Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor

Background The transition from exponential to stationary phase in Streptomyces coelicolor is accompanied by a major metabolic switch and results in a strong activation of secondary metabolism. Here we have explored the underlying reorganization of the metabolome by combining computational predictions based on constraint-based modeling and detailed transcriptomics time course observations. Results We reconstructed the stoichiometric matrix of S. coelicolor, including the major antibiotic biosynthesis pathways, and performed flux balance analysis to predict flux changes that occur when the cell switches from biomass to antibiotic production. We defined the model input based on observed fermenter culture data and used a dynamically varying objective function to represent the metabolic switch. The predicted fluxes of many genes show highly significant correlation to the time series of the corresponding gene expression data. Individual mispredictions identify novel links between antibiotic production and primary metabolism. Conclusion Our results show the usefulness of constraint-based modeling for providing a detailed interpretation of time course gene expression data

Implications of the Babinet Principle for Casimir Interactions

We formulate the Babinet Principle (BP) as a relation between the scattering amplitudes for electromagnetic waves, and combine it with multiple scattering techniques to derive new properties of Casimir forces. We show that the Casimir force exerted by a planar conductor or dielectric on a self- complementary perforated planar mirror is approximately half that on a uniform mirror independent of the distance between them. The BP suggests that Casimir edge effects are anomalously small, supporting results obtained earlier in special cases. Finally, we illustrate how the BP can be used to estimate Casimir forces between perforated planar mirrors

Issues on the molecular-beam epitaxial growth of p-SiGe inverted-modulation-doped structures

The influence of boron segregation and silicon cap-layer thickness on two-dimensional hole gases (2-DHGs) has been investigated in Si/Si0.8Ge0.2/Si inverted-modulation-doped heterostructures grown by solid-source molecular-beam epitaxy. Boron segregation, which is significant in structures with small spacer layers, can be suppressed by growth interruption after the boron doping. How growth interruption affected the electrical properties of the 2-DHG and the boron doping profile as measured by secondary ion mass spectroscopy are reported. We report also on the role played by the unpassivated silicon cap, and compare carrier transport at the normal and inverted interfaces

Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels

Background Inflammatory bowel disease (IBD), is a debilitating group of chronic diseases including Crohn’s Disease (CD) and ulcerative colitis (UC), which causes inflammation of the gut and affects millions of people worldwide. At different taxonomic levels, the structure of the gut microbiota is significantly altered in IBD patients compared to that of healthy individuals. However, it is unclear how these IBD-affected bacterial groups are related to other common bacteria in the gut, and how they are connected across different disease conditions at the global scale. Results In this study, using faecal samples from patients with IBD, we show through diversity analysis of the microbial community structure based on the 16S rRNA gene that the gut microbiome of IBD patients is less diverse compared to healthy individuals. Furthermore, we have identified which bacterial groups change in abundance in both CD and UC compared to healthy controls. A substantial imbalance was observed across four major bacterial phyla including Firmicutes, Bacteroidetes, Proteobacteria and Actinobacteria, which together constitute >98% of the gut microbiota. Next, we reconstructed a bacterial family co-abundance network based on the correlation of abundance profiles obtained from the public gut microbiome data of >22000 samples of faecal and gut biopsies taken from both diseased and healthy individuals. The data was compiled using the EBI metagenomics database [1]. By mapping IBD-altered bacterial families to the network, we show that the bacterial families which exhibit an increased abundance in IBD conditions are not well connected to other groups, implying that these families generally do not coexist together with common gut organisms. Whereas, the bacterial families whose abundance is reduced or did not change in IBD conditions compared to healthy conditions are very well connected to other bacterial groups, suggesting they are highly important groups of bacteria in the gut that can coexist with other bacteria across a range of conditions. Conclusions IBD patients exhibited a less diverse gut microbiome compared to healthy individuals. Bacterial groups which changed in IBD patients were found to be groups which do not co-exist well with common commensal gut bacteria, whereas bacterial groups which did not change in patients with IBD were found to commonly co-exist with commensal gut microbiota. This gives a potential insight into the dynamics of the gut microbiota in patients with IBD

Satellite data interpretation of causes and controls on groundwater-seawater flow directions, Merseyside, UK: implications for assessing saline intrusions

International audienceGroundwater in the Triassic Sherwood Sandstone aquifer, Liverpool, UK, has locally elevated chloride concentrations (~4000 mg/l) in parts of the coastal region although there is freshwater right up to the coast line in other areas. The aquifer is cut my numerous faults with vertical displacements of as much 300 m. SPOT satellite data have been used for the Merseyside area of Liverpool. The satellite data revealed and confirmed the location of some of the main faults since the fault zones of the aquifer have low permeability (due to grain crushing, cataclasis, and clay smearing). Where fault zones outcrop at the surface, below the well-developed regolith, there is locally elevated soil water and thus anomalous vegetation patterns in comparison to unfaulted and highly porous aquifer. The ability to identify fault zones by this satellite-based method strongly suggests that they are at least partially sealing, sub-vertical features in the aquifer. Digitally enhanced and processed satellite data were used to define the relative proportions of sand and clay in the near-coastal (inter-tidal) part of the Mersey estuary. Sand-dominated sediment has higher pixel values in comparison with clay deposits in the near infrared spectral region (NIR). Where open and weathered fault rocks crop out at the surface near the intertidal zone, water movement in these potential surface water conduits is limited where the intertidal zone is clay-dominated since clay will plug the conduit. Where these weathered and open fault-rocks crop out against sand-dominated parts of the coastline, fresh water outflux into the seawater has been imaged using the satellite data. Furthermore, the high and low chloride concentration parts of the aquifer are separated by major, sub-vertical fault zones and have allowed a very steep water table gradient to remain in the aquifer

Wave function-dependent mobility and suppression of interface roughness scattering in a strained SiGe p-channel field-effect structure

The 4 K Hall mobility has been measured in a top-gated, inverted, modulation-doped Si/Si0.8Ge0.2 structure having a Si:B doping layer beneath the alloy. From comparisons with theoretical calculations, we argue that, unlike an ordinary enhancement-mode SiGe p-channel metal–oxide–semiconductor structure, this configuration leads to a decrease of interface roughness scattering with increasing sheet carrier density. We also speculate on the nature of the interface charge observed in these structures at low temperature

Quantum transport of strongly interacting photons in a one-dimensional nonlinear waveguide

We present a theoretical technique for solving the quantum transport problem of a few photons through a one-dimensional, strongly nonlinear waveguide. We specifically consider the situation where the evolution of the optical field is governed by the quantum nonlinear Schr\"odinger equation (NLSE). Although this kind of nonlinearity is quite general, we focus on a realistic implementation involving cold atoms loaded in a hollow-core optical fiber, where the atomic system provides a tunable nonlinearity that can be large even at a single-photon level. In particular, we show that when the interaction between photons is effectively repulsive, the transmission of multi-photon components of the field is suppressed. This leads to anti-bunching of the transmitted light and indicates that the system acts as a single-photon switch. On the other hand, in the case of attractive interaction, the system can exhibit either anti-bunching or bunching, which is in stark contrast to semiclassical calculations. We show that the bunching behavior is related to the resonant excitation of bound states of photons inside the system.Comment: 22 pages, 24 figure

Instability and Fluctuations of Flux Lines with Point Impurities in a Parallel Current

A parallel current can destabilize a single flux line (FL), or an array of FLs. We consider the effects of pinning by point impurities on this instability. The presence of impurities destroys the long-range order of a flux lattice, leading to the so called Bragg glass (BrG) phase. We first show that the long-range topological order of the BrG is also destroyed by a parallel current. Nonetheless, some degree of short-range order should remain, whose destruction by thermal and impurity fluctuations, as well as the current, is studied here. To this end, we employ a cage model for a single FL in the presence of impurities and current, and study it analytically (by replica variational methods), and numerically (using a transfer matrix technique). The results are in good agreement, and in conjunction with a Lindemann criterion, provide the boundary in the magnetic field--temperature plane for destruction of short-range order. In all cases, we find that the addition of impurities or current (singly or in combination) leads to further increase in equilibrium FL fluctuations. Thus pinning to point impurities does not stabilize FLs in a parallel current $j_z$, although the onset of this instability is much delayed due to large potential barriers that diverge as $j_z^{-\mu}$.Comment: 10 pages, 6 figure