Variation between freshwater and terrestrial fungal communities on decaying bamboo culms

Fungal communities on decaying culms of a bamboo host (Phyllostachys bambusoides) from freshwater and adjacent terrestrial habitats were identified. Collections were made at Xiao Bai Long Mountain, Yiliang, Yunnan, China in the winter and summer. In each collection, 100 similar-sized bamboo culms were collected, comprising 50 submerged samples from a stream and 50 terrestrial samples from adjacent riparian vegetation. A total of 82 fungal taxa were recorded from the samples, including 30 ascomycetes and 52 anamorphic fungi. The frequency of occurrence of these fungi were recorded and the Shannon–Weiner indices (H′) were applied to evaluate fungal diversity. The results showed that variation of the fungal diversity between the summer and winter collections was insignificant (0.2<p<0.5). Fungal diversity on submerged bamboo however, was significantly higher than that on terrestrial bamboo (p<0.001). Further findings were that: (1) some commonly recorded freshwater and terrestrial taxa were found in both habitats, but overall there were only 15 overlapping species between the two habitats; (2) the dominant species in each habitat were considerably different, and (3) only a few fungi were dominant, while most species were rare, being recorded only once or twice. Factors responsible for the distribution patterns and variations in composition of the fungal communities are discussed.     

Prediction of protease types in a hybridization space

Regulating most physiological processes by controlling the activation, synthesis, and turnover of proteins, proteases play pivotal regulatory roles in conception, birth, digestion, growth, maturation, ageing, and death of all organisms. Different types of proteases have different functions and biological processes. Therefore, it is important for both basic research and drug discovery to consider the following two problems. (1) Given the sequence of a protein, can we identify whether it is a protease or non-protease? (2) If it is, what protease type does it belong to? Although the two problems can be solved by various experimental means, it is both time-consuming and costly to do so. The avalanche of protein sequences generated in the post-genetic era has challenged us to develop an automated method for making a fast and reliable identification. By hybridizing the functional domain composition and pseudo-amino acid composition, we have introduced a new method called "FunD-PseAA predictor" that is operated in a hybridization space. To avoid redundancy and bias, demonstrations were performed on a dataset where none of the proteins has >or=25% sequence identity to any other. The overall success rate thus obtained by the jackknife cross-validation test in identifying protease and non-protease was 92.95%, and that in identifying the protease type was 94.75% among the following six types: (1) aspartic, (2) cysteine, (3) glutamic, (4) metallo, (5) serine, and (6) threonine. Demonstration was also made on an independent dataset, and the corresponding overall success rates were 98.36% and 97.11%, respectively, suggesting the FunD-PseAA predictor is very powerful and may become a useful tool in bioinformatics and proteomics.     

Binding of Src to Na+/K+-ATPase forms a functional signaling complex

We have shown that ouabain activates Src, resulting in subsequent tyrosine phosphorylation of multiple effectors. Here, we tested if the Na+/K+-ATPase and Src can form a functional signaling complex. In LLC-PK1 cells the Na+/K+-ATPase and Src colocalized in the plasma membrane. Fluorescence resonance energy transfer analysis indicated that both proteins were in close proximity, suggesting a direct interaction. GST pulldown assay showed a direct, ouabain-regulated, and multifocal interaction between the 1 subunit of Na+/K+-ATPase and Src. Although the interaction between the Src kinase domain and the third cytosolic domain (CD3) of 1 is regulated by ouabain, the Src SH3SH2 domain binds to the second cytosolic domain constitutively. Functionally, binding of Src to either the Na+/K+-ATPase or GST-CD3 inhibited Src activity. Addition of ouabain, but not vanadate, to the purified Na+/K+-ATPase/Src complex freed the kinase domain and restored the Src activity. Consistently, exposure of intact cells to ouabain apparently increased the distance between the Na+/K+-ATPase and Src. Concomitantly, it also stimulated tyrosine phosphorylation of the proteins that are associated with the Na+/K+-ATPase. These new findings illustrate a novel molecular mechanism of signal transduction involving the interaction of a P-type ATPase and a nonreceptor tyrosine kinase.     

Ena/VASP proteins regulate cortical neuronal positioning

Development of the multilayered cerebral cortex involves extensive regulated migration of neurons arising from the deeper germinative layers of the mammalian brain. The anatomy and formation of the cortical layers has been well characterized; however, the underlying molecular mechanisms that control the migration and the final positioning of neurons within the cortex remain poorly understood. Here, we report evidence for a key role of Ena/VASP proteins, a protein family implicated in the spatial control of actin assembly and previously shown to negatively regulate fibroblast cell speeds, in cortical development. Ena/VASP proteins are highly expressed in the developing cortical plate in cells bordering Reelin-expressing Cajal-Retzius cells and in the intermediate zone through which newly born cells migrate. Inhibition of Ena/VASP function through retroviral injections in utero led to aberrant placement of early-born pyramidal neurons in the superficial layers of both the embryonic and the postnatal cortex in a cell-autonomous fashion. The abnormally placed pyramidal neurons exhibited grossly normal morphology and polarity. Our results are consistent with a model in which Ena/VASP proteins function in vivo to control the position of neurons in the mouse neocortex.     

Enhanced learning and memory in GAT1 heterozygous mice

γ-Aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the central nervous system. The termination of GABA transmission is through the action of a family of membrane proteins, called GABA transporters (GAT1-4). It is well established that GABA system is involved in the modulation of memory. Our previous study showed that homozygous GAT1(-/-) mice exhibited impaired hippocampus-dependent learning and memory. To evaluate the impact of endogenous reduced GABA reuptake on mice cognitive behaviors, the ability of learning and memory of heterozygous GAT1(+/-) mice was detected by the passive avoidance paradigm and Morris water maze. The hole board paradigm was also used to measure changes in anxiety-related behavior or exploratory behavior in such mice. As one form of synaptic plasticity, long-term potentiation was recorded in the mouse hippocampal CA1 area. We found that GAT1(+/-) mice displayed increased learning and memory, decreased anxiety-like behaviors, and highest synaptic plasticity compared with wild-type and homozygous GAT1(-/-) mice. Our results suggest that a moderate reduction in GAT1 activity causes the enhancement of learning and memory in mice.     

Structure insights into mechanisms of ATP hydrolysis and the activation of human heat-shock protein 90

The activation of molecular chaperone heat-shock protein 90 (Hsp90) is dependent on ATP binding and hydrolysis, which occurs in the N-terminal domains of protein. Here, we have determined three crystal structures of the N-terminal domain of human Hsp90 in native and in complex with ATP and ATP analog, providing a clear view of the catalytic mechanism of ATP hydrolysis by Hsp90. Additionally, the binding of ATP leads the N-terminal domains to be an intermediate state that could be used to partially explain why the isolated N-terminal domain of Hsp90 has very weak ATP hydrolytic activity.     

Abundance and age of viable resting eggs of the calanoid copepod Boeckella poppei Mrázek in sediments: evidence of egg banks in two Antarctic maritime lakes

The existence of egg banks not only ensures the survival of zooplankton through harsh periods, but could also affect microevolutionary dynamics. Whether zooplankton at high latitudes can build up an egg bank in sediments, as occurs at lower latitudes, is still unknown. The distribution and age of viable resting eggs of the calanoid copepod Boeckella poppei Mrázek in sediments of two small freshwater lakes on King George Island were determined by slicing sediment cores at 1-cm intervals. Most viable resting eggs were found near the sediment surface, with abundance sharply declining to very low values at the depth of 5?cm, although eggs were present as deep as 9?cm in the sediments of Yanouhu Lake. The egg abundances in Xihu Lake and Yanouhu Lake were estimated to be 9.2?×?10⁴ and 7.2?×?10⁴?eggs?m^?2, respectively. ²¹⁰Pb dating indicated a relatively constant sedimentation rate (0.023?cm?year^?1) in Xihu Lake, which was used to estimate the mean age (46.8?year), the maximum age (195.7?year), and the mortality rate (1.64?% year^?1) of resting eggs of B. poppei in Xihu Lake. The accumulation of resting eggs with long-term viability in sediments provided the first evidence for the existence of egg banks in two Antarctic maritime lakes. An egg bank may serve as an overwintering strategy for B. poppei in Antarctica, enhance their ability to cope with random extreme changes, and contribute to their broad distribution.     

Mangiferin aglycone attenuates radiation-induced damage on human intestinal epithelial cells

Recent studies suggest that mangiferin aglycone (norathyriol) has great potential as a novel radioprotector without any known toxic side effects. In this study, we assessed the protective effects of mangiferin aglycone against radiation-induced injuries on normal human intestinal epithelial cells (HIECs), while using mangiferin as a reference compound. The in vitro experiments showed that pretreatment of either mangiferin aglycone or mangiferin could inhibit cytotoxic effects of ionizing irradiation (IR) on HIECs. Cellular changes were estimated by measuring cell viability, clonogenic surviving rate, and apoptotic rate. Compared to mangiferin, we found mangiferin aglycone had greater radioprotective effects of mangiferin aglycone on HIECs. It has been demonstrated that the cytotoxicity of ionizing radiation relates to its capacity to induce DNA damage. In view of this, we monitored DNA double-strand breaks (DSBs) using γH2AX foci formation to test whether mangiferin aglycone and mangiferin could modulate genotoxic effects of radiation. It shows that mangiferin aglycone could eliminate 46.8% of the total DSBs of the cells exposed to 2 Gy IR, which is significantly better than mangiferin. Complementing earlier results from our group, it appears possible to conclude that mangiferin aglycone presents potential useful effects on IR-induced damage and may be a better radioprotective agent than mangiferin therapeutically.     

Predicting protein oxidation sites with feature selection and analysis approach

Protein oxidation is a ubiquitous post-translational modification that plays important roles in various physiological and pathological processes. Owing to the fact that protein oxidation can also take place as an experimental artifact or caused by oxygen in the air during the process of sample collection and analysis, and that it is both time-consuming and expensive to determine the protein oxidation sites purely by biochemical experiments, it would be of great benefit to develop in silico methods for rapidly and effectively identifying protein oxidation sites. In this study, we developed a computational method to address this problem. Our method was based on the nearest neighbor algorithm in which, however, the maximum relevance minimum redundancy and incremental feature selection approaches were incorporated. From the initial 735 features, 16 features were selected as the optimal feature set. Of such 16 optimized features, 10 features were associated with the position-specific scoring matrix conservation scores, three with the amino acid factors, one with the propensity of conservation of residues on protein surface, one with the side chain count of carbon atom deviation from mean, and one with the solvent accessibility. It was observed that our prediction model achieved an overall success rate of 75.82%, indicating that it is quite encouraging and promising for practical applications. Also, the 16 optimal features obtained through this study may provide useful clues and insights for in-depth understanding the action mechanism of protein oxidation.