The route to transcription initiation determines the mode of transcriptional bursting in E. coli

Transcription is fundamentally noisy, leading to significant heterogeneity across bacterial populations. Noise is often attributed to burstiness, but the underlying mechanisms and their dependence on the mode of promotor regulation remain unclear. Here, we measure E. coli single cell mRNA levels for two stress responses that depend on bacterial sigma factors with different mode of transcription initiation (sigma (70) and sigma (54)). By fitting a stochastic model to the observed mRNA distributions, we show that the transition from low to high expression of the sigma (70)-controlled stress response is regulated via the burst size, while that of the sigma (54)-controlled stress response is regulated via the burst frequency. Therefore, transcription initiation involving sigma (54) differs from other bacterial systems, and yields bursting kinetics characteristic of eukaryotic systems. Transcription noise in bacteria is often attributed to burstiness, but the mechanisms are unclear. Here, the authors show that the transition from low to high expression can be regulated via burst size or burst frequency, depending on the mode of transcription initiation determined by different sigma factors

Carrageenan Is a Potent Inhibitor of Papillomavirus Infection

Certain sexually transmitted human papillomavirus (HPV) types are causally associated with the development of cervical cancer. Our recent development of high-titer HPV pseudoviruses has made it possible to perform high-throughput in vitro screens to identify HPV infection inhibitors. Comparison of a variety of compounds revealed that carrageenan, a type of sulfated polysaccharide extracted from red algae, is an extremely potent infection inhibitor for a broad range of sexually transmitted HPVs. Although carrageenan can inhibit herpes simplex viruses and some strains of HIV in vitro, genital HPVs are about a thousand-fold more susceptible, with 50% inhibitory doses in the low ng/ml range. Carrageenan acts primarily by preventing the binding of HPV virions to cells. This finding is consistent with the fact that carrageenan resembles heparan sulfate, an HPV cell-attachment factor. However, carrageenan is three orders of magnitude more potent than heparin, a form of cell-free heparan sulfate that has been regarded as a highly effective model HPV inhibitor. Carrageenan can also block HPV infection through a second, postattachment heparan sulfate–independent effect. Carrageenan is in widespread commercial use as a thickener in a variety of cosmetic and food products, ranging from sexual lubricants to infant feeding formulas. Some of these products block HPV infectivity in vitro, even when diluted a million-fold. Clinical trials are needed to determine whether carrageenan-based products are effective as topical microbicides against genital HPVs

Regulation of cardiac ryanodine receptor function by the cyclic-GMP dependent protein kinase G

Background: The cGMP-dependent protein kinase G (PKG) phosphorylates the cardiac ryanodine receptor (RyR2) in vitro. We aimed to determine whether modulation of endogenous PKG alters RyR2-mediated spontaneous Ca2+ release and whether this effect is linked to a change in RyR2 phosphorylation. Methods: & Results: Human embryonic kidney (HEK293) cells with inducible RyR2 expression were treated with the cGMP analogue 8-Br-cGMP (100 μM) to activate endogenous PKG. In cells transfected with luminal Ca2+ sensor, D1ER, PKG activation significantly reduced the threshold for RyR2-mediated spontaneous Ca2+ release (93.9 ± 0.4% of store size with vehicle vs. 91.7 ± 0.8% with 8-Br-cGMP, P = 0.04). Mutation of the proposed PKG phosphorylation sites, S2808 and S2030, either individually or as a combination, prevented the decrease in Ca2+ release threshold induced by endogenous PKG activation. Interestingly, despite a functional dependence on expression of RyR2 phosphorylation sites, 8-Br-cGMP activation of PKG did not promote a detectable change in S2808 phosphorylation (P = 0.9). Paradoxically, pharmacological inhibition of PKG with KT 5823 (1 μM) also reduced the threshold for spontaneous Ca2+ release through RyR2 without affecting S2808 phosphorylation. Silencing RNA knockdown of endogenous PKG expression also had no quantifiable effect on RyR2 S2808 phosphorylation (P = 0.9). However, unlike PKG inhibition with KT 5823, PKG knockdown did not alter spontaneous Ca2+ release propensity or luminal Ca2+ handling. Conclusion: In an intact cell model, activation of endogenous PKG reduces the threshold for RyR2-mediated spontaneous Ca2+ release in a manner dependent on the RyR2 phosphorylation sites S2808 and S2030. This study clarifies the regulation of RyR2 Ca2+ release by endogenous PKG and functionally implicates the role of RyR2 phosphorylation.Fil: Gonano, Luis Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigaciones Cardiovasculares "Dr. Horacio Eugenio Cingolani". Universidad Nacional de La Plata. Facultad de Ciencias Médicas. Centro de Investigaciones Cardiovasculares "Dr. Horacio Eugenio Cingolani"; Argentina. University of Otago; Nueva ZelandaFil: Aitken Buck, Hamish M.. University of Otago; Nueva ZelandaFil: Chakraborty, Akash D.. University of Otago; Nueva ZelandaFil: Worthington, Luke P. I.. University of Otago; Nueva ZelandaFil: Cully, Tanya R.. University of Otago; Nueva ZelandaFil: Lamberts, Regis R.. University of Otago; Nueva ZelandaFil: Vila Petroff, Martin Gerarde. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigaciones Cardiovasculares "Dr. Horacio Eugenio Cingolani". Universidad Nacional de La Plata. Facultad de Ciencias Médicas. Centro de Investigaciones Cardiovasculares "Dr. Horacio Eugenio Cingolani"; ArgentinaFil: Jones, Peter P.. University of Otago; Nueva Zeland

Understanding consumer demand for new transport technologies and services, and implications for the future of mobility

The transport sector is witnessing unprecedented levels of disruption. Privately owned cars that operate on internal combustion engines have been the dominant modes of passenger transport for much of the last century. However, recent advances in transport technologies and services, such as the development of autonomous vehicles, the emergence of shared mobility services, and the commercialization of alternative fuel vehicle technologies, promise to revolutionise how humans travel. The implications are profound: some have predicted the end of private car dependent Western societies, others have portended greater suburbanization than has ever been observed before. If transport systems are to fulfil current and future needs of different subpopulations, and satisfy short and long-term societal objectives, it is imperative that we comprehend the many factors that shape individual behaviour. This chapter introduces the technologies and services most likely to disrupt prevailing practices in the transport sector. We review past studies that have examined current and future demand for these new technologies and services, and their likely short and long-term impacts on extant mobility patterns. We conclude with a summary of what these new technologies and services might mean for the future of mobility.Comment: 15 pages, 0 figures, book chapte

Depth-resolved measurement of the Meissner screening profile in a niobium thin film from spin-lattice relaxation of the implanted β\beta-emitter 8^{8}Li

We report measurements of the Meissner screening profile in a Nb(300 nm)/Al$_{2}$O$_{3}$ thin film using $^{8}$Li $\beta$-detected nuclear magnetic resonance ($\beta$-NMR). The NMR probe $^{8}$Li was ion-implanted into the Nb film at energies $\leq$ 20 keV, corresponding to mean stopping depths comparable to Nb's magnetic penetration depth $\lambda$. $^{8}$Li's strong dipole-dipole coupling with the host $^{93}$Nb nuclei provided a "cross-relaxation" channel that dominated in low magnetic fields, which conferred indirect sensitivity to the local magnetic field via the spin-lattice relaxation (SLR) rate $1/T_{1}$. From a fit of the $1/T_{1}$ data to a model accounting for its dependence on temperature, magnetic field, and $^{8}$Li$^{+}$ implantation energy, we obtained a magnetic penetration depth $\lambda_{0}$ = 51.5(22) nm, consistent with a relatively short carrier mean-free-path $\ell$ = 18.7(29) nm typical of similarly prepared Nb films. The results presented here constitute an important step towards using $^{8}$Li $\beta$-NMR to characterize bulk Nb samples with engineered surfaces, which are often used in the fabrication of particle accelerators.Comment: 16 pages, 4 figure

Genome-Wide Studies of Histone Demethylation Catalysed by the Fission Yeast Homologues of Mammalian LSD1

In order to gain a more global view of the activity of histone demethylases, we report here genome-wide studies of the fission yeast SWIRM and polyamine oxidase (PAO) domain homologues of mammalian LSD1. Consistent with previous work we find that the two S. pombe proteins, which we name Swm1 and Swm2 (after SWIRM1 and SWIRM2), associate together in a complex. However, we find that this complex specifically demethylates lysine 9 in histone H3 (H3K9) and both up- and down-regulates expression of different groups of genes. Using chromatin-immunoprecipitation, to isolate fragments of chromatin containing either H3K4me2 or H3K9me2, and DNA microarray analysis (ChIP-chip), we have studied genome-wide changes in patterns of histone methylation, and their correlation with gene expression, upon deletion of the swm1+ gene. Using hyper-geometric probability comparisons we uncover genetic links between lysine-specific demethylases, the histone deacetylase Clr6, and the chromatin remodeller Hrp1. The data presented here demonstrate that in fission yeast the SWIRM/PAO domain proteins Swm1 and Swm2 are associated in complexes that can remove methyl groups from lysine 9 methylated histone H3. In vitro, we show that bacterially expressed Swm1 also possesses lysine 9 demethylase activity. In vivo, loss of Swm1 increases the global levels of both H3K9me2 and H3K4me2. A significant accumulation of H3K4me2 is observed at genes that are up-regulated in a swm1 deletion strain. In addition, H3K9me2 accumulates at some genes known to be direct Swm1/2 targets that are down-regulated in the swm1¿ strain. The in vivo data indicate that Swm1 acts in concert with the HDAC Clr6 and the chromatin remodeller Hrp1 to repress gene expression. In addition, our in vitro analyses suggest that the H3K9 demethylase activity requires an unidentified post-translational modification to allow it to act. Thus, our results highlight complex interactions between histone demethylase, deacetylase and chromatin remodelling activities in the regulation of gene expression

The effect of the national minimum wage on the UK small business sector : a geographical analysis

A national minimum wage (NMW) was introduced into the United Kingdom in 1999 as part of New Labour's active labour-market approach. The level has been uprated on several occasions since then. Most research suggests that the NMW has benefited low-paid workers while having little adverse impact on employment levels. This paper explores the regional impact of the NMW on the small business sector, using data from the Federation of Small Businesses' biennial survey, the largest business survey in the United Kingdom. Overall, just over 21% of businesses with employees uprated employees and just under 10% of employees have benefited from pay uprates. The impact has varied across industries, with the greatest effects in the hotels and catering sector. In general, affected businesses have anticipated that they would be able to absorb the costs, although in some cases at the expense of a slight decline in profitability. The impact of the NMW also varies across the regions, having the least impact in London and the South East and the greatest impact in the 'north'. In the northern regions, businesses are less able to absorb the increased costs and more likely to respond by increasing prices. This has potential implications for the competitiveness of small and medium-sized enterprises in these regions, which is more likely to be based around price and cost advantages than their counterparts in the south. The Low Pay Commission therefore should give greater attention to the geographical impacts of the NMW in its evaluation and when proposing future increases in the rate

A modeling assessment of the role of reversible scavenging in controlling oceanic dissolved Cu and Zn distributions

The balance of processes that control elemental distributions in the modern oceans is important in understanding both their internal recycling and the rate and nature of their eventual output to sediment. Here we seek to evaluate the likely controls on the vertical profiles of Cu and Zn. Though the concentrations of both Cu and Zn increase with depth, Cu increases in a more linear fashion than Zn, which exhibits a typical "nutrient-type" profile. Both elements are bioessential, and biological uptake and regeneration has often been cited as an important process in controlling their vertical distribution. In this study, we investigate the likely importance of another key vertical process, that of passive scavenging on sinking particles, via a simple one-dimensional model of reversible scavenging. We find that, despite the absence of lateral or vertical water advection, mixing, diffusion, or biological uptake, our reversible scavenging model is very successful in replicating dissolved Cu concentration profiles on a range of geographic scales. We provide preliminary constraints on the scavenging coefficients for Cu for a spectrum of particle types (calcium carbonate, opal, particulate organic carbon, and dust) while emphasizing the fit of the shape of the modeled profile to that of the tracer data. In contrast to Cu, and reaffirming the belief that Zn behaves as a true micronutrient, the scavenging model is a poor match to the shape of oceanic Zn profiles. Modeling a single vertical process simultaneously highlights the importance of lateral advection in generating high Zn concentrations in the deep Pacific. Key Points A 1-D reversible scavenging model is applied to oceanic [Cu] and [Zn]Dissolved Cu is well described by the process of reversible scavengingDissolved Zn is not, reflecting its behaviour as a true nutrient-type element ©2013. American Geophysical Union. All Rights Reserved