ALBERT

Description: Microbial electrochemical systems exploit the metabolism of microorganisms to generate electrical energy or a useful product. In the past couple of decades, the application of microbial electrochemical systems has increased from the use of wastewaters to produce electricity to a versatile technology that can use numerous sources for the extraction of electrons on the one hand, while on the other hand these electrons can be used to serve an ever increasing number of functions. Extremophilic microorganisms grow in environments that are hostile to most forms of life and their utilization in microbial electrochemical systems has opened new possibilities to oxidize substrates in the anode and produce novel products in the cathode. For example, extremophiles can be used to oxidize sulfur compounds in acidic pH to remediate wastewaters, generate electrical energy from marine sediment microbial fuel cells at low temperatures, desalinate wastewaters and act as biosensors of low amounts of organic carbon. In this review, we will discuss the recent advances that have been made in using microbial catalysts under extreme conditions and show possible new routes that extremophilic microorganisms open for microbial electrochemical systems.

Description: The Qiyugou deposit, in the Xiong’er terrane, Qinling Orogen, is an auriferous breccia pipe developed in continental collision setting. The breccia pipe exhibits variable-sized clasts and clast mixing, which are typical of fluidized breccias. Brecciation, alteration, and gold mineralization are related to granite porphyry emplaced at c. 134 Ma. However, the relationships of the CO2-rich ore-forming fluids with the tectonic setting, structural control, granite magma evolution, and hydrothermal brecciation have not been clearly discussed. New fluid inclusion data presented in this paper indicate that the formation of the Qiyugou deposit includes: (1) an early stage defined by K-feldspar-epidote-quartz-pyrite assemblage; (2) a middle stage of quartz-polymetallic sulphides; and (3) a late stage typified by quartz-carbonate±adularia. Alteration and mineralization resulted from escape of hot (〉320 °C), high-salinity (〉40 wt% NaCl eq.) magmatic fluid exsolved during the final stage of crystallization of the granite porphyry. Significant pressure drop from 85–90 to 20–38 MPa resulted in breccia formation and precipitation of quartz, sulphides, and gold. A vapour phase was produced at 355–403 °C due to fluid boiling, and then was cooled and condensed under near-critical conditions to a moderately saline, warm liquid. Aqueous-carbonic inclusions were formed by trapping of heterogeneous fluids unmixed from the original H2O-CO2-NaCl fluid. Late magmatic-hydrothermal fluid mixed with meteoric fluid, and was cooled and diluted to produce lukewarm, low-salinity fluid that precipitated clear quartz and calcite with little or no mineralization. Our review of the literature suggests that the brecciation and mineralization likely coincided with sinistral transtensive faulting during 140–120 Ma. Therefore, synthesis of the foregoing geochemical information with pertinent geological information from the literature lead us to propose that fluidization and seismic pumping were important in the breccia formation and associated gold mineralization at Qiyugou.

Description: Motivation: Human miRNAs have recently been found to have important roles in viral replication. Understanding the patterns and details of human miRNA interactions during virus–host interactions may help uncover novel antiviral therapies. Based on the abundance of knowledge available regarding protein–protein interactions (PPI), virus–host protein interactions, experimentally validated human miRNA-target pairs and transcriptional regulation of human miRNAs, it is possible to explore the complex regulatory network that exists between viral proteins and human miRNAs at the system level. Results: By integrating current data regarding the virus–human interactome and human miRNA-target pairs, the overlap between targets of viral proteins and human miRNAs was identified and found to represent topologically important proteins (e.g. hubs or bottlenecks) at the global center of the human PPI network. Viral proteins and human miRNAs were also found to significantly target human PPI pairs. Furthermore, an overlap analysis of virus targets and transcription factors (TFs) of human miRNAs revealed that viral proteins preferentially target human miRNA TFs, representing a new pattern of virus–host interactions. Potential feedback loops formed by viruses, human miRNAs and miRNA TFs were also identified, and these may be exploited by viruses resulting in greater virulence and more effective replication strategies. Contact: boxc@bmi.ac.cn or ni.ming@163.com or sqwang@bmi.ac.cn Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Numerous public microarray datasets are valuable resources for the scientific communities. Several online tools have made great steps to use these data by querying related datasets with users’ own gene signatures or expression profiles. However, dataset annotation and result exhibition still need to be improved. Results: ExpTreeDB is a database that allows for queries on human and mouse microarray experiments from Gene Expression Omnibus with gene signatures or profiles. Compared with similar applications, ExpTreeDB pays more attention to dataset annotations and result visualization. We introduced a multiple-level annotation system to depict and organize original experiments. For example, a tamoxifen-treated cell line experiment is hierarchically annotated as ‘agent-〉drug-〉estrogen receptor antagonist-〉tamoxifen’. Consequently, retrieved results are exhibited by an interactive tree-structured graphics, which provide an overview for related experiments and might enlighten users on key items of interest. Availability and implementation: The database is freely available at http://biotech.bmi.ac.cn/ExpTreeDB . Web site is implemented in Perl, PHP, R, MySQL and Apache. Contact: boxc@bmi.ac.cn Supplementary information: Supplementary data are available at Bioinformatics online.