We welcome suggestions for research to highlight in Aliquots. The items should be primary research articles (no reviews, editorials or commentaries) published within the last two months in a peer-reviewed journal. Please send the article citation (PDF if available) and any other feedback about the column to: aliquots@vanderbilt.edu.
Pick a peck of proper proteins
Identifying new disease biomarkers hinges on determining which proteins are present in a sample. Proteomics methods like liquid chromatography-tandem mass spectrometry break proteins down into thousands of fragments (peptides) that must be compared to known proteins. Since a single peptide can be common to many proteins, such methods often overestimate the number of proteins in a sample.
To facilitate protein identification, Bing Zhang, Ph.D., David Tabb, Ph.D., and colleagues have created an open-source protein assembly tool called IDPicker (http://fenchurch.mc.vanderbilt.edu/lab/software.html). They characterized the tool's accuracy of protein identification using mass spectrometry data sets of human and yeast protein samples. The team reports in the Journal of Proteome Research that the technique simplifies candidate protein lists, improves accuracy of protein identification, and groups proteins of related function together to help investigators decipher the biological lessons presented by each sample.
— Melissa Marino
Cre-ating tools for gene manipulation
It has become possible in recent years to make precise genetic modifications in the mouse — in specific tissues or at specific times during development. One approach for making these “conditional” changes is the Cre/LoxP system, which takes advantage of the Cre recombinase protein to modify gene targets. This system uses a single promoter to “drive” expression of Cre, but the available promoters often drive Cre production in too many different cell types.
To address this limitation, Guoqiang Gu, Ph.D., and colleagues explored expressing Cre as two inactive fragments under the control of separate promoters. They report in Nucleic Acids Research the successful reconstitution of Cre activity from two pieces of the protein, each modified to contain a protein interaction domain that “zips” the fragments together. The pieced-together Cre was active in both cultured cells and transgenic animals, suggesting that the approach can be used to study gene function in cells expressing two different protein markers.
— Leigh MacMillan
Poking holes in toxin structure
More than half of all humans harbor the bacterium Helicobacter pylori — a risk factor for gastric cancer and ulcers — in their stomachs, where it produces a toxin capable of punching holes in stomach cell membranes.
In the Proceedings of the National Academy of Sciences, Borden Lacy, Ph.D., Tim Cover, M.D., and colleagues describe the structure of a key piece of the pore-forming toxin VacA. They determined that this “p55 domain,” which mediates binding of VacA to host cells, resembles a sock, with a globular “toe” region and a triangular helix making up the “heel” and “calf.” This structure fits nicely into the previously described flower-shaped structure of the VacA complex thought to assemble on the host cell membrane. The researchers identified two strictly conserved regions likely important for assembly of the pore complex and binding to host cells. Targeting these regions could be key to developing a vaccine that offers protection against multiple strains of H. pylori.
— Melissa Marino
Vaccine candidate for RSV
Respiratory syncytial virus (RSV) — the No. 1 cause of respiratory disease and hospitalization in children under age 5 — is especially dangerous for premature infants, the elderly and immunocompromised patients. Despite years of efforts, there are no FDA-approved vaccines to prevent RSV disease.
James Crowe, M.D., and colleagues are trying a new vaccine vector: Venezuelan equine encephalitis replicon particles (VRPs). Other studies have shown that VRPs induce a protective response at the mucosal surface, which would offer an advantage in combating respiratory viruses like RSV. The investigators engineered VRPs expressing RSV surface proteins and showed that intranasal delivery of these RSV-VRP vaccine candidates to mice and cotton rats induced immune responses comparable to or greater than those following wild-type virus infection. The RSV-VRPs also protected vaccinated animals against an intranasal RSV challenge. The findings, reported in the Journal of Virology, support further development of RSV-VRPs as an RSV vaccine candidate. Vanderbilt has applied for a patent to support the use of this vaccine strategy.
— Leigh MacMillan
Past Aliquots
June 22, 2012
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