Concentration oscillations in single cells : the roles of intracellular noise and intercellular coupling

Concentration oscillations are a ubiquitous characteristic of intracellular dynamics. The period of these oscillations can vary from few seconds to many hours, well known examples being calcium oscillations (seconds to minutes), glycolytic oscillations (minutes) and circadian rhythms (1 day). Considerable advances into understanding the mechanisms and functionality of concentration oscillations have been made since glycolytic oscillations were observed in the late 1950s, and mathematical methods have been an essential part of this process. With increasing ability to experimentally measure oscillations in single cells as well as in cell ensembles, the gold standard of modelling is to provide tools that can elucidate how the system-wide dynamics in complex organisms emerge from a system of single cells. Both abstract and detailed mechanistic models are complementary in the insight they can bring, and for networks of coupled cells considerations such as intrinsic intracellular noise, cellular heterogeneity and coupling strength are all expected to play a part. Here, we investigate separately the potential roles played by intrinsic noise arising from finite numbers of interacting molecules and by coupling among cellular oscillators. Regarding the former, it is well known that internal or molecular noise induces concentration oscillations in chemical systems whose deterministic models exhibit damped oscillations. We show, using the linear-noise approximation of the chemical master equation, that noise can also induce oscillations in biochemical systems whose deterministic descriptions admit no damped oscillations, i.e., systems with a stable node. This non-intuitive phenomenon is remarkable since, unlike noise-induced oscillations in systems with damped deterministic oscillations, it cannot be explained by noise excitation of the deterministic resonant frequency of the system. We here prove the following general properties of stable-node noise-induced oscillations for systems with two species: (i) the upper bound of their frequency is given by the geometric mean of the real eigenvalues of the Jacobian of the system, (ii) the upper bound of the Q-factor of the oscillations is inversely proportional to the distance between the real eigenvalues of the Jacobian, and (iii) these oscillations are not necessarily exhibited by all interacting chemical species in the system. The existence and properties of stable-node oscillations are verified by stochastic simulations of the Brusselator, a cascade Brusselator reaction system, and two other simple chemical systems involving autocatalysis and trimerization. We also show that external noise induces stable node oscillations with different properties than those stimulated by internal noise. Having demonstrated and explored this non-intuitive effect of noise, we extend the work to investigate the phenomenon of noise induced oscillations in cellular reaction systems characterised by the ‘bursty’ production of one or more species. Experiments have shown that proteins are typically translated in sharp bursts and similar bursty phenomena have been observed for protein import into subcellular compartments. We investigate the effect of such burstiness on the stochastic properties of downstream pathways by considering two identical systems with equal mean input rates, except in one system molecules (e.g., proteins) are input one at a time and in the other molecules are input in bursts according to some probability distribution. We find that the stochastic behaviour falls in three categories: (i) both systems display or do not display noise-induced oscillations; (ii) the non-bursty input system displays noiseinduced oscillations whereas the bursty input system does not; (iii) the reverse of (ii). We derive necessary conditions for these three cases to classify pathways involving autocatalysis, trimerization and genetic feedback loops. Our results suggest that single cell rhythms can be controlled by regulation of burstiness in protein production. We go on to investigate roles played by intercellular coupling in whole organ-level oscillations with an experimental analysis of circadian rhythms in Arabidopsis thaliana †. Circadian clocks in animals are known to be tightly coupled among the cells of some tissues, and this coupling profoundly affects cellular rhythmicity. However, research on the clock in plant cells has largely ignored intercellular coupling. Our research group used luciferase reporter gene imaging to monitor circadian rhythms in leaves of Arabidopsis thaliana plants, with both a lower resolution, high throughput method and a high-resolution (cellular level), lower throughput method. Leaves were grown and imaged in a variety of light conditions to test the relative importance of intercellular coupling and cellular coupling to the environmental signal. We analysed the high throughput data and described the circadian phase by the timing of peak expression. Leaves grown for three weeks without entrainment reproducibly showed spatio-temporal waves of gene expression, consistent with intercellular coupling. A range of patterns was observed among the leaves, rather than a unique spatio-temporal pattern, although some patterns were more often observed. All of the measured leaves exposed to lightdark entrainment cycles had fully synchronised rhythms, which could desynchronise rather quickly when placed in a non-entraining environment (i.e., constant light conditions). After four days in constant light some of these leaves were as desynchronised as leaves grown without any rhythmic input, as described by the phase coherence across the leaf. The same fast transition was observed in the reverse experimental scenario, i.e., applying light-dark cycles to leaves grown in constant light resulted in full synchronisation within two to four days. From these results we conclude that single-cell circadian oscillators were coupled far more strongly to external light-dark cycles than to the other cellular oscillators. Leaves did not spontaneously completely desynchronise, which is consistent with a presence of intercellular coupling among heterogeneous clocks. We also developed a methodology, based on the notion of two functional spatial scales of expression across the leaf, to analyse the high-resolution microscope data and determine whether there is a difference in the phase of circadian expression between vein cells and mesophyll cells in the leaf. The result from a single leaf suggests that the global phase wave dominates the phase behaviour but that there are small delays in the veins compared to their nearby mesophyll cells. This result can be validated by applying the methodology developed here to new microscope leaf data which is currently being collected in the research group. † This work was performed as a collaboration between David Toner (DT) and Benedicte Wenden (BW). BW designed and carried out the experiments, DT performed the data analysis and led on data visualisation

A Controlled Study on the Characterisation of Bioaerosols Emissions from Compost

Bioaerosol emissions arising from biowaste treatment are an issue of public concern. To better characterise the bioaerosols, and to assess a range of measurement methods, we aerosolised green waste compost under controlled conditions. Viable and non-viable Andersen samplers, cyclone samplers and a real time bioaerosol detection system (Spectral Intensity Bioaerosol Sensor (SIBS)) were deployed simultaneously. The number-weighted fraction of fluorescent particles was in the range 22–26% of all particles for low and high emission scenarios. Overall fluorescence spectral profiles seen by the SIBS exhibited several peaks across the 16 wavelength bands from 298 to 735 nm. The size-fractionated endotoxin profile showed most endotoxin resided in the 2.1–9 μm aerodynamic diameter fraction, though up to 27% was found in a finer size fraction. A range of microorganisms were detected through culture, Matrix Assisted Laser Desorption and Ionisation Time of Flight Mass Spectrometry (MALDI-TOF) and quantitative polymerase chain reaction (qPCR), including Legionella pneumophila serogroup 1. These findings contribute to our knowledge of the physico-chemical and biological characteristics of bioaerosols from composting sites, as well as informing future monitoring approaches and data interpretation for bioaerosol measurement

The Newtonian limit of spacetimes for accelerated particles and black holes

Solutions of vacuum Einstein's field equations describing uniformly accelerated particles or black holes belong to the class of boost-rotation symmetric spacetimes. They are the only explicit solutions known which represent moving finite objects. Their Newtonian limit is analyzed using the Ehlers frame theory. Generic spacetimes with axial and boost symmetries are first studied from the Newtonian perspective. The results are then illustrated by specific examples such as C-metric, Bonnor-Swaminarayan solutions, self-accelerating "dipole particles", and generalized boost-rotation symmetric solutions describing freely falling particles in an external field. In contrast to some previous discussions, our results are physically plausible in the sense that the Newtonian limit corresponds to the fields of classical point masses accelerated uniformly in classical mechanics. This corroborates the physical significance of the boost-rotation symmetric spacetimes

Superstring Cosmology

Aspects of superstring cosmology are reviewed with an emphasis on the cosmological implications of duality symmetries in the theory. The string effective actions are summarized and toroidal compactification to four dimensions reviewed. Global symmetries that arise in the compactification are discussed and the duality relationships between the string effective actions are then highlighted. Higher-dimensional Kasner cosmologies are presented and interpreted in both string and Einstein frames, and then given in dimensionally reduced forms. String cosmologies containing both non-trivial Neveu-Schwarz/Neveu-Schwarz and Ramond-Ramond fields are derived by employing the global symmetries of the effective actions. Anisotropic and inhomogeneous cosmologies in four-dimensions are also developed. The review concludes with a detailed analysis of the pre-big bang inflationary scenario. The generation of primordial spectra of cosmological perturbations in such a scenario is discussed. Possible future directions offered in the Horava-Witten theory are outlined.Comment: 161 pages, latex with epsf, 15 figures. Minor changes, additional references and figures. Version to appear in Physics Report

Correlations in the chemical composition of rural background atmospheric aerosol in the UK determined in real time using time-of-flight mass spectrometry

An aerosol time-of-flight mass spectrometer (ATOFMS) was used to determine, in real time, the size and chemical composition of individual particles in the atmosphere at the remote inland site of Eskdalemuir, Scotland. A total of 51980 particles, in the size range 0.3–7.4 µm, were detected between the 25th and 30th June 2001. Rapid changes in the number density, size and chemical composition of the atmospheric aerosol were observed. These changes are attributed to two distinct types of air mass; a polluted air mass that had passed over the British mainland before reaching Eskdalemuir, interposed between two cleaner air masses that had arrived directly from the sea. Such changes in the background aerosol could clearly be very important to studies of urban aerosols and attempts at source apportionment. The results of an objective method of data analysis are presented. Correlations were sought between the occurrence of: lithium, potassium, rubidium, caesium, beryllium, strontium, barium, ammonium, amines, nitrate, nitrite, boron, mercury, sulfate, phosphate, fluorine, chlorine, bromine, iodine and carbon (both elemental and organic hydrocarbon) in both fine (d 2.5 µm) particle fractions. Several previously unreported correlations were observed, for instance between the elements lithium, beryllium and boron. The results suggest that about 2 in 3 of all fine particles (by number rather than by mass), and 1 in 2 of all coarse particles containing carbon, consisted of elemental carbon rather than organic hydrocarbon (although a bias in the sensitivity of the ATOFMS could have affected these numbers). The ratio of the number of coarse particles containing nitrate anions to the number of particles containing chloride anions exceeded unity when the air mass had travelled over the British mainland. The analysis also illustrates that an air mass of marine origin that had travelled slowly over agricultural land can accumulate amines and ammonium

Pair Creation of Dilaton Black Holes

We consider dilaton gravity theories in four spacetime dimensions parametrised by a constant $a$, which controls the dilaton coupling, and construct new exact solutions. We first generalise the C-metric of Einstein-Maxwell theory ($a=0$) to solutions corresponding to oppositely charged dilaton black holes undergoing uniform acceleration for general $a$. We next develop a solution generating technique which allows us to ``embed" the dilaton C-metrics in magnetic dilaton Melvin backgrounds, thus generalising the Ernst metric of Einstein-Maxwell theory. By adjusting the parameters appropriately, it is possible to eliminate the nodal singularities of the dilaton C-metrics. For $a<1$ (but not for $a\ge 1$), it is possible to further restrict the parameters so that the dilaton Ernst solutions have a smooth euclidean section with topology $S^2\times S^2-{\rm\{pt\}}$, corresponding to instantons describing the pair production of dilaton black holes in a magnetic field. A different restriction on the parameters leads to smooth instantons for all values of $a$ with topology $S^2\times \R^2$.Comment: 22 pages, EFI-93-51, FERMILAB-Pub-93/272-A, UMHEP-393. (Asymptotics of Ernst solutions clarified, typos repaired

Whole genome sequencing refines stratification and therapy of patients with clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is the most common form of kidney cancer, but a comprehensive description of its genomic landscape is lacking. We report the whole genome sequencing of 778 ccRCC patients enrolled in the 100,000 Genomes Project, providing for a detailed description of the somatic mutational landscape of ccRCC. We identify candidate driver genes, which as well as emphasising the major role of epigenetic regulation in ccRCC highlight additional biological pathways extending opportunities for therapeutic interventions. Genomic characterisation identified patients with divergent clinical outcome; higher number of structural copy number alterations associated with poorer prognosis, whereas VHL mutations were independently associated with a better prognosis. The observations that higher T-cell infiltration is associated with better overall survival and that genetically predicted immune evasion is not common supports the rationale for immunotherapy. These findings should inform personalised surveillance and treatment strategies for ccRCC patients

Accelerating electromagnetic magic field from the C-metric

Various aspects of the C-metric representing two rotating charged black holes accelerated in opposite directions are summarized and its limits are considered. A particular attention is paid to the special-relativistic limit in which the electromagnetic field becomes the "magic field" of two oppositely accelerated rotating charged relativistic discs. When the acceleration vanishes the usual electromagnetic magic field of the Kerr-Newman black hole with gravitational constant set to zero arises. Properties of the accelerated discs and the fields produced are studied and illustrated graphically. The charges at the rim of the accelerated discs move along spiral trajectories with the speed of light. If the magic field has some deeper connection with the field of the Dirac electron, as is sometimes conjectured because of the same gyromagnetic ratio, the "accelerating magic field" represents the electromagnetic field of a uniformly accelerated spinning electron. It generalizes the classical Born's solution for two uniformly accelerated monopole charges.Comment: 22 pages, 5 figure

The effect of nurses' preparedness and nurse practitioner status on triage call management in primary care: a secondary analysis of cross-sectional data from the ESTEEM Trial

Background: Nurse-led telephone triage is increasingly used to manage demand for GP consultations in UK general practice. Previous studies are equivocal about the relationship between clinical experience and the call outcomes of nurse triage. Most research is limited to investigating nurse telephone triage in out-of-hours settings. Objective: To investigate whether the professional characteristics of primary care nurses undertaking computer decision supported software telephone triage are related to call disposition. Design: Questionnaire survey of nurses delivering the nurse intervention arm of the ESTEEM trial, to capture role type (practice nurse or nurse practitioner), prescriber status, number of years’ nursing experience, graduate status, previous experience of triage, and perceived preparedness for triage. Our main outcome was the proportion of triaged patients recommended for follow-up within the practice (call disposition), including all contact types (face-to-face, telephone or home visit), by a GP or nurse. Settings: : 15 General Practices and 7012 patients receiving the nurse triage intervention in four regions of the U.K. Participants: : 45 Nurse Practitioners (NPs) and Practice Nurse (PNs) trained in the use of CDSS. Methods: We investigated the associations between nursing characteristics and triage call disposition for patient ‘same-day’ appointment requests in general practice using multivariable logistic regression modelling. Results: Valid responses from 35 nurses (78%) from 14 practices: 31/35 (89%) had ≥10 years’ experience with 24/35 (69%) having ≥20 years. Most patient contacts (3842/4605; 86%) were recommended for follow-up within the practice. Nurse practitioners were less likely to recommend patients for follow-up odds ratio (OR) 0.19, 95% confidence interval (CI) 0.07; 0.49 than practice nurses. Nurses who reported that their previous experience had prepared them less well for triage were more likely to recommend patients for follow-up (OR 3.17, 95% CI 1.18; 5.55). Conclusion: Nurse characteristics were associated with disposition of triage calls to within practice follow-up. Nurse practitioners or those who reported feeling ‘more prepared’ for the role were more likely to manage the call definitively. Practices considering nurse triage should ensure that nurses transitioning into new roles feel adequately prepared. While standardised training is necessary, it may not be sufficient to ensure successful implementation