Analysis of bymovirus resistance genes on proximal barley chromosome 4HL provides the basis for precision breeding for BaMMV/BaYMV resistance

Key message

Unlocking allelic diversity of the bymovirus resistance gene rym11 located on proximal barley chromosome 4HL and diagnostic markers provides the basis for precision breeding for BaMMV/BaYMV resistance.

Abstract

The recessive resistance gene rym11 on barley chromosome 4HL confers broad-spectrum and complete resistance to all virulent European isolates of Barley mild mosaic virus and Barley yellow mosaic virus (BaMMV/BaYMV). As previously reported, rym11-based resistance is conferred by a series of alleles of naturally occurring deletions in the gene HvPDIL5-1, encoding a protein disulfide isomerase-like protein. Here, a novel resistance-conferring allele of rym11 is reported that, in contrast to previously identified resistance-conferring variants of the gene HvPDIL5-1, carries a single non-synonymous amino acid substitution. Allelism was confirmed by crossing to genotypes carrying previously known rym11 alleles. Crossing rym11 genotypes with a cultivar carrying the recessive resistance gene rym1, which was reported to reside on the same chromosome arm 4HL like rym11, revealed allelism of both loci. This allelic state was confirmed by re-sequencing HvPDIL5-1 in the rym1 genotype, detecting the haplotype of the rym11-d allele. Diagnostic PCR-based markers were established to differentiate all seven resistance-conferring alleles of the rym11 locus providing precise tools for marker-assisted selection (MAS) of rym11 in barley breeding.     

The effects of temperature and exercise training on swimming performance in juvenile qingbo (Spinibarbus sinensis)

To investigate the effects of temperature and exercise training on swimming performance in juvenile qingbo (Spinibarbus sinensis), we measured the following: (1) the resting oxygen consumption rate $ \left( {{\dot{\text{M}}\text{O}}_{{ 2 {\text{rest}}}} } \right) $ , critical swimming speed (U _crit) and active oxygen consumption rate $ \left( {{\dot{\text{M}}\text{O}}_{{ 2 {\text{active}}}} } \right) $ of fish at acclimation temperatures of 10, 15, 20, 25 and 30 °C and (2) the $ \dot{M}{\text{O}}_{{ 2 {\text{rest}}}} $ , U _crit and $ \dot{M}{\text{O}}_{{ 2 {\text{active}}}} $ of both exercise-trained (exhaustive chasing training for 14 days) and control fish at both low and high acclimation temperatures (15 and 25 °C). The relationship between U _crit and temperature (T) approximately followed a bell-shaped curve as temperature increased: U _crit = 8.21/{1 + [(T ? 27.2)/17.0]²} (R ² = 0.915, P < 0.001, N = 40). The optimal temperature for maximal U _crit (8.21 BL s^?1) in juvenile qingbo was 27.2 °C. Both the $ \dot{M}{\text{O}}_{{ 2 {\text{active}}}} $ and the metabolic scope (MS, $ \dot{M}{\text{O}}_{{ 2 {\text{active}}}} - \dot{M}{\text{O}}_{{ 2 {\text{rest}}}} $ ) of qingbo increased with temperature from 10 to 25 °C (P < 0.05), but there were no significant differences between fish acclimated to 25 and 30 °C. The relationships between $ \dot{M}{\text{O}}_{{ 2 {\text{active}}}} $ or MS and temperature were described as $ {\dot{\text{M}}\text{O}}_{{ 2 {\text{active}}}} = 1,214.29/\left\{ {1 + \left[ {\left( {T - 28.8} \right)/10.6} \right]^{2} } \right\}\;\left( {R^{2} = 0.911,\;P < 0.001,\;N = 40} \right) $ and MS = 972.67/{1 + [(T ? 28.0)/9.34]²} (R ² = 0.878, P < 0.001, N = 40). The optimal temperatures for $ \dot{M}{\text{O}}_{{ 2 {\text{active}}}} $ and MS in juvenile qingbo were 28.8 and 28.0 °C, respectively. Exercise training resulted in significant increases in both U _crit and $ \dot{M}{\text{O}}_{{ 2 {\text{active}}}} $ at a low temperature (P < 0.05), but training exhibited no significant effect on either U _crit or $ \dot{M}{\text{O}}_{{ 2 {\text{active}}}} $ at a high temperature. These results suggest that exercise training had different effects on swimming performance at different temperatures. These differences may be related to changes in aerobic metabolic capability, arterial oxygen delivery, available dissolved oxygen, imbalances in ion fluxes and stimuli to remodel tissues with changes in temperature.     

Genomics-based high-resolution mapping of the BaMMV/BaYMV resistance gene rym11 in barley (Hordeum vulgare L.)

Soil-borne barley yellow mosaic virus disease, caused by different strains of Barley yellow mosaic virus (BaYMV) and Barley mild mosaic virus (BaMMV), is one of the most important diseases of winter barley (Hordeum vulgare L.) in Europe and East Asia. The recessive resistance gene rym11 located in the centromeric region of chromosome 4HL is effective against all so far known strains of BaMMV and BaYMV in Germany. In order to isolate this gene, a high-resolution mapping population (10,204 meiotic events) has been constructed. F₂ plants were screened with co-dominant flanking markers and segmental recombinant inbred lines (RILs) were tested for resistance to BaMMV under growth chamber and field conditions. Tightly linked markers were developed by exploiting (1) publicly available barley EST sequences, (2) employing barley synteny to rice, Brachypodium distachyon and sorghum and (3) using next-generation sequencing data of barley. Using this approach, the genetic interval was efficiently narrowed down from the initial 10.72 % recombination to 0.074 % recombination. A marker co-segregating with rym11 was developed providing the basis for gene isolation and efficient marker-assisted selection.     

Deriving fluorometer-specific values of relative PSI fluorescence intensity from quenching of F 0 fluorescence in leaves of Arabidopsis thaliana and Zea mays

The effect of stepwise increments of red light intensities on pulse-amplitude modulated (PAM) chlorophyll (Chl) fluorescence from leaves of A. thaliana and Z. mays was investigated. Minimum and maximum fluorescence were measured before illumination (F ₀ and F _M, respectively) and at the end of each light step ( $ F^{\prime}_{0} $ and $ F^{\prime}_{\text{M}} $ , respectively). Calculated $ F^{\prime}_{0} $ values derived from F ₀, F _M and $ F^{\prime}_{\text{M}} $ fluorescence according to Oxborough and Baker (1997) were lower than the corresponding measured $ F^{\prime}_{0} $ values. Based on the concept that calculated $ F^{\prime}_{0} $ values are under-estimated because the underlying theory ignores PSI fluorescence, a method was devised to gain relative PSI fluorescence intensities from differences between calculated and measured $ F^{\prime}_{0} $ . This method yields fluorometer-specific PSI data as its input data (F ₀, F _M, $ F^{\prime}_{0} $ and $ F^{\prime}_{\text{M}} $ ) depend solely on the spectral properties of the fluorometer used. Under the present conditions, the PSI contribution to F ₀ fluorescence was 0.24 in A. thaliana and it was independent on the light acclimation status; the corresponding value was 0.50 in Z. mays. Correction for PSI fluorescence affected Z. mays most: the linear relationship between PSI and PSII photochemical yields was clearly shifted toward the one-to-one proportionality line and maximum electron transport was increased by 50 %. Further, correction for PSI fluorescence increased the PSII reaction center-specific parameter, 1/F ₀ ? 1/F _M, up to 50 % in A. thaliana and up to 400 % in Z. mays.     

Heritability for resistance to Puccinia psidii Winter rust in Eucalyptus grandis Hill ex Maiden in Southwestern Brazil

The climates of the central and southern regions of São Paulo state in Brazil favor pathogens such as Puccinia psidii Winter, which causes a common and severe disease in Eucalyptus plantations under 2 years old. We studied genetic parameters including genotype by environment interaction (G × E) of resistance to P. psidii rust in Eucalyptus grandis at nine sites in São Paulo State. Open-pollinated progeny from ten ‘provenances’ were established in a randomized complete block design; at individual sites there were from 134 to 160 progenies, from four to eight blocks, and five to six trees per plot. Significant provenance and progeny(provenance) differences were detected, as was G × E involving progeny(provenance). However, the G × E involved little if any rank changes, indicating that selection can be done efficiently at a single site, if the disease level is sufficient. The estimated coefficient of genetic variation among the progeny within provenances $ \left( {{{{\widehat{\mathrm{CV}}}}_{\mathrm{g}}}} \right) $ was high and variable among the sites (ranging from 11 % to 36.7 %), demonstrating different expression of genetic variability among the sites. The estimated heritability at the individual-tree level $ \left( {{{\widehat{h}}^2}} \right) $ and within a plot $ \left( {\widehat{h}_{\mathrm{w}}^2} \right) $ ranged from low to intermediate (ranging from 0.04 to 0.46) and was high at the progeny-mean level $ \left( {\widehat{h}_{\mathrm{f}}^2} \right) $ (ranging from 0.30 to 0.86). Our study shows good prospects of controlling this disease by selection among and within progenies in a single site.     

Stress fermentation strategies for the production of hyperthermostable superoxide dismutase from Thermus thermophilus HB27: effects of ions

In this study, we explored how ammonium and metal ion stresses affected the production of recombinant hyperthermostable manganese superoxide dismutase (Mn-SOD). To improve Mn-SOD production, fed-batch culture in shake flasks and bioreactor fermentation were undertaken to examine the effects of $ {\text{NH}}_{ 4}^{{^{ + } }} $ and Mn²⁺ feeding. Under the optimized feeding time and concentrations of $ {\text{NH}}_{ 4}^{{^{ + } }} $ and Mn²⁺, the maximal SOD activity obtained from bioreactor fermentation reached some 480 U/ml, over 4 times higher than that in batch cultivation (113 U/ml), indicating a major enhancement of the concentration of Mn-SOD in the scale-up of hyperthermostable Mn-SOD production. In contrast, when the fed-batch culture with appropriate $ {\text{NH}}_{ 4}^{{^{ + } }} $ and Mn²⁺ feeding was carried out in the same 5-L stirred tank bioreactor, a maximal SOD concentration of some 450 U/ml was obtained, again indicating substantial increase in SOD activity as a result of $ {\text{NH}}_{ 4}^{{^{ + } }} $ and Mn²⁺ feeding. The isoelectric point (pI) of the sample was found to be 6.2. It was highly stable at 90 °C and circular dichroism measurements indicated a high α-helical content of 70 % as well, consistent with known SOD properties. This study indicates that $ {\text{NH}}_{ 4}^{{^{ + } }} $ and Mn²⁺ play important roles in Mn-SOD expression. Stress fermentation strategies established in this study are useful for large-scale efficient production of hyperthermostable Mn-SOD and may also be valuable for the scale-up of other extremozymes.     

Synchronicity of movement paths of barren-ground caribou and tundra wolves

Movement patterns of highly mobile animals can reveal life history strategies and ecological relationships. We hypothesized that wolves (Canis lupus) would display similar movement patterns as their prey, barren-ground caribou (Rangifer tarandus groenlandicus), and that movements of the two species would co-vary with season. We tested for interspecific movement dynamics using animal locations from wolves and caribou monitored concurrently from mid-October to June, across the Northwest Territories and Nunavut, Canada. We used a correlated random walk as a null model to test for pattern in movements and the bearing procedure to detect whether movements were consistently directional. There was a statistical difference between the movements of caribou and wolves (F _1,9 = 13.232, P = 0.005), when compared to a correlated random walk, and a significant interaction effect between season and species (F _1,9 = 6.815, P = 0.028). During winter, the movements of caribou were strongly correlated with the 80°–90° ( $\overline{X}$ X ¯ r = 0.859, SE = 0.065) and 270°–280° ( $\overline{X}$ X ¯ r = 0.875, SE = 0.059) bearing classes suggesting an east–west movement gradient. Wolf movements during winter showed large variation in direction, but were generally east to west. Peak mean correlation for caribou movements during spring was distinct at 40°–50° ( $\overline{X}$ X ¯ r = 0.978, SE = 0.006) revealing movement to the north-east calving grounds. During spring, wolf movements correlated with the 80°–90° ( $\overline{X}$ X ¯ r = 0.861, SE = 0.043) and 270°–280° ( $\overline{X}$ X ¯ r = 0.850, SE = 0.064) bearing class. Directionality of movement suggested that during winter, caribou and wolves had a similar distribution at the large spatial scales we tested. During spring migration, however, caribou and wolves employed asynchronous movement strategies. Our findings demonstrate the utility of the correlated random walk and bearing procedure for quantifying the movement patterns of co-occurring species.     

Dissection of resistance to soil-borne yellow-mosaic-inducing viruses of barley (BaMMV,BaYMV, BaYMV-2) in a complex breeders' cross by means of SSRs and simultaneous mapping of BaYMV/BaYMV-2 resistance of var. 'Chikurin Ibaraki 1'

Ninety-three F(1)-derived doubled haploid (DH) lines from a complex breeders' cross involving the Japanese genotype 'Chikurin Ibaraki 1', which is resistant to barley mild mosaic virus (BaMMV) and two strains of barley yellow mosaic virus (BaYMV and BaYMV-2), three susceptible varieties ('Hamu', 'Julia' and a breeding line) and cv. 'Carola', which carries rym4 conferring resistance to BaMMV and BaYMV, were analysed for resistance to BaMMV, BaYMV and BaYMV-2. The DH lines fell into four phenotypic classes. In addition to completely resistant and susceptible genotypes, DHs were observed which were either resistant to BaMMV and BaYMV or to BaYMV and BaYMV-2. For BaMMV and BaYMV-2 resistance, segregation ratios approaching 1r:1s were observed, suggesting the presence of single resistance genes. In contrast, the segregation ratio for BaYMV fits a 3r:1s segregation ratio, suggesting the presence of two independently inherited genes. From the genetic analysis, we conclude that a resistance locus effective against BaYMV and BaYMV-2 originates from Chikurin Ibaraki 1 and segregates independently from the Carola-derived rym4 resistance that is effective against BaYMV and BaMMV. The BaMMV resistance in Chikurin Ibaraki 1 has probably been lost during population development. This hypothesis was tested using a simple-sequence repeat (SSR) marker (Bmac29) linked to rym4. All BaMMV-resistant DH lines supported amplification of the rym4-resistance diagnostic allele. To identify the genetic location of the Chikurin Ibaraki 1-derived resistance against BaYMV/BaYMV-2, bulked DNA samples were constructed from the four resistance classes, and bulked segregant analysis was performed using a genome-wide collection of SSRs. Differentiating alleles were observed at two linked SSRs on chromosome 5H. The location of this BaYMV/BaYMV-2 resistance locus was confirmed and further resolved by linkage analysis on the whole population using a total of five linked SSRs.     

Enhanced accuracy of kinetic information from CT-CPMG experiments by transverse rotating-frame spectroscopy

Micro-to-millisecond motions of proteins transmit pivotal signals for protein function. A powerful technique for the measurement of these motions is nuclear magnetic resonance spectroscopy. One of the most widely used methodologies for this purpose is the constant-time Carr–Purcell–Meiboom–Gill (CT-CPMG) relaxation dispersion experiment where kinetic and structural information can be obtained at atomic resolution. Extraction of accurate kinetics determined from CT-CPMG data requires refocusing frequencies that are much larger than the nuclei’s exchange rate between states. We investigated the effect when fast processes are probed by CT-CPMG experiments via simulation and show that if the intrinsic relaxation rate $ \left( {R_{2,0}^{CT - CPMG} } \right) $ ( R 2 , 0 CT ? CPMG ) is not known a priori the extraction of accurate kinetics is hindered. Errors on the order of 50 % in the exchange rate are attained when processes become fast, but are minimized to 5 % with a priori $ R_{2,0}^{CT - CPMG} $ R 2 , 0 CT ? CPMG information. To alleviate this shortcoming, we developed an experimental scheme probing $ R_{2,0}^{CT - CPMG} $ R 2 , 0 CT ? CPMG with large amplitude spin-lock fields, which specifically contains the intrinsic proton longitudinal Eigenrelaxation rate. Our approach was validated with ubiquitin and the Oscillatoria agardhii agglutinin (OAA). For OAA, an underestimation of 66 % in the kinetic rates was observed if $ R_{2,0}^{CT - CPMG}\, $ R 2 , 0 CT ? CPMG is not included during the analysis of CT-CPMG data and result in incorrect kinetics and imprecise amplitude information. This was overcome by combining CT-CPMG with $ R_{2,0}^{CT - CPMG} $ R 2 , 0 CT ? CPMG measured with a high power R_1ρ experiment. In addition, the measurement of $ R_{2,0}^{CT - CPMG} $ R 2 , 0 CT ? CPMG removes the ambiguities in choosing between different models that describe CT-CPMG data.     

Stochastic population growth in spatially heterogeneous environments

Classical ecological theory predicts that environmental stochasticity increases extinction risk by reducing the average per-capita growth rate of populations. For sedentary populations in a spatially homogeneous yet temporally variable environment, a simple model of population growth is a stochastic differential equation dZ _t = μ Z _t dt + σ Z _t dW _t , t ≥ 0, where the conditional law of Z _t+Δt ? Z _t given Z _t = z has mean and variance approximately z μΔt and z ² σ ²Δt when the time increment Δt is small. The long-term stochastic growth rate ${\lim_{t \to \infty} t^{-1}\log Z_t}$ for such a population equals ${\mu -\frac{\sigma^2}{2}}$ . Most populations, however, experience spatial as well as temporal variability. To understand the interactive effects of environmental stochasticity, spatial heterogeneity, and dispersal on population growth, we study an analogous model ${{\bf X}_t = (X_t^1, \ldots, X_t^n)}$ , t ≥ 0, for the population abundances in n patches: the conditional law of X _t+Δt given X _t = x is such that the conditional mean of ${X_{t+\Delta t}^i - X_t^i}$ is approximately ${[x^i \mu_i + \sum_j (x^j D_{ji} - x^i D_{ij})] \Delta t}$ where μ _i is the per capita growth rate in the ith patch and D _ij is the dispersal rate from the ith patch to the jth patch, and the conditional covariance of ${X_{t+\Delta t}^i - X_t^i}$ and ${X_{t + \Delta t}^j - X_t^j}$ is approximately x ⁱ x ^j σ _ij Δt for some covariance matrix Σ = (σ _ij ). We show for such a spatially extended population that if ${S_t = X_t^1 + \cdots + X_t^n}$ denotes the total population abundance, then Y _t = X _t /S _t , the vector of patch proportions, converges in law to a random vector Y _∞ as ${t \to \infty}$ , and the stochastic growth rate ${\lim_{t \to \infty} t^{-1}\log S_t}$ equals the space-time average per-capita growth rate ${\sum_i \mu_i \mathbb{E}[Y_\infty^i]}$ experienced by the population minus half of the space-time average temporal variation ${\mathbb{E}[\sum_{i,j}\sigma_{ij}Y_\infty^i Y_\infty^j]}$ experienced by the population. Using this characterization of the stochastic growth rate, we derive an explicit expression for the stochastic growth rate for populations living in two patches, determine which choices of the dispersal matrix D produce the maximal stochastic growth rate for a freely dispersing population, derive an analytic approximation of the stochastic growth rate for dispersal limited populations, and use group theoretic techniques to approximate the stochastic growth rate for populations living in multi-scale landscapes (e.g. insects on plants in meadows on islands). Our results provide fundamental insights into “ideal free” movement in the face of uncertainty, the persistence of coupled sink populations, the evolution of dispersal rates, and the single large or several small (SLOSS) debate in conservation biology. For example, our analysis implies that even in the absence of density-dependent feedbacks, ideal-free dispersers occupy multiple patches in spatially heterogeneous environments provided environmental fluctuations are sufficiently strong and sufficiently weakly correlated across space. In contrast, for diffusively dispersing populations living in similar environments, intermediate dispersal rates maximize their stochastic growth rate.     

Comparing red deer (Cervus elaphus L.) and wild boar (Sus scrofa L.) dispersal patterns in southern Belgium

This study analyses the natal dispersal of red deer and wild boar in order to compare their dispersal capabilities in southern Belgium and to evaluate the relevance of management unit areas (MUA) designed for their monitoring. Dispersal was studied thanks to a mark-recovery method based on 111 red deer fawns and 1,613 piglets. The recovery rate of ear-tagged animals was 68 and 40 %, respectively. In both species, sub-adult males moved on longer distances ( $ \mathop{x}\limits^{-} $ red deer?=?4.82+/?4.17 km and $ \mathop{x}\limits^{-} $ wild boar?=?4.90+/?5.65 km) than females and juveniles $ \mathop{x}\limits^{-} $ (red deer?=?1.84+/?1.46 km and $ \mathop{x}\limits^{-} $ wild boar?=?2.49+/?3.74 km). Taking into account the age and sex categories, we found no difference between species in dispersal mean distance. But we observed higher maximal dispersal distances in wild boar compared to red deer. The natal home range mean sizes were 5.29 km² (+/?4.87) for red deer and 6.23 km² (+/?4.60) for wild boar. Red deer and wild boar showed similar dispersal rates according to age and sex category: 53 and 42 % in sub-adult males and 14 and 16 % in females and juveniles. Our results confirmed the higher proportion of philopatry in females and juveniles of both species compared to sub-adult males more likely to disperse. Wild boar of any sex or age seemed to be less sensitive than red deer to infrastructure (road, rail, river) network on which the management unit area limits are currently based.     

Head impact accelerations for brain strain-related responses in contact sports: a model-based investigation

Both linear \((\mathbf{a}_{\mathrm{lin}})\) and rotational \((\mathbf{a}_{\mathrm{rot}} )\) accelerations contribute to head impacts on the field in contact sports; however, they are often isolated in injury studies. It is critical to evaluate the feasibility of estimating brain responses using isolated instead of full degrees-of-freedom (DOFs) accelerations. In this study, we investigated the sensitivities of regional brain strain-related responses to resultant \(\mathbf{a}_{\mathrm{lin}}\) and \(\mathbf{a}_{\mathrm{rot}}\) as well as the relative contributions of these acceleration components to the responses via random sampling and linear regression using parameterized, triangulated head impacts with kinematic variable values based on on-field measurements. Two independently established and validated finite element models of the human head were employed to evaluate model-consistency and dependency in results: the Dartmouth Head Injury Model and Simulated Injury Monitor. For the majority of the brain, volume-weighted regional peak strain, strain rate, and von Mises stress accumulated from the simulation significantly correlated with the product of the magnitude and duration of \(\mathbf{a}_{\mathrm{rot}}\) , or effectively, the rotational velocity, but not to \(\mathbf{a}_{\mathrm{lin}}\) . Responses from \(\mathbf{a}_{\mathrm{rot}}\) -only were comparable to the full-DOF counterparts especially when normalized by injury-causing thresholds (e.g., volume fractions of large differences virtually diminished (i.e., \(<\) 1 %) at typical difference percentage levels of 1–4 % on average). These model-consistent results support the inclusion of both rotational acceleration magnitude and duration into kinematics-based injury metrics and demonstrate the feasibility of estimating strain-related responses from isolated \(\mathbf{a}_{\mathrm{rot}}\) for analyses of strain-induced injury relevant to contact sports without significant loss of accuracy, especially for the cerebrum.     

Estimation of viscosity from passage time of liquids flowing through a microchannel array

Recently, a microchannel flow analyzer (MC-FAN) has been used to study the flow properties of blood. However, the correlation between blood passage time measured by use of the MC-FAN and hemorheology has not been clarified. In this study, a simple model is proposed for estimation of liquid viscosity from the passage time t _p of liquids. The t _p data for physiological saline were well represented by the model. According to the model, the viscosity of Newtonian fluids was estimated reasonably well from the t _p data. For blood samples, although the viscosity $ \eta_{\text{mc}} $ estimated from t _p was shown to be smaller than the viscosity $ \eta_{{450{\text{s}}^{ - 1} }} $ measured by use of a rotatory viscometer at a shear rate of 450 s^?1, $ \eta_{\text{mc}} $ was correlated with $ \eta_{{450{\text{s}}^{ - 1} }} $ . An empirical equation for estimation of $ \eta_{{450{\text{s}}^{ - 1} }} $ from $ \eta_{\text{mc}} $ of blood samples is proposed.     

Release of non-exchangeable {}^{{{\text{15}}}}{\text{NH}}^{{\text{ + }}}_{{\text{4}}} from subgrade, decomposed granite substrates and uptake by non-mycorrhizal and mycorrhizal California native annual grass, Vulpia microstachys

Release rates of recently fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ from non-exchangeable interlayer sites in 2:1 silicate minerals were determined for decomposed granite (DG) saprolites from three locations in California, USA. Recently-fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release from the DG substrate was quantified by extracting diffused $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ with H-resin, as well as a native, annual grass Vulpia microstachys. The $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release data varied with via the method of extraction, which included H-resin pre-treatments (Na⁺ or H⁺) and V. microstachys uptake (mycorrhizal inoculated or uninoculated). After 6 weeks (1008 h), more $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ was recovered from fixed interlayer positions by the H-resins as compared to uptake by V. microstachys. The H⁺ treated H-resins recovered more released $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ (≈94 mg ${\text{NH}}^{{\text{ + }}}_{{\text{4}}} - {\text{N}}\;{\text{kg}}^{1} $ or (12%) of total fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ ) in two of the three DG samples as compared to the Na⁺ treated resins, (which recovered ≈70–78 mg ${\text{NH}}^{{\text{ + }}}_{{\text{4}}} - {\text{N}}\;{\text{kg}}^{{{\text{ - 1}}}} $ (or 9–10%) of the total fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ ). The V. microstachys assimilated 8–9% of the total fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ with mycorrhizal inoculum as compared to only 2% without a mycorrhizal inoculum, over the same time period. The fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release kinetics from the H-resin experiments were most accurately described by first order and power function models, and can be characterized as biphasic using a heterogeneous diffusion model. Uptake of both the ¹⁵N and ambient, unlabelled N from the soils was closely related to plant biomass. There was no significant difference in percent of N per unit of biomass between the control and mycorrhizal treatments. The findings presented here indicate that observed, long-term $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release rates from DG in studies utilizing resins, may overestimate the levels of fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ made available to plants and microorganisms. Additionally, the study suggested that mycorrhizae facilitate the acquisition and plant uptake of fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ , resulting in markedly increased plant biomass production.     

Theoretical study of the reaction of CH2XO (X = F, Cl, Br) radicals with the NO radical

In this paper, we focus on the multiple-channel reactions of CH₂XO (X = F, Cl, Br) radicals with the NO radical by means of direct dynamic methods. All structures of the stationary points were obtained at the MP2/6-311+G(d,p) level and vibrational frequency analysis was also performed at this level of theory. The minimum energy path (MEP) was obtained via the intrinsic reaction coordinate (IRC) theory at the MP2/6-311+G(d,p) level, and higher-level energetic information was refined by the MC-QCISD method. The rate constants for the three hydrogen abstraction reaction channels over the temperature range 200–1,500 K were calculated by the improved canonical variational transition state theory (ICVT) with a correction for small-curvature tunneling (SCT). The rate constants calculated in this manner were in good agreement with the available experimental data, and the three-parameter rate–temperature formulae for the temperature range 200–1,500 K were $ {k_{1{\text{a}} }}(T)=0.32\times {10^{-18 }}{T^{1.83 }}\exp \left( {1748.54/T} \right) $ , $ {k_{2{\text{a}} }}(T)=0.22\times {10^{-19 }}{T^{2.19 }}\exp \left( {1770.19/T} \right) $ , $ {k_{3{\text{a}} }}(T)=0.88\times {10^{-20 }}{T^{2.20 }}\exp \left( {1513.82/T} \right) $ (in units of cm³ molecule^?1?s^?1).     

Investigation of the possibility of exceeding the Greenwald density limit during ECRH in T-10

In T-10 experiments, attempts were made to significantly exceed the Greenwald limit $\bar n_{Gr} $ during high-power (P _ab=750 kW) electron-cyclotron resonance heating (ECRH) and gas puffing. Formally, the density limit $(\bar n_e )_{\lim } $ exceeding the Greenwald limit $({{(\bar n_e )_{\lim } } \mathord{\left/ {\vphantom {{(\bar n_e )_{\lim } } {\bar n_{Gr} }}} \right. \kern-0em} {\bar n_{Gr} }} = 1.8)$ was achieved for q _L=8.2. However, as q _L decreased, the ratio ${{(\bar n_e )_{\lim } } \mathord{\left/ {\vphantom {{(\bar n_e )_{\lim } } {\bar n_{Gr} }}} \right. \kern-0em} {\bar n_{Gr} }}$ also decreased, approaching unity at q _L≈3. It was suggested that the “current radius” (i.e., the radius of the magnetic surface enclosing the bulk of the plasma current I _p), rather than the limiter radius, was the parameter governing the value of $(\bar n_e )_{\lim } $ . In the ECRH experiments, no substantial degradation of plasma confinement was observed up to $\bar n_e \sim 0.9(\bar n_e )_{\lim } $ regardless of the ratio ${{(\bar n_e )_{\lim } } \mathord{\left/ {\vphantom {{(\bar n_e )_{\lim } } {\bar n_{Gr} }}} \right. \kern-0em} {\bar n_{Gr} }}$ . In different scenarios of the density growth up to $(\bar n_e )_{\lim } $ , two types of disruptions related to the density limit were observed.     

Partitioning of oxygen uptake and cost of surfacing during swimming in the air-breathing catfish Pangasianodon hypophthalmus

Though air-breathing has probably evolved mainly as a response to hypoxia, it may provide an important oxygen supplement when metabolism is elevated, as for example during swimming. Due to the increased travelling distance involved when an air-breathing fish swims to and from the surface, and the increased drag when the surface is breached, it can be proposed that air-breathing results in a rise in the apparent cost of transport. In order to investigate this hypothesis, it is necessary to use a fish that is able to swim equally well with and without access to air. The striped catfish Pangasianodon hypophthalmus has been shown to have a sufficiently high capacity for aquatic oxygen uptake in normoxia, to allow for such a comparison. Here, we measured the partitioning of oxygen uptake ( $ \dot{M}{\text{O}}_{2} $ ) during swimming and recovery, and calculated the apparent cost of transport with and without access to air, under normoxic conditions. Aerial $ \dot{M}{\text{O}}_{2} $ constituted 25–40 % of the total $ \dot{M}{\text{O}}_{2} $ during swimming and less than 15 % during recovery. The net cost of transport was 25 % lower in fish that did not air-breathe compared to fish that did, showing that the cost of surfacing can be substantial. This is the first study to measure partitioning in an air-breathing fish during swimming at velocities close to the critical swimming speed.     

Age structure, growth and mortality estimates of an endemic Ptychobarbus dipogon (Regan, 1905) (Cyprinidae: Schizothoracinae) in the Lhasa River, Tibet

Ptychobarbus dipogon is an endemic fish in the Yarlung Tsangpo River, but its biology is poorly known. We sampled 582 specimens (total length, TL, between 70.6 and 593.0 mm) from April 2004 to August 2006 in the Lhasa River, Tibet. We estimated ages based on the counts of alternating opaque and translucent zones (annuli) in thin transverse sections of lapilli otoliths. Ages ranged from 1⁺ to 23⁺ years for males and 1⁺ to 44⁺ for females. The observed 44⁺ years was the oldest reported for schizothoracine fishes. Females attained a larger size than males. The TL–weight relationship was W?=?7.12?×?10^?6 TL ^3.006 for combined sexes. The growth parameters fitted von Bertalanffy growth functions were $L_\infty = 598.66\,{\text{mm}}$ , k?=?0.0898 year^?1, t ₀?=??0.7261 year and $W_\infty = 1585.38\;{\text{g}}$ for females and $L_\infty = 494.23{\text{ mm}}$ , k?=?0.1197 year^?1, t ₀?=??0.7296 year and $W_\infty = 904.88{\text{ g}}$ for males. The longevities of 32.7 year for females and 24.3 year for males were similar to the observed ages. Using an empirical model we estimated the instantaneous rate of total mortality (Z) at 0.28 per year in the lower reaches. Z in the upper and middle stocks was close to the M because of unexploited or lightly exploited stock. Protracted longevity, slow growth, low natural mortality and large body size were typical characteristics of P. dipogon. The current declining trend of P. dipogon could be prevented by altering fishing regulations.     

Hyperfine interactions and electron distribution in FeIIFeI and FeIFeI models for the active site of the [FeFe] hydrogenases: Mössbauer spectroscopy studies of low-spin FeI

Mössbauer studies of [{μ-S(CH₂C(CH₃)₂CH₂S}(μ-CO)Fe^IIFe^I(PMe₃)₂(CO)₃]PF₆ (1 _OX ), a model complex for the oxidized state of the [FeFe] hydrogenases, and the parent Fe^IFe^I derivative are reported. The paramagnetic 1 _OX is part of a series featuring a dimethylpropanedithiolate bridge, introducing steric hindrance with profound impact on the electronic structure of the diiron complex. Well-resolved spectra of 1 _OX allow determination of the magnetic hyperfine couplings for the low-spin distal Fe^I ( $ {\text{Fe}}^{\text{I}} _{\text{ D}} $ Fe D I ) site, A _x,y,z  = [?24 (6), ?12 (2), 20 (2)] MHz, and the detection of significant internal fields (approximately 2.3 T) at the low-spin ferrous site, confirmed by density functional theory (DFT) calculations. Mössbauer spectra of 1 _OX show nonequivalent sites and no evidence of delocalization up to 200 K. Insight from the experimental hyperfine tensors of the Fe^I site is used in correlation with DFT to reveal the spatial distribution of metal orbitals. The Fe–Fe bond in [Fe₂{μ-S(CH₂C(CH₃)₂CH₂S}(PMe₃)₂(CO)₄] (1) involving two $ d_{{z^{2} }} $ d z 2 -type orbitals is crucial in keeping the structure intact in the presence of strain. On oxidation, the distal iron site is not restricted by the Fe–Fe bond, and thus the more stable isomer results from inversion of the square pyramid, rotating the $ d_{{z^{2} }} $ d z 2 orbital of $ {\text{Fe}}^{\text{I}} _{\text{ D}} $ Fe D I . DFT calculations imply that the Mössbauer properties can be traced to this $ d_{{z^{2} }} $ d z 2 orbital. The structure of the magnetic hyperfine coupling tensor, A, of the low-spin Fe^I in 1 _OX is discussed in the context of the known A tensors for the oxidized states of the [FeFe] hydrogenases.     

A Mathematical Model Supports a Key Role for Ae4 (Slc4a9) in Salivary Gland Secretion

We develop a mathematical model of a salivary gland acinar cell with the objective of investigating the role of two \(\mathrm{Cl}^-/\mathrm{HCO}_3^-\) exchangers from the solute carrier family 4 (Slc4), Ae2 (Slc4a2) and Ae4 (Slc4a9), in fluid secretion. Water transport in this type of cell is predominantly driven by \(\mathrm{Cl}^-\) movement. Here, a basolateral \(\mathrm{Na}^+/ \mathrm{K}^+\) adenosine triphosphatase pump (NaK-ATPase) and a \(\mathrm{Na}^+\)–\(\mathrm{K}^+\)–\(2 \mathrm{Cl}^-\) cotransporter (Nkcc1) are primarily responsible for concentrating the intracellular space with \(\mathrm{Cl}^-\) well above its equilibrium potential. Gustatory and olfactory stimuli induce the release of \(\mathrm{Ca}^{2+}\) ions from the internal stores of acinar cells, which triggers saliva secretion. \(\mathrm{Ca}^{2+}\)-dependent \(\mathrm{Cl}^-\) and \(\mathrm{K}^+\) channels promote ion secretion into the luminal space, thus creating an osmotic gradient that promotes water movement in the secretory direction. The current model for saliva secretion proposes that \(\mathrm{Cl}^-/ \mathrm{HCO}_3^-\) anion exchangers (Ae), coupled with a basolateral \(\mathrm{Na}^+/\hbox {proton}\) (\(\hbox {H}^+\)) (Nhe1) antiporter, regulate intracellular pH and act as a secondary \(\mathrm{Cl}^-\) uptake mechanism (Nauntofte in Am J Physiol Gastrointest Liver Physiol 263(6):G823–G837, 1992; Melvin et al. in Annu Rev Physiol 67:445–469, 2005.  https://doi.org/10.1146/annurev.physiol.67.041703.084745). Recent studies demonstrated that Ae4 deficient mice exhibit an approximate \(30\%\) decrease in gland salivation (Peña-Münzenmayer et al. in J Biol Chem 290(17):10677–10688, 2015). Surprisingly, the same study revealed that absence of Ae2 does not impair salivation, as previously suggested. These results seem to indicate that the Ae4 may be responsible for the majority of the secondary \(\mathrm{Cl}^-\) uptake and thus a key mechanism for saliva secretion. Here, by using ‘in-silico’ Ae2 and Ae4 knockout simulations, we produced mathematical support for such controversial findings. Our results suggest that the exchanger’s cotransport of monovalent cations is likely to be important in establishing the osmotic gradient necessary for optimal transepithelial fluid movement.