Computer prediction of allergen proteins from sequence-derived protein structural and physicochemical properties

BACKGROUND: Computational methods have been developed for predicting allergen proteins from sequence segments that show identity, homology, or motif match to a known allergen. These methods achieve good prediction accuracies, but are less effective for novel proteins with no similarity to any known allergen. METHODS: This work tests the feasibility of using a statistical learning method, support vector machines, as such a method. The prediction system is trained and tested by using 1005 allergen proteins from the Allergome database and 22,469 non-allergen proteins from 7871 Pfam families. RESULTS: Testing results by an independent set of 229 allergen and 6717 non-allergen proteins from 7871 Pfam families show that 93.0% and 99.9% of these are correctly predicted, which are comparable to the best results of other methods. Of the 18 novel allergen proteins non-homologous to any other proteins in the Swissprot database, 88.9% is correctly predicted. A further screening of 168,128 proteins in the Swissprot database finds that 2.9% of the proteins are predicted as allergen proteins, which is consistent with the estimated numbers from motif-based methods. CONCLUSIONS: Our study suggests that SVM is a potentially useful method for predicting allergen proteins and it has certain capability for predicting novel allergen proteins. Our software can be accessed at .     

Identification of neutralizing linear epitopes from the VP1 capsid protein of Enterovirus 71 using synthetic peptides

Enterovirus 71 (EV71) is the main causative agent of Hand, foot and mouth disease (HFMD) and has been associated with severe neurological diseases resulting in high mortalities. Currently, there is no vaccine available and treatment is limited to palliative care. In this study, antisera were raised in mice against 95 overlapping synthetic peptides spanning the VP1 capsid protein of EV71. Two peptides, SP55 and SP70, containing amino acid 163-177 and 208-222 of VP1, respectively, are capable of eliciting neutralizing antibodies against EV71 in the in vitro microneutralization assay. SP70 was identified to be particularly potent in eliciting a neutralizing antibody titer comparable to that obtained with a whole virion-immune serum. Immunization of mice with either SP55 or SP70 triggered an EV71-specific IgG response as high as that obtained with the whole virion as immunogen. The IgG sub-typing revealed that the neutralizing antibodies elicited by both synthetic peptides are likely belonging to the IgG1 sub-type. Alignment with databases showed that the amino acid residues of SP70 are highly conserved amongst the VP1 sequences of EV71 strains from various sub-genogroups. Altogether, these data indicate that SP70 represents a promising candidate for an effective synthetic peptide-based vaccine against EV71.     

Predicting Failure Load of the Femur with Simulated Osteolytic Defects using Noninvasive Imaging Technique in a Simplified Load Case

Currently, there is no proven sensitive or specific method for predicting pathological fracture of the femur. The clinical management of lytic femoral metastases is based on geometric measurement of the bone, of the defect, or both. However, the mechanical behavior of a structure depends on both its material and geometric properties. Our hypothesis is that a change in bone structural properties as the result of tumor induced osteolysis determines the fracture risk in bones with skeletal metastases. We developed a method of QCT (Quantitative Computed Tomography) combined with engineering beam analysis as a noninvasive tool for measuring the material and geometric properties of the femur with simulated lytic defects in the intertrochanteric region. In this ex-vivo study we prove that engineering beam structural analysis applied to serial transaxial QCT scans through human femora with simulated lytic defects at the proximal femur predicts the load at failure and location of fracture better than current clinical guidelines. Structural rigidity measured by QCT in this study may be used to predict the load carrying capacity of femurs with metastatic defects and, furthermore, may be used when the tumor has weakened the bone sufficiently such that pathological fracture is imminent and prophylactic stabilization is necessary.

Induction of apoptosis by crambene protects mice against acute pancreatitis via anti-inflammatory pathways

Apoptosis is a teleologically beneficial form of cell death in acute pancreatitis. Our previous work has demonstrated that induction of pancreatic acinar cell apoptosis by crambene protects mice against acute pancreatitis. However, little is known about how the induction of apoptosis reduces the severity of acute pancreatitis. Because the clearance of apoptotic cells might suppress inflammation and critically regulate immune responses, we postulate that clearance of apoptotic cells stimulates an anti-inflammatory response, which has a protective action against acute pancreatitis. To test this hypothesis, induction of apoptosis in acute pancreatitis in vivo and co-cultures of peritoneal resident macrophages with apoptotic acinar cells in vitro were used as experimental systems, testing expression of phagocytic receptors and levels of inflammatory mediators. Moreover, neutralizing anti-interleukin (IL)-10 monoclonal antibody (2.5 mg/kg) was used before the induction of apoptosis in acute pancreatitis, testing whether the protection from apoptosis induction would be removed. Our study showed that clearance of apoptotic acinar cells, which may occur essentially through the CD36-positive macrophage, stimulates the release of anti-inflammatory mediators like IL-10. IL-10 plays an important role in crambene-induced protection in acute pancreatitis. Thus, induction of pancreatic acinar cell apoptosis by crambene protects mice against acute pancreatitis via induction of anti-inflammatory pathways.     

A female-specific pentraxin, CrOctin, bridges pattern recognition receptors to bacterial phosphoethanolamine

Pathogen recognition and binding are crucial functions of innate immunity. It has been observed that the short pentraxin superfamily including C-reactive protein (CRP) and serum amyloid P component are pathogen pattern recognition receptors (PRR) in the plasma. We isolated and characterized a novel and distinctive pentraxin from the plasma of horseshoe crab, Carcinoscorpius rotundicauda, henceforth named CrOctin, which binds to bacteria via phosphoethanolamine (PE), a chemical component present on lipid A and core polysaccharide moieties of bacterial lipopolysaccharide (LPS). Infection enhances the formation of the PRR interactome constituting CrOctin, CRP and galactose-binding protein. In particular, infection increases the affinity of CRP to CrOctin by 1000-fold. Furthermore, we observed that by binding to PE, CrOctin acts as a linker that bridges the PRR interactome to the inner core of LPS. On the other hand, under normal physiological conditions, binding of CrOctin to PE appears to obscure other PRR from interacting directly with PE. Interestingly, the cluster of "CrOctin-interactive PRR" is sex specific. We report, for the first time, the change in PRR protein profiles with a distinctive gender difference during Pseudomonas infection.     

Differential effects of ceramide species on exocytosis in rat PC12 cells

Increases in several ceramide species have been shown by non-targeted lipid profiling (lipidomics) of the rat hippocampus after kainate lesions (Guan et al. FASEB J 20:1152–1161, 2006). This study was carried out to examine possible effects of ceramide species on exocytosis. Significant increase in membrane capacitance in voltage-clamped rat pheochromocytoma (PC12) cells, an indication of exocytosis, was detected immediately after external application of C2, C6, and C18 ceramide. In contrast, no increase in capacitance was found after addition of C16 and C20 ceramide, or DMSO vehicle. The effect of ceramide on exocytosis was dependent on the integrity of lipid rafts. Treatment of cells with the cholesterol binding agent/disruptor of lipid rafts, methyl β cyclodextrin, prior to addition of C18 ceramide suppressed the increase in capacitance induced by this lipid species. The ability of C2, C6 and C18 ceramide to trigger exocytosis was confirmed using total internal reflection fluorescence microscopy (TIRFM) experiments. External application of these species caused an exponential decrease in the number of subplasmalemmal neuropeptide Y (NPY)-enhanced green fluorescence protein (EGFP) labeled vesicles, indicating exocytosis. Interestingly, C18 is also the ceramide species that showed the greatest increase in the rat hippocampus after kainate excitotoxicity. It is postulated that C18 ceramide might facilitate exocytosis of glutamate from damaged neurons, thus propagating neuronal injury.