Langmuir probe study of an inductively coupled magnetic-pole-enhanced helium plasma

This study reports the effects of RF power and filling gas pressure variation on the plasma parameters, including the electron number density n _e , electron temperature T _e , plasma potential V _p , skin depth δ, and electron energy probability functions (EEPFs) in a low-pressure inductively coupled helium plasma source with magnetic pole enhancement. An RF compensated Langmuir probe is used to measure these plasma parameters. It is observed that the electron number density increases with both the RF power and the filling gas pressure. Conversely, the electron temperature decreases with increasing RF power and gas pressure. It is also noted that, at low RF powers and gas pressures, the EEPFs are non-Maxwellian, while at RF powers of ≥50 W, they evolve into a Maxwellian distribution. The dependences of the skin depth and plasma potential on the RF power are also studied and show a decreasing trend.     

Natively oxidized amino acid residues in the spinach cytochrome <Emphasis Type="Italic">b</Emphasis><Subscript><Emphasis Type="Italic">6</Emphasis></Subscript><Emphasis Type="Italic">f</Emphasis> complex

The cytochrome b ₆ f complex of oxygenic photosynthesis produces substantial levels of reactive oxygen species (ROS). It has been observed that the ROS production rate by b ₆ f is 10–20 fold higher than that observed for the analogous respiratory cytochrome bc₁ complex. The types of ROS produced (O₂^{??, 1}O₂, and, possibly, H₂O₂) and the site(s) of ROS production within the b ₆ f complex have been the subject of some debate. Proposed sources of ROS have included the heme b _p , PQ _p ^?? (possible sources for O₂^??), the Rieske iron–sulfur cluster (possible source of O₂^?? and/or ¹O₂), Chl a (possible source of ¹O₂), and heme c _n (possible source of O₂^?? and/or H₂O₂). Our working hypothesis is that amino acid residues proximal to the ROS production sites will be more susceptible to oxidative modification than distant residues. In the current study, we have identified natively oxidized amino acid residues in the subunits of the spinach cytochrome b ₆ f complex. The oxidized residues were identified by tandem mass spectrometry using the MassMatrix Program. Our results indicate that numerous residues, principally localized near p-side cofactors and Chl a, were oxidatively modified. We hypothesize that these sites are sources for ROS generation in the spinach cytochrome b ₆ f complex.     

The potential for non-adaptive origins of evolutionary innovations in central carbon metabolism

Background

Biological systems are rife with examples of pre-adaptations or exaptations. They range from the molecular scale – lens crystallins, which originated from metabolic enzymes – to the macroscopic scale, such as feathers used in flying, which originally served thermal insulation or waterproofing. An important class of exaptations are novel and useful traits with non-adaptive origins. Whether such origins could be frequent cannot be answered with individual examples, because it is a question about a biological system’s potential for exaptation.We here take a step towards answering this question by analyzing central carbon metabolism, and novel traits that allow an organism to survive on novel sources of carbon and energy. We have previously applied flux balance analysis to this system and predicted the viability of 10¹⁵ metabolic genotypes on each of ten different carbon sources.

Results

We here use this exhaustive genotype-phenotype map to ask whether a central carbon metabolism that is viable on a given, focal carbon source C – the equivalent of an adaptation in our framework – is usually or rarely viable on one or more other carbon sources C _new – a potential exaptation. We show that most metabolic genotypes harbor potential exaptations, that is, they are viable on one or more carbon sources C _new . The nature and number of these carbon sources depends on the focal carbon source C itself, and on the biochemical similarity between C and C _new . Moreover, metabolisms that show a higher biomass yield on C, and that are more complex, i.e., they harbor more metabolic reactions, are viable on a greater number of carbon sources C _new .

Conclusions

A high potential for exaptation results from correlations between the phenotypes of different genotypes, and such correlations are frequent in central carbon metabolism. If they are similarly abundant in other metabolic or biological systems, innovations may frequently have non-adaptive (“exaptive”) origins.

     

Characteristics of a transverse RF discharge in Xe/Cl<Subscript>2</Subscript> mixtures

Results are presented from the study of the electrical and optical characteristics of a transverse RF discharge in Xe/Cl₂ mixtures at pressures of p≤400 Pa. The working mixture was excited by a modulated RF discharge (f=1.76 MHz) with a transverse electrode configuration (L≤17 cm). The emission spectrum in the spectral range of 210–600 nm and the waveforms of the discharge current, discharge voltage, and plasma emission intensity were investigated. The UV emission power from the discharge was studied as a function of the pressure and composition of a Xe/Cl₂ mixture. It is shown that a discharge in a xenon-chlorine mixture acts as planar excimer-halogen lamp operating in the spectral range of 220–450 nm, which contains a system of overlapping XeCl(D, B-X; B, C-A) and Cl₂(D′-A′) bands. Transverse RF discharges in Xe/Cl₂ mixtures can be used to create a wideband lamp with two 50-cm² planar apertures and the low circulation rate of the working mixture.     

Transition into the improved core confinement mode as a possible mechanism for additional electron heating observed in the lower hybrid current drive experiments at the FT-2 tokamak

In experiments on lower hybrid current drive (LHCD) carried out at the FT-2 tokamak, a substantial increase in the central electron temperature T _e (r = 0 cm) from 550 to 700 eV was observed. A complex simulation procedure is used to explain a fairly high LHCD efficiency and the observed additional heating, which can be attributed to a transition into the improved core confinement (ICC) mode. For numerical simulations, data obtained in experiments with deuterium plasma at 〈n _e 〉 = 1.6 × 10¹⁹ m^–3 were used. Simulations by the GRILL3D, FRTC, and ASTRA codes have shown that the increase in the density and central temperature is apparently caused by a significant suppression of heat transport in the electron component. The mechanism for transition into the improved confinement mode at r < 3 cm can be associated with the broadening of the plasma current channel due to the lower hybrid drive of the current carried by superthermal and runaway electrons. In this case, the magnetic shear s = (r/q)(dq/dr) in the axial region of the plasma column almost vanishes during the RF pulse. In this study, the effect of lower hybrid waves on the plasma parameters, resulting in a transition into the ICC mode, is considered. New experimental and calculated data are presented that evidence in favor of such a transition. Special attention is paid to the existence of a threshold for the transition into the ICC mode in deuterium plasma.     

Physical Parameters of a Reactor-Stellarator with Small Ripples of the Helical Magnetic Field

The paper describes the calculation data on the physical parameters of a reactor-stellarator, where the nonuniformities of the helical field are smaller than the toroidal magnetic field nonuniformities: ε_h < ε_t. Unlike the previous studies, where the ion-component transport coefficients had the collision frequency dependence proportional to ν^1/2, this being equivalent to the ε_h > ε_t case, in the present calculations, these coefficients were assumed to be in proportion to the first power of the collision frequency, D_i ∝ ν for ν_eff < 2ω_E, and to D_i ∝ ν^?1 for the inverse inequality. Here, ω_E is the rotation frequency of plasma in the radial electric field. As before, the plasma electrons corresponded to the mode of D_e ∝ ν^?1. As initial parameters for numerical calculations, a reactor with R = 8 m, r_p = 2 m, and B₀ = 5 Т was taken. A numerical code was used to solve the set of equations that describes the plasma space?time behavior in the reactor-stellarator under the conditions of equal diffusion fluxes. The start of reactor operation in the mode of thermonuclear burning was provided by heating sources with a power of several tens of megawatts. Steady-state operating conditions of a self-sustained thermonuclear reaction were attained by maintaining the plasma density through DT fuel pellet injection into the plasma.     

A Planar Source of Atmospheric-Pressure Plasma Jet

In a single-barrier discharge with voltage sharpening and low gas consumption (up to 1 L/min), plane atmospheric pressure plasma jets with a width of up to 3 cm and length of up to 4 cm in air are formed in the slit geometry of the discharge zone. The energy, temperature, and spectral characteristics of the obtained jets have been measured. The radiation spectrum contains intense maxima corresponding to vibrational transitions of the second positive system of molecular nitrogen N₂ (C³Π _u → B³Π _g ) and comparatively weak transition lines of the first positive system of the N ₂ ⁺ ion (B²Σ _u ⁺ → X²Σ _g ). By an example of inactivation of the Staphylococcus aureus culture (strain ATCC 209), it is shown that plasma is a source of chemically active particles providing the inactivation of microorganisms.     

Microwave electrode discharge in nitrogen: Structure and characteristics of the electrode region

The parameters of the electrode region of an electrode microwave discharge in nitrogen are studied by emission spectroscopy. The radial and axial distributions of the intensities of the bands of the second (N₂(C ³Π _u → B ³Π _g )) and first (N₂(B ³Π _g → A ³Σ _u ⁺ )) positive systems of molecular nitrogen and the first negative system of nitrogen ions (N ₂ ⁺ (B ²Σ _u ⁺ → X ²Σ _g ⁺ )), the radial profiles of the electric field E and the electron density N _e , and the absolute populations of the vibrational levels v _C = 0–4 of the C ³Π _u excited state of N₂ and the vibrational level v _Bi = 0 of the B ²Σ _u ⁺ excited state of a molecular nitrogen ion are determined. The population temperature of the first vibrational level T _V of the ground electronic state X ¹Σ _g ⁺ of N₂ and the excitation temperature T _C of the C ³Π _u state in the electrode region of the discharge are measured. The radius of the spherical region and the spatially integrated plasma emission spectra are studied as functions of the incident microwave power and gas pressure. A method for determining the electron density and the microwave field strength from the plasma emission characteristics is described in detail.     

Interaction of near-IR laser radiation with plasma of a continuous optical discharge

The interaction of 1.07-μm laser radiation with plasma of a continuous optical discharge (COD) in xenon and argon at a pressure of p = 3–25 bar and temperature of T = 15 kK has been studied. The threshold power required to sustain COD is found to decrease with increasing gas pressure to P _t < 30 W in xenon at p > 20 bar and to P _t < 350 W in argon at p > 15 bar. This effect is explained by an increase in the coefficient of laser radiation absorption to 20?25 cm^–1 in Xe and 1?2 cm^–1 in Ar due to electronic transitions between the broadened excited atomic levels. The COD characteristics also depend on the laser beam refraction in plasma. This effect can be partially compensated by a tighter focusing of the laser beam. COD is applied as a broadband light source with a high spectral brightness.     

Characterization of extracellular yeast peptide factors and their stress-protective effect on probiotic lactic acid bacteria

Protective effect of the extracellular peptide fraction (reactivating factors, RF) produced by yeasts of various taxonomic groups (Saccharomyces cerevisiae, Kluyveromyces lactis, Candida utilis, and Yarrowia lipolytica) on probiotic lactic acid bacteria (LAB) Lactobacillus casei, L. acidophilus, and L. reuteri under bile salt (BS)-induced stress was shown. RF of all yeasts were shown to be of peptide nature; the active component of the S. cerevisiae RF was identified as a combination of low-molecular polypeptides with molecular masses of 0.6 to 1.5 kDa. The protective and reactivating effects of the yeast factors were not species-specific and were similar to those of the Luteococcus japonicus subsp. casei RF. In BS-treated cells of the tester bacteria, a protective effect was observed after 10-min preincubation of the LAB cell suspension with yeast RF: the number of surviving cells (CFU) was 2 to 4.5 times higher than in the control. The reactivating effect was observed when RF was added to LAB cell suspensions not later than 15 min after stress treatment. It was less pronounced than the protector effect, with the CFU number 1 to 3 times that of the control. Both the protector and the reactivating effects were most pronounced in the S. cerevisiae and decreased in the row C. utilis > K. lactis > Y. lipolytica. The efficiency of protective action of yeast RF was found to depend on the properties of recipient LAB cells, with the L. casei strain being most sensitive to BS treatment. In both variants, the highest protective effect of RF (increase in the CFU number) was observed for L. acidophilus, while the least pronounced one was observed for L. casei. The reasons for application of the LAB strains combining high stress resistance and high response to stress-protecting metabolites, including RF factors, as probiotics, is discussed.     

Cyanobacteria consumption by cladocerans: a case study on facilitation

Eutrophic systems are stressful for zooplankton species, especially for small organisms (<?1000 μm) that are inefficient in consuming large colonies or filaments of cyanobacteria. Certain mechanisms, however, enable organisms to coexist in spite of the stress related to poor food quality or manageability of the diet. The present work suggests that coprophagy is recurrent behavior in cladocerans that may facilitate the survival and growth of some species in eutrophic systems. We chose three clones of Moina macrocopa that inhabit eutrophic systems. The species selected as possible facilitators were the cladocerans Simocephalus vetulus and Daphnia similis, and the ostracod Heterocypris incongruens, because they are cosmopolitan, have high rates of cyanobacterial filtration and in some cases coexist with Moina. The design used for the demographic experiments of the three clones of M. macrocopa was based on the source of nutrition and consisted of a control diet of Scenedesmus acutus (1?×?10⁶ cells ml), a diet of undigested cyanobacteria (10?×?10⁶ cells ml), and this same diet after digestion by D. similis, S. vetulus or H. incongruens. The excreta of the cladocerans was a deficient diet for Moina, whose populations decreased by more than 1 individual per day. On the contrary, fecal pellets of the ostracod were a diet that allowed Moina to have positive population growth (0.3 day^?1). Our results help to explain the high densities achieved by cladocerans in eutrophic tropical water bodies where cyanobacterial blooms are normal.     

Water sources and water-use efficiency of desert plants in different habitats in Dunhuang,NW China

To understand habitat associated differences in desert plant water-use patterns, water stable oxygen isotope composition was used to determine water source and leaf carbon isotope composition (δ ¹³C) was used to estimate long-term water-use efficiency in three typical habitats (saline land, sandy land and Gobi) in Dunhuang. The primary findings are: (1) in the three habitats, plant species used mainly deep soil water (>120 cm), except for Kalidium foliatum in the saline land, which relied primarily on 0–40 cm soil water; (2) in the saline land and Gobi habitat, Alhagi sparsifolia had the most negative foliar δ ¹³C; in the sandy land, Elaeagnus angustifolia leaf was enriched in ¹³C than the other three species in 2011, but no species differences in foliar δ ¹³C was observed among the four species in 2012; (3) common species (Tamarix ramosissima and A. sparsifolia) may alter their water sources to cope with habitat differences associated changes in soil water availability with deeper water sources were used in the Gobi habitat with lower soil water content (SWC) compared to in the saline land and sandy land; (4) we detected significant habitat differences in foliar δ ¹³C in A. sparsifolia which may have resulted from differences in SWC and soil electrical conductivity. However, no habitat differences in foliar δ ¹³C were observed in T. ramosissima, which may attribute to the strong genetic control in T. ramosissima or the ability to access stable deep soil water. Overall, the results suggest that extremely arid climate, root distribution and soil properties worked together to determine plant water uptake in Dunhuang area.     

Exocyst Complex Member EXOC5 Is Required for Survival of Hair Cells and Spiral Ganglion Neurons and Maintenance of Hearing

The exocyst, an octameric protein complex consisting of Exoc1 through Exoc8, was first determined to regulate exocytosis by targeting vesicles to the plasma membrane in yeast to mice. In addition to this fundamental role, the exocyst complex has been implicated in other cellular processes. In this study, we investigated the role of the exocyst in cochlear development and hearing by targeting EXOC5, a central exocyst component. Deleting Exoc5 in the otic epithelium with widely used Cre lines resulted in early lethality. Thus, we generated two different inner ear-specific Exoc5 knockout models by crossing Gfi1^Cre mice with Exoc5^f/f mice for hair cell-specific deletion (Gfi1^Cre/+;Exoc5^f/f) and by in utero delivery of rAAV-iCre into the otocyst of embryonic day 12.5 for deletion throughout the otic epithelium (rAAV2/1-iCre;Exoc5^f/f). Gfi1^Cre/+;Exoc5^f/f mice showed relatively normal hair cell morphology until postnatal day 20, after which hair cells underwent apoptosis accompanied by disorganization of stereociliary bundles, resulting in progressive hearing loss. rAAV2/1-iCre;Exoc5^f/f mice exhibited abnormal neurite morphology, followed by apoptotic degeneration of spiral ganglion neurons (SGNs) and hair cells, which led to profound and early-onset hearing loss. These results demonstrate that Exoc5 is essential for the normal development and survival of cochlear hair cells and SGNs, as well as the functional maintenance of hearing.     

Genetic redundancy in the catabolism of methylated amines in the yeast <Emphasis Type="Italic">Scheffersomyces stipitis</Emphasis>

The catabolism of choline as a source of nitrogen in budding yeasts is thought to proceed via the intermediates trimethylamine, dimethylamine and methylamine before the release of ammonia. The present study investigated the utilisation of choline and its downstream intermediates as nitrogen sources in the yeast Scheffersomyces stipitis using a reverse genetics approach. Six genes (AMO1, AMO2, SFA1, FGH1, PICST_49761, PICST_63000) that have previously been predicted to be directly or indirectly involved in the catabolism of methylated amines were individually deleted. The growth of each deletion mutant was assayed on minimal media with methylamine, dimethylamine, trimethylamine or choline as the sole nitrogen source. The two amine oxidase-encoding genes AMO1 and AMO2 appeared to be functionally redundant for growth on methylated amines as both deletion mutants displayed growth on all nitrogen sources tested. However, deletion of AMO1 resulted in a pronounced growth lag on all four methylated amines while deletion of AMO2 only caused a growth lag when methylamine was the sole nitrogen source. The glutathione-dependent formaldehyde dehydrogenase-encoding gene SFA1 was found to be absolutely essential for growth on all methylated amines tested while deletion of the S-formylglutathione hydrolase gene FGH1 caused a pronounced growth lag on dimethylamine, trimethylamine and choline. The putative cytochrome P450 monooxygenase-encoding genes PICST_49761 and PICST_63000 were considered likely candidates for demethylation of di- and trimethylamine but produced no discernable phenotype on any of the tested nitrogen sources when deleted. This study revealed notable instances of genetic redundancies in the choline catabolic pathway, which are discussed.     

Anomalous pinch in the T-11M tokamak in an enhanced-collisionality regime

The formation of a peaked bell-shaped profile of the electron density n _e (r) in the T-11M tokamak (B _t=1 T, R/a = 0.7/0.2 m, I _p = 100 kA, t _shot ≤ 300 ms, Li and C limiters) was observed in Li experiments carried out in the near-plateau collisionality regime (the collisionality parameter at one-half of the minor radius was v* ≥ 0.5) under the conditions of low hydrogen recycling and intense hydrogen influx from the plasma edge. It is well known that peaked n _e (r) profiles are observed in collisionless regimes at v* values as low as 10^?1–10^?2 or in impurity-contaminated discharges, in which this effect can be attributed to the impurity accumulation on the plasma column axis. Moreover, a bell-shaped n _e (r) profile in discharges with low n _e can result from the ionization of hydrogen atoms at the column axis, where they arrive from the plasma edge due to cascade charge-exchange. In quasi-steady lithium discharges in T-11M, however, peaked n _e (r) profiles were observed at a relatively high central electron density n _e (0) and relatively high collision frequency, such that the influence of impurities on the n _e (r) profile could be ignored (Z _eff = 1.1±0.1). To explain this effect, one has to assume that the pinching of hydrogen ions in T-11M is anomalous. The lower estimate of the observed pinch velocity is 4 ± 1 m/s, which is three to five times higher than the velocity of the neoclassical (Ware) pinch, characteristic of these conditions. The work is devoted to the experimental study of this effect.     

Plasma diagnostics from intensities of resonance line series of He-like ions

The possibility of using the relative intensities of the 1snp ¹P₁–1s ^{2 1}S0 transitions with n = 3–6 in He-like multicharged ions to diagnose plasma in a nonstationary ionization state is considered. The calculations performed for F VIII ions show that, at electron temperatures of T _e = 10–100 eV, the intensity ratios are sensitive to the plasma electron density in the range of N _e = 10¹⁶–10²⁰ cm^–3. The universal calculated dependences can be used to diagnose various kinds of recombining or ionizing plasmas containing such ions.     

Simulations of the Ion Current to a Probe in Plasma with Allowance for Ionization and Ion–Neutral Collisions: II. Cylindrical Probe

The ion current to a cylindrical probe is considered with allowance for volume ionization, ion–neutral collisions, and the ion orbital moment. A model based on the molecular dynamics method and applicable in a wide range of plasma parameters (r_p/λ_D= 0.01–100, r_i/λ_D= 0.002–200, ν_i/ω_0i= 0.01–0.05, and T_i/T_e = 0?0.01) is proposed A convenient representation of the dependence of the relative ion current density on the Langmuir coefficient β² and a technique for determining the plasma density from simulation results are offered.     

1,4-Dioxane degradation potential of members of the genera <Emphasis Type="Italic">Pseudonocardia</Emphasis> and <Emphasis Type="Italic">Rhodococcus</Emphasis>

In recent years, several strains capable of degrading 1,4-dioxane have been isolated from the genera Pseudonocardia and Rhodococcus. This study was conducted to evaluate the 1,4-dioxane degradation potential of phylogenetically diverse strains in these genera. The abilities to degrade 1,4-dioxane as a sole carbon and energy source and co-metabolically with tetrahydrofuran (THF) were evaluated for 13 Pseudonocardia and 12 Rhodococcus species. Pseudonocardia dioxanivorans JCM 13855^T, which is a 1,4-dioxane degrading bacterium also known as P. dioxanivorans CB1190, and Rhodococcus aetherivorans JCM 14343^T could degrade 1,4-dioxane as the sole carbon and energy source. In addition to these two strains, ten Pseudonocardia strains could degrade THF, but no Rhodococcus strains could degrade THF. Of the ten Pseudonocardia strains, Pseudonocardia acacia JCM 16707^T and Pseudonocardia asaccharolytica JCM 10410^T degraded 1,4-dioxane co-metabolically with THF. These results indicated that 1,4-dioxane degradation potential, including degradation for growth and by co-metabolism with THF, is possessed by selected strains of Pseudonocardia and Rhodococcus, although THF degradation potential appeared to be widely distributed in Pseudonocardia. Analysis of soluble di-iron monooxygenase (SDIMO) α-subunit genes in THF and/or 1,4-dioxane degrading strains revealed that not only THF and 1,4-dioxane monooxygenases but also propane monooxygenase-like SDIMOs can be involved in 1,4-dioxane degradation.