Redox rhythm reinforces the circadian clock to gate immune response.

Recent studies have shown that in addition to the transcriptional circadian clock, many organisms, including Arabidopsis, have a circadian redox rhythm driven by the organism's metabolic activities. It has been hypothesized that the redox rhythm is linked to the circadian clock, but the mechanism and the biological significance of this link have only begun to be investigated. Here we report that the master immune regulator NPR1 (non-expressor of pathogenesis-related gene 1) of Arabidopsis is a sensor of the plant's redox state and regulates transcription of core circadian clock genes even in the absence of pathogen challenge. Surprisingly, acute perturbation in the redox status triggered by the immune signal salicylic acid does not compromise the circadian clock but rather leads to its reinforcement. Mathematical modelling and subsequent experiments show that NPR1 reinforces the circadian clock without changing the period by regulating both the morning and the evening clock genes. This balanced network architecture helps plants gate their immune responses towards the morning and minimize costs on growth at night. Our study demonstrates how a sensitive redox rhythm interacts with a robust circadian clock to ensure proper responsiveness to environmental stimuli without compromising fitness of the organism.

Short distance phase shifts revisited: tracking clock-shifted homing pigeons (Rock Dove Columba livia) close to the loft

Clock-shifted homing pigeons (Rock Dove Columba livia) were tracked from familiar release sites using a direction recorder. At relatively short distances from the home loft (

The effect of clock jitter on the performance of continuous-time delta-sigma ADC for GNSS signals

Next generation Global Navigation Satellite System (GNSS) receivers will operate in multiple navigation bands. An efficient way to achieve this with lower power and cost is to employ BandPass Sampling (BPS); nevertheless, the sampling operation injects large amounts of jitter noise, which degrades the performance of the receiver. Continuous–Time (CT) Delta–Sigma (ΔΣ) modulators are capable of suppressing this noise but the impact of clock jitter at the output of the Digital– to–Analog Converter (DAC) in the feedback path of the modulator should be taken into account. This paper presents an analytical approach for describing clock jitter in GNSS receivers when a CT–ΔΣ modulator is utilized for Analog–to–Digital Conversion (ADC). The validity of the presented approach is verified through time–domain simulations using a behavioural model of the fourth–order CT–ΔΣ modulator with 1–bit NRZ DAC feedback pulse.

In vivo characterization of the circadian clock output gene usp2

Life on earth is subject to the repeated change between day and night periods. All organisms that undergo these alterations have to anticipate consequently the adaptation of their physiology and possess an endogenous periodicity of about 24 hours called circadian rhythm from the Latin circa (about) and diem (day). At the molecular level, virtually all cells of an organism possess a molecular clock which drives rhythmic gene expression and output functions. Besides altered rhythmicity in constant conditions, impaired clock function causes pathophysiological conditions such as diabetes or hypertension. These data unveil a part of the mechanisms underlying the well-described epidemiology of shift work and highlight the function of clock-driven regulatory mechanisms. The post-translational modification of proteins by the ubiquitin polypeptide is a central mechanism to regulate their stability and activity and is capital for clock function. Similarly to the majority of biological processes, it is reversible. Deubiquitylation is carried out by a wide variety of about ninety deubiquitylating enzymes and their function remains poorly understood, especially in vivo. This class of proteolytic enzymes is parted into five families including the Ubiquitin-Specific Proteases (USP), which is the most important with about sixty members. Among them, the Ubiquitin-Specific Protease 2 (Usp2) gene encodes two protein isoforms, USP2-45 and USP2-69. The first is ubiquitously expressed under the control of the circadian clock and displays all features of core clock genes or its closest outputs effectors. Additionally, Usp2-45 was also found to be induced by the mineralocorticoid hormone aldosterone and thought to participate in Na+ reabsorption and blood pressure regulation by Epithelial Na+ Channel ENaC in the kidneys. During my thesis, I aimed to characterize the role of Usp2 in vivo with respect to these two areas, by taking advantage of a total constitutive knockout mouse model. In the first project I aimed to validate the role of USP2-45 in Na+ homeostasis and blood pressure regulation by the kidneys. I found no significant alterations of diurnal Na+ homeostasis and blood pressure in these mice, indicating that Usp2 does not play a substantial role in this process. In urine analyses, we found that our Usp2-KO mice are actually hypercalciuric. In a second project, I aimed to understand the causes of this phenotype. I found that the observed hypercalciuria results essentially from intestinal hyperabsorption. These data reveal a new role for Usp2 as an output effector of the circadian clock in dietary Ca2+ metabolism in the intestine.

The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils?

The use of nucleotide and amino acid sequences allows improved understanding of the timing of evolutionary events of life on earth. Molecular estimates of divergence times are, however, controversial and are generally much more ancient than suggested by the fossil record. The limited number of genes and species explored and pervasive variations in evolutionary rates are the most likely sources of such discrepancies. Here we compared concatenated amino acid sequences of 129 proteins from 36 eukaryotes to determine the divergence times of several major clades, including animals, fungi, plants, and various protists. Due to significant variations in their evolutionary rates, and to handle the uncertainty of the fossil record, we used a Bayesian relaxed molecular clock simultaneously calibrated by six paleontological constraints. We show that, according to 95% credibility intervals, the eukaryotic kingdoms diversified 950-1,259 million years ago (Mya), animals diverged from choanoflagellates 761-957 Mya, and the debated age of the split between protostomes and deuterostomes occurred 642-761 Mya. The divergence times appeared to be robust with respect to prior assumptions and paleontological calibrations. Interestingly, these relaxed clock time estimates are much more recent than those obtained under the assumption of a global molecular clock, yet bilaterian diversification appears to be approximate to100 million years more ancient than the Cambrian boundary.

Characterisation of an amphioxus Fringe gene and the evolution of the vertebrate segmentation clock

In mouse and chick embryos, cyclic expression of lunatic fringe has an important role in the regulation of mesoderm segmentation. We have isolated a Fringe gene from the protochordate amphioxus. Amphioxus is the closest living relative of the vertebrates, and has mesoderm that is definitively segmented in a manner that is similar to, and probably homologous with, that of vertebrates. AmphiFringe is placed basal to vertebrate Fringe genes in molecular phylogenetic analyses, indicating that the duplications that formed radical-, manic- and lunatic fringe are specific to the vertebrate lineage. AmphiFringe expression was detected in the anterior neural plate of early neurulae, where it resolved into a series of segmental patches by the mid-neurulae stage. No AmphiFringe transcripts were detected in the mesoderm. Based on these observations, we propose a model depicting a successive recruitment of Fringe in the maintenance then regulation of segmentation during vertebrate evolution.

Modeling the observed proton aurora and ionospheric convection responses to changes in the IMF clock angle: 2. Persistence of ionospheric convection

We apply a numerical model of time-dependent ionospheric convection to two directly driven reconnection pulses during a 15-min interval of southward IMF on 26 November 2000. The model requires an input magnetopause reconnection rate variation, which is here derived from the observed variation in the upstream IMF clock angle, q. The reconnection rate is mapped to an ionospheric merging gap, the MLT extent of which is inferred from the Doppler-shifted Lyman-a emission on newly opened field lines, as observed by the FUV instrument on the IMAGE spacecraft. The model is used to reproduce a variety of features observed during this event: SuperDARN observations of the ionospheric convection pattern and transpolar voltage; FUV observations of the growth of patches of newly opened flux; FUVand in situ observations of the location of the Open-Closed field line Boundary (OCB) and a cusp ion step. We adopt a clock angle dependence of the magnetopause reconnection electric field, mapped to the ionosphere, of the form Enosin4(q/2) and estimate the peak value, Eno, by matching observed and modeled variations of both the latitude, LOCB, of the dayside OCB (as inferred from the equatorward edge of cusp proton emissions seen by FUV) and the transpolar voltage FPC (as derived using the mapped potential technique from SuperDARN HF radar data). This analysis also yields the time constant tOCB with which the open-closed boundary relaxes back toward its equilibrium configuration. For the case studied here, we find tOCB = 9.7 ± 1.3 min, consistent with previous inferences from the observed response of ionospheric flow to southward turnings of the IMF. The analysis confirms quantitatively the concepts of ionospheric flow excitation on which the model is based and explains some otherwise anomalous features of the cusp precipitation morphology.

Modeling the observed proton aurora and ionospheric convection responses to changes in the IMF clock angle: 1. Persistence of cusp proton aurora

We employ a numerical model of cusp ion precipitation and proton aurora emission to fit variations of the peak Doppler-shifted Lyman-a intensity observed on 26 November 2000 by the SI-12 channel of the FUV instrument on the IMAGE satellite. The major features of this event appeared in response to two brief swings of the interplanetary magnetic field (IMF) toward a southward orientation. We reproduce the observed spatial distributions of this emission on newly opened field lines by combining the proton emission model with a model of the response of ionospheric convection. The simulations are based on the observed variations of the solar wind proton temperature and concentration and the interplanetary magnetic field clock angle. They also allow for the efficiency, sampling rate, integration time and spatial resolution of the FUV instrument. The good match (correlation coefficient 0.91, significant at the 98% level) between observed and modeled variations confirms the time constant (about 4 min) for the rise and decay of the proton emissions predicted by the model for southward IMF conditions. The implications for the detection of pulsed magnetopause reconnection using proton aurora are discussed for a range of interplanetary conditions.

Disruption of the circadian clock within the cardiomyocyte influences myocardial contractile function, metabolism, and gene expression

Virtually every mammalian cell, including cardiomyocytes, possesses an intrinsic circadian clock. The role of this transcriptionally based molecular mechanism in cardiovascular biology is poorly understood. We hypothesized that the circadian clock within the cardiomyocyte influences diurnal variations in myocardial biology. We, therefore, generated a cardiomyocyte-specific circadian clock mutant (CCM) mouse to test this hypothesis. At 12 wk of age, CCM mice exhibit normal myocardial contractile function in vivo, as assessed by echocardiography. Radiotelemetry studies reveal attenuation of heart rate diurnal variations and bradycardia in CCM mice (in the absence of conduction system abnormalities). Reduced heart rate persisted in CCM hearts perfused ex vivo in the working mode, highlighting the intrinsic nature of this phenotype. Wild-type, but not CCM, hearts exhibited a marked diurnal variation in responsiveness to an elevation in workload (80 mmHg plus 1 mu M epinephrine) ex vivo, with a greater increase in cardiac power and efficiency during the dark (active) phase vs. the light (inactive) phase. Moreover, myocardial oxygen consumption and fatty acid oxidation rates were increased, whereas cardiac efficiency was decreased, in CCM hearts. These observations were associated with no alterations in mitochondrial content or structure and modest mitochondrial dysfunction in CCM hearts. Gene expression microarray analysis identified 548 and 176 genes in atria and ventricles, respectively, whose normal diurnal expression patterns were altered in CCM mice. These studies suggest that the cardiomyocyte circadian clock influences myocardial contractile function, metabolism, and gene expression.

Beyond the road : Beat writing and its socio-cultural contexts

This study looks at the contribution of Beat Generation writers to the post-World-War II reinvigoration of the American literary tradition. It challenges the reductive judgements of many critics and demonstrates that the Beat phenomenon was as much an expression of its historical moment as a rebellion against it.