Hydra: software for tailored processing of H/D exchange data from MS or tandem MS analyses

Background  

Hydrogen/deuterium exchange mass spectrometry (H/DX-MS) experiments implemented to characterize protein interaction and protein folding generate large quantities of data. Organizing, processing and visualizing data requires an automated solution, particularly when accommodating new tandem mass spectrometry modes for H/DX measurement. We sought to develop software that offers flexibility in defining workflows so as to support exploratory treatments of H/DX-MS data, with a particular focus on the analysis of very large protein systems and the mining of tandem mass spectrometry data.     

The priming effect of halogenated phospholipids on the functional responses of human neutrophils

Halogenated lipids formed in the reactions with myeloperoxidase (MPO)-derived species may contribute to the regulation of the functional activity of cells. In the present study we have investigated the effects of chloro- and bromohydrins formed in the HOCl and HOBr reactions, respectively, with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) on three different functional responses of human neutrophils: H₂O₂ generation, degranulation (MPO exocytosis), and cell aggregation. It was shown that POPC chloro- and bromohydrins (POPC-Cl and POPC-Br) induced the priming of neutrophils, resulting in significant upregulation of cell responses to neutrophil stimulators such as N-formyl-Met-Leu-Phe and lectin from Solanum tuberosum. The stimulating effects of POPC-Cl and POPC-Br were observed at low micromolar concentrations (liposomal concentration of POPC, 0.5–5 μM; the content of POPC-Cl or POPC-Br, 38 ± 3% of total lipids) after a short exposure (about 5 min) of the neutrophils to POPC-Cl or POPC-Br. These results suggest that halogenated lipids formed in vivo via MPO-dependent reactions may be considered as a new class of biologically active substances that are potentially able to contribute to the priming of myeloid cells in the sites of inflammation and serve as inflammatory response modulators.     

Lectin-induced activation of plasma membrane NADPH oxidase in cholesterol-depleted human neutrophils

The gp91phox subunit of flavocytochrome b₅₅₈ is the catalytic core of the phagocyte plasma membrane NADPH oxidase. Its activation occurs within lipid rafts and requires translocation of four subunits to flavocytochrome b₅₅₈. gp91phox is the only glycosylated subunit of NADPH oxidase and no data exist about the structure or function of its glycans. Glycans, however, bind to lectins and this can stimulate NADPH oxidase activity. Given this information, we hypothesized that lectin–gp91phox interactions would facilitate the assembly of a functionally active NADPH oxidase in the absence of lipid rafts. To test this, we used lectins with different carbohydrate-binding specificity to examine the effects on H₂O₂ generation by human neutrophils treated with the lipid raft disrupting agent methyl-β-cyclodextrin (MβCD). MβCD treatment removed membrane cholesterol, caused changes in cell morphology, inhibited lectin-induced cell aggregation, and delayed lectin-induced assembly of the NADPH oxidase complex. More importantly, MβCD treatment either stimulated or inhibited H₂O₂ production in a lectin-dependent manner. Together, these results show selectivity in lectin binding to gp91phox, and provide evidence for the biochemical structures of the gp91phox glycans. Furthermore, the data also indicate that in the absence of lipid rafts, neutrophil NADPH oxidase activity can be altered by these select lectins.     

Key enzymes of degradation and angiogenesis as factors of tumor progression for squamous-cell cervical carcinoma

Destruction of the connective tissue matrix (CTM) and angiogenesis are the two processes playing a key role in tumor progression. Matrix metalloproteinases (MMPs) play a leading role in processes of tissue destruction. Tissue collagenases MMP-1 and MT1-MMP hydrolyze fibrillar collagens constituting the base of CTM and enable tumor invasion. Gelatinases A and B (MMP-2 and MMP-9) hydrolyze type IV collagen which is the main component of basal membranes and contribute to the development of metastases. Endogenous activators and inhibitors are involved in the regulation of expression and activity of these enzymes. MMP-9 was shown to release vascular endothelial growth factor (VEGF), the principal inductor of angiogenesis, bound to CTM. Angiotensin-converting enzyme (ACE) is involved in the induction of VEGF synthesis and stimulation of endothelial cell proliferation mediated by angiotensin II (AII) and its type 1 receptor (AT1R). Experiments reported in the present article addressed the distinctive features of expression of key degradation and angiogenesis enzymes in squamous cell carcinoma (SCC) of the cervix. MMP-1, MT1-MMP, MMP-2, and MMP-9 and their endogenous regulators TIMP-1 and TIMP-2, as well as ACE, were the objects of research. Experiments were performed with clinical specimens including tumor tissue samples, for which presence or absence of metastasis to regional lymph nodes was taken into account, and morphologically normal tissue samples. Increased expression of MMP-1, MT1-MMP, and MMP-9 and decreased expression of TIMP-1 and TIMP-2 were shown to make the principal contribution to the destructive (invasive) potential of cervical carcinomas; the effect of changes in MMP-2 expression was less pronounced. Dramatically increased expression of MMP-1 and MMP-9 was evident in metastasizing tumors. ACE activity in tumor samples was generally higher than activity in normal tissue. Substantial expression of MMP-1, MMP-2, MMP-9, and ACE was detected in morphologically normal tissue adjacent to the tumor; this can contribute to increased destructive potential of a tumor. The data reported are important for understanding the mechanisms of tumor progression, have prognostic value, and may affect the choice of individual therapeutic strategy for the patients.     

血红细胞超氧化物歧化酶(SOD)制备工艺的研究初报

本文报告了本实验室设计的由血红细胞自溶液60℃热变性, 乙醇——氯仿法除血红蛋白,旋转蒸发法减压浓缩抽去氯仿、乙醇,硫酸铵分级盐析法沉降SOD,Sepbadex G-75层析提纯SOD等步骤构成的一条成本低、设计合理、简便实用的分离纯化SOD的工艺路线。     

Generation of H2O2 by Human Neutrophils and Changes of Cytosolic Ca2+ and pH of Rat Thymocytes in Response to Galactoside-Binding Proteins (Lectins or Immunoglobulins)

In contrast to plant agglutinins, biological activities of animal/human lectins are not well defined yet. Testing a panel of seven mammalian carbohydrate-binding proteins we have found that the dimeric lectin from chicken liver (CL-16) was a stimulator of H₂O₂ release from human neutrophils as well as effector for induction of cytosolic Ca²⁺ and pH increase in rat thymocytes. Activity of this lectin was comparable to potent galactoside-specific plant lectins such as Viscum album L. agglutinin. The activities of the tested plant lectins depended significantly on their nominal carbohydrate specificity as well as on the source. The results indicate that endogenous lectins may be involved in the regulation of neutrophil and lymphocyte functions by elicitation of selective biosignaling reactions.     

Histological and immunohistochemical effects of Curcuma longa on activation of rat hepatic stellate cells after cadmium induced hepatotoxicity

The liver is a target for toxic chemicals such as cadmium (Cd). When the liver is damaged, hepatic stellate cells (HSC) are activated and transformed into myofibroblast-like cells, which are responsible for liver fibrosis. Curcuma longa has been reported to exert a hepato-protective effect under various pathological conditions. We investigated the effects of C. longa administration on HSC activation in response to Cd induced hepatotoxicity. Forty adult male albino rats were divided into: group 1 (control), group 2 (Cd treated), group 3 (C. longa treated) and group 4 (Cd and C. longa treated). After 6 weeks, liver specimens were prepared for light and electron microscopy examination of histological changes and immunohistochemical localization of alpha smooth muscle actin (αSMA) as a specific marker for activated HSC. Activated HSC with a positive αSMA immune reaction were not detected in groups 1 and 3. Large numbers of activated HSC with αSMA immune reactions were observed in group 2 in addition to Cd induced hepatotoxic changes including excess collagen deposition in thickened portal triads, interlobular septa with hepatic lobulation, inflammatory cell infiltration, a significant increase in Kupffer cells and degenerated hepatocytes. In group 4, we observed a significant decrease in HSC that expressed αSMA with amelioration of the hepatotoxic changes. C. longa administration decreased HSC activation and ameliorated hepatotoxic changes caused by Cd in adult rats.