Monoclonal antibodies were produced to Streptomyces lividans spore surface antigens. One particular hybridoma cell line, 43H6, produced a monoclonal antibody that reacted exclusively with ...Streptomyces cluster group 21 in an enzyme-linked immunosorbent assay (ELISA). Antibody 43H6 was found to be of subclass IgG1, kappa light chain. Western blot (immunoblot) analysis revealed that 43H6 recognized a major outer spore polypeptide of about 37 000 Da. The epitope was stably maintained in S. lividans spores over at least seven sporulation cycles on laboratory medium and for at least 14 weeks in sterile soil systems. The species group specificity of antibody 43H6 was exploited in the development of an immunocapture technique for the isolation of streptomycetes from soil. Magnetic beads coated with antibody 43H6 were mixed with soil samples seeded with S. lividans spores. Spore-bead complexes were recovered using magnets. Treatment of beads with blocking agents and the inclusion of detergents in the recovery system lessened non-specific binding of spores to beads and improved recovery. In buffer solutions decreasing the spore concentration increased the recovery values for a fixed bead concentration. At a spore concentration of 5 X 10(7) ml-1 the recovery was 4.3% whilst at 5 X 10(7) ml-1 it was 76% for a fixed bead concentration of 0.6 mg ml-1. Using a bead concentration of 2 mg per 10(9) soil, approximately 30% of the target spore population of 10(6) c.f.u. was recovered from sterile soil and 4% from non-sterile soil. This method offers a rapid means of selectively recovering and concentrating Streptomyces spores from soil samples.
The concept of a network motif-a small set of interacting genes which produce a predictable behaviour at the network level-has attracted considerable attention amongst network analysts. It is of ...particular interest to synthetic biology, a new discipline which aims to apply engineering principles to biological systems. The modular nature of network motifs would make them ideal candidates for the basic components of an engineered organism. In this paper we investigate the relationship between the presence of network motifs and oscillatory dynamics in a yeast transcriptional network and a set of computational networks, evolved to exhibit oscillatory behaviour. Our results do not support the hypothesis that network motifs are critical to network dynamics, possibly because they are tightly connected to many other components of the complex cell-wide transcriptional network.
Many different clustering algorithms have been applied to biological networks, with varying degrees of success. The output of a clustering algorithm may be hard to interpret in biological terms ...because such networks are often large and highly interconnected, with structural and functional modules overlapping to varying degrees. In this paper we describe an evolutionary network clustering algorithm specifically designed for the analysis of large, complex biological networks. It identifies variably sized, overlapping clusters of nodes. The identification of points of overlap between clusters facilitates the analysis of the biological nature of crosstalk between functional units in the network. We apply two variants of the algorithm (one using probabilistic weights on edges and one ignoring them) to a recently published network of functional gene interactions in the yeast Saccharomyces cerevisiae and assess the biological validity of the resulting clusters in terms of ontological similarity
Many biological systems can be modeled as networks. Hence, network analysis is of increasing importance to systems biology. We describe an evolutionary algorithm for selecting clusters of nodes ...within a large network based upon network topology together with a measure of the relevance of nodes to a set of independently identified genes of interest. We apply the algorithm to a previously published integrated functional network of yeast genes, using a set of query genes derived from a whole genome screen of yeast strains with a mutation in a telomere uncapping gene. We find that the algorithm identifies biologically plausible clusters of genes which are related to the cell cycle, and which contain interactions not previously identified as potentially important. We conclude that the algorithm is valuable for the querying of complex networks, and the generation of biological hypotheses.
Two major families of peptidylprolyl cis‐trans‐isomerases, the cyclophilins and the structurally unrelated FK506‐binding proteins (FKBPs), have been identified as cellular factors involved in protein ...folding in vitro. Here we report on the biochemical characterization of a second prolyl isomerase of Bacillus subtilis that was purified from a cyclophilin‐negative (ppiB null) mutant and was shown to be the trigger factor (TigBS). N‐terminal sequencing of 27 amino acid residues of the purified protein revealed 100% identity to the deduced sequence encoded by the tig gene, sequenced as a part of the B. subtilis genome project. The tigBS gene, located at 246° on the genetic map upstream of the clpX and lonA, B genes, encodes an acidic protein (pI 4.3) of 47.5 kDa. Purified and recombinant TigBS‐His proteins share the same substrate specificity and catalytic activity (kcat/Km of 1.5 μM−1 s−1); both are inhibited by the macrolide FK506 with IC50 the range of 500 nM. We also demonstrate that the prolyl isomerase activity of TigBS is mediated by an internal domain of about 13 kDa (homologous to FKPB12) that represents the catalytic core of the trigger factor.
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