Apex Peptide Elution Chain Selection: A New Strategy for Selecting Precursors in 2D-LC-MALDI-TOF/TOF Experiments on Complex Biological Samples

LC-MALDI provides an often overlooked opportunity to exploit the separation between LC-MS and MS/MS stages of a 2D-LC-MS-based proteomics experiment, that is, by making a smarter selection for precursor fragmentation. Apex Peptide Elution Chain Selection (APECS) is a simple and powerful method for intensity-based peptide selection in a complex sample separated by 2D-LC, using a MALDI-TOF/TOF instrument. It removes the peptide redundancy present in the adjacent first-dimension (typically strong cation exchange, SCX) fractions by constructing peptide elution profiles that link the precursor ions of the same peptide across SCX fractions. Subsequently, the precursor ion most likely to fragment successfully in a given profile is selected for fragmentation analysis, selecting on precursor intensity and absence of adjacent ions that may cofragment. To make the method independent of experiment-specific tolerance criteria, we introduce the concept of the branching factor, which measures the likelihood of false clustering of precursor ions based on past experiments. By validation with a complex proteome sample of Arabidopsis thaliana, APECS identified an equivalent number of peptides as a conventional data-dependent acquisition method but with a 35% smaller work load. Consequently, reduced sample depletion allowed further selection of lower signal-to-noise ratio precursor ions, leading to a larger number of identified unique peptides.

Trans-trapezium carpo-metacarpal dislocation of the thumb

We report a case of carpo-metacarpal dislocation associated with an isolated horizontal fracture of the trapezium. It is a rare lesion which is difficult to diagnose by standard radiography, and CT may be necessary for the diagnosis and correct treatment. In our case, stable osteosynthesis was achieved by internal screw fixation, and at follow-up there was an unrestricted, painless range of motion of the thum

Gallstone ileus treated with non-surgical conservative methods: a case report

INTRODUCTION: The preoperative diagnosis of gallstone ileus is challenging due to the variability of its presentation, often resulting in late diagnosis. Controversy remains regarding the management of gallstone ileus; surgery is the standard treatment, but also less invasive approaches have proven to be successful. We present an unusual case of gallstone ileus and its conservative treatment. CASE PRESENTATION: We describe the case of a 49-year-old Caucasian woman with a bowel sub-occlusion, treated conservatively. The imaging technique (plain abdominal X-ray and computed tomography scan) led to a diagnosis of gallstones ileus. A surgical intervention was not performed. Instead, she underwent extracorporeal shock-wave lithotripsy to fragment the stones, mechanical intestinal dilatation for ileocolic stenosis and endoscopic removal of the gallstone. The presence of an apricot shell contributed to the bowel occlusion and was removed. The intervention was successful and without complications. CONCLUSIONS: Given the variability of the gallstone ileus presentation, surgery could not be the only treatment for our patient. In our case report, we show that colonoscopy could be a non-invasive approach that allows for diagnosis and treatment at the same time. The available data do not show a higher rate of recurrent biliary disease in cases where this method has been used, therefore in select patients, a conservative treatment could be an effective solution

Metastasis to parotid gland from non Head and Neck tumors

Most primary tumors spreading metastasis to the parotid gland are usually located in the head and neck region, nonetheless, rarely, parotid gland can also be the target of metastatic localization site of distant primary tumors. The purpose of this study was to describe a clinical series of metastasis to the parotid gland from distant primary tumors (non Head & Neck)

Trans-nasal endoscopic and intra-oral combined approach for odontogenic cysts

Maxillary cysts are a common finding in maxillofacial surgery, dentistry and otolaryngology. Treatment is surgical; a traditional approach includes Caldwell-Luc and other intra-oral approaches. In this article, we analyse the outcomes of 9 patients operated on using a combined intra-oral and trans-nasal approach to the aforementioned disease. Although the number of patients is small, the good results of this study suggest that the combined approach might be a reliable treatment option

Direct and indirect costs in the conservative management of undisplaced scaphoid fractures

The scaphoid is the most commonly fractured carpal bone, and preferable treatment of undisplaced fractures is controversial. In order to assess the socio-economic impact of treatment modalities, we analysed the cost of conservative management of 54 undisplaced scaphoid fractures. Global costs amounted to 14.077 Swiss francs (9385 euros) per patient. Direct costs represent only 10% of global costs. No significant correlation was found between costs and timing of diagnosis, hand dominance or complications. Thirty-four percent of patients were able to resume their job with the wrist immobilised without complication, but at an obvious impact on indirect and global costs. If early resumption of professional activities during conservative treatment of undisplaced scaphoid fractures does not impair successful fracture healing, patients should be encouraged to return to work as early as possible, as is routinely done after percutaneous fracture fixation. This will contribute to massively reducing the cost of conservative treatmen

Biomarker Discovery In Chronic Obstructive Pulmonary Disease (COPD) Using Epithelial Lining Fluid:A Proteomic Approach

RATIONALE Chronic Obstructive Pulmonary Disease (COPD) is the third most frequent disease worldwide with increasing mortality. Cigarette smoking is the principle risk factor and 15-20% of smokers develop COPD. Epithelial Lining Fluid (ELF) covers the internal part of the airways and can be collected during bronchoscopy. ELF appears to be well-suited for proteomic analysis, since it contains a higher concentration of proteins (150-300 μg /mL) than other lung fluids and can be obtained from different locations of the lungs. No comprehensive proteomic analysis of human ELF has been performed to date, which makes ELF a highly interesting fluid for biomarker discovery in COPD. AIM To discover proteins that change in abundance in ELF from COPD patients versus healthy controls using a quantitative proteomics approach. METHODS The ELF proteome from COPD patients and healthy controls was studied by 1D polyacrylamide gel electrophoresis in the presence of SDS followed by in-gel tryptic digestion to establish the methodology and assess the feasibility of such an approach. Approximately 40 gel slices were obtained from each lane of the gel (corresponding to one patient). Digested samples were analyzed by nanoChip-LC-MS/MS using an ion trap. We performed a quantitative pilot study of ELF from 4 COPD patients and 4 healthy controls (table 1) to test for statistically significant differences in protein levels. ELF samples were digested by trypsin, labeled with stable isotope-containing reagents (iTRAQ®, 8-plex) and processed by strong cation-exchange chromatography followed by nanoLC-MS/MS. In order to validate the results, a second quantitative analysis of an independent sample set (4 COPD vs 4 healthy) using the same methodological approach was done. RESULTS The 1D electrophoretic approach resulted in more than 300 identified proteins. Most of the identified proteins were present in both COPD and healthy samples, although some proteins were only identified either in healthy control or in COPD samples. The quantitative studies showed that a number of proteins was significantly different between ELF of COPD patients and controls, including 4 up-regulated proteins in common in both studies. CONCLUSIONS This is the first study in ELF of COPD patients and healthy controls in which such a large number of proteins has been identified. The obtained results show the feasibility of this proteomic approach and the possibility to discover proteins that are differentially expressed in ELF of COPD patients and controls. We are currently validating these proteins further by western blot and immunohistochemistry

Experimental and numerical analysis of supersonic blade profiles developed for highly loaded impulse type steam turbine stages

The paper describes the results of a numerical and experimental research program addressing the aerodynamic investigation on the performance of blade profiles specifically developed for application in highly loaded impulse type turbine stages. The industrial requirements driving toward the adoption of highly loaded stage solutions are presented, along with an estimation of the profiles operating parameters. Two stator vanes and one rotor blade profile have been developed and extensively tested by means of flow field measurements and schlieren visualization in a transonic blow-down wind tunnel for linear cascades. Experimental results for the relevant operating conditions are presented, providing validation data for the CFD model used for blade design and evidencing that the main goals of the design optimization procedure have been achieved

Regulation of ykrL (htpX) by Rok and YkrK, a Novel Type of Regulator in Bacillus subtilis

Expression of ykrL of Bacillus subtilis, encoding a close homologue of the Escherichia coli membrane protein quality control protease HtpX, was shown to be upregulated under membrane protein overproduction stress. Using DNA affinity chromatography, two proteins were found to bind to the promoter region of ykrL: Rok, known as a repressor of competence and genes for extracytoplasmic functions, and YkrK, a novel type of regulator encoded by the gene adjacent to ykrL but divergently transcribed. Electrophoretic mobility shift assays showed Rok and YkrK binding to the ykrL promoter region as well as YkrK binding to the ykrK promoter region. Comparative bioinformatic analysis of the ykrL promoter regions in related Bacillus species revealed a consensus motif, which was demonstrated to be the binding site of YkrK. Deletion of rok and ykrK in a PykrL-gfp reporter strain showed that both proteins are repressors of ykrL expression. In addition, conditions which activated PykrL (membrane protein overproduction, dissipation of the membrane potential, and salt and phenol stress) point to the involvement of YkrL in membrane protein quality control