Biotic interactions enhance survival and fitness in the caddisfly <Emphasis Type="Italic">Micropterna sequax</Emphasis> (Trichoptera: Limnephilidae)

Fish-based index of biotic integrity (F-IBI) is widely used to assess river ecosystems. With survey data from the Yellow River fishery resources in the 1980s and 2008, fish composition and abundance, vertical distribution, trophic structure, reproductive guilds and tolerance in the river’s upstream, midstream, downstream, and estuary were examined, and F-IBI systems were established for each reach to assess river ecosystem health. Results showed that compared to the 1980s, the number of fish species in 2008 sharply declined in the midstream and downstream reaches, percentage of benthic fish species decreased in upstream and estuary, the number and percentage of omnivorous species decreased in all reaches, and percentage of tolerant fish species increased 15 times in upstream but decreased in midstream and downstream. The F-IBI scores in the four reaches in the 1980s were all higher than those in 2008 and decreased from upstream to estuary; the healthy conditions indicated by F-IBI scores in the 1980s were “good,” “fair,” “poor,” and “fair” from upstream to estuary and “degraded” to “poor” in all the reaches in 2008. This indicated that the river ecosystem has degraded from the 1980s to 2008. This was also shown by variations in water chemistry.     

How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

RNA-seq is now the technology of choice for genome-wide differential gene expression experiments, but it is not clear how many biological replicates are needed to ensure valid biological interpretation of the results or which statistical tools are best for analyzing the data. An RNA-seq experiment with 48 biological replicates in each of two conditions was performed to answer these questions and provide guidelines for experimental design. With three biological replicates, nine of the 11 tools evaluated found only 20%–40% of the significantly differentially expressed (SDE) genes identified with the full set of 42 clean replicates. This rises to >85% for the subset of SDE genes changing in expression by more than fourfold. To achieve >85% for all SDE genes regardless of fold change requires more than 20 biological replicates. The same nine tools successfully control their false discovery rate at ≲5% for all numbers of replicates, while the remaining two tools fail to control their FDR adequately, particularly for low numbers of replicates. For future RNA-seq experiments, these results suggest that at least six biological replicates should be used, rising to at least 12 when it is important to identify SDE genes for all fold changes. If fewer than 12 replicates are used, a superior combination of true positive and false positive performances makes edgeR and DESeq2 the leading tools. For higher replicate numbers, minimizing false positives is more important and DESeq marginally outperforms the other tools.     

The effect of electrodialytic treatment and Na2H2EDTA addition on methanogenic activity of copper-amended anaerobic granular sludge: treatment costs and energy consumption

The effect of electrodialytic treatment in terms of a current density, pH and Na₂H₂EDTA addition on the methanogenic activity of copper-amended anaerobic granular sludge taken from the UASB reactor from paper mill was evaluated. Moreover, the specific energy consumption and simplified operational and treatment costs were calculated. Addition of Na₂H₂EDTA (at pH 7.7) to copper-amended sludge resulted in the highest microbial activity (62 mg CH₄-COD g VSS⁻¹ day⁻¹) suggesting that Na₂H₂EDTA decreased the toxic effects of copper on the methanogenic activity of the anaerobic granular sludge. The highest methane production (159 %) was also observed upon Na₂H₂EDTA addition and simultaneous electricity application (pH 7.7). The energy consumption during the treatment was 560, 840, 1400 and 1680 kW h m⁻³ at current densities of 0.23, 0.34, 0.57 and 0.69 mA cm⁻², respectively. This corresponded to a treatment costs in terms of electricity expenditure from 39.2 to 117.6 € per cubic meter of sludge.     

Proteolytic cleavage of covalently linked cell wall proteins by Candida albicans Sap9 and Sap10

The cell wall of the human-pathogenic fungus Candida albicans is a robust but also dynamic structure which mediates adaptation to changing environmental conditions during infection. Sap9 and Sap10 are cell surface-associated proteases which function in C. albicans cell wall integrity and interaction with human epithelial cells and neutrophils. In this study, we have analyzed the enzymatic properties of Sap9 and Sap10 and investigated whether these proteases cleave proteins on the fungal cell surface. We show that Sap9 and Sap10, in contrast to other aspartic proteases, exhibit a near-neutral pH optimum of proteolytic activity and prefer the processing of peptides containing basic or dibasic residues. However, both proteases also cleaved at nonbasic sites, and not all tested peptides with dibasic residues were processed. By digesting isolated cell walls with Sap9 or Sap10, we identified the covalently linked cell wall proteins (CWPs) Cht2, Ywp1, Als2, Rhd3, Rbt5, Ecm33, and Pga4 as in vitro protease substrates. Proteolytic cleavage of the chitinase Cht2 and the glucan-cross-linking protein Pir1 by Sap9 was verified using hemagglutinin (HA) epitope-tagged versions of both proteins. Deletion of the SAP9 and SAP10 genes resulted in a reduction of cell-associated chitinase activity similar to that upon deletion of CHT2, suggesting a direct influence of Sap9 and Sap10 on Cht2 function. In contrast, cell surface changes elicited by SAP9 and SAP10 deletion had no major impact on the phagocytosis and killing of C. albicans by human macrophages. We propose that Sap9 and Sap10 influence distinct cell wall functions by proteolytic cleavage of covalently linked cell wall proteins.     

Citrulline-modified phage display: a novel high-throughput discovery approach for the identification of citrulline-containing ligands

Phage display is a high-throughput technology used to identify ligands for a given target. A drawback of the approach is the absence of PTMs in phage-displayed peptides. The applicability of phage display could be broadened considerably by the implementation of PTMs in this system. The aim of this study was to investigate the possible application of citrullination, a PTM of an arginine into a citrulline amino acid, in filamentous (M13) and lytic (T7) phage display. After in vitro citrullination of T7 and M13 phages, citrullination was confirmed and the infectivity of both citrullinated and non-citrullinated phage was compared by titer determination. We demonstrated the successful in vitro citrullination of T7 and M13 phage-displayed peptides. This in vitro modification did not affect the viability or infectivity of the T7 virions, a necessary prerequisite for the implementation of this approach in T7 phage display. For M13 phage, however, the infecting phage titer decreased five-fold upon citrullination, limiting the use of this modification in M13 phage display. In conclusion, in vitro citrullination can be applied in T7 phage display giving rise to a high-throughput and sensitive approach to identify citrulline-containing ligands by the use of the strengths of phage display technology.     

CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks

SUMMARY: Network motifs in integrated molecular networks represent functional relationships between distinct data types. They aggregate to form dense topological structures corresponding to functional modules which cannot be detected by traditional graph clustering algorithms. We developed CyClus3D, a Cytoscape plugin for clustering composite three-node network motifs using a 3D spectral clustering algorithm. AVAILABILITY: Via the Cytoscape plugin manager or http://bioinformatics.psb.ugent.be/software/details/CyClus3D.     

Synthesis of novel 5-amino-thiazolo[4,5-d]pyrimidines as E. coli and S. aureus SecA inhibitors

An efficient synthesis of a library of 5-amino-thiazolo[4,5-d]pyrimidines is reported. Regioselective displacements of chlorines, as well as regioselective diazotation reactions are described, which allow the introduction of structural diversity on the scaffold by consecutive reactions. Screening of this focused library led to the discovery of SecA inhibitors from Escherichia coli and Staphylococcus aureus.