exit icon). View larger image

Like plants and animals, different types of E. coli thrive in different environments. Now, scientists can even predict which environments—such as the bladder, stomach or blood—are most amenable to the growth of various strains, including pathogenic ones. A research team led by Bernhard Palsson Exit icon of the University of California, San Diego, accomplished this by using genome data to reconstruct the metabolic networks of 55 E. coli strains. The metabolic models, which identify differences in the ability to manufacture certain compounds and break down various nutrients, shed light on how certain E. coli strains become pathogenic and how to potentially control them. One approach could be depriving the deadly strains of the nutrients they need to survive in their niches. The researchers plan to use their new method to study other bacteria, such as those that cause staph infections.

This work also was funded by NIH’s National Cancer Institute.

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Stop the (Biological) Clock

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Molecular structure of the three proteins in blue-green algae’s circadian clock.  Credit: Johnson Lab, Vanderbilt University.
Molecular structure of the three proteins in blue-green algae’s circadian clock. Credit: Johnson Lab, Vanderbilt University.

Many microorganisms can sense whether it’s day or night and adjust their activity accordingly. In tiny blue-green algae, the “quartz-crystal” of the time-keeping circadian clock consists of only three proteins, making it the simplest clock found in nature. Researchers led by Carl Johnson of Vanderbilt University recently found that, by manipulating these clock proteins, they could lock the algae into continuously expressing its daytime genes, even during the nighttime.

Why would one want algae to act like it’s always daytime? The kind used in Johnson’s study is widely harnessed to produce commercial products, from drugs to biofuels. But even when grown in constant light, algae with a normal circadian clock typically decrease production of biomolecules when nighttime genes are expressed. When the researchers grew the algae with the daytime genes locked “on” in constant light, the microorganism’s output increased by as much as 700 percent. This proof of concept experiment may be applicable to improving the commercial production of compounds such as insulin and some anti-cancer drugs.

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Circadian Rhythms Fact Sheet

Meet Shanta Dhar

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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.

Detailing Key Structures of HIV

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Structure of Env. Credit: The Scripps Research Institute.
This model shows a birds-eye view of the structure of Env, a protein on the HIV surface that enables it to infect cells, bound to neutralizing antibodies. Credit: The Scripps Research Institute.

In a statement on World AIDS Day 2013, NIH leaders wrote, “In the 25 years that have passed since the first annual commemoration of World AIDS Day, extraordinary scientific progress has been made in the fight against HIV/AIDS. That progress has turned an HIV diagnosis from an almost-certain death sentence to what is now for many, a manageable medical condition and nearly normal lifespan. We have come far, yet not far enough.”

One area of progress is in understanding the structural biology of HIV, the virus that causes AIDS. Capturing details about the virus’ shape has helped scientists better understand how HIV operates and pinpoint its Achilles’ heels. Recently, scientists got a closer look at two key pieces of the virus.

In one study, researchers developed the most detailed picture yet of Env, a three-segment protein on the HIV surface that allows the virus to infect cells. The work illuminated the complex process by which the protein assembles, undergoes radical shape changes during infection and interacts with neutralizing antibodies, which can block many strains of HIV from infecting human cells. The findings also may guide the development of HIV vaccines.

In another study, researchers created the best image yet of the cocoon-like container, or capsid, that carries HIV’s genome. Capsids have been difficult to study because individual imaging techniques had not produced high enough detail. By combining several cutting-edge imaging methods, the scientists pieced together the individual polygonal units of the capsid like a jigsaw puzzle to determine its structure in detail. Now that they know how HIV’s inner vessel looks, the research team is searching for its cracks—potential targets for drug development.

Learn more:
Imaging HIV’S Inner Shell Article from Inside Life Science
Key HIV Protein Structure Revealed Article from NIH Research Matters
Interactive HIV Structural Model