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VLF ground data from Porojarvi in N. Finland has been presented. Spectrograms reveal frequent occurrence of power line harmonic radiation (PLHR), originating from the Finnish power system and from heavy industrial plant. The radiation is seen to penetrate the magnetosphere since numerous occurrences of PLHR triggered emissions are seen. Risers predominate but fallers and hooks are also observed. A well-established 1D Vlasov simulation code has been used to simulate these emissions, using plausible magnetospheric data for a range of L values from L = 4 to L = 5.5. The code is able to reproduce risers fallers and hooks in close agreement with observations. The results shed considerable insight into the generation structure of both risers and fallers.Key words. Electromagnetics (numerical methods) · Ionosphere (wave-particle interactions) · Magnetospheric physics (plasma waves and instabilities)

It has been suggested that whistler-induced electron precipitation (WEP) may be the most significant inner radiation belt loss process for some electron energy ranges. One area of uncertainty lies in identifying a typical estimate of the precipitating fluxes from the examples given in the literature to date. Here we aim to solve this difficulty through modelling satellite and ground-based observations of onset and decay of the precipitation and its effects in the ionosphere by examining WEP-produced Trimpi perturbations in subionospheric VLF transmissions. In this study we find that typical Trimpi are well described by the effects of WEP spectra derived from the AE-5 inner radiation belt model for typical precipitating energy fluxes. This confirms the validity of the radiation belt lifetimes determined in previous studies using these flux parameters. We find that the large variation in observed Trimpi perturbation size occurring over time scales of minutes to hours is primarily due to differing precipitation flux levels rather than changing WEP spectra. Finally, we show that high-time resolution measurements during the onset of Trimpi perturbations should provide a useful signature for discriminating WEP Trimpi from non-WEP Trimpi, due to the pulsed nature of the WEP arrival.

Background: cancellation of planned surgery impacts substantially on patients and health systems. This study describes the incidence and reasons for cancellation of inpatient surgery in the UK NHS. Methods: we conducted a prospective observational cohort study over 7 consecutive days in March 2017 in 245 NHS hospitals. Occurrences and reasons for previous surgical cancellations were recorded. Using multilevel logistic regression, we identified patient- and hospital-level factors associated with cancellation due to inadequate bed capacity. Results: we analysed data from 14 936 patients undergoing planned surgery. A total of 1499 patients (10.0%) reported previous cancellation for the same procedure; contemporaneous hospital census data indicated that 13.9% patients attending inpatient operations were cancelled on the day of surgery. Non-clinical reasons, predominantly inadequate bed capacity, accounted for a large proportion of previous cancellations. Independent risk factors for cancellation due to inadequate bed capacity included requirement for postoperative critical care [odds ratio (OR)=2.92; 95% confidence interval (CI), 2.12–4.02; PConclusions: a significant proportion of patients presenting for surgery have experienced a previous cancellation for the same procedure. Cancer surgery is relatively protected, but bed capacity, including postoperative critical care requirements, are significant risk factors for previous cancellations.

A theoretical model to study electromagnetic ion cyclotron (EMIC) waves in kappa-Maxwellian plasma is developed. The plasma is assumed to have five components, i.e., electrons, cool and hot protons, and singly charged helium and oxygen ions. The kappa-Maxwellian anisotropic particle distribution function is assumed for the hot protons. We use the Kyoto University Plasma Dispersion Analysis Package, a full dispersion solver developed at Kyoto University, to obtain the numerical results and delineate the oxygen, helium, and proton bands. Higher harmonics of the EMIC waves are also studied, and the effects of the kappa distribution on the growth of these waves are clearly demonstrated. Our results are applied to Cluster spacecraft observations of EMIC waves in the inner magnetosphere.

Using a well-established magnetospheric very-low-frequency (VLF) ray tracing method, in this work we trace the propagation of individual rising- and falling-frequency elements of VLF chorus from their generation point in the equatorial region of the magnetosphere through to at least one reflection at the lower-hybrid resonance point. Unlike recent work by Bortnik and co-workers, whose emphasis was on demonstrating that magnetospheric hiss has its origins in chorus, we here track the motion in the equatorial plane of the whole chorus element, paying particular regard to movement across field lines, rotation, and compression or expansion of the wave pulse. With a generation point for rising chorus at the equator, it was found the element wave pulse remained largely field aligned in the generation region. However, for a falling tone generation point at 4000 km upstream from the equator, by the time the pulse crosses the equator the wavefield had substantial obliquity, displacement, and compression, which has substantial implications for the theory of falling chorus generation.

A wide variety of commercial products can be potentially made from monomeric sugars produced by the dilute acid hydrolysis of lignocellulosic biomass. However, this process is accompanied by side products such as furfural that hinder microbial growth and fermentation. To investigate the mechanism of furfural inhibition, mRNA microarrays of an ethanologenic strain of Escherichia coli (LY180) were compared immediately prior to and 15 min after a moderate furfural challenge. Expression of genes and regulators associated with the biosynthesis of cysteine and methionine was increased by furfural, consistent with a limitation of these critical metabolites. This was in contrast to a general stringent response and decreased expression of many other biosynthetic genes. Of the 20 amino acids individually tested as supplements (100 μM each), cysteine and methionine were the most effective in increasing furfural tolerance with serine (precursor of cysteine), histidine, and arginine of lesser benefit. Supplementation with other reduced sulfur sources such as d -cysteine and thiosulfate also increased furfural tolerance. In contrast, supplementation with taurine, a sulfur source that requires 3 molecules of NADPH for sulfur assimilation, was of no benefit. Furfural tolerance was also increased by inserting a plasmid encoding pntAB , a cytoplasmic NADH/NADPH transhydrogenase. Based on these results, a model is proposed for the inhibition of growth in which the reduction of furfural by YqhD, an enzyme with a low K m for NADPH, depletes NADPH sufficiently to limit the assimilation of sulfur into amino acids (cysteine and methionine) by CysIJ (sulfite reductase).

The efficiency of energetic electron cyclotron acceleration in the Earth’s magnetosphere in different regimes of electron resonant interaction with parallel propagating whistler mode waves of variable frequency, specifically, with chorus ELF-VLF emissions, is considered. The regime of stochastic acceleration, typical of the interaction between particles and noise-like emissions, and particle acceleration in the regime of nonlinear trapping by a quasimonochromatic wave field are discussed. The specific feature of the latter regime consists in its non-diffuse character, i.e., the definite sign of the energy variation depending on the frequency variation in the wave packet. The trapped electron energy becomes higher if frequency increases within an element, which is typical of chorus emissions. For the parameters typical of chorus emissions (the amplitude of a wave magnetic field B ∼ = 102 nT, the initial frequency ω ∼ 0.3ω H , and the frequency variation &Dω ∼ 0.15ω H , where ω H is the electron gyrofrequency), the energy increase during one act of such an interaction at L = 4−5 exceeds the rms variation in the energy of untrapped electron (during stochastic acceleration) by one-two orders of magnitude. The estimates indicate that a considerable fraction (several tens of percent) of the chorus element energy can be absorbed by electrons accelerated in the trapping regime during a single hop.

Acceleration of relativistic electrons in an inhomogeneous geomagnetic field during their resonant interaction with longitudinally propagating whistler-mode waves of varying frequency has been considered. Specific features of acceleration of electrons trapped by the wave field have been studied. Previous estimates of the efficiency of such acceleration have been generalized with regard to relativistic effects, and the simple formula for energy gain in a wide range of initial energies has been obtained. It has been indicated that the energy gain during a single interaction between electron and a whistler-mode wave packet, with typical parameters of an element of chorus emissions in the Earth’s magnetosphere, can reach several keV. The conditions of this acceleration mechanism realization are discussed. Specifically, it has been found that, in the case of chorus emissions in the Earth’s magnetosphere, this mechanism can be effective for electrons with perpendicular energies several times as high as such an energy of electrons generating chorus.

A linear theory for the backward wave oscillator generation regime of whistler waves in the Earth’s magnetosphere is presented. Using a parabolic profile of the magnetic field and a linear expression for the resonant current in the case of a zeroth order distribution function with a step discontinuity in the velocity component parallel to the magnetic field, the modes of the system are investigated by means of a search procedure. The existence of at least one mode exponentially growing in time is indicative of absolute instability, and such modes have been found. Therefore, an earlier prediction of such a regime, based on the homogeneous magnetic field model, is confirmed. The dependence of growth rates on the frequency mismatch and energetic electron density has been studied. These results yield the characteristic spatial profile and temporal growth rate of small-amplitude whistler-wave disturbances, which are likely to be the seeds for chorus emissions.

The well-known phenomena of triggered VLF emissions and the related VLF chorus are due to strongly nonlinear wave particle interactions between cyclotron resonant keV/MeV electrons and a narrow band or band limited VLF wavefield, taking place in the equatorial region of the magnetosphere. Nearly all theoretical and numerical work in this field assumes the VLF wavefield is parallel propagating or ‘ducted’ along the field line by field aligned density irregularities. Although complex, the causative mechanisms are very amenable to both numerical modelling and to theoretical and even analytic analysis.

The scattering of VLF sub-ionospheric transmissions by sprite plasma through horizontal angles up to 180/spl deg/ shows that sprite plasma is highly conducting. Following a simple transmission-line (one-dimensional-wave) model in 1997, two-dimensional and three-dimensional models have been produced. Here, we compare the results of the three models, and show that all require a uniform conductivity of at least 30 /spl mu/S/m, corresponding to an electron density at 70 km altitude of /spl sim/10/sup 10/ m/sup -3/ (/spl sim/10/sup 4/ electrons per cc), and so about 10/sup 5//cc at 55 km. The latter ionization density is about that of the daytime E-region, and over six orders of magnitude above the ambient density at 55 km. By contrast, the "early/fast" events, as defined by the Stanford group, do not exhibit scatter angles above 15/spl deg/, suggesting that the sprite conductivity rises too slowly (as the plasma cools) to reach adequate backscatter within the time allowed by the "early/fast" definition.

Red sprites consist of multiple ionised columns extending above a thunderstorm from ~30 km to ~90 km. Electron densities in these columns are very much larger than the ambient background, perhaps fives times at 70 km. These highly ionized structures cause observable perturbations in subionospheric VLF transmissions known as "VLF Sprites". Three models of initial sprite electron density are considered, and using a realistic ionization relaxation model the time dependence of electron density is derived. A 3-D Born propagation code of is used to compute the time profile of a VLF sprite. Two profiles show good agreement with the time signature experimentally observed, in that scattered amplitude and phase decrease linearly log(t). These simulations provide insight into the nature and structure of sprite columns, and indicate an additional constraint which should be applied to red sprite creation models.

We have isolated cosmids that complement a Pseudomonas aeruginosa export-impaired mutant by increasing growth on lipid agar, a medium that requires lipase expression and export. These cosmids encode a previously unidentified lipase, LipC, which has high homology to the P. aeruginosa lipA gene product. Like LipA, LipC activity requires the chaperone activity of the lipB gene product and a functional xcp gene cluster for export. However, expression of LipC is barely detectable in a wild-type background. Transposon insertions that increase lipC promoter activity have been obtained that inactivate two pilus biogenesis genes, pilX and pilY1. This suggests that these proteins either directly or indirectly repress the expression of LipC and may be involved in transducing an extracellular signal that regulates this lipase.

Modeling studies show that the exclusion of the propagating VLF wave from the ionospheric region results in the decline of Trimpi magnitude with patch altitude. In large models such as Long Wave Propagation Capability (LWPC) this exclusion does not occur inherently in the code, and high-altitude precipitation modeling can produce results that are not consistent with observations from ground-based experiments. The introduction to LWPC of realistic wave attenuation of the height gain functions in the ionosphere solves these computational problems. This work presents the first modeling of (Born) Trimpi scattering at long ranges, taking into account global inhomogeneities and continuous mode conversion along all paths, by employing the full conductivity perturbation matrix. The application of the more realistic height gain functions allows the prediction of decreasing Trimpi activity with increasing latitude, primarily through the mechanism of excluding the VLF wave from regions of high conductivity and scattering efficiency. Ground-based observations from Faraday and Rothera, Antarctica, in September and October 1995 of Trimpi occurring on the NPM (Hawaii) path provide data that are consistent with these predictions. Latitudinal variations in Trimpi occurrence near L = 2.5, with a significant decrease of about 70% occurrence between L = 2.4 and L = 2.8, have been observed at higher L shell resolution than in previous studies (i.e., 2 < L < 3).

Red sprites were discovered by chance in 1989 when a low-light TV system was pointed above an active thunderstorm. Red sprites are associated with columns of ionization in the Earth-ionosphere waveguide, from above the thunderstorm into the D region of the ionosphere. The ionized columns have been detected through “VLF sprites,” perturbations of the phase and/or amplitude of subionospheric VLF transmissions, which can be used to study the electrical properties of red sprites. There is extensive experimental evidence that VLF sprites may involve wide scattering angles and can produce back scattered radiation. Here we present a numerical and theoretical study of the scattering of subionospheric VLF transmissions caused by the plasma columns associated with red sprites. Comparison of the VLF scattering from sprites is made between a non-Born rigorous model which assumes the sprites are infinite columns of constant conductivity, and a three dimensional Born scattering code. Both formulations show excellent agreement with one another. The formulations predict VLF sprites similar to those experimentally observed for all scattering angles. This shows that the conclusions of previous studies into VLF sprites making use of the non-Born formulations of Rodger et al [1997a, b] are valid. The modeling provides strong evidence that red sprite plasma is highly ionized in comparison with the ambient nighttime ionosphere, being nearly 5 orders of magnitude greater than the ambient at some heights.

Many strains of Pseudomonas syringae produce retractile pili that act as receptors for lytic bacteriophage φ6. As these are also characteristics of type IV pili, it was postulated that P. syringae may possess genes for type IV pilus biogenesis. A cosmid clone bank of P. syringae pv. tomato DC3000 genomic DNA was used to complement a mutant of Pseudomonas aeruginosa defective in the PilD (XcpA) prepilin peptidase gene by selection for restoration of extracellular protein secretion, a function also known to require PilD. A cosmid able to complement this mutant was also able to complement mutations in the pilB and pilC genes, suggesting that, if the organization of these genes is similar to that of P. aeruginosa, the cosmid may contain the P. syringae pilA. This was confirmed by sequencing a region from this plasmid that was shown to hybridize at low stringency to the P. aeruginosa pilA gene. The deduced P. syringae PilA polypeptide possesses the characteristic properties of the type IV pilins. Heterologous expression of the P. syringae pilA in P. aeruginosa was also shown, conferring not only φ6 phage sensitivity to P. aeruginosa pilA mutants but also sensitivity to PO4, a lytic bacteriophage specific for the pilus of P. aeruginosa. This suggests that additional components might be present in the mature pilus of P. aeruginosa that are the true receptors for this phage. Chromosomal mutations in P. syringae pv. tomato DC3000 pilA and pilD genes were shown to abolish its sensitivity to bacteriophage φ6. To determine the importance of P. syringae pilus in plant leaf interactions, these mutations were tested under laboratory and field conditions. Although little effect was seen on pathogenicity, culturable leaf-associated population sizes of the pilA mutant were significantly different from those of the wild-type parent. In addition, the expression of the DC3000 pilA gene appears to contribute to the UV tolerance of P. syringae and may play a role in survival on the plant leaf surface.

This paper investigates the numerical modelling of VLF Trimpis produced by a D region inhomogeneity on the Great Circle Path . Two different codes are used. The first is a 2D finite element method (FEM) code , whose solutions are rigorous and valid in the strong scattering or non-Born limit. The second code is a fully 3D model that invokes the Born approximation. The predicted Trimpis from these codes compare closely, thus confirming the validity of both models. The modal scattering matrices have a comparable structure, and indicate strong scattering between the dominant TM modes. Analysis of the scattering matrix from the FEM code delineates the Born regime. For a LIE with a radius of 100kms, the Born approximation becomes invalid at an electron density perturbation of about 8 el/cc.

Pseudomonas aeruginosa is a prolific exporter of virulence factors and contains three of the four protein secretion systems that have been described in gram-negative bacteria. The P. aeruginosa type II general secretory pathway (GSP) is used to export the largest number of proteins from this organism, including lipase, phospholipase C, alkaline phosphatase, exotoxin A, elastase and LasA. Although these exoproteins contain no sequence similarity, they are specifically and efficiently transported by the secretion apparatus. Bacterial homologues of XcpQ (GspD), the only outer membrane component of this system, have been proposed to play the role of gatekeeper, by presumably interacting and recognizing the exported substrates to allow their passage through the outer membrane. While determining the phenotype of nonpolar deletions in each of the xcp genes, we have shown that a deletion of the P. aeruginosa strain K xcpQ does not completely abolish protein secretion. As the proposed function of XcpQ should be requisite for secretion, we searched for additional factors that could carry out this role. A cosmid DNA library from a PAK strain deleted for xcpP-Z was tested for its ability to increase protein secretion by screening for enhanced growth on lipid agar, a medium that selects for the secretion of lipase. In this manner, we have identified an XcpQ homologue, XqhA, that is solely responsible for the residual export observed in a deltaxcpQ strain, although it is not required for efficient secretion in wild-type P. aeruginosa. We have also demonstrated that this protein is capable of recognizing all of the exoproteins of P. aeruginosa, arguing against the proposed role of members of the secretin family as determinants of specificity.

Pseudomonas aeruginosa exports a number of hydrolytic enzymes and toxins using the type II or general secretion pathway, found in a variety of Gram-negative bacteria and requiring the functions of at least 12 gene products (XcpP-Z and PilD/XcpA in P. aeruginosa). A number of these gene products are homologues of components of the type IV pilus biogenesis system, including four proteins, XcpT-W, which are highly similar to the pilin subunit in their size, localization and post-translational modifications. These proteins, in addition to the pilin subunit, are cleaved and methylated by the PilD/XcpA prepilin peptidase, but their interactions with other components of the export apparatus are unclear. Using a medium developed for the selection of export-proficient P. aeruginosa strains, we have isolated temperature-sensitive mutations in the xcpT gene and extragenic suppressors for one of the mutants. These suppressors fall into two classes, one that maps outside of the xcpP-Z gene cluster and may define additional cellular functions that are required for export, and a second that maps to the xcpR gene product and indicates a potential protein-protein interaction connecting two different cellular compartments and required for the assembly or function of the export apparatus.

[1] Recently much progress has been made in the simulation and theoretical understanding of rising frequency triggered emissions and rising chorus. Both PIC and Vlasov VHS codes produce risers in the region downstream from the equator toward which the VLF waves are traveling. The VHS code only produces fallers or downward hooks with difficulty due to the coherent nature of wave particle interaction across the equator. With the VHS code we now confine the interaction region to be the region upstream from the equator, where inhomogeneity factor S is positive. This suppresses correlated wave particle interaction effects across the equator and the tendency of the code to trigger risers, and permits the formation of a proper falling tone generation region. The VHS code now easily and reproducibly triggers falling tones. The evolution of resonant particle current JE in space and time shows a generation point at −5224 km and the wavefield undergoes amplification of some 25 dB in traversing the nonlinear generation region. The current component parallel to wave magnetic field (JB) is positive, whereas it is negative for risers. The resonant particle trap shows an enhanced distribution function or ‘hill’, whereas risers have a ‘hole’. According to recent theory (Omura et al., 2008, 2009) sweeping frequency is due primarily to the advective term. The nonlinear frequency shift term is now negative (∼−12 Hz) and the sweep rate of −800 Hz/s is approximately nonlinear frequency shift divided by TN, the transition time, of the order of a trapping time.

Chorus emissions are triggered from the linear cyclotron instability driven by the temperature anisotropy of energetic electrons (10–100 keV) in the magnetosphere. Chorus emissions grow as an absolute nonlinear instability near the magnetic equator due to the presence of an electromagnetic electron hole in velocity space. The transition process from the linear wave growth at a constant frequency to the nonlinear wave growth with a rising tone frequency is due to formation of a resonant current — J B anti-parallel to the wave magnetic field. The rising-tone frequency introduces a phase shift to the electron hole at the equator, and results in a resonant current component anti-parallel to the wave electric field — J E , which causes the nonlinear wave growth. To confirm this triggering mechanism, we perform Vlasov Hybrid Simulations with J B and without J B . The run without J B does not reproduce chorus emissions, while the run with J B does successfully reproduce chorus emissions. The nonlinear frequency shift ω 1 due to J B plays a critical role in the triggering process. The nonlinear transition time T N for the frequency shift is found to be of the same order as the nonlinear trapping period, which is confirmed by simulations and observation. The established frequency sweep rate is ω 1 / T N , which gives an optimum wave amplitude of chorus emissions.

[1] Chorus emissions are triggered from the linear cyclotron instability driven by the temperature anisotropy of energetic electrons (10–100 keV) in the magnetosphere. Chorus emissions grow as an absolute nonlinear instability near the magnetic equator because of the presence of an electromagnetic electron hole in velocity space. The transition process from the linear wave growth at a constant frequency to the nonlinear wave growth with a rising tone frequency is due to formation of a resonant current −JB antiparallel to the wave magnetic field. The rising-tone frequency introduces a phase shift to the electron hole at the equator and results in a resonant current component antiparallel to the wave electric field −JE, which causes the nonlinear wave growth. To confirm this triggering mechanism, we perform Vlasov hybrid simulations with JB and without JB. The run without JB does not reproduce chorus emissions, while the run with JB does successfully reproduce chorus emissions. The nonlinear frequency shift ω1 due to JB plays a critical role in the triggering process. The nonlinear transition time TN for the frequency shift is found to be of the same order as the nonlinear trapping period, which is confirmed by simulations and observation. The established frequency sweep rate is ω1/TN, which gives an optimum wave amplitude of chorus emissions.

Four components of the apparatus of extracellular protein secretion of Pseudomonas aeruginosa, Xcpt, -U, -V, and -W (XcpT-W), are synthesized as precursors with short N-terminal leader peptides that share sequence similarity with the pilin subunit of this organism. A specialized leader peptidase/methylase, product of the pilD gene, has been shown to cleave the leader peptide from prepilin and to methylate the N-terminal phenylalanine of the mature pilin. Antibodies were prepared against XcpT-W and used to purify each of these proteins. Sequence analysis of XcpT-W has shown that these proteins, like mature pilin, contain N-methylphenylalanine as the N-terminal amino acid. Analysis of cellular fractions from wild-type and pilD mutant strains of P. aeruginosa showed that the precursor forms of XcpT-W are located predominantly in the bacterial inner membrane, and their localization is not altered after PilD-mediated removal of the leader sequence. These studies demonstrate that the biogenesis of the apparatus of extracellular protein secretion and that of type IV pili share a requirement for PilD. This bifunctional enzyme, acting in the inner membrane, cleaves the leader peptides from precursors of pilins and XcpT-W and subsequently methylates the amino group of the N-terminal phenylalanine of each of its substrates.

Precursors of the type IV pilins of a number of bacterial pathogens, as well as related proteins involved in extracellular protein export and DNA uptake, are synthesized with short basic leader sequences. Maturation of these proteins involves two consecutive posttranslational modifications. The leader sequence is first proteolytically removed by specialized endopeptidases, of which the prototype is encoded by the pilD gene of Pseudomonas aeruginosa. Subsequently, the amino termini of these proteins are methylated. Here we demonstrate that PilD, in addition to cleaving the amino-terminal leader sequences of prepilin, also catalyzes N-methylation of the amino-terminal phenylalanine of the mature pilin, using S-adenosyl-L-methionine as a methyl donor. Thus, to our knowledge, PilD is the first characterized bacterial N-methyltransferase. Complete inhibition of N-methylation, but not peptide cleavage, by structural analogues of S-adenosyl-L-methionine suggests that PilD is a bifunctional enzyme with proteolytic and methylation activities carried out within two distinct active sites.

The work considers the highly anisotropic electron distribution functions observed by Bell and co-workers at Stanford in the magnetosphere. IOt is maintained that Bells' observations provide evidence for the existence of step like deformations in electron distribution function, and that his observations may be due to such steps. The origin of such steps at the top of hiss band emissions is explained, and the implications for triggering of emissions and chorus is explained.

[1] Chorus emissions are generated by a nonlinear mechanism involving wave‐particle interactions with energetic electrons. Discrete chorus wave packets are narrowband tones usually rising (sometimes falling) in frequency. We investigate frequency sweep rates of chorus wave packets measured by the Wideband data (WBD) instrument onboard the Cluster spacecraft. In particular, we study the relationship between the sweep rates and the plasma density measured by the WHISPER active sounder. We have observed increasing values of the sweep rate for decreasing plasma densities. We have compared our results with results of simulations of triggered emissions as well as with estimates based on the backward wave oscillator model for chorus emissions. We demonstrate a reasonable agreement of our experimental results with theoretical ones. Citation: Macusova, E., et al. (2010), Observations of the relationship between frequency sweep rates of chorus wave packets and plasma density

The current Verenium cellulosic ethanol process is based on the dilute-acid pretreatment of a biomass feedstock, followed by a two-stage fermentation of the pentose sugar-containing hydrolysate by a genetically modified ethanologenic Escherichia coli strain and a separate simultaneous saccharification-fermentation (SSF) of the cellulosic fraction by a genetically modified ethanologenic Klebsiella oxytoca strain and a fungal enzyme cocktail. In order to reduce unit operations and produce a fermentation beer with higher ethanol concentrations to reduce distillation costs, we have proposed to develop a simultaneous saccharification co-fermentation (SScF) process, where the fermentation of the pentose-containing hydrolysate and cellulosic fraction occurs within the same fermentation vessel. In order to accomplish this goal, improvements in the ethanologens must be made to address a number of issues that arise, including improved hydrolysate tolerance, co-fermentation of the pentose and hexose sugars and increased ethanol tolerance. Using a variety of approaches, including transcriptomics, strain adaptation, metagenomics and directed evolution, this work describes the efforts of a team of scientists from Verenium, University of Florida, Massachusetts Institute of Technology and Genomatica to improve the E. coli and K. oxytoca ethanologens to meet these requirements.

We review theoretical and numerical studies of VLF triggered emissions generated by manmade signals propagating in the whistler mode in the magnetosphere. Instead of listing all the past studies on the subject we select some of those works which give important ideas and the theoretical basis for future studies. The main purpose of the paper is to clarify what problems remain unresolved and to make suggestions for future studies. We first describe the phenomenon of VLF triggered emissions and give a brief review of experiments and observations. We then summarize the basic physics of VLF wave-particle interactions, which is indispensable for an understanding of the triggering mechanisms. We review important ideas and theories, as well as numerical models so far employed, summarize the present understanding of the phenomenon and consider briefly those problems which need further study. Especially, we focus our attention on numerical simulations whose capabilities in nonlinear physics are increasing with the increasing power of supercomputers.

The interaction of Pseudomonas aeruginosa with a human lung pneumocyte cell line (A549) was studied. Wild-type strain PAK adhered efficiently to the A549 cells, while an isogenic mutant, carrying a mutation in the pilin structural gene, adhered at 10 to 20% of the wild-type levels. Another nonpiliated mutant of P. aeruginosa PAK, defective in the pleiotropic regulatory gene rpoN, did not adhere to A549 cells, suggesting the presence of a second, RpoN-controlled adhesin on the bacterial surface. Endocytosis of wild-type P. aeruginosa PAK by A549 cells was also demonstrated. A significant fraction of the internalized bacteria were recovered in a viable form after several hours of residence within the A549 cells. When examined by electron microscopy, intracellular bacteria were located in membranous vesicles, and no evidence of killing by lysosomal mechanisms was observed. These studies raise the possibility that during chronic respiratory tract infections in immunocompromised patients, P. aeruginosa may persist in intracellular compartments and therefore be protected from the defense mechanisms of the host.

The polar pili of Pseudomonas aeruginosa are composed of monomers of the pilin structural subunits. The biogenesis of pili involves the synthesis of pilin precursor, cleavage of a six-amino-acid leader peptide, membrane translocation, and assembly of monomers into a filamentous structure extending from the bacterial surface. This report describes three novel genes necessary for the formation of pili. DNA sequences adjacent to pilA, the pilin structural gene, were cloned and mutagenized with transposon Tn5. Each of the insertions were introduced into the chromosome of P. aeruginosa PAK by gene replacement. The effect of the Tn5 insertions in the bacterial chromosome on pilus assembly was assessed by electron microscopy and sensitivity of mutants to a pilus-specific bacteriophage. The resultant mutants were also tested for synthesis and membrane localization of the pilin antigen in order to define the genes required for maturation, export, and assembly of pilin. A 4.0-kilobase-pair region of DNA adjacent to the pilin structural gene was found to be essential for formation of pili. This region was sequenced and found to contain three open reading frames coding for 62-, 38- to 45-, and 28- to 32-kilodalton proteins (pilB, pilC, and pilD, respectively). Three proteins of similar molecular weight were expressed in Escherichia coli from the 4.0-kilobase-pair fragment flanking pilA with use of a T7 promoter-polymerase expression system. The results of the analyses of the three genes and the implications for pilin assembly and maturation are discussed.

SUMMARY: Methylobacterium extorquens AM1 contains a novel c-type cytochrome, called cytochrome c-553, previously thought to be a precursor of the electron acceptor (cytochrome c L) for methanol dehydrogenase. Its amino acid composition and serological characteristics show that it has no structural relationship to cytochrome c L. It usually comprises less than 5% of the total c-type cytochromes. In a moxD mutant, which contains neither methanol dehydrogenase nor cytochrome c L, it comprises 30% of the soluble cytochrome and it has been purified and characterized from that mutant. Cytochrome c-553 is large (M r 23000), acidic and monohaem, with a redox potential of 194 mV. It reacts rapidly and completely with CO but is not autoxidizable. It is not autoreducible, and it is not an electron acceptor from methanol dehydrogenase or methylamine dehydrogenase, nor an important electron donor to the oxidase. It is able to accept electrons from cytochrome c L and to donate electrons to cytochrome c H. It is present in the soluble fraction (presumably periplasmic) and membrane fraction of wild-type bacteria during growth on a wide range of growth substrates, but its function in these bacteria or in the moxD mutant has not been determined.

[1] In this study we report on ground-based observations of short bursts of relativistic electron precipitation (REP), detected by a subionospheric propagation sensor in Sodankyla, Finland during 2005. In two ∼4 hour case study periods from L = 5.2, around local midnight, several hundred short-lived radio wave perturbations were observed, covering a wide range of arrival azimuths. The vast majority (∼99%) of these perturbations were not simultaneous with perturbations on other paths, consistent with a precipitation “rainstorm” producing ionospheric changes of small spatial sizes around the Sodankyla receiver. The recovery time of these radio wave perturbations are ∼1.2 s, which is consistent with the modeled effects of a burst of >2 MeV precipitating electrons. This agrees with satellite observations of the microburst energy spectrum. The energetic nature of the precipitation which produces the FAST perturbations suggests that they should be observable in both day and night conditions. While it is widely assumed that satellite-detected REP microbursts are due to wave-particle interactions with very low-frequency chorus waves, the energy spectra predicted by our current models of chorus propagation and wave-particle interaction are not consistent with the experimentally observed radio wave perturbations presented here or previously reported satellite observations of REP microbursts. The results inferred from both the satellite and subionospheric observations, namely the absence of a large, dominant component of

[1] The dependence of the frequency spectrum of individual chorus elements on the position of the observation point in and near the generation region is analyzed using recent Cluster data obtained on two different geomagnetically active days. The source of night-side chorus is localized using multicomponent measurements of the wave electric and magnetic fields. We have revealed that the spectrum of the chorus elements lacks the lower frequencies at the center of the source region. One possible explanation of this effect is provided by applying the backward wave oscillator model of chorus generation to these data. According to this model, the chorus frequency is determined by the parallel velocity corresponding to a steplike deformation in the distribution function of resonant electrons. This velocity decreases during the generation of an element as the electrons move through the source region. Thus, only a part of a chorus element is visible inside this region. For the typical case of rising-tone chorus elements, the lower frequencies are generated downstream with respect to the chorus propagation and, hence, disappear as a receiver is moved upstream towards the center of the source region. Citation: Trakhtengerts, V. Y., A. G. Demekhov, E. E. Titova, B. V. Kozelov, O. Santolik, E. Macusova, D. Gurnett, J. S. Pickett, M. J. Rycroft, and D. Nunn (2007), Formation of VLF chorus frequency spectrum: Cluster data and comparison with the backward wave oscillator model, Geophys. Res. Lett., 34, L02104, doi:10.1029/2006GL027953.

In this study we examine energetic electron precipitation fluxes driven by lightning, in order to determine the global distribution of energy deposited into the middle atmosphere. Previous studies using lightning-driven precipitation burst rates have estimated losses from the inner radiation belts. In order to confirm the reliability of those rates and the validity of the conclusions drawn from those studies, we have analyzed New Zealand data to test our global understanding of troposphere to magnetosphere coupling. We examine about 10000h of AbsPAL recordings made from 17 April 2003 through to 26 June 2004, and analyze subionospheric very-low frequency (VLF) perturbations observed on transmissions from VLF transmitters in Hawaii (NPM) and western Australia (NWC). These observations are compared with those previously reported from the Antarctic Peninsula. The perturbation rates observed in the New Zealand data are consistent with those predicted from the global distribution of the lightning sources, once the different experimental configurations are taken into account. Using lightning current distributions rather than VLF perturbation observations we revise previous estimates of typical precipitation bursts at L~2.3 to a mean precipitation energy flux of ~1×10-3 ergs cm-2s-1. The precipitation of energetic electrons by these bursts in the range L=1.9-3.5 will lead to a mean rate of energy deposited into the atmosphere of 3×10-4 ergs cm-2min-1, spatially varying from a low of zero above some ocean regions to highs of ~3-6×10-3 ergs cm-2min-1 above North America and its conjugate region.

In this study we consider the dependence of precipitation fluxes arising from whistler-induced radiation belt losses on the strength of the associated lightning's return stroke current. As a result of this work, it will be possible to use lightning activity data sets to estimate globally induced precipitation flux rates and thus determine the lightning-induced effect on the radiation belts more accurately. Four study days were selected, during which a high proportion of the lightning activity occurring near the east coast of North America produced observable Trimpi effects on VLF transmitter signals propagating in the region of the Antarctic Peninsula (similar toL = 2-2.5). The lack of lightning in Antarctica gives this location a unique advantage for this study. The functional dependence of the relative scattered field amplitude with the return stroke peak current of the lightning discharge suggests that during these events diffusion conditions are occurring near the precipitating radiation belt particles loss cone due to strong whistler wave fields, probably caused by ducted signals. The range of observed Trimpi scatter amplitude of -10 to -35 dB was produced by precipitation bursts with energy fluxes estimated to range over 6.5-0.4 x 10(-3) ergs cm(-2) s(-1). The largest fluxes were found to be driven by lightning currents of about 250 kA, while the smallest detectable fluxes relate to lightning currents of 70 kA. Although 3 of the 4 study days showed a high degree of consistency between the levels of lightning return stroke peak current required to produce any given perturbation scatter amplitude value, conditions were significantly different on 23 April 1994. On this day, observed Trimpi signatures were 6-7 dB greater for any given lightning intensity than on the other study days. These events are consistent with a significantly harder radiation belt precipitation spectra, probably caused by geomagnetic storm-time acceleration processes of radiation belt electrons.

The material in this report summarizes the Diversa technical effort in development of a biocatalyst for the biodesulfurization of Petro Star diesel as well as an economic report of standalone and combined desulfurization options, prepared by Pelorus and Anvil, to support and inform the development of a commercially viable process. We will discuss goals of the projected as originally stated and their modification as guided by parallel efforts to evaluate commercialization economics and process parameters. We describe efforts to identify novel genes and hosts for the generation of an optimal biocatalyst, analysis of diesel fuels (untreated, chemically oxidized and hydrotreated) for organosulfur compound composition and directed evolution of enzymes central to the biodesulfurization pathway to optimize properties important for their use in a biocatalyst. Finally we will summarize the challenges and issues that are central to successful development of a viable biodesulfurization process.

A number of increasingly sophisticated and realistic models have been developed in order to investigate the interaction between sub-ionospherically propagating VLF waves and regions of enhanced electron density in the D-region caused by lightning induced electron precipitation (LIEs). These LIEs can result in phase and amplitude perturbations on received VLF signals that are referred to as Trimpis. It is important, for comparison with experimentally observed Trimpi effects, that the spatial extent of the D-region electron density perturbation is modeled accurately. Here, it is argued that most previous modeling has used patch sizes that are typically up to 100 km in both latitudinal and longitudinal extent, which are generally smaller than those that actually occur for real lightning induced electron precipitation events. It would also appear that maximum ?Ne values assumed have often been too large and patches have been incorrectly modeled as circular rather than elliptical in horizontal extent. Consequently, in the present work, Trimpi perturbations are determined for LIEs with smaller maximum ?Ne, larger spatial extent and elliptical shape. Calculations of VLF Trimpis have been made as a function of the horizontal coordinates of the LIE centre, over the whole rectangular corridor linking transmitter and receiver. The Trimpi modelling program is fully 3D, and takes account of modal mixing at the LIE. The underlying theory assumes weak Born scattering, but the code calculates a non-Born skin depth attenuation function for the LIE in question. The LIE is modelled as an electron density enhancement with a Gaussian profile in all coordinates. Results for a large elliptical LIE ~ 200 x 600 kms show that significant Trimpis, ~-0.4dB in amplitude and ~+4 degrees in phase are predicted, using modest maximum ?Ne values ~ 1.5 el/cc. Such an electron density enhancement is well within the range that would be expected to result from experimentally observed fluxes of electron precipitation following wave particle interactions with whistler-mode waves. This shows the continued viability of the original explanation of whistler-induced electron precipitation as the mechanism for the “Classical Trimpi”.

Protein export by Gram-negative bacteria requires devoted machineries to allow for the passage of hydrolytic enzymes and toxins through the cell envelope. The Type II export machinery has a number of distinct characteristics, which include its role as an extension of Sec-dependent secretion, its ability to recognize and export fully folded substrates efficiently and, perhaps most significantly, the relationship between a subset of its gene products with the Type IV pilus-biogenesis apparatus. An important question is whether we can extrapolate our knowledge, albeit limited, of Type IV pilus biogenesis to understand the structure and function of the Type II export apparatus. This and other questions relating to the energetics of assembly and specificity of the apparatus are addressed in this article.