A temporal switch model for estimating transcriptional activity in gene expression

Motivation: The analysis and mechanistic modelling of time series gene expression data provided by techniques such as microarrays, NanoString, reverse transcription–polymerase chain reaction and advanced sequencing are invaluable for developing an understanding of the variation in key biological processes. We address this by proposing the estimation of a flexible dynamic model, which decouples temporal synthesis and degradation of mRNA and, hence, allows for transcriptional activity to switch between different states. Results: The model is flexible enough to capture a variety of observed transcriptional dynamics, including oscillatory behaviour, in a way that is compatible with the demands imposed by the quality, time-resolution and quantity of the data. We show that the timing and number of switch events in transcriptional activity can be estimated alongside individual gene mRNA stability with the help of a Bayesian reversible jump Markov chain Monte Carlo algorithm. To demonstrate the methodology, we focus on modelling the wild-type behaviour of a selection of 200 circadian genes of the model plant Arabidopsis thaliana. The results support the idea that using a mechanistic model to identify transcriptional switch points is likely to strongly contribute to efforts in elucidating and understanding key biological processes, such as transcription and degradation

Ionization, Kinematics, and Extent of the Diffuse Ionized Gas Halo of NGC 5775

We present key results from deep spectra of the Diffuse Ionized Gas (DIG) halo of the edge-on galaxy NGC 5775. [NII]6583 has been detected up to about z=13 kpc above the plane in one of two vertically oriented long slits -- making this the spiral galaxy with the greatest spectroscopically detected halo extent in emission. Key diagnostic line ratios have been measured up to about z=8 kpc, allowing the source of ionization and physical state to be probed. Ionization by a dilute radiation field from massive stars in the disk can explain some of the line ratio behavior, but departures from this picture are clearly indicated, most strongly by the rise of [OIII]/Halpha with z. Velocities of the gas in both slits approach the systemic velocity of the galaxy at several kpc above the plane. We interpret this trend as a decrease in rotation velocity with z, with essentially no rotation at heights of several kpc. Such a trend was observed in the edge-on galaxy NGC 891, but here much more dramatically. This falloff is presumably due to the gravitational potential changing with z, but will also depend on the hydrodynamic nature of the disk-halo cycling of gas and projection effects. More detailed modeling of the ionization and kinematics of this and other edge-ons will be presented in future papers.Comment: figures 1, 2a-d and 3 included. ApJ Letters, in pres

Infrared Spectroscopy of the Diffuse Ionized Halo of NGC 891

We present infrared spectroscopy from the Spitzer Space Telescope at one disk position and two positions at a height of 1 kpc from the disk in the edge-on spiral NGC 891, with the primary goal of studying halo ionization. Our main result is that the [Ne III]/[Ne II] ratio, which provides a measure of the hardness of the ionizing spectrum free from the major problems plaguing optical line ratios, is enhanced in the extraplanar pointings relative to the disk pointing. Using a 2D Monte Carlo-based photo-ionization code which accounts for the effects of radiation field hardening, we find that this trend cannot be reproduced by any plausible photo-ionization model, and that a secondary source of ionization must therefore operate in gaseous halos. We also present the first spectroscopic detections of extraplanar PAH features in an external normal galaxy. If they are in an exponential layer, very rough emission scale-heights of 330-530 pc are implied for the various features. Extinction may be non-negligible in the midplane and reduce these scale-heights significantly. There is little significant variation in the relative emission from the various features between disk and extraplanar environment. Only the 17.4 micron feature is significantly enhanced in the extraplanar gas compared to the other features, possibly indicating a preference for larger PAHs in the halo.Comment: 35 pages in ApJ preprint format, 8 figures, accepted for publication in ApJ. Minor change to Introduction to give appropriate credit to earlier, related wor

Robustness from flexibility in the fungal circadian clock

Background Robustness is a central property of living systems, enabling function to be maintained against environmental perturbations. A key challenge is to identify the structures in biological circuits that confer system-level properties such as robustness. Circadian clocks allow organisms to adapt to the predictable changes of the 24-hour day/night cycle by generating endogenous rhythms that can be entrained to the external cycle. In all organisms, the clock circuits typically comprise multiple interlocked feedback loops controlling the rhythmic expression of key genes. Previously, we showed that such architectures increase the flexibility of the clock's rhythmic behaviour. We now test the relationship between flexibility and robustness, using a mathematical model of the circuit controlling conidiation in the fungus Neurospora crassa. Results The circuit modelled in this work consists of a central negative feedback loop, in which the frequency (frq) gene inhibits its transcriptional activator white collar-1 (wc-1), interlocked with a positive feedback loop in which FRQ protein upregulates WC-1 production. Importantly, our model reproduces the observed entrainment of this circuit under light/dark cycles with varying photoperiod and cycle duration. Our simulations show that whilst the level of frq mRNA is driven directly by the light input, the falling phase of FRQ protein, a molecular correlate of conidiation, maintains a constant phase that is uncoupled from the times of dawn and dusk. The model predicts the behaviour of mutants that uncouple WC-1 production from FRQ's positive feedback, and shows that the positive loop enhances the buffering of conidiation phase against seasonal photoperiod changes. This property is quantified using Kitano's measure for the overall robustness of a regulated system output. Further analysis demonstrates that this functional robustness is a consequence of the greater evolutionary flexibility conferred on the circuit by the interlocking loop structure. Conclusions Our model shows that the behaviour of the fungal clock in light-dark cycles can be accounted for by a transcription-translation feedback model of the central FRQ-WC oscillator. More generally, we provide an example of a biological circuit in which greater flexibility yields improved robustness, while also introducing novel sensitivity analysis techniques applicable to a broader range of cellular oscillators

Was Jesus volgens Lukas se vertelling ’n politieke faktor?

Was Jesus in any sense politically involved in the social and cultural activities of his day? The answer is yes and no! An analysis of the social-political situation in Palestine during Jesus’ ministry shows that political aspirations and religious convictions were interlaced. It was a complex situation in which the political, social, economical and religious background contributed to the understanding of the message of Jesus. The Romans, priests, Sadducees, Pharisees, Zealots and Essenes, each chose their own social-political solution. According to Luke, Jesus had his own stance regarding the poor, the infirm, and aspects like riches oppression, injustice and violence. He manifested a strong concern for the poor; called upon those with surplus possessions to use them to benefit the poor and recommended to his disciples to find ways to enable the poor to participate fully in community life (cf. Luke 14:12-14). Jesus also did not submit to the social patterns and political practices to which the Romans were committed. Although he rejected violence, as manifested in the attitude of the Zealots, Jesus was al least potentially a serious threat to Roman rule in Palestine in propagating a new community style of love and humility

Ionization Sources and Physical Conditions in the Diffuse Ionized Gas Halos of Four Edge-On Galaxies

Deep long-slit spectra of the diffuse ionized gas halos of the edge-on spiral galaxies NGC 4302 and UGC 10288 are presented. These data, along with previously presented data for NGC 5775 and NGC 891, are used to address the issue of how DIG halos are energized. Composite photo-ionization/shock models are generally better at explaining runs of line ratios in these galaxies than photo-ionization models alone. Models of line ratios in NGC 5775 require a greater contribution from shocks for filamentary regions than for non-filamentary regions to explain the run of [OIII]/Halpha. In either case, the [SII]/[NII] ratio is not well fit by the models. Composite models for UGC 10288 are successful at reproducing the run of [SII]/[NII] for all but the the highest values of [NII]/Halpha; however, the run of [OIII]/Halpha vs. [NII]/Halpha does not show any discernible trend, making it difficult to determine whether or not shocks make a contribution. We also examine whether the data can be explained simply by an increase in temperature with z in a pure photo-ionization model. Runs of [SII]/Halpha, [NII]/Halpha, and [SII]/[NII] in each of the four galaxies are consistent with such an increase. However, the runs of [OIII]/Halpha vs. z in NGC 5775 and UGC 10288 require unusually high ionization fractions of O^{++} that can not be explained without invoking a secondary ionization source or at the very least a much higher temperature for the [OIII]-emitting component than for the [SII]- and [NII]-emitting component. An increase in temperature with z is generally more successful at explaining the [OIII]/Halpha run in NGC 891.Comment: 42 pages in aaspp4.sty format. This includes the 19 figures. Reference added. Accepted for publication in Ap

Direct measurement of transcription rates reveals multiple mechanisms for configuration of the Arabidopsis ambient temperature response

Background Sensing and responding to ambient temperature is important for controlling growth and development of many organisms, in part by regulating mRNA levels. mRNA abundance can change with temperature, but it is unclear whether this results from changes in transcription or decay rates, and whether passive or active temperature regulation is involved. Results Using a base analog labelling method, we directly measured the temperature coefficient, Q10, of mRNA synthesis and degradation rates of the Arabidopsis transcriptome. We show that for most genes, transcript levels are buffered against passive increases in transcription rates by balancing passive increases in the rate of decay. Strikingly, for temperature-responsive transcripts, increasing temperature raises transcript abundance primarily by promoting faster transcription relative to decay and not vice versa, suggesting a global transcriptional process exists that controls mRNA abundance by temperature. This is partly accounted for by gene body H2A.Z which is associated with low transcription rate Q10, but is also influenced by other marks and transcription factor activities. Conclusions Our data show that less frequent chromatin states can produce temperature responses simply by virtue of their rarity and the difference between their thermal properties and those of the most common states, and underline the advantages of directly measuring transcription rate changes in dynamic systems, rather than inferring rates from changes in mRNA abundance. Background The mechanism for ambient temperature sensing in plants is unclear. Control of transcript levels is believed to be important in responses to temperature [1-4] but affects of ambient temperature on transcription and mRNA decay rates have not been measured. According to the work of Arrhenius [5] the temperature coefficient (Q10) of biochemical reactions is expected to be 2 to 3 at biological temperatures: yet less than 2% of Arabidopsis thaliana genes have a two-fold or greater difference in expression level between 17°C and 27°C [6]. The remaining genes either have rates buffered against changing temperatures, or passive increases in transcription rate must be offset by a balanced increase in decay rate, leading to higher turnover but static steady state levels. Despite this fundamental uncertainty, steady state transcriptomic responses to ambient temperature have been used to infer a role for chromatin modifications in temperature signaling [2,7]. 4-Thiouracil (4SU) is a non-toxic base analogue that has been shown to be incorporated into mammalian and yeast mRNA during transcription [8-12]. Biotinylation and column separation allow 4SU-labeled RNA to be separated from unlabeled RNA, and transcriptomic analysis using the separated samples can be used to simultaneously calculate mRNA synthesis and decay rates [8]. Here we use 4SU labeling to measure transcription rates and determine the Q10 genome-wide of mRNA synthesis and decay rates in Arabidopsis thaliana. We show that ambient temperature has large passive effects on both mRNA synthesis and decay rates, and that where temperature controls transcript abundance it does so by regulating transcription relative to decay and not vice versa. Our analysis suggests that transcription factor binding sites and epigenetic state combine to create a complex network of temperature responses in plants. Results Cells incorporate 4SU into RNA and this has been exploited in mammalian cells [8,11,12] and in yeast [13] to measure mRNA synthesis and decay rates. In order to determine whether plants can take up 4SU we floated intact seedlings in MS medium and monitored 4SU incorporation into RNA by biotinylation and dot blot (Figure S1a in Additional file 1). This clearly showed that plants incorporate 4SU from the environment into RNA and that concentrations as low as 1 mM lead to a signal detectable above background within 1 hour (Figure 1B). The resulting RNA could be separated from unlabeled RNA by biotinylation and passage through a streptavidin column as described previously. At 1.5 mM the flow-through can be depleted of detectable 4SU-labeled RNA, whilst labeled plant RNA is highly concentrated in the fraction recovered from the column [8,13] (Figure S1c in Additional file 1). To maximize recovery we chose a low concentration of 4SU at 1.5 mM [8] as high labeling frequencies are known to lead to binding of fewer more frequently labeled transcripts to the columns and reduce recovery. At this concentration Arabidopsis plants treated with 4SU showed the same growth and survival as control plants (Figure S2a in Additional file 1), suggesting 4SU has low toxicity in plants, as in other organisms. Therefore, 4SU dynamics in Arabidopsis seedlings resemble those described for other experimental systems. Preliminary experiments showed that RNA turnover was faster at 27°C compared to 12°C (Figure S2b in Additional file 1), suggesting that temperature generally affected transcription rates

Chandra Observation of the Edge-on Galaxy NGC 3556 (M 108): Violent Galactic Disk-halo Interaction Revealed

We present a 60 ks Chandra ACIS-S observation of the isolated edge-on spiral NGC 3556, together with a multiwavelength analysis of various discrete X-ray sources and diffuse X-ray features. Among 33 discrete X-ray sources detected within the I_B = 25 mag per square arcsec isophote ellipse of the galaxy, we identify a candidate for the galactic nucleus, an ultraluminous X-ray source that might be an accreting intermediate-mass black hole, a possible X-ray binary with a radio counterpart, and two radio-bright giant HII regions. We detect large amounts of extraplanar diffuse X-ray emission, which extends about 10 kpc radially in the disk and >~ 4 kpc away from the galactic plane. The diffuse X-ray emission exhibits significant substructures, possibly representing various blown-out superbubbles or chimneys of hot gas heated in massive star forming regions. This X-ray-emitting gas has temperatures in the range of ~ 2-7 x 10^6 K and has a total cooling rate of ~ 2 x 10^40 erg/s. The energy can be easily supplied by supernova blast-waves in the galaxy. These results demonstrate NGC 3556 as being a galaxy undergoing vigorous disk-halo interaction. The halo in NGC 3556 is considerably less extended, however, than that of NGC 4631, in spite of many similarities between the two galaxies. This may be due to the fact that NGC 3556 is isolated whereas NGC 4631 is interacting. Thus NGC 3556 presents a more pristine environment for studying the disk-halo interaction.Comment: 30 pages, 12 figures. To appear in ApJ. Please see http://www.astro.umass.edu/~wqd/papers/n3556/n3556.pdf for a high resolution versio