A synthetic route to fully substituted chiral cyclopentylamine derivatives: precursors of carbanucleosides

Removal of silyl protection from D-glucose derived substrate 6 afforded 7, which upon acetonide deprotection followed by reaction with N-benzylhydroxylamine furnished two isomeric isoxazolidinocyclopentane derivatives via spontaneous cyclization of an in situ generated nitrone. The methyl xanthate derivative of the tertiary hydroxyl group of one isomer was isolated and subjected to radical deoxygenation reaction to form epimeric products, while with the other isomer it underwent spontaneous 1,2-elimination to form a mixture of the two possible endocyclic olefins. Hydrogenolytic cleavage of the isoxazolidine rings of the purified products followed by insertion of 5-amino-4-chloropyrimidine moiety and purine ring construction smoothly afforded structurally unique carbanucleoside analogues. Various spectroscopic methods on the synthesized compounds and X-ray analysis on one important intermediate were used to assign the structures and stereochemistry of the products.

Fully automated software solution for protein quantitation by global metabolic labeling with stable isotopes

Metabolic stable isotope labeling is increasingly employed for accurate protein (and metabolite) quantitation using mass spectrometry (MS). It provides sample-specific isotopologues that can be used to facilitate comparative analysis of two or more samples. Stable Isotope Labeling by Amino acids in Cell culture (SILAC) has been used for almost a decade in proteomic research and analytical software solutions have been established that provide an easy and integrated workflow for elucidating sample abundance ratios for most MS data formats. While SILAC is a discrete labeling method using specific amino acids, global metabolic stable isotope labeling using isotopes such as (15)N labels the entire element content of the sample, i.e. for (15)N the entire peptide backbone in addition to all nitrogen-containing side chains. Although global metabolic labeling can deliver advantages with regard to isotope incorporation and costs, the requirements for data analysis are more demanding because, for instance for polypeptides, the mass difference introduced by the label depends on the amino acid composition. Consequently, there has been less progress on the automation of the data processing and mining steps for this type of protein quantitation. Here, we present a new integrated software solution for the quantitative analysis of protein expression in differential samples and show the benefits of high-resolution MS data in quantitative proteomic analyses.

Effects of fully open-air CO2 elevation on leaf ultrastructure, photosynthesis and yield of two soybean cultivars.

The objective of this study was to investigate the effect of elevated (550 ± 17 μmol mol−1) CO2 concentration ([CO2]) on leaf ultrastructure, leaf photosynthesis and seed yield of two soybean cultivars [Glycine max (L.) Merr. cv. Zhonghuang 13 and cv. Zhonghuang 35] at the Free-Air Carbon dioxide Enrichment (FACE) experimental facility in North China. Photosynthetic acclimation occurred in soybean plants exposed to long-term elevated [CO2] and varied with cultivars and developmental stages. Photosynthetic acclimation occurred at the beginning bloom (R1) stage for both cultivars, but at the beginning seed (R5) stage only for Zhonghuang 13. No photosynthetic acclimation occurred at the beginning pod (R3) stage for either cultivar. Elevated [CO2] increased the number and size of starch grains in chloroplasts of the two cultivars. Soybean leaf senescence was accelerated under elevated [CO2], determined by unclear chloroplast membrane and blurred grana layer at the beginning bloom (R1) stage. The different photosynthesis response to elevated [CO2] between cultivars at the beginning seed (R5) contributed to the yield difference under elevated [CO2]. Elevated [CO2] significantly increased the yield of Zhonghuang 35 by 26% with the increased pod number of 31%, but not for Zhonghuang 13 without changes of pod number. We conclude that the occurrence of photosynthetic acclimation at the beginning seed (R5) stage for Zhonghuang 13 restricted the development of extra C sink under elevated [CO2], thereby limiting the response to elevated [CO2] for the seed yield of this cultivar.

Solutions of the fully compressible semi-geostrophic system

The fully compressible semi-geostrophic system is widely used in the modelling of large-scale atmospheric flows. In this paper, we prove rigorously the existence of weak Lagrangian solutions of this system, formulated in the original physical coordinates. In addition, we provide an alternative proof of the earlier result on the existence of weak solutions of this system expressed in the so-called geostrophic, or dual, coordinates. The proofs are based on the optimal transport formulation of the problem and on recent general results concerning transport problems posed in the Wasserstein space of probability measures.

Efficient fully nonlinear data assimilation for geophysical fluid dynamics

A potential problem with Ensemble Kalman Filter is the implicit Gaussian assumption at analysis times. Here we explore the performance of a recently proposed fully nonlinear particle filter on a high-dimensional but simplified ocean model, in which the Gaussian assumption is not made. The model simulates the evolution of the vorticity field in time, described by the barotropic vorticity equation, in a highly nonlinear flow regime. While common knowledge is that particle filters are inefficient and need large numbers of model runs to avoid degeneracy, the newly developed particle filter needs only of the order of 10-100 particles on large scale problems. The crucial new ingredient is that the proposal density cannot only be used to ensure all particles end up in high-probability regions of state space as defined by the observations, but also to ensure that most of the particles have similar weights. Using identical twin experiments we found that the ensemble mean follows the truth reliably, and the difference from the truth is captured by the ensemble spread. A rank histogram is used to show that the truth run is indistinguishable from any of the particles, showing statistical consistency of the method.

Claviceps purpurea expressing polygalacturonases escaping PGIP inhibition fully infects PvPGIP2 wheat transgenic plants but its infection is delayed in wheat transgenic plants with increased level of pectin methyl esterification

Claviceps purpurea is a biotrophic fungal pathogen of grasses causing the ergot disease. The infection process of C. purpurea on rye flowers is accompanied by pectin degradation and polygalacturonase (PG) activity represents a pathogenicity factor. Wheat is also infected by C. purpurea and we tested whether the presence of polygalacturonase inhibiting protein (PGIP) can affect pathogen infection and ergot disease development. Wheat transgenic plants expressing the bean PvPGIP2 did not show a clear reduction of disease symptoms when infected with C. purpurea. To ascertain the possible cause underlying this lack of improved resistance of PvPGIP2 plants, we expressed both polygalacturonases present in the C. purpurea genome, cppg1 and cppg2 in Pichia pastoris. In vitro assays using the heterologous expressed PGs and PvPGIP2 showed that neither PG is inhibited by this inhibitor. To further investigate the role of PG in the C. purpurea/wheat system, we demonstrated that the activity of both PGs of C. purpurea is reduced on highly methyl esterified pectin. Finally, we showed that this reduction in PG activity is relevant in planta, by inoculating with C. purpurea transgenic wheat plants overexpressing a pectin methyl esterase inhibitor (PMEI) and showing a high degree of pectin methyl esterification. We observed reduced disease symptoms in the transgenic line compared with null controls. Together, these results highlight the importance of pectin degradation for ergot disease development in wheat and sustain the notion that inhibition of pectin degradation may represent a possible route to control of ergot in cereals.

Curl free pressure gradients over orography in a solution of the fully compressible Euler equations with implicit treatment of acoustic and gravity waves

Steep orography can cause noisy solutions and instability in models of the atmosphere. A new technique for modelling flow over orography is introduced which guarantees curl free gradients on arbitrary grids, implying that the pressure gradient term is not a spurious source of vorticity. This mimetic property leads to better hydrostatic balance and better energy conservation on test cases using terrain following grids. Curl-free gradients are achieved by using the co-variant components of velocity over orography rather than the usual horizontal and vertical components. In addition, gravity and acoustic waves are treated implicitly without the need for mean and perturbation variables or a hydrostatic reference profile. This enables a straightforward description of the implicit treatment of gravity waves. Results are presented of a resting atmosphere over orography and the curl-free pressure gradient formulation is advantageous. Results of gravity waves over orography are insensitive to the placement of terrain-following layers. The model with implicit gravity waves is stable in strongly stratified conditions, with N∆t up to at least 10 (where N is the Brunt-V ̈ais ̈al ̈a frequency). A warm bubble rising over orography is simulated and the curl free pressure gradient formulation gives much more accurate results for this test case than a model without this mimetic property.

Occurrence probability, width and number of steps of cusp precipitation for fully pulsed reconnection at the dayside magnetopause

We discuss the characteristics of magnetosheath plasma precipitation in the “cusp” ionosphere for when the reconnection at the dayside magnetopause takes place only in a series of pulses. It is shown that even in this special case, the low-altitude cusp precipitation is continuous, unless the intervals between the pulses are longer than observed intervals between magnetopause flux transfer event (FTE) signatures. We use FTE observation statistics to predict, for this case of entirely pulsed reconnection, the occurrence frequency, the distribution of latitudinal widths, and the number of ion dispersion steps of the cusp precipitation for a variety of locations of the reconnection site and a range of values of the local de-Hoffman Teller velocity. It is found that the cusp occurrence frequency is comparable with observed values for virtually all possible locations of the reconnection site. The distribution of cusp width is also comparable with observations and is shown to be largely dependent on the distribution of the mean reconnection rate, but pulsing the reconnection does very slightly increase the width of that distribution compared with the steady state case. We conclude that neither cusp occurrence probability nor width can be used to evaluate the relative occurrence of reconnection behaviors that are entirely pulsed, pulsed but continuous and quasi-steady. We show that the best test of the relative frequency of these three types of reconnection is to survey the distribution of steps in the cusp ion dispersion characteristics.

FORCe: fully online and automated artifact removal for brain-computer interfacing

A fully automated and online artifact removal method for the electroencephalogram (EEG) is developed for use in brain-computer interfacing. The method (FORCe) is based upon a novel combination of wavelet decomposition, independent component analysis, and thresholding. FORCe is able to operate on a small channel set during online EEG acquisition and does not require additional signals (e.g. electrooculogram signals). Evaluation of FORCe is performed offline on EEG recorded from 13 BCI particpants with cerebral palsy (CP) and online with three healthy participants. The method outperforms the state-of the-art automated artifact removal methods Lagged auto-mutual information clustering (LAMIC) and Fully automated statistical thresholding (FASTER), and is able to remove a wide range of artifact types including blink, electromyogram (EMG), and electrooculogram (EOG) artifacts.