An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network

Organisms from all domains of life use gene regulation networks to control cell growth, identity, function, and responses to environmental challenges. Although accurate global regulatory models would provide critical evolutionary and functional insights, they remain incomplete, even for the best studied organisms. Efforts to build comprehensive networks are confounded by challenges including network scale, degree of connectivity, complexity of organism–environment interactions, and difficulty of estimating the activity of regulatory factors. Taking advantage of the large number of known regulatory interactions in Bacillus subtilis and two transcriptomics datasets (including one with 38 separate experiments collected specifically for this study), we use a new combination of network component analysis and model selection to simultaneously estimate transcription factor activities and learn a substantially expanded transcriptional regulatory network for this bacterium. In total, we predict 2,258 novel regulatory interactions and recall 74% of the previously known interactions. We obtained experimental support for 391 (out of 635 evaluated) novel regulatory edges (62% accuracy), thus significantly increasing our understanding of various cell processes, such as spore formation.

Perceptual biases, affect, and behavior in the relationships of dependents and self-critics

Aspects of interpersonal, personality, and cognitive models of depression were tested in a college sample. The perceptions and actual interpersonal behaviors of dependent and self-critical women and their romantic partners were assessed during a conflict-resolution task. Dependent women were characterized by positive biases in the perception of lovingness expressed within the relationship. The partners of dependent women, however, experienced a decrease in positive affect and a trend toward increasing hostility during the conflict-resolution task. Self-critical women were objectively rated as less loving and more hostile, and their partners were also rated as less loving. Self-critics also exhibited negative biases in self-perceptions of submissiveness. The results are interpreted within a comprehensive framework integrating various elements of interpersonal, personality, and cognitive models of depression.

Contributions of crust proteins to spore surface properties in Bacillus subtilis

Surface properties, such as adhesion and hydrophobicity, constrain dispersal of bacterial spores in the environment. In Bacillus subtilis, these properties are influenced by the outermost layer of the spore, the crust. Previous work has shown that two clusters, cotVWXYZ and cgeAB, encode the protein components of the crust. Here, we characterize the respective roles of these genes in surface properties using Bacterial Adherence to Hydrocarbons assays, negative staining of polysaccharides by India ink and Transmission Electron Microscopy. We showed that inactivation of crust genes caused increases in spore relative hydrophobicity, disrupted the spore polysaccharide layer, and impaired crust structure and attachment to the rest of the coat. We also found that cotO, previously identified for its role in outer coat formation, is necessary for proper encasement of the spore by the crust. In parallel, we conducted fluorescence microscopy experiments to determine the full network of genetic dependencies for subcellular localization of crust proteins. We determined that CotZ is required for the localization of most crust proteins, while CgeA is at the bottom of the genetic interaction hierarchy.

Perceptual biases, affect, and behavior in the relationships of dependents and self-critics

Aspects of interpersonal, personality, and cognitive models of depression were tested in a college sample. The perceptions and actual interpersonal behaviors of dependent and self-critical women and their romantic partners were assessed during a conflict-resolution task. Dependent women were characterized by positive biases in the perception of lovingness expressed within the relationship. The partners of dependent women, however, experienced a decrease in positive affect and a trend toward increasing hostility during the conflict-resolution task. Self-critical women were objectively rated as less loving and more hostile, and their partners were also rated as less loving. Self-critics also exhibited negative biases in self-perceptions of submissiveness. The results are interpreted within a comprehensive framework integrating various elements of interpersonal, personality, and cognitive models of depression.

The role of the plastic surgeon in the management of surgical infection

At our Medical Center, our reconstructive service has actively sought referrals of acute and chronic infections by declaring an interest in undertaking the integrated management and reconstruction of these cases. The practices of the two senior surgeons were reviewed for three academic years (1992 to 1995). Cases of surgical infection were analyzed as to site, ablative procedures, and reconstructive procedures. In total, 139 patients with 147 infections were identified. Sites of infection included head and neck (9.5 percent), trunk and pelvis (39.5 percent), upper extremity (22 percent), and lower extremity (29 percent). One-hundred thirty-one ablative procedures were done on this group, as were 126 reconstructive procedures, including 17 fasciocutaneous flaps, 26 pedicled muscle flaps, and 28 microsurgical flaps. With a mean follow-up of 14 months, 92 percent of these patients had resolution of infection. The 8 percent failure group included recurrences, amputation, and death. This series demonstrates that a plastic surgery service can attract a diverse population of surgical infections and manage them successfully with ablation and a wide variety of reconstructive procedures. The coordination of ablation and reconstruction may be optimally performed by the plastic surgeon.

Engineering a probiotic Bacillus subtilis for acetaldehyde removal: A hag locus integration to robustly express acetaldehyde dehydrogenase

We have addressed critical challenges in probiotic design to develop a commercially viable bacterial strain capable of removing the intestinal toxin, acetaldehyde. In this study, we report the engineering of the hag locus, a σD-dependent flagellin expression site, as a stable location for robust enzyme production. We demonstrate constitutive gene expression in relevant conditions driven by the endogenous hag promoter, following a deletion of the gene encoding a post-translational regulator of σD, FlgM, and a point mutation to abrogate the binding of the translational inhibitor CsrA. Reporter constructs demonstrate activity at the hag locus after germination, with a steady increase in heterologous expression throughout outgrowth and vegetative growth. To evaluate the chassis as a spore-based probiotic solution, we identified the physiologically relevant ethanol metabolic pathway and the subsequent accumulation of gut-derived acetaldehyde following alcohol consumption. We integrated a Cupriavidus necator aldehyde dehydrogenase gene (acoD) into the hag locus under the control of the flagellin promoter and observed a rapid reduction in acetaldehyde levels in gut-simulated conditions post-germination. This work demonstrates a promising approach for the development of genetically engineered spore-based probiotics.

Bacillus subtilis ZB423: 90-Day repeat dose oral (gavage) toxicity study in Wistar rats

The novel genetically modified probiotic Bacillus subtilis ZB423 was assessed in a 90-day repeated-dose oral toxicity study adhering to Good Laboratory Practice (GLP) and Organization for Economic Cooperation and Development (OECD) guidelines. Spray-dried spores at a concentration of 1.1E12 CFU/g were administered at doses of 130, 260, and 519 mg/kg body weight/day correlating to 1.43 × 1011, 2.86 × 1011, and 5.71 × 1011 CFU/kg/day, respectively, by oral gavage to Wistar rats for a period of 90 consecutive days. Results showed no toxicologically relevant findings for B. subtilis ZB423 from measured parameters. The no observed adverse effect level (NOAEL) of B. subtilis ZB423 is 519 mg/kg body weight/day corresponding to 5.71 × 1011 CFU/kg/day for lyophilized B. subtilis ZB423 spores under the test conditions employed.