Developing a taxonomy for strategising in industrial networks

The purposes of the project described here were (1) to develop a taxonomy of terms relating to strategy used in industrial networks research studies, and (2) to compare manual qualitative content analysis with a computer-assisted text mining approach to taxonomy creation in a social science context. The unit of analysis was abstracts from the IMP research database (publicly available at www.impgroup.org). The main sample used in the analysis comprised 107 abstracts that contained 'strategy' as a keyword. There were marked similarities between the lists of key terms generated by the manual content analysis and by the text mining approach. Where there were differences between the lists of key terms, it was not possible to say whether these were because of unconscious biases in the manual analysis (analysts finding what they expected to find), or because of inadequacies in the text mining approach (which can only identify terms that exist within the data and cannot 'understand' meanings that are implied, but not explicitly stated, by authors)

Immunoreactivity of the AAA plus chaperone ClpB from Leptospira interrogans with sera from Leptospira-infected animals

Citation: Krajewska, J., Arent, Z., Wieckowski, D., Zolkiewski, M., & Kedzierska-Mieszkowska, S. (2016). Immunoreactivity of the AAA plus chaperone ClpB from Leptospira interrogans with sera from Leptospira-infected animals. Bmc Microbiology, 16, 8. doi:10.1186/s12866-016-0774-8Leptospira interrogans is a spirochaete responsible for leptospirosis in mammals. The molecular mechanisms of the Leptospira virulence remain mostly unknown. Recently, it has been demonstrated that L. interrogans ClpB (ClpB(Li)) is essential for bacterial survival under stressful conditions and also during infection. The aim of this study was to provide further insight into the role of ClpB in L. interrogans and answer the question whether ClpB(Li) as a potential virulence factor may be a target of the humoral immune response during leptospiral infections in mammals. Results: ClpB(Li) consists of 860 amino acid residues with a predicted molecular mass of 96.3 kDa and shows multi-domain organization similar to that of the well-characterized ClpB from Escherichia coli. The amino acid sequence identity between ClpB(Li) and E. coli ClpB is 52 %. The coding sequence of the clpB(Li) gene was cloned and expressed in E. coli BL21(DE3) strain. Immunoreactivity of the recombinant ClpB(Li) protein was assessed with the sera collected from Leptospira-infected animals and uninfected healthy controls. Western blotting and ELISA analysis demonstrated that ClpB(Li) activates the host immune system, as evidenced by an increased level of antibodies against ClpB(Li) in the sera from infected animals, as compared to the control group. Additionally, ClpB(Li) was found in kidney tissues of Leptospira-infected hamsters. Conclusions: ClpB(Li) is both synthesized and immunogenic during the infectious process, further supporting its involvement in the pathogenicity of Leptospira. In addition, the immunological properties of ClpB(Li) point to its potential value as a diagnostic antigen for the detection of leptospirosis

Supportive networks among companies: Key factors of success and failure

The role of entrepreneurial networks in the development of Small and Medium-sized Enterprises (SMEs) and the associated entrepreneurial activities are a core topic in both the networks and IMP literature. However the effectiveness of these networks remains little understood. This paper investigates a specific form of formal entrepreneurial network: the supportive networks among companies. More precisely, it seeks to identify the key factors of success and failure of these networks in their actions to support small and new business development by focusing on the interactions between the three categories of actors embedded in these networks. Eleven case studies were undertaken focusing on three French supportive networks between companies. The results showed that convergent interests - altruistic as well as economic - shared both between and within companies is the overarching reason why supportive action succeeds. We also found that interactions driven by non-trading interests contribute favourably to the development of the dynamics of these networks

Repurposing p97 inhibitors for chemical modulation of the bacterial ClpB–DnaK bichaperone system

The ClpB–DnaK bichaperone system reactivates aggregated cellular proteins and is essential for survival of bacteria, fungi, protozoa, and plants under stress. AAA+ ATPase ClpB is a promising target for the development of antimicrobials because a loss of its activity is detrimental for survival of many pathogens and no apparent ClpB orthologs are found in metazoans. We investigated ClpB activity in the presence of several compounds that were previously described as inhibitor leads for the human AAA+ ATPase p97, an antitumor target. We discovered that N2,N4-dibenzylquinazoline-2,4-diamine (DBeQ), the least potent among the tested p97 inhibitors, binds to ClpB with a Kd∼60 μM and inhibits the casein-activated, but not the basal, ATPase activity of ClpB with an IC50∼5 μM. The remaining p97 ligands, which displayed a higher affinity toward p97, did not affect the ClpB ATPase. DBeQ also interacted with DnaK with a Kd∼100 μM and did not affect the DnaK ATPase but inhibited the DnaK chaperone activity in vitro. DBeQ inhibited the reactivation of aggregated proteins by the ClpB–DnaK bichaperone system in vitro with an IC50∼5 μM and suppressed the growth of cultured Escherichia coli. The DBeQ-induced loss of E. coli proliferation was exacerbated by heat shock but was nearly eliminated in a ClpB-deficient E. coli strain, which demonstrates a significant selectivity of DBeQ toward ClpB in cells. Our results provide chemical validation of ClpB as a target for developing novel antimicrobials. We identified DBeQ as a promising lead compound for structural optimization aimed at selective targeting of ClpB and/or DnaK

Determinants of Affinity and Activity of the Anti-Sigma Factor AsiA

The AsiA protein is a T4 bacteriophage early gene product that regulates transcription of host and viral genes. Monomeric AsiA binds tightly to the σ70 subunit of Escherichia coli RNA polymerase, thereby inhibiting transcription from bacterial promoters and phage early promoters and co-activating transcription from phage middle promoters. Results of structural studies have identified amino acids at the protomer-protomer interface in dimeric AsiA and at the monomeric AsiA-σ70 interface and demonstrated substantial overlap in the sets of residues that comprise each. Here we evaluate the contributions of individual interfacial amino acid side chains to protomer-protomer affinity in AsiA homodimers, to monomeric AsiA affinity for σ70, and to AsiA function in transcription. Sedimentation equilibrium, dynamic light scattering, electrophoretic mobility shift and transcription activity measurements were used to assess affinity and function of site-specific AsiA mutants. Alanine substitutions for solvent-inaccessible residues positioned centrally in the protomer-protomer interface of the AsiA homodimer – V14, I17, and I40 – resulted in the largest changes in free energy of dimer association, whereas alanine substitutions at other interfacial positions had little effect. These residues also contribute significantly to AsiA-dependent regulation of RNA polymerase activity, as do additional residues positioned at the periphery of the interface (K20 and F21). Notably, the relative contributions of a given amino acid side chain to RNA polymerase inhibition and activation (MotA-independent) by AsiA are very similar in most cases. The mainstay for intermolecular affinity and AsiA function appears to be I17. Our results define the core interfacial residues of AsiA, establish roles for many of the interfacial amino acids, are in agreement with the tenets underlying protein-protein interactions and interfaces, and will be beneficial for a general, comprehensive understanding of the mechanistic underpinnings of bacterial RNA polymerase regulation