Infectivity of mine soils from Southeast Spain

A bioassay was carried out to measure the mycorrhizal population levels in five soils disturbed by mining activities. Mycorrhizal infection of Medicago sativa (as test plant) was always less than 56%, and in some cases there was no mycorrhization. Thus degradation of soil by mining brings about a decrease in mycorrhizal inoculum potential. No relationship was found between the number of spores and either infectivity or soil characteristics.     

Taxonomic proposal for a deep branching bacterial phylogenetic lineage: transfer of the family Thermodesulfobiaceae to Thermodesulfobiales ord. nov., Thermodesulfobiia classis nov. and Thermodesulfobiota phyl. nov

The family Thermodesulfobiaceae, comprising one genus Thermodesulfobium with two validly published species, is currently assigned to order Thermoanaerobacterales within the class Clostridia of the phylum Bacillota. At the same time, the very first 16S rRNA gene sequence-based phylogenetic studies of representatives of the genus pointed out great differences between Thermodesulfobium and other members of the phylum Bacillota. Subsequent studies of new Thermodesulfobium representatives supported deep phylogenetic branching of this lineage within bacterial tree, implying that it represents a novel phylum. The results of the phylogenomic analysis performed in the frames of the present work confirm previous findings and suggest that Thermodesulfobium represents a distinct phylum-level lineage. Thus, we propose the transfer of the family Thermodesulfobiaceae to the new order Thermodesulfobiales within the new class Thermodesulfobiia and the new phylum Thermodesulfobiota.     

MicroRNA–mRNA interaction network using TSK-type recurrent neural fuzzy network

MicroRNAs are short non-coding RNAs that can regulate gene expression during various crucial cell processes such as differentiation, proliferation and apoptosis. Changes in expression profiles of miRNA play an important role in the development of many cancers, including CRC. Therefore, the identification of cancer related miRNAs and their target genes are important for cancer biology research. In this paper, we applied TSK-type recurrent neural fuzzy network (TRNFN) to infer miRNA–mRNA association network from paired miRNA, mRNA expression profiles of CRC patients. We demonstrated that the method we proposed achieved good performance in recovering known experimentally verified miRNA–mRNA associations. Moreover, our approach proved successful in identifying 17 validated cancer miRNAs which are directly involved in the CRC related pathways. Targeting such miRNAs may help not only to prevent the recurrence of disease but also to control the growth of advanced metastatic tumors. Our regulatory modules provide valuable insights into the pathogenesis of cancer.     

Fragment-based discovery of focal adhesion kinase inhibitors

Chemically diverse fragment hits of focal adhesion kinase (FAK) were discovered by surface plasmon resonance (SPR) screening of our in-house fragment library. Site specific binding of the primary hits was confirmed in a competition setup using a high-affinity ATP-site inhibitor of FAK. Protein crystallography revealed the binding mode of 41 out of 48 selected fragment hits within the ATP-site. Structural comparison of the fragment binding modes with a DFG-out inhibitor of FAK initiated first synthetic follow-up optimization leading to improved binding affinity.     

NemChR-DB: a database of parasitic nematode chemosensory G-protein coupled receptors

Nematode Chemosensory G-Protein Coupled Receptors have expanded within nematodes, where they play important roles in foraging and host-seeking behaviour. Nematode Chemosensory G-Protein Coupled Receptors are most highly expressed during free-living stages when chemosensory signalling is required for host detection and nematode activation in various parasitic nematodes, and therefore position Nematode Chemosensory G-Protein Coupled Receptors at the transition from infective to parasitic stages, making them important regulators to study in terms of host-seeking and host specificity. To facilitate the analysis of Nematode Chemosensory G-Protein Coupled Receptors, here we describe an integrative database of nematode chemoreceptors called NemChR-DB. This database enables users to study diverse parasitic nematode chemoreceptors, functionally explore sequence entries through structural and literature-based annotations, and perform cross-species comparisons.     

Explaining and Predicting Allostery with Allosteric Database and Modern Analytical Techniques

Allostery is a phenomenon that the protein activity is regulated when a non-functional site on it is bounded. This phenomenon is important in life process and disease therapy. However, it is difficult to study allostery due to the lack of knowledge. Facing this demand, we have created Allosteric Database (ASD) 10 years before to collect numerous kinds of allosteric data. In this review, we will introduce the 4 categories of data in ASD. For each category, we further reviewed how researchers applied ASD data to conduct studies. We focused on their research topics, analytical methods and conclusions. Several discoveries of new drug targets and allosteric modulators driven by ASD are also summarized. We hope this review could inspire researchers with new utilities of ASD data.