Rock-eating mycorrhizas: their role in plant nutrition and biogeochemical cycles

A decade ago, tunnels inside mineral grains were found that were likely formed by hyphae of ectomycorrhizal (EcM) fungi. This observation implied that EcM fungi can dissolve mineral grains. The observation raised several questions on the ecology of these ¿rock-eating¿ fungi. This review addresses the roles of these rock-eating EcM associations in plant nutrition, biogeochemical cycles and pedogenesis. Research approaches ranged from molecular to ecosystem level scales. Nutrient deficiencies change EcM seedling exudation patterns of organic anions and thus their potential to mobilise base cations from minerals. This response was fungal species-specific. Some EcM fungi accelerated mineral weathering. While mineral weathering could also increase the concentrations of phytotoxic aluminium in the soil solution, some EcM fungi increase Al tolerance through an enhanced exudation of oxalate. Through their contribution to Al transport, EcM hyphae could be agents in pedogenesis, especially podzolisation. A modelling study indicated that mineral tunnelling is less important than surface weathering by EcM fungi. With both processes taken together, the contribution of EcM fungi to weathering may be significant. In the field vertical niche differentiation of EcM fungi was shown for EcM root tips and extraradical mycelium. In the field EcM fungi and tunnel densities were correlated. Our results support a role of rock-eating EcM fungi in plant nutrition and biogeochemical cycles. EcM fungal species-specific differences indicate the need for further research with regard to this variation in functional traits

MIMOX: a web tool for phage display based epitope mapping

BACKGROUND: Phage display is widely used in basic research such as the exploration of protein-protein interaction sites and networks, and applied research such as the development of new drugs, vaccines, and diagnostics. It has also become a promising method for epitope mapping. Research on new algorithms that assist and automate phage display based epitope mapping has attracted many groups. Most of the existing tools have not been implemented as an online service until now however, making it less convenient for the community to access, utilize, and evaluate them. RESULTS: We present MIMOX, a free web tool that helps to map the native epitope of an antibody based on one or more user supplied mimotopes and the antigen structure. MIMOX was coded in Perl using modules from the Bioperl project. It has two sections. In the first section, MIMOX provides a simple interface for ClustalW to align a set of mimotopes. It also provides a simple statistical method to derive the consensus sequence and embeds JalView as a Java applet to view and manage the alignment. In the second section, MIMOX can map a single mimotope or a consensus sequence of a set of mimotopes, on to the corresponding antigen structure and search for all of the clusters of residues that could represent the native epitope. NACCESS is used to evaluate the surface accessibility of the candidate clusters; and Jmol is embedded to view them interactively in their 3D context. Initial case studies show that MIMOX can reproduce mappings from existing tools such as FINDMAP and 3DEX, as well as providing novel, rational results. CONCLUSION: A web-based tool called MIMOX has been developed for phage display based epitope mapping. As a publicly available online service in this area, it is convenient for the community to access, utilize, and evaluate, complementing other existing programs. MIMOX is freely available at

Algorithm for automatic detection of self-similarity and prediction of residual central respiratory events during continuous positive airway pressure

STUDY OBJECTIVES: Sleep-disordered breathing is a significant risk factor for cardiometabolic and neurodegenerative diseases. High loop gain (HLG) is a driving mechanism of central sleep apnea or periodic breathing. This study presents a computational approach that identifies "expressed/manifest" HLG via a cyclical self-similarity feature in effort-based respiration signals. METHODS: Working under the assumption that HLG increases the risk of residual central respiratory events during continuous positive airway pressure (CPAP), the full night similarity, computed during diagnostic non-CPAP polysomnography (PSG), was used to predict residual central events during CPAP (REC), which we defined as central apnea index (CAI) higher than 10. Central apnea labels are obtained both from manual scoring by sleep technologists and from an automated algorithm developed for this study. The Massachusetts General Hospital sleep database was used, including 2466 PSG pairs of diagnostic and CPAP titration PSG recordings. RESULTS: Diagnostic CAI based on technologist labels predicted REC with an area under the curve (AUC) of 0.82 ± 0.03. Based on automatically generated labels, the combination of full night similarity and automatically generated CAI resulted in an AUC of 0.85 ± 0.02. A subanalysis was performed on a population with technologist-labeled diagnostic CAI higher than 5. Full night similarity predicted REC with an AUC of 0.57 ± 0.07 for manual and 0.65 ± 0.06 for automated labels. CONCLUSIONS: The proposed self-similarity feature, as a surrogate estimate of expressed respiratory HLG and computed from easily accessible effort signals, can detect periodic breathing regardless of admixed obstructive features such as flow limitation and can aid the prediction of REC