Tag Archives: genetic

Penn Vet-Temple team characterizes genetic mutations linked to a form of blindness

Achromatopsia is a rare, inherited vision disorder that affects the eye’s cone cells, resulting in problems with daytime vision, clarity and color perception. It often strikes people early in life, and currently there is no cure for the condition.

One of the most promising avenues for developing a cure, however, is through gene therapy, and to create those therapies requires animal models of disease that closely replicate the human condition.

In a new study, a collaboration between University of Pennsylvania and Temple University scientists has identified two naturally occurring genetic mutations in dogs that result in achromatopsia. Having identified the mutations responsible, they used structural modeling and molecular dynamics on the Titan supercomputer at Oak Ridge National Laboratory and the Stampede supercomputer at the Texas Advanced Computing Center to simulate how the mutations would impact the resulting protein, showing that the mutations destabilized a molecular channel essential to light signal transduction.

The findings provide new insights into the molecular cause of this form of blindness and also present new opportunities for conducting preclinical assessments of curative gene therapy for achromatopsia in both dogs and humans.

“Our work in the dogs, in vitro and in silico shows us the consequences of these mutations in disrupting the function of these crucial channels,” said Karina Guziewicz, senior author on the study and a senior research investigator at Penn’s School of Veterinary Medicine. “Everything we found suggests that gene therapy will be the best approach to treating this disease, and we are looking forward to taking that next step.”

The study was published in the journal PLOS ONE and coauthored by Penn Vet’s Emily V. Dutrow and Temple’s Naoto Tanaka. Additional coauthors from Penn Vet included Gustavo D. Aguirre, Keiko Miyadera, Shelby L. Reinstein, William R. Crumley and Margret L. Casal. Temple’s team, all from the College of Science and Technology, included Lucie Delemotte, Christopher M. MacDermaid, Michael L. Klein and Jacqueline C. Tanaka. Christopher J. Dixon of Veterinary Vision in the United Kingdom also contributed.

The research began with a German shepherd that was brought to Penn Vet’s Ryan Hospital. The owners were worried about its vision.

“This dog displayed a classical loss of cone vision; it could not see well in daylight but had no problem in dim light conditions,” said Aguirre, professor of medical genetics and ophthalmology at Penn Vet.

The Penn Vet researchers wanted to identify the genetic cause, but the dog had none of the “usual suspects,” the known gene mutations responsible for achromatopsia in dogs. To find the new mutation, the scientists looked at five key genes that play a role in phototransduction, or the process by which light signals are transmitted through the eye to the brain.

They found what they were looking for on the CNGA3 gene, which encodes a cyclic nucleotide channel and plays a key role in transducing visual signals. The change was a “missense” mutation, meaning that the mutation results in the production of a different amino acid. Meanwhile, they heard from colleague Dixon that he had examined Labrador retrievers with similar symptoms. When the Penn team performed the same genetic analysis, they found a different mutation on the same part of the same gene where the shepherd’s mutation was found. Neither mutation had ever been characterized previously in dogs.

“The next step was to take this further and look at the consequences of these particular mutations,” Guziewicz said.

The group had the advantage of using the Titan and Stampede supercomputers, which can simulate models of the atomic structure of proteins and thereby elucidate how the protein might function. That work revealed that both mutations disrupted the function of the channel, making it unstable.

“The computational approach allows us to model, right down to the atomic level, how small changes in protein sequence can have a major impact on signaling,” said MacDermaid, assistant professor of research at Temple’s Institute for Computational Molecular Science. “We can then use these insights to help us understand and refine our experimental and clinical work.”

The Temple researchers recreated these mutated channels and showed that one resulted in a loss of channel function. Further in vitro experiments showed that the second mutation caused the channels to be routed improperly within the cell.

Penn Vet researchers have had success in treating various forms of blindness in dogs with gene therapy, setting the stage to treat human blindness. In human achromatopsia, nearly 100 different mutations have been identified in the CNGA3 gene, including the very same one identified in the German shepherd in this study.

The results, therefore, lay the groundwork for designing gene therapy constructs that can target this form of blindness with the same approach.

The study was supported by the Foundation Fighting Blindness, the National Eye Institute, the National Science Foundation, the European Union Seventh Framework Program, Hope for Vision, the Macula Vision Research Foundation and the Van Sloun Fund for Canine Genetic Research.

Source: University of Pennsylvania 

Ant-Man possible? Scientists shrink ants to study mechanisms that control DNA expression

By shrinking ants to sizes smaller than exist in nature, biologists present a useful model for understanding how environmental factors can influence DNA expression to create a range of outcomes.

This may not be exactly what the Marvel’s Ant-Man story has but still close enough to be amazing! 


In the pages of Marvel comic books, Ant-Man manipulates fictional subatomic particles in order to shrink and fight crime as one of Earth’s mightiest heroes.

In real life, a team of biologists has now achieved similar shrinking results by manipulating ants’ DNA. The work won’t produce any superpowers, but it presents a useful model for understanding how environmental factors can influence DNA expression to create a range of outcomes in a population.

The work is published online in the journal Nature Communications. Sebastian Alvarado, a postdoctoral fellow at Stanford, conducted the research as a graduate student at McGill University, working alongside fellow graduate student Rajendhran Rajakumar, and professors Ehab Abouheif and Moshe Szyf, all of McGill.


Video : Stanford researcher explains the science behind Ant-Man

The experiment was designed as a means to study variation in quantitative traits. These are individual qualities, such as height or body weight, that can naturally vary across a defined range in a population. This variation is usually driven by the degree that environmental or other factors influence the expression of a particular gene, which makes ants an excellent test model.

In an ant colony, queens, workers and soldiers share similar genetics. But early in ant development, social, nutritional and chemical cues cause some genes to be more active, ultimately creating a wide range of body sizes, each specialized to a different task in the colony.

Many of these changes are controlled by DNA methylation, a process in which molecules are added to sections of DNA sequences. These additions affect how the DNA is interpreted and expressed, thus influencing an organism’s development or behavior.

“A lot of growth and development and sizing mechanisms that exist across the animal kingdom are found to be regulated by the same DNA methylation processes,” Alvarado said.

In the experiment, Alvarado and his colleagues at McGill exposed ant larvae to drugs that either increased or decreased the amount of DNA methylation. In doing so, they created ants that were larger within a caste and even significantly smaller than what exists in a natural population.

They then traced this size change to a specific growth factor gene, and found that across the population, varying degrees of DNA methylation to that gene directly corresponded to body size. A 20 percent modification in DNA methylation yielded a 20 percent change in body size, for example.

“This helps explain at a molecular level how continuums exist between two very discrete variables,” said Alvarado, who is now a member of biology Professor Russell Fernald’s lab at Stanford. “We can now look at diversity within a population by considering what expressions exist in between these variables and the actual molecular mechanism that controls that difference.”

Drawing a stronger connection between how environment and genetic factors influence DNA expression, Alvarado said, could have payoff in mapping the genetic basis of diseases and understanding evolutionary changes.

Source: Stanford News