The Mycobacterium tuberculosis regulatory network and hypoxia.

We have taken the first steps towards a complete reconstruction of the Mycobacterium tuberculosis regulatory network based on ChIP-Seq and combined this reconstruction with system-wide profiling of messenger RNAs, proteins, metabolites and lipids during hypoxia and re-aeration. Adaptations to hypoxia are thought to have a prominent role in M. tuberculosis pathogenesis. Using ChIP-Seq combined with expression data from the induction of the same factors, we have reconstructed a draft regulatory network based on 50 transcription factors. This network model revealed a direct interconnection between the hypoxic response, lipid catabolism, lipid anabolism and the production of cell wall lipids. As a validation of this model, in response to oxygen availability we observe substantial alterations in lipid content and changes in gene expression and metabolites in corresponding metabolic pathways. The regulatory network reveals transcription factors underlying these changes, allows us to computationally predict expression changes, and indicates that Rv0081 is a regulatory hub.

Very early hallucinatory experiences: a school-based study.

BACKGROUND: The prevalence and clinical significance of hallucinatory experiences among children below 7 years of age remain unknown. We aimed to determine the independent influences of sensory deficits, the presence of an imaginary companion and metacognition on hallucinatory experiences. We assumed that hallucinatory experiences were associated with (a) sensory deficits, (b) the presence of an imaginary companion (IC) and (c) metacognition defaults (i.e. first- and second-order theory of mind default). METHODS: All children in the third year of preschool from a region of Northern France underwent medical screening. We compared the prevalence rates of visual, auditory and audio-visual hallucinatory experiences based on (a) the presence of visual or auditory deficits, (b) the actual presence of an IC and (c) metacognition. The analyses were adjusted for age. RESULTS: A total of 1,087 children aged between 5 and 7 years were included. The prevalence rates of auditory, visual and audio-visual hallucinatory experiences were 15.8%, 12.5% and 5.8%, respectively. The prevalences of different types of hallucinatory experiences were not significantly different according to sensory deficit. The prevalences of all types of hallucinatory experiences were significantly higher among children with an IC and among children with metacognition defaults. CONCLUSIONS: The association between hallucinatory experiences and sensory deficits might concern only long-lasting deficits. The association with the presence of an IC confirms experimental findings of the likelihood of perceiving words among meaningless auditory stimuli. Relations between hallucinatory experiences and theory of mind need to be addressed in longitudinal studies.

Global analysis of mRNA stability in Mycobacterium tuberculosis.

Mycobacterium tuberculosis (MTB) is a highly successful pathogen that infects over a billion people. As with most organisms, MTB adapts to stress by modifying its transcriptional profile. Remodeling of the transcriptome requires both altering the transcription rate and clearing away the existing mRNA through degradation, a process that can be directly regulated in response to stress. To understand better how MTB adapts to the harsh environs of the human host, we performed a global survey of the decay rates of MTB mRNA transcripts. Decay rates were measured for 2139 of the ~4000 MTB genes, which displayed an average half-life of 9.5 min. This is nearly twice the average mRNA half-life of other prokaryotic organisms where these measurements have been made. The transcriptome was further stabilized in response to lowered temperature and hypoxic stress. The generally stable transcriptome described here, and the additional stabilization in response to physiologically relevant stresses, has far-ranging implications for how this pathogen is able to adapt in its human host.

KP-1212/1461, a nucleoside designed for the treatment of HIV by viral mutagenesis.

We report the activities of a novel nucleoside analog against HIV. This nucleoside (KP-1212) is not a chain terminator but exerts its antiviral effects via mutagenesis of the viral genome. Serial passaging of HIV in the presence of KP-1212 causes an increase in the mutation rate of the virus leading to viral ablation. HIV strains resistant to KP-1212 have not yet been isolated. Quite to the contrary, virus treated with KP-1212 exhibited an increased sensitivity not only to KP-1212 but also to another nucleoside reverse transcriptase inhibitor (NRTI), zidovudine. HIV strains resistant to other NRTIs (e.g. zidovudine, lamivudine, stavudine, abacavir, etc.) exhibited no cross-resistance towards KP-1212. Multiple assays confirmed that KP-1212 has a favorable (low) genotoxicity profile when compared to some approved antiviral nucleosides. In addition, KP-1212 is not toxic to mitochondria nor does it exhibit any inhibitory effects on mitochondrial DNA synthesis.

The DNA-binding network of Mycobacterium tuberculosis.

Mycobacterium tuberculosis (MTB) infects 30% of all humans and kills someone every 20-30 s. Here we report genome-wide binding for ~80% of all predicted MTB transcription factors (TFs), and assayed global expression following induction of each TF. The MTB DNA-binding network consists of ~16,000 binding events from 154 TFs. We identify >50 TF-DNA consensus motifs and >1,150 promoter-binding events directly associated with proximal gene regulation. An additional ~4,200 binding events are in promoter windows and represent strong candidates for direct transcriptional regulation under appropriate environmental conditions. However, we also identify >10,000 'dormant' DNA-binding events that cannot be linked directly with proximal transcriptional control, suggesting that widespread DNA binding may be a common feature that should be considered when developing global models of coordinated gene expression.

Mapping and manipulating the Mycobacterium tuberculosis transcriptome using a transcription factor overexpression-derived regulatory network.

BACKGROUND: Mycobacterium tuberculosis senses and responds to the shifting and hostile landscape of the host. To characterize the underlying intertwined gene regulatory network governed by approximately 200 transcription factors of M. tuberculosis, we have assayed the global transcriptional consequences of overexpressing each transcription factor from an inducible promoter. RESULTS: We cloned and overexpressed 206 transcription factors in M. tuberculosis to identify the regulatory signature of each. We identified 9,335 regulatory consequences of overexpressing each of 183 transcription factors, providing evidence of regulation for 70% of the M. tuberculosis genome. These transcriptional signatures agree well with previously described M. tuberculosis regulons. The number of genes differentially regulated by transcription factor overexpression varied from hundreds of genes to none, with the majority of expression changes repressing basal transcription. Exploring the global transcriptional maps of transcription factor overexpressing (TFOE) strains, we predicted and validated the phenotype of a regulator that reduces susceptibility to a first line anti-tubercular drug, isoniazid. We also combined the TFOE data with an existing model of M. tuberculosis metabolism to predict the growth rates of individual TFOE strains with high fidelity. CONCLUSION: This work has led to a systems-level framework describing the transcriptome of a devastating bacterial pathogen, characterized the transcriptional influence of nearly all individual transcription factors in M. tuberculosis, and demonstrated the utility of this resource. These results will stimulate additional systems-level and hypothesis-driven efforts to understand M. tuberculosis adaptations that promote disease.

Colony morphotypes on Congo red agar segregate along species and drug susceptibility lines in the Mycobacterium avium-intracellulare complex.

Isolates of the Mycobacterium avium-intracellulare complex (MAC) have long been known to segregate into transparent opaque and rough colony morphotypes that differ from each other in clinically important parameters including drug susceptibility and virulence. Here the authors report additional morphotypic variation that occurs on two levels: interspecific (between M. avium and M. intracellulare) and intraspecific (within individual M. avium isolates). Clinical isolates of M. avium grown on Congo red (CR) plates formed red, pink or mixed (red and white) opaque colonies, while M. intracellulare isolates formed purely white opaque colonies. A quantitative CR binding assay showed that this interspecific differential applies to transparent as well as opaque colony variants; however, it was less pronounced among laboratory reference strains than among recent clinical isolates. Opaque colonies of M. avium isolates with 'mixed' phenotypes segregated into stable opaque red and white variants with shared IS1245 banding patterns (intraspecific segregation). White segregants of M. avium were more flocculent and significantly more resistant to ciprofloxacin and rifamycin drugs than were red segregants. Thus, cultivation on CR agar revealed a previously unknown multidrug resistant colony morphotype of M. avium.