Male-sterile mutation alters Zea m 1 (β-expansin 1) accumulation in a maize mutant

gaMS-2 is a gametophytic male-sterile mutant of maize, with sterile pollen grains developmentally blocked at the binucleate stage. To characterise differentially expressed proteins in gaMS-2 pollen, we compared protein profiles of anthers and mature pollen from heterozygous GaMS-2/gaMS-2 plants and wild type (wt) plants by two-dimensional electrophoresis (2-DE). A basic protein present at a greatly reduced level in GaMS-2/gaMS-2 anthers was subsequently identified by tandem mass spectrometry as Zea m 1 (a glycoprotein of 31 kDa), the major group-1 allergen of maize pollen and a member of the -expansin 1 family. Moreover, we show that Zea m 1 can be deglycosylated by peptide N-glycosidase F. After deglycosylation, four major isoforms—Zea m 1a (more acetic), Zea m 1b, Zea m1c and Zea m 1d (more basic)—can be discriminated in wt anther in 2-DE immunoblots probed with a monoclonal antibody against the group-1 pollen allergen, whereas all the isoforms, especially Zea m 1a, exist at reduced levels in GaMS-2/gaMS-2 anthers. Furthermore, the reduced Zea m 1 accumulation in the mutant appears to occur in immature pollen but not in anther sporophytic tissues. Finally, we separated sterile pollen grains (at the mononucleate stage) from fertile ones using 42% Percoll solution, and found that Zea m 1 is barely detectable in sterile pollen grains. Together, our results indicate that a reduced Zea m 1 level is associated with the sterile phenotype of gaMS-2.W. Wang and M. Scali contributed equally to this study     

Sample size calculations for noninferiority trials with Poisson distributed count data

Clinical trials with Poisson distributed count data as the primary outcome are common in various medical areas such as relapse counts in multiple sclerosis trials or the number of attacks in trials for the treatment of migraine. In this article, we present approximate sample size formulae for testing noninferiority using asymptotic tests which are based on restricted or unrestricted maximum likelihood estimators of the Poisson rates. The Poisson outcomes are allowed to be observed for unequal follow‐up schemes, and both the situations that the noninferiority margin is expressed in terms of the difference and the ratio are considered. The exact type I error rates and powers of these tests are evaluated and the accuracy of the approximate sample size formulae is examined. The test statistic using the restricted maximum likelihood estimators (for the difference test problem) and the test statistic that is based on the logarithmic transformation and employs the maximum likelihood estimators (for the ratio test problem) show favorable type I error control and can be recommended for practical application. The approximate sample size formulae show high accuracy even for small sample sizes and provide power values identical or close to the aspired ones. The methods are illustrated by a clinical trial example from anesthesia.     

Curtailment in single‐arm two‐stage phase II oncology trials

Two‐stage designs that allow for early stopping if the treatment is ineffective are commonly used in phase II oncology trials. A limitation of current designs is that early stopping is only allowed at the end of the first stage, even if it becomes evident during the trial that a significant result is unlikely. One way to overcome this limitation is to implement stochastic curtailment procedures that enable stopping the trial whenever the conditional power is below a pre‐specified threshold θ. In this paper, we present the results for implementing curtailment rules in either only the second stage or both stages of the designs. In total, 102 scenarios with different parameter settings were investigated using conditional power thresholds θ between 0 and 1 in steps of 0.01. An increase in θ results not only in a decrease of the actual Type I error rate and power but also of the expected sample size. Therefore, a reasonable balance has to be found when selecting a specific threshold value in the planning phase of a curtailed two‐stage design. Given that the effect of curtailment highly depends on the underlying design parameters, no general recommendation for θ can be made. However, up to , the loss in power was less than 5% for all investigated scenarios while savings of up to 50% in expected sample size occurred. In general, curtailment is most appropriate when the outcome can be observed fast or when accrual is slow so that adequate information for making early and frequent decisions is available.     

Primary structure, recombinant expression, and molecular characterization of Phl p 4, a major allergen of timothy grass (Phleum pratense)

Grass pollen allergy is one of the most important allergic diseases world-wide. Several meadow grasses, like timothy grass and rye grass, contribute to allergic sensitizations, but also allergens from extensively cultivated cereals, especially rye, make a profound contribution. The group 4 allergens are well known as important major allergens of grasses. We have cloned for the first time group 4 sequences from Phleum pratense, Lolium perenne, Secale cereale, Triticum aestivum, and Hordeum vulgare, and investigated the IgE-reactivity of recombinant Phl p 4 as a candidate for allergy diagnostic and therapeutic applications.     

Increased Activity of the Vacuolar Monosaccharide Transporter TMT1 Alters Cellular Sugar Partitioning,Sugar Signaling,and Seed Yield in Arabidopsis

The extent to which vacuolar sugar transport activity affects molecular, cellular, and developmental processes in Arabidopsis (Arabidopsis thaliana) is unknown. Electrophysiological analysis revealed that overexpression of the tonoplast monosaccharide transporter TMT1 in a tmt1-2::tDNA mutant led to increased proton-coupled monosaccharide import into isolated mesophyll vacuoles in comparison with wild-type vacuoles. TMT1 overexpressor mutants grew faster than wild-type plants on soil and in high-glucose (Glc)-containing liquid medium. These effects were correlated with increased vacuolar monosaccharide compartmentation, as revealed by nonaqueous fractionation and by chlorophyll_ab-binding protein1 and nitrate reductase1 gene expression studies. Soil-grown TMT1 overexpressor plants respired less Glc than wild-type plants and only about half the amount of Glc respired by tmt1-2::tDNA mutants. In sum, these data show that TMT activity in wild-type plants limits vacuolar monosaccharide loading. Remarkably, TMT1 overexpressor mutants produced larger seeds and greater total seed yield, which was associated with increased lipid and protein content. These changes in seed properties were correlated with slightly decreased nocturnal CO₂ release and increased sugar export rates from detached source leaves. The SUC2 gene, which codes for a sucrose transporter that may be critical for phloem loading in leaves, has been identified as Glc repressed. Thus, the observation that SUC2 mRNA increased slightly in TMT1 overexpressor leaves, characterized by lowered cytosolic Glc levels than wild-type leaves, provided further evidence of a stimulated source capacity. In summary, increased TMT activity in Arabidopsis induced modified subcellular sugar compartmentation, altered cellular sugar sensing, affected assimilate allocation, increased the biomass of Arabidopsis seeds, and accelerated early plant development.Sugars fulfill an extraordinarily wide range of functions in plants as well as in other organisms. They serve as valuable energy resources that are easy to store and remobilize. Sugars are required for the synthesis of cell walls and carbohydrate polymers. They are also necessary for starch accumulation and serve as precursors for a range of primary and secondary plant intermediates. From a chemical point of view, sugars represent a large class of metabolites. Among the prominent members in higher plants are the monosaccharides Glc and Fru and the disaccharide Suc (ap Rees, 1994).In contrast to heterotrophic organisms, plants are able to synthesize sugars de novo and to degrade them via oxidative or fermentative metabolism (Heldt, 2005). Net sugar accumulation in plants takes place during the day, whereas net degradation of stored carbohydrate reserves takes place the following night. In higher plants, autotrophic and heterotrophic organs appear to be interconnected by phloem for long-distance transport of sugars (Ruiz-Medrano et al., 2001). Accordingly, sugars must be transported within cells, between cells, and between plant organs. Given these factors, along with the outstanding importance of sugars, it is not surprising that plants sense intracellular sugar availability and use this information to coordinate the expression of many genes (Koch, 1996; Moore et al., 2003).In Arabidopsis (Arabidopsis thaliana), about 60 genes code for putative monosaccharide transport proteins and about 10 genes encode predicted disaccharide carriers (Lalonde et al., 2004). Transport of neutral sugars has been monitored across the plasma membrane, the chloroplast envelope, and the vacuolar membrane (Weber et al., 2000; Niittylä et al., 2004; Martinoia et al., 2007). So far, all sugar carriers residing in the plant plasma membrane have been characterized to catalyze proton-coupled sugar movement (Sauer, 1992; Büttner and Sauer, 2000; Carpaneto et al., 2005). In contrast, both facilitated diffusion and proton-driven antiport mechanisms have been described for monosaccharide and Suc transport across the vacuolar membrane (Thom and Komor, 1984; Daie and Wilusz, 1987; Martinoia et al., 1987; Shiratake et al., 1997; Neuhaus, 2007).In plants, vacuoles fulfill critical functions in the long-term and temporary storage of sugars, sugar alcohols, and other primary metabolites such as carboxylates and amino acids (Dietz et al., 1990; Rentsch and Martinoia, 1991; Martinoia and Rentsch, 1992; Emmerlich et al., 2003). Recently, the first solute carriers responsible for vacuolar Suc and inositol transport have been identified (Endler et al., 2006; Schneider et al., 2008). In addition, TMT (for tonoplast monosaccharide transporter) and VGT (for vacuolar Glc transporter) were the first vacuolar carrier proteins proven to have transport capacity for both Glc and Fru (Wormit et al., 2006; Aluri and Büttner, 2007).TMT exists in three isoforms in Arabidopsis (TMT1–TMT3), and orthologs have been found in other plant species like grapevine (Vitis vinifera), barley (Hordeum vulgare), and rice (Oryza sativa; Wormit et al., 2006). In Arabidopsis, the genes TMT1 and TMT2 are expressed in various tissues, whereas TMT3 is hardly expressed throughout the entire plant life cycle (Wormit et al., 2006). Interestingly, TMT1 and TMT2 are induced by Glc, salt, drought, and cold stress (Wormit et al., 2006), and vacuoles isolated from a TMT1 loss-of-function (T-DNA) Arabidopsis mutant showed reduced Glc import capacity in comparison with corresponding wild-type organelles (Wormit et al., 2006). Moreover, after transfer into the cold, these mutant leaves showed impaired ability to accumulate Glc and Fru, underscoring the in vivo function of TMT under selected conditions (Wormit et al., 2006).However, it is unknown to what extent overexpression of a vacuolar sugar carrier affects subcellular sugar allocation in Arabidopsis. In addition, whether increased vacuolar sugar transport influences sugar signaling, plant development, or organ properties has not been determined. Thus, it is unknown how important controlled activity of vacuolar monosaccharide transport is to plant development or physiological properties. To reveal whether TMT activity affects these processes, we created TMT1-overexpressing Arabidopsis lines and analyzed their physiological and molecular feedbacks.     

Nitrogen supply affects arbuscular mycorrhizal colonization of Artemisia vulgaris in a phosphate-polluted field site

Root colonization by arbuscular mycorrhizal fungi (AMF) was investigated in industrially polluted grassland characterized by exceptionally high phosphorus levels (up to 120 g kg(-1) soil). Along a pollution-induced nitrogen gradient, soil and tissue element concentrations of Artemisia vulgaris plants and their mycorrhizal status were determined. Additionally, we compared mycorrhization rates and above-ground biomass of A. vulgaris at N-fertilized and control plots in the N-poor area. Despite high soil and tissue P concentrations, plants from N-deficient plots, which were characterized by low tissue N concentrations and N : P ratios, were strongly colonized by AMF, whereas at a plot with comparable P levels, but higher soil and plant N concentrations and N : P ratios, mycorrhization rates were significantly lower. Correlation analyses revealed a negative relationship between percentage root colonization of A. vulgaris by AMF and both tissue N concentration and N : P ratio. Accordingly, in the fertilization experiment, control plants had higher mycorrhization rates than N-fertilized plants, whereas the species attained higher biomass at N-fertilized plots. The results suggest that N deficiency stimulates root colonization by AMF in this extraordinarily P-rich field site.     

A Comparison of Procedures for Adaptive Choice of Location Tests in Flexible Two‐Stage Designs

Although linear rank statistics for the two‐sample problem are distribution free tests, their power depends on the distribution of the data. In the planning phase of an experiment, researchers are often uncertain about the shape of this distribution and so the choice of test statistic for the analysis and the determination of the required sample size are based on vague information. Adaptive designs with interim analysis can potentially overcome both problems. And in particular, adaptive tests based on a selector statistic are a solution to the first. We investigate whether adaptive tests can be usefully implemented in flexible two‐stage designs to gain power. In a simulation study, we compare several methods for choosing a test statistic for the second stage of an adaptive design based on interim data with the procedure that applies adaptive tests in both stages. We find that the latter is a sensible approach that leads to the best results in most situations considered here. The different methods are illustrated using a clinical trial example.     

A global survey of gene regulation during cold acclimation in Arabidopsis thaliana

Many temperate plant species such as Arabidopsis thaliana are able to increase their freezing tolerance when exposed to low, nonfreezing temperatures in a process called cold acclimation. This process is accompanied by complex changes in gene expression. Previous studies have investigated these changes but have mainly focused on individual or small groups of genes. We present a comprehensive statistical analysis of the genome-wide changes of gene expression in response to 14 d of cold acclimation in Arabidopsis, and provide a large-scale validation of these data by comparing datasets obtained for the Affymetrix ATH1 Genechip and MWG 50-mer oligonucleotide whole-genome microarrays. We combine these datasets with existing published and publicly available data investigating Arabidopsis gene expression in response to low temperature. All data are integrated into a database detailing the cold responsiveness of 22,043 genes as a function of time of exposure at low temperature. We concentrate our functional analysis on global changes marking relevant pathways or functional groups of genes. These analyses provide a statistical basis for many previously reported changes, identify so far unreported changes, and show which processes predominate during different times of cold acclimation. This approach offers the fullest characterization of global changes in gene expression in response to low temperature available to date.     

Structural and immunological properties of arabinogalactan polysaccharides from pollen of timothy grass (Phleum pratense L.)

Extracts from pollen of timothy grass (Phleum pratense L.) contain up to 20% arabinogalactan proteins (AGPs). Separation of the AGP polysaccharide moieties by tryptic digestion, size exclusion chromatography (GPC), and reverse phase HPLC yielded arabinogalactan fractions AG-1 and AG-2 with molecular weights of approximately 15,000 and approximately 60,000Da, respectively. The backbones of both polysaccharides are composed of (1-->6)-linked beta-D-galactopyranosides with beta-D-GlcUAp or 4-O-Me-beta-D-GlcUAp at their terminal ends as revealed by chemical analysis, FT-IR, MALDI-MS, and NMR spectroscopy. AG-1 contains a small number of beta-l-Araf side chains while AG-2 possesses a variety of (1-->3)-linked units, which consist of beta-l-Araf-(1-->, alpha-l-Araf-(1-->3)-beta-l-Araf-(1-->, and alpha-l-Araf-(1-->5)-beta-l-Araf-(1--> as well as a small number of longer arabinogalactan side chains. In contrast to crude pollen extracts, the immunological properties of the arabinogalactan mixture reveal an IgG4 reactivity instead of IgE reactivity. Structural properties of timothy pollen arabinogalactan might thus influence the immune response.