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.     

Molecular models of the Mojave rattlesnake (Crotalus scutulatus scutulatus) venom metalloproteinases reveal a structural basis for differences in hemorrhagic activities

Rattlesnake venom can differ in composition and in metalloproteinase-associated activities. The molecular basis for this intra-species variation in Crotalus scutulatus scutulatus (Mojave rattlesnake) remains an enigma. To understand the molecular basis for intra-species variation of metalloproteinase-associated activities, we modeled the three-dimensional structures of four metalloproteinases based on the amino acid sequence of four variations of the proteinase domain of the C. s. scutulatus metalloproteinase gene (GP1, GP2, GP3, and GP4). For comparative purposes, we modeled the atrolysin metalloproteinases of C. atrox as well. All molecular models shared the same topology. While the atrolysin metalloproteinase molecular models contained highly conserved substrate binding sites, the Mojave rattlesnake metalloproteinases showed higher structural divergence when superimposed onto each other. The highest structural divergence among the four C. s. scutulatus molecular models was located at the northern cleft wall and the S’₁-pocket of the substrate binding site, molecular regions that modulate substrate selectivity. Molecular dynamics and field potential maps for each C. s. scutulatus metalloproteinase model demonstrated that the non-hemorrhagic metalloproteinases (GP2 and GP3) contain highly basic molecular and field potential surfaces while the hemorrhagic metalloproteinases GP1 and atrolysin C showed extensive acidic field potential maps and shallow but less dynamic active site pockets. Hence, differences in the spatial arrangement of the northern cleft wall, the S’₁-pocket, and the physico-chemical environment surrounding the catalytic site contribute to differences in metalloproteinase activities in the Mojave rattlesnake. Our results provide a structural basis for variation of metalloproteinase-associated activities in the rattlesnake venom of the Mojave rattlesnake.     

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。     

Iron Oxide Nanoparticles as Nano-adsorbents: A Possible Way to Reduce Arsenic Phytotoxicity in Indian Mustard Plant (Brassica juncea L.)

Journal of Plant Growth Regulation - Application of nanoparticles (NPs) is very effective in reducing metal toxicity. The present study was designed to determine the effectiveness of iron oxide...     

The predatory mite Hypoaspis miles: biological and demographic characteristics on two prey species, the mushroom sciarid fly, Lycoriella solani, and the mould mite, Tyrophagus putrescentiae

The biology of Hypoaspis miles Berlese (Acarina: Hypoaspidae) fed on mushroom sciarid larvae (Lycoriella solani Winnertz) (Diptera: Lycoriidae) and mould mites (Tyrophagus putrescentiae Schrank) (Acari: Acaridae), was investigated by laboratory experiments at 20 °C, 75% r.h. and LD16:D8 hours. H. miles had a significantly shorter development time and a significantly lower juvenile mortality when fed on sciarid larvae than on mould mites, the development time being 14.5 days and the mortality 3.5% on the former prey. The preoviposition and postoviposition periods of H. miles were not uninfluenced by the prey species and were 5–9 and 32–37 days, respectively. Oviposition periods of 53.2 and 68.5 days and female longevities of 82 and 109.6 days were observed on diets of sciarid larvae and mould mites, respectively. Male longevity (168–219 days) was uninfluenced by the prey species. The egg production of H. miles on sciarid larvae was estimated to be 44.4 ± 4.33 eggs per female, as compared to 22.43 ± 1.79 eggs per female on mould mites. The sex-ratio of the offspring was significantly influenced by the prey species, the ratios (/(+)) being 0.66 on sciarid larvae and 0.54 on mould mites. The net reproductive rate (R₀) for H. miles fed on sciarid larvae was approximately 27 which was three times higher than for mites feeding on mould mites. The innate capacity of increase (r_m) was highest (0.0747 day^–1) when sciarid larvae served as food, giving a doubling time of 9.3 days as compared to 12.8 days on mould mites. The generation times were 44.28 on sciarid larvae and 40.67 days on mould mites. The daily food consumption rate of juvenile and adult H. miles was 0.24 and 0.86 sciarid larvae and 10.8 and 21.7 mould mites, respectively. In terms of weight consumed, however, the consumption of sciarid larvae was 2–3.5 times the weight of mould mites. The ratio of females to males influenced the oviposition period and egg production of H. miles, with virgin females laying fewer eggs over a longer period of time as compared with females with access to males. The egg production in relation to the sex-ratio was described by models predicting a maximum number of eggs per female of 22.3 to be attained at a sex ratio of 0.69 (/(+)) and a maximum daily number of eggs per female of 0.33 to be attained at a sex ratio of 0.37 (/(+)).     

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.