An integrated machine learning approach for predicting DosR-regulated genes in Mycobacterium tuberculosis.

BACKGROUND: DosR is an important regulator of the response to stress such as limited oxygen availability in Mycobacterium tuberculosis. Time course gene expression data enable us to dissect this response on the gene regulatory level. The mRNA expression profile of a regulator, however, is not necessarily a direct reflection of its activity. Knowing the transcription factor activity (TFA) can be exploited to predict novel target genes regulated by the same transcription factor. Various approaches have been proposed to reconstruct TFAs from gene expression data. Most of them capture only a first-order approximation to the complex transcriptional processes by assuming linear gene responses and linear dynamics in TFA, or ignore the temporal information in data from such systems. RESULTS: In this paper, we approach the problem of inferring dynamic hidden TFAs using Gaussian processes (GP). We are able to model dynamic TFAs and to account for both linear and nonlinear gene responses. To test the validity of the proposed approach, we reconstruct the hidden TFA of p53, a tumour suppressor activated by DNA damage, using published time course gene expression data. Our reconstructed TFA is closer to the experimentally determined profile of p53 concentration than that from the original study. We then apply the model to time course gene expression data obtained from chemostat cultures of M. tuberculosis under reduced oxygen availability. After estimation of the TFA of DosR based on a number of known target genes using the GP model, we predict novel DosR-regulated genes: the parameters of the model are interpreted as relevance parameters indicating an existing functional relationship between TFA and gene expression. We further improve the prediction by integrating promoter sequence information in a logistic regression model. Apart from the documented DosR-regulated genes, our prediction yields ten novel genes under direct control of DosR. CONCLUSIONS: Chemostat cultures are an ideal experimental system for controlling noise and variability when monitoring the response of bacterial organisms such as M. tuberculosis to finely controlled changes in culture conditions and available metabolites. Nonlinear hidden TFA dynamics of regulators can be reconstructed remarkably well with Gaussian processes from such data. Moreover, estimated parameters of the GP can be used to assess whether a gene is controlled by the reconstructed TFA or not. It is straightforward to combine these parameters with further information, such as the presence of binding motifs, to increase prediction accuracy.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

A Bayesian Change point model for differential gene expression patterns of the DosR regulon of Mycobacterium tuberculosis.

BACKGROUND: Low oxygen availability has been shown previously to stimulate M. tuberculosis to establish non-replicative persistence in vitro. The two component sensor/regulator dosRS is a major mediator in the transcriptional response of M. tuberculosis to hypoxia and controls a regulon of approximately 50 genes that are induced under this condition. The aim of this study was to determine whether the induction of the entire DosR regulon is triggered as a synchronous event or if induction can unfold as a cascade of events as the differential expression of subsets of genes is stimulated by different oxygen availabilities. RESULTS: A novel aspect of our work is the use of chemostat cultures of M. tuberculosis which allowed us to control environmental conditions very tightly. We exposed M. tuberculosis to a sudden drop in oxygen availability in chemostat culture and studied the transcriptional response of the organism during the transition from a high oxygen level (10% dissolved oxygen tension or DOT) to a low oxygen level (0.2% DOT) using DNA microarrays. We developed a Bayesian change point analysis method that enabled us to detect subtle shifts in the timing of gene induction. It results in probabilities of a change in gene expression at certain time points. A computational analysis of potential binding sites upstream of the DosR-controlled genes shows how the transcriptional responses of these genes are influenced by the affinity of these binding sites to DosR. Our study also indicates that a subgroup of DosR-controlled genes is regulated indirectly. CONCLUSION: The majority of the dosR-dependent genes were up-regulated at 0.2% DOT, which confirms previous findings that these genes are triggered by hypoxic environments. However, our change point analysis also highlights genes which were up-regulated earlier at levels of about 8% DOT indicating that they respond to small fluctuations in oxygen availability. Our analysis shows that there are pairs of divergent genes where one gene in the pair is up-regulated before the other, presumably for a flexible response to a constantly changing environment in the host.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Enhanced heterogeneity of rpoB in Mycobacterium tuberculosis found at low pH.

OBJECTIVES: The aim of this study was to gain an insight into the molecular mechanisms of the evolution of rifampicin resistance in response to controlled changes in the environment. METHODS: We determined the proportion of rpoB mutants in the chemostat culture and characterized the sequence of mutations found in the rifampicin resistance-determining region of rpoB in a steady-state chemostat at pH 7.0 and 6.2. RESULTS: The overall proportion of rpoB mutants of strain H37Rv remained constant for 37 days at pH 7.0, ranging between 3.6 x 10(-8) and 8.9 x 10(-8); however, the spectrum of mutations varied. The most commonly detected mutation, serine to leucine mutation at codon 531 (S531L), increased from 40% to 89%, while other mutations (S531W, H526Y, H526D, H526R, S522L and D516V) decreased over the 37 day sampling period. Changing the pH from 7.0 to 6.2 did not significantly alter the overall proportion of mutants, but resulted in a decrease in the percentage of strains harbouring S531L (from 89% to 50%) accompanied by an increase in the range of different mutations from 4 to 12. CONCLUSIONS: The data confirm that the fitness of strains with the S531L mutation is greater than that of strains containing other mutations. We also conclude that at low pH the environment is permissive for a wider spectrum of mutations, which may provide opportunities for a successful mutant to survive

Ionized nebulae surrounding brightest cluster galaxies

We present IFU observations of six emission-line nebulae that surround the central galaxy of cool core clusters. Qualitatively similar nebulae are observed in cool core clusters even when the dynamics and possibly formation and excitation source are different. Evidence for a nearby secondary galaxy disturbing a nebula, as well as AGN and starburst driven outflows are presented as possible formation mechanisms. One nebula has a rotation velocity of the same amplitude as the underlying molecular reservoir, which implies that the excitation or formation of a nebula does not require any disturbance of the molecular reservoir within the central galaxy. Bulk flows and velocity shears of a few hundred km/s are seen across all nebulae. The majority lack any ordered rotation, their configurations are not stable so the nebulae must be constantly reshaping, dispersing and reforming. The dimmer nebulae are co-spatial with dust features whilst the more luminous are not. Significant variation in the ionization state of the gas is seen in all nebulae through the non-uniform [NII]/H_alpha ratio. There is no correlation between the line ratio and H_alpha surface brightness, but regions with excess blue or UV light have lower line ratios. This implies that UV from massive, young stars act in combination with an underlying heating source that produces the observed low-ionization spectra.Comment: 12 pages, accepted for publication in MNRA

Chandra and XMM-Newton X-ray observations of AWM 7 - I: Investigating X-ray surface brightness fluctuations

We investigate the levels of small scale structure in surface brightness images of the core of the X-ray bright cool-core galaxy cluster AWM 7. After subtraction of a model of the smooth cluster emission, we find a number of approximately radial surface brightness depressions which are not present in simulated images and are seen in both the Chandra and XMM-Newton data. The depressions are most strongly seen in the south of the cluster and have a magnitude of around 4 per cent in surface brightness. We see these features in both an energy band sensitive to the density (0.6 to 5 keV) and a band more sensitive to the pressure (3.5 to 7.5 keV). Histograms of surface brightness in the data, when compared to realisations of a smooth model, reveal stronger surface brightness variations. We use the Delta-variance technique to characterise the magnitude of the fluctuations as a function of length scale. We find that the spectrum in the 0.6 to 5 keV band is flatter than expected for Kolmogorov index fluctuations. If characterised by a power spectrum, on large scales it would have an index around -1.7, rather than -3.7. The implied 3D density fluctuations have a standard deviation of around 4 per cent. The implied 3D pressure variations are at most 4 per cent. Most of the longer-scale power in the density spectrum is contributed by the southern half of the cluster, where the depressions are seen. The density variations implied by the spectrum of the northern sector have a standard deviation of about 2 per cent.Comment: 17 pages, accepted by MNRAS, high resolution version available at http://www-xray.ast.cam.ac.uk/papers/awm7.pd

A Study of Problem Solving Using Blocks Vehicle in a STEAM Course for Lower Elementary Levels

STEAM education is currently one of the most important parts of the elementary school curriculum. If STEAM learning can cultivate good problem-solving ability, it will also help improve judgment and thinking abilities. Several voices in the literature have argued for cooperative learning in STEAM courses. Although the effectiveness of course learning often is evaluated using course feedback forms, there is comparatively little emphasis on whether a course succeeds in realizing cooperative learning. For a course involving self-propelled toy-brick cars, there is little research on the application of low-grade pupils. Therefore, based on the integration of STEAM courses into self-propelled toy-brick car learning, this study applied two learning strategies of cooperative learning and individual learning to low-grade pupils in the second grade in elementary schools. After completing the course problem-solving ability indicators were measured and analyzed using the problem-solving ability test. The results show that the mean score of the experimental group in the problem-solving ability test was higher than that of the control group. In the problem-solving ability test, the scores of the two groups were also significantly different, which suggests that cooperative learning is more effective than individual learning strategies.acceptedVersio

Assessment of the Physicochemical Properties of Chrysotile-Containing Brake Debris Pertaining to Toxicity

Grinding and drilling of chrysotile asbestos-containing brake pads during the 20thcentury led torelease of chrysotile, resulting in varying levels of workplace exposures of mechanics. Despite expo-sures, excess risk of mesothelioma remains in doubt.Objectives:The toxicity of particulates is primarily derived through a combination of physicochemicalproperties and dose and as such this study aimed to determine properties of asbestos-containingbrake debris (BD) which may influence pathogenicity and potential of mesothelioma.Materials and Methods:Chrysotile-containing brake pads were ground–to reflect occupational activ-ities, aerosolized, and size-fractionated to isolate respirable fractions. Analysis of morphology, biodur-ability, surface charge, and interactions with macrophages were undertaken.Results:The respirable fraction of BD contained15–17% free chrysotile fibers thereby constituting asmall but relevant potential long fiber dose. Acellular biodurability studies showed rapid dissolutionand fragmentation of chrysotile fibers that was consistent for pure chrysotile control and BD samples.Conclusions:The long, free, respirable chrysotile fibers were present in BD, yet were of low bio-dur-ability; incubation in artificial lysosomal fluid led to destruction of free fibers

The black hole masses of extremely luminous radio-WISE selected galaxies

We present near-IR photometry and spectroscopy of 30 extremely luminous radio and mid-IR selected galaxies. With bolometric luminosities exceeding $\sim10^{13}$ $\rm{L_{\odot}}$ and redshifts ranging from $z = 0.880-2.853$, we use VLT instruments X-shooter and ISAAC to investigate this unique population of galaxies. Broad multi-component emission lines are detected in 18 galaxies and we measure the near-IR lines $\rm{H\rm{\beta}}$, $\text{[OIII]}\rm{\lambda}\rm{\lambda}4959,5007$ and $\rm{H\rm{\alpha}}$ in six, 15 and 13 galaxies respectively, with 10 $\rm{Ly\alpha}$ and five CIV lines additionally detected in the UVB arm. We use the broad $\text{[OIII]}\rm{\lambda}5007$ emission lines as a proxy for the bolometric AGN luminosity, and derive lower limits to supermassive black hole masses of $10^{7.9}$-$10^{9.4}$ $\text{M}_{\odot}$ with expectations of corresponding host masses of $10^{10.4}$-$10^{12.0}$ $\text{M}_{\odot}$. We measure $\rm{\lambda}_{Edd}$ > 1 for eight of these sources at a $2\sigma$ significance. Near-IR photometry and SED fitting are used to compare stellar masses directly. We detect both Balmer lines in five galaxies and use these to infer a mean visual extinction of $A_{V}$ = 2.68 mag. Due to non-detections and uncertainties in our $\rm{H\rm{\beta}}$ emission line measurements, we simulate a broad $\rm{H\rm{\beta}}$ line of FWHM = 1480 $\rm{kms^{-1}}$ to estimate extinction for all sources with measured $\rm{H\rm{\alpha}}$ emission. We then use this to infer a mean $A_{V}=3.62$ mag, demonstrating the highly-obscured nature of these galaxies, with the consequence of increasing our estimates of black-hole masses by an 0.5 orders of magnitude in the most extreme and obscured cases.Comment: Accepted for publication in MNRAS. 14 pages (+8 page appendix), 11 figures and 9 table