Recently Published Articles
Editorial for Journal of Proteomics and Genomics Research
Abstract:
An editorial announcing the journal’s launch sets expectations for data standards, reproducibility, and integrative omics studies with clinical relevance.
Optimization and ZSPORE Analysis of Affinity Purification Coupled with Tandem Mass Spectrometry in Mammalian Cells
Abstract:
Defining protein-protein interactions is essential for understanding the mechanisms by which cells regulate basic functions, such as metabolism, transcription, and signal transduction. Affinity purification followed by tandem mass spectrometry (AP-MS) has application for discovery of new interactors regulating various cellular processes. Here we optimize the purification method for AP-MS and develop a simplified unbiased analytical tool, Z-score plus prey occurrence and reproducibility (ZSPORE) for data analysis. Using this pipeline we achieve a higher efficiency of AP-MS and enhanced identification of high confidence interacting proteins (HCIP) in mammalian cells. When applied to analysis of the innate immune interactome, these methods enhanced HCIP identification. In addition, we investigated the GRB2 complex, which is associated with signal transduction and cell growth. Twenty-four known GRB2 interacting proteins were identified plus 26 new GRB2 binding partner...
Eukaryotic Signature Proteins
Abstract:
Eukaryotic Signature Proteins (ESPs) are proteins that delineate the eukaryotes from the archaea and bacteria. They have no recognisable homologues in any prokaryotic genome, but their homologues are present in all main branches of eukaryotes. ESPs are thus likely to have descended from ancient proteins that have existed since the first eukaryotic cell. The last dataset of ESPs was calculated more than a decade ago, thus with advances in technology and the rapid completion of many evolutionary important genomes, this dataset required recalculating. This study recalculated the Giardia lamblia ESP dataset and provides a procedure to calculate signature proteins beginning with any species. The G. lamblia ESP dataset contained a range of proteins including many associated with the membrane, cytoskeleton, nucleus and protein synthesis. ESP datasets have implications on current models of eukaryotic evolution, having high importance in phylogenetic analysis due to ESPs�...
RETRACTED: 3D-Method for Determining the Imaging Quality of Ultrasound Probes
Abstract:
Monitoring ultrasonic probe quality remains an important problem which impacts diagnostic accuracy. Here we present a quantitative method to assess probe quality primarily based on measuring probe maximum contrast (dB) and dynamic range. Contrast relevant parameters of 26 transducer models manufactured by five manufacturers were measured with a novel Random Void Phantom (RVP) approach. 3D-data were acquired and analysed to determine image quality. Acoustic contrast values ranging from 15dB to 36dB were observed. By examining artefact producing side lobes, the novel RVP approach presented here per...
Lung Cancer and Isolated Adrenal Metastases: Different Disease?
Abstract:
Distant metastases generally indicate disseminated disease and the standard treatment for these patients is palliative chemotherapy. Retrospective series showed that selected patients with metastatic lung cancer and a solitary extrathoracic disease could be effectively treated with curative intention by resection of both primary tumor and the single site of metastatic disease. According to current data, adrenalectomy might be considered as an alternative option for patients with isolated adrenal metastases. Significant morbidity and mortality may be happened by these procedures, and a cautious analysis of pros and cons should be discussed with the patient. We present a review of the literature and updated recommendations focusing lung cancer with solitary adrenal metastasis.