A quantitative systems pharmacology workflow toward optimal design and biomarker stratification of atopic dermatitis clinical trials.

BACKGROUND: The development of atopic dermatitis (AD) drugs is challenged by many disease phenotypes and trial design options, which are hard to explore experimentally. OBJECTIVE: We aimed to optimize AD trial design using simulations. METHODS: We constructed a quantitative systems pharmacology model of AD and standard of care (SoC) treatments and generated a phenotypically diverse virtual population whose parameter distribution was derived from known relationships between AD biomarkers and disease severity and calibrated using disease severity evolution under SoC regimens. RESULTS: We applied this workflow to the immunomodulator OM-85, currently being investigated for its potential use in AD, and calibrated the investigational treatment model with the efficacy profile of an existing trial (thereby enriching it with plausible marker levels and dynamics). We assessed the sensitivity of trial outcomes to trial protocol and found that for this particular example the choice of end point is more important than the choice of dosing regimen and patient selection by model-based responder enrichment could increase the expected effect size. A global sensitivity analysis revealed that only a limited subset of baseline biomarkers is needed to predict the drug response of the full virtual population. CONCLUSIONS: This AD quantitative systems pharmacology workflow built around knowledge of marker-severity relationships as well as SoC efficacy can be tailored to specific development cases to optimize several trial protocol parameters and biomarker stratification and therefore has promise to become a powerful model-informed AD drug development and personalized medicine tool.

What is a supercoiling-sensitive gene? Insights from topoisomerase I inhibition in the Gram-negative bacterium Dickeya dadantii.

DNA supercoiling is an essential mechanism of bacterial chromosome compaction, whose level is mainly regulated by topoisomerase I and DNA gyrase. Inhibiting either of these enzymes with antibiotics leads to global supercoiling modifications and subsequent changes in global gene expression. In previous studies, genes responding to DNA relaxation induced by DNA gyrase inhibition were categorised as 'supercoiling-sensitive'. Here, we studied the opposite variation of DNA supercoiling in the phytopathogen Dickeya dadantii using the non-marketed antibiotic seconeolitsine. We showed that the drug is active against topoisomerase I from this species, and analysed the first transcriptomic response of a Gram-negative bacterium to topoisomerase I inhibition. We find that the responding genes essentially differ from those observed after DNA relaxation, and further depend on the growth phase. We characterised these genes at the functional level, and also detected distinct patterns in terms of expression level, spatial and orientational organisation along the chromosome. Altogether, these results highlight that the supercoiling-sensitivity is a complex feature, which depends on the action of specific topoisomerases, on the physiological conditions, and on their genomic context. Based on previous in vitro expression data of several promoters, we propose a qualitative model of SC-dependent regulation that accounts for many of the contrasting transcriptomic features observed after DNA gyrase or topoisomerase I inhibition.

Carbon catabolite repression in pectin digestion by the phytopathogen Dickeya dadantii.

The catabolism of pectin from plant cell walls plays a crucial role in the virulence of the phytopathogen Dickeya dadantii. In particular, the timely expression of pel genes encoding major pectate lyases is essential to circumvent the plant defense systems and induce massive pectinolytic activity during the maceration phase. Previous studies identified the role of a positive feedback loop specific to the pectin-degradation pathway, whereas the precise signals controlling the dynamics of pectate lyase expression were unclear. Here, we show that the latter is controlled by a metabolic switch involving both glucose and pectin. We measured the HPLC concentration profiles of the key metabolites related to these two sources of carbon, cAMP and 2-keto-3-deoxygluconate, and developed a dynamic and quantitative model of the process integrating the associated regulators, cAMP receptor protein and KdgR. The model describes the regulatory events occurring at the promoters of two major pel genes, pelE and pelD. It highlights that their activity is controlled by a mechanism of carbon catabolite repression, which directly controls the virulence of D. dadantii. The model also shows that quantitative differences in the binding properties of common regulators at these two promoters resulted in a qualitatively different role of pelD and pelE in the metabolic switch, and also likely in conditions of infection, justifying their evolutionary conservation as separate genes in this species.

Bacterium isolated from coffee waste pulp biosorps lead: Investigation of EPS mediated mechanism.

Kleibsiella pneumoniae Kpn555, isolated from coffee waste pulp showed high level of tolerance to lead with a minimum inhibitory concentration of 900 mg/L. On its growth in nutrient broth supplemented with lead, brown clumps were visualised at the bottom of the flask. On scanning and transmission electron microscopic studies the brown clumps were corroborated to be bacterial cells with lead biosorbed on the cell surface and accumulated inside the cytoplasm. Biochemical and FT-IR analysis of the extracellular polymeric substance produced on exposure to lead revealed its chemical nature as glycolipid with protein moieties. Purified EPS (100 mg/L) could remove 50% of lead from aqueous solution (200 mg/L). Isolation of plasmid from Klebsiella pneumoniae Kpn555 revealed the presence of a plasmid of size 30-40 kb. This capability of the bacteria was proven to be plasmid mediated as the Escherichia coli DH5α cells transformed with the plasmid of Klebsiella pneumoniae Kpn555 also could tolerate 900 mg/L of lead and form brown clumps. This study shows that these bacteria, aided by EPS could serve as an effective agent for the removal of lead from contaminated water environmental samples.

Separation and quantification of 2-keto-3-deoxy-gluconate (KDG) a major metabolite in pectin and alginate degradation pathways.

A rapid and sensitive High Performance Liquid Chromatography (HPLC) method with photometric and fluorescence detection is developed for routine analysis of 2-Keto-3-deoxy-gluconate (KDG), a catabolite product of pectin and alginate. These polysaccharides are primary-based compounds for biofuel production and for generation of high-value-added products. HPLC is performed, after derivatization of the 2-oxo-acid groups of the metabolite with o-phenylenediamine (oPD), using a linear gradient of trifluoroacetic acid and acetonitrile. Quantification is accomplished with an internal standard method. The gradient is optimized to distinguish KDG from its close structural analogues such as 5-keto-4-deoxyuronate (DKI) and 2,5-diketo-3-deoxygluconate (DKII). The proposed method is simple, highly sensitive and accurate for time course analysis of pectin or alginate degradation.

DNA Supercoiling: an Ancestral Regulator of Gene Expression in Pathogenic Bacteria?

DNA supercoiling acts as a global and ancestral regulator of bacterial gene expression. In this review, we advocate that it plays a pivotal role in host-pathogen interactions by transducing environmental signals to the bacterial chromosome and coordinating its transcriptional response. We present available evidence that DNA supercoiling is modulated by environmental stress conditions relevant to the infection process according to ancestral mechanisms, in zoopathogens as well as phytopathogens. We review the results of transcriptomics studies obtained in widely distant bacterial species, showing that such structural transitions of the chromosome are associated to a complex transcriptional response affecting a large fraction of the genome. Mechanisms and computational models of the transcriptional regulation by DNA supercoiling are then discussed, involving both basal interactions of RNA Polymerase with promoter DNA, and more specific interactions with regulatory proteins. A final part is specifically focused on the regulation of virulence genes within pathogenicity islands of several pathogenic bacterial species.

CSF thyrotropin-releasing hormone concentrations differ in patients with schizoaffective disorder from patients with schizophrenia or mood disorders.

OBJECTIVE: To determine if there were differences in CSF-TRH concentrations among several acute major psychiatric disorders and to investigate the effects of antipsychotic treatment on CSF-TRH levels. METHOD: CSF-TRH concentrations were measured in 62 psychiatric inpatients during an acute phase of illness after a drug-free period. CSF-TRH measurements were repeated in 14 of these patients after 4 weeks of antipsychotic treatment. RESULTS: Post-hoc tests (Tukey HSD) revealed significant differences among patients with schizoaffective disorder and both schizophrenia (P<0.03) and major depression (P<0.01). There were no significant differences between pre and posttreatment levels of CSF-TRH in the 14 patients treated with conventional agents for 4 weeks (1.54 pg/ml vs. 1.47 pg/ml). However, patients with a reduction in CSF-TRH concentration had a significantly better symptom response measured by the Brief Psychiatric Rating Scale (BPRS) positive factor (61% in six subjects) vs. those who had an increase in posttreatment CSF-TRH (29% in eight subjects; t=2.2; d.f.=12; P<0.04). CONCLUSIONS: These results provide further evidence for a neuromodulatory role for TRH and suggest a re-examination of its behavioral effects and interactions with brain neurotransmitter systems relevant to major psychotic and mood disorders.

Are sex offenders treatable? A research overview.

OBJECTIVE: Recent legislation in several states providing for civil commitment and preventive detention of sexually violent persons has stirred legal, clinical, and public policy controversies. The mandate for psychiatric evaluation and treatment has an impact on public mental health systems, requiring clinicians and public administrators to direct attention to treatment options. It is a common view that no treatments work for disorders involving sexual aggression. The authors examine this assumption by reviewing research on the effectiveness of treatment for adult male sex offenders. METHODS: MEDLINE was searched for key reviews and papers published during the years 1970 through 1998 that presented outcome data for sex offenders in treatment programs, individual case reports, and other clinically and theoretically important information. RESULTS: Although rigorous research designs are difficult to achieve, studies comparing treated and untreated sex offenders have been done. Measurement of outcome is flawed, with recidivism rates underestimating actual recurrence of the pathological behavior. Outcome research suggests a reduction in recidivism of 30 percent over seven years, with comparable effectiveness for hormonal and cognitive-behavioral treatments. Institutionally based treatment is associated with poorer outcome than outpatient treatment, and the nature of the offender's criminal record is an important prognostic factor. CONCLUSIONS: Although treatment does not eliminate sexual crime, research supports the view that treatment can decrease sex offense and protect potential victims. However, given the limitations in scientific knowledge and accuracy of outcome data, as well as the potential high human costs of prognostic uncertainty, any commitment to a social project substituting treatment for imprisonment of sexual aggressors must be accompanied by vigorous research.

Strategies for treatment-resistant depression.

Clinical depression is a common disorder with serious implications that is often misdiagnosed or underestimated. More than 50% of suicides are associated with a major depressive disorder, and depression can adversely impact a variety of other medical conditions. Although > or = 70% of depressions can respond to appropriate medications, few patients actually receive adequate medical therapy. This article reviews the definition of adequate therapy for depression, discusses common comorbid conditions, and examines the issue of true treatment resistance. Practical strategies for treatment-resistant depression, including switching classes of antidepressant drugs, combination therapy, augmentation strategies, and somatic therapies, are incorporated into a treatment algorithm.