Catching The Common Cold Virus Genome

A new study by Brigham Young University researchers on the virus behind nearly half of all cold infections explains how and where evolution occurs in the rhinovirus genome and what this means for possible vaccines."There are a lot of different approaches to treating the cold, none of which seem to be effective," said Keith Crandall, professor of biology and co-author of the study. "This is partly because we haven't spent a lot of time studying the virus and its history to see how it's responding to the human immune system and drugs."

The BYU team studied genomic sequences available online and used computer algorithms to estimate how the rhinovirus is related to other viruses.

According to Nicole Lewis-Rogers, a postdoctoral fellow in the Biology Department and lead author on the study, the rhinovirus is similar to the polio virus, whose vaccine was announced in 1955. But while the polio virus has just three subspecies, the rhinovirus has more than 100 subspecies, which continually evolve.

"These viruses could be under the same constraints and yet change differently," Lewis-Rogers said. "That's why it is so hard to create a vaccine."

Through a computer program developed at BYU, Lewis-Rogers' team was able to identify the parts of the virus genome that enable resistance to drugs and the human immune system.

The immune system does a good job of recognizing viral contaminants and getting rid of them, as do new drugs, but the rhinovirus has responded to these defenses by changing its genome so that it is not so easily recognized.

"The virus is evolving solutions against the immune system and drugs," Crandall said. "The more we can learn about how the virus evolves solutions, the better we can rid the body of these infections."

Understanding where change occurs in the virus genome will help virologists who work to design drugs that target the rhinovirus.

"If you've got 10,000 bits of information, this narrows it down to a handful," Lewis-Rogers said. "Here is where you can start looking."

Lewis-Rogers and Crandall hope scientists will use these insights to build better drugs to combat the virus in the most effective way.

The study is reported in the April issue of the journal Molecular Biology and Evolution. BYU undergraduate Matthew Bendall is also a co-author on the study, which was funded by the USDA. Bendall will next pursue a master's in bioinformatics at BYU.

Broccoli May Help Protect Against Respiratory Conditions Like Asthma

Here's another reason to eat your broccoli: UCLA researchers report that a naturally occurring compound found in broccoli and other cruciferous vegetables may help protect against respiratory inflammation that causes conditions like asthma, allergic rhinitis and chronic obstructive pulmonary disease.Published in the March edition of the journal Clinical Immunology, the research shows that sulforaphane, a chemical in broccoli, triggers an increase of antioxidant enzymes in the human airway that offers protection against the onslaught of free radicals that we breathe in every day in polluted air, pollen, diesel exhaust and tobacco smoke. A supercharged form of oxygen, free radicals can cause oxidative tissue damage, which leads to inflammation and respiratory conditions like asthma.

"This is one of the first studies showing that broccoli sprouts — a readily available food source — offered potent biologic effects in stimulating an antioxidant response in humans," said Dr. Marc Riedl, the study's principal investigator and an assistant professor of clinical immunology and allergy at the David Geffen School of Medicine at UCLA.

"We found a two- to three-fold increase in antioxidant enzymes in the nasal airway cells of study participants who had eaten a preparation of broccoli sprouts," Riedl said. "This strategy may offer protection against inflammatory processes and could lead to potential treatments for a variety of respiratory conditions."

The UCLA team worked with 65 volunteers who were given varying oral doses of either broccoli or alfalfa sprout preparations for three days. Broccoli sprouts are the richest natural source of sulforaphane; the alfalfa sprouts, which do not contain the compound, served as a placebo.

Rinses of nasal passages were collected at the beginning and end of the study to assess the gene expression of antioxidant enzymes in cells of the upper airways. Researchers found significant increases of antioxidant enzymes at broccoli sprout doses of 100 grams and higher, compared with the placebo group.

The maximum broccoli sprout dosage of 200 grams generated a 101-percent increase of an antioxidant enzyme called GSTP1 and a 199-percent increase of another key enzyme called NQO1.

"A major advantage of sulforaphane is that it appears to increase a broad array of antioxidant enzymes, which may help the compound's effectiveness in blocking the harmful effects of air pollution," Riedl said.

According to the authors, no serious side effects occurred in study participants receiving broccoli sprouts, demonstrating that this may be an effective, safe antioxidant strategy to help reduce the inflammatory impact of free radicals.

Riedl notes that more research needs to be done to examine the benefits of sulforaphane for specific respiratory conditions. It is too early to recommend a particular dosage.

Riedl recommends including broccoli and other cruciferous vegetables as part of a healthy diet.

The study was supported by the National Institutes of Health, the National Institute of Environmental Health Sciences and the U.S. Environmental Protection Agency.

Other study authors include Dr. Andrew Saxon of the Hart and Louis Lyon Laboratory, division of clinical immunology and allergy in the department of medicine at the David Geffen School of Medicine at UCLA, and Dr. David Diaz-Sanchez of the human studies division of the U.S. Environmental Protection Agency.

Calculating Gene And Protein Connections In Parkinson's Disease Model

A novel approach to analyzing cellular data is yielding new understanding of Parkinson's disease's destructive pathways.Researchers have created an algorithm that meshes existing data to produce a clearer step-by-step flow chart of how cells respond to stimuli. Using this new method, Whitehead Institute and Massachusetts Institute of Technology scientists have analyzed alpha-synuclein toxicity to identify genes and pathways that can affect cell survival. Misfolded copies of the alpha-synuclein protein in brain cells are a hallmark of Parkinson's disease.

Until now, data on gene expression and protein production have not been consistently analyzed together, leaving gaps in researchers' understanding of how various genes and proteins interact to form a cell's response to a stimulus. This new method could speed the development of therapies for a variety of diseases, including Parkinson's disease.

The scientists have employed this new computational technique to analyze alpha-synuclein, a mysterious protein that is associated with Parkinson's disease.

Cells are constantly adapting to various stimuli, including changes in their environment and mutations, through an intricate web of molecular interactions. Knowledge of these changes is crucial for developing new treatments for diseases. To decipher how a cell responds to various stimuli, laboratories worldwide have been turning to new technologies that produce vast amounts of data. Such data typically exists in two major forms: genetic screen data (the results from deleting a gene from a cell's genome and seeing what observable traits appear in the cell) and information on the cellular levels of messenger RNA (mRNA, which is the template for proteins).

Historically, these two types of data have largely been analyzed independently of each other, revealing only glimpses of the cell's internal workings. Each type of data is actually biased toward identifying different aspects of cellular response, something that researchers had not realized until now. However, the new algorithm, known as ResponseNet, exploits these biases and allows for combined analysis.

In this combined analysis, both data types are integrated with molecular interactions data into a diagram that connects the experimentally identified proteins and genes. While this typically results in an extraordinarily complicated diagram, sometimes jokingly referred to as a "hairball", ResponseNet is designed to whittle the hairball down to the most probable pathways connecting various genes and proteins.

Esti Yeger-Lotem, a postdoctoral researcher in the laboratories of Whitehead Member Susan Lindquist and of Ernest Fraenkel at MIT's Biological Engineering department and co-author of the Nature Genetics article, says that by analyzing those probable pathways, a systems view of the cellular response emerges. "This allows for a more complete understanding of cellular response and can reveal hidden components of the response that may be targeted by drugs," she says.

According to Laura Riva, a postdoctoral researcher in MIT's biological engineering department and one of the designers of the algorithm, ResponseNet is potentially very useful for researchers.

"It is a powerful approach for interpreting experimental data because it can efficiently analyze tens of thousands of nodes and interactions," says Riva, who is also a co-author on the article. "The output of ResponseNet is a sparse network connecting some of the genetic data to some of the transcriptional data via intermediate proteins. Biologists can look at the network and understand which pathways are perturbed, and they can use it to generate testable hypotheses."

To demonstrate ResponseNet's capabilities, Yeger-Lotem entered the data from screens of 5,500 yeast strains (Saccharomyces cerevisiae). These strains are based on a yeast model that creates large amounts of the protein alpha-synuclein, thereby mimicking the toxic effects of alpha-synuclein accumulation in Parkinson's disease patients' brain cells.

Ernest Fraenkel, Assistant Professor of Biological Engineering at MIT, says that the alpha-synuclein data are an excellent test case for the algorithm, which has lead to new insights from existing data.

"The connection between alpha-synuclein and Parkinson's disease is enigmatic," says Fraenkel. "We have wonderful data from the yeast model, but despite this richness of data, so little is known about what alpha-synuclein really does in the cell."

Using these data, ResponseNet identified several links between alpha-synuclein toxicity and basic cell processes, including those used to recycle proteins and to usher the cell through its normal life cycle.

Surprisingly, ResponseNet also tied alpha-synuclein toxicity to a highly-conserved pathway targeted by cholesterol-lowering statin drugs and another pathway targeted by the immunosuppressing drug rapamycin.

To confirm ResponseNet's links and to test how these two pathways could affect alpha-synuclein toxicity, researchers added either rapamycin or the statin lovastatin to yeast model cultures. When the researchers added a low dose of rapamycin to the yeast model, the drug was toxic to the yeast. When lovastatin was added, the yeast reduced their growth rate, an indicator that the yeast had gotten sicker. However, when researchers added the molecule ubiquinone (also known as coenzyme Q10 or CoQ10), which is farther downstream in the statin network and possibly undersynthesized in alpha-synuclein-containing yeast, ubiquinone modestly suppressed alpha-synuclein toxicity.

All of these results validated the hypotheses based on ResponseNet's network.

"ResponseNet provides a wealth of new information," says Lindquist, who is also a Howard Hughes Medical Institute investigator and a professor of biology at MIT. "Some of the things we have found offer a promise to speed the development of new therapeutic strategies for Parkinson's disease. For the sake of the patients involved, let's hope they hold true in a human brain."

Full Citation: "Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity"

Nature Genetics, online February 22, 2009