September 18, 2009

Aliquots — research highlights from VUMC laboratories

Improved protein assembly

Proteomics methods – which break proteins down into thousands of fragments (peptides) that must be compared to known proteins – are important tools for identifying new disease biomarkers. But a typical experiment can generate tens of thousands of fragments that must be matched to protein sequences in a database, requiring an automated analysis system to identify the proteins present in a sample.

David Tabb, Ph.D., and colleagues developed an open-source protein assembly tool called IDPicker to help identify proteins from such large data sets. In the August issue of the Journal of Proteome Research, the investigators report recent improvements to the tool.

The researchers evaluated the new software with multiple data sets and compared the performance of IDPicker to another commonly used program (PeptideProphet). The new version, they report, is more robust against false positives and improves peptide identification and sensitivity.

These advances position IDPicker (available at: for high peptide discrimination and reliable protein assembly in large-scale proteomics studies.

Melissa Marino


Speeding up TB testing

Mycobacterium tuberculosis – the bacterium responsible for tuberculosis – often takes several weeks to grow in the lab. This slow growth limits the usefulness of culture-based methods in assessing the effectiveness of an antibiotic regimen against tuberculosis.

Yi-Wei Tang, M.D., Ph.D., and colleagues have developed two real-time PCR methods for detecting and quantifying mycobacterial DNA and mRNA isolated directly from sputum samples. The researchers tested the effectiveness of these assays in 65 patients with newly diagnosed TB that were receiving a first-line anti-TB drug regimen.

In the September issue of Clinical Chemistry, they report that both assays were better at detecting TB than a standard acid-fast stain method for diagnosis. The mRNA assay, they found, was better at monitoring the efficacy of therapy. The mRNA assay results correlated with mycobacterial culture to anti-TB drugs, but the DNA assay showed a high false-positive rate. The results suggest that this mRNA assay may allow for rapid monitoring of response to anti-TB therapy.

Melissa Marino


Stomach bug’s cancer factors

Helicobacter pylori – a bacterial species found in the stomachs of more than half of all humans – is the strongest known risk factor for gastric adenocarcinoma, but only a fraction of infected persons will develop cancer. The genetic diversity of H. pylori strains has hindered identification of factors that mediate carcinogenesis.

To find such factors, Richard Peek, M.D., and colleagues compared the proteins expressed by two related H. pylori strains – one that induces inflammation, but not cancer, and another (derived from the first) that causes gastric cancer in two rodent models. Using a proteomics approach

H. pylori

The findings, reported in the August issue of Molecular & Cellular Proteomics, provide a foundation for further studies of the roles of bacterial virulence factors in H. pylori-induced gastric cancer.

Leigh MacMillan


Children increase stroke risk

High gravidity (number of pregnancies) and high parity (number of births) have been associated with an increased risk of stroke in women. Although the biologic effects of pregnancy may account for this, a study of Chinese women and their husbands indicates chronic stress and lifestyle risk factors related to childrearing may also be contributing factors.

The study, published in the August issue of Stroke, examined a large cohort of Chinese women enrolled in the Shanghai Women’s Health Study as well as their husbands. Xianglan Zhang, M.D., M.P.H., and colleagues

Leslie Hast


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:

Past Aliquots

June 22, 2012
June 8, 2012
May 11, 2012
April 27, 2012
April 13, 2012
March 30, 2012
March 16, 2012