Pectate distribution and esterification in Dubautia leaves and soybean nodules,studied with a fluorescent hybridization probe

Carbohydrate-hybridization probes (Vreeland and Laetsch, 1989, Planta (177, 423–434) were used to localize the homogalacturonan (pectate) component of pectins in the cell walls of leaves and soybean root nodules. Leaves of two species of the dicotyledon Dubautia were compared; these species contain much pectin but differ in their tissue water relations with respect to their cell-wall properties. Maturation of the primary cell walls in nodules was studied in the Bradyrhizobium japonicum-Glycine max symbiosis. Probe labelling was based on the divalent-cation-mediated association between pectate in tissue sections and fluorescein-conjugated pectate fragments. Pectate was also labelled by mixed-dimer formation with fluorescent polyguluronate derived from alginate. The specificity of the probe for unesterified polygalacturonate was indicated by increased cell-wall labelling after chemical or enzymatic deesterification of tissue sections, in contrast to elimination of labelling by chemical esterification. Postfixation of tissue sections improved retention of soluble pectate. Pectate differences were found in the leaves among cell types, in degree of esterification, and between plant species. The cell walls of soybean nodules were strongly labelled by the pectate probe in nodules one week and three weeks after infection. Pectate was more highly esterified in the central infected zone than in the surrouding cortex. Within the infected zone, walls of uninfected cells and infected cells were similarly labelled by the pectate probe. The results indicate that the pectate molecular probe provides detailed information on pectate distribution at the cellular level for investigations of cell-wall structure, development and physiology.Abbreviations EDTA ethylenedinitrilotetraacetic acid (ethylenediaminetetraacetic acid) - NMR nuclear magnetic resonance spectroscopy - TTB 1,3,5-triazido-2,4,6-trinitrobenene     

In Vivo Quantification Reveals Extensive Natural Variation in Mitochondrial Form and Function in Caenorhabditis briggsae

We have analyzed natural variation in mitochondrial form and function among a set of Caenorhabditis briggsae isolates known to harbor mitochondrial DNA structural variation in the form of a heteroplasmic nad5 gene deletion (nad5Δ) that correlates negatively with organismal fitness. We performed in vivo quantification of 24 mitochondrial phenotypes including reactive oxygen species level, membrane potential, and aspects of organelle morphology, and observed significant among-isolate variation in 18 traits. Although several mitochondrial phenotypes were non-linearly associated with nad5Δ levels, most of the among-isolate phenotypic variation could be accounted for by phylogeographic clade membership. In particular, isolate-specific mitochondrial membrane potential was an excellent predictor of clade membership. We interpret this result in light of recent evidence for local adaptation to temperature in C. briggsae. Analysis of mitochondrial-nuclear hybrid strains provided support for both mtDNA and nuclear genetic variation as drivers of natural mitochondrial phenotype variation. This study demonstrates that multicellular eukaryotic species are capable of extensive natural variation in organellar phenotypes and highlights the potential of integrating evolutionary and cell biology perspectives.     

The male determinant of self-incompatibility in Brassica oleracea is located in the pollen coating

An in vitro bioassay has been developed to explore the role of the pollen coating in the pollen/stigma interaction in Brassica oleracea . In the assay, coating is removed from pollen grains, supplemented with protein fractions isolated from coatings of different S (self incompatibility) haplotypes, and then—using micromanipulation—interposed between individual pollen grains and the stigmatic surface. Normally, the coating used is of the same haplotype as the pollen in the experiment—thus constituting an 'extension' of its own coat—but carrying the supplemented protein fractions. Initial experiments confirmed preliminary data that the pollen coating contained the male determinant of self incompatibility (SI); not only did the addition of 'self' coating (i.e. that with the same S -haplotype as the stigma) prevent the success of a compatible cross pollination, but a 'cross' coating (i.e. that with a different S -haplotype from the stigma) could induce the germination and growth of self pollen. Protein supplementation experiments demonstrated that the pollen-held determinant is contained within the water soluble component of the pollen coat, while further analysis revealed that the active molecular species possesses an M_r10 kDa. More extensive fractionation by gel filtration and reverse phase HPLC was used to isolate a family of basic, cysteine-rich proteins (PCP-A: P ollen C oat P roteins-class A)—one of which is known to bind to stigmatically-expressed components of the S -locus in Brassica . Introduction of the PCP-A protein fraction into the bioassay confirmed the male determinant of SI as a protein, and probably a member of the PCP-A protein family.     

Inhibition of cGMP-dependent protein kinase II by its own splice isoform

cGMP- and cAMP-dependent protein kinases (cGK I, cGK II, and cAK) are important mediators of many signaling pathways that increase cyclic nucleotide concentrations and ultimately phosphorylation of substrates vital to cellular functions. Here we demonstrate a novel mRNA splice isoform of cGK II arising from alternative 5' splicing within exon 11. The novel splice variant encodes a protein (cGK II Delta(441-469)) lacking 29 amino acids of the cGK II Mg-ATP-binding/catalytic domain, including the conserved glycine-rich loop consensus motif Gly-x-Gly-x-x-Gly-x-Val which interacts with ATP in the protein kinase family of enzymes. cGK II Delta(441-469) has no intrinsic enzymatic activity itself, however, it antagonizes cGK II and cGK I, but not cAK. Thus, the activation and cellular functions of cGK II may be determined not only by intracellular cGMP levels but also by alternative splicing which may regulate the balance of expression of cGK II versus its own inhibitor, cGK II Delta(441-469).     

Advantages of granivory in seasonal environments: feeding ecology of an arboreal seed predator in Amazonian forests

Specialized seed predators are uncommon in arboreal vertebrate assemblages, and the hypothesis that consuming seeds of immature fruits – which may be available for relatively long periods compared to mature fruit – could reduce seasonal food scarcity experienced by generalist frugivores remains largely untested. To test this hypothesis, we examined the diet and feeding ecology of bald‐faced saki monkeys Pithecia irrorata in a largely intact forest mosaic of southeastern Peru based on systematic monitoring of five habituated groups over a three‐year period and compared the relative availability of ripe and unripe fruits in their diet. Plant phenology data from individual tree crowns showed that, compared to ripe fruits, immature fruits were available in more tree species, in greater quantities, and for longer periods. Despite pronounced community‐wide seasonal changes in fruit production at our study area, feeding patterns of bald‐faced saki remained largely invariant: fruits comprised approximately 95% of the species’ monthly diet, with seeds alone accounting for 75%, with no major monthly dietary shifts. The flexible exploitation by this species of a consistently available food supply for which it faces little competition likely reduces foraging effort and consumption of less desirable foods, even during prolonged periods of overall fruit scarcity. The relative rarity of immature fruit specialists in tropical forests may reflect the fact that processing the hard pericarps and neutralizing the toxicities of immature seeds present substantial evolutionary hurdles that few arboreal vertebrate species have overcome.     

A novel adaptive method for the analysis of next-generation sequencing data to detect complex trait associations with rare variants due to gene main effects and interactions

There is solid evidence that rare variants contribute to complex disease etiology. Next-generation sequencing technologies make it possible to uncover rare variants within candidate genes, exomes, and genomes. Working in a novel framework, the kernel-based adaptive cluster (KBAC) was developed to perform powerful gene/locus based rare variant association testing. The KBAC combines variant classification and association testing in a coherent framework. Covariates can also be incorporated in the analysis to control for potential confounders including age, sex, and population substructure. To evaluate the power of KBAC: 1) variant data was simulated using rigorous population genetic models for both Europeans and Africans, with parameters estimated from sequence data, and 2) phenotypes were generated using models motivated by complex diseases including breast cancer and Hirschsprung's disease. It is demonstrated that the KBAC has superior power compared to other rare variant analysis methods, such as the combined multivariate and collapsing and weight sum statistic. In the presence of variant misclassification and gene interaction, association testing using KBAC is particularly advantageous. The KBAC method was also applied to test for associations, using sequence data from the Dallas Heart Study, between energy metabolism traits and rare variants in ANGPTL 3,4,5 and 6 genes. A number of novel associations were identified, including the associations of high density lipoprotein and very low density lipoprotein with ANGPTL4. The KBAC method is implemented in a user-friendly R package.     

Piecing together our woodlands – Interview with Suzanne Prober

Over nearly three decades, Suzanne Prober has played a pivotal role in shifting research in Australian agricultural landscapes to include a focus on native woodlands, and to examine ways woodland conservation can co‐exist with production, contributing to new models for conservation within multi‐use landscapes.     

The new higher level classification of eukaryotes with emphasis on the taxonomy of protists

This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional "kingdoms." The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.     

Large,Omega-3 Rich,Pelagic Diatoms under Arctic Sea Ice: Sources and Implications for Food Webs

Pelagic primary production in Arctic seas has traditionally been viewed as biologically insignificant until after the ice breakup. There is growing evidence however, that under-ice blooms of pelagic phytoplankton may be a recurrent occurrence. During the springs of 2011 and 2012, we found substantial numbers (201–5713 cells m⁻³) of the large centric diatom (diameter >250 µm) Coscinodiscus centralis under the sea ice in the Canadian Arctic Archipelago near Resolute Bay, Nunavut. The highest numbers of these pelagic diatoms were observed in Barrow Strait. Spatial patterns of fatty acid profiles and stable isotopes indicated two source populations for C. centralis: a western origin with low light conditions and high nutrients, and a northern origin with lower nutrient levels and higher irradiances. Fatty acid analysis revealed that pelagic diatoms had significantly higher levels of polyunsaturated fatty acids (mean ± SD: 50.3±8.9%) compared to ice-associated producers (30.6±10.3%) in our study area. In particular, C. centralis had significantly greater proportions of the long chain omega-3 fatty acid, eicosapentaenoic acid (EPA), than ice algae (24.4±5.1% versus 13.7±5.1%, respectively). Thus, C. centralis represented a significantly higher quality food source for local herbivores than ice algae, although feeding experiments did not show clear evidence of copepod grazing on C. centralis. Our results suggest that C. centralis are able to initiate growth under pack ice in this area and provide further evidence that biological productivity in ice-covered seas may be substantially higher than previously recognized.