Nonlinear dust-acoustic structures in space plasmas with superthermal electrons,positrons, and ions

Some features of nonlinear dust-acoustic (DA) structures are investigated in a space plasma consisting of superthermal electrons, positrons, and positive ions in the presence of negatively charged dust grains with finite-temperature by employing a pseudo-potential technique in a hydrodynamic model. For this purpose, it is assumed that the electrons, positrons, and ions obey a kappa-like (κ) distribution in the background of adiabatic dust population. In the linear analysis, it is found that the dispersion relation yield two positive DA branches, i.e., the slow and fast DA waves. The upper branch (fast DA waves) corresponds to the case in which both (negatively charged) dust particles and (positively charged) ion species oscillate in phase with electrons and positrons. On the other hand, the lower branch (slow DA waves) corresponds to the case in which only dust particles oscillate in phase with electrons and positrons, while ion species are in antiphase with them. On the other hand, the fully nonlinear analysis shows that the existence domain of solitons and their characteristics depend strongly on the dust charge, ion charge, dust temperature, and the spectral index κ. It is found that the minimum/maximum Mach number increases as the spectral index κ increases. Also, it is found that only solitons with negative polarity can propagate and that their amplitudes increase as the parameter κ increases. Furthermore, the domain of Mach number shifts to the lower values, when the value of the dust charge Z _d increases. Moreover, it is found that the Mach number increases with an increase in the dust temperature. Our analysis confirms that, in space plasmas with highly charged dusts, the presence of superthermal particles (electrons, positrons, and ions) may facilitate the formation of DA solitary waves. Particularly, in two cases of hydrogen ions H⁺ (Z _i = 1) and doubly ionized Helium atoms He²⁺ (Z _i = 2), the mentioned results are the same. Additionally, the mentioned dusty plasma does not support DA solitons with positive polarity (compressive solitons). Furthermore, our analysis confirms that DA double layers cannot exist in such a system. Moreover, the positron density has not a considerable effect on the behavior of DA solitons in our model.     

Compressive and rarefactive DIA solitons beyond the KdV limit

The modified Gardner equation (MGE), showing the existence of compressive and rarefactive dust-ion-acoustic (DIA) solitons in a nonplanar dusty plasma (containing inertial ions, Boltzmann electrons, and negatively charged stationary dust) beyond the KdV Korteweg-de Vries (KdV) limit, is derived and numerically solved. The basic features of the compressive and rarefactive cylindrical and spherical DIA solitons, which are found to exist beyond the KdV limit, i.e., exist for μ ∼ 2/3 (where μ = Z _n n _d0/n _i0, z _d is the number of electrons residing onto the dust grain surface, n _d0(n _i0) is the dust (ion) number density at equilibrium, and μ ∼ 2/3 means that μ is not equal to 2/3, but it is around 2/3) are identified. These solitons (which can be referred to as DIA Gardner solitons (DIA-GSs)) are completely different from the KdV solitons because μ = 2/3 corresponds to the vanishing of the nonlinear coefficient of the KdV equation, and μ ∼ 2/3 corresponds to extremely large amplitude KdV solitons for which the validity of the reductive perturbation method breaks down. It is also shown that the properties of the nonplanar (cylindrical and spherical) DIA-GSs are significantly different from those of the one dimensional planar ones.     

Influence of Daily Short-Term Temperature Drops on Respiration to Photosynthesis Ratio in Chilling-Sensitive Plants

Cucumber (Cucumis sativus L.), tomato (Solanum lycopersicum L.), and sweet pepper (Capsicum annuum L.) plants were subjected daily over 13 days to short-term (2 h) temperature drops to 12, 8, 4, and 1°C (DROP treatments) at the end of night periods, and effects of these chilling treatments on the ratio of dark respiration in leaves (R_d) to gross photosynthesis (A_g) were examined. The results showed that DROP treatments affected the R_d/A_g ratio in leaves: this ratio increased significantly in cucumber and tomato plants and was slightly affected in pepper plants. When the temperature drops to 12°C were applied, the increase in R_d/A_g ratio in cucumber and tomato plants was entirely due to the rise in R_d. In the case of temperature drops to 8°C and below, the increase in R_d/A_g was determined by both elevation of R_d and the concurrent decrease in Ag. In cucumber plants, the extent of Ag and R_d changes increased with the DROP severity, i.e., with lowering the temperature of DROP treatment. The inhibition of photosynthesis by DROP treatment in cucumber plants was accompanied by the diminished efficiency of light energy use for photosynthesis and by the increase in the light compensation point. The elevation in R_d/A_g ratio in cucumber plants was accompanied by the decline in growth characteristics, such as accumulation of aboveground biomass, plant height, and leaf area. It was concluded that the R/A ratio is an important indicator characterizing the adaptive potential of chilling-sensitive plant species and their response to daily short-term temperature drops.     

Chlorophylls <Emphasis Type="Italic">d</Emphasis> and <Emphasis Type="Italic">f</Emphasis> and their role in primary photosynthetic processes of cyanobacteria

The finding of unique Chl d- and Chl f-containing cyanobacteria in the last decade was a discovery in the area of biology of oxygenic photosynthetic organisms. Chl b, Chl c, and Chl f are considered to be accessory pigments found in antennae systems of photosynthetic organisms. They absorb energy and transfer it to the photosynthetic reaction center (RC), but do not participate in electron transport by the photosynthetic electron transport chain. However, Chl d as well as Chl a can operate not only in the light-harvesting complex, but also in the photosynthetic RC. The long-wavelength (Q_y) Chl d and Chl f absorption band is shifted to longer wavelength (to 750 nm) compared to Chl a, which suggests the possibility for oxygenic photosynthesis in this spectral range. Such expansion of the photosynthetically active light range is important for the survival of cyanobacteria when the intensity of light not exceeding 700 nm is attenuated due to absorption by Chl a and other pigments. At the same time, energy storage efficiency in photosystem 2 for cyanobacteria containing Chl d and Chl f is not lower than that of cyanobacteria containing Chl a. Despite great interest in these unique chlorophylls, many questions related to functioning of such pigments in primary photosynthetic processes are still not elucidated. This review describes the latest advances in the field of Chl d and Chl f research and their role in primary photosynthetic processes of cyanobacteria.     

The invariance of production per unit of food consumed in fish populations

The amount of biomass production per unit of food consumed (P/Q) represents an important quantity in ecosystem functioning, because it indicates how efficient a population transforms ingested food into biomass. Several investigations have noticed that P/Q remains relatively constant (or invariant) across fish population that feed at the same food-type level (carnivorous/herbivorous). Nevertheless, theoretical explanation for this invariant is still lacking. In this paper, we demonstrate that P/Q remains invariant across fish populations with stable-age distribution. Three key assumptions underpin the P/Q invariant: (1) the ratio between natural mortality M and von Bertalanffy growth parameter k (M/k ratio) should remain invariant across fish populations; (2) a parameter defining the fraction of ingested food available for growth needs to remain constant across fish that feed at the same trophic level; (3) third, the ratio between length at age 0 (\(l_0\)) and asymptotic length (\(l_\infty\)) should be constant across fish populations. The influence of these assumptions on the P/Q estimates were numerically assessed considering fish populations of different lifespan. Numerical evaluations show that the most critical condition highly relates to the first assumption, M/k. Results are discussed in the context of the reliability of the required assumption to consider the P/Q invariant in stable-age distributed fish populations.     

Genetic drift and uniform selection shape evolution of most traits in <Emphasis Type="Italic">Eugenia dysenterica</Emphasis> DC. (Myrtaceae)

Knowing how microevolutionary processes, such as genetic drift and natural selection, shape variation in adaptive traits is strategic for conservation measures. One way to estimate local adaptation is to compare divergences in quantitative traits (Q_ST) and neutral loci (F_ST). Therefore, we have assessed the pattern of phenotypic and molecular genetic divergence among natural subpopulations of the fruit tree Eugenia dysenterica DC. A provenance and progeny test was performed to assess the quantitative traits of the subpopulations collected in a wide distribution area of the species in the Brazilian Cerrado. The sampled environments are in a biodiversity hotspot with heterogeneous soil and climate conditions. By associating quantitative trait variation in initial seedling development with neutral microsatellite marker variation, we tested the local adaptation of the traits by the Q_ST–F_ST contrast. Genetic drift was prevalent in the phenotypic differentiation among the subpopulations, although the traits seedling emergence time and root green mass, which are relevant for adaptation to the Cerrado climate, showed signs of uniform selection. Our results suggest that E. dysenterica has a spatial genetic structure divided into two large groups, separated by a line that divides the Cerrado biome in a southwestern to northeastern direction. This structure must be taken into account for managing E. dysenterica genetic resources both for conservation and breeding purposes.     

Effect of high light intensity on the photosynthetic apparatus of two hybrid lines of <Emphasis Type="Italic">Paulownia</Emphasis> grown on soils with different salinity

The objective of this investigation was to evaluate the simultaneous action of light stress and salinity. Pulse amplitude modulated chlorophyll fluorescence, P₇₀₀ redox state, and pigment analysis were used to assess the impact of high light intensity on Paulownia tomentosa × fortunei and Paulownia elongata × elongata grown on soils with different salinity. It was found that light stress reduced the amount of pigments and the efficiency of photochemical energy conversion, inhibited the maximum and the effective quantum yields of PSII photochemistry, decreased photochemical quenching and photosynthetic rate. Data also showed influence on the primary quinone acceptor (Q_A) reoxidation, which led to the restriction of the electron flow from Q_A to plastoquinone and stimulation of the cyclic electron flow. The possible reasons for the increased effects of the light stress under conditions of high salt concentration in soil for Paulownia tomentosa × fortunei are discussed.     

Space-charge-limited current in a plane vacuum diode discharged by an electron current pulse

An unsteady discharge of a relativistic vacuum diode is studied analytically. The amplitude and rise time of the discharge current pulse are determined as functions of the input parameters of the problem. It is found that, in a nonrelativistic limit, the maximum attainable amplitude of the discharge current pulse is equal to J_Alim = 9/4J_CL, where J_CL is the vacuum-diode limiting current prescribed by the 3/2 law. The parameters of the dipole moment of the layer formed above the grid anode are found in the nonrelativistic limit.     

Simple generalisation of a mesophyll resistance model for various intracellular arrangements of chloroplasts and mitochondria in C<Subscript>3</Subscript> leaves

The classical definition of mesophyll conductance (g _m) represents an apparent parameter (g _m,app) as it places (photo)respired CO₂ at the same compartment where the carboxylation by Rubisco takes place. Recently, Tholen and co-workers developed a framework, in which g _m better describes a physical diffusional parameter (g _m,dif). They partitioned mesophyll resistance (r _m,dif = 1/g _m,dif) into two components, cell wall and plasmalemma resistance (r _wp) and chloroplast resistance (r _ch), and showed that g _m,app is sensitive to the ratio of photorespiratory (F) and respiratory (R _d) CO₂ release to net CO₂ uptake (A): g _m,app = g _m,dif/[1?+?ω(F?+?R _d)/A], where ω is the fraction of r _ch in r _m,dif. We herein extend the framework further by considering various scenarios for the intracellular arrangement of chloroplasts and mitochondria. We show that the formula of Tholen et al. implies either that mitochondria, where (photo)respired CO₂ is released, locate between the plasmalemma and the chloroplast continuum or that CO₂ in the cytosol is completely mixed. However, the model of Tholen et al. is still valid if ω is replaced by ω(1?σ), where σ is the fraction of (photo)respired CO₂ that experiences r _ch (in addition to r _wp and stomatal resistance) if this CO₂ is to escape from being refixed. Therefore, responses of g _m,app to (F?+?R _d)/A lie somewhere between no sensitivity in the classical method (σ =1) and high sensitivity in the model of Tholen et al. (σ =0).     

Temporary immersion systems for the mass propagation of sweet cherry cultivars and cherry rootstocks: development of a micropropagation procedure and effect of culture conditions on plant quality

Sweet cherry (Prunus avium L.) varieties and cherry rootstocks are an important part of the fruit industry, and difficulties associated with mass propagation provide an opportunity for the use of temporary immersion systems (TIS). We show the establishment of culture procedures for four genotypes: the rootstocks Maxma-14 and Colt and the varieties ‘Van’ and ‘Rainier.’ The starting explants were internodal segments from seedlings kept in solid propagation medium (PM) (Driver-Kuniyuki Walnut (DKW) base supplemented with indole butyric acid, benzyl amino purine; ascorbic acid, myo-inositol, and agar). Segments were cultured under TIS for 14 d and led to whole plant generation after 30 d of culturing in solid rooting media, which depended on whether they are varieties or rootstocks. A 15-d acclimatization phase led to establishment in greenhouse. The efficiency of TIS was specifically analyzed for the two best PM-derivative media and compared to cultures using solid medium. A number of shoots (P _x), biomass (Q _x), and sucrose consumption (SC) were evaluated for these purposes. The results showed that Maxma-14, Colt, and ‘Van’ TIS cultures had improved performance in comparison to solid cultures, whereas ‘Rainier’ showed no differences. The number of immersions influenced all of the productive parameters (P _x, Q _x, and SC), whereas genotype affected P _x, and the time of immersion influenced SC. The best Q _x and P _x values were obtained with the rootstocks Maxma-14 and Colt, as well as the variety Van; these showed no hyperhydration. Physiological studies show that 14-d TIS-produced shoots represented an intermediate stage between solid-derived and adult plants, although the photosynthetic efficiencies of these materials revealed a lack of autotrophic ability at this point.     

Evidences and magnitude of nighttime transpiration derived from <Emphasis Type="Italic">Populus euphratica</Emphasis> in the extreme arid region of China

Extensive research has found that nighttime transpiration (E _n) is positively correlated to the vapour pressure deficit (VPD), that suggested E _n was highest during the night under high temperatures and low humidity along with high soil water availability, typically for the riparian forest in the extreme arid region of China. This study used the heat ratio method to measure sap velocity (V _s) for mature and saplings Populus euphratica Oliv., and then E _n was conservatively calculated as total nocturnal sap flow (F _s, the product of V _s and sapwood area A _s) between 01:00 to 06:00. A gas exchange system was used to measure the leaf transpiration rate (T _r) and stomatal conductance (g _s) of saplings. For mature trees, nighttime V _s was extensive and logarithmic correlated to VPD (similar to daytime). For saplings, g _s and T _r was extensive in different months, and also a strong logarithmic relationship was found between V _s and VPD for both daytime and nighttime periods. Both of stem sap flow and leaf gas exchange suggusted the occurrence of E _n, whether mature or sapling trees. E _n contribution to daily transpiration (E _d) was high just as expected for P. euphratica, which was confirmed by proportional E _n to E _d (E _n/E _d) means taken in 2012 (24.99%) and 2013 (34.08%). Compared to mature trees, E _n/E _d of saplings in 2013 was lower with means of 12.06%, that supported further by the shorter duration times and less T _r,n (16.64%) and g _s,n (26.45%) of leaf, suggesting that E _n magnitude is associated to individual the tree size, that effect to stored water of individual trees, although this hypothesis requires further research.     

Study of Electromagnetic Electron Cyclotron Waves for Kappa Distribution with AC Field in the Magnetosphere of Saturn

Parallel propagating electromagnetic electron cyclotron (EMEC) waves in the extended plasma sheet (~12R_S) and in the outer magnetosphere (~18R_S) of Saturn have been studied. A dispersion relation for parallel propagating relativistic EMEC waves has been applied to the magnetosphere of Saturn, and comparisons have been made with the data of Voyager 1 at these radial distances. The detailed investigations for EMEC waves have been done in the presence of the perpendicular AC electric field, using the kappa distribution function. The relativistic temporal growth rate is calculated by the method of characteristic solution with the data provided by Voyager 1. The effect of the suprathermal electron density, temperature anisotropy, frequency of AC electric field, thermal energy of ions, and relativistic factor on the temporal growth rate of EMEC wave emission has been studied. The simulation results show that the growth of parallel propagating EMEC waves is significantly affected by variations in the temperature anisotropy, electron density, ion thermal energy, and relativistic factor in both the extended plasma sheet and the outer magnetosphere of Saturn. The temperature anisotropy (T⊥/T_║), ion thermal energy (K_BT_║i), and electron density (n₀) have been found to be a major source of free energy for parallel propagating EMEC waves in both regions.     

Impacts on Micro- and Macro-Structure of Thermally Stabilised Whey Protein-Pectin Complexes: A Fluorescence Approach

Stability of whey protein-pectin complexes is an essential criterion for their application in different food matrices. The impact of process parameters on micro- and macro-structural characteristics of thermally stabilised whey protein-pectin complexes was investigated using fluorescence spectroscopy, ζ-potential measurements, dynamic light scattering and phase separation. Complexes prepared from whey protein isolate (WPI) and pectins with different degrees of esterification (HMP, LMP) were generated at different biopolymer concentrations (WPI + pectin: 5.0 % + 1.0 %, c _{h i g h} ; 2.75 % + 0.55 %, c _{m e d} ; 0.5 % + 0.1 %, c _{l o w} ), heating temperatures (80-90^°C) and pH levels (6.1-4.0). Micro- and macro-structural characteristics of the complexes depended on concentration level and degree of esterification, with complexes being more sensitive towards environmental changes at c _{l o w} than at c _{m e d} and c _{h i g h} . WPI-LMP complexes exhibited sizes <1 μm suitable for micro-encapsulation, whereas WPI-HMP complexes at c _{m e d} achieved sizes from 1-10 μm and at c _{h i g h} from 10-200 μm underlining their potential as fat-replacers and structuring agents, respectively. Slopes and intercepts derived from intensity ratios of fluorescence spectra gave insights into the state of unfolding of β-lactoglobulin within the complexes and thus about the protective effect of pectin addition.     

Dynamic changes in energy metabolism and electron transport of photosystem II in <Emphasis Type="Italic">Nicotiana tabacum</Emphasis> infested by nymphs of <Emphasis Type="Italic">Bemisia tabaci</Emphasis> (Middle East-Asia Minor 1)

Bemisia tabaci Middle East-Asia Minor 1 (MEAM1) infestation adversely affected photosynthesis of host plants. In the current study, chlorophyll a fluorescence was measured to determine the effects of MEAM1 nymph infestation of tobacco local and systemic leaves on energy metabolism and electron transport of photosystemII(PSII). The results showed that the density of PSII reaction centres per excited cross section (CS) (RC/CS) of infested and systemic leaves was reduced at 14 and 20 days. In systemic leaves, the number of PSII closed reaction centres (1-qP) increased significantly at 14 and 20 days. Absorption flux per Q_A^? reducing PSII reaction centre (RC) (ABS/RC), trapped energy flux per RC (TRo/RC), and electron transport per RC (ETo/RC) of infested and systemic leaves increased with MEAM1 nymph infestation. The most obvious increase in absorption flux per CS (ABS/CSo) and trapped energy flux per CS (TRo/CSo) of infested and systemic leaves occurred at 14 days. MEAM1 nymph infestation significantly reduced the energy required for PSII Q_A to be completely reduced (Sm) in tobacco leaves. These results suggested that MEAM1 nymph infestation caused changes in light-harvesting antenna system and deactivation of the reaction centre, resulting in the reduction of photons absorbed by reaction centres per unit area. MEAM1 nymph infestation, particularly the 3rd instar nymphs, decreased light utilization ability and increased excess excitation energy in tobacco leaves. With MEAM1 nymph infestation, the relative electron transport capacity of the entire electron transport chain decreased, and more light energy was used to reduce Q_A.     

Leaf functional trait responses to changes in water status differ among three oak (<Emphasis Type="Italic">Quercus</Emphasis>) species

We monitored differences in rates of foliar carbon-compound increases with progressive drought as an indicator of sink limitation status and subsequent drought tolerance. We postulate that species which increase foliar carbohydrates and protein-precipitable phenolics (PPP) more quickly than related species over the same time period and drought conditions have stronger sink limitations and are therefore less drought tolerant. Quercus macrocarpa, Q. shumardii, and Q. virginiana saplings were subjected to two treatments for approximately 3.5 months: (1) watered, which received the equivalent of average weekly precipitation for College Station, TX, USA, and (2) droughted, in which precipitation was reduced by 100%. Q. virginiana’s photosynthesis (A) and stomatal conductance (g_s) were 44 and 54% greater, respectively, than the other species in the drought treatment. Q. virginiana’s g_s also increased more dramatically with watering and subsequent increases in predawn leaf water potential. This plasticity suggests Q. virginiana is best equipped to deal with sporadic rainfall events and soil moisture changes, at least in the short term. Results indicate that the three species allocate carbon from photosynthate in different ways. Q. shumardii had the most soluble sugar in its foliage but had the least PPP, while Q. virginiana and macrocarpa had more PPP and less sugar than Q. shumardii. Diameter:height growth rate was greatest in Q. shumardii. Foliar protein-precipitable phenolic content appears to be more affected by factors other than drought. Differences in species’ physiological responses to drought may result in stand composition shifts with future climate alterations.     

Stability and electronic properties of praseodymium-doped silicon clusters PrSin (<Emphasis Type="Italic">n</Emphasis> = 12–21)

The neutral PrSi _n (n = 12–21) species considering various spin configurations were systematically studied using PBE0 and B3LYP schemes in combination with relativistic small-core potentials (ECP28MWB) for Pr atoms and cc-pVTZ basis set for Si atoms. The total energy, growth-pattern, equilibrium geometry, relative stability, hardness, charge transfer, and magnetic moments are calculated and discussed. The results reveal that when n < 20, the ground-state structure of PrSi _n evaluated to be prolate clusters. Starting from n = 20, the ground-state structures of PrSi _n are evaluated to be endohedral cagelike clusters. Although the relative stabilities based on various binding energies and different functional is different from each other, the consensus is that the PrSi₁₃, PrSi₁₆, PrSi₁₈, and PrSi₂₀ are more stable than the others, especially the PrSi₂₀. Analyses of hardness show that introducing Pr into Si _n (n = 12–21) elevates the photochemical sensitivity, especially for PrSi₂₀. Calculated result of magnetic moment and charge transfer shows that the 4f electrons of Pr in the clusters are changed, especially in endohedral structures such as PrSi₂₀, in which one electron transfers from 4f to 5d orbital. That is, the 4f electron of Pr in the clusters participates in bonding. The way to participate in bonding is that a 4f electron transfers to 5d orbital. Although the 4f electron of Pr atom participates in bonding, the total magnetic moment of PrSi _n is equal to that of isolated Pr atom. The charge always transfers from Pr atom to Si _n cluster for the ground state structures of PrSi_n (n = 12–19), but charge transfer is reverse for n ≥ 20. The largest charge transfer for endohedral structure reveals that the bonding between Pr and Si _n is ionic in nature and very strong. The fullerenelike structure of PrSi₂₀ is the most stable among all of these clusters and can act as the building blocks for novel functional nanotubes.     

Enantiomer-Selective Photo-Induced Reaction of Protonated Tryptophan with Disaccharides in the Gas Phase

In order to investigate chemical evolution in interstellar molecular clouds, enantiomer-selective photo-induced chemical reactions between an amino acid and disaccharides in the gas phase were examined using a tandem mass spectrometer containing an electrospray ionization source and a cold ion trap. Ultraviolet photodissociation mass spectra of cold gas-phase noncovalent complexes of protonated tryptophan (Trp) enantiomers with disaccharides consisting of two d-glucose units, such as d-maltose or d-cellobiose, were obtained by photoexcitation of the indole ring of Trp. NH₂CHCOOH loss via cleavage of the C_α–C_β bond in Trp induced by hydrogen atom transfer from the NH₃ ⁺ group of a protonated Trp was observed in a noncovalent heterochiral H⁺(l-Trp)(d-maltose) complex. In contrast, a photo-induced chemical reaction forming the product ion with m/z 282 occurs in homochiral H⁺(d-Trp)(d-maltose). For d-cellobiose, both NH₂CHCOOH elimination and the m/z 282 product ion were observed, and no enantiomer-selective phenomena occurred. The m/z 282 product ion indicates that the photo-induced C-glycosylation, which links d-glucose residues to the indole moiety of Trp via a C–C bond, can occur in cold gas-phase noncovalent complexes, and its enantiomer-selectivity depends on the structure of the disaccharide.     

Identification of methylated flavonoid regioisomeric metabolites using enzymatic semisynthesis and liquid chromatography-tandem mass spectrometry

Discrimination of isomeric methylated metabolites is an important step toward identifying genes responsible for methylation, but presents substantial challenges because authentic standards are often unavailable and mass spectra of isomers have been considered indistinguishable. In this report, an approach is described for identifying methyl group positions in multiply methylated flavonoid metabolites using combinations of tandem mass spectrometry, liquid chromatography retention, and site-selective methylation by recombinant O-methyltransferases from Solanum habrochaites LA1777. The basis for observed fragment ions in tandem mass spectra of multiply methylated myricetin was further established using enzymatic incorporation of deuterium-labeled methyl groups using S-adenosylmethionine-d ₃ as precursor.     

Characterization and fine mapping of <Emphasis Type="Italic">osh15</Emphasis>(<Emphasis Type="Italic">t</Emphasis>), a novel dwarf mutant gene in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Plant height is one of the most important agronomic traits of plant architecture, and also affects grain yield in rice. In this study, we obtained a novel dwarf rice mutant of japonica variety Shennong9816, designated Shennong9816d. Compared with wild-type, the Shennong9816d plant height was significantly reduced, and the tiller number significantly increased. Additionally, the mutant yield component, and the number of large and small vascular bundles were significantly decreased compared with wild-type. Genetic analysis indicated that the Shennong9816d dwarf phenotype was controlled by a recessive nuclear gene, while the plant was shown to be sensitive to gibberellic acid. Using a large F₂ population derived from a cross between Shennong9816d and the indica rice variety Habataki, the osh15(t) gene was fine mapped between RM20891 and RM20898, within a physical distance of 73.78 kb. Sequencing analysis showed that Shennong9816d carries a 1 bp mutation and a 30 bp insertion in the OSH15 region. These results suggest that osh15(t) is a novel allelic mutant originally derived from japonica variety Shennong9816, which may be useful for introducing the semi-dwarf phenotype to improve plant architecture in rice breeding practice.     

Double-check: validation of diagnostic statistics for PLS-DA models in metabolomics studies

Partial Least Squares-Discriminant Analysis (PLS-DA) is a PLS regression method with a special binary ‘dummy’ y-variable and it is commonly used for classification purposes and biomarker selection in metabolomics studies. Several statistical approaches are currently in use to validate outcomes of PLS-DA analyses e.g. double cross validation procedures or permutation testing. However, there is a great inconsistency in the optimization and the assessment of performance of PLS-DA models due to many different diagnostic statistics currently employed in metabolomics data analyses. In this paper, properties of four diagnostic statistics of PLS-DA, namely the number of misclassifications (NMC), the Area Under the Receiver Operating Characteristic (AUROC), Q ² and Discriminant Q ² (DQ ²) are discussed. All four diagnostic statistics are used in the optimization and the performance assessment of PLS-DA models of three different-size metabolomics data sets obtained with two different types of analytical platforms and with different levels of known differences between two groups: control and case groups. Statistical significance of obtained PLS-DA models was evaluated with permutation testing. PLS-DA models obtained with NMC and AUROC are more powerful in detecting very small differences between groups than models obtained with Q ² and Discriminant Q ² (DQ ²). Reproducibility of obtained PLS-DA models outcomes, models complexity and permutation test distributions are also investigated to explain this phenomenon. DQ ² and Q ² (in contrary to NMC and AUROC) prefer PLS-DA models with lower complexity and require higher number of permutation tests and submodels to accurately estimate statistical significance of the model performance. NMC and AUROC seem more efficient and more reliable diagnostic statistics and should be recommended in two group discrimination metabolomic studies.